From 261371c8320e92f9a4416b180fa6651b18f2ae94 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 7 Jul 2022 13:03:27 -0700 Subject: [PATCH 001/127] #220 Update extract-semmed-sh --- extract-semmeddb.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/extract-semmeddb.sh b/extract-semmeddb.sh index fbe27f10..61a0472f 100755 --- a/extract-semmeddb.sh +++ b/extract-semmeddb.sh @@ -22,8 +22,8 @@ semmed_output_file=${1:-"${BUILD_DIR}/kg2-semmeddb-tuplelist.json"} ## supply a default value for the build_flag string build_flag=${2:-""} -semmed_ver=VER43 -semmed_year=2021 +semmed_ver=VER30 +semmed_year=2022 semmed_dir=${BUILD_DIR}/semmeddb semmed_output_dir=`dirname "${semmed_output_file}"` semmed_sql_file=semmed${semmed_ver}_${semmed_year}_R_WHOLEDB.sql From fa6859792bfbbe81ff0edece359beae9813ff1d5 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 7 Jul 2022 13:27:34 -0700 Subject: [PATCH 002/127] #220 Undo changes to extract-semmed.sh --- extract-semmeddb.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/extract-semmeddb.sh b/extract-semmeddb.sh index 61a0472f..fbe27f10 100755 --- a/extract-semmeddb.sh +++ b/extract-semmeddb.sh @@ -22,8 +22,8 @@ semmed_output_file=${1:-"${BUILD_DIR}/kg2-semmeddb-tuplelist.json"} ## supply a default value for the build_flag string build_flag=${2:-""} -semmed_ver=VER30 -semmed_year=2022 +semmed_ver=VER43 +semmed_year=2021 semmed_dir=${BUILD_DIR}/semmeddb semmed_output_dir=`dirname "${semmed_output_file}"` semmed_sql_file=semmed${semmed_ver}_${semmed_year}_R_WHOLEDB.sql From 8b4d1725e24465f506502673353deabe8a56c80b Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 7 Jul 2022 14:49:02 -0700 Subject: [PATCH 003/127] #220 Update umls-config.prop --- umls-config.prop | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/umls-config.prop b/umls-config.prop index 44e20a4b..fb4cd681 100644 --- a/umls-config.prop +++ b/umls-config.prop @@ -1,11 +1,11 @@ # Configuration Properties File -#Mon Apr 29 13:17:42 PDT 2019 +#Thu Jul 07 14:48:42 PDT 2022 mmsys_output_stream=gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.remove_obsolete_data=false gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.confirm_selections=false install_lvg=false gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.calculate_md5s=false -release_version=2018AB +release_version=2022AA gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.subset_dir=/home/ubuntu/kg2-build/umls/META gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.suppressed_sabttys=DMDICD10|HT;DMDICD10|PT;DMDUMD|ET;DMDUMD|PT;DMDUMD|RT;ICPCBAQ|CP;ICPCBAQ|PT;ICPCDAN|CP;ICPCDAN|PT;ICPCDUT|CP;ICPCDUT|PT;ICPCFIN|CP;ICPCFIN|PT;ICPCFRE|CP;ICPCFRE|PT;ICPCGER|CP;ICPCGER|PT;ICPCHEB|CP;ICPCHEB|PT;ICPCHUN|CP;ICPCHUN|PT;ICPCITA|CP;ICPCITA|PT;ICPCNOR|CP;ICPCNOR|PT;ICPCPOR|CP;ICPCPOR|PT;ICPCSPA|CP;ICPCSPA|PT;ICPCSWE|CP;ICPCSWE|PT;LNC-DE-AT|LN;LNC-DE-AT|LO;LNC-DE-AT|LVDN;LNC-DE-CH|OOSN;LNC-DE-CH|OSN;LNC-DE-DE|LN;LNC-DE-DE|LO;LNC-EL-GR|LN;LNC-EL-GR|LO;LNC-ES-AR|LN;LNC-ES-AR|LO;LNC-ES-AR|OOSN;LNC-ES-AR|OSN;LNC-ES-CH|OOSN;LNC-ES-CH|OSN;LNC-ES-ES|LN;LNC-ES-ES|LO;LNC-ET-EE|LN;LNC-ET-EE|LO;LNC-FR-BE|LN;LNC-FR-BE|LO;LNC-FR-CA|LN;LNC-FR-CA|LO;LNC-FR-CH|OOSN;LNC-FR-CH|OSN;LNC-FR-FR|LC;LNC-FR-FR|LN;LNC-FR-FR|LO;LNC-FR-FR|OLC;LNC-IT-CH|OOSN;LNC-IT-CH|OSN;LNC-IT-IT|LN;LNC-IT-IT|LO;LNC-KO-KR|LN;LNC-KO-KR|LO;LNC-NL-NL|LN;LNC-NL-NL|LO;LNC-PT-BR|LN;LNC-PT-BR|LO;LNC-PT-BR|OOSN;LNC-PT-BR|OSN;LNC-RU-RU|LN;LNC-RU-RU|LO;LNC-TR-TR|LN;LNC-TR-TR|LO;LNC-ZH-CN|LN;LNC-ZH-CN|SMQ;MSHCZE|ET;MSHCZE|MH;MSHCZE|PEP;MSHDUT|MH;MSHDUT|SY;MSHFIN|MH;MSHFRE|ET;MSHFRE|MH;MSHFRE|PEP;MSHGER|DSV;MSHGER|ET;MSHGER|MH;MSHGER|PEP;MSHITA|ET;MSHITA|MH;MSHITA|PEP;MSHJPN|PT;MSHJPN|SY;MSHLAV|EP;MSHLAV|MH;MSHLAV|PEP;MSHNOR|DSV;MSHNOR|ET;MSHNOR|MH;MSHNOR|PEP;MSHPOL|MH;MSHPOL|SY;MSHPOR|ET;MSHPOR|MH;MSHPOR|PEP;MSHRUS|MH;MSHRUS|SY;MSHSCR|ET;MSHSCR|MH;MSHSCR|PEP;MSHSPA|ET;MSHSPA|MH;MSHSPA|PEP;MSHSWE|MH;MSHSWE|TQ;SCTSPA|FN;SCTSPA|IS;SCTSPA|MTH_FN;SCTSPA|MTH_IS;SCTSPA|MTH_OAF;SCTSPA|MTH_OAP;SCTSPA|MTH_OAS;SCTSPA|MTH_OF;SCTSPA|MTH_OP;SCTSPA|MTH_PT;SCTSPA|MTH_SY;SCTSPA|OAF;SCTSPA|OAP;SCTSPA|OAS;SCTSPA|OF;SCTSPA|OP;SCTSPA|PT;SCTSPA|SB;SCTSPA|SY;WHOFRE|HT;WHOFRE|IT;WHOFRE|OS;WHOFRE|PT;WHOGER|HT;WHOGER|IT;WHOGER|OS;WHOGER|PT;WHOPOR|HT;WHOPOR|IT;WHOPOR|OS;WHOPOR|PT;WHOSPA|HT;WHOSPA|IT;WHOSPA|OS;WHOSPA|PT gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.remove_mth_only=false @@ -22,19 +22,19 @@ install_umls=true install_lex=false gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.database=MySQL 5.6 mmsys_input_stream=gov.nih.nlm.umls.mmsys.io.NLMFileMetamorphoSysInputStream -meta_source_uri=/home/ubuntu/kg2-build/umls/2018AB-full +meta_source_uri=/home/ubuntu/kg2-build/umls/2022AA-full gov.nih.nlm.umls.mmsys.filter.SourceListFilter.base_url=http\://www.nlm.nih.gov/research/umls/sourcereleasedocs/ gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.max_field_length=4000 gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.versioned_output=false install_meta=true gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.remove_editor_suppressible_data=false gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.remove_source_tty_suppressible_data=false -umls_destination_uri=/home/ubuntu/kg2-build/umls/2018AB +umls_destination_uri=/home/ubuntu/kg2-build/umls/2022AA gov.nih.nlm.umls.mmsys.filter.SourceListFilter.selected_sources=AIR|AIR;ALT|ALT;AOD|AOD;AOT|AOT;ATC|ATC;BI|BI;CCC|CCC;CCPSS|CCPSS;CCS|CCS;CCS_10|CCS;CDT|CDT;CHV|CHV;COSTAR|COSTAR;CPM|CPM;CPTSP|CPT;CPT|CPT;CSP|CSP;CST|CST;CVX|CVX;DDB|DDB;DMDICD10|ICD10;DMDUMD|UMD;DRUGBANK|DRUGBANK;DSM-5|DSM-5;DXP|DXP;FMA|FMA;GO|GO;GS|GS;HCDT|HCPCS;HCPCS|HCPCS;HCPT|CPT;HGNC|HGNC;HL7V2.5|HL7V2.5;HL7V3.0|HL7V3.0;HLREL|HLREL;HPO|HPO;ICD10AE|ICD10;ICD10AMAE|ICD10AM;ICD10AM|ICD10AM;ICD10CM|ICD10CM;ICD10DUT|ICD10;ICD10PCS|ICD10PCS;ICD10|ICD10;ICD9CM|ICD9CM;ICF-CY|ICF;ICF|ICF;ICNP|ICNP;ICPC2EDUT|ICPC2EENG;ICPC2EENG|ICPC2EENG;ICPC2ICD10DUT|ICPC2ICD10ENG;ICPC2ICD10ENG|ICPC2ICD10ENG;ICPC2P|ICPC2P;ICPC|ICPC;ICPCBAQ|ICPC;ICPCDAN|ICPC;ICPCDUT|ICPC;ICPCFIN|ICPC;ICPCFRE|ICPC;ICPCGER|ICPC;ICPCHEB|ICPC;ICPCHUN|ICPC;ICPCITA|ICPC;ICPCNOR|ICPC;ICPCPOR|ICPC;ICPCSPA|ICPC;ICPCSWE|ICPC;JABL|JABL;KCD5|KCD5;LCH|LCH;LCH_NW|LCH;LNC-DE-AT|LNC;LNC-DE-CH|LNC;LNC-DE-DE|LNC;LNC-EL-GR|LNC;LNC-ES-AR|LNC;LNC-ES-CH|LNC;LNC-ES-ES|LNC;LNC-ET-EE|LNC;LNC-FR-BE|LNC;LNC-FR-CA|LNC;LNC-FR-CH|LNC;LNC-FR-FR|LNC;LNC-IT-CH|LNC;LNC-IT-IT|LNC;LNC-KO-KR|LNC;LNC-NL-NL|LNC;LNC-PT-BR|LNC;LNC-RU-RU|LNC;LNC-TR-TR|LNC;LNC-ZH-CN|LNC;LNC|LNC;MCM|MCM;MDR|MDR;MDRCZE|MDR;MDRDUT|MDR;MDRFRE|MDR;MDRGER|MDR;MDRHUN|MDR;MDRITA|MDR;MDRJPN|MDR;MDRPOR|MDR;MDRSPA|MDR;MED-RT|MED-RT;MEDCIN|MEDCIN;MEDLINEPLUS|MEDLINEPLUS;MMSL|MMSL;MMX|MMX;MSH|MSH;MSHCZE|MSH;MSHDUT|MSH;MSHFIN|MSH;MSHFRE|MSH;MSHGER|MSH;MSHITA|MSH;MSHJPN|MSH;MSHLAV|MSH;MSHNOR|MSH;MSHPOL|MSH;MSHPOR|MSH;MSHRUS|MSH;MSHSCR|MSH;MSHSPA|MSH;MSHSWE|MSH;MTH|MTH;MTHCMSFRF|MTHCMSFRF;MTHHH|HCPCS;MTHICD9|ICD9CM;MTHICPC2EAE|ICPC2EENG;MTHICPC2ICD10AE|ICPC2ICD10ENG;MTHMST|MTHMST;MTHMSTFRE|MTHMST;MTHMSTITA|MTHMST;MTHSPL|MTHSPL;MVX|MVX;NANDA-I|NANDA-I;NCBI|NCBI;NCI|NCI;NCI_BRIDG|NCI;NCI_BioC|NCI;NCI_CDC|NCI;NCI_CDISC-GLOSS|NCI;NCI_CDISC|NCI;NCI_CRCH|NCI;NCI_CTCAE|NCI;NCI_CTCAE_3|NCI;NCI_CTCAE_5|NCI;NCI_CTEP-SDC|NCI;NCI_CTRP|NCI;NCI_CareLex|NCI;NCI_DCP|NCI;NCI_DICOM|NCI;NCI_DTP|NCI;NCI_FDA|NCI;NCI_GAIA|NCI;NCI_GENC|NCI;NCI_ICH|NCI;NCI_JAX|NCI;NCI_KEGG|NCI;NCI_NCI-GLOSS|NCI;NCI_NCI-HGNC|NCI;NCI_NCI-HL7|NCI;NCI_NCPDP|NCI;NCI_NICHD|NCI;NCI_PI-RADS|NCI;NCI_PID|NCI;NCI_RENI|NCI;NCI_UCUM|NCI;NCI_ZFin|NCI;NCISEER|NCISEER;NDDF|NDDF;NDFRT|NDFRT;NDFRT_FDASPL|NDFRT;NDFRT_FMTSME|NDFRT;NEU|NEU;NIC|NIC;NOC|NOC;NUCCPT|NUCCPT;OMIM|OMIM;OMS|OMS;PCDS|PCDS;PDQ|PDQ;PNDS|PNDS;PPAC|PPAC;PSY|PSY;QMR|QMR;RAM|RAM;RCD|RCD;RCDAE|RCD;RCDSA|RCD;RCDSY|RCD;RXNORM|RXNORM;SCTSPA|SNOMEDCT;SNM|SNM;SNMI|SNMI;SNOMEDCT_US|SNOMEDCT;SNOMEDCT_VET|SNOMEDCT;SOP|SOP;SPN|SPN;TKMT|TKMT;ULT|ULT;UMD|UMD;USPMG|USPMG;USP|USP;UWDA|UWDA;VANDF|VANDF;WHO|WHO;WHOFRE|WHO;WHOGER|WHO;WHOPOR|WHO;WHOSPA|WHO gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.truncate=false gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream.character_encoding=UTF-8 active_filters=gov.nih.nlm.umls.mmsys.filter.SourceListFilter;gov.nih.nlm.umls.mmsys.filter.PrecedenceFilter;gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter gov.nih.nlm.umls.mmsys.filter.PrecedenceFilter.precedence=MTH|PN;RXNORM|MIN;MTHCMSFRF|PT;RXNORM|SCD;RXNORM|SBD;RXNORM|SCDG;RXNORM|SBDG;RXNORM|IN;RXNORM|PSN;RXNORM|SCDF;RXNORM|SBDF;RXNORM|SCDC;RXNORM|DFG;RXNORM|DF;RXNORM|SBDC;RXNORM|BN;RXNORM|PIN;RXNORM|BPCK;RXNORM|GPCK;RXNORM|SY;RXNORM|TMSY;MSH|MH;MSH|TQ;MSH|PEP;MSH|ET;MSH|XQ;MSH|PXQ;MSH|NM;SNOMEDCT_US|PT;SNOMEDCT_US|FN;SNOMEDCT_US|SY;SNOMEDCT_US|PTGB;SNOMEDCT_US|SYGB;SNOMEDCT_US|MTH_PT;SNOMEDCT_US|MTH_FN;SNOMEDCT_US|MTH_SY;SNOMEDCT_US|MTH_PTGB;SNOMEDCT_US|MTH_SYGB;SNOMEDCT_US|SB;SNOMEDCT_US|XM;SNOMEDCT_VET|PT;SNOMEDCT_VET|FN;SNOMEDCT_VET|SY;SNOMEDCT_VET|SB;HPO|PT;HPO|SY;HPO|ET;HPO|OP;HPO|IS;NCBI|SCN;MTHSPL|MTH_RXN_DP;MTHSPL|DP;MTHSPL|SU;ATC|RXN_PT;ATC|PT;VANDF|PT;VANDF|CD;VANDF|IN;USP|CD;USP|IN;USPMG|HC;USPMG|PT;MMX|MTH_RXN_CD;MMX|MTH_RXN_BD;MMX|CD;MMX|BD;DRUGBANK|IN;DRUGBANK|SY;DRUGBANK|FSY;MSH|N1;MSH|PCE;MSH|CE;CPM|PT;NEU|PT;NEU|ACR;NEU|SY;NEU|OP;NEU|IS;FMA|PT;FMA|SY;FMA|AB;FMA|OP;FMA|IS;UWDA|PT;UWDA|SY;UMD|PT;UMD|SY;UMD|ET;UMD|RT;GS|CD;MMSL|CD;GS|MTH_RXN_BD;GS|BD;MMSL|MTH_RXN_BD;MMSL|BD;MMSL|SC;MMSL|MS;MMSL|GN;MMSL|BN;ATC|RXN_IN;ATC|IN;MMSL|IN;VANDF|AB;GS|MTH_RXN_CD;VANDF|MTH_RXN_CD;NDDF|MTH_RXN_CDC;NDDF|CDC;NDDF|CDD;NDDF|CDA;NDDF|IN;NDDF|DF;NDFRT|MTH_RXN_RHT;NDFRT|HT;MED-RT|PT;MED-RT|FN;NDFRT|FN;NDFRT|PT;MED-RT|SY;NDFRT|SY;NDFRT|AB;SPN|PT;MDR|PT;MDR|MTH_PT;MDR|HG;MDR|MTH_HG;MDR|OS;MDR|MTH_OS;MDR|HT;MDR|MTH_HT;MDR|LLT;MDR|MTH_LLT;MDR|SMQ;MDR|MTH_SMQ;MDR|AB;CPT|PT;CPT|SY;CPT|ETCLIN;CPT|POS;CPT|GLP;CPT|ETCF;CPT|MP;HCPT|PT;HCPCS|PT;CDT|PT;CDT|OP;MVX|PT;CVX|PT;CVX|RXN_PT;CVX|AB;HCDT|PT;HCPCS|MP;HCPT|MP;ICD10AE|PT;ICD10|PT;ICD10AE|PX;ICD10|PX;ICD10AE|PS;ICD10|PS;ICD10AMAE|PT;ICD10AM|PT;ICD10AMAE|PX;ICD10AM|PX;ICD10AMAE|PS;ICD10AM|PS;OMIM|PT;OMIM|PHENO;OMIM|PHENO_ET;OMIM|PTAV;OMIM|PTCS;OMIM|ETAL;OMIM|ET;OMIM|HT;OMIM|ACR;MEDCIN|PT;MEDCIN|FN;MEDCIN|XM;MEDCIN|SY;HGNC|PT;HGNC|ACR;HGNC|MTH_ACR;HGNC|NA;HGNC|SYN;ICNP|PT;ICNP|MTH_PT;ICNP|XM;PNDS|PT;PNDS|HT;PNDS|XM;PDQ|PT;PDQ|HT;PDQ|PSC;PDQ|SY;PDQ|MTH_SY;CHV|PT;MEDLINEPLUS|PT;NCI|PT;NCI|SY;NCI_BioC|SY;NCI_PI-RADS|PT;NCI_CareLex|PT;NCI_CareLex|SY;NCI_CDC|PT;NCI_CDISC|PT;NCI_CDISC|SY;NCI|CSN;NCI_DCP|PT;NCI_DCP|SY;NCI|DN;NCI_DTP|PT;NCI_DTP|SY;NCI|FBD;NCI_FDA|AB;NCI_CTRP|PT;NCI_CTRP|SY;NCI_CTRP|DN;NCI_FDA|PT;NCI_FDA|SY;NCI|HD;NCI_GENC|PT;NCI_GENC|CA2;NCI_GENC|CA3;NCI_CRCH|PT;NCI_CRCH|SY;NCI_DICOM|PT;NCI_CDISC-GLOSS|PT;NCI_CDISC-GLOSS|SY;NCI_BRIDG|PT;NCI_RENI|DN;NCI_BioC|PT;NCI|CCN;NCI_CTCAE|PT;NCI_CTCAE_5|PT;NCI_CTCAE_3|PT;NCI_CTEP-SDC|PT;NCI_CTEP-SDC|SY;NCI|CCS;NCI_JAX|PT;NCI_JAX|SY;NCI_KEGG|PT;NCI_ICH|AB;NCI_ICH|PT;NCI_NCI-HL7|AB;NCI_NCI-HGNC|PT;NCI_NCI-HGNC|SY;NCI_NCI-HL7|PT;NCI_UCUM|AB;NCI_UCUM|PT;NCI_KEGG|AB;NCI_KEGG|SY;NCI_NICHD|PT;NCI_NICHD|SY;NCI_PID|PT;NCI_NCPDP|PT;NCI_GAIA|PT;NCI_GAIA|SY;NCI_ZFin|PT;NCI_NCI-GLOSS|PT;NCI_ICH|SY;NCI_NCI-HL7|SY;NCI_UCUM|SY;NCI_NCPDP|SY;NCI_ZFin|SY;NCI_NCI-GLOSS|SY;NCI|OP;NCI_NICHD|OP;NCI|AD;NCI|CA2;NCI|CA3;NCI|BN;NCI|AB;MTHICPC2EAE|PT;ICPC2EENG|PT;MTHICPC2ICD10AE|PT;SOP|PT;ICF|HT;ICF|PT;ICF|MTH_HT;ICF|MTH_PT;ICF-CY|HT;ICF-CY|PT;ICF-CY|MTH_HT;ICF-CY|MTH_PT;ICPC2ICD10ENG|PT;ICPC|PX;ICPC|PT;ICPC|PS;ICPC|PC;ICPC|CX;ICPC|CP;ICPC|CS;ICPC|CC;ICPC2EENG|CO;ICPC|CO;MTHICPC2EAE|AB;ICPC2EENG|AB;ICPC2P|PTN;ICPC2P|MTH_PTN;ICPC2P|PT;ICPC2P|MTH_PT;ICPC2P|OPN;ICPC2P|MTH_OPN;ICPC2P|OP;ICPC2P|MTH_OP;AOT|PT;AOT|ET;HCPCS|OP;HCDT|OP;HCPT|OP;HCPCS|OM;HCPCS|OAM;GO|PT;GO|MTH_PT;GO|ET;GO|MTH_ET;GO|SY;GO|MTH_SY;GO|OP;GO|MTH_OP;GO|OET;GO|MTH_OET;GO|IS;GO|MTH_IS;PDQ|ET;PDQ|CU;PDQ|MTH_LV;PDQ|LV;PDQ|MTH_AB;PDQ|MTH_ACR;PDQ|ACR;PDQ|AB;PDQ|BD;PDQ|FBD;PDQ|OP;PDQ|CCN;PDQ|CHN;PDQ|MTH_CHN;PDQ|IS;PDQ|MTH_BD;NCBI|USN;NCBI|USY;NCBI|SY;NCBI|UCN;NCBI|CMN;NCBI|UE;NCBI|EQ;NCBI|AUN;NCBI|UAUN;LNC|LN;LNC|MTH_LN;LNC|OSN;LNC|CN;LNC|MTH_CN;LNC|LPN;LNC|LPDN;LNC|HC;LNC|HS;LNC|OLC;LNC|LC;LNC|XM;LNC|LS;LNC|LO;LNC|MTH_LO;LNC|OOSN;LNC|LA;ICD10CM|PT;ICD9CM|PT;MDR|OL;MDR|MTH_OL;ICD10CM|HT;ICD9CM|HT;CCS_10|HT;CCS_10|MD;CCS_10|MV;CCS_10|SD;CCS_10|SP;CCS_10|XM;CCS|HT;CCS|MD;CCS|SD;CCS|MV;CCS|SP;CCS|XM;ICPC2ICD10ENG|XM;ICD10AE|HT;ICD10PCS|PT;ICD10PCS|PX;ICD10PCS|HX;ICD10PCS|MTH_HX;ICD10PCS|HT;ICD10PCS|HS;ICD10PCS|AB;ICD10|HT;ICD10AE|HX;ICD10|HX;ICD10AE|HS;ICD10|HS;ICD10AMAE|HT;ICD10AM|HT;UMD|HT;ICPC|HT;NUCCPT|PT;NUCCPT|OP;NUCCPT|MP;HL7V3.0|CSY;HL7V3.0|PT;HL7V2.5|PT;HL7V3.0|CDO;HL7V3.0|VS;HL7V3.0|BR;HL7V3.0|CPR;HL7V3.0|CR;HL7V3.0|NPT;HL7V3.0|OP;HL7V3.0|ONP;HL7V2.5|HTN;CPT|HT;CDT|HT;MTHHH|HT;CCC|PT;CCC|HT;NIC|IV;NIC|HC;NANDA-I|PT;NANDA-I|HT;NANDA-I|HC;NANDA-I|RT;OMS|MTH_SI;OMS|PR;OMS|TG;OMS|HT;OMS|PQ;OMS|IVC;OMS|SI;OMS|SCALE;NIC|AC;NOC|OC;NOC|ID;NIC|HT;NOC|HT;NOC|HC;CCC|MTH_HT;CCC|MP;ALT|PT;ALT|HT;MTH|CV;MTH|XM;MTH|PT;MTH|SY;MTH|RT;ICD10CM|ET;MTHICD9|ET;ICD10CM|AB;ICD9CM|AB;PSY|PT;PSY|HT;PSY|ET;MEDLINEPLUS|ET;MEDLINEPLUS|SY;MEDLINEPLUS|HT;LCH_NW|PT;LCH|PT;MSH|HT;MSH|HS;MSH|DEV;MSH|DSV;MSH|QAB;MSH|QEV;MSH|QSV;MSH|PM;LCH_NW|XM;CPT|AB;HCPT|AB;HCPCS|AB;WHO|PT;WHO|OS;WHO|HT;WHO|IT;SNMI|PT;SNMI|PX;SNMI|HT;SNMI|HX;SNMI|RT;SNMI|SY;SNMI|SX;SNMI|AD;SNM|PT;SNM|RT;SNM|HT;SNM|SY;SNM|RS;RCD|PT;RCD|OP;RCD|SY;RCD|IS;RCD|AT;RCD|AS;RCD|AB;RCDSA|PT;RCDSY|PT;RCDAE|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-gov.nih.nlm.umls.mmsys.io.NLMFileMetamorphoSysInputStream.meta_source_uri=/home/ubuntu/kg2-build/umls/2018AB-full +gov.nih.nlm.umls.mmsys.io.NLMFileMetamorphoSysInputStream.meta_source_uri=/home/ubuntu/kg2-build/umls/2022AA-full gov.nih.nlm.umls.mmsys.filter.SuppressibleFilter.confirm_default_suppressible_sabttys= gov.nih.nlm.umls.mmsys.filter.SourceListFilter.enforce_dep_source_selection=true From 771f54bcc44b9f81d9460d280926f04ff16f2ec9 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 8 Jul 2022 11:26:44 -0700 Subject: [PATCH 004/127] #220 Update extract-umls.sh --- extract-umls.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/extract-umls.sh b/extract-umls.sh index 98dd682c..29627694 100755 --- a/extract-umls.sh +++ b/extract-umls.sh @@ -20,7 +20,7 @@ source ${config_dir}/master-config.shinc output_dir=${1:-${BUILD_DIR}} umls_cui_file=${2:-${BUILD_DIR}/umls_cuis.tsv} -umls_ver=2020AA +umls_ver=2022AA umls_file_base=${umls_ver}-metathesaurus umls2rdf_release=rtx-2.2 umls2rdf_pkgname=umls2rdf-${umls2rdf_release} @@ -46,7 +46,7 @@ cp ${CODE_DIR}/umls-config.prop ${config_file} ## unpack UMLS zip archive unzip ${umls_dir}/umls-${umls_file_base}.zip -d ${umls_dir}/ -mv ${umls_dir}/2020AA/META/* ${umls_dest_dir} +mv ${umls_dir}/2022AA/META/* ${umls_dest_dir} mysql_user=`grep 'user = ' ${mysql_conf} | sed 's/user = //g'` mysql_password=`grep 'password = ' ${mysql_conf} | sed 's/password = //g'` From b1fb9156118523018110cb8a5fcc2e389a6f3159 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 8 Jul 2022 11:34:47 -0700 Subject: [PATCH 005/127] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e5335832..1523e6e3 100644 --- a/README.md +++ b/README.md @@ -210,7 +210,7 @@ which are in the `us-west-2` AWS region) and you will need to have an AWS authentication key pair that is configured to be able to read from (and write to) the bucket(s), so that the build script can download a copy of the full Unified Medical Language System (UMLS) distribution. The full UMLS distribution -(including SNOMED CT) (`umls-2020AA-metathesaurus.zip`; IANAL, but it appears +(including SNOMED CT) (`umls-2022AA-metathesaurus.zip`; IANAL, but it appears that the UMLS is encumbered by a license preventing redistribution so I have not hosted them on a public server for download; but you can get it for free at the [UMLS website](https://www.nlm.nih.gov/research/umls/) if you agree to the UMLS From 7d03e506aa7f56da6352ac42d9a2b9d981a40422 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 8 Jul 2022 11:44:01 -0700 Subject: [PATCH 006/127] #220 Update extract-chembl.sh --- extract-chembl.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/extract-chembl.sh b/extract-chembl.sh index ef8f2d62..0bb0b32c 100755 --- a/extract-chembl.sh +++ b/extract-chembl.sh @@ -18,7 +18,7 @@ config_dir=`dirname "$0"` source ${config_dir}/master-config.shinc chembl_dir=${BUILD_DIR}/chembl -chembl_version=27 +chembl_version=30 chembl_db_tarball=chembl_${chembl_version}_mysql.tar.gz chembl_sql_file=${chembl_dir}/chembl_${chembl_version}/chembl_${chembl_version}_mysql/chembl_${chembl_version}_mysql.dmp From 0b99fd76fe5150649b0a244e783dcacf58a3091b Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 8 Jul 2022 12:04:38 -0700 Subject: [PATCH 007/127] #220 Update extract-drugbank.sh --- extract-drugbank.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/extract-drugbank.sh b/extract-drugbank.sh index 530f9b4c..b4e375cd 100755 --- a/extract-drugbank.sh +++ b/extract-drugbank.sh @@ -18,9 +18,10 @@ date config_dir=`dirname "$0"` source ${config_dir}/master-config.shinc +drugbank_version=5.1.9 output_file=${1:-"${BUILD_DIR}/drugbank.xml"} -xml_filename="drugbank.xml.gz" +xml_filename=drugbank-${drugbank_version}.xml.gz ${s3_cp_cmd} s3://${s3_bucket}/${xml_filename} ${BUILD_DIR} gzip -cdf ${BUILD_DIR}/${xml_filename} > ${output_file} From 30a10a092c2f861c066d20a72ac99f3e74824a00 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 11 Jul 2022 08:55:57 -0700 Subject: [PATCH 008/127] #220 Update extract-ensembl.sh --- extract-ensembl.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/extract-ensembl.sh b/extract-ensembl.sh index dc8026f4..5ad77e72 100755 --- a/extract-ensembl.sh +++ b/extract-ensembl.sh @@ -15,7 +15,7 @@ date config_dir=`dirname "$0"` source ${config_dir}/master-config.shinc -ensembl_release=103 +ensembl_release=106 ensembl_json_file=${1:-"${BUILD_DIR}/ensembl/ensembl_genes_homo_sapiens.json"} output_dir=`dirname ${ensembl_json_file}` From 33fbec305296e88006defc0d3dbc07cfb6da0d16 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 11 Jul 2022 10:54:58 -0700 Subject: [PATCH 009/127] #220 Update extract-drugcentral.sh --- extract-drugcentral.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/extract-drugcentral.sh b/extract-drugcentral.sh index c57d246a..677e9353 100755 --- a/extract-drugcentral.sh +++ b/extract-drugcentral.sh @@ -25,7 +25,7 @@ drugcentral_database=drugcentral mkdir -p ${drugcentral_dir} -drugcentral_date=20200918 +drugcentral_date=2021_09_01 source="https://unmtid-shinyapps.net/download/DrugCentral/${drugcentral_date}/drugcentral-pgdump_${drugcentral_date}.sql.gz" download_filename=${drugcentral_dir}/drugcentral.sql.gz From 22d539d732d1dd0273150a3b4b67a70b390c716f Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 12 Jul 2022 11:21:57 -0700 Subject: [PATCH 010/127] #220 Update kg2-versions.md --- kg2-versions.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/kg2-versions.md b/kg2-versions.md index d5b95b0d..499d4f61 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -1,3 +1,34 @@ +# 2.7.7 +**Date: 2022.XX.XX** + +Counts: +- Nodes: 10,370,747 +- Edges: 54,078,936 + +Issues: +- Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) +- Additional issues that arose during the build: + +Build info: +- Biolink Model version: 2.2.11 +- Build host: `buildkg2.rtx.ai` +- Build directory: `/home/ubuntu/kg2-build` +- Build code branch: `master` +- Neo4j endpoint CNAME: `kg2-7-6.rtx.ai` +- Neo4j endpoint hostname: `kg2endpoint2.rtx.ai` +- Tracking issue for the build: Issue [#202](https://github.com/RTXteam/RTX-KG2/issues/202) +- Major knowledge source versions: + - SemMedDB: `23 (2021)` + - UMLS: `2022AA` + - ChEMBL: `30` + - DrugBank: `5.1.9` + - Ensembl: `106` + - GO annotations: `2021-07-01` + - UniProtKB: `2022_02` + - UniChem: `385` + - DrugCentral: `48` + - KEGG: `103.0` + # 2.7.6 **Date: 2022.05.10** From 4217b3f6d9502f5cd1508c8ef9ceeb3a883a6b8c Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 12 Jul 2022 14:31:12 -0700 Subject: [PATCH 011/127] #220 Update version and kegg rule --- extract-kegg.sh | 4 ---- update_version.py | 55 +++++++++++++++++++++++++++-------------------- 2 files changed, 32 insertions(+), 27 deletions(-) diff --git a/extract-kegg.sh b/extract-kegg.sh index 712ca2a2..89a0b9a8 100755 --- a/extract-kegg.sh +++ b/extract-kegg.sh @@ -20,10 +20,6 @@ source ${config_dir}/master-config.shinc output_file=${1:-"${BUILD_DIR}/kegg.json"} -cache_control_helper_link="https://raw.githubusercontent.com/RTXteam/RTX/master/code/reasoningtool/kg-construction/cache_control_helper.py" - -curl -L ${cache_control_helper_link} > ${CODE_DIR}/cache_control_helper.py - ${VENV_DIR}/bin/python3 -u ${CODE_DIR}/query_kegg.py ${output_file} date diff --git a/update_version.py b/update_version.py index 423bbfc7..562e52aa 100755 --- a/update_version.py +++ b/update_version.py @@ -17,6 +17,9 @@ __email__ = '' __status__ = 'Prototype' +VERSION = '2.7.7' +VERSION_FILE = 'kg2-version.txt' + def get_args(): arg_parser = argparse.ArgumentParser(description='update_version.py: \ @@ -34,26 +37,32 @@ def get_args(): if __name__ == '__main__': - args = get_args() - input_file_name = args.versionFile - increment_major = args.increment_major - increment_minor = args.increment_minor - assert not (increment_major and increment_minor), "cannot specify both --increment_major and --increment_minor at the same time" - input_file = open(input_file_name, "r") - for line in input_file: - input_file.close() - output_file = open(input_file_name, "w") - old_version = line.split(".") - graph_ver = old_version[0] - major_ver = int(old_version[1]) - minor_ver = int(old_version[2]) - if increment_major: - major_ver += 1 - minor_ver = 0 - elif increment_minor: - minor_ver += 1 - new_version = graph_ver + "." + str(major_ver) + "." + str(minor_ver) - output_file.write(new_version) - output_file.close() - print("KG2 version: " + new_version) - break + output_file = open(VERSION_FILE, 'w') + output_file.write(VERSION) + output_file.close() + print("KG2 version: " VERSION) + + + # args = get_args() + # input_file_name = args.versionFile + # increment_major = args.increment_major + # increment_minor = args.increment_minor + # assert not (increment_major and increment_minor), "cannot specify both --increment_major and --increment_minor at the same time" + # input_file = open(input_file_name, "r") + # for line in input_file: + # input_file.close() + # output_file = open(input_file_name, "w") + # old_version = line.split(".") + # graph_ver = old_version[0] + # major_ver = int(old_version[1]) + # minor_ver = int(old_version[2]) + # if increment_major: + # major_ver += 1 + # minor_ver = 0 + # elif increment_minor: + # minor_ver += 1 + # new_version = graph_ver + "." + str(major_ver) + "." + str(minor_ver) + # output_file.write(new_version) + # output_file.close() + # print("KG2 version: " + new_version) + # break From 1101b6a5918b6a4b4c159e1a2dc8aaf7539c5895 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 12 Jul 2022 15:05:00 -0700 Subject: [PATCH 012/127] #220 Add prefixes --- curies-to-urls-map.yaml | 78 +++++++++++++++++++++++++++++++++++++---- kg2_util.py | 2 +- 2 files changed, 73 insertions(+), 7 deletions(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index e7af73e4..9317bd6d 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -7,12 +7,18 @@ use_for_bidirectional_mapping: AEO: http://purl.obolibrary.org/obo/AEO_ - AIR: https://identifiers.org/umls/AIR/ + - + alliancegenome: 'https://www.alliancegenome.org/' + - + apollo: 'https://github.com/GMOD/Apollo' - AraPort: http://purl.uniprot.org/araport/ - ARG: http://purl.obolibrary.org/obo/ARG_ - ARO: http://purl.obolibrary.org/obo/ARO_ + - + AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=' - ATC: http://purl.bioontology.org/ontology/ATC/ - @@ -21,18 +27,22 @@ use_for_bidirectional_mapping: BFO: http://purl.obolibrary.org/obo/BFO_ - bibo: http://purl.org/ontology/bibo/ -# - -# biolink: https://w3id.org/biolink/vocab/ - - biolink: https://w3id.org/linkml/ + biolink: https://w3id.org/biolink/vocab/ +# - +# biolink: https://w3id.org/linkml/ - biolink_download_source: https://raw.githubusercontent.com/biolink/biolink-model/master/ + - + bioschemas: 'https://bioschemas.org/' - BRO: http://bioontology.org/ontologies/BiomedicalResourceOntology.owl# - BSPO: http://purl.obolibrary.org/obo/BSPO_ - BTO: http://purl.obolibrary.org/obo/BTO_ + - + CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=' - CARO: http://purl.obolibrary.org/obo/CARO_ - @@ -49,22 +59,40 @@ use_for_bidirectional_mapping: CHEMBL.TARGET: "https://identifiers.org/chembl.target:" - CHMO: http://purl.obolibrary.org/obo/CHMO_ + - + CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/' - CL: http://purl.obolibrary.org/obo/CL_ - clinicaltrials: "https://identifiers.org/clinicaltrials:" + - + CLINVAR: 'http://identifiers.org/clinvar' - CLO: http://purl.obolibrary.org/obo/CLO_ + - + COAR_RESOURCE: 'http://purl.org/coar/resource_type/' + - + COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/' - CP: http://purl.obolibrary.org/obo/CP_ - - CPT: http://purl.bioontology.org/ontology/CPT/ + CPT: https://www.ama-assn.org/practice-management/cpt/ + - + CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc=' + - + CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc=' + - + CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc=' + - + CTD: 'http://ctdbase.org/' - CVDO: http://purl.obolibrary.org/obo/CVDO_ - dbpedia: http://dbpedia.org/resource/ - dc: http://purl.org/dc/elements/1.1/ + - + dcat: 'http://www.w3.org/ns/dcat#' - dcid: 'https://datacommons.org/browser/' - @@ -74,7 +102,7 @@ use_for_bidirectional_mapping: - DDANAT: http://purl.obolibrary.org/obo/DDANAT_ - - DGIdb: http://www.dgidb.org/ + DGIdb: https://www.dgidb.org/interaction_types - dictybase.gene: "https://identifiers.org/dictybase.gene:" - @@ -101,6 +129,14 @@ use_for_bidirectional_mapping: ECTO: http://purl.obolibrary.org/obo/ECTO_ - EDAM: http://purl.bioontology.org/ontology/edam/ + - + EDAM-DATA: 'http://edamontology.org/data_' + - + EDAM-FORMAT: 'http://edamontology.org/format_' + - + EDAM-OPERATION: 'http://edamontology.org/operation_' + - + EDAM-TOPIC: 'http://edamontology.org/topic_' - EFO: http://purl.bioontology.org/ontology/EFO/ - @@ -121,6 +157,8 @@ use_for_bidirectional_mapping: ExO: http://purl.obolibrary.org/obo/ExO_ - FAO: http://purl.obolibrary.org/obo/FAO_ + - + fabio: 'http://purl.org/spar/fabio/' - FBbt: http://purl.obolibrary.org/obo/FBbt_ - @@ -137,8 +175,18 @@ use_for_bidirectional_mapping: FMA: http://purl.obolibrary.org/obo/FMA_ - foaf: http://xmlns.com/foaf/0.1/ + - + foodb.compound: 'http://foodb.ca/foods/' + - + foodb.food: 'http://foodb.ca/compounds/' - FOODON: http://purl.obolibrary.org/obo/FOODON_ + - + FYECO: 'https://www.pombase.org/term/' + - + FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology + - + GAMMA: 'http://translator.renci.org/GAMMA_' - GARD: http://purl.obolibrary.org/obo/GARD_ - @@ -151,12 +199,16 @@ use_for_bidirectional_mapping: GENO: http://purl.obolibrary.org/obo/GENO_ - GEO: http://purl.obolibrary.org/obo/GEO_ + - + gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#' - GO: http://purl.obolibrary.org/obo/GO_ - GOREL: http://purl.obolibrary.org/obo/GOREL_ - GO_REF: "https://identifiers.org/GO_REF:" + - + gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#' - GTPI: https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId= - @@ -206,7 +258,9 @@ use_for_bidirectional_mapping: - KEGG_source: "https://www.genome.jp" - - LOINC: http://purl.bioontology.org/ontology/LNC/ + linkml: 'https://w3id.org/linkml/' + - + LOINC: http://loinc.org/rdf/ - MA: http://purl.obolibrary.org/obo/MA_ - @@ -231,8 +285,12 @@ use_for_bidirectional_mapping: miRBase: http://identifiers.org/mirbase - miRGate: http://mirgate.bioinfo.cnio.es + - + mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:' - MMO: http://purl.obolibrary.org/obo/MMO_ + - + MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_' - MOD: http://purl.obolibrary.org/obo/MOD_ - @@ -295,6 +353,8 @@ use_for_bidirectional_mapping: OMIABIS: http://purl.obolibrary.org/obo/OMIABIS_ - OMIM: http://purl.obolibrary.org/obo/OMIM_ + - + OMIM.PS: 'https://www.omim.org/phenotypicSeries/' - OMIMDiseaseCluster: http://purl.obolibrary.org/obo/DC_ - @@ -441,6 +501,10 @@ use_for_bidirectional_mapping: VT: http://purl.obolibrary.org/obo/VT_ - wb: "https://identifiers.org/wb:" + - + WBls: 'http://purl.obolibrary.org/obo/WBBL_' + - + WBbt: 'http://purl.obolibrary.org/obo/WBBT_' - WIKIDATA: 'https://www.wikidata.org/wiki/' - @@ -541,6 +605,8 @@ use_for_contraction_only: ICD9: http://purl.obolibrary.org/obo/ICD9_ - KEGG: http://purl.obolibrary.org/obo/KEGG_ + - + LOINC: http://purl.bioontology.org/ontology/LNC/ - MEDDRA: http://purl.obolibrary.org/obo/MedDRA_ - diff --git a/kg2_util.py b/kg2_util.py index 080e4056..20b8a953 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -125,7 +125,7 @@ BASE_URL_IDENTIFIERS_ORG_REGISTRY = \ 'https://registry.identifiers.org/registry/' -BASE_URL_BIOLINK_CONCEPTS = 'https://w3id.org/linkml/' +BASE_URL_BIOLINK_CONCEPTS = 'https://w3id.org/biolink/vocab/' BASE_URL_BIOLINK_ONTOLOGY = 'https://w3id.org/biolink/biolink-model' BASE_URL_BIOLINK_META = 'https://w3id.org/biolink/biolinkml/meta/' BASE_URL_CHEMBL_COMPOUND = BASE_BASE_URL_IDENTIFIERS_ORG + 'chembl.compound:' From 49baa9c4434f1819f3d2b35c9240ea5ebf740232 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 14 Jul 2022 11:39:28 -0700 Subject: [PATCH 013/127] #222 Comment out unused predicates --- predicate-remap.yaml | 568 +++++++++++++++++++++---------------------- 1 file changed, 284 insertions(+), 284 deletions(-) diff --git a/predicate-remap.yaml b/predicate-remap.yaml index be5e25dc..ff4cbcd0 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -408,10 +408,10 @@ DGIdb:activator: rename: - entity_positively_regulates_entity - biolink:entity_positively_regulates_entity -DGIdb:adduct: - rename: - - directly_interacts_with - - biolink:directly_interacts_with +# DGIdb:adduct: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with DGIdb:affects: rename: - affects @@ -440,10 +440,10 @@ DGIdb:antisense_oligonucleotide: rename: - decreases_expression_of - biolink:decreases_expression_of -DGIdb:binder: - rename: - - directly_interacts_with - - biolink:directly_interacts_with +# DGIdb:binder: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with DGIdb:blocker: rename: - decreases_activity_of @@ -452,18 +452,18 @@ DGIdb:blocker: # rename: # - decreases_activity_of # - biolink:decreases_activity_of -DGIdb:chaperone: - rename: - - directly_interacts_with - - biolink:directly_interacts_with -DGIdb:cleavage: - rename: - - affects_degradation_of - - biolink:affects_degradation_of -DGIdb:cofactor: - rename: - - directly_interacts_with - - biolink:directly_interacts_with +# DGIdb:chaperone: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +# DGIdb:cleavage: +# rename: +# - affects_degradation_of +# - biolink:affects_degradation_of +# DGIdb:cofactor: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with # DGIdb:gating_inhibitor: # rename: # - decreases_activity_of @@ -484,18 +484,18 @@ DGIdb:inverse_agonist: rename: - decreases_activity_of - biolink:decreases_activity_of -DGIdb:ligand: - rename: - - directly_interacts_with - - biolink:directly_interacts_with +# DGIdb:ligand: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with DGIdb:modulator: rename: - affects_activity_of - biolink:affects_activity_of -DGIdb:multitarget: - rename: - - directly_interacts_with - - biolink:directly_interacts_with +# DGIdb:multitarget: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with DGIdb:negative_modulator: rename: - decreases_activity_of @@ -504,10 +504,10 @@ DGIdb:partial_agonist: rename: - increases_activity_of - biolink:increases_activity_of -DGIdb:partial_antagonist: - rename: - - decreases_activity_of - - biolink:decreases_activity_of +# DGIdb:partial_antagonist: +# rename: +# - decreases_activity_of +# - biolink:decreases_activity_of # DGIdb:positive_allosteric_modulator: # rename: # - increases_activity_of @@ -516,22 +516,22 @@ DGIdb:positive_modulator: rename: - increases_activity_of - biolink:increases_activity_of -DGIdb:potentiator: - rename: - - increases_activity_of - - biolink:increases_activity_of -DGIdb:product_of: - rename: - - derives_from - - biolink:derives_from -DGIdb:stimulator: - rename: - - increases_activity_of - - biolink:increases_activity_of -DGIdb:substrate: - rename: - - increases_degradation_of - - biolink:increases_degradation_of +# DGIdb:potentiator: +# rename: +# - increases_activity_of +# - biolink:increases_activity_of +# DGIdb:product_of: +# rename: +# - derives_from +# - biolink:derives_from +# DGIdb:stimulator: +# rename: +# - increases_activity_of +# - biolink:increases_activity_of +# DGIdb:substrate: +# rename: +# - increases_degradation_of +# - biolink:increases_degradation_of DGIdb:suppressor: rename: - decreases_activity_of @@ -540,14 +540,14 @@ DGIdb:vaccine: rename: - decreases_activity_of - biolink:decreases_activity_of -DOID-PROPERTY:derives_from: - rename: - - derives_from - - biolink:derives_from -DOID-PROPERTY:has_symptom: - rename: - - has_phenotype - - biolink:has_phenotype +# DOID-PROPERTY:derives_from: +# rename: +# - derives_from +# - biolink:derives_from +# DOID-PROPERTY:has_symptom: +# rename: +# - has_phenotype +# - biolink:has_phenotype DRUGBANK:activator: rename: - entity_positively_regulates_entity @@ -780,10 +780,10 @@ DRUGBANK:weak_inhibitor: rename: - entity_negatively_regulates_entity - biolink:entity_negatively_regulates_entity -DrugCentral:5271: - rename: - - diagnoses - - biolink:diagnoses +# DrugCentral:5271: +# rename: +# - diagnoses +# - biolink:diagnoses DrugCentral:activator: rename: - entity_positively_regulates_entity @@ -2227,22 +2227,22 @@ MONDO:predisposes_towards: rename: - contributes_to - biolink:contributes_to -NBO-PROPERTY:by_means: - rename: - - actively_involved_in - - biolink:actively_involved_in -NBO-PROPERTY:has_participant: - rename: - - has_participant - - biolink:has_participant -NBO-PROPERTY:in_response_to: - invert: - - causes - - biolink:causes -NBO-PROPERTY:is_about: - rename: - - related_to - - biolink:related_to +# NBO-PROPERTY:by_means: +# rename: +# - actively_involved_in +# - biolink:actively_involved_in +# NBO-PROPERTY:has_participant: +# rename: +# - has_participant +# - biolink:has_participant +# NBO-PROPERTY:in_response_to: +# invert: +# - causes +# - biolink:causes +# NBO-PROPERTY:is_about: +# rename: +# - related_to +# - biolink:related_to NCIT:abnormal_cell_affected_by_chemical_or_drug: delete: null NCIT:abnormality_associated_with_allele: @@ -2317,10 +2317,10 @@ NCIT:biomarker_type_includes_gene: delete: null NCIT:biomarker_type_includes_gene_product: delete: null -NCIT:C15220: # diagnosis - rename: - - diagnoses - - biolink:diagnoses +# NCIT:C15220: # diagnosis +# rename: +# - diagnoses +# - biolink:diagnoses NCIT:cdrh_parent_of: invert: - subclass_of @@ -2901,10 +2901,10 @@ NCIT:qualifier_applies_to: rename: - related_to - biolink:related_to -NCIT:R40: - rename: - - located_in - - biolink:located_in +# NCIT:R40: +# rename: +# - located_in +# - biolink:located_in NCIT:R81: rename: - related_to @@ -2913,66 +2913,66 @@ NCIT:R82: rename: - part_of - biolink:part_of -NCIT:R88: # disease is stage - rename: - - related_to - - biolink:related_to -NCIT:R89: - rename: - - has_phenotype - - biolink:has_phenotype -NCIT:R108: - rename: - - has_phenotype - - biolink:has_phenotype -NCIT:R115: - rename: - - has_phenotype - - biolink:has_phenotype -NCIT:R145: - rename: - - located_in - - biolink:located_in -NCIT:R155: - rename: - - located_in - - biolink:located_in -NCIT:R156: - rename: - - located_in - - biolink:located_in +# NCIT:R88: # disease is stage +# rename: +# - related_to +# - biolink:related_to +# NCIT:R89: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R108: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R115: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R145: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R155: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R156: +# rename: +# - located_in +# - biolink:located_in NCIT:R163: rename: - related_to - biolink:related_to -NCIT:R165: - rename: - - located_in - - biolink:located_in -NCIT:R166: - rename: - - located_in - - biolink:located_in -NCIT:R167: - rename: - - located_in - - biolink:located_in -NCIT:R168: - rename: - - located_in - - biolink:located_in -NCIT:R169: - rename: - - located_in - - biolink:located_in -NCIT:R170: - rename: - - located_in - - biolink:located_in -NCIT:R171: - rename: - - located_in - - biolink:located_in +# NCIT:R165: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R166: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R167: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R168: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R169: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R170: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R171: +# rename: +# - located_in +# - biolink:located_in NCIT:regimen_has_accepted_use_for_disease: rename: - treats @@ -3045,10 +3045,10 @@ OBO:bspo#parallel_to: rename: - coexists_with - biolink:coexists_with -OBO:doid#has_symptom: - rename: - - has_phenotype - - biolink:has_phenotype +# OBO:doid#has_symptom: +# rename: +# - has_phenotype +# - biolink:has_phenotype OBO:envo#has_increased_levels_of: rename: - related_to @@ -3065,18 +3065,18 @@ OBO:exo#interacts_with_an_exposure_receptor_via: rename: - interacts_with - biolink:interacts_with -OBO:exo.obo#interacts_with: - rename: - - interacts_with - - biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_stressor_via: - rename: - - interacts_with - - biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_receptor_via: - rename: - - interacts_with - - biolink:interacts_with +# OBO:exo.obo#interacts_with: +# rename: +# - interacts_with +# - biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_stressor_via: +# rename: +# - interacts_with +# - biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_receptor_via: +# rename: +# - interacts_with +# - biolink:interacts_with OBO:has_role: rename: - related_to @@ -3101,14 +3101,14 @@ OBO:nbo#is_about: rename: - related_to - biolink:related_to -OBO:uo#is_unit_of: - invert: - - related_to - - biolink:related_to -OIO:hasDbXref: - rename: - - close_match - - biolink:close_match +# OBO:uo#is_unit_of: +# invert: +# - related_to +# - biolink:related_to +# OIO:hasDbXref: +# rename: +# - close_match +# - biolink:close_match OMIM:allelic_variant_of: rename: - is_sequence_variant_of @@ -3185,14 +3185,14 @@ ORPHANET:C017: rename: - related_to - biolink:related_to -PATO:0000085: # sensitivity toward - rename: - - associated_with_sensitivity_to - - biolink:associated_with_sensitivity_to -PATO:correlates_with: - rename: - - correlated_with - - biolink:correlated_with +# PATO:0000085: # sensitivity toward +# rename: +# - associated_with_sensitivity_to +# - biolink:associated_with_sensitivity_to +# PATO:correlates_with: +# rename: +# - correlated_with +# - biolink:correlated_with PATO:decreased_in_magnitude_relative_to: rename: - related_to @@ -3899,10 +3899,10 @@ RO:0002452: # has symptom rename: - has_phenotype - biolink:has_phenotype -RO:0002470: - rename: - - related_to - - biolink:related_to +# RO:0002470: +# rename: +# - related_to +# - biolink:related_to RO:0002473: rename: - composed_primarily_of @@ -4361,14 +4361,14 @@ SEMMEDDB:xref: - biolink:related_to SIO:000001: delete: null -SIO:000983: - rename: - - biomarker_for - - biolink:biomarker_for -SIO:001331: # diagnosis - rename: - - diagnoses - - biolink:diagnoses +# SIO:000983: +# rename: +# - biomarker_for +# - biolink:biomarker_for +# SIO:001331: # diagnosis +# rename: +# - diagnoses +# - biolink:diagnoses # SO:adjacent_to: # rename: # - coexists_with @@ -4417,90 +4417,90 @@ SO:has_origin: # invert: # - gene_product_of # - biolink:gene_product_of -UBERON:anastomoses_with: - rename: - - coexists_with - - biolink:coexists_with -UBERON:anteriorly_connected_to: - rename: - - coexists_with - - biolink:coexists_with -UBERON:channel_for: - rename: - - coexists_with - - biolink:coexists_with -UBERON:channels_from: - rename: - - coexists_with - - biolink:coexists_with -UBERON:channels_into: - rename: - - coexists_with - - biolink:coexists_with -UBERON:conduit_for: - rename: - - coexists_with - - biolink:coexists_with -UBERON:distally_connected_to: - rename: - - coexists_with - - biolink:coexists_with +# UBERON:anastomoses_with: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:anteriorly_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channel_for: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channels_from: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channels_into: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:conduit_for: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:distally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with # UBERON:existence_starts_and_ends_during: # rename: # - coexists_with # - biolink:coexists_with -UBERON:extends_fibers_into: - rename: - - coexists_with - - biolink:coexists_with -UBERON:filtered_through: - rename: - - coexists_with - - biolink:coexists_with -UBERON:in_central_side_of: - rename: - - coexists_with - - biolink:coexists_with -UBERON:in_innermost_side_of: - rename: - - coexists_with - - biolink:coexists_with -UBERON:in_outermost_side_of: - rename: - - coexists_with - - biolink:coexists_with -UBERON:indirectly_supplies: - rename: - - coexists_with - - biolink:coexists_with -UBERON:posteriorly_connected_to: - rename: - - coexists_with - - biolink:coexists_with -UBERON:protects: - rename: - - coexists_with - - biolink:coexists_with -UBERON:proximally_connected_to: - rename: - - coexists_with - - biolink:coexists_with -UBERON:sexually_homologous_to: - rename: - - coexists_with - - biolink:coexists_with -UBERON:site_of: - invert: - - occurs_in - - biolink:occurs_in -UBERON:subdivision_of: - invert: - - has_part - - biolink:has_part -UBERON:synapsed_by: - rename: - - related_to - - biolink:related_to +# UBERON:extends_fibers_into: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:filtered_through: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_central_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_innermost_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_outermost_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:indirectly_supplies: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:posteriorly_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:protects: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:proximally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:sexually_homologous_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:site_of: +# invert: +# - occurs_in +# - biolink:occurs_in +# UBERON:subdivision_of: +# invert: +# - has_part +# - biolink:has_part +# UBERON:synapsed_by: +# rename: +# - related_to +# - biolink:related_to UBERON_CORE:anastomoses_with: rename: - coexists_with @@ -4581,22 +4581,22 @@ UBERON_CORE:synapsed_by: rename: - coexists_with - biolink:coexists_with -UBERON_NONAMESPACE:connected_to: - rename: - - related_to - - biolink:related_to -UBERON_NONAMESPACE:distally_connected_to: - rename: - - coexists_with - - biolink:coexists_with -UBERON_NONAMESPACE:innervated_by: - rename: - - related_to - - biolink:related_to -UBERON_NONAMESPACE:subdivision_of: - rename: - - coexists_with - - biolink:coexists_with +# UBERON_NONAMESPACE:connected_to: +# rename: +# - related_to +# - biolink:related_to +# UBERON_NONAMESPACE:distally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON_NONAMESPACE:innervated_by: +# rename: +# - related_to +# - biolink:related_to +# UBERON_NONAMESPACE:subdivision_of: +# rename: +# - coexists_with +# - biolink:coexists_with UMLS:has_physiologic_effect: rename: - causes @@ -4719,10 +4719,10 @@ UMLS:supported_concept_property_in: delete: null UMLS:supported_concept_relationship_in: delete: null -UO-PROPERTY:is_unit_of: - rename: - - related_to - - biolink:related_to +# UO-PROPERTY:is_unit_of: +# rename: +# - related_to +# - biolink:related_to VANDF:has_ingredient: rename: - has_part From 9ac17fb92aed7853e0b258e8347efede126ccf5d Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 14 Jul 2022 11:46:52 -0700 Subject: [PATCH 014/127] #220 Updating kg2-versions.md --- kg2-versions.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/kg2-versions.md b/kg2-versions.md index 499d4f61..717e332d 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -7,14 +7,16 @@ Counts: Issues: - Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) +- Issue [#221](https://github.com/RTXteam/RTX-KG2/issues/221) +- Issue [#222](https://github.com/RTXteam/RTX-KG2/issues/222) - Additional issues that arose during the build: Build info: -- Biolink Model version: 2.2.11 +- Biolink Model version: 2.4.2 - Build host: `buildkg2.rtx.ai` - Build directory: `/home/ubuntu/kg2-build` - Build code branch: `master` -- Neo4j endpoint CNAME: `kg2-7-6.rtx.ai` +- Neo4j endpoint CNAME: `kg2-7-7.rtx.ai` - Neo4j endpoint hostname: `kg2endpoint2.rtx.ai` - Tracking issue for the build: Issue [#202](https://github.com/RTXteam/RTX-KG2/issues/202) - Major knowledge source versions: From 704625f1b5df8e7e349f9fdc862ce502be405063 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 20 Jul 2022 12:20:29 -0700 Subject: [PATCH 015/127] #220 Correct name for drugbank file --- extract-drugbank.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/extract-drugbank.sh b/extract-drugbank.sh index b4e375cd..99a6ad20 100755 --- a/extract-drugbank.sh +++ b/extract-drugbank.sh @@ -21,7 +21,7 @@ source ${config_dir}/master-config.shinc drugbank_version=5.1.9 output_file=${1:-"${BUILD_DIR}/drugbank.xml"} -xml_filename=drugbank-${drugbank_version}.xml.gz +xml_filename=drugbank_${drugbank_version}.xml.gz ${s3_cp_cmd} s3://${s3_bucket}/${xml_filename} ${BUILD_DIR} gzip -cdf ${BUILD_DIR}/${xml_filename} > ${output_file} From 04e3a28a3b26bd927bb2a007df857eae95f5173d Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 20 Jul 2022 13:17:52 -0700 Subject: [PATCH 016/127] #221 Updates to predicate-remap.yaml --- predicate-remap.yaml | 114 +++++++++++++++++++++++++++++++++++++++---- 1 file changed, 105 insertions(+), 9 deletions(-) diff --git a/predicate-remap.yaml b/predicate-remap.yaml index ff4cbcd0..cd96892e 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -400,6 +400,66 @@ CL:lacks_plasma_membrane_part: rename: - lacks_part - biolink:lacks_part +CPT:has_add_on_code: + rename: + - related_to + - biolink:related_to +CPT:mapped_to: + rename: + - related_to + - biolink:related_to +CTD:affects_abundance_of: + rename: + - affects_abundance_of + - biolink:affects_abundance_of +CTD:affects_folding_of: + rename: + - affects_folding_of + - biolink:affects_folding_of +CTD:affects_molecular_modification_of: + rename: + - affects_molecular_modification_of + - biolink:affects_molecular_modification_of +CTD:affects_synthesis_of: + rename: + - affects_synthesis_of + - biolink:affects_synthesis_of +CTD:decreases_folding_of: + rename: + - decreases_folding_of + - biolink:decreases_folding_of +CTD:decreases_localization_of: + rename: + - decreases_localization_of + - biolink:decreases_localization_of +CTD:decreases_metabolic_processing_of: + rename: + - decreases_metabolic_processing_of + - biolink:decreases_metabolic_processing_of +CTD:decreases_molecular_modification_of: + rename: + - decreases_molecular_modification_of + - biolink:decreases_molecular_modification_of +CTD:increases_folding_of: + rename: + - increases_folding_of + - biolink:increases_folding_of +CTD:increases_localization_of: + rename: + - increases_localization_of + - biolink:increases_localization_of +CTD:increases_metabolic_processing_of: + rename: + - increases_metabolic_processing_of + - biolink:increases_metabolic_processing_of +CTD:increases_molecular_modification_of: + rename: + - increases_molecular_modification_of + - biolink:increases_molecular_modification_of +CTD:increases_synthesis_of: + rename: + - increases_synthesis_of + - biolink:increases_synthesis_of DDANAT:develops_from: rename: - develops_from @@ -3710,7 +3770,15 @@ RO:0002254: RO:0002256: rename: - causes - - biolink:causes + - biolink: +RO:0002263: + rename: + - acts_upstream_of + - biolink:acts_upstream_of +RO:0002264: + rename: + - acts_upstream_of_or_within + - biolink:acts_upstream_of_or_within RO:0002285: invert: - precedes @@ -3891,6 +3959,10 @@ RO:0002433: rename: - overlaps - biolink:overlaps +RO:0002434: + rename: + - interacts_with + - biolink:interacts_with RO:0002451: rename: - related_to @@ -4039,10 +4111,18 @@ RO:0003001: invert: - produces - biolink:produces +RO:0003003: + rename: + - increases_expression_of + - biolink:increases_expression_of RO:0003304: rename: - contributes_to - biolink:contributes_to +RO:0003309: + rename: + - exacerbates + - biolink:exacerbates RO:0004001: rename: - causes @@ -4099,10 +4179,26 @@ RO:0004029: rename: - associated_with - biolink:associated_with -RO:0004030: - invert: - - causes - - biolink:causes +# RO:0004030: +# invert: +# - causes +# - biolink: +RO:0004032: + rename: + - acts_upstream_of_or_within_positive_effect + - biolink:acts_upstream_of_or_within_positive_effect +RO:0004033: + rename: + - acts_upstream_of_or_within_negative_effect + - biolink:acts_upstream_of_or_within_negative_effect +RO:0004034: + rename: + - acts_upstream_of_positive_effect + - biolink:acts_upstream_of_positive_effect +RO:0004035: + rename: + - acts_upstream_of_negative_effect + - biolink:acts_upstream_of_negative_effect RO:0009001: rename: - related_to @@ -4255,8 +4351,8 @@ SEMMEDDB:compared_with: - biolink:related_to SEMMEDDB:complicates: rename: - - interacts_with - - biolink:interacts_with + - exacerbates + - biolink:exacerbates SEMMEDDB:converts_to: invert: - derives_from @@ -4279,8 +4375,8 @@ SEMMEDDB:inhibits: - biolink:entity_negatively_regulates_entity SEMMEDDB:interacts_with: rename: - - physically_interacts_with - - biolink:physically_interacts_with + - interacts_with + - biolink:interacts_with SEMMEDDB:isa: rename: - subclass_of From beefa1f71aedc07a78675b0f9283f38152016a32 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 26 Jul 2022 10:36:15 -0700 Subject: [PATCH 017/127] #221 Created predicate_remap_new.yaml --- predicate_remap_new.yaml | 3850 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 3850 insertions(+) create mode 100644 predicate_remap_new.yaml diff --git a/predicate_remap_new.yaml b/predicate_remap_new.yaml new file mode 100644 index 00000000..d7eb3916 --- /dev/null +++ b/predicate_remap_new.yaml @@ -0,0 +1,3850 @@ +BFO:0000050: + operation: invert + core_predicate: biolink:has_part +BFO:0000051: + operation: rename + core_predicate: biolink:has_part +BFO:0000054: + operation: rename + core_predicate: biolink:related_to +BFO:0000055: + operation: rename + core_predicate: biolink:has_part +# BFO:0000056: +# invert: +# - has_participant +# - biolink:has_participant +BFO:0000062: + operation: invert + core_predicate: biolink:precedes +BFO:0000063: + operation: rename + core_predicate: biolink:precedes +BFO:0000066: + operation: rename + core_predicate: biolink:occurs_in +BFO:0000067: + operation: rename + core_predicate: biolink:occurs_in +BFO:0000068: + operation: rename + core_predicate: biolink:related_to +BFO:0000069: + operation: rename + core_predicate: biolink:related_to +BFO:0000117: + operation: rename + core_predicate: biolink:has_part +BFO:0000167: + operation: rename + core_predicate: biolink:has_participant +BSPO:0000096: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000097: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000098: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000099: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000100: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000102: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000104: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000107: + operation: rename + core_predicate: biolink:located_in +BSPO:0000108: + operation: rename + core_predicate: biolink:located_in +BSPO:0000110: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000113: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0000120: + operation: rename + core_predicate: biolink:located_in +BSPO:0000121: + operation: rename + core_predicate: biolink:located_in +BSPO:0000122: + operation: rename + core_predicate: biolink:located_in +BSPO:0000123: + operation: rename + core_predicate: biolink:located_in +BSPO:0000124: + operation: rename + core_predicate: biolink:located_in +BSPO:0000125: + operation: rename + core_predicate: biolink:located_in +BSPO:0000126: + operation: rename + core_predicate: biolink:located_in +BSPO:0001100: + operation: rename + core_predicate: biolink:located_in +BSPO:0001101: + operation: rename + core_predicate: biolink:located_in +BSPO:0001106: + operation: invert + core_predicate: biolink:has_part +BSPO:0001107: + operation: rename + core_predicate: biolink:located_in +BSPO:0001108: + operation: invert + core_predicate: biolink:has_part +BSPO:0001113: + operation: invert + core_predicate: biolink:has_part +BSPO:0001115: + operation: invert + core_predicate: biolink:has_part +BSPO:0005001: + operation: rename + core_predicate: biolink:overlaps +BSPO:0015001: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015002: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015003: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015005: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015006: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015007: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015008: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015009: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015012: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015014: + operation: rename + core_predicate: biolink:coexists_with +BSPO:0015101: + operation: rename + core_predicate: biolink:located_in +BSPO:0015102: + operation: rename + core_predicate: biolink:located_in +BSPO:0015202: + operation: rename + core_predicate: biolink:located_in +BTO:develops_from: + operation: rename + core_predicate: biolink:develops_from +BTO:related_to: + operation: rename + core_predicate: biolink:related_to +CHEBI:has_functional_parent: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEBI:has_parent_hydride: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEBI:is_conjugate_acid_of: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEBI:is_conjugate_base_of: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEBI:is_enantiomer_of: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEBI:is_substituent_group_from: + operation: invert + core_predicate: biolink:has_part +CHEBI:is_tautomer_of: + operation: rename + core_predicate: biolink:chemically_similar_to +CHEMBL.MECHANISM:activator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +CHEMBL.MECHANISM:agonist: + operation: rename + core_predicate: biolink:increases_activity_of +CHEMBL.MECHANISM:allosteric_antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +CHEMBL.MECHANISM:antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +CHEMBL.MECHANISM:antisense_inhibitor: + operation: rename + core_predicate: biolink:decreases_expression_of +CHEMBL.MECHANISM:binding_agent: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:blocker: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:chelating_agent: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:cross-linking_agent: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:degrader: + operation: rename + core_predicate: biolink:increases_degradation_of +CHEMBL.MECHANISM:disrupting_agent: + operation: rename + core_predicate: biolink:disrupts +CHEMBL.MECHANISM:equivalent_to: + operation: rename + core_predicate: biolink:same_as +CHEMBL.MECHANISM:hydrolytic_enzyme: + operation: rename + core_predicate: biolink:increases_degradation_of +CHEMBL.MECHANISM:inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:inverse_agonist: + operation: rename + core_predicate: biolink:decreases_activity_of +CHEMBL.MECHANISM:modulator: + operation: rename + core_predicate: biolink:entity_regulates_entity +CHEMBL.MECHANISM:negative_allosteric_modulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:negative_modulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:opener: + operation: rename + core_predicate: biolink:increases_activity_of +CHEMBL.MECHANISM:other: + operation: delete +CHEMBL.MECHANISM:overlaps_with: + operation: rename + core_predicate: biolink:overlaps +CHEMBL.MECHANISM:oxidative_enzyme: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:partial_agonist: + operation: rename + core_predicate: biolink:increases_activity_of +CHEMBL.MECHANISM:positive_allosteric_modulator: + operation: rename + core_predicate: biolink:increases_activity_of +CHEMBL.MECHANISM:positive_modulator: + operation: rename + core_predicate: biolink:increases_activity_of +CHEMBL.MECHANISM:proteolytic_enzyme: + operation: rename + core_predicate: biolink:increases_degradation_of +CHEMBL.MECHANISM:reducing_agent: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:releasing_agent: + operation: rename + core_predicate: biolink:increases_expression_of +CHEMBL.MECHANISM:rnai_inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:sequestering_agent: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:stabiliser: + operation: rename + core_predicate: biolink:increases_stability_of +CHEMBL.MECHANISM:subset_of: + operation: rename + core_predicate: biolink:subclass_of +CHEMBL.MECHANISM:substrate: + operation: rename + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:superset_of: + operation: invert + core_predicate: biolink:subclass_of +CL:has_completed: + operation: rename + core_predicate: biolink:has_completed +CL:has_high_plasma_membrane_amount: + operation: rename + core_predicate: biolink:has_increased_amount +CL:has_low_plasma_membrane_amount: + operation: rename + core_predicate: biolink:has_decreased_amount +CL:has_not_completed: + operation: rename + core_predicate: biolink:has_not_completed +CL:lacks_part: + operation: rename + core_predicate: biolink:lacks_part +CL:lacks_plasma_membrane_part: + operation: rename + core_predicate: biolink:lacks_part +CPT:has_add_on_code: + operation: rename + core_predicate: biolink:related_to +CPT:mapped_to: + operation: rename + core_predicate: biolink:related_to +CTD:affects_abundance_of: + operation: rename + core_predicate: biolink:affects_abundance_of +CTD:affects_folding_of: + operation: rename + core_predicate: biolink:affects_folding_of +CTD:affects_molecular_modification_of: + operation: rename + core_predicate: biolink:affects_molecular_modification_of +CTD:affects_synthesis_of: + operation: rename + core_predicate: biolink:affects_synthesis_of +CTD:decreases_folding_of: + operation: rename + core_predicate: biolink:decreases_folding_of +CTD:decreases_localization_of: + operation: rename + core_predicate: biolink:decreases_localization_of +CTD:decreases_metabolic_processing_of: + operation: rename + core_predicate: biolink:decreases_metabolic_processing_of +CTD:decreases_molecular_modification_of: + operation: rename + core_predicate: biolink:decreases_molecular_modification_of +CTD:increases_folding_of: + operation: rename + core_predicate: biolink:increases_folding_of +CTD:increases_localization_of: + operation: rename + core_predicate: biolink:increases_localization_of +CTD:increases_metabolic_processing_of: + operation: rename + core_predicate: biolink:increases_metabolic_processing_of +CTD:increases_molecular_modification_of: + operation: rename + core_predicate: biolink:increases_molecular_modification_of +CTD:increases_synthesis_of: + operation: rename + core_predicate: biolink:increases_synthesis_of +DDANAT:develops_from: + operation: rename + core_predicate: biolink:develops_from +DGIdb:activator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +# DGIdb:adduct: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +DGIdb:affects: + operation: rename + core_predicate: biolink:affects +DGIdb:agonist: + operation: rename + core_predicate: biolink:increases_activity_of +DGIdb:allosteric_modulator: + operation: rename + core_predicate: biolink:affects_activity_of +DGIdb:antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DGIdb:antibody: + operation: rename + core_predicate: biolink:molecularly_interacts_with +# DGIdb:antisense: +# rename: +# - decreases_expression_of +# - biolink:decreases_expression_of +DGIdb:antisense_oligonucleotide: + operation: rename + core_predicate: biolink:decreases_expression_of +# DGIdb:binder: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +DGIdb:blocker: + operation: rename + core_predicate: biolink:decreases_activity_of +# DGIdb:channel_blocker: +# rename: +# - decreases_activity_of +# - biolink:decreases_activity_of +# DGIdb:chaperone: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +# DGIdb:cleavage: +# rename: +# - affects_degradation_of +# - biolink:affects_degradation_of +# DGIdb:cofactor: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +# DGIdb:gating_inhibitor: +# rename: +# - decreases_activity_of +# - biolink:decreases_activity_of +DGIdb:inducer: + operation: rename + core_predicate: biolink:increases_activity_of +DGIdb:inhibitor: + operation: rename + core_predicate: biolink:decreases_activity_of +DGIdb:inhibitory_allosteric_modulator: + operation: rename + core_predicate: biolink:decreases_activity_of +DGIdb:inverse_agonist: + operation: rename + core_predicate: biolink:decreases_activity_of +# DGIdb:ligand: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +DGIdb:modulator: + operation: rename + core_predicate: biolink:affects_activity_of +# DGIdb:multitarget: +# rename: +# - directly_interacts_with +# - biolink:directly_interacts_with +DGIdb:negative_modulator: + operation: rename + core_predicate: biolink:decreases_activity_of +DGIdb:partial_agonist: + operation: rename + core_predicate: biolink:increases_activity_of +# DGIdb:partial_antagonist: +# rename: +# - decreases_activity_of +# - biolink:decreases_activity_of +# DGIdb:positive_allosteric_modulator: +# rename: +# - increases_activity_of +# - biolink:increases_activity_of +DGIdb:positive_modulator: + operation: rename + core_predicate: biolink:increases_activity_of +# DGIdb:potentiator: +# rename: +# - increases_activity_of +# - biolink:increases_activity_of +# DGIdb:product_of: +# rename: +# - derives_from +# - biolink:derives_from +# DGIdb:stimulator: +# rename: +# - increases_activity_of +# - biolink:increases_activity_of +# DGIdb:substrate: +# rename: +# - increases_degradation_of +# - biolink:increases_degradation_of +DGIdb:suppressor: + operation: rename + core_predicate: biolink:decreases_activity_of +DGIdb:vaccine: + operation: rename + core_predicate: biolink:decreases_activity_of +# DOID-PROPERTY:derives_from: +# rename: +# - derives_from +# - biolink:derives_from +# DOID-PROPERTY:has_symptom: +# rename: +# - has_phenotype +# - biolink:has_phenotype +DRUGBANK:activator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:adduct: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:aggregation_inhibitor: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:agonist: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:allosteric_modulator: + operation: rename + core_predicate: biolink:affects_activity_of +DRUGBANK:antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:antibody: + operation: rename + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:antisense_oligonucleotide: + operation: rename + core_predicate: biolink:decreases_expression_of +DRUGBANK:atc-code: + operation: rename + core_predicate: biolink:close_match +DRUGBANK:atc-code-level: + operation: rename + core_predicate: biolink:related_to +DRUGBANK:binder: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:binding: + operation: rename + core_predicate: biolink:physically_interacts_with +DRUGBANK:blocker: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:category: + operation: rename + core_predicate: biolink:subclass_of +DRUGBANK:chaperone: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:chelator: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:cleavage: + operation: rename + core_predicate: biolink:affects_degradation_of +DRUGBANK:cofactor: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:component_of: + operation: invert + core_predicate: biolink:has_part +DRUGBANK:degradation: + operation: rename + core_predicate: biolink:affects_degradation_of +DRUGBANK:deoxidizer: + operation: rename + core_predicate: biolink:decreases_molecular_modification_of +DRUGBANK:desensitize_the_target: + operation: rename + core_predicate: biolink:decreases_response_to +DRUGBANK:downregulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:drug-interaction: + operation: rename + core_predicate: biolink:physically_interacts_with +DRUGBANK:external-identifier: + operation: rename + core_predicate: biolink:same_as +DRUGBANK:external-identifier-protein: + operation: rename + core_predicate: biolink:derives_from +DRUGBANK:gene_replacement: + operation: rename + core_predicate: biolink:close_match +DRUGBANK:group: + operation: rename + core_predicate: biolink:related_to +DRUGBANK:inactivator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:incorporation_into_and_destabilization: + operation: rename + core_predicate: biolink:affects_degradation_of +DRUGBANK:inducer: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:inhibition_of_synthesis: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitory_allosteric_modulator: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:intercalation: + operation: rename + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:inverse_agonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:ligand: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:modulator: + operation: rename + core_predicate: biolink:entity_regulates_entity +DRUGBANK:multitarget: + operation: rename + core_predicate: biolink:directly_interacts_with +DRUGBANK:negative_modulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:neutralizer: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:nucleotide_exchange_blocker: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:oxidizer: + operation: rename + core_predicate: biolink:increases_molecular_modification_of +DRUGBANK:partial_agonist: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:partial_antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:pathway: + operation: rename + core_predicate: biolink:has_participant +DRUGBANK:positive_allosteric_modulator: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:positive_modulator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:potentiator: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:product_of: + operation: rename + core_predicate: biolink:derives_from +DRUGBANK:regulator: + operation: rename + core_predicate: biolink:entity_regulates_entity +DRUGBANK:stabilization: + operation: rename + core_predicate: biolink:increases_stability_of +DRUGBANK:stimulator: + operation: rename + core_predicate: biolink:increases_activity_of +DRUGBANK:substrate: + operation: rename + core_predicate: biolink:physically_interacts_with +DRUGBANK:suppressor: + operation: rename + core_predicate: biolink:decreases_activity_of +DRUGBANK:target: + operation: rename + core_predicate: biolink:physically_interacts_with +DRUGBANK:translocation_inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:weak_inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +# DrugCentral:5271: +# rename: +# - diagnoses +# - biolink:diagnoses +DrugCentral:activator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +DrugCentral:agonist: + operation: rename + core_predicate: biolink:increases_activity_of +DrugCentral:allosteric_antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DrugCentral:allosteric_modulator: + operation: rename + core_predicate: biolink:affects_activity_of +DrugCentral:antagonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DrugCentral:antibody_binding: + operation: rename + core_predicate: biolink:molecularly_interacts_with +DrugCentral:antisense_inhibitor: + operation: rename + core_predicate: biolink:decreases_expression_of +DrugCentral:binding_agent: + operation: rename + core_predicate: biolink:directly_interacts_with +DrugCentral:blocker: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:contraindication: + operation: rename + core_predicate: biolink:contraindicated_for +# DrugCentral:diagnosis: # A drug that helps diagnose a condition +# rename: +# - related_to +# - biolink:related_to +DrugCentral:gating_inhibitor: + operation: rename + core_predicate: biolink:decreases_activity_of +# DrugCentral:has_faers: +# rename: +# - causes_adverse_event +# - biolink:causes_adverse_event +DrugCentral:has_role: + operation: rename + core_predicate: biolink:related_to +DrugCentral:indication: + operation: rename + core_predicate: biolink:treats +DrugCentral:inhibitor: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:inverse_agonist: + operation: rename + core_predicate: biolink:decreases_activity_of +DrugCentral:modulator: + operation: rename + core_predicate: biolink:entity_regulates_entity +DrugCentral:negative_allosteric_modulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:negative_modulator: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:off-label_use: + operation: rename + core_predicate: biolink:treats +DrugCentral:opener: + operation: rename + core_predicate: biolink:increases_activity_of +DrugCentral:PA: # PA stands for "Pharmacological Action" + operation: rename + core_predicate: biolink:subclass_of +DrugCentral:partial_agonist: + operation: rename + core_predicate: biolink:increases_activity_of +DrugCentral:pharmacological_chaperone: + operation: rename + core_predicate: biolink:directly_interacts_with +DrugCentral:positive_allosteric_modulator: + operation: rename + core_predicate: biolink:increases_activity_of +DrugCentral:positive_modulator: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +# DrugCentral:reduce_risk: +# rename: +# - prevents +# - biolink:prevents +DrugCentral:releasing_agent: + operation: rename + core_predicate: biolink:increases_expression_of +DrugCentral:struct2atc: + operation: rename + core_predicate: biolink:close_match +DrugCentral:substrate: + operation: rename + core_predicate: biolink:physically_interacts_with +DrugCentral:symptomatic_treatment: + operation: rename + core_predicate: biolink:treats +EFO:0000784: + operation: rename + core_predicate: biolink:located_in +EFO:0001697: + operation: invert + core_predicate: biolink:related_to +EFO:0006351: + operation: rename + core_predicate: biolink:related_to +EFO:is_executed_in: + operation: rename + core_predicate: biolink:related_to +ENVO:01001307: + operation: rename + core_predicate: biolink:coexists_with +FMA:SIB: + operation: delete +FMA:adheres_to: + operation: rename + core_predicate: biolink:physically_interacts_with +FMA:adjacent_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:afferent_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:anatomical_entity_observed_in: + operation: delete +FMA:anterior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:anteroinferior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:anterolateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:anteromedial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:anterosuperior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:arterial_supply_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:articulates_with: + operation: rename + core_predicate: biolink:coexists_with +FMA:attaches_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:bounded_by: + operation: rename + core_predicate: biolink:coexists_with +FMA:bounds: + operation: rename + core_predicate: biolink:coexists_with +FMA:branch_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:connected_to: + operation: rename + core_predicate: biolink:related_to +FMA:connection_type_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:constitutional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:contained_in: + operation: invert + core_predicate: biolink:has_part +FMA:contains: + operation: rename + core_predicate: biolink:has_part +FMA:continuation_branch_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:continuous_distally_with: + operation: rename + core_predicate: biolink:coexists_with +FMA:continuous_proximally_with: + operation: rename + core_predicate: biolink:coexists_with +FMA:continuous_with: + operation: rename + core_predicate: biolink:related_to +FMA:corresponds_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:derives: + operation: invert + core_predicate: biolink:derives_from +FMA:derives_from: + operation: rename + core_predicate: biolink:derives_from +FMA:development_type_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:developmental_stage_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:develops_from: + operation: rename + core_predicate: biolink:develops_from +FMA:develops_into: + operation: rename + core_predicate: biolink:develops_from +FMA:direct_cell_shape_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:direct_left_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:direct_right_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:distal_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:drains_into: + operation: rename + core_predicate: biolink:coexists_with +FMA:efferent_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:external_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:formed_by: + operation: rename + core_predicate: biolink:coexists_with +FMA:forms: + operation: rename + core_predicate: biolink:coexists_with +FMA:full_grown_phenotype_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:fuses_with: + operation: rename + core_predicate: biolink:coexists_with +FMA:fusion_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:germ_origin_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_adherent: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_arterial_supply: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_branch: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_connection_type: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_constitutional_part: + operation: rename + core_predicate: biolink:has_part +FMA:has_continuation_branch: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_development_type: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_developmental_stage: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_direct_cell_shape: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_full_grown_phenotype: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_fusion: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_germ_origin: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_inherent_3d_shape: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_insertion: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_location: + operation: rename + core_predicate: biolink:located_in +FMA:has_lymphatic_drainage: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_member: + operation: rename + core_predicate: biolink:has_part +FMA:has_nerve_supply: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_observed_anatomical_entity: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_origin: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_part: + operation: rename + core_predicate: biolink:has_part +FMA:has_primary_segmental_supply: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_projection: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_regional_part: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_related_developmental_entity: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_secondary_segmental_supply: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_segmental_composition: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_segmental_supply: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_tributary: + operation: rename + core_predicate: biolink:coexists_with +FMA:has_venous_drainage: + operation: rename + core_predicate: biolink:coexists_with +FMA:homonym_for: + operation: delete +FMA:homonym_of: + operation: rename + core_predicate: biolink:related_to +FMA:inferior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:inferolateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:inferomedial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:inherent_3d_shape_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:insertion_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:internal_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:lateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:left_lateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:left_medial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:location_of: + operation: invert + core_predicate: biolink:located_in +FMA:lymphatic_drainage_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:matures_from: + operation: rename + core_predicate: biolink:coexists_with +FMA:matures_into: + operation: rename + core_predicate: biolink:coexists_with +FMA:medial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:member_of: + operation: invert + core_predicate: biolink:has_part +FMA:merges_with: + operation: rename + core_predicate: biolink:coexists_with +FMA:nerve_supply_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:origin_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:part_of: + operation: invert + core_predicate: biolink:has_part +FMA:posterior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:posteroinferior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:posterolateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:posteromedial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:posterosuperior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:primary_segmental_supply_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:projects_from: + operation: rename + core_predicate: biolink:coexists_with +FMA:projects_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:proximal_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:receives_attachment_from: + operation: rename + core_predicate: biolink:coexists_with +FMA:receives_drainage_from: + operation: rename + core_predicate: biolink:coexists_with +FMA:receives_input_from: + operation: rename + core_predicate: biolink:coexists_with +FMA:receives_projection: + operation: rename + core_predicate: biolink:coexists_with +FMA:regional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:related_developmental_entity_of: + operation: invert + core_predicate: biolink:related_to +FMA:related_object: + operation: rename + core_predicate: biolink:related_to +FMA:related_part: + operation: rename + core_predicate: biolink:coexists_with +FMA:right_lateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:right_medial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:secondary_segmental_supply_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:segmental_composition_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:segmental_supply_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:sends_output_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:superior_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:superolateral_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:superomedial_to: + operation: rename + core_predicate: biolink:coexists_with +FMA:surrounded_by: + operation: rename + core_predicate: biolink:coexists_with +FMA:surrounds: + operation: rename + core_predicate: biolink:coexists_with +FMA:transforms_from: + operation: invert + core_predicate: biolink:precedes +FMA:transforms_into: + operation: rename + core_predicate: biolink:precedes +FMA:tributary_of: + operation: rename + core_predicate: biolink:coexists_with +FMA:venous_drainage_of: + operation: rename + core_predicate: biolink:coexists_with +FOODON:00001301: + operation: rename + core_predicate: biolink:model_of +FOODON:00001563: + operation: rename + core_predicate: biolink:has_part +FOODON:00002420: + operation: rename + core_predicate: biolink:has_part +GENEPIO:0001739: + operation: invert + core_predicate: biolink:precedes +GO:SIB: + operation: delete +GO:acts_upstream_of: + operation: rename + core_predicate: biolink:affects +GO:acts_upstream_of_negative_effect: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within: + operation: rename + core_predicate: biolink:affects +GO:acts_upstream_of_or_within_negative_effect: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within_positive_effect: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +GO:acts_upstream_of_positive_effect: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +GO:colocalizes_with: + operation: rename + core_predicate: biolink:colocalizes_with +GO:contributes_to: + operation: rename + core_predicate: biolink:contributes_to +GO:enables: + operation: rename + core_predicate: biolink:enables +GO:ends_during: + operation: rename + core_predicate: biolink:related_to +GO:happens_during: + operation: rename + core_predicate: biolink:related_to +GO:has_occurrence: + operation: rename + core_predicate: biolink:capable_of +GO:has_part: + operation: rename + core_predicate: biolink:has_part +GO:inverse_ends_during: + operation: rename + core_predicate: biolink:related_to +GO:inverse_happens_during: + operation: delete +GO:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +GO:involved_in: + operation: invert + core_predicate: biolink:has_participant +GO:is_active_in: + operation: rename + core_predicate: biolink:actively_involved_in +GO:isa: + operation: rename + core_predicate: biolink:subclass_of +GO:located_in: + operation: rename + core_predicate: biolink:located_in +GO:negatively_regulated_by: + operation: invert + core_predicate: biolink:entity_negatively_regulates_entity +GO:negatively_regulates: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +GO:occurs_in: + operation: rename + core_predicate: biolink:occurs_in +GO:part_of: + operation: invert + core_predicate: biolink:has_part +GO:positively_regulated_by: + operation: invert + core_predicate: biolink:entity_positively_regulates_entity +GO:positively_regulates: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +GO:regulated_by: + operation: invert + core_predicate: biolink:entity_regulates_entity +GO:regulates: + operation: rename + core_predicate: biolink:entity_regulates_entity +GOREL:0000040: + operation: rename + core_predicate: biolink:causes +GOREL:0002003: + operation: rename + core_predicate: biolink:affects_localization_of +GOREL:0002004: + operation: rename + core_predicate: biolink:increases_degradation_of +# GOREL:0002005: +# rename: +# - related_to +# - biolink:related_to +GOREL:0012006: + operation: rename + core_predicate: biolink:related_to +HANCESTRO:0301: + operation: rename + core_predicate: biolink:related_to +HANCESTRO:0308: # has country of origin + operation: rename + core_predicate: biolink:related_to +HANCESTRO:0330: + operation: rename + core_predicate: biolink:related_to +HCPCS:mapped_from: + operation: delete +HCPCS:mapped_to: + operation: rename + core_predicate: biolink:related_to +HMDB:at_cellular_location: + operation: rename + core_predicate: biolink:located_in +HMDB:at_tissue: + operation: rename + core_predicate: biolink:located_in +HMDB:disease: + operation: rename + core_predicate: biolink:related_to +HMDB:has_protein_association: + operation: rename + core_predicate: biolink:related_to +HMDB:in_biospecimen: + operation: rename + core_predicate: biolink:located_in +HMDB:in_pathway: + operation: invert + core_predicate: biolink:has_participant +HP:SIB: + operation: delete +IAO:0000039: + operation: rename + core_predicate: biolink:related_to +IAO:0000136: + operation: rename + core_predicate: biolink:related_to +IAO:0000219: + operation: rename + core_predicate: biolink:related_to +ICD10PCS:SIB: + operation: delete +ICD9:SIB: + operation: delete +IDO:0000664: + operation: invert + core_predicate: biolink:contributes_to +JensenLab:associated_with: + operation: rename + core_predicate: biolink:gene_associated_with_condition +KEGG:compound_to_enzyme: + operation: rename + core_predicate: biolink:interacts_with +KEGG:compound_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:compound_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_reaction: + operation: rename + core_predicate: biolink:catalyzes +KEGG:glycan_to_enzyme: + operation: rename + core_predicate: biolink:interacts_with +KEGG:glycan_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:glycan_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:pathway_to_compound: + operation: rename + core_predicate: biolink:has_participant +KEGG:pathway_to_drug: + operation: rename + core_predicate: biolink:has_participant +KEGG:pathway_to_glycan: + operation: rename + core_predicate: biolink:has_participant +KEGG:reaction_to_enzyme: + operation: invert + core_predicate: biolink:catalyzes +KEGG:reaction_to_pathway: + operation: invert + core_predicate: biolink:has_participant +LOINC:adjustment_of: + operation: delete +LOINC:analyzed_by: + operation: delete +LOINC:analyzes: + operation: rename + core_predicate: biolink:related_to +LOINC:answer_to: + operation: delete +LOINC:archetype_of: + operation: delete +LOINC:associated_with: + operation: rename + core_predicate: biolink:correlated_with +LOINC:challenge_of: + operation: delete +LOINC:class_of: + operation: rename + core_predicate: biolink:subclass_of +LOINC:component_of: + operation: invert + core_predicate: biolink:has_part +LOINC:count_of: + operation: delete +LOINC:divisor_of: + operation: delete +LOINC:evaluation_of: + operation: delete +LOINC:fragments_for_synonyms_of: + operation: delete +LOINC:has_action_guidance: + operation: rename + core_predicate: biolink:related_to +LOINC:has_adjustment: + operation: rename + core_predicate: biolink:related_to +LOINC:has_aggregation_view: + operation: rename + core_predicate: biolink:related_to +LOINC:has_answer: + operation: rename + core_predicate: biolink:related_to +LOINC:has_approach_guidance: + operation: rename + core_predicate: biolink:related_to +LOINC:has_archetype: + operation: rename + core_predicate: biolink:subclass_of +LOINC:has_challenge: + operation: rename + core_predicate: biolink:related_to +LOINC:has_class: + operation: invert + core_predicate: biolink:subclass_of +LOINC:has_component: + operation: rename + core_predicate: biolink:has_part +LOINC:has_count: + operation: rename + core_predicate: biolink:related_to +LOINC:has_divisor: + operation: rename + core_predicate: biolink:related_to +LOINC:has_evaluation: + operation: rename + core_predicate: biolink:related_to +LOINC:has_exam: + operation: rename + core_predicate: biolink:related_to +LOINC:has_fragments_for_synonyms: + operation: rename + core_predicate: biolink:has_input +LOINC:has_given_pharmaceutical_substance: + operation: delete +LOINC:has_imaged_location: + operation: rename + core_predicate: biolink:occurs_in +LOINC:has_imaging_focus: + operation: rename + core_predicate: biolink:located_in +LOINC:has_lateral_anatomic_location: + operation: rename + core_predicate: biolink:coexists_with +LOINC:has_lateral_location_presence: + operation: rename + core_predicate: biolink:coexists_with +LOINC:has_loinc_number: + operation: delete +LOINC:has_member: + operation: rename + core_predicate: biolink:has_part +LOINC:has_method: + operation: rename + core_predicate: biolink:related_to +LOINC:has_modality_subtype: + operation: rename + core_predicate: biolink:related_to +LOINC:has_modality_type: + operation: rename + core_predicate: biolink:related_to +LOINC:has_multipart: + operation: delete +LOINC:has_object_guidance: + operation: rename + core_predicate: biolink:related_to +LOINC:has_parent_group: + operation: rename + core_predicate: biolink:subclass_of +LOINC:has_pharmaceutical_route: + operation: rename + core_predicate: biolink:related_to +LOINC:has_presence_guidance: + operation: delete +LOINC:has_property: + operation: delete +LOINC:has_scale: + operation: rename + core_predicate: biolink:related_to +LOINC:has_subject: + operation: rename + core_predicate: biolink:has_participant +LOINC:has_suffix: + operation: rename + core_predicate: biolink:related_to +LOINC:has_supersystem: + operation: invert + core_predicate: biolink:has_part +LOINC:has_system: + operation: rename + core_predicate: biolink:has_input +LOINC:has_time_aspect: + operation: rename + core_predicate: biolink:related_to +LOINC:has_time_modifier: + operation: rename + core_predicate: biolink:related_to +LOINC:has_timing_of: + operation: rename + core_predicate: biolink:related_to +LOINC:has_view_type: + operation: rename + core_predicate: biolink:related_to +LOINC:is_action_guidance_for: + operation: delete +LOINC:is_aggregation_view_of: + operation: delete +LOINC:is_approach_guidance_for: + operation: delete +LOINC:is_exam_for: + operation: delete +LOINC:is_given_pharmaceutical_substance_for: + operation: invert + core_predicate: biolink:has_participant +LOINC:is_imaged_location_for: + operation: delete +LOINC:is_imaging_focus_of: + operation: delete +LOINC:is_lateral_anatomic_location_of: + operation: delete +LOINC:is_modality_subtype_for: + operation: delete +LOINC:is_modality_type_for: + operation: delete +LOINC:is_object_guidance_for: + operation: delete +LOINC:is_pharmaceutical_route_for: + operation: delete +LOINC:is_presence_guidance_for: + operation: rename + core_predicate: biolink:subclass_of +LOINC:is_presence_of_lateral_location: + operation: delete +LOINC:is_subject_of: + operation: delete +LOINC:is_timing_for: + operation: delete +LOINC:is_view_type_for: + operation: delete +LOINC:loinc_number_of: + operation: delete +LOINC:mapped_from: + operation: delete +LOINC:mapped_to: + operation: rename + core_predicate: biolink:related_to +LOINC:measured_by: + operation: rename + core_predicate: biolink:related_to +LOINC:measures: + operation: delete +LOINC:member_of: + operation: invert + core_predicate: biolink:has_part +LOINC:method_of: + operation: delete +LOINC:mth_expanded_form_of: + operation: delete +LOINC:mth_has_expanded_form: + operation: rename + core_predicate: biolink:related_to +LOINC:multipart_of: + operation: invert + core_predicate: biolink:has_part +LOINC:parent_group_of: + operation: delete +LOINC:property_of: + operation: rename + core_predicate: biolink:related_to +LOINC:scale_of: + operation: delete +LOINC:suffix_of: + operation: delete +LOINC:supersystem_of: + operation: delete +LOINC:system_of: + operation: delete +LOINC:time_aspect_of: + operation: delete +LOINC:time_modifier_of: + operation: delete +MESH:AQ: + operation: delete +MESH:QB: + operation: delete +MESH:RO: + operation: rename + core_predicate: biolink:related_to +MESH:SIB: + operation: delete +MESH:has_mapping_qualifier: + operation: rename + core_predicate: biolink:related_to +MESH:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +MESH:isa: + operation: rename + core_predicate: biolink:subclass_of +MESH:mapped_from: + operation: delete +MESH:mapped_to: + operation: rename + core_predicate: biolink:related_to +MESH:mapping_qualifier_of: + operation: delete +MI:0192: # acetylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0194: # cleavage reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0195: # covalent bonding + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0197: # deacetylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0203: # dephosphorylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0204: # deubiquitination reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0210: # hydroxylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0211: # lipid addition + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0212: # lipoprotein cleavage reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0213: # methylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0214: # myristoylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0216: # palmitoylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0217: # phosphorylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0220: # ubiquitination reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0403: # colocalization + operation: rename + core_predicate: biolink:colocalizes_with +MI:0407: # direct interaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0408: # disulfide bond + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0414: # enzymatic reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0556: # transglutamination reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0557: # adp_ribosylation_reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0559: # glycosylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0566: # sumoylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0567: # neddylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0569: # deneddylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0570: # protein cleavage + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0572: # dna cleavage + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0844: # phosphotransfer reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0871: # demethylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0882: # atpase reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0883: # gtpase reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0902: # rna reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:0914: # association + operation: rename + core_predicate: biolink:interacts_with +MI:0915: # physical associaiton + operation: rename + core_predicate: biolink:physically_interacts_with +MI:0945: # oxidoreductase activity electron transfer reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:1126: # self interaction + operation: rename + core_predicate: biolink:interacts_with +MI:1127: # putative self interaction + operation: rename + core_predicate: biolink:interacts_with +MI:1148: # ampylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:1237: # proline isomerization reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:1310: # de-ADP-ribosylation reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MI:2364: # proximity + operation: rename + core_predicate: biolink:colocalizes_with +MI:2252: # guanine nucleotide exchange factor reaction + operation: rename + core_predicate: biolink:directly_interacts_with +MONDO:0100332: # disease has primary infectious agent + operation: invert + core_predicate: biolink:causes +MONDO:0100333: # disease caused by reactivation of latent infectious agent + operation: invert + core_predicate: biolink:causes +MONDO:disease_causes_feature: + operation: rename + core_predicate: biolink:causes +MONDO:disease_has_basis_in_accumulation_of: + operation: rename + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_basis_in_development_of: + operation: rename + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_major_feature: + operation: rename + core_predicate: biolink:has_part +MONDO:disease_responds_to: + operation: invert + core_predicate: biolink:treats +MONDO:disease_shares_features_of: + operation: rename + core_predicate: biolink:related_to +MONDO:disease_triggers: + operation: rename + core_predicate: biolink:causes +MONDO:equivalentTo: + operation: rename + core_predicate: biolink:same_as +MONDO:has_onset: + operation: rename + core_predicate: biolink:related_to +MONDO:has_onset_before: + operation: rename + core_predicate: biolink:related_to +MONDO:has_onset_during_or_after: + operation: rename + core_predicate: biolink:related_to +MONDO:part_of_progression_of_disease: + operation: invert + core_predicate: biolink:has_part +MONDO:predisposes_towards: + operation: rename + core_predicate: biolink:contributes_to +# NBO-PROPERTY:by_means: +# rename: +# - actively_involved_in +# - biolink:actively_involved_in +# NBO-PROPERTY:has_participant: +# rename: +# - has_participant +# - biolink:has_participant +# NBO-PROPERTY:in_response_to: +# invert: +# - causes +# - biolink:causes +# NBO-PROPERTY:is_about: +# rename: +# - related_to +# - biolink:related_to +NCIT:abnormal_cell_affected_by_chemical_or_drug: + operation: delete +NCIT:abnormality_associated_with_allele: + operation: delete +NCIT:activity_of_allele: + operation: delete +NCIT:allele_absent_from_wild-type_chromosomal_location: + operation: rename + core_predicate: biolink:located_in +NCIT:allele_has_abnormality: + operation: rename + core_predicate: biolink:causes +NCIT:allele_has_activity: + operation: rename + core_predicate: biolink:has_molecular_consequence +NCIT:allele_in_chromosomal_location: + operation: rename + core_predicate: biolink:located_in +NCIT:allele_plays_altered_role_in_process: + operation: rename + core_predicate: biolink:affects +NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: + operation: rename + core_predicate: biolink:affects +NCIT:anatomic_structure_has_location: + operation: delete +NCIT:anatomic_structure_is_physical_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:anatomy_originated_from_biological_process: + operation: delete +NCIT:associated_with_malfunction_of_gene_product: + operation: delete +NCIT:biological_process_has_associated_location: + operation: rename + core_predicate: biolink:affects +NCIT:biological_process_has_initiator_chemical_or_drug: + operation: delete +NCIT:biological_process_has_initiator_process: + operation: delete +NCIT:biological_process_has_result_anatomy: + operation: rename + core_predicate: biolink:has_output +NCIT:biological_process_has_result_biological_process: + operation: rename + core_predicate: biolink:causes +NCIT:biological_process_has_result_chemical_or_drug: + operation: rename + core_predicate: biolink:produces +NCIT:biological_process_involves_chemical_or_drug: + operation: invert + core_predicate: biolink:actively_involved_in +NCIT:biological_process_involves_gene_product: + operation: delete +NCIT:biological_process_is_part_of_process: + operation: delete +NCIT:biological_process_results_from_biological_process: + operation: delete +NCIT:biomarker_type_includes_gene: + operation: delete +NCIT:biomarker_type_includes_gene_product: + operation: delete +# NCIT:C15220: # diagnosis +# rename: +# - diagnoses +# - biolink:diagnoses +NCIT:cdrh_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cell_type_is_associated_with_eo_disease: + operation: delete +NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: + operation: delete +NCIT:chemical_or_drug_affects_abnormal_cell: + operation: rename + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_cell_type_or_tissue: + operation: rename + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_gene_product: + operation: rename + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_mechanism_of_action: + operation: rename + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_physiologic_effect: + operation: rename + core_predicate: biolink:causes +NCIT:chemical_or_drug_initiates_biological_process: + operation: rename + core_predicate: biolink:causes +NCIT:chemical_or_drug_is_metabolized_by_enzyme: + operation: delete +NCIT:chemical_or_drug_is_product_of_biological_process: + operation: delete +NCIT:chemical_or_drug_metabolism_is_associated_with_allele: + operation: delete +NCIT:chemical_or_drug_plays_role_in_biological_process: + operation: delete +NCIT:chemotherapy_regimen_has_component: + operation: delete +NCIT:chromosomal_location_of_allele: + operation: delete +NCIT:chromosomal_location_of_wild-type_gene: + operation: delete +NCIT:chromosome_involved_in_cytogenetic_abnormality: + operation: delete +NCIT:chromosome_mapped_to_disease: + operation: rename + core_predicate: biolink:causes +NCIT:completely_excised_anatomy_has_procedure: + operation: delete +NCIT:completely_excised_anatomy_may_have_procedure: + operation: delete +NCIT:complex_has_physical_part: + operation: rename + core_predicate: biolink:has_part +NCIT:concept_in_subset: + operation: delete +NCIT:conceptual_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:ctcae_5_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cytogenetic_abnormality_involves_chromosome: + operation: rename + core_predicate: biolink:affects +NCIT:data_element_of: + operation: delete +NCIT:disease_excludes_abnormal_cell: + operation: delete +NCIT:disease_excludes_cytogenetic_abnormality: + operation: delete +NCIT:disease_excludes_finding: + operation: delete +NCIT:disease_excludes_metastatic_anatomic_site: + operation: delete +NCIT:disease_excludes_molecular_abnormality: + operation: delete +NCIT:disease_excludes_normal_cell_origin: + operation: delete +NCIT:disease_excludes_normal_tissue_origin: + operation: delete +NCIT:disease_excludes_primary_anatomic_site: + operation: delete +NCIT:disease_has_abnormal_cell: + operation: delete +NCIT:disease_has_accepted_treatment_with_regimen: + operation: delete +NCIT:disease_has_associated_anatomic_site: + operation: rename + core_predicate: biolink:affects +NCIT:disease_has_associated_disease: + operation: rename + core_predicate: biolink:has_real_world_evidence_of_association_with +NCIT:disease_has_associated_gene: + operation: delete +NCIT:disease_has_cytogenetic_abnormality: + operation: delete +NCIT:disease_has_finding: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_metastatic_anatomic_site: + operation: rename + core_predicate: biolink:affects +NCIT:disease_has_molecular_abnormality: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_normal_cell_origin: + operation: delete +NCIT:disease_has_normal_tissue_origin: + operation: rename + core_predicate: biolink:causes +NCIT:disease_has_primary_anatomic_site: + operation: rename + core_predicate: biolink:affects +NCIT:disease_is_grade: + operation: rename + core_predicate: biolink:related_to +NCIT:disease_is_marked_by_gene: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_is_stage: + operation: rename + core_predicate: biolink:related_to +NCIT:disease_mapped_to_chromosome: + operation: delete +NCIT:disease_mapped_to_gene: + operation: delete +NCIT:disease_may_have_abnormal_cell: + operation: rename + core_predicate: biolink:affects +NCIT:disease_may_have_associated_disease: + operation: rename + core_predicate: biolink:related_to +NCIT:disease_may_have_cytogenetic_abnormality: + operation: delete +NCIT:disease_may_have_finding: + operation: rename + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_molecular_abnormality: + operation: rename + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_normal_cell_origin: + operation: delete +NCIT:endogenous_product_related_to: + operation: delete +NCIT:enzyme_metabolizes_chemical_or_drug: + operation: rename + core_predicate: biolink:increases_metabolic_processing_of +NCIT:eo_anatomy_is_associated_with_eo_disease: + operation: delete +NCIT:eo_disease_has_associated_cell_type: + operation: rename + core_predicate: biolink:affects +NCIT:eo_disease_has_associated_eo_anatomy: + operation: rename + core_predicate: biolink:affects +NCIT:eo_disease_has_property_or_attribute: + operation: rename + core_predicate: biolink:related_to +NCIT:eo_disease_maps_to_human_disease: + operation: delete +NCIT:excised_anatomy_has_procedure: + operation: delete +NCIT:excised_anatomy_may_have_procedure: + operation: delete +NCIT:gene_associated_with_disease: + operation: rename + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_encodes_gene_product: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_found_in_organism: + operation: rename + core_predicate: biolink:in_taxon +NCIT:gene_has_abnormality: + operation: delete +NCIT:gene_has_physical_location: + operation: rename + core_predicate: biolink:located_in +NCIT:gene_in_chromosomal_location: + operation: rename + core_predicate: biolink:located_in +NCIT:gene_involved_in_molecular_abnormality: + operation: rename + core_predicate: biolink:actively_involved_in +NCIT:gene_involved_in_pathogenesis_of_disease: + operation: rename + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_is_biomarker_of: + operation: rename + core_predicate: biolink:biomarker_for +NCIT:gene_is_biomarker_type: + operation: rename + core_predicate: biolink:subclass_of +NCIT:gene_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_mapped_to_disease: + operation: rename + core_predicate: biolink:affects +NCIT:gene_mutant_encodes_gene_product_sequence_variation: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_plays_role_in_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_affected_by_chemical_or_drug: + operation: delete +NCIT:gene_product_encoded_by_gene: + operation: delete +NCIT:gene_product_expressed_in_tissue: + operation: rename + core_predicate: biolink:expressed_in +NCIT:gene_product_has_abnormality: + operation: rename + core_predicate: biolink:affects +NCIT:gene_product_has_associated_anatomy: + operation: rename + core_predicate: biolink:expressed_in +NCIT:gene_product_has_biochemical_function: + operation: rename + core_predicate: biolink:capable_of +NCIT:gene_product_has_chemical_classification: + operation: rename + core_predicate: biolink:subclass_of +NCIT:gene_product_has_gene_product_variant: + operation: delete +NCIT:gene_product_has_organism_source: + operation: rename + core_predicate: biolink:in_taxon +NCIT:gene_product_has_structural_domain_or_motif: + operation: rename + core_predicate: biolink:has_part +NCIT:gene_product_is_biomarker_of: + operation: rename + core_predicate: biolink:biomarker_for +NCIT:gene_product_is_biomarker_type: + operation: rename + core_predicate: biolink:subclass_of +NCIT:gene_product_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_is_physical_part_of: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_malfunction_associated_with_disease: + operation: rename + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_product_plays_role_in_biological_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: + operation: rename + core_predicate: biolink:is_sequence_variant_of +NCIT:gene_product_variant_of_gene_product: + operation: rename + core_predicate: biolink:is_sequence_variant_of +NCIT:genetic_biomarker_related_to: + operation: rename + core_predicate: biolink:biomarker_for +NCIT:has_cdrh_parent: + operation: delete +NCIT:has_conceptual_part: + operation: delete +NCIT:has_ctcae_5_parent: + operation: delete +NCIT:has_data_element: + operation: rename + core_predicate: biolink:related_to +NCIT:has_free_acid_or_base_form: + operation: delete +NCIT:has_gene_product_element: + operation: delete +NCIT:has_inc_parent: + operation: rename + core_predicate: biolink:subclass_of +NCIT:has_nichd_parent: + operation: rename + core_predicate: biolink:subclass_of +NCIT:has_pharmaceutical_administration_method: + operation: rename + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_basic_dose_form: + operation: rename + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_intended_site: + operation: rename + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_release_characteristics: + operation: rename + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_state_of_matter: + operation: rename + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_transformation: + operation: rename + core_predicate: biolink:related_to +NCIT:has_physical_part_of_anatomic_structure: + operation: delete +NCIT:has_salt_form: + operation: rename + core_predicate: biolink:chemically_similar_to +NCIT:has_target: + operation: rename + core_predicate: biolink:physically_interacts_with +NCIT:human_disease_maps_to_eo_disease: + operation: rename + core_predicate: biolink:related_to +NCIT:inc_parent_of: + operation: delete +NCIT:imaged_anatomy_has_procedure: + operation: delete +NCIT:is_abnormal_cell_of_disease: + operation: rename + core_predicate: biolink:related_to +NCIT:is_abnormality_of_gene: + operation: delete +NCIT:is_abnormality_of_gene_product: + operation: delete +NCIT:is_associated_anatomic_site_of: + operation: delete +NCIT:is_associated_anatomy_of_gene_product: + operation: delete +NCIT:is_associated_disease_of: + operation: rename + core_predicate: biolink:correlated_with +NCIT:is_biochemical_function_of_gene_product: + operation: delete +NCIT:is_chemical_classification_of_gene_product: + operation: delete +NCIT:is_chromosomal_location_of_gene: + operation: delete +NCIT:is_component_of_chemotherapy_regimen: + operation: invert + core_predicate: biolink:has_part +NCIT:is_cytogenetic_abnormality_of_disease: + operation: invert + core_predicate: biolink:correlated_with +NCIT:is_finding_of_disease: + operation: delete +NCIT:is_grade_of_disease: + operation: delete +NCIT:is_location_of_anatomic_structure: + operation: rename + core_predicate: biolink:located_in +NCIT:is_location_of_biological_process: + operation: delete +NCIT:is_marked_by_gene_product: + operation: delete +NCIT:is_mechanism_of_action_of_chemical_or_drug: + operation: delete +NCIT:is_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_molecular_abnormality_of_disease: + operation: rename + core_predicate: biolink:biomarker_for +NCIT:is_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:is_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_abnormal_cell_of_disease: + operation: delete +NCIT:is_not_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:is_not_finding_of_disease: + operation: delete +NCIT:is_not_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_not_molecular_abnormality_of_disease: + operation: delete +NCIT:is_not_normal_cell_origin_of_disease: + operation: delete +NCIT:is_not_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_organism_source_of_gene_product: + operation: invert + core_predicate: biolink:in_taxon +NCIT:is_physical_location_of_gene: + operation: delete +NCIT:is_physiologic_effect_of_chemical_or_drug: + operation: delete +NCIT:is_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_property_or_attribute_of_eo_disease: + operation: delete +NCIT:is_qualified_by: + operation: rename + core_predicate: biolink:related_to +NCIT:is_related_to_endogenous_product: + operation: rename + core_predicate: biolink:related_to +NCIT:is_stage_of_disease: + operation: delete +NCIT:is_structural_domain_or_motif_of_gene_product: + operation: delete +NCIT:is_target: + operation: delete +NCIT:kind_is_domain_of: + operation: delete +NCIT:kind_is_range_of: + operation: delete +NCIT:may_be_abnormal_cell_of_disease: + operation: delete +NCIT:may_be_associated_disease_of_disease: + operation: delete +NCIT:may_be_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:may_be_finding_of_disease: + operation: delete +NCIT:may_be_molecular_abnormality_of_disease: + operation: delete +NCIT:may_be_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:molecular_abnormality_involves_gene: + operation: delete +NCIT:neoplasm_has_special_category: + operation: rename + core_predicate: biolink:subclass_of +NCIT:nichd_parent_of: + operation: delete +NCIT:organism_has_gene: + operation: invert + core_predicate: biolink:in_taxon +NCIT:partially_excised_anatomy_has_procedure: + operation: delete +NCIT:partially_excised_anatomy_may_have_procedure: + operation: delete +NCIT:pathogenesis_of_disease_involves_gene: + operation: delete +NCIT:pathway_has_gene_element: + operation: rename + core_predicate: biolink:has_participant +NCIT:pharmaceutical_administration_method_of: + operation: delete +NCIT:pharmaceutical_basic_dose_form_of: + operation: delete +NCIT:pharmaceutical_intended_site_of: + operation: delete +NCIT:pharmaceutical_release_characteristics_of: + operation: delete +NCIT:pharmaceutical_state_of_matter_of: + operation: delete +NCIT:pharmaceutical_transformation_of: + operation: delete +NCIT:procedure_has_completely_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_has_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_has_imaged_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_has_target_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_has_partially_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_may_have_completely_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_may_have_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:procedure_may_have_partially_excised_anatomy: + operation: rename + core_predicate: biolink:located_in +NCIT:process_altered_by_allele: + operation: delete +NCIT:process_includes_biological_process: + operation: rename + core_predicate: biolink:has_participant +NCIT:process_initiates_biological_process: + operation: rename + core_predicate: biolink:causes +NCIT:process_involves_gene: + operation: rename + core_predicate: biolink:has_participant +NCIT:qualifier_applies_to: + operation: rename + core_predicate: biolink:related_to +# NCIT:R40: +# rename: +# - located_in +# - biolink:located_in +NCIT:R81: + operation: rename + core_predicate: biolink:related_to +NCIT:R82: + operation: rename + core_predicate: biolink:part_of +# NCIT:R88: # disease is stage +# rename: +# - related_to +# - biolink:related_to +# NCIT:R89: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R108: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R115: +# rename: +# - has_phenotype +# - biolink:has_phenotype +# NCIT:R145: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R155: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R156: +# rename: +# - located_in +# - biolink:located_in +NCIT:R163: + operation: rename + core_predicate: biolink:related_to +# NCIT:R165: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R166: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R167: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R168: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R169: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R170: +# rename: +# - located_in +# - biolink:located_in +# NCIT:R171: +# rename: +# - located_in +# - biolink:located_in +NCIT:regimen_has_accepted_use_for_disease: + operation: rename + core_predicate: biolink:treats +NCIT:related_to_genetic_biomarker: + operation: delete +NCIT:role_has_domain: + operation: rename + core_predicate: biolink:related_to +NCIT:role_has_parent: + operation: rename + core_predicate: biolink:subclass_of +NCIT:role_has_range: + operation: rename + core_predicate: biolink:related_to +NCIT:role_is_parent_of: + operation: delete +NCIT:special_category_includes_neoplasm: + operation: delete +NCIT:subset_includes_concept: + operation: invert + core_predicate: biolink:subclass_of +NCIT:target_anatomy_has_procedure: + operation: delete +NCIT:tissue_is_expression_site_of_gene_product: + operation: delete +NDDF:dose_form_of: + operation: delete +NDDF:has_dose_form: + operation: rename + core_predicate: biolink:subclass_of +NDDF:has_ingredient: + operation: rename + core_predicate: biolink:has_part +NDDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +OBI:0000293: + operation: rename + core_predicate: biolink:has_participant +OBI:0000295: + operation: invert + core_predicate: biolink:has_participant +OBI:0000299: + operation: rename + core_predicate: biolink:has_output +OBI:0000417: # achieves planned objective + operation: rename + core_predicate: biolink:has_output +OBI:0001927: + operation: invert + core_predicate: biolink:related_to +OBO:INO_0000154: + operation: rename + core_predicate: biolink:related_to +OBO:bspo#parallel_to: + operation: rename + core_predicate: biolink:coexists_with +# OBO:doid#has_symptom: +# rename: +# - has_phenotype +# - biolink:has_phenotype +OBO:envo#has_increased_levels_of: + operation: rename + core_predicate: biolink:related_to +OBO:exo#interacts_with: + operation: rename + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_stressor_via: + operation: rename + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_receptor_via: + operation: rename + core_predicate: biolink:interacts_with +# OBO:exo.obo#interacts_with: +# rename: +# - interacts_with +# - biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_stressor_via: +# rename: +# - interacts_with +# - biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_receptor_via: +# rename: +# - interacts_with +# - biolink:interacts_with +OBO:has_role: + operation: rename + core_predicate: biolink:related_to +OBO:MF#manifestationOf: + operation: rename + core_predicate: biolink:manifestation_of +OBO:nbo#by_means: + operation: invert + core_predicate: biolink:actively_involved_in +OBO:nbo#has_participant: + operation: rename + core_predicate: biolink:has_participant +OBO:nbo#in_response_to: + operation: invert + core_predicate: biolink:causes +OBO:nbo#is_about: + operation: rename + core_predicate: biolink:related_to +# OBO:uo#is_unit_of: +# invert: +# - related_to +# - biolink:related_to +# OIO:hasDbXref: +# rename: +# - close_match +# - biolink:close_match +OMIM:allelic_variant_of: + operation: rename + core_predicate: biolink:is_sequence_variant_of +OMIM:has_allelic_variant: + operation: delete +OMIM:has_inheritance_type: + operation: rename + core_predicate: biolink:related_to +OMIM:has_manifestation: + operation: invert + core_predicate: biolink:subclass_of +OMIM:has_phenotype: + operation: rename + core_predicate: biolink:has_phenotype +OMIM:inheritance_type_of: + operation: delete +OMIM:manifestation_of: + operation: rename + core_predicate: biolink:manifestation_of +OMIM:phenotype_of: + operation: invert + core_predicate: biolink:has_phenotype +ORPHANET:317343: + operation: rename + core_predicate: biolink:causes +ORPHANET:317344: + operation: rename + core_predicate: biolink:causes +ORPHANET:317345: + operation: rename + core_predicate: biolink:correlated_with +ORPHANET:317346: + operation: rename + core_predicate: biolink:causes +ORPHANET:317348: + operation: rename + core_predicate: biolink:actively_involved_in +ORPHANET:317349: + operation: rename + core_predicate: biolink:actively_involved_in +ORPHANET:327767: + operation: rename + core_predicate: biolink:actively_involved_in +ORPHANET:410295: + operation: rename + core_predicate: biolink:causes +ORPHANET:410296: + operation: rename + core_predicate: biolink:causes +ORPHANET:465410: + operation: rename + core_predicate: biolink:biomarker_for +ORPHANET:C016: + operation: rename + core_predicate: biolink:related_to +ORPHANET:C017: + operation: rename + core_predicate: biolink:related_to +# PATO:0000085: # sensitivity toward +# rename: +# - associated_with_sensitivity_to +# - biolink:associated_with_sensitivity_to +# PATO:correlates_with: +# rename: +# - correlated_with +# - biolink:correlated_with +PATO:decreased_in_magnitude_relative_to: + operation: rename + core_predicate: biolink:related_to +PATO:has_cross_section: + operation: rename + core_predicate: biolink:related_to +PATO:has_relative_magnitude: + operation: rename + core_predicate: biolink:related_to +PATO:increased_in_magnitude_relative_to: + operation: rename + core_predicate: biolink:related_to +PATO:reciprocal_of: + operation: rename + core_predicate: biolink:related_to +PATO:towards: + operation: invert + core_predicate: biolink:actively_involved_in +PDQ:associated_disease: + operation: rename + core_predicate: biolink:correlated_with +PDQ:associated_genetic_condition: + operation: delete +PDQ:component_of: + operation: invert + core_predicate: biolink:has_part +PDQ:has_component: + operation: rename + core_predicate: biolink:has_part +PR:has_gene_template: + operation: rename + core_predicate: biolink:gene_product_of +PR:confers_resistance_to: + operation: rename + core_predicate: biolink:decreases_activity_of +PR:lacks_part: + operation: rename + core_predicate: biolink:lacks_part +PR:non-covalently_bound_to: + operation: rename + core_predicate: biolink:physically_interacts_with +PSY:RO: + operation: rename + core_predicate: biolink:related_to +PSY:RB: + operation: invert + core_predicate: biolink:subclass_of +PSY:use: + operation: rename + core_predicate: biolink:subclass_of +PSY:used_for: + operation: invert + core_predicate: biolink:has_input +PathWhiz:has_bound: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_compound: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_element_collection: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_element_in_bound: + operation: rename + core_predicate: biolink:has_part +PathWhiz:has_enzyme: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_left_element: + operation: rename + core_predicate: biolink:has_input +PathWhiz:has_location: + operation: rename + core_predicate: biolink:occurs_in +PathWhiz:has_nucleic_acid: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_protein: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_protein_in_complex: + operation: rename + core_predicate: biolink:has_part +PathWhiz:has_reaction: + operation: rename + core_predicate: biolink:has_participant +PathWhiz:has_right_element: + operation: rename + core_predicate: biolink:has_output +PathWhiz:in_species: + operation: rename + core_predicate: biolink:occurs_in +REACT:has_element: + operation: rename + core_predicate: biolink:has_part +REACT:has_event: + operation: rename + core_predicate: biolink:has_participant +REACT:has_input: + operation: rename + core_predicate: biolink:has_input +REACT:has_member: + operation: rename + core_predicate: biolink:has_part +REACT:has_output: + operation: rename + core_predicate: biolink:has_output +REACT:in_species: + operation: rename + core_predicate: biolink:occurs_in +REACT:linked_to_disease: + operation: rename + core_predicate: biolink:related_to +REACT:negatively_regulates: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +REACT:negatively_regulates_gene_expression: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +REACT:positively_regulates: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +REACT:positively_regulates_gene_expression: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +REACT:related_to: + operation: rename + core_predicate: biolink:related_to +REACT:is_requirement_for: + operation: rename + core_predicate: biolink:entity_regulates_entity +REPODB:clinically_tested_approved_unknown_phase: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_0: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1_or_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2_or_phase_3: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_3: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_0: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1_or_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2_or_phase_3: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_3: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_0: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: + operation: rename + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_3: + operation: rename + core_predicate: biolink:treats +RO:0000052: + operation: rename + core_predicate: biolink:related_to +RO:0000053: + operation: rename + core_predicate: biolink:related_to +RO:0000056: + operation: invert + core_predicate: biolink:has_participant +RO:0000057: + operation: rename + core_predicate: biolink:has_participant +RO:0000059: + operation: rename + core_predicate: biolink:related_to +RO:0000086: + operation: rename + core_predicate: biolink:related_to +RO:0000087: + operation: rename + core_predicate: biolink:related_to +RO:0001000: + operation: rename + core_predicate: biolink:derives_from +RO:0001015: + operation: invert + core_predicate: biolink:located_in +RO:0001019: + operation: rename + core_predicate: biolink:has_part +RO:0001022: + operation: invert + core_predicate: biolink:causes +RO:0001025: + operation: rename + core_predicate: biolink:located_in +RO:0002001: + operation: rename + core_predicate: biolink:related_to +RO:0002002: + operation: rename + core_predicate: biolink:related_to +RO:0002005: + operation: rename + core_predicate: biolink:related_to +RO:0002007: + operation: invert + core_predicate: biolink:has_part +RO:0002008: + operation: rename + core_predicate: biolink:related_to +RO:0002082: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002083: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002087: + operation: invert + core_predicate: biolink:precedes +RO:0002090: + operation: rename + core_predicate: biolink:precedes +RO:0002092: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002093: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002100: + operation: rename + core_predicate: biolink:overlaps +RO:0002101: # fasciculates with + operation: rename + core_predicate: biolink:overlaps +RO:0002102: + operation: rename + core_predicate: biolink:overlaps +RO:0002103: + operation: rename + core_predicate: biolink:interacts_with +RO:0002104: + operation: rename + core_predicate: biolink:has_plasma_membrane_part +RO:0002120: + operation: rename + core_predicate: biolink:interacts_with +RO:0002130: + operation: rename + core_predicate: biolink:interacts_with +RO:0002131: + operation: rename + core_predicate: biolink:overlaps +RO:0002134: + operation: rename + core_predicate: biolink:related_to +RO:0002150: + operation: rename + core_predicate: biolink:related_to +RO:0002159: + operation: rename + core_predicate: biolink:related_to +RO:0002160: + operation: rename + core_predicate: biolink:in_taxon +RO:0002162: + operation: rename + core_predicate: biolink:in_taxon +RO:0002170: + operation: rename + core_predicate: biolink:related_to +RO:0002176: + operation: rename + core_predicate: biolink:related_to +RO:0002177: + operation: rename + core_predicate: biolink:related_to +RO:0002178: + operation: rename + core_predicate: biolink:related_to +RO:0002179: + operation: rename + core_predicate: biolink:related_to +RO:0002180: + operation: rename + core_predicate: biolink:has_part +RO:0002200: + operation: rename + core_predicate: biolink:has_phenotype +RO:0002202: + operation: rename + core_predicate: biolink:develops_from +RO:0002203: + operation: rename + core_predicate: biolink:develops_from +RO:0002207: + operation: rename + core_predicate: biolink:develops_from +RO:0002211: + operation: rename + core_predicate: biolink:process_regulates_process +RO:0002212: + operation: rename + core_predicate: biolink:process_negatively_regulates_process +RO:0002213: + operation: rename + core_predicate: biolink:process_positively_regulates_process +RO:0002215: + operation: rename + core_predicate: biolink:capable_of +RO:0002216: + operation: invert + core_predicate: biolink:has_participant +RO:0002219: + operation: rename + core_predicate: biolink:coexists_with +RO:0002220: + operation: rename + core_predicate: biolink:coexists_with +RO:0002221: + operation: rename + core_predicate: biolink:coexists_with +RO:0002223: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002224: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002225: + operation: rename + core_predicate: biolink:develops_from +RO:0002226: + operation: rename + core_predicate: biolink:develops_from +RO:0002229: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002230: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002231: + operation: rename + core_predicate: biolink:occurs_in +RO:0002232: + operation: rename + core_predicate: biolink:occurs_in +RO:0002233: + operation: rename + core_predicate: biolink:has_input +RO:0002234: + operation: rename + core_predicate: biolink:has_output +RO:0002241: + operation: rename + core_predicate: biolink:related_to +RO:0002254: + operation: rename + core_predicate: biolink:related_to +RO:0002256: + operation: rename + core_predicate: biolink: +RO:0002263: + operation: rename + core_predicate: biolink:acts_upstream_of +RO:0002264: + operation: rename + core_predicate: biolink:acts_upstream_of_or_within +RO:0002285: + operation: invert + core_predicate: biolink:precedes +RO:0002292: + operation: invert + core_predicate: biolink:expressed_in +RO:0002295: + operation: rename + core_predicate: biolink:entity_regulates_entity +RO:0002296: + operation: rename + core_predicate: biolink:has_output +RO:0002297: + operation: rename + core_predicate: biolink:has_output +RO:0002298: + operation: rename + core_predicate: biolink:has_output +RO:0002299: + operation: rename + core_predicate: biolink:has_output +RO:0002303: + operation: rename + core_predicate: biolink:located_in +RO:0002309: + operation: rename + core_predicate: biolink:related_to +RO:0002313: + operation: rename + core_predicate: biolink:affects_transport_of +RO:0002314: + operation: rename + core_predicate: biolink:related_to +RO:0002315: + operation: rename + core_predicate: biolink:causes +RO:0002322: + operation: rename + core_predicate: biolink:related_to +RO:0002328: + operation: rename + core_predicate: biolink:related_to +RO:0002331: + operation: rename + core_predicate: biolink:actively_involved_in +RO:0002332: + operation: rename + core_predicate: biolink:related_to +RO:0002334: + operation: invert + core_predicate: biolink:entity_regulates_entity +RO:0002338: + operation: rename + core_predicate: biolink:related_to +RO:0002339: + operation: rename + core_predicate: biolink:related_to +RO:0002340: + operation: rename + core_predicate: biolink:affects_transport_of +RO:0002341: + operation: rename + core_predicate: biolink:related_to +RO:0002342: + operation: rename + core_predicate: biolink:related_to +RO:0002343: + operation: rename + core_predicate: biolink:affects +RO:0002344: + operation: rename + core_predicate: biolink:related_to +RO:0002345: + operation: rename + core_predicate: biolink:affects_transport_of +RO:0002348: + operation: rename + core_predicate: biolink:related_to +RO:0002349: + operation: rename + core_predicate: biolink:related_to +RO:0002350: + operation: invert + core_predicate: biolink:has_part +RO:0002351: + operation: rename + core_predicate: biolink:has_part +RO:0002352: + operation: invert + core_predicate: biolink:has_input +RO:0002353: + operation: invert + core_predicate: biolink:has_output +RO:0002354: + operation: invert + core_predicate: biolink:has_output +RO:0002355: + operation: rename + core_predicate: biolink:affects +RO:0002356: + operation: rename + core_predicate: biolink:related_to +RO:0002371: + operation: rename + core_predicate: biolink:related_to +RO:0002372: + operation: rename + core_predicate: biolink:related_to +RO:0002373: + operation: rename + core_predicate: biolink:related_to +RO:0002374: + operation: rename + core_predicate: biolink:related_to +RO:0002376: + operation: invert + core_predicate: biolink:has_part +RO:0002380: + operation: invert + core_predicate: biolink:has_part +RO:0002385: + operation: rename + core_predicate: biolink:related_to +RO:0002387: + operation: rename + core_predicate: biolink:related_to +RO:0002411: + operation: rename + core_predicate: biolink:precedes +RO:0002412: + operation: rename + core_predicate: biolink:precedes +RO:0002433: + operation: rename + core_predicate: biolink:overlaps +RO:0002434: + operation: rename + core_predicate: biolink:interacts_with +RO:0002451: + operation: rename + core_predicate: biolink:related_to +RO:0002452: # has symptom + operation: rename + core_predicate: biolink:has_phenotype +# RO:0002470: +# rename: +# - related_to +# - biolink:related_to +RO:0002473: + operation: rename + core_predicate: biolink:composed_primarily_of +RO:0002488: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002489: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002491: + operation: rename + core_predicate: biolink:coexists_with +RO:0002492: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002493: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002494: + operation: rename + core_predicate: biolink:related_to +RO:0002495: + operation: rename + core_predicate: biolink:related_to +RO:0002496: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002497: + operation: rename + core_predicate: biolink:temporally_related_to +RO:0002500: + operation: rename + core_predicate: biolink:capable_of +RO:0002503: + operation: rename + core_predicate: biolink:actively_involved_in +RO:0002505: + operation: rename + core_predicate: biolink:has_participant +RO:0002507: + operation: invert + core_predicate: biolink:causes +RO:0002509: + operation: invert + core_predicate: biolink:causes +RO:0002524: + operation: rename + core_predicate: biolink:has_part +RO:0002551: + operation: rename + core_predicate: biolink:has_part +RO:0002565: + operation: rename + core_predicate: biolink:has_participant +RO:0002568: + operation: rename + core_predicate: biolink:related_to +RO:0002571: + operation: invert + core_predicate: biolink:has_part +RO:0002572: + operation: invert + core_predicate: biolink:has_part +RO:0002573: + operation: rename + core_predicate: biolink:related_to +RO:0002576: + operation: invert + core_predicate: biolink:has_part +# RO:0002578: +# rename: +# - entity_regulates_entity +# - biolink:entity_regulates_entity +RO:0002588: + operation: rename + core_predicate: biolink:has_output +RO:0002590: + operation: rename + core_predicate: biolink:has_input +RO:0002591: + operation: rename + core_predicate: biolink:affects +RO:0002592: + operation: rename + core_predicate: biolink:affects +RO:0002608: + operation: invert + core_predicate: biolink:causes +RO:0002610: + operation: rename + core_predicate: biolink:correlated_with +# RO:0002629: +# rename: +# - entity_positively_regulates_entity +# - biolink:entity_positively_regulates_entity +# RO:0002630: +# rename: +# - entity_negatively_regulates_entity +# - biolink:entity_negatively_regulates_entity +RO:0003000: + operation: rename + core_predicate: biolink:produces +RO:0003001: + operation: invert + core_predicate: biolink:produces +RO:0003003: + operation: rename + core_predicate: biolink:increases_expression_of +RO:0003304: + operation: rename + core_predicate: biolink:contributes_to +RO:0003309: + operation: rename + core_predicate: biolink:exacerbates +RO:0004001: + operation: rename + core_predicate: biolink:causes +RO:0004007: + operation: rename + core_predicate: biolink:has_participant +RO:0004008: + operation: rename + core_predicate: biolink:has_output +RO:0004009: + operation: rename + core_predicate: biolink:has_input +RO:0004019: + operation: invert + core_predicate: biolink:causes +RO:0004020: + operation: rename + core_predicate: biolink:has_participant +RO:0004021: + operation: rename + core_predicate: biolink:has_participant +RO:0004022: + operation: rename + core_predicate: biolink:has_phenotype +RO:0004024: + operation: rename + core_predicate: biolink:disrupts +RO:0004025: + operation: rename + core_predicate: biolink:disrupts +RO:0004026: + operation: rename + core_predicate: biolink:disease_has_location +RO:0004027: + operation: rename + core_predicate: biolink:related_to +RO:0004028: + operation: invert + core_predicate: biolink:causes +RO:0004029: + operation: rename + core_predicate: biolink:associated_with +# RO:0004030: +# invert: +# - causes +# - biolink: +RO:0004032: + operation: rename + core_predicate: biolink:acts_upstream_of_or_within_positive_effect +RO:0004033: + operation: rename + core_predicate: biolink:acts_upstream_of_or_within_negative_effect +RO:0004034: + operation: rename + core_predicate: biolink:acts_upstream_of_positive_effect +RO:0004035: + operation: rename + core_predicate: biolink:acts_upstream_of_negative_effect +RO:0009001: + operation: rename + core_predicate: biolink:related_to +RO:0009004: + operation: rename + core_predicate: biolink:related_to +RO:0009501: + operation: invert + core_predicate: biolink:causes +RO:0012003: + operation: rename + core_predicate: biolink:affects +RO:0012008: # results in fusion of + operation: rename + core_predicate: biolink:affects +RO:0013001: # has synaptic IO in + operation: rename + core_predicate: biolink:related_to +RO:0014001: # disease has infectious agent + operation: rename + core_predicate: biolink:related_to +RO:participates_in: + operation: invert + core_predicate: biolink:has_participant +RXNORM:consists_of: + operation: rename + core_predicate: biolink:has_part +RXNORM:constitutes: + operation: invert + core_predicate: biolink:has_part +RXNORM:contained_in: + operation: invert + core_predicate: biolink:has_part +RXNORM:contains: + operation: rename + core_predicate: biolink:has_part +RXNORM:dose_form_of: + operation: delete +RXNORM:doseformgroup_of: + operation: delete +RXNORM:form_of: + operation: delete +RXNORM:has_dose_form: + operation: rename + core_predicate: biolink:subclass_of +RXNORM:has_doseformgroup: + operation: rename + core_predicate: biolink:subclass_of +RXNORM:has_form: + operation: rename + core_predicate: biolink:related_to +RXNORM:has_ingredient: + operation: rename + core_predicate: biolink:has_part +RXNORM:has_ingredients: + operation: delete +RXNORM:has_part: + operation: rename + core_predicate: biolink:has_part +RXNORM:has_precise_ingredient: + operation: delete +RXNORM:has_quantified_form: + operation: rename + core_predicate: biolink:close_match +RXNORM:has_tradename: + operation: rename + core_predicate: biolink:related_to +RXNORM:ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:ingredients_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +RXNORM:isa: + operation: rename + core_predicate: biolink:subclass_of +RXNORM:part_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:precise_ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:quantified_form_of: + operation: delete +RXNORM:reformulated_to: + operation: rename + core_predicate: biolink:related_to +RXNORM:reformulation_of: + operation: delete +RXNORM:tradename_of: + operation: delete +SEMMEDDB:1532: + operation: delete +SEMMEDDB:administered_to: + operation: rename + core_predicate: biolink:affects +SEMMEDDB:affects: + operation: rename + core_predicate: biolink:affects +SEMMEDDB:associated_with: + operation: rename + core_predicate: biolink:related_to +SEMMEDDB:augments: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:causes: + operation: rename + core_predicate: biolink:causes +SEMMEDDB:coexists_with: + operation: rename + core_predicate: biolink:coexists_with +SEMMEDDB:compared_with: + operation: rename + core_predicate: biolink:related_to +SEMMEDDB:complicates: + operation: rename + core_predicate: biolink:exacerbates +SEMMEDDB:converts_to: + operation: invert + core_predicate: biolink:derives_from +SEMMEDDB:diagnoses: + operation: rename + core_predicate: biolink:diagnoses +SEMMEDDB:disrupts: + operation: rename + core_predicate: biolink:disrupts +SEMMEDDB:higher_than: + operation: rename + core_predicate: biolink:related_to +SEMMEDDB:inhibits: + operation: rename + core_predicate: biolink:entity_negatively_regulates_entity +SEMMEDDB:interacts_with: + operation: rename + core_predicate: biolink:interacts_with +SEMMEDDB:isa: + operation: rename + core_predicate: biolink:subclass_of +SEMMEDDB:location_of: + operation: invert + core_predicate: biolink:located_in +SEMMEDDB:lower_than: + operation: rename + core_predicate: biolink:related_to +SEMMEDDB:manifestation_of: + operation: rename + core_predicate: biolink:manifestation_of +SEMMEDDB:measurement_of: + operation: delete +SEMMEDDB:measures: + operation: rename + core_predicate: biolink:related_to +SEMMEDDB:method_of: + operation: delete +SEMMEDDB:nom: + operation: delete +SEMMEDDB:occurs_in: + operation: rename + core_predicate: biolink:occurs_in +SEMMEDDB:part_of: + operation: invert + core_predicate: biolink:has_part +SEMMEDDB:precedes: + operation: rename + core_predicate: biolink:precedes +SEMMEDDB:predisposes: + operation: rename + core_predicate: biolink:predisposes +SEMMEDDB:prep: + operation: delete +SEMMEDDB:prevents: + operation: rename + core_predicate: biolink:prevents +SEMMEDDB:process_of: + operation: rename + core_predicate: biolink:occurs_in +SEMMEDDB:produces: + operation: rename + core_predicate: biolink:produces +SEMMEDDB:same_as: + operation: rename + core_predicate: biolink:close_match +SEMMEDDB:stimulates: + operation: rename + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:treats: + operation: rename + core_predicate: biolink:treats +SEMMEDDB:uses: + operation: rename + core_predicate: biolink:has_input +SEMMEDDB:verb: + operation: delete +SEMMEDDB:xref: + operation: rename + core_predicate: biolink:related_to +SIO:000001: + operation: delete +# SIO:000983: +# rename: +# - biomarker_for +# - biolink:biomarker_for +# SIO:001331: # diagnosis +# rename: +# - diagnoses +# - biolink:diagnoses +# SO:adjacent_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# SO:contains: +# rename: +# - has_part +# - biolink:has_part +# SO:derives_from: +# rename: +# - coexists_with +# - biolink:coexists_with +# SO:guided_by: +# rename: +# - related_to +# - biolink:related_to +SO:has_origin: + operation: rename + core_predicate: biolink:coexists_with +# SO:has_part: +# rename: +# - has_part +# - biolink:has_part +# SO:has_quality: +# rename: +# - related_to +# - biolink:related_to +# SO:non_functional_homolog_of: +# rename: +# - homologous_to +# - biolink:homologous_to +# SO:member_of: +# invert: +# - has_part +# - biolink:has_part +# SO:overlaps: +# rename: +# - overlaps +# - biolink:overlaps +# SO:transcribed_from: +# rename: +# - gene_product_of +# - biolink:gene_product_of +# SO:transcribed_to: +# invert: +# - gene_product_of +# - biolink:gene_product_of +# UBERON:anastomoses_with: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:anteriorly_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channel_for: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channels_from: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:channels_into: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:conduit_for: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:distally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:existence_starts_and_ends_during: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:extends_fibers_into: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:filtered_through: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_central_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_innermost_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:in_outermost_side_of: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:indirectly_supplies: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:posteriorly_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:protects: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:proximally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:sexually_homologous_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON:site_of: +# invert: +# - occurs_in +# - biolink:occurs_in +# UBERON:subdivision_of: +# invert: +# - has_part +# - biolink:has_part +# UBERON:synapsed_by: +# rename: +# - related_to +# - biolink:related_to +UBERON_CORE:anastomoses_with: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:anteriorly_connected_to: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:channel_for: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:channels_from: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:channels_into: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:conduit_for: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:distally_connected_to: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:extends_fibers_into: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:filtered_through: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:in_central_side_of: + operation: rename + core_predicate: biolink:located_in +UBERON_CORE:in_innermost_side_of: + operation: rename + core_predicate: biolink:located_in +UBERON_CORE:in_outermost_side_of: + operation: rename + core_predicate: biolink:located_in +UBERON_CORE:indirectly_supplies: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:posteriorly_connected_to: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:protects: + operation: rename + core_predicate: biolink:related_to +UBERON_CORE:proximally_connected_to: + operation: rename + core_predicate: biolink:coexists_with +UBERON_CORE:sexually_homologous_to: + operation: rename + core_predicate: biolink:homologous_to +UBERON_CORE:site_of: + operation: rename + core_predicate: biolink:occurs_in +UBERON_CORE:subdivision_of: + operation: rename + core_predicate: biolink:part_of +UBERON_CORE:synapsed_by: + operation: rename + core_predicate: biolink:coexists_with +# UBERON_NONAMESPACE:connected_to: +# rename: +# - related_to +# - biolink:related_to +# UBERON_NONAMESPACE:distally_connected_to: +# rename: +# - coexists_with +# - biolink:coexists_with +# UBERON_NONAMESPACE:innervated_by: +# rename: +# - related_to +# - biolink:related_to +# UBERON_NONAMESPACE:subdivision_of: +# rename: +# - coexists_with +# - biolink:coexists_with +UMLS:has_physiologic_effect: + operation: rename + core_predicate: biolink:causes +UMLS:RB: + operation: rename + core_predicate: biolink:related_to +# UMLS:RN: +# rename: +# - related_to +# - biolink:related_to +UMLS:RO: + operation: rename + core_predicate: biolink:related_to +UMLS:RQ: + operation: rename + core_predicate: biolink:related_to +UMLS:SIB: + operation: delete +UMLS:SY: + operation: rename + core_predicate: biolink:close_match +UMLS:class_code_classified_by: + operation: rename + core_predicate: biolink:related_to +UMLS:classifies_class_code: + operation: delete +UMLS:component_of: + operation: invert + core_predicate: biolink:has_part +UMLS:context_binding_of: + operation: delete +UMLS:exhibited_by: + operation: rename + core_predicate: biolink:related_to +UMLS:exhibits: + operation: delete +UMLS:form_of: + operation: delete +UMLS:has_component: + operation: rename + core_predicate: biolink:has_part +UMLS:has_context_binding: + operation: rename + core_predicate: biolink:related_to +UMLS:has_form: + operation: rename + core_predicate: biolink:related_to +UMLS:has_mapping_qualifier: + operation: rename + core_predicate: biolink:related_to +UMLS:has_owning_affiliate: + operation: invert + core_predicate: biolink:has_part +UMLS:has_owning_section: + operation: delete +UMLS:has_owning_subsection: + operation: delete +UMLS:has_structural_class: + operation: rename + core_predicate: biolink:related_to +UMLS:has_supported_concept_property: + operation: rename + core_predicate: biolink:related_to +UMLS:has_supported_concept_relationship: + operation: rename + core_predicate: biolink:related_to +UMLS:larger_than: + operation: rename + core_predicate: biolink:related_to +UMLS:mapped_from: + operation: delete +UMLS:mapped_to: + operation: rename + core_predicate: biolink:related_to +UMLS:may_be_qualified_by: + operation: rename + core_predicate: biolink:related_to +UMLS:may_qualify: + operation: delete +UMLS:measured_by: + operation: delete +UMLS:measures: + operation: rename + core_predicate: biolink:related_to +UMLS:owning_affiliate_of: + operation: delete +UMLS:owning_section_of: + operation: rename + core_predicate: biolink:related_to +UMLS:owning_subsection_of: + operation: invert + core_predicate: biolink:has_part +UMLS:related_to: + operation: rename + core_predicate: biolink:related_to +UMLS:supported_concept_property_in: + operation: delete +UMLS:supported_concept_relationship_in: + operation: delete +# UO-PROPERTY:is_unit_of: +# rename: +# - related_to +# - biolink:related_to +VANDF:has_ingredient: + operation: rename + core_predicate: biolink:has_part +VANDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +VANDF:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +VANDF:isa: + operation: rename + core_predicate: biolink:subclass_of +biolink:in_taxon: + operation: keep +biolink:part_of: + operation: invert + core_predicate: biolink:has_part +biolink:subclass_of: + operation: keep +oboFormat:xref: + operation: rename + core_predicate: biolink:close_match +owl:inverseOf: + operation: rename + core_predicate: biolink:related_to +owl:sameAs: + operation: rename + core_predicate: biolink:same_as +rdf:type: + operation: rename + core_predicate: biolink:related_to +rdfs:subClassOf: + operation: rename + core_predicate: biolink:subclass_of +rdfs:subPropertyOf: + operation: rename + core_predicate: biolink:subclass_of From 5408253f5d23d31ad2f5587ee52b32c81ce31796 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 26 Jul 2022 11:26:20 -0700 Subject: [PATCH 018/127] #221 Update predicate_remap_new.yaml --- predicate_remap_new.yaml | 109 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 108 insertions(+), 1 deletion(-) diff --git a/predicate_remap_new.yaml b/predicate_remap_new.yaml index d7eb3916..8cdfcb37 100644 --- a/predicate_remap_new.yaml +++ b/predicate_remap_new.yaml @@ -188,12 +188,24 @@ CHEMBL.MECHANISM:activator: CHEMBL.MECHANISM:agonist: operation: rename core_predicate: biolink:increases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: increases + object_aspect_qualifier: activity CHEMBL.MECHANISM:allosteric_antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity CHEMBL.MECHANISM:antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity CHEMBL.MECHANISM:antisense_inhibitor: operation: rename core_predicate: biolink:decreases_expression_of @@ -227,6 +239,10 @@ CHEMBL.MECHANISM:inhibitor: CHEMBL.MECHANISM:inverse_agonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity CHEMBL.MECHANISM:modulator: operation: rename core_predicate: biolink:entity_regulates_entity @@ -279,7 +295,7 @@ CHEMBL.MECHANISM:subset_of: core_predicate: biolink:subclass_of CHEMBL.MECHANISM:substrate: operation: rename - core_predicate: biolink:physically_interacts_with + core_predicate: biolink:increases_degradation_of CHEMBL.MECHANISM:superset_of: operation: invert core_predicate: biolink:subclass_of @@ -319,6 +335,9 @@ CTD:affects_molecular_modification_of: CTD:affects_synthesis_of: operation: rename core_predicate: biolink:affects_synthesis_of +CTD:decreases_degradation_of: + operation: rename + core_predicate: biolink:decreases_degradation_of CTD:decreases_folding_of: operation: rename core_predicate: biolink:decreases_folding_of @@ -368,6 +387,14 @@ DGIdb:allosteric_modulator: DGIdb:antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreases + object_aspect_qualifier: activity DGIdb:antibody: operation: rename core_predicate: biolink:molecularly_interacts_with @@ -385,6 +412,10 @@ DGIdb:antisense_oligonucleotide: DGIdb:blocker: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity # DGIdb:channel_blocker: # rename: # - decreases_activity_of @@ -411,12 +442,24 @@ DGIdb:inducer: DGIdb:inhibitor: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DGIdb:inhibitory_allosteric_modulator: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DGIdb:inverse_agonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity # DGIdb:ligand: # rename: # - directly_interacts_with @@ -431,6 +474,10 @@ DGIdb:modulator: DGIdb:negative_modulator: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DGIdb:partial_agonist: operation: rename core_predicate: biolink:increases_activity_of @@ -464,9 +511,17 @@ DGIdb:positive_modulator: DGIdb:suppressor: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreases + object_aspect_qualifier: activity DGIdb:vaccine: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity # DOID-PROPERTY:derives_from: # rename: # - derives_from @@ -484,6 +539,10 @@ DRUGBANK:adduct: DRUGBANK:aggregation_inhibitor: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:agonist: operation: rename core_predicate: biolink:increases_activity_of @@ -493,6 +552,10 @@ DRUGBANK:allosteric_modulator: DRUGBANK:antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:antibody: operation: rename core_predicate: biolink:molecularly_interacts_with @@ -577,12 +640,20 @@ DRUGBANK:inhibitor: DRUGBANK:inhibitory_allosteric_modulator: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:intercalation: operation: rename core_predicate: biolink:molecularly_interacts_with DRUGBANK:inverse_agonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:ligand: operation: rename core_predicate: biolink:directly_interacts_with @@ -598,9 +669,17 @@ DRUGBANK:negative_modulator: DRUGBANK:neutralizer: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:nucleotide_exchange_blocker: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:oxidizer: operation: rename core_predicate: biolink:increases_molecular_modification_of @@ -610,6 +689,10 @@ DRUGBANK:partial_agonist: DRUGBANK:partial_antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:pathway: operation: rename core_predicate: biolink:has_participant @@ -640,6 +723,10 @@ DRUGBANK:substrate: DRUGBANK:suppressor: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DRUGBANK:target: operation: rename core_predicate: biolink:physically_interacts_with @@ -662,12 +749,20 @@ DrugCentral:agonist: DrugCentral:allosteric_antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DrugCentral:allosteric_modulator: operation: rename core_predicate: biolink:affects_activity_of DrugCentral:antagonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DrugCentral:antibody_binding: operation: rename core_predicate: biolink:molecularly_interacts_with @@ -690,6 +785,10 @@ DrugCentral:contraindication: DrugCentral:gating_inhibitor: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity # DrugCentral:has_faers: # rename: # - causes_adverse_event @@ -706,6 +805,10 @@ DrugCentral:inhibitor: DrugCentral:inverse_agonist: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity DrugCentral:modulator: operation: rename core_predicate: biolink:entity_regulates_entity @@ -2612,6 +2715,10 @@ PR:has_gene_template: PR:confers_resistance_to: operation: rename core_predicate: biolink:decreases_activity_of + qualified_predicate: biolink:causes + qualifiers: + object_direction_qualifier: decreased + object_aspect_qualifier: activity PR:lacks_part: operation: rename core_predicate: biolink:lacks_part From 730b50dd80504863680d9039d492703f47be6ced Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 26 Jul 2022 12:03:22 -0700 Subject: [PATCH 019/127] #221 Updates predicate_remap_new.yaml --- predicate_remap_new.yaml | 2038 ++++++++++++++++++++------------------ 1 file changed, 1050 insertions(+), 988 deletions(-) diff --git a/predicate_remap_new.yaml b/predicate_remap_new.yaml index 8cdfcb37..ba08b423 100644 --- a/predicate_remap_new.yaml +++ b/predicate_remap_new.yaml @@ -2,13 +2,13 @@ BFO:0000050: operation: invert core_predicate: biolink:has_part BFO:0000051: - operation: rename + operation: keep core_predicate: biolink:has_part BFO:0000054: - operation: rename + operation: keep core_predicate: biolink:related_to BFO:0000055: - operation: rename + operation: keep core_predicate: biolink:has_part # BFO:0000056: # invert: @@ -18,91 +18,91 @@ BFO:0000062: operation: invert core_predicate: biolink:precedes BFO:0000063: - operation: rename + operation: keep core_predicate: biolink:precedes BFO:0000066: - operation: rename + operation: keep core_predicate: biolink:occurs_in BFO:0000067: - operation: rename + operation: keep core_predicate: biolink:occurs_in BFO:0000068: - operation: rename + operation: keep core_predicate: biolink:related_to BFO:0000069: - operation: rename + operation: keep core_predicate: biolink:related_to BFO:0000117: - operation: rename + operation: keep core_predicate: biolink:has_part BFO:0000167: - operation: rename + operation: keep core_predicate: biolink:has_participant BSPO:0000096: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000097: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000098: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000099: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000100: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000102: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000104: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000107: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000108: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000110: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000113: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0000120: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000121: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000122: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000123: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000124: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000125: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0000126: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0001100: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0001101: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0001106: operation: invert core_predicate: biolink:has_part BSPO:0001107: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0001108: operation: invert @@ -114,278 +114,338 @@ BSPO:0001115: operation: invert core_predicate: biolink:has_part BSPO:0005001: - operation: rename + operation: keep core_predicate: biolink:overlaps BSPO:0015001: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015002: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015003: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015005: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015006: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015007: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015008: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015009: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015012: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015014: - operation: rename + operation: keep core_predicate: biolink:coexists_with BSPO:0015101: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0015102: - operation: rename + operation: keep core_predicate: biolink:located_in BSPO:0015202: - operation: rename + operation: keep core_predicate: biolink:located_in BTO:develops_from: - operation: rename + operation: keep core_predicate: biolink:develops_from BTO:related_to: - operation: rename + operation: keep core_predicate: biolink:related_to CHEBI:has_functional_parent: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEBI:has_parent_hydride: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEBI:is_conjugate_acid_of: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEBI:is_conjugate_base_of: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEBI:is_enantiomer_of: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEBI:is_substituent_group_from: operation: invert core_predicate: biolink:has_part CHEBI:is_tautomer_of: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to CHEMBL.MECHANISM:activator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity CHEMBL.MECHANISM:agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: increases object_aspect_qualifier: activity CHEMBL.MECHANISM:allosteric_antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity CHEMBL.MECHANISM:antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity CHEMBL.MECHANISM:antisense_inhibitor: - operation: rename + operation: keep core_predicate: biolink:decreases_expression_of CHEMBL.MECHANISM:binding_agent: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:blocker: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity CHEMBL.MECHANISM:chelating_agent: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:cross-linking_agent: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:degrader: - operation: rename + operation: keep core_predicate: biolink:increases_degradation_of CHEMBL.MECHANISM:disrupting_agent: - operation: rename + operation: keep core_predicate: biolink:disrupts CHEMBL.MECHANISM:equivalent_to: - operation: rename + operation: keep core_predicate: biolink:same_as CHEMBL.MECHANISM:hydrolytic_enzyme: - operation: rename + operation: keep core_predicate: biolink:increases_degradation_of CHEMBL.MECHANISM:inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity CHEMBL.MECHANISM:inverse_agonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity CHEMBL.MECHANISM:modulator: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity CHEMBL.MECHANISM:negative_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity CHEMBL.MECHANISM:negative_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity CHEMBL.MECHANISM:opener: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of CHEMBL.MECHANISM:other: operation: delete CHEMBL.MECHANISM:overlaps_with: - operation: rename + operation: keep core_predicate: biolink:overlaps CHEMBL.MECHANISM:oxidative_enzyme: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:partial_agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of CHEMBL.MECHANISM:positive_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of CHEMBL.MECHANISM:positive_modulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of CHEMBL.MECHANISM:proteolytic_enzyme: - operation: rename + operation: keep core_predicate: biolink:increases_degradation_of CHEMBL.MECHANISM:reducing_agent: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:releasing_agent: - operation: rename + operation: keep core_predicate: biolink:increases_expression_of CHEMBL.MECHANISM:rnai_inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity CHEMBL.MECHANISM:sequestering_agent: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with CHEMBL.MECHANISM:stabiliser: - operation: rename + operation: keep core_predicate: biolink:increases_stability_of CHEMBL.MECHANISM:subset_of: - operation: rename + operation: keep core_predicate: biolink:subclass_of CHEMBL.MECHANISM:substrate: - operation: rename + operation: keep core_predicate: biolink:increases_degradation_of CHEMBL.MECHANISM:superset_of: operation: invert core_predicate: biolink:subclass_of CL:has_completed: - operation: rename + operation: keep core_predicate: biolink:has_completed CL:has_high_plasma_membrane_amount: - operation: rename + operation: keep core_predicate: biolink:has_increased_amount CL:has_low_plasma_membrane_amount: - operation: rename + operation: keep core_predicate: biolink:has_decreased_amount CL:has_not_completed: - operation: rename + operation: keep core_predicate: biolink:has_not_completed CL:lacks_part: - operation: rename + operation: keep core_predicate: biolink:lacks_part CL:lacks_plasma_membrane_part: - operation: rename + operation: keep core_predicate: biolink:lacks_part CPT:has_add_on_code: - operation: rename + operation: keep core_predicate: biolink:related_to CPT:mapped_to: - operation: rename + operation: keep core_predicate: biolink:related_to CTD:affects_abundance_of: - operation: rename + operation: keep core_predicate: biolink:affects_abundance_of +CTD:affects_export: + operation: keep + core_predicate: biolink:affects_secretion_of CTD:affects_folding_of: - operation: rename + operation: keep core_predicate: biolink:affects_folding_of CTD:affects_molecular_modification_of: - operation: rename + operation: keep core_predicate: biolink:affects_molecular_modification_of +CTD:affects_mutation_rate_of: + operation: keep + core_predicate: biolink:affects_mutation_rate +CTD:affects_RNA_splicing: + operation: keep + core_predicate: biolink:affects_splicing_of +CTD:affects_secretion_of: + operation: keep + core_predicate: biolink:affects_secretion_of +CTD:affects_splicing_of: + operation: keep + core_predicate: biolink:affects_splicing_of CTD:affects_synthesis_of: - operation: rename + operation: keep core_predicate: biolink:affects_synthesis_of +CTD:affects_transport_of: + operation: keep + core_predicate: biolink:affects_transport_of +CTD:affects_uptake_of: + operation: keep + core_predicate: biolink:affects_uptake_of CTD:decreases_degradation_of: - operation: rename + operation: keep core_predicate: biolink:decreases_degradation_of CTD:decreases_folding_of: - operation: rename + operation: keep core_predicate: biolink:decreases_folding_of CTD:decreases_localization_of: - operation: rename + operation: keep core_predicate: biolink:decreases_localization_of CTD:decreases_metabolic_processing_of: - operation: rename + operation: keep core_predicate: biolink:decreases_metabolic_processing_of CTD:decreases_molecular_modification_of: - operation: rename + operation: keep core_predicate: biolink:decreases_molecular_modification_of +CTD:decreases_mutation_rate_of: + operation: keep + core_predicate: biolink:decreases_mutation_rate_of +CTD:decreases_RNA_splicing: + operation: keep + core_predicate: biolink:decreases_splicing_of +CTD:decreases_secretion_of: + operation: keep + core_predicate: biolink:decreases_secretion_of +CTD:decreases_splicing_of: + operation: keep + core_predicate: biolink:decreases_splicing_of +CTD:decreases_stability_of: + operation: keep + core_predicate: biolink:decreases_stability_of +CTD:decreases_transport_of: + operation: keep + core_predicate: biolink:decreases_transport_of +CTD:decreases_uptake_of: + operation: keep + core_predicate: biolink:decreases_uptake_of CTD:increases_folding_of: - operation: rename + operation: keep core_predicate: biolink:increases_folding_of CTD:increases_localization_of: - operation: rename + operation: keep core_predicate: biolink:increases_localization_of CTD:increases_metabolic_processing_of: - operation: rename + operation: keep core_predicate: biolink:increases_metabolic_processing_of CTD:increases_molecular_modification_of: - operation: rename + operation: keep core_predicate: biolink:increases_molecular_modification_of +CTD:increases_mutation_rate_of: + operation: keep + core_predicate: biolink:increases_mutation_rate_of +CTD:increases_RNA_splicing: + operation: keep + core_predicate: increases_splicing_of +CTD:increases_secretion_of: + operation: keep + core_predicate: increases_secretion_of +CTD:increases_splicing_of: + operation: keep + core_predicate: increases_splicing_of CTD:increases_synthesis_of: - operation: rename + operation: keep core_predicate: biolink:increases_synthesis_of +CTD:increases_uptake_of: + operation: keep + core_predicate: biolink:increases_uptake_of +CTD:positive_correlation: + operation: keep + core_predicate: biolink:positively_correlated_with DDANAT:develops_from: - operation: rename + operation: keep core_predicate: biolink:develops_from DGIdb:activator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity # DGIdb:adduct: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with DGIdb:affects: - operation: rename + operation: keep core_predicate: biolink:affects DGIdb:agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DGIdb:allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:affects_activity_of DGIdb:antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: @@ -396,531 +456,531 @@ DGIdb:antagonist: object_direction_qualifier: decreases object_aspect_qualifier: activity DGIdb:antibody: - operation: rename + operation: keep core_predicate: biolink:molecularly_interacts_with # DGIdb:antisense: -# rename: +# keep: # - decreases_expression_of # - biolink:decreases_expression_of DGIdb:antisense_oligonucleotide: - operation: rename + operation: keep core_predicate: biolink:decreases_expression_of # DGIdb:binder: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with DGIdb:blocker: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity # DGIdb:channel_blocker: -# rename: +# keep: # - decreases_activity_of # - biolink:decreases_activity_of # DGIdb:chaperone: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with # DGIdb:cleavage: -# rename: +# keep: # - affects_degradation_of # - biolink:affects_degradation_of # DGIdb:cofactor: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with # DGIdb:gating_inhibitor: -# rename: +# keep: # - decreases_activity_of # - biolink:decreases_activity_of DGIdb:inducer: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DGIdb:inhibitor: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DGIdb:inhibitory_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DGIdb:inverse_agonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity # DGIdb:ligand: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with DGIdb:modulator: - operation: rename + operation: keep core_predicate: biolink:affects_activity_of # DGIdb:multitarget: -# rename: +# keep: # - directly_interacts_with # - biolink:directly_interacts_with DGIdb:negative_modulator: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DGIdb:partial_agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of # DGIdb:partial_antagonist: -# rename: +# keep: # - decreases_activity_of # - biolink:decreases_activity_of # DGIdb:positive_allosteric_modulator: -# rename: +# keep: # - increases_activity_of # - biolink:increases_activity_of DGIdb:positive_modulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of # DGIdb:potentiator: -# rename: +# keep: # - increases_activity_of # - biolink:increases_activity_of # DGIdb:product_of: -# rename: +# keep: # - derives_from # - biolink:derives_from # DGIdb:stimulator: -# rename: +# keep: # - increases_activity_of # - biolink:increases_activity_of # DGIdb:substrate: -# rename: +# keep: # - increases_degradation_of # - biolink:increases_degradation_of DGIdb:suppressor: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreases object_aspect_qualifier: activity DGIdb:vaccine: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity # DOID-PROPERTY:derives_from: -# rename: +# keep: # - derives_from # - biolink:derives_from # DOID-PROPERTY:has_symptom: -# rename: +# keep: # - has_phenotype # - biolink:has_phenotype DRUGBANK:activator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity DRUGBANK:adduct: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:aggregation_inhibitor: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:affects_activity_of DRUGBANK:antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:antibody: - operation: rename + operation: keep core_predicate: biolink:molecularly_interacts_with DRUGBANK:antisense_oligonucleotide: - operation: rename + operation: keep core_predicate: biolink:decreases_expression_of DRUGBANK:atc-code: - operation: rename + operation: keep core_predicate: biolink:close_match DRUGBANK:atc-code-level: - operation: rename + operation: keep core_predicate: biolink:related_to DRUGBANK:binder: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:binding: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with DRUGBANK:blocker: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:category: - operation: rename + operation: keep core_predicate: biolink:subclass_of DRUGBANK:chaperone: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:chelator: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:cleavage: - operation: rename + operation: keep core_predicate: biolink:affects_degradation_of DRUGBANK:cofactor: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:component_of: operation: invert core_predicate: biolink:has_part DRUGBANK:degradation: - operation: rename + operation: keep core_predicate: biolink:affects_degradation_of DRUGBANK:deoxidizer: - operation: rename + operation: keep core_predicate: biolink:decreases_molecular_modification_of DRUGBANK:desensitize_the_target: - operation: rename + operation: keep core_predicate: biolink:decreases_response_to DRUGBANK:downregulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:drug-interaction: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with DRUGBANK:external-identifier: - operation: rename + operation: keep core_predicate: biolink:same_as DRUGBANK:external-identifier-protein: - operation: rename + operation: keep core_predicate: biolink:derives_from DRUGBANK:gene_replacement: - operation: rename + operation: keep core_predicate: biolink:close_match DRUGBANK:group: - operation: rename + operation: keep core_predicate: biolink:related_to DRUGBANK:inactivator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:incorporation_into_and_destabilization: - operation: rename + operation: keep core_predicate: biolink:affects_degradation_of DRUGBANK:inducer: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:inhibition_of_synthesis: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:inhibitory_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:intercalation: - operation: rename + operation: keep core_predicate: biolink:molecularly_interacts_with DRUGBANK:inverse_agonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:ligand: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:modulator: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity DRUGBANK:multitarget: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:negative_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:neutralizer: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:nucleotide_exchange_blocker: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:oxidizer: - operation: rename + operation: keep core_predicate: biolink:increases_molecular_modification_of DRUGBANK:partial_agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:partial_antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:pathway: - operation: rename + operation: keep core_predicate: biolink:has_participant DRUGBANK:positive_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:positive_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity DRUGBANK:potentiator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:product_of: - operation: rename + operation: keep core_predicate: biolink:derives_from DRUGBANK:regulator: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity DRUGBANK:stabilization: - operation: rename + operation: keep core_predicate: biolink:increases_stability_of DRUGBANK:stimulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DRUGBANK:substrate: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with DRUGBANK:suppressor: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DRUGBANK:target: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with DRUGBANK:translocation_inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DRUGBANK:weak_inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity # DrugCentral:5271: -# rename: +# keep: # - diagnoses # - biolink:diagnoses DrugCentral:activator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity DrugCentral:agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DrugCentral:allosteric_antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DrugCentral:allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:affects_activity_of DrugCentral:antagonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DrugCentral:antibody_binding: - operation: rename + operation: keep core_predicate: biolink:molecularly_interacts_with DrugCentral:antisense_inhibitor: - operation: rename + operation: keep core_predicate: biolink:decreases_expression_of DrugCentral:binding_agent: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DrugCentral:blocker: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DrugCentral:contraindication: - operation: rename + operation: keep core_predicate: biolink:contraindicated_for # DrugCentral:diagnosis: # A drug that helps diagnose a condition -# rename: +# keep: # - related_to # - biolink:related_to DrugCentral:gating_inhibitor: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity # DrugCentral:has_faers: -# rename: +# keep: # - causes_adverse_event # - biolink:causes_adverse_event DrugCentral:has_role: - operation: rename + operation: keep core_predicate: biolink:related_to DrugCentral:indication: - operation: rename + operation: keep core_predicate: biolink:treats DrugCentral:inhibitor: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DrugCentral:inverse_agonist: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity DrugCentral:modulator: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity DrugCentral:negative_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DrugCentral:negative_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity DrugCentral:off-label_use: - operation: rename + operation: keep core_predicate: biolink:treats DrugCentral:opener: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DrugCentral:PA: # PA stands for "Pharmacological Action" - operation: rename + operation: keep core_predicate: biolink:subclass_of DrugCentral:partial_agonist: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DrugCentral:pharmacological_chaperone: - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with DrugCentral:positive_allosteric_modulator: - operation: rename + operation: keep core_predicate: biolink:increases_activity_of DrugCentral:positive_modulator: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity # DrugCentral:reduce_risk: -# rename: +# keep: # - prevents # - biolink:prevents DrugCentral:releasing_agent: - operation: rename + operation: keep core_predicate: biolink:increases_expression_of DrugCentral:struct2atc: - operation: rename + operation: keep core_predicate: biolink:close_match DrugCentral:substrate: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with DrugCentral:symptomatic_treatment: - operation: rename + operation: keep core_predicate: biolink:treats EFO:0000784: - operation: rename + operation: keep core_predicate: biolink:located_in EFO:0001697: operation: invert core_predicate: biolink:related_to EFO:0006351: - operation: rename + operation: keep core_predicate: biolink:related_to EFO:is_executed_in: - operation: rename + operation: keep core_predicate: biolink:related_to ENVO:01001307: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:SIB: operation: delete FMA:adheres_to: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with FMA:adjacent_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:afferent_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:anatomical_entity_observed_in: operation: delete FMA:anterior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:anteroinferior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:anterolateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:anteromedial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:anterosuperior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:arterial_supply_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:articulates_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:attaches_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:bounded_by: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:bounds: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:branch_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:connected_to: - operation: rename + operation: keep core_predicate: biolink:related_to FMA:connection_type_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:constitutional_part_of: operation: invert @@ -929,270 +989,270 @@ FMA:contained_in: operation: invert core_predicate: biolink:has_part FMA:contains: - operation: rename + operation: keep core_predicate: biolink:has_part FMA:continuation_branch_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:continuous_distally_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:continuous_proximally_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:continuous_with: - operation: rename + operation: keep core_predicate: biolink:related_to FMA:corresponds_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:derives: operation: invert core_predicate: biolink:derives_from FMA:derives_from: - operation: rename + operation: keep core_predicate: biolink:derives_from FMA:development_type_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:developmental_stage_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:develops_from: - operation: rename + operation: keep core_predicate: biolink:develops_from FMA:develops_into: - operation: rename + operation: keep core_predicate: biolink:develops_from FMA:direct_cell_shape_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:direct_left_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:direct_right_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:distal_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:drains_into: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:efferent_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:external_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:formed_by: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:forms: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:full_grown_phenotype_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:fuses_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:fusion_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:germ_origin_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_adherent: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_arterial_supply: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_branch: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_connection_type: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_constitutional_part: - operation: rename + operation: keep core_predicate: biolink:has_part FMA:has_continuation_branch: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_development_type: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_developmental_stage: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_direct_cell_shape: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_full_grown_phenotype: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_fusion: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_germ_origin: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_inherent_3d_shape: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_insertion: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_location: - operation: rename + operation: keep core_predicate: biolink:located_in FMA:has_lymphatic_drainage: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_member: - operation: rename + operation: keep core_predicate: biolink:has_part FMA:has_nerve_supply: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_observed_anatomical_entity: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_origin: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_part: - operation: rename + operation: keep core_predicate: biolink:has_part FMA:has_primary_segmental_supply: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_projection: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_regional_part: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_related_developmental_entity: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_secondary_segmental_supply: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_segmental_composition: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_segmental_supply: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_tributary: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:has_venous_drainage: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:homonym_for: operation: delete FMA:homonym_of: - operation: rename + operation: keep core_predicate: biolink:related_to FMA:inferior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:inferolateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:inferomedial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:inherent_3d_shape_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:insertion_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:internal_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:lateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:left_lateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:left_medial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:location_of: operation: invert core_predicate: biolink:located_in FMA:lymphatic_drainage_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:matures_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:matures_into: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:medial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:member_of: operation: invert core_predicate: biolink:has_part FMA:merges_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:nerve_supply_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:origin_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:part_of: operation: invert core_predicate: biolink:has_part FMA:posterior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:posteroinferior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:posterolateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:posteromedial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:posterosuperior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:primary_segmental_supply_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:projects_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:projects_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:proximal_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:receives_attachment_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:receives_drainage_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:receives_input_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:receives_projection: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:regional_part_of: operation: invert @@ -1201,64 +1261,64 @@ FMA:related_developmental_entity_of: operation: invert core_predicate: biolink:related_to FMA:related_object: - operation: rename + operation: keep core_predicate: biolink:related_to FMA:related_part: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:right_lateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:right_medial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:secondary_segmental_supply_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:segmental_composition_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:segmental_supply_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:sends_output_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:superior_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:superolateral_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:superomedial_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:surrounded_by: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:surrounds: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:transforms_from: operation: invert core_predicate: biolink:precedes FMA:transforms_into: - operation: rename + operation: keep core_predicate: biolink:precedes FMA:tributary_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FMA:venous_drainage_of: - operation: rename + operation: keep core_predicate: biolink:coexists_with FOODON:00001301: - operation: rename + operation: keep core_predicate: biolink:model_of FOODON:00001563: - operation: rename + operation: keep core_predicate: biolink:has_part FOODON:00002420: - operation: rename + operation: keep core_predicate: biolink:has_part GENEPIO:0001739: operation: invert @@ -1266,46 +1326,46 @@ GENEPIO:0001739: GO:SIB: operation: delete GO:acts_upstream_of: - operation: rename + operation: keep core_predicate: biolink:affects GO:acts_upstream_of_negative_effect: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity GO:acts_upstream_of_or_within: - operation: rename + operation: keep core_predicate: biolink:affects GO:acts_upstream_of_or_within_negative_effect: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity GO:acts_upstream_of_or_within_positive_effect: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity GO:acts_upstream_of_positive_effect: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity GO:colocalizes_with: - operation: rename + operation: keep core_predicate: biolink:colocalizes_with GO:contributes_to: - operation: rename + operation: keep core_predicate: biolink:contributes_to GO:enables: - operation: rename + operation: keep core_predicate: biolink:enables GO:ends_during: - operation: rename + operation: keep core_predicate: biolink:related_to GO:happens_during: - operation: rename + operation: keep core_predicate: biolink:related_to GO:has_occurrence: - operation: rename + operation: keep core_predicate: biolink:capable_of GO:has_part: - operation: rename + operation: keep core_predicate: biolink:has_part GO:inverse_ends_during: - operation: rename + operation: keep core_predicate: biolink:related_to GO:inverse_happens_during: operation: delete @@ -1316,22 +1376,22 @@ GO:involved_in: operation: invert core_predicate: biolink:has_participant GO:is_active_in: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in GO:isa: - operation: rename + operation: keep core_predicate: biolink:subclass_of GO:located_in: - operation: rename + operation: keep core_predicate: biolink:located_in GO:negatively_regulated_by: operation: invert core_predicate: biolink:entity_negatively_regulates_entity GO:negatively_regulates: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity GO:occurs_in: - operation: rename + operation: keep core_predicate: biolink:occurs_in GO:part_of: operation: invert @@ -1340,58 +1400,58 @@ GO:positively_regulated_by: operation: invert core_predicate: biolink:entity_positively_regulates_entity GO:positively_regulates: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity GO:regulated_by: operation: invert core_predicate: biolink:entity_regulates_entity GO:regulates: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity GOREL:0000040: - operation: rename + operation: keep core_predicate: biolink:causes GOREL:0002003: - operation: rename + operation: keep core_predicate: biolink:affects_localization_of GOREL:0002004: - operation: rename + operation: keep core_predicate: biolink:increases_degradation_of # GOREL:0002005: -# rename: +# keep: # - related_to # - biolink:related_to GOREL:0012006: - operation: rename + operation: keep core_predicate: biolink:related_to HANCESTRO:0301: - operation: rename + operation: keep core_predicate: biolink:related_to HANCESTRO:0308: # has country of origin - operation: rename + operation: keep core_predicate: biolink:related_to HANCESTRO:0330: - operation: rename + operation: keep core_predicate: biolink:related_to HCPCS:mapped_from: operation: delete HCPCS:mapped_to: - operation: rename + operation: keep core_predicate: biolink:related_to HMDB:at_cellular_location: - operation: rename + operation: keep core_predicate: biolink:located_in HMDB:at_tissue: - operation: rename + operation: keep core_predicate: biolink:located_in HMDB:disease: - operation: rename + operation: keep core_predicate: biolink:related_to HMDB:has_protein_association: - operation: rename + operation: keep core_predicate: biolink:related_to HMDB:in_biospecimen: - operation: rename + operation: keep core_predicate: biolink:located_in HMDB:in_pathway: operation: invert @@ -1399,13 +1459,13 @@ HMDB:in_pathway: HP:SIB: operation: delete IAO:0000039: - operation: rename + operation: keep core_predicate: biolink:related_to IAO:0000136: - operation: rename + operation: keep core_predicate: biolink:related_to IAO:0000219: - operation: rename + operation: keep core_predicate: biolink:related_to ICD10PCS:SIB: operation: delete @@ -1415,10 +1475,10 @@ IDO:0000664: operation: invert core_predicate: biolink:contributes_to JensenLab:associated_with: - operation: rename + operation: keep core_predicate: biolink:gene_associated_with_condition KEGG:compound_to_enzyme: - operation: rename + operation: keep core_predicate: biolink:interacts_with KEGG:compound_to_pathway: operation: invert @@ -1430,10 +1490,10 @@ KEGG:enzyme_to_pathway: operation: invert core_predicate: biolink:has_participant KEGG:enzyme_to_reaction: - operation: rename + operation: keep core_predicate: biolink:catalyzes KEGG:glycan_to_enzyme: - operation: rename + operation: keep core_predicate: biolink:interacts_with KEGG:glycan_to_pathway: operation: invert @@ -1442,13 +1502,13 @@ KEGG:glycan_to_reaction: operation: invert core_predicate: biolink:has_participant KEGG:pathway_to_compound: - operation: rename + operation: keep core_predicate: biolink:has_participant KEGG:pathway_to_drug: - operation: rename + operation: keep core_predicate: biolink:has_participant KEGG:pathway_to_glycan: - operation: rename + operation: keep core_predicate: biolink:has_participant KEGG:reaction_to_enzyme: operation: invert @@ -1461,19 +1521,19 @@ LOINC:adjustment_of: LOINC:analyzed_by: operation: delete LOINC:analyzes: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:answer_to: operation: delete LOINC:archetype_of: operation: delete LOINC:associated_with: - operation: rename + operation: keep core_predicate: biolink:correlated_with LOINC:challenge_of: operation: delete LOINC:class_of: - operation: rename + operation: keep core_predicate: biolink:subclass_of LOINC:component_of: operation: invert @@ -1487,116 +1547,116 @@ LOINC:evaluation_of: LOINC:fragments_for_synonyms_of: operation: delete LOINC:has_action_guidance: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_adjustment: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_aggregation_view: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_answer: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_approach_guidance: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_archetype: - operation: rename + operation: keep core_predicate: biolink:subclass_of LOINC:has_challenge: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_class: operation: invert core_predicate: biolink:subclass_of LOINC:has_component: - operation: rename + operation: keep core_predicate: biolink:has_part LOINC:has_count: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_divisor: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_evaluation: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_exam: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_fragments_for_synonyms: - operation: rename + operation: keep core_predicate: biolink:has_input LOINC:has_given_pharmaceutical_substance: operation: delete LOINC:has_imaged_location: - operation: rename + operation: keep core_predicate: biolink:occurs_in LOINC:has_imaging_focus: - operation: rename + operation: keep core_predicate: biolink:located_in LOINC:has_lateral_anatomic_location: - operation: rename + operation: keep core_predicate: biolink:coexists_with LOINC:has_lateral_location_presence: - operation: rename + operation: keep core_predicate: biolink:coexists_with LOINC:has_loinc_number: operation: delete LOINC:has_member: - operation: rename + operation: keep core_predicate: biolink:has_part LOINC:has_method: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_modality_subtype: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_modality_type: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_multipart: operation: delete LOINC:has_object_guidance: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_parent_group: - operation: rename + operation: keep core_predicate: biolink:subclass_of LOINC:has_pharmaceutical_route: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_presence_guidance: operation: delete LOINC:has_property: operation: delete LOINC:has_scale: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_subject: - operation: rename + operation: keep core_predicate: biolink:has_participant LOINC:has_suffix: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_supersystem: operation: invert core_predicate: biolink:has_part LOINC:has_system: - operation: rename + operation: keep core_predicate: biolink:has_input LOINC:has_time_aspect: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_time_modifier: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_timing_of: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:has_view_type: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:is_action_guidance_for: operation: delete @@ -1624,7 +1684,7 @@ LOINC:is_object_guidance_for: LOINC:is_pharmaceutical_route_for: operation: delete LOINC:is_presence_guidance_for: - operation: rename + operation: keep core_predicate: biolink:subclass_of LOINC:is_presence_of_lateral_location: operation: delete @@ -1639,10 +1699,10 @@ LOINC:loinc_number_of: LOINC:mapped_from: operation: delete LOINC:mapped_to: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:measured_by: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:measures: operation: delete @@ -1654,7 +1714,7 @@ LOINC:method_of: LOINC:mth_expanded_form_of: operation: delete LOINC:mth_has_expanded_form: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:multipart_of: operation: invert @@ -1662,7 +1722,7 @@ LOINC:multipart_of: LOINC:parent_group_of: operation: delete LOINC:property_of: - operation: rename + operation: keep core_predicate: biolink:related_to LOINC:scale_of: operation: delete @@ -1681,148 +1741,148 @@ MESH:AQ: MESH:QB: operation: delete MESH:RO: - operation: rename + operation: keep core_predicate: biolink:related_to MESH:SIB: operation: delete MESH:has_mapping_qualifier: - operation: rename + operation: keep core_predicate: biolink:related_to MESH:inverse_isa: operation: invert core_predicate: biolink:subclass_of MESH:isa: - operation: rename + operation: keep core_predicate: biolink:subclass_of MESH:mapped_from: operation: delete MESH:mapped_to: - operation: rename + operation: keep core_predicate: biolink:related_to MESH:mapping_qualifier_of: operation: delete MI:0192: # acetylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0194: # cleavage reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0195: # covalent bonding - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0197: # deacetylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0203: # dephosphorylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0204: # deubiquitination reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0210: # hydroxylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0211: # lipid addition - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0212: # lipoprotein cleavage reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0213: # methylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0214: # myristoylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0216: # palmitoylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0217: # phosphorylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0220: # ubiquitination reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0403: # colocalization - operation: rename + operation: keep core_predicate: biolink:colocalizes_with MI:0407: # direct interaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0408: # disulfide bond - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0414: # enzymatic reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0556: # transglutamination reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0557: # adp_ribosylation_reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0559: # glycosylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0566: # sumoylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0567: # neddylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0569: # deneddylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0570: # protein cleavage - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0572: # dna cleavage - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0844: # phosphotransfer reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0871: # demethylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0882: # atpase reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0883: # gtpase reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0902: # rna reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:0914: # association - operation: rename + operation: keep core_predicate: biolink:interacts_with MI:0915: # physical associaiton - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with MI:0945: # oxidoreductase activity electron transfer reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:1126: # self interaction - operation: rename + operation: keep core_predicate: biolink:interacts_with MI:1127: # putative self interaction - operation: rename + operation: keep core_predicate: biolink:interacts_with MI:1148: # ampylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:1237: # proline isomerization reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:1310: # de-ADP-ribosylation reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MI:2364: # proximity - operation: rename + operation: keep core_predicate: biolink:colocalizes_with MI:2252: # guanine nucleotide exchange factor reaction - operation: rename + operation: keep core_predicate: biolink:directly_interacts_with MONDO:0100332: # disease has primary infectious agent operation: invert @@ -1831,50 +1891,50 @@ MONDO:0100333: # disease caused by reactivation of latent infectious agent operation: invert core_predicate: biolink:causes MONDO:disease_causes_feature: - operation: rename + operation: keep core_predicate: biolink:causes MONDO:disease_has_basis_in_accumulation_of: - operation: rename + operation: keep core_predicate: biolink:disease_has_basis_in MONDO:disease_has_basis_in_development_of: - operation: rename + operation: keep core_predicate: biolink:disease_has_basis_in MONDO:disease_has_major_feature: - operation: rename + operation: keep core_predicate: biolink:has_part MONDO:disease_responds_to: operation: invert core_predicate: biolink:treats MONDO:disease_shares_features_of: - operation: rename + operation: keep core_predicate: biolink:related_to MONDO:disease_triggers: - operation: rename + operation: keep core_predicate: biolink:causes MONDO:equivalentTo: - operation: rename + operation: keep core_predicate: biolink:same_as MONDO:has_onset: - operation: rename + operation: keep core_predicate: biolink:related_to MONDO:has_onset_before: - operation: rename + operation: keep core_predicate: biolink:related_to MONDO:has_onset_during_or_after: - operation: rename + operation: keep core_predicate: biolink:related_to MONDO:part_of_progression_of_disease: operation: invert core_predicate: biolink:has_part MONDO:predisposes_towards: - operation: rename + operation: keep core_predicate: biolink:contributes_to # NBO-PROPERTY:by_means: -# rename: +# keep: # - actively_involved_in # - biolink:actively_involved_in # NBO-PROPERTY:has_participant: -# rename: +# keep: # - has_participant # - biolink:has_participant # NBO-PROPERTY:in_response_to: @@ -1882,7 +1942,7 @@ MONDO:predisposes_towards: # - causes # - biolink:causes # NBO-PROPERTY:is_about: -# rename: +# keep: # - related_to # - biolink:related_to NCIT:abnormal_cell_affected_by_chemical_or_drug: @@ -1892,22 +1952,22 @@ NCIT:abnormality_associated_with_allele: NCIT:activity_of_allele: operation: delete NCIT:allele_absent_from_wild-type_chromosomal_location: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:allele_has_abnormality: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:allele_has_activity: - operation: rename + operation: keep core_predicate: biolink:has_molecular_consequence NCIT:allele_in_chromosomal_location: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:allele_plays_altered_role_in_process: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:anatomic_structure_has_location: operation: delete @@ -1919,20 +1979,20 @@ NCIT:anatomy_originated_from_biological_process: NCIT:associated_with_malfunction_of_gene_product: operation: delete NCIT:biological_process_has_associated_location: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:biological_process_has_initiator_chemical_or_drug: operation: delete NCIT:biological_process_has_initiator_process: operation: delete NCIT:biological_process_has_result_anatomy: - operation: rename + operation: keep core_predicate: biolink:has_output NCIT:biological_process_has_result_biological_process: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:biological_process_has_result_chemical_or_drug: - operation: rename + operation: keep core_predicate: biolink:produces NCIT:biological_process_involves_chemical_or_drug: operation: invert @@ -1948,7 +2008,7 @@ NCIT:biomarker_type_includes_gene: NCIT:biomarker_type_includes_gene_product: operation: delete # NCIT:C15220: # diagnosis -# rename: +# keep: # - diagnoses # - biolink:diagnoses NCIT:cdrh_parent_of: @@ -1959,22 +2019,22 @@ NCIT:cell_type_is_associated_with_eo_disease: NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: operation: delete NCIT:chemical_or_drug_affects_abnormal_cell: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:chemical_or_drug_affects_cell_type_or_tissue: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:chemical_or_drug_affects_gene_product: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:chemical_or_drug_has_mechanism_of_action: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:chemical_or_drug_has_physiologic_effect: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:chemical_or_drug_initiates_biological_process: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:chemical_or_drug_is_metabolized_by_enzyme: operation: delete @@ -1993,14 +2053,14 @@ NCIT:chromosomal_location_of_wild-type_gene: NCIT:chromosome_involved_in_cytogenetic_abnormality: operation: delete NCIT:chromosome_mapped_to_disease: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:completely_excised_anatomy_has_procedure: operation: delete NCIT:completely_excised_anatomy_may_have_procedure: operation: delete NCIT:complex_has_physical_part: - operation: rename + operation: keep core_predicate: biolink:has_part NCIT:concept_in_subset: operation: delete @@ -2011,7 +2071,7 @@ NCIT:ctcae_5_parent_of: operation: invert core_predicate: biolink:subclass_of NCIT:cytogenetic_abnormality_involves_chromosome: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:data_element_of: operation: delete @@ -2036,10 +2096,10 @@ NCIT:disease_has_abnormal_cell: NCIT:disease_has_accepted_treatment_with_regimen: operation: delete NCIT:disease_has_associated_anatomic_site: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:disease_has_associated_disease: - operation: rename + operation: keep core_predicate: biolink:has_real_world_evidence_of_association_with NCIT:disease_has_associated_gene: operation: delete @@ -2049,7 +2109,7 @@ NCIT:disease_has_finding: operation: invert core_predicate: biolink:biomarker_for NCIT:disease_has_metastatic_anatomic_site: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:disease_has_molecular_abnormality: operation: invert @@ -2057,55 +2117,55 @@ NCIT:disease_has_molecular_abnormality: NCIT:disease_has_normal_cell_origin: operation: delete NCIT:disease_has_normal_tissue_origin: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:disease_has_primary_anatomic_site: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:disease_is_grade: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:disease_is_marked_by_gene: operation: invert core_predicate: biolink:biomarker_for NCIT:disease_is_stage: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:disease_mapped_to_chromosome: operation: delete NCIT:disease_mapped_to_gene: operation: delete NCIT:disease_may_have_abnormal_cell: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:disease_may_have_associated_disease: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:disease_may_have_cytogenetic_abnormality: operation: delete NCIT:disease_may_have_finding: - operation: rename + operation: keep core_predicate: biolink:has_phenotype NCIT:disease_may_have_molecular_abnormality: - operation: rename + operation: keep core_predicate: biolink:has_phenotype NCIT:disease_may_have_normal_cell_origin: operation: delete NCIT:endogenous_product_related_to: operation: delete NCIT:enzyme_metabolizes_chemical_or_drug: - operation: rename + operation: keep core_predicate: biolink:increases_metabolic_processing_of NCIT:eo_anatomy_is_associated_with_eo_disease: operation: delete NCIT:eo_disease_has_associated_cell_type: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:eo_disease_has_associated_eo_anatomy: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:eo_disease_has_property_or_attribute: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:eo_disease_maps_to_human_disease: operation: delete @@ -2114,39 +2174,39 @@ NCIT:excised_anatomy_has_procedure: NCIT:excised_anatomy_may_have_procedure: operation: delete NCIT:gene_associated_with_disease: - operation: rename + operation: keep core_predicate: biolink:gene_associated_with_condition NCIT:gene_encodes_gene_product: operation: invert core_predicate: biolink:gene_product_of NCIT:gene_found_in_organism: - operation: rename + operation: keep core_predicate: biolink:in_taxon NCIT:gene_has_abnormality: operation: delete NCIT:gene_has_physical_location: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:gene_in_chromosomal_location: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:gene_involved_in_molecular_abnormality: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in NCIT:gene_involved_in_pathogenesis_of_disease: - operation: rename + operation: keep core_predicate: biolink:gene_associated_with_condition NCIT:gene_is_biomarker_of: - operation: rename + operation: keep core_predicate: biolink:biomarker_for NCIT:gene_is_biomarker_type: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:gene_is_element_in_pathway: operation: invert core_predicate: biolink:has_participant NCIT:gene_mapped_to_disease: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:gene_mutant_encodes_gene_product_sequence_variation: operation: invert @@ -2159,33 +2219,33 @@ NCIT:gene_product_affected_by_chemical_or_drug: NCIT:gene_product_encoded_by_gene: operation: delete NCIT:gene_product_expressed_in_tissue: - operation: rename + operation: keep core_predicate: biolink:expressed_in NCIT:gene_product_has_abnormality: - operation: rename + operation: keep core_predicate: biolink:affects NCIT:gene_product_has_associated_anatomy: - operation: rename + operation: keep core_predicate: biolink:expressed_in NCIT:gene_product_has_biochemical_function: - operation: rename + operation: keep core_predicate: biolink:capable_of NCIT:gene_product_has_chemical_classification: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:gene_product_has_gene_product_variant: operation: delete NCIT:gene_product_has_organism_source: - operation: rename + operation: keep core_predicate: biolink:in_taxon NCIT:gene_product_has_structural_domain_or_motif: - operation: rename + operation: keep core_predicate: biolink:has_part NCIT:gene_product_is_biomarker_of: - operation: rename + operation: keep core_predicate: biolink:biomarker_for NCIT:gene_product_is_biomarker_type: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:gene_product_is_element_in_pathway: operation: invert @@ -2194,19 +2254,19 @@ NCIT:gene_product_is_physical_part_of: operation: invert core_predicate: biolink:has_participant NCIT:gene_product_malfunction_associated_with_disease: - operation: rename + operation: keep core_predicate: biolink:gene_associated_with_condition NCIT:gene_product_plays_role_in_biological_process: operation: invert core_predicate: biolink:has_participant NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: - operation: rename + operation: keep core_predicate: biolink:is_sequence_variant_of NCIT:gene_product_variant_of_gene_product: - operation: rename + operation: keep core_predicate: biolink:is_sequence_variant_of NCIT:genetic_biomarker_related_to: - operation: rename + operation: keep core_predicate: biolink:biomarker_for NCIT:has_cdrh_parent: operation: delete @@ -2215,53 +2275,53 @@ NCIT:has_conceptual_part: NCIT:has_ctcae_5_parent: operation: delete NCIT:has_data_element: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_free_acid_or_base_form: operation: delete NCIT:has_gene_product_element: operation: delete NCIT:has_inc_parent: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:has_nichd_parent: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:has_pharmaceutical_administration_method: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_pharmaceutical_basic_dose_form: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_pharmaceutical_intended_site: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_pharmaceutical_release_characteristics: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_pharmaceutical_state_of_matter: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_pharmaceutical_transformation: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:has_physical_part_of_anatomic_structure: operation: delete NCIT:has_salt_form: - operation: rename + operation: keep core_predicate: biolink:chemically_similar_to NCIT:has_target: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with NCIT:human_disease_maps_to_eo_disease: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:inc_parent_of: operation: delete NCIT:imaged_anatomy_has_procedure: operation: delete NCIT:is_abnormal_cell_of_disease: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:is_abnormality_of_gene: operation: delete @@ -2272,7 +2332,7 @@ NCIT:is_associated_anatomic_site_of: NCIT:is_associated_anatomy_of_gene_product: operation: delete NCIT:is_associated_disease_of: - operation: rename + operation: keep core_predicate: biolink:correlated_with NCIT:is_biochemical_function_of_gene_product: operation: delete @@ -2291,7 +2351,7 @@ NCIT:is_finding_of_disease: NCIT:is_grade_of_disease: operation: delete NCIT:is_location_of_anatomic_structure: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:is_location_of_biological_process: operation: delete @@ -2302,7 +2362,7 @@ NCIT:is_mechanism_of_action_of_chemical_or_drug: NCIT:is_metastatic_anatomic_site_of_disease: operation: delete NCIT:is_molecular_abnormality_of_disease: - operation: rename + operation: keep core_predicate: biolink:biomarker_for NCIT:is_normal_cell_origin_of_disease: operation: invert @@ -2337,10 +2397,10 @@ NCIT:is_primary_anatomic_site_of_disease: NCIT:is_property_or_attribute_of_eo_disease: operation: delete NCIT:is_qualified_by: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:is_related_to_endogenous_product: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:is_stage_of_disease: operation: delete @@ -2368,7 +2428,7 @@ NCIT:may_be_normal_cell_origin_of_disease: NCIT:molecular_abnormality_involves_gene: operation: delete NCIT:neoplasm_has_special_category: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:nichd_parent_of: operation: delete @@ -2382,7 +2442,7 @@ NCIT:partially_excised_anatomy_may_have_procedure: NCIT:pathogenesis_of_disease_involves_gene: operation: delete NCIT:pathway_has_gene_element: - operation: rename + operation: keep core_predicate: biolink:has_participant NCIT:pharmaceutical_administration_method_of: operation: delete @@ -2397,125 +2457,125 @@ NCIT:pharmaceutical_state_of_matter_of: NCIT:pharmaceutical_transformation_of: operation: delete NCIT:procedure_has_completely_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_has_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_has_imaged_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_has_target_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_has_partially_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_may_have_completely_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_may_have_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:procedure_may_have_partially_excised_anatomy: - operation: rename + operation: keep core_predicate: biolink:located_in NCIT:process_altered_by_allele: operation: delete NCIT:process_includes_biological_process: - operation: rename + operation: keep core_predicate: biolink:has_participant NCIT:process_initiates_biological_process: - operation: rename + operation: keep core_predicate: biolink:causes NCIT:process_involves_gene: - operation: rename + operation: keep core_predicate: biolink:has_participant NCIT:qualifier_applies_to: - operation: rename + operation: keep core_predicate: biolink:related_to # NCIT:R40: -# rename: +# keep: # - located_in # - biolink:located_in NCIT:R81: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:R82: - operation: rename + operation: keep core_predicate: biolink:part_of # NCIT:R88: # disease is stage -# rename: +# keep: # - related_to # - biolink:related_to # NCIT:R89: -# rename: +# keep: # - has_phenotype # - biolink:has_phenotype # NCIT:R108: -# rename: +# keep: # - has_phenotype # - biolink:has_phenotype # NCIT:R115: -# rename: +# keep: # - has_phenotype # - biolink:has_phenotype # NCIT:R145: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R155: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R156: -# rename: +# keep: # - located_in # - biolink:located_in NCIT:R163: - operation: rename + operation: keep core_predicate: biolink:related_to # NCIT:R165: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R166: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R167: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R168: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R169: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R170: -# rename: +# keep: # - located_in # - biolink:located_in # NCIT:R171: -# rename: +# keep: # - located_in # - biolink:located_in NCIT:regimen_has_accepted_use_for_disease: - operation: rename + operation: keep core_predicate: biolink:treats NCIT:related_to_genetic_biomarker: operation: delete NCIT:role_has_domain: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:role_has_parent: - operation: rename + operation: keep core_predicate: biolink:subclass_of NCIT:role_has_range: - operation: rename + operation: keep core_predicate: biolink:related_to NCIT:role_is_parent_of: operation: delete @@ -2531,175 +2591,175 @@ NCIT:tissue_is_expression_site_of_gene_product: NDDF:dose_form_of: operation: delete NDDF:has_dose_form: - operation: rename + operation: keep core_predicate: biolink:subclass_of NDDF:has_ingredient: - operation: rename + operation: keep core_predicate: biolink:has_part NDDF:ingredient_of: operation: invert core_predicate: biolink:has_part OBI:0000293: - operation: rename + operation: keep core_predicate: biolink:has_participant OBI:0000295: operation: invert core_predicate: biolink:has_participant OBI:0000299: - operation: rename + operation: keep core_predicate: biolink:has_output OBI:0000417: # achieves planned objective - operation: rename + operation: keep core_predicate: biolink:has_output OBI:0001927: operation: invert core_predicate: biolink:related_to OBO:INO_0000154: - operation: rename + operation: keep core_predicate: biolink:related_to OBO:bspo#parallel_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with # OBO:doid#has_symptom: -# rename: +# keep: # - has_phenotype # - biolink:has_phenotype OBO:envo#has_increased_levels_of: - operation: rename + operation: keep core_predicate: biolink:related_to OBO:exo#interacts_with: - operation: rename + operation: keep core_predicate: biolink:interacts_with OBO:exo#interacts_with_an_exposure_stressor_via: - operation: rename + operation: keep core_predicate: biolink:interacts_with OBO:exo#interacts_with_an_exposure_receptor_via: - operation: rename + operation: keep core_predicate: biolink:interacts_with # OBO:exo.obo#interacts_with: -# rename: +# keep: # - interacts_with # - biolink:interacts_with # OBO:exo.obo#interacts_with_an_exposure_stressor_via: -# rename: +# keep: # - interacts_with # - biolink:interacts_with # OBO:exo.obo#interacts_with_an_exposure_receptor_via: -# rename: +# keep: # - interacts_with # - biolink:interacts_with OBO:has_role: - operation: rename + operation: keep core_predicate: biolink:related_to OBO:MF#manifestationOf: - operation: rename + operation: keep core_predicate: biolink:manifestation_of OBO:nbo#by_means: operation: invert core_predicate: biolink:actively_involved_in OBO:nbo#has_participant: - operation: rename + operation: keep core_predicate: biolink:has_participant OBO:nbo#in_response_to: operation: invert core_predicate: biolink:causes OBO:nbo#is_about: - operation: rename + operation: keep core_predicate: biolink:related_to # OBO:uo#is_unit_of: # invert: # - related_to # - biolink:related_to # OIO:hasDbXref: -# rename: +# keep: # - close_match # - biolink:close_match OMIM:allelic_variant_of: - operation: rename + operation: keep core_predicate: biolink:is_sequence_variant_of OMIM:has_allelic_variant: operation: delete OMIM:has_inheritance_type: - operation: rename + operation: keep core_predicate: biolink:related_to OMIM:has_manifestation: operation: invert core_predicate: biolink:subclass_of OMIM:has_phenotype: - operation: rename + operation: keep core_predicate: biolink:has_phenotype OMIM:inheritance_type_of: operation: delete OMIM:manifestation_of: - operation: rename + operation: keep core_predicate: biolink:manifestation_of OMIM:phenotype_of: operation: invert core_predicate: biolink:has_phenotype ORPHANET:317343: - operation: rename + operation: keep core_predicate: biolink:causes ORPHANET:317344: - operation: rename + operation: keep core_predicate: biolink:causes ORPHANET:317345: - operation: rename + operation: keep core_predicate: biolink:correlated_with ORPHANET:317346: - operation: rename + operation: keep core_predicate: biolink:causes ORPHANET:317348: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in ORPHANET:317349: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in ORPHANET:327767: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in ORPHANET:410295: - operation: rename + operation: keep core_predicate: biolink:causes ORPHANET:410296: - operation: rename + operation: keep core_predicate: biolink:causes ORPHANET:465410: - operation: rename + operation: keep core_predicate: biolink:biomarker_for ORPHANET:C016: - operation: rename + operation: keep core_predicate: biolink:related_to ORPHANET:C017: - operation: rename + operation: keep core_predicate: biolink:related_to # PATO:0000085: # sensitivity toward -# rename: +# keep: # - associated_with_sensitivity_to # - biolink:associated_with_sensitivity_to # PATO:correlates_with: -# rename: +# keep: # - correlated_with # - biolink:correlated_with PATO:decreased_in_magnitude_relative_to: - operation: rename + operation: keep core_predicate: biolink:related_to PATO:has_cross_section: - operation: rename + operation: keep core_predicate: biolink:related_to PATO:has_relative_magnitude: - operation: rename + operation: keep core_predicate: biolink:related_to PATO:increased_in_magnitude_relative_to: - operation: rename + operation: keep core_predicate: biolink:related_to PATO:reciprocal_of: - operation: rename + operation: keep core_predicate: biolink:related_to PATO:towards: operation: invert core_predicate: biolink:actively_involved_in PDQ:associated_disease: - operation: rename + operation: keep core_predicate: biolink:correlated_with PDQ:associated_genetic_condition: operation: delete @@ -2707,377 +2767,377 @@ PDQ:component_of: operation: invert core_predicate: biolink:has_part PDQ:has_component: - operation: rename + operation: keep core_predicate: biolink:has_part PR:has_gene_template: - operation: rename + operation: keep core_predicate: biolink:gene_product_of PR:confers_resistance_to: - operation: rename + operation: keep core_predicate: biolink:decreases_activity_of qualified_predicate: biolink:causes qualifiers: object_direction_qualifier: decreased object_aspect_qualifier: activity PR:lacks_part: - operation: rename + operation: keep core_predicate: biolink:lacks_part PR:non-covalently_bound_to: - operation: rename + operation: keep core_predicate: biolink:physically_interacts_with PSY:RO: - operation: rename + operation: keep core_predicate: biolink:related_to PSY:RB: operation: invert core_predicate: biolink:subclass_of PSY:use: - operation: rename + operation: keep core_predicate: biolink:subclass_of PSY:used_for: operation: invert core_predicate: biolink:has_input PathWhiz:has_bound: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_compound: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_element_collection: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_element_in_bound: - operation: rename + operation: keep core_predicate: biolink:has_part PathWhiz:has_enzyme: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_left_element: - operation: rename + operation: keep core_predicate: biolink:has_input PathWhiz:has_location: - operation: rename + operation: keep core_predicate: biolink:occurs_in PathWhiz:has_nucleic_acid: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_protein: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_protein_in_complex: - operation: rename + operation: keep core_predicate: biolink:has_part PathWhiz:has_reaction: - operation: rename + operation: keep core_predicate: biolink:has_participant PathWhiz:has_right_element: - operation: rename + operation: keep core_predicate: biolink:has_output PathWhiz:in_species: - operation: rename + operation: keep core_predicate: biolink:occurs_in REACT:has_element: - operation: rename + operation: keep core_predicate: biolink:has_part REACT:has_event: - operation: rename + operation: keep core_predicate: biolink:has_participant REACT:has_input: - operation: rename + operation: keep core_predicate: biolink:has_input REACT:has_member: - operation: rename + operation: keep core_predicate: biolink:has_part REACT:has_output: - operation: rename + operation: keep core_predicate: biolink:has_output REACT:in_species: - operation: rename + operation: keep core_predicate: biolink:occurs_in REACT:linked_to_disease: - operation: rename + operation: keep core_predicate: biolink:related_to REACT:negatively_regulates: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity REACT:negatively_regulates_gene_expression: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity REACT:positively_regulates: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity REACT:positively_regulates_gene_expression: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity REACT:related_to: - operation: rename + operation: keep core_predicate: biolink:related_to REACT:is_requirement_for: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity REPODB:clinically_tested_approved_unknown_phase: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_0: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_1: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_1_or_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_2_or_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_suspended_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_0: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_1: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_1_or_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_2_or_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_terminated_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_0: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_1: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_2: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats REPODB:clinically_tested_withdrawn_phase_3: - operation: rename + operation: keep core_predicate: biolink:treats RO:0000052: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0000053: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0000056: operation: invert core_predicate: biolink:has_participant RO:0000057: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0000059: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0000086: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0000087: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0001000: - operation: rename + operation: keep core_predicate: biolink:derives_from RO:0001015: operation: invert core_predicate: biolink:located_in RO:0001019: - operation: rename + operation: keep core_predicate: biolink:has_part RO:0001022: operation: invert core_predicate: biolink:causes RO:0001025: - operation: rename + operation: keep core_predicate: biolink:located_in RO:0002001: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002002: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002005: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002007: operation: invert core_predicate: biolink:has_part RO:0002008: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002082: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002083: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002087: operation: invert core_predicate: biolink:precedes RO:0002090: - operation: rename + operation: keep core_predicate: biolink:precedes RO:0002092: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002093: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002100: - operation: rename + operation: keep core_predicate: biolink:overlaps RO:0002101: # fasciculates with - operation: rename + operation: keep core_predicate: biolink:overlaps RO:0002102: - operation: rename + operation: keep core_predicate: biolink:overlaps RO:0002103: - operation: rename + operation: keep core_predicate: biolink:interacts_with RO:0002104: - operation: rename + operation: keep core_predicate: biolink:has_plasma_membrane_part RO:0002120: - operation: rename + operation: keep core_predicate: biolink:interacts_with RO:0002130: - operation: rename + operation: keep core_predicate: biolink:interacts_with RO:0002131: - operation: rename + operation: keep core_predicate: biolink:overlaps RO:0002134: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002150: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002159: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002160: - operation: rename + operation: keep core_predicate: biolink:in_taxon RO:0002162: - operation: rename + operation: keep core_predicate: biolink:in_taxon RO:0002170: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002176: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002177: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002178: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002179: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002180: - operation: rename + operation: keep core_predicate: biolink:has_part RO:0002200: - operation: rename + operation: keep core_predicate: biolink:has_phenotype RO:0002202: - operation: rename + operation: keep core_predicate: biolink:develops_from RO:0002203: - operation: rename + operation: keep core_predicate: biolink:develops_from RO:0002207: - operation: rename + operation: keep core_predicate: biolink:develops_from RO:0002211: - operation: rename - core_predicate: biolink:process_regulates_process + operation: keep + core_predicate: biolink:regulates RO:0002212: - operation: rename + operation: keep core_predicate: biolink:process_negatively_regulates_process RO:0002213: - operation: rename + operation: keep core_predicate: biolink:process_positively_regulates_process RO:0002215: - operation: rename + operation: keep core_predicate: biolink:capable_of RO:0002216: operation: invert core_predicate: biolink:has_participant RO:0002219: - operation: rename + operation: keep core_predicate: biolink:coexists_with RO:0002220: - operation: rename + operation: keep core_predicate: biolink:coexists_with RO:0002221: - operation: rename + operation: keep core_predicate: biolink:coexists_with RO:0002223: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002224: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002225: - operation: rename + operation: keep core_predicate: biolink:develops_from RO:0002226: - operation: rename + operation: keep core_predicate: biolink:develops_from RO:0002229: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002230: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002231: - operation: rename + operation: keep core_predicate: biolink:occurs_in RO:0002232: - operation: rename + operation: keep core_predicate: biolink:occurs_in RO:0002233: - operation: rename + operation: keep core_predicate: biolink:has_input RO:0002234: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002241: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002254: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002256: - operation: rename + operation: keep core_predicate: biolink: RO:0002263: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of RO:0002264: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of_or_within RO:0002285: operation: invert @@ -3086,85 +3146,85 @@ RO:0002292: operation: invert core_predicate: biolink:expressed_in RO:0002295: - operation: rename + operation: keep core_predicate: biolink:entity_regulates_entity RO:0002296: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002297: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002298: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002299: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002303: - operation: rename + operation: keep core_predicate: biolink:located_in RO:0002309: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002313: - operation: rename + operation: keep core_predicate: biolink:affects_transport_of RO:0002314: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002315: - operation: rename + operation: keep core_predicate: biolink:causes RO:0002322: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002328: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002331: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in RO:0002332: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002334: operation: invert core_predicate: biolink:entity_regulates_entity RO:0002338: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002339: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002340: - operation: rename + operation: keep core_predicate: biolink:affects_transport_of RO:0002341: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002342: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002343: - operation: rename + operation: keep core_predicate: biolink:affects RO:0002344: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002345: - operation: rename + operation: keep core_predicate: biolink:affects_transport_of RO:0002348: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002349: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002350: operation: invert core_predicate: biolink:has_part RO:0002351: - operation: rename + operation: keep core_predicate: biolink:has_part RO:0002352: operation: invert @@ -3176,22 +3236,22 @@ RO:0002354: operation: invert core_predicate: biolink:has_output RO:0002355: - operation: rename + operation: keep core_predicate: biolink:affects RO:0002356: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002371: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002372: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002373: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002374: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002376: operation: invert @@ -3200,71 +3260,71 @@ RO:0002380: operation: invert core_predicate: biolink:has_part RO:0002385: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002387: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002411: - operation: rename + operation: keep core_predicate: biolink:precedes RO:0002412: - operation: rename + operation: keep core_predicate: biolink:precedes RO:0002433: - operation: rename + operation: keep core_predicate: biolink:overlaps RO:0002434: - operation: rename + operation: keep core_predicate: biolink:interacts_with RO:0002451: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002452: # has symptom - operation: rename + operation: keep core_predicate: biolink:has_phenotype # RO:0002470: -# rename: +# keep: # - related_to # - biolink:related_to RO:0002473: - operation: rename + operation: keep core_predicate: biolink:composed_primarily_of RO:0002488: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002489: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002491: - operation: rename + operation: keep core_predicate: biolink:coexists_with RO:0002492: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002493: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002494: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002495: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002496: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002497: - operation: rename + operation: keep core_predicate: biolink:temporally_related_to RO:0002500: - operation: rename + operation: keep core_predicate: biolink:capable_of RO:0002503: - operation: rename + operation: keep core_predicate: biolink:actively_involved_in RO:0002505: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0002507: operation: invert @@ -3273,16 +3333,16 @@ RO:0002509: operation: invert core_predicate: biolink:causes RO:0002524: - operation: rename + operation: keep core_predicate: biolink:has_part RO:0002551: - operation: rename + operation: keep core_predicate: biolink:has_part RO:0002565: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0002568: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002571: operation: invert @@ -3291,140 +3351,140 @@ RO:0002572: operation: invert core_predicate: biolink:has_part RO:0002573: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0002576: operation: invert core_predicate: biolink:has_part # RO:0002578: -# rename: +# keep: # - entity_regulates_entity # - biolink:entity_regulates_entity RO:0002588: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0002590: - operation: rename + operation: keep core_predicate: biolink:has_input RO:0002591: - operation: rename + operation: keep core_predicate: biolink:affects RO:0002592: - operation: rename + operation: keep core_predicate: biolink:affects RO:0002608: operation: invert core_predicate: biolink:causes RO:0002610: - operation: rename + operation: keep core_predicate: biolink:correlated_with # RO:0002629: -# rename: +# keep: # - entity_positively_regulates_entity # - biolink:entity_positively_regulates_entity # RO:0002630: -# rename: +# keep: # - entity_negatively_regulates_entity # - biolink:entity_negatively_regulates_entity RO:0003000: - operation: rename + operation: keep core_predicate: biolink:produces RO:0003001: operation: invert core_predicate: biolink:produces RO:0003003: - operation: rename + operation: keep core_predicate: biolink:increases_expression_of RO:0003304: - operation: rename + operation: keep core_predicate: biolink:contributes_to RO:0003309: - operation: rename + operation: keep core_predicate: biolink:exacerbates RO:0004001: - operation: rename + operation: keep core_predicate: biolink:causes RO:0004007: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0004008: - operation: rename + operation: keep core_predicate: biolink:has_output RO:0004009: - operation: rename + operation: keep core_predicate: biolink:has_input RO:0004019: operation: invert core_predicate: biolink:causes RO:0004020: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0004021: - operation: rename + operation: keep core_predicate: biolink:has_participant RO:0004022: - operation: rename + operation: keep core_predicate: biolink:has_phenotype RO:0004024: - operation: rename + operation: keep core_predicate: biolink:disrupts RO:0004025: - operation: rename + operation: keep core_predicate: biolink:disrupts RO:0004026: - operation: rename + operation: keep core_predicate: biolink:disease_has_location RO:0004027: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0004028: operation: invert core_predicate: biolink:causes RO:0004029: - operation: rename + operation: keep core_predicate: biolink:associated_with # RO:0004030: # invert: # - causes # - biolink: RO:0004032: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of_or_within_positive_effect RO:0004033: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of_or_within_negative_effect RO:0004034: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of_positive_effect RO:0004035: - operation: rename + operation: keep core_predicate: biolink:acts_upstream_of_negative_effect RO:0009001: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0009004: - operation: rename + operation: keep core_predicate: biolink:related_to RO:0009501: operation: invert core_predicate: biolink:causes RO:0012003: - operation: rename + operation: keep core_predicate: biolink:affects RO:0012008: # results in fusion of - operation: rename + operation: keep core_predicate: biolink:affects RO:0013001: # has synaptic IO in - operation: rename + operation: keep core_predicate: biolink:related_to RO:0014001: # disease has infectious agent - operation: rename + operation: keep core_predicate: biolink:related_to RO:participates_in: operation: invert core_predicate: biolink:has_participant RXNORM:consists_of: - operation: rename + operation: keep core_predicate: biolink:has_part RXNORM:constitutes: operation: invert @@ -3433,7 +3493,7 @@ RXNORM:contained_in: operation: invert core_predicate: biolink:has_part RXNORM:contains: - operation: rename + operation: keep core_predicate: biolink:has_part RXNORM:dose_form_of: operation: delete @@ -3442,29 +3502,29 @@ RXNORM:doseformgroup_of: RXNORM:form_of: operation: delete RXNORM:has_dose_form: - operation: rename + operation: keep core_predicate: biolink:subclass_of RXNORM:has_doseformgroup: - operation: rename + operation: keep core_predicate: biolink:subclass_of RXNORM:has_form: - operation: rename + operation: keep core_predicate: biolink:related_to RXNORM:has_ingredient: - operation: rename + operation: keep core_predicate: biolink:has_part RXNORM:has_ingredients: operation: delete RXNORM:has_part: - operation: rename + operation: keep core_predicate: biolink:has_part RXNORM:has_precise_ingredient: operation: delete RXNORM:has_quantified_form: - operation: rename + operation: keep core_predicate: biolink:close_match RXNORM:has_tradename: - operation: rename + operation: keep core_predicate: biolink:related_to RXNORM:ingredient_of: operation: invert @@ -3476,7 +3536,7 @@ RXNORM:inverse_isa: operation: invert core_predicate: biolink:subclass_of RXNORM:isa: - operation: rename + operation: keep core_predicate: biolink:subclass_of RXNORM:part_of: operation: invert @@ -3487,7 +3547,7 @@ RXNORM:precise_ingredient_of: RXNORM:quantified_form_of: operation: delete RXNORM:reformulated_to: - operation: rename + operation: keep core_predicate: biolink:related_to RXNORM:reformulation_of: operation: delete @@ -3496,147 +3556,147 @@ RXNORM:tradename_of: SEMMEDDB:1532: operation: delete SEMMEDDB:administered_to: - operation: rename + operation: keep core_predicate: biolink:affects SEMMEDDB:affects: - operation: rename + operation: keep core_predicate: biolink:affects SEMMEDDB:associated_with: - operation: rename + operation: keep core_predicate: biolink:related_to SEMMEDDB:augments: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity SEMMEDDB:causes: - operation: rename + operation: keep core_predicate: biolink:causes SEMMEDDB:coexists_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with SEMMEDDB:compared_with: - operation: rename + operation: keep core_predicate: biolink:related_to SEMMEDDB:complicates: - operation: rename + operation: keep core_predicate: biolink:exacerbates SEMMEDDB:converts_to: operation: invert core_predicate: biolink:derives_from SEMMEDDB:diagnoses: - operation: rename + operation: keep core_predicate: biolink:diagnoses SEMMEDDB:disrupts: - operation: rename + operation: keep core_predicate: biolink:disrupts SEMMEDDB:higher_than: - operation: rename + operation: keep core_predicate: biolink:related_to SEMMEDDB:inhibits: - operation: rename + operation: keep core_predicate: biolink:entity_negatively_regulates_entity SEMMEDDB:interacts_with: - operation: rename + operation: keep core_predicate: biolink:interacts_with SEMMEDDB:isa: - operation: rename + operation: keep core_predicate: biolink:subclass_of SEMMEDDB:location_of: operation: invert core_predicate: biolink:located_in SEMMEDDB:lower_than: - operation: rename + operation: keep core_predicate: biolink:related_to SEMMEDDB:manifestation_of: - operation: rename + operation: keep core_predicate: biolink:manifestation_of SEMMEDDB:measurement_of: operation: delete SEMMEDDB:measures: - operation: rename + operation: keep core_predicate: biolink:related_to SEMMEDDB:method_of: operation: delete SEMMEDDB:nom: operation: delete SEMMEDDB:occurs_in: - operation: rename + operation: keep core_predicate: biolink:occurs_in SEMMEDDB:part_of: operation: invert core_predicate: biolink:has_part SEMMEDDB:precedes: - operation: rename + operation: keep core_predicate: biolink:precedes SEMMEDDB:predisposes: - operation: rename + operation: keep core_predicate: biolink:predisposes SEMMEDDB:prep: operation: delete SEMMEDDB:prevents: - operation: rename + operation: keep core_predicate: biolink:prevents SEMMEDDB:process_of: - operation: rename + operation: keep core_predicate: biolink:occurs_in SEMMEDDB:produces: - operation: rename + operation: keep core_predicate: biolink:produces SEMMEDDB:same_as: - operation: rename + operation: keep core_predicate: biolink:close_match SEMMEDDB:stimulates: - operation: rename + operation: keep core_predicate: biolink:entity_positively_regulates_entity SEMMEDDB:treats: - operation: rename + operation: keep core_predicate: biolink:treats SEMMEDDB:uses: - operation: rename + operation: keep core_predicate: biolink:has_input SEMMEDDB:verb: operation: delete SEMMEDDB:xref: - operation: rename + operation: keep core_predicate: biolink:related_to SIO:000001: operation: delete # SIO:000983: -# rename: +# keep: # - biomarker_for # - biolink:biomarker_for # SIO:001331: # diagnosis -# rename: +# keep: # - diagnoses # - biolink:diagnoses # SO:adjacent_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # SO:contains: -# rename: +# keep: # - has_part # - biolink:has_part # SO:derives_from: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # SO:guided_by: -# rename: +# keep: # - related_to # - biolink:related_to SO:has_origin: - operation: rename + operation: keep core_predicate: biolink:coexists_with # SO:has_part: -# rename: +# keep: # - has_part # - biolink:has_part # SO:has_quality: -# rename: +# keep: # - related_to # - biolink:related_to # SO:non_functional_homolog_of: -# rename: +# keep: # - homologous_to # - biolink:homologous_to # SO:member_of: @@ -3644,11 +3704,11 @@ SO:has_origin: # - has_part # - biolink:has_part # SO:overlaps: -# rename: +# keep: # - overlaps # - biolink:overlaps # SO:transcribed_from: -# rename: +# keep: # - gene_product_of # - biolink:gene_product_of # SO:transcribed_to: @@ -3656,75 +3716,75 @@ SO:has_origin: # - gene_product_of # - biolink:gene_product_of # UBERON:anastomoses_with: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:anteriorly_connected_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:channel_for: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:channels_from: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:channels_into: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:conduit_for: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:distally_connected_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:existence_starts_and_ends_during: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:extends_fibers_into: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:filtered_through: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:in_central_side_of: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:in_innermost_side_of: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:in_outermost_side_of: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:indirectly_supplies: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:posteriorly_connected_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:protects: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:proximally_connected_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:sexually_homologous_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON:site_of: @@ -3736,108 +3796,108 @@ SO:has_origin: # - has_part # - biolink:has_part # UBERON:synapsed_by: -# rename: +# keep: # - related_to # - biolink:related_to UBERON_CORE:anastomoses_with: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:anteriorly_connected_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:channel_for: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:channels_from: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:channels_into: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:conduit_for: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:distally_connected_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:extends_fibers_into: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:filtered_through: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:in_central_side_of: - operation: rename + operation: keep core_predicate: biolink:located_in UBERON_CORE:in_innermost_side_of: - operation: rename + operation: keep core_predicate: biolink:located_in UBERON_CORE:in_outermost_side_of: - operation: rename + operation: keep core_predicate: biolink:located_in UBERON_CORE:indirectly_supplies: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:posteriorly_connected_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:protects: - operation: rename + operation: keep core_predicate: biolink:related_to UBERON_CORE:proximally_connected_to: - operation: rename + operation: keep core_predicate: biolink:coexists_with UBERON_CORE:sexually_homologous_to: - operation: rename + operation: keep core_predicate: biolink:homologous_to UBERON_CORE:site_of: - operation: rename + operation: keep core_predicate: biolink:occurs_in UBERON_CORE:subdivision_of: - operation: rename + operation: keep core_predicate: biolink:part_of UBERON_CORE:synapsed_by: - operation: rename + operation: keep core_predicate: biolink:coexists_with # UBERON_NONAMESPACE:connected_to: -# rename: +# keep: # - related_to # - biolink:related_to # UBERON_NONAMESPACE:distally_connected_to: -# rename: +# keep: # - coexists_with # - biolink:coexists_with # UBERON_NONAMESPACE:innervated_by: -# rename: +# keep: # - related_to # - biolink:related_to # UBERON_NONAMESPACE:subdivision_of: -# rename: +# keep: # - coexists_with # - biolink:coexists_with UMLS:has_physiologic_effect: - operation: rename + operation: keep core_predicate: biolink:causes UMLS:RB: - operation: rename + operation: keep core_predicate: biolink:related_to # UMLS:RN: -# rename: +# keep: # - related_to # - biolink:related_to UMLS:RO: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:RQ: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:SIB: operation: delete UMLS:SY: - operation: rename + operation: keep core_predicate: biolink:close_match UMLS:class_code_classified_by: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:classifies_class_code: operation: delete @@ -3847,23 +3907,23 @@ UMLS:component_of: UMLS:context_binding_of: operation: delete UMLS:exhibited_by: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:exhibits: operation: delete UMLS:form_of: operation: delete UMLS:has_component: - operation: rename + operation: keep core_predicate: biolink:has_part UMLS:has_context_binding: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:has_form: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:has_mapping_qualifier: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:has_owning_affiliate: operation: invert @@ -3873,53 +3933,53 @@ UMLS:has_owning_section: UMLS:has_owning_subsection: operation: delete UMLS:has_structural_class: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:has_supported_concept_property: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:has_supported_concept_relationship: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:larger_than: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:mapped_from: operation: delete UMLS:mapped_to: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:may_be_qualified_by: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:may_qualify: operation: delete UMLS:measured_by: operation: delete UMLS:measures: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:owning_affiliate_of: operation: delete UMLS:owning_section_of: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:owning_subsection_of: operation: invert core_predicate: biolink:has_part UMLS:related_to: - operation: rename + operation: keep core_predicate: biolink:related_to UMLS:supported_concept_property_in: operation: delete UMLS:supported_concept_relationship_in: operation: delete # UO-PROPERTY:is_unit_of: -# rename: +# keep: # - related_to # - biolink:related_to VANDF:has_ingredient: - operation: rename + operation: keep core_predicate: biolink:has_part VANDF:ingredient_of: operation: invert @@ -3928,30 +3988,32 @@ VANDF:inverse_isa: operation: invert core_predicate: biolink:subclass_of VANDF:isa: - operation: rename + operation: keep core_predicate: biolink:subclass_of biolink:in_taxon: operation: keep + core_predicate: biolink:in_taxon biolink:part_of: operation: invert core_predicate: biolink:has_part biolink:subclass_of: operation: keep + core_predicate: biolink:in_taxon oboFormat:xref: - operation: rename + operation: keep core_predicate: biolink:close_match owl:inverseOf: - operation: rename + operation: keep core_predicate: biolink:related_to owl:sameAs: - operation: rename + operation: keep core_predicate: biolink:same_as rdf:type: - operation: rename + operation: keep core_predicate: biolink:related_to rdfs:subClassOf: - operation: rename + operation: keep core_predicate: biolink:subclass_of rdfs:subPropertyOf: - operation: rename + operation: keep core_predicate: biolink:subclass_of From a1f5b7537b401234c84ccd8aebe7942cdb88d71a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 4 Aug 2022 15:00:12 -0700 Subject: [PATCH 020/127] Create remap_predicate_remap.py --- remap_predicate_remap.py | 437 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 437 insertions(+) create mode 100644 remap_predicate_remap.py diff --git a/remap_predicate_remap.py b/remap_predicate_remap.py new file mode 100644 index 00000000..3ae88beb --- /dev/null +++ b/remap_predicate_remap.py @@ -0,0 +1,437 @@ +#! /usr/bin/venv python3 + +""" + Purpose: Remap entries in predicate_remap.yaml according to biolink_model 3.0 +""" +from collections import OrderedDict + +import yaml + + +OUTPUT_FILE_PATH = "predicate_remap_biolink_3.0.yaml" +BIOLINK_MODEL_FILE_PATH = "biolink-model.yaml" +PREDICATE_REMAP_OLD_FILE_PATH = "predicate_remap.yaml" +QUALIFIER_MAPPING_DICT = {"biolink:negatively_regulates": """ + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +""", + "biolink:positively_regulates": """ + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +""", + "biolink:affects_abundance_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: abundance +""", + "biolink:decreases_abundance_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: abundance + - object_direction: decreased +""", + "biolink:decreases_synthesis_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: decreased +""", + "biolink:decreases_expression_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +""", + "biolink:increases_degradation_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +""", + "biolink:increases_abundance_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: abundance + - object_direction: increased +""", + "biolink:increases_synthesis_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: increased +""", + "biolink:increases_expression_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +""", + "biolink:decreases_degradation_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +""", + "biolink:affects_synthesis_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: synthesis +""", + "biolink:affects_expression_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: expression +""", + "biolink:affects_degradation_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +""", + "biolink:affects_activity_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +""", + "biolink:decreases_activity_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +""", + "biolink:increases_activity_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +""", + "biolink:affects_expression_in": """ + core_predicate: biolink:affects +""", + "biolink:affects_folding_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: folding +""", + "biolink:decreases_folding_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: decreased +""", + "biolink:increases_folding_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: increased +""", + "biolink:affects_localization_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: localization +""", + "biolink:decreases_localization_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +""", + "biolink:increases_localization_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +""", + "biolink:affects_metabolic_processing_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: processing +""", + "biolink:decreases_metabolic_processing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +""", + "biolink:increases_metabolic_processing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +""", + "biolink:affects_molecular_modification_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +""", + "biolink:decreases_molecular_modification_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +""", + "biolink:increases_molecular_modification_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +""", + "biolink:affects_mutation_rate_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: mutation_rate +""", + "biolink:decreases_mutation_rate_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +""", + "biolink:increases_mutation_rate_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +""", + "biolink:affects_splicing_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +""", + "biolink:decreases_splicing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +""", + "biolink:increases_splicing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +""", + "biolink:affects_stability_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: stability +""", + "biolink:decreases_stability_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: decreased +""", + "biolink:increases_stability_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: increased +""", + "biolink:affects_transport_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +""", + "biolink:decreases_transport_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: decreased +""", + "biolink:increases_transport_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: increased +""", + "biolink:affects_uptake_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +""", + "biolink:decreases_uptake_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +""", + "biolink:increases_uptake_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +""", + "biolink:affects_secretion_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +""", + "biolink:decreases_secretion_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +""", + "biolink:increases_secretion_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +""" + } + + +def get_mapped_predicates(): + # Get info from the existing predicate-remap.yaml + # Note yaml.full_load does not retain comments + with open(PREDICATE_REMAP_OLD_FILE_PATH, "r") as fp: + predicate_remap_dict = yaml.full_load(fp) + + for key, value_dict in predicate_remap_dict.items(): + for operation, values in value_dict.items(): + # disregards current "keep" operation, changes "rename" to "keep + if operation == "rename": + new_value = ["keep"] + elif operation in ("invert", "delete"): + new_value = [operation] + + # add biolink predicate to list + if values is not None: + new_value.append(values[1]) + predicate_remap_dict[key] = new_value + + return predicate_remap_dict + + +def get_biolink_predicates(): + with open(BIOLINK_MODEL_FILE_PATH, "r") as fp: + # convert biolink-model.yaml into a dictionary + biolink_dict = yaml.full_load(fp) + + # create a dict for valid predicates + valid_dict = {} + + # create a dictionary for the remapped predicates + predicates_dict = {} + + # iterate over the biolink dictionary to remap predicates + # while also generating a list of predicates + for biolink_key, biolink_value in biolink_dict["slots"].items(): + + deprecated = False + + # build a dictionary of biolink predicates + if biolink_key == "related to": + valid_dict[biolink_key] = "keep" + elif type(biolink_value) == dict and "is_a" in biolink_value.keys() \ + and biolink_value["is_a"] in valid_dict.keys(): + if "inverse" in biolink_value.keys(): + valid_dict[biolink_key] = "invert" + else: + valid_dict[biolink_key] = "keep" + + # Add flag for deprecated + if "deprecated" in biolink_value.keys(): + deprecated = True + + # If key is in valid_dict, add it to `predicates_dict` + if biolink_key in valid_dict.keys(): + for key, value_list in biolink_value.items(): + # Map predicates to `related to` + if key in ("exact_mappings", "broad_mappings", "narrow_mappings") and value_list is not None: + # value_list is a list of predicates + for predicate in value_list: + if predicate not in predicates_dict: + operation = valid_dict[biolink_key] + biolink_predicate = "biolink:" + "_".join(biolink_key.split()) + # Filter out undesired KPs + if predicate.split(":", 1)[0] not in ("SNOMED", "SNOMEDCT", "GAMMA"): + if operation != "invert": + predicates_dict[predicate] = [operation, biolink_predicate] + else: + invert_predicate = "biolink:" + "_".join(biolink_value["inverse"].split()) + predicates_dict[predicate] = [operation, invert_predicate] + + if deprecated: + predicates_dict[predicate].append("deprecated") + + return predicates_dict + + +def remap_predicates(predicates_dict, predicate_map_dict): + # print(predicate_map_dict) + print(predicates_dict) + + # Add data from the old predicate_remap.yaml to the predicates dict + for predicate, value_list in predicate_map_dict.items(): + if predicate not in predicates_dict: + predicates_dict[predicate] = value_list + + ordered_dict = OrderedDict(sorted(predicates_dict.items())) + + with open(OUTPUT_FILE_PATH, "w") as ofp, open("remap.log", "w") as log: + text = "" + for key, value in ordered_dict.items(): + # print(f"{key} {value}") + operation = value[0] + if len(value) > 1: + biolink_predicate = value[1] + ofp.write(f"{key}: \n operation: {operation}") # (key + ":\n operation: keep") + # Check if the predicate is in the qualifiers dict and has a "keep" operation + if operation == "keep" and biolink_predicate in QUALIFIER_MAPPING_DICT.keys(): + text = QUALIFIER_MAPPING_DICT[biolink_predicate] + elif operation == "delete": + text = "\n" + else: + text = "\n core_predicate: " + biolink_predicate + "\n" + + # Write to log predicates that are deprecated but not covered in qualifier map + if len(value) == 3 and value[1] not in QUALIFIER_MAPPING_DICT.keys(): + log.write(f"{key} {value[1]} {operation}\n") + + ofp.write(text) + + print("Completed") + + return + + +if __name__ == "__main__": + predicates = get_biolink_predicates() + mapped_predicates = get_mapped_predicates() + remap_predicates(predicates, mapped_predicates) From 9ffd6bd6006033a1bc346ecb59207de38fd50bf7 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 4 Aug 2022 16:19:40 -0700 Subject: [PATCH 021/127] #220 Create predicate-remap-biolink-3.0.yaml --- predicate-remap-biolink-3.0.yaml | 437 +++++++++++++++++++++++++++++++ 1 file changed, 437 insertions(+) create mode 100644 predicate-remap-biolink-3.0.yaml diff --git a/predicate-remap-biolink-3.0.yaml b/predicate-remap-biolink-3.0.yaml new file mode 100644 index 00000000..3ae88beb --- /dev/null +++ b/predicate-remap-biolink-3.0.yaml @@ -0,0 +1,437 @@ +#! /usr/bin/venv python3 + +""" + Purpose: Remap entries in predicate_remap.yaml according to biolink_model 3.0 +""" +from collections import OrderedDict + +import yaml + + +OUTPUT_FILE_PATH = "predicate_remap_biolink_3.0.yaml" +BIOLINK_MODEL_FILE_PATH = "biolink-model.yaml" +PREDICATE_REMAP_OLD_FILE_PATH = "predicate_remap.yaml" +QUALIFIER_MAPPING_DICT = {"biolink:negatively_regulates": """ + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +""", + "biolink:positively_regulates": """ + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +""", + "biolink:affects_abundance_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: abundance +""", + "biolink:decreases_abundance_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: abundance + - object_direction: decreased +""", + "biolink:decreases_synthesis_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: decreased +""", + "biolink:decreases_expression_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +""", + "biolink:increases_degradation_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +""", + "biolink:increases_abundance_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: abundance + - object_direction: increased +""", + "biolink:increases_synthesis_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: increased +""", + "biolink:increases_expression_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +""", + "biolink:decreases_degradation_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +""", + "biolink:affects_synthesis_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: synthesis +""", + "biolink:affects_expression_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: expression +""", + "biolink:affects_degradation_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +""", + "biolink:affects_activity_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +""", + "biolink:decreases_activity_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +""", + "biolink:increases_activity_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +""", + "biolink:affects_expression_in": """ + core_predicate: biolink:affects +""", + "biolink:affects_folding_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: folding +""", + "biolink:decreases_folding_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: decreased +""", + "biolink:increases_folding_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: increased +""", + "biolink:affects_localization_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: localization +""", + "biolink:decreases_localization_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +""", + "biolink:increases_localization_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +""", + "biolink:affects_metabolic_processing_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: processing +""", + "biolink:decreases_metabolic_processing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +""", + "biolink:increases_metabolic_processing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +""", + "biolink:affects_molecular_modification_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +""", + "biolink:decreases_molecular_modification_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +""", + "biolink:increases_molecular_modification_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +""", + "biolink:affects_mutation_rate_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: mutation_rate +""", + "biolink:decreases_mutation_rate_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +""", + "biolink:increases_mutation_rate_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +""", + "biolink:affects_splicing_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +""", + "biolink:decreases_splicing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +""", + "biolink:increases_splicing_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +""", + "biolink:affects_stability_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: stability +""", + "biolink:decreases_stability_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: decreased +""", + "biolink:increases_stability_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: increased +""", + "biolink:affects_transport_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +""", + "biolink:decreases_transport_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: decreased +""", + "biolink:increases_transport_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: increased +""", + "biolink:affects_uptake_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +""", + "biolink:decreases_uptake_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +""", + "biolink:increases_uptake_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +""", + "biolink:affects_secretion_of": """ + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +""", + "biolink:decreases_secretion_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +""", + "biolink:increases_secretion_of": """ + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +""" + } + + +def get_mapped_predicates(): + # Get info from the existing predicate-remap.yaml + # Note yaml.full_load does not retain comments + with open(PREDICATE_REMAP_OLD_FILE_PATH, "r") as fp: + predicate_remap_dict = yaml.full_load(fp) + + for key, value_dict in predicate_remap_dict.items(): + for operation, values in value_dict.items(): + # disregards current "keep" operation, changes "rename" to "keep + if operation == "rename": + new_value = ["keep"] + elif operation in ("invert", "delete"): + new_value = [operation] + + # add biolink predicate to list + if values is not None: + new_value.append(values[1]) + predicate_remap_dict[key] = new_value + + return predicate_remap_dict + + +def get_biolink_predicates(): + with open(BIOLINK_MODEL_FILE_PATH, "r") as fp: + # convert biolink-model.yaml into a dictionary + biolink_dict = yaml.full_load(fp) + + # create a dict for valid predicates + valid_dict = {} + + # create a dictionary for the remapped predicates + predicates_dict = {} + + # iterate over the biolink dictionary to remap predicates + # while also generating a list of predicates + for biolink_key, biolink_value in biolink_dict["slots"].items(): + + deprecated = False + + # build a dictionary of biolink predicates + if biolink_key == "related to": + valid_dict[biolink_key] = "keep" + elif type(biolink_value) == dict and "is_a" in biolink_value.keys() \ + and biolink_value["is_a"] in valid_dict.keys(): + if "inverse" in biolink_value.keys(): + valid_dict[biolink_key] = "invert" + else: + valid_dict[biolink_key] = "keep" + + # Add flag for deprecated + if "deprecated" in biolink_value.keys(): + deprecated = True + + # If key is in valid_dict, add it to `predicates_dict` + if biolink_key in valid_dict.keys(): + for key, value_list in biolink_value.items(): + # Map predicates to `related to` + if key in ("exact_mappings", "broad_mappings", "narrow_mappings") and value_list is not None: + # value_list is a list of predicates + for predicate in value_list: + if predicate not in predicates_dict: + operation = valid_dict[biolink_key] + biolink_predicate = "biolink:" + "_".join(biolink_key.split()) + # Filter out undesired KPs + if predicate.split(":", 1)[0] not in ("SNOMED", "SNOMEDCT", "GAMMA"): + if operation != "invert": + predicates_dict[predicate] = [operation, biolink_predicate] + else: + invert_predicate = "biolink:" + "_".join(biolink_value["inverse"].split()) + predicates_dict[predicate] = [operation, invert_predicate] + + if deprecated: + predicates_dict[predicate].append("deprecated") + + return predicates_dict + + +def remap_predicates(predicates_dict, predicate_map_dict): + # print(predicate_map_dict) + print(predicates_dict) + + # Add data from the old predicate_remap.yaml to the predicates dict + for predicate, value_list in predicate_map_dict.items(): + if predicate not in predicates_dict: + predicates_dict[predicate] = value_list + + ordered_dict = OrderedDict(sorted(predicates_dict.items())) + + with open(OUTPUT_FILE_PATH, "w") as ofp, open("remap.log", "w") as log: + text = "" + for key, value in ordered_dict.items(): + # print(f"{key} {value}") + operation = value[0] + if len(value) > 1: + biolink_predicate = value[1] + ofp.write(f"{key}: \n operation: {operation}") # (key + ":\n operation: keep") + # Check if the predicate is in the qualifiers dict and has a "keep" operation + if operation == "keep" and biolink_predicate in QUALIFIER_MAPPING_DICT.keys(): + text = QUALIFIER_MAPPING_DICT[biolink_predicate] + elif operation == "delete": + text = "\n" + else: + text = "\n core_predicate: " + biolink_predicate + "\n" + + # Write to log predicates that are deprecated but not covered in qualifier map + if len(value) == 3 and value[1] not in QUALIFIER_MAPPING_DICT.keys(): + log.write(f"{key} {value[1]} {operation}\n") + + ofp.write(text) + + print("Completed") + + return + + +if __name__ == "__main__": + predicates = get_biolink_predicates() + mapped_predicates = get_mapped_predicates() + remap_predicates(predicates, mapped_predicates) From 0060ba6741658290583b0f51a6ccdcb8e7859400 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 5 Aug 2022 13:05:20 -0700 Subject: [PATCH 022/127] #220 Update predicate-remap-biolink-3.0.yaml --- predicate-remap-biolink-3.0.yaml | 5562 ++++++++++++++++++++++++++++-- 1 file changed, 5282 insertions(+), 280 deletions(-) diff --git a/predicate-remap-biolink-3.0.yaml b/predicate-remap-biolink-3.0.yaml index 3ae88beb..ea50289e 100644 --- a/predicate-remap-biolink-3.0.yaml +++ b/predicate-remap-biolink-3.0.yaml @@ -1,437 +1,5439 @@ -#! /usr/bin/venv python3 - -""" - Purpose: Remap entries in predicate_remap.yaml according to biolink_model 3.0 -""" -from collections import OrderedDict - -import yaml - - -OUTPUT_FILE_PATH = "predicate_remap_biolink_3.0.yaml" -BIOLINK_MODEL_FILE_PATH = "biolink-model.yaml" -PREDICATE_REMAP_OLD_FILE_PATH = "predicate_remap.yaml" -QUALIFIER_MAPPING_DICT = {"biolink:negatively_regulates": """ +BFO:0000050: + operation: invert + core_predicate: biolink:has_part +BFO:0000051: + operation: keep + core_predicate: biolink:has_part +BFO:0000054: + operation: keep + core_predicate: biolink:related_to +BFO:0000055: + operation: keep + core_predicate: biolink:has_part +BFO:0000056: + operation: invert + core_predicate: biolink:has_participant +BFO:0000062: + operation: invert + core_predicate: biolink:precedes +BFO:0000063: + operation: keep + core_predicate: biolink:precedes +BFO:0000066: + operation: keep + core_predicate: biolink:occurs_in +BFO:0000067: + operation: keep + core_predicate: biolink:occurs_in +BFO:0000068: + operation: keep + core_predicate: biolink:related_to +BFO:0000069: + operation: keep + core_predicate: biolink:related_to +BFO:0000117: + operation: keep + core_predicate: biolink:has_part +BFO:0000167: + operation: keep + core_predicate: biolink:has_participant +BSPO:0000096: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000097: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000098: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000099: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000100: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000102: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000104: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000107: + operation: keep + core_predicate: biolink:located_in +BSPO:0000108: + operation: keep + core_predicate: biolink:located_in +BSPO:0000110: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000113: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000120: + operation: keep + core_predicate: biolink:located_in +BSPO:0000121: + operation: keep + core_predicate: biolink:located_in +BSPO:0000122: + operation: keep + core_predicate: biolink:located_in +BSPO:0000123: + operation: keep + core_predicate: biolink:located_in +BSPO:0000124: + operation: keep + core_predicate: biolink:located_in +BSPO:0000125: + operation: keep + core_predicate: biolink:located_in +BSPO:0000126: + operation: keep + core_predicate: biolink:located_in +BSPO:0001100: + operation: keep + core_predicate: biolink:located_in +BSPO:0001101: + operation: keep + core_predicate: biolink:located_in +BSPO:0001106: + operation: invert + core_predicate: biolink:has_part +BSPO:0001107: + operation: keep + core_predicate: biolink:located_in +BSPO:0001108: + operation: invert + core_predicate: biolink:has_part +BSPO:0001113: + operation: invert + core_predicate: biolink:has_part +BSPO:0001115: + operation: invert + core_predicate: biolink:has_part +BSPO:0005001: + operation: keep + core_predicate: biolink:overlaps +BSPO:0015001: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015002: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015003: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015005: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015006: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015007: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015008: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015009: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015012: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015014: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015101: + operation: keep + core_predicate: biolink:located_in +BSPO:0015102: + operation: keep + core_predicate: biolink:located_in +BSPO:0015202: + operation: keep + core_predicate: biolink:located_in +BSPO:parallel_to: + operation: keep + core_predicate: biolink:coexists_with +BTO:develops_from: + operation: keep + core_predicate: biolink:develops_from +BTO:related_to: + operation: keep + core_predicate: biolink:related_to +CHEBI:25212: + operation: invert + core_predicate: biolink:has_metabolite +CHEBI:has_functional_parent: + operation: keep + core_predicate: biolink:chemically_similar_to +CHEBI:has_parent_hydride: + operation: keep + core_predicate: biolink:subclass_of +CHEBI:is_conjugate_acid_of: + operation: keep + core_predicate: biolink:related_to +CHEBI:is_conjugate_base_of: + operation: keep + core_predicate: biolink:related_to +CHEBI:is_enantiomer_of: + operation: keep + core_predicate: biolink:close_match +CHEBI:is_substituent_group_from: + operation: invert + core_predicate: biolink:has_part +CHEBI:is_tautomer_of: + operation: keep + core_predicate: biolink:close_match +CHEMBL.MECHANISM:activator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +CHEMBL.MECHANISM:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:allosteric_antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antisense_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +CHEMBL.MECHANISM:binding_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:blocker: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:chelating_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:cross-linking_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:degrader: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:disrupting_agent: + operation: keep + core_predicate: biolink:disrupts +CHEMBL.MECHANISM:equivalent_to: + operation: keep + core_predicate: biolink:same_as +CHEMBL.MECHANISM:hydrolytic_enzyme: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:inhibitor: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:modulator: + operation: keep + core_predicate: biolink:regulates +CHEMBL.MECHANISM:negative_allosteric_modulator: + operation: keep core_predicate: biolink:regulates qualified_predicate: biolink:causes qualifiers: - object_aspect: activity_or_abundance - object_direction: decreased -""", - "biolink:positively_regulates": """ +CHEMBL.MECHANISM:negative_modulator: + operation: keep core_predicate: biolink:regulates qualified_predicate: biolink:causes qualifiers: - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:opener: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:other: + operation: delete +CHEMBL.MECHANISM:overlaps_with: + operation: keep + core_predicate: biolink:overlaps +CHEMBL.MECHANISM:oxidative_enzyme: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:partial_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:positive_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:positive_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:proteolytic_enzyme: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:reducing_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:releasing_agent: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +CHEMBL.MECHANISM:rnai_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:sequestering_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:stabiliser: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability - object_direction: increased -""", - "biolink:affects_abundance_of": """ +CHEMBL.MECHANISM:subset_of: + operation: keep + core_predicate: biolink:subclass_of +CHEMBL.MECHANISM:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:superset_of: + operation: invert + core_predicate: biolink:subclass_of +CL:has_completed: + operation: keep + core_predicate: biolink:has_completed +CL:has_high_plasma_membrane_amount: + operation: keep + core_predicate: biolink:has_increased_amount +CL:has_low_plasma_membrane_amount: + operation: keep + core_predicate: biolink:has_decreased_amount +CL:has_not_completed: + operation: keep + core_predicate: biolink:has_not_completed +CL:lacks_part: + operation: keep + core_predicate: biolink:lacks_part +CL:lacks_plasma_membrane_part: + operation: keep + core_predicate: biolink:lacks_part +CPT:has_add_on_code: + operation: keep + core_predicate: biolink:related_to +CPT:mapped_to: + operation: keep + core_predicate: biolink:related_to +CPT:panel_element_of: + operation: invert + core_predicate: biolink:has_part +CPT:panel_element_of_possibly_included: + operation: invert + core_predicate: biolink:has_part +CTD:affects_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +CTD:affects_abundance_of: + operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: abundance -""", - "biolink:decreases_abundance_of": """ +CTD:affects_acetylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_acylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_alkylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_amination: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_binding: + operation: keep + core_predicate: biolink:directly_interacts_with +CTD:affects_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_carboxylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_cleavage: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_degradation_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_ethylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_export: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +CTD:affects_farnesylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_folding_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: folding +CTD:affects_geranoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glycation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_import: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +CTD:affects_lipidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_methylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: mutation_rate +CTD:affects_myristoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_nitrosation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_oxidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_prenylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_reduction: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_response_to: + operation: invert + core_predicate: biolink:response_affected_by +CTD:affects_ribosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_secretion_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +CTD:affects_splicing_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +CTD:affects_sulfation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_sumoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_synthesis_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: synthesis +CTD:affects_transport_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +CTD:affects_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_uptake_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +CTD:decreases_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +CTD:decreases_acetylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_acylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_alkylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_amination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_carboxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_cleavage: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_degradation_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_ethylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_export: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +CTD:decreases_farnesylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_folding_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: decreased +CTD:decreases_geranoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glycation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_import: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +CTD:decreases_lipidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_localization_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +CTD:decreases_metabolic_processing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +CTD:decreases_methylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_molecular_interaction_with: + operation: keep + core_predicate: biolink:decreases_molecular_interaction +CTD:decreases_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_mutagenesis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +CTD:decreases_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +CTD:decreases_myristoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_nitrosation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_oxidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_prenylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_reduction: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_response_to: + operation: keep + core_predicate: biolink:decreases_response_to +CTD:decreases_response_to_substance: + operation: keep + core_predicate: biolink:decreases_response_to +CTD:decreases_ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_secretion_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +CTD:decreases_splicing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +CTD:decreases_stability_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: decreased +CTD:decreases_sulfation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_sumoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_transport_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: decreased +CTD:decreases_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_uptake_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +CTD:increases_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +CTD:increases_acetylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_acylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_alkylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_amination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_carboxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_cleavage: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CTD:increases_ethylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_export: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +CTD:increases_farnesylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_folding_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: increased +CTD:increases_geranoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glycation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CTD:increases_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_import: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +CTD:increases_lipidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_localization_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +CTD:increases_metabolic_processing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +CTD:increases_methylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_molecular_interaction_with: + operation: keep + core_predicate: biolink:increases_molecular_interaction +CTD:increases_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_mutagenesis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +CTD:increases_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +CTD:increases_myristoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_nitrosation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_oxidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_prenylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_reduction: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_response_to: + operation: keep + core_predicate: biolink:increases_response_to +CTD:increases_ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_secretion_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +CTD:increases_splicing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +CTD:increases_sulfation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_sumoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_synthesis_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: increased +CTD:increases_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_uptake_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +CTD:inferred: + operation: keep + core_predicate: biolink:affects +CTD:marker_mechanism: + operation: keep + core_predicate: biolink:contributes_to +CTD:negative_correlation: + operation: keep + core_predicate: biolink:negatively_correlated_with +CTD:positive_correlation: + operation: keep + core_predicate: biolink:positively_correlated_with +CTD:prediction_hypothesis: + operation: keep + core_predicate: biolink:affects +DDANAT:develops_from: + operation: keep + core_predicate: biolink:develops_from +DGIdb:activator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +DGIdb:adduct: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:affects: + operation: keep + core_predicate: biolink:affects +DGIdb:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DGIdb:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:antibody: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DGIdb:antisense_oligonucleotide: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: abundance + - object_aspect: expression - object_direction: decreased -""", - "biolink:decreases_synthesis_of": """ +DGIdb:binder: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:blocker: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: - - object_aspect: synthesis + qualifiers: + - object_aspect: activity - object_direction: decreased -""", - "biolink:decreases_expression_of": """ +DGIdb:channel_blocker: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: - - object_aspect: expression + qualifiers: + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_degradation_of": """ +DGIdb:chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:cleavage: + operation: keep core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - - object_direction: increased -""", - "biolink:increases_abundance_of": """ +DGIdb:cofactor: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:gating_inhibitor: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: abundance - - object_direction: increased -""", - "biolink:increases_synthesis_of": """ + - object_aspect: activity + - object_direction: decreased +DGIdb:inducer: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: synthesis + - object_aspect: activity - object_direction: increased -""", - "biolink:increases_expression_of": """ +DGIdb:inhibitor: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: expression - - object_direction: increased -""", - "biolink:decreases_degradation_of": """ + - object_aspect: activity + - object_direction: decreased +DGIdb:inhibitory_allosteric_modulator: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: degradation + - object_aspect: activity - object_direction: decreased -""", - "biolink:affects_synthesis_of": """ +DGIdb:inverse_agonist: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: synthesis -""", - "biolink:affects_expression_of": """ + - object_aspect: activity + - object_direction: decreased +DGIdb:ligand: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:modulator: + operation: keep core_predicate: biolink:affects qualifiers: - - object_aspect: expression -""", - "biolink:affects_degradation_of": """ + - object_aspect: activity +DGIdb:multitarget: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:negative_modulator: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: degradation -""", - "biolink:affects_activity_of": """ + - object_aspect: activity + - object_direction: decreased +DGIdb:partial_agonist: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - object_aspect: activity -""", - "biolink:decreases_activity_of": """ + - object_direction: increased +DGIdb:partial_antagonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_activity_of": """ +DGIdb:positive_modulator: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -""", - "biolink:affects_expression_in": """ +DGIdb:potentiator: + operation: keep core_predicate: biolink:affects -""", - "biolink:affects_folding_of": """ + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:product_of: + operation: keep + core_predicate: biolink:derives_from +DGIdb:stimulator: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: folding -""", - "biolink:decreases_folding_of": """ + - object_aspect: activity + - object_direction: increased +DGIdb:substrate: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +DGIdb:suppressor: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: folding + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_folding_of": """ +DGIdb:vaccine: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: folding + - object_aspect: activity + - object_direction: decreased +DOID-PROPERTY:derives_from: + operation: invert + core_predicate: biolink:derives_into +DOID-PROPERTY:has_symptom: + operation: keep + core_predicate: biolink:has_phenotype +DRUGBANK:activator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:adduct: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:aggregation_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity - object_direction: increased -""", - "biolink:affects_localization_of": """ +DRUGBANK:allosteric_modulator: + operation: keep core_predicate: biolink:affects qualifiers: - - object_aspect: localization -""", - "biolink:decreases_localization_of": """ + - object_aspect: activity +DRUGBANK:antagonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: localization + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_localization_of": """ +DRUGBANK:antibody: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:antisense_oligonucleotide: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +DRUGBANK:atc-code: + operation: keep + core_predicate: biolink:close_match +DRUGBANK:atc-code-level: + operation: keep + core_predicate: biolink:related_to +DRUGBANK:binder: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:binding: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:blocker: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:category: + operation: keep + core_predicate: biolink:subclass_of +DRUGBANK:chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:chelator: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:cleavage: + operation: keep + core_predicate: biolink:affects qualifiers: - - object_aspect: localization - - object_direction: increased -""", - "biolink:affects_metabolic_processing_of": """ + - object_aspect: degradation +DRUGBANK:cofactor: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:component_of: + operation: invert + core_predicate: biolink:has_part +DRUGBANK:degradation: + operation: keep core_predicate: biolink:affects qualifiers: - - object_aspect: processing -""", - "biolink:decreases_metabolic_processing_of": """ + - object_aspect: degradation +DRUGBANK:deoxidizer: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: localization + - object_aspect: molecular_modification - object_direction: decreased -""", - "biolink:increases_metabolic_processing_of": """ +DRUGBANK:desensitize_the_target: + operation: keep + core_predicate: biolink:decreases_response_to +DRUGBANK:downregulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:drug-interaction: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:external-identifier: + operation: keep + core_predicate: biolink:same_as +DRUGBANK:external-identifier-protein: + operation: keep + core_predicate: biolink:derives_from +DRUGBANK:gene_replacement: + operation: keep + core_predicate: biolink:close_match +DRUGBANK:group: + operation: keep + core_predicate: biolink:related_to +DRUGBANK:inactivator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:incorporation_into_and_destabilization: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +DRUGBANK:inducer: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: localization + - object_aspect: activity - object_direction: increased -""", - "biolink:affects_molecular_modification_of": """ +DRUGBANK:inhibition_of_synthesis: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitory_allosteric_modulator: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification -""", - "biolink:decreases_molecular_modification_of": """ + - object_aspect: activity + - object_direction: decreased +DRUGBANK:intercalation: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:inverse_agonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: activity + - object_direction: decreased +DRUGBANK:ligand: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:modulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DRUGBANK:multitarget: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:negative_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:neutralizer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:nucleotide_exchange_blocker: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_molecular_modification_of": """ +DRUGBANK:oxidizer: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -""", - "biolink:affects_mutation_rate_of": """ +DRUGBANK:partial_agonist: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: mutation_rate -""", - "biolink:decreases_mutation_rate_of": """ + - object_aspect: activity + - object_direction: increased +DRUGBANK:partial_antagonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: mutation_rate + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_mutation_rate_of": """ +DRUGBANK:pathway: + operation: invert + core_predicate: biolink:has_participant +DRUGBANK:positive_allosteric_modulator: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: mutation_rate + - object_aspect: activity - object_direction: increased -""", - "biolink:affects_splicing_of": """ +DRUGBANK:positive_modulator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:potentiator: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: splicing -""", - "biolink:decreases_splicing_of": """ + - object_aspect: activity + - object_direction: increased +DRUGBANK:product_of: + operation: keep + core_predicate: biolink:derives_from +DRUGBANK:regulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DRUGBANK:stabilization: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: splicing + - object_aspect: stability + - object_direction: increased +DRUGBANK:stimulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:suppressor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity - object_direction: decreased -""", - "biolink:increases_splicing_of": """ +DRUGBANK:target: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:translocation_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:treats: + operation: keep + core_predicate: biolink:treats +DRUGBANK:weak_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:5271: + operation: keep + core_predicate: biolink:diagnoses +DrugCentral:PA: + operation: keep + core_predicate: biolink:subclass_of +DrugCentral:activator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DrugCentral:agonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: splicing + - object_aspect: activity - object_direction: increased -""", - "biolink:affects_stability_of": """ +DrugCentral:allosteric_antagonist: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: stability -""", - "biolink:decreases_stability_of": """ + - object_aspect: activity + - object_direction: decreased +DrugCentral:allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DrugCentral:antagonist: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: stability + - object_aspect: activity + - object_direction: decreased +DrugCentral:antibody_binding: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DrugCentral:antisense_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression - object_direction: decreased -""", - "biolink:increases_stability_of": """ +DrugCentral:binding_agent: + operation: keep + core_predicate: biolink:directly_interacts_with +DrugCentral:blocker: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:contraindication: + operation: keep + core_predicate: biolink:contraindicated_for +DrugCentral:gating_inhibitor: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: stability + - object_aspect: activity + - object_direction: decreased +DrugCentral:has_role: + operation: keep + core_predicate: biolink:related_to +DrugCentral:indication: + operation: keep + core_predicate: biolink:treats +DrugCentral:inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DrugCentral:modulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DrugCentral:negative_allosteric_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:negative_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:off-label_use: + operation: keep + core_predicate: biolink:treats +DrugCentral:opener: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity - object_direction: increased -""", - "biolink:affects_transport_of": """ +DrugCentral:partial_agonist: + operation: keep core_predicate: biolink:affects + qualified_predicate: biolink:causes qualifiers: - - object_aspect: transport -""", - "biolink:decreases_transport_of": """ + - object_aspect: activity + - object_direction: increased +DrugCentral:pharmacological_chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DrugCentral:positive_allosteric_modulator: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: transport - - object_direction: decreased -""", - "biolink:increases_transport_of": """ + - object_aspect: activity + - object_direction: increased +DrugCentral:positive_modulator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DrugCentral:releasing_agent: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: transport + - object_aspect: expression - object_direction: increased -""", - "biolink:affects_uptake_of": """ +DrugCentral:struct2atc: + operation: keep + core_predicate: biolink:close_match +DrugCentral:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +DrugCentral:symptomatic_treatment: + operation: keep + core_predicate: biolink:treats +EFO:0000784: + operation: keep + core_predicate: biolink:located_in +EFO:0001697: + operation: invert + core_predicate: biolink:related_to +EFO:0006351: + operation: keep + core_predicate: biolink:related_to +EFO:is_executed_in: + operation: keep + core_predicate: biolink:related_to +ENVO:01001307: + operation: keep + core_predicate: biolink:coexists_with +FMA:SIB: + operation: delete +FMA:adheres_to: + operation: keep + core_predicate: biolink:physically_interacts_with +FMA:adjacent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:afferent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anatomical_entity_observed_in: + operation: delete +FMA:anterior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anteroinferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anterolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anteromedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anterosuperior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:arterial_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:articulates_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:attaches_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:bounded_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:bounds: + operation: keep + core_predicate: biolink:coexists_with +FMA:branch_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:connected_to: + operation: keep + core_predicate: biolink:related_to +FMA:connection_type_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:constitutional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:contained_in: + operation: invert + core_predicate: biolink:has_part +FMA:contains: + operation: keep + core_predicate: biolink:has_part +FMA:continuation_branch_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_distally_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_proximally_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_with: + operation: keep + core_predicate: biolink:related_to +FMA:corresponds_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:derives: + operation: invert + core_predicate: biolink:derives_from +FMA:derives_from: + operation: invert + core_predicate: biolink:derives_into +FMA:development_type_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:developmental_stage_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:develops_from: + operation: keep + core_predicate: biolink:develops_from +FMA:develops_into: + operation: keep + core_predicate: biolink:develops_from +FMA:direct_cell_shape_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:direct_left_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:direct_right_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:distal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:drains_into: + operation: keep + core_predicate: biolink:coexists_with +FMA:efferent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:external_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:formed_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:forms: + operation: keep + core_predicate: biolink:coexists_with +FMA:full_grown_phenotype_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:fuses_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:fusion_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:germ_origin_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_adherent: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_arterial_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_branch: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_connection_type: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_constitutional_part: + operation: keep + core_predicate: biolink:has_part +FMA:has_continuation_branch: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_development_type: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_developmental_stage: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_direct_cell_shape: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_full_grown_phenotype: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_fusion: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_germ_origin: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_inherent_3d_shape: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_insertion: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_location: + operation: keep + core_predicate: biolink:located_in +FMA:has_lymphatic_drainage: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_member: + operation: keep + core_predicate: biolink:has_part +FMA:has_nerve_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_observed_anatomical_entity: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_origin: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_part: + operation: keep + core_predicate: biolink:has_part +FMA:has_primary_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_projection: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_regional_part: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_related_developmental_entity: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_secondary_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_segmental_composition: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_tributary: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_venous_drainage: + operation: keep + core_predicate: biolink:coexists_with +FMA:homonym_for: + operation: delete +FMA:homonym_of: + operation: keep + core_predicate: biolink:related_to +FMA:inferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inferolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inferomedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inherent_3d_shape_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:insertion_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:internal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:left_lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:left_medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:location_of: + operation: invert + core_predicate: biolink:located_in +FMA:lymphatic_drainage_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:matures_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:matures_into: + operation: keep + core_predicate: biolink:coexists_with +FMA:medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:member_of: + operation: invert + core_predicate: biolink:has_part +FMA:merges_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:nerve_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:origin_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:part_of: + operation: invert + core_predicate: biolink:has_part +FMA:posterior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posteroinferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posterolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posteromedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posterosuperior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:primary_segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:projects_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:projects_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:proximal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_attachment_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_drainage_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_input_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_projection: + operation: keep + core_predicate: biolink:coexists_with +FMA:regional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:related_developmental_entity_of: + operation: keep + core_predicate: biolink:related_to +FMA:related_object: + operation: keep + core_predicate: biolink:related_to +FMA:related_part: + operation: keep + core_predicate: biolink:coexists_with +FMA:right_lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:right_medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:secondary_segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:segmental_composition_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:sends_output_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superomedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:surrounded_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:surrounds: + operation: keep + core_predicate: biolink:coexists_with +FMA:transforms_from: + operation: invert + core_predicate: biolink:precedes +FMA:transforms_into: + operation: keep + core_predicate: biolink:precedes +FMA:tributary_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:venous_drainage_of: + operation: keep + core_predicate: biolink:coexists_with +FOODON:00001301: + operation: keep + core_predicate: biolink:model_of +FOODON:00001563: + operation: keep + core_predicate: biolink:has_part +FOODON:00002420: + operation: keep + core_predicate: biolink:has_part +GENEPIO:0001739: + operation: invert + core_predicate: biolink:precedes +GENO:0000382: + operation: keep + core_predicate: biolink:has_variant_part +GENO:0000790: + operation: keep + core_predicate: biolink:related_condition +GENO:0000840: + operation: keep + core_predicate: biolink:gene_associated_with_condition +GENO:0000841: + operation: keep + core_predicate: biolink:gene_associated_with_condition +GO:SIB: + operation: delete +GO:acts_upstream_of: + operation: keep + core_predicate: biolink:affects +GO:acts_upstream_of_negative_effect: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within: + operation: keep + core_predicate: biolink:affects +GO:acts_upstream_of_or_within_negative_effect: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within_positive_effect: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:acts_upstream_of_positive_effect: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:colocalizes_with: + operation: keep + core_predicate: biolink:colocalizes_with +GO:contributes_to: + operation: keep + core_predicate: biolink:contributes_to +GO:enables: + operation: keep + core_predicate: biolink:enables +GO:ends_during: + operation: keep + core_predicate: biolink:related_to +GO:happens_during: + operation: keep + core_predicate: biolink:related_to +GO:has_occurrence: + operation: keep + core_predicate: biolink:capable_of +GO:has_part: + operation: keep + core_predicate: biolink:has_part +GO:inverse_ends_during: + operation: keep + core_predicate: biolink:related_to +GO:inverse_happens_during: + operation: delete +GO:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +GO:involved_in: + operation: invert + core_predicate: biolink:has_participant +GO:is_active_in: + operation: keep + core_predicate: biolink:actively_involved_in +GO:isa: + operation: keep + core_predicate: biolink:subclass_of +GO:located_in: + operation: keep + core_predicate: biolink:located_in +GO:negatively_regulated_by: + operation: invert + core_predicate: biolink:entity_negatively_regulates_entity +GO:negatively_regulates: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:occurs_in: + operation: keep + core_predicate: biolink:occurs_in +GO:part_of: + operation: invert + core_predicate: biolink:has_part +GO:positively_regulated_by: + operation: invert + core_predicate: biolink:entity_positively_regulates_entity +GO:positively_regulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:regulated_by: + operation: invert + core_predicate: biolink:entity_regulates_entity +GO:regulates: + operation: keep + core_predicate: biolink:entity_regulates_entity +GOREL:0000040: + operation: keep + core_predicate: biolink:causes +GOREL:0001004: + operation: keep + core_predicate: biolink:located_in +GOREL:0001006: + operation: keep + core_predicate: biolink:affects +GOREL:0002003: + operation: keep core_predicate: biolink:affects qualifiers: - - object_aspect: uptake -""", - "biolink:decreases_uptake_of": """ + - object_aspect: localization +GOREL:0002004: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +GOREL:0002005: + operation: keep + core_predicate: biolink:related_to +GOREL:0012006: + operation: keep + core_predicate: biolink:related_to +GTEx:affects_expression_in: + operation: keep + core_predicate: biolink:affects +HANCESTRO:0301: + operation: keep + core_predicate: biolink:related_to +HANCESTRO:0308: + operation: keep + core_predicate: biolink:related_to +HANCESTRO:0330: + operation: keep + core_predicate: biolink:related_to +HCPCS:mapped_from: + operation: delete +HCPCS:mapped_to: + operation: keep + core_predicate: biolink:related_to +HMDB:at_cellular_location: + operation: keep + core_predicate: biolink:located_in +HMDB:at_tissue: + operation: keep + core_predicate: biolink:located_in +HMDB:disease: + operation: keep + core_predicate: biolink:related_to +HMDB:has_protein_association: + operation: keep + core_predicate: biolink:related_to +HMDB:in_biospecimen: + operation: keep + core_predicate: biolink:located_in +HMDB:in_pathway: + operation: invert + core_predicate: biolink:has_participant +HP:SIB: + operation: delete +IAO:0000039: + operation: keep + core_predicate: biolink:related_to +IAO:0000136: + operation: keep + core_predicate: biolink:related_to +IAO:0000142: + operation: keep + core_predicate: biolink:mentions +IAO:0000219: + operation: keep + core_predicate: biolink:related_to +ICD10PCS:SIB: + operation: delete +ICD9:SIB: + operation: delete +IDO:0000664: + operation: invert + core_predicate: biolink:contributes_to +JensenLab:associated_with: + operation: keep + core_predicate: biolink:gene_associated_with_condition +KEGG:compound_to_enzyme: + operation: keep + core_predicate: biolink:interacts_with +KEGG:compound_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:compound_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_reaction: + operation: keep + core_predicate: biolink:catalyzes +KEGG:glycan_to_enzyme: + operation: keep + core_predicate: biolink:interacts_with +KEGG:glycan_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:glycan_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:pathway_to_compound: + operation: keep + core_predicate: biolink:has_participant +KEGG:pathway_to_drug: + operation: keep + core_predicate: biolink:has_participant +KEGG:pathway_to_glycan: + operation: keep + core_predicate: biolink:has_participant +KEGG:reaction_to_enzyme: + operation: invert + core_predicate: biolink:catalyzes +KEGG:reaction_to_pathway: + operation: invert + core_predicate: biolink:has_participant +LOINC:adjustment_of: + operation: delete +LOINC:analyzed_by: + operation: delete +LOINC:analyzes: + operation: keep + core_predicate: biolink:related_to +LOINC:answer_to: + operation: delete +LOINC:archetype_of: + operation: delete +LOINC:associated_with: + operation: keep + core_predicate: biolink:correlated_with +LOINC:challenge_of: + operation: delete +LOINC:class_of: + operation: keep + core_predicate: biolink:subclass_of +LOINC:component_of: + operation: invert + core_predicate: biolink:has_part +LOINC:count_of: + operation: delete +LOINC:divisor_of: + operation: delete +LOINC:evaluation_of: + operation: delete +LOINC:fragments_for_synonyms_of: + operation: delete +LOINC:has_action_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_adjustment: + operation: keep + core_predicate: biolink:related_to +LOINC:has_aggregation_view: + operation: keep + core_predicate: biolink:related_to +LOINC:has_answer: + operation: keep + core_predicate: biolink:related_to +LOINC:has_approach_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_archetype: + operation: keep + core_predicate: biolink:subclass_of +LOINC:has_challenge: + operation: keep + core_predicate: biolink:related_to +LOINC:has_class: + operation: invert + core_predicate: biolink:subclass_of +LOINC:has_component: + operation: keep + core_predicate: biolink:has_part +LOINC:has_count: + operation: keep + core_predicate: biolink:related_to +LOINC:has_divisor: + operation: keep + core_predicate: biolink:related_to +LOINC:has_evaluation: + operation: keep + core_predicate: biolink:related_to +LOINC:has_exam: + operation: keep + core_predicate: biolink:related_to +LOINC:has_fragments_for_synonyms: + operation: keep + core_predicate: biolink:has_input +LOINC:has_given_pharmaceutical_substance: + operation: delete +LOINC:has_imaged_location: + operation: keep + core_predicate: biolink:occurs_in +LOINC:has_imaging_focus: + operation: keep + core_predicate: biolink:located_in +LOINC:has_lateral_anatomic_location: + operation: keep + core_predicate: biolink:coexists_with +LOINC:has_lateral_location_presence: + operation: keep + core_predicate: biolink:coexists_with +LOINC:has_loinc_number: + operation: delete +LOINC:has_member: + operation: keep + core_predicate: biolink:has_part +LOINC:has_method: + operation: keep + core_predicate: biolink:related_to +LOINC:has_modality_subtype: + operation: keep + core_predicate: biolink:related_to +LOINC:has_modality_type: + operation: keep + core_predicate: biolink:related_to +LOINC:has_multipart: + operation: delete +LOINC:has_object_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_parent_group: + operation: keep + core_predicate: biolink:subclass_of +LOINC:has_pharmaceutical_route: + operation: keep + core_predicate: biolink:related_to +LOINC:has_presence_guidance: + operation: delete +LOINC:has_property: + operation: delete +LOINC:has_scale: + operation: keep + core_predicate: biolink:related_to +LOINC:has_subject: + operation: keep + core_predicate: biolink:has_participant +LOINC:has_suffix: + operation: keep + core_predicate: biolink:related_to +LOINC:has_supersystem: + operation: invert + core_predicate: biolink:has_part +LOINC:has_system: + operation: keep + core_predicate: biolink:has_input +LOINC:has_time_aspect: + operation: keep + core_predicate: biolink:related_to +LOINC:has_time_modifier: + operation: keep + core_predicate: biolink:related_to +LOINC:has_timing_of: + operation: keep + core_predicate: biolink:related_to +LOINC:has_view_type: + operation: keep + core_predicate: biolink:related_to +LOINC:is_action_guidance_for: + operation: delete +LOINC:is_aggregation_view_of: + operation: delete +LOINC:is_approach_guidance_for: + operation: delete +LOINC:is_exam_for: + operation: delete +LOINC:is_given_pharmaceutical_substance_for: + operation: invert + core_predicate: biolink:has_participant +LOINC:is_imaged_location_for: + operation: delete +LOINC:is_imaging_focus_of: + operation: delete +LOINC:is_lateral_anatomic_location_of: + operation: delete +LOINC:is_modality_subtype_for: + operation: delete +LOINC:is_modality_type_for: + operation: delete +LOINC:is_object_guidance_for: + operation: delete +LOINC:is_pharmaceutical_route_for: + operation: delete +LOINC:is_presence_guidance_for: + operation: keep + core_predicate: biolink:subclass_of +LOINC:is_presence_of_lateral_location: + operation: delete +LOINC:is_subject_of: + operation: delete +LOINC:is_timing_for: + operation: delete +LOINC:is_view_type_for: + operation: delete +LOINC:loinc_number_of: + operation: delete +LOINC:mapped_from: + operation: delete +LOINC:mapped_to: + operation: keep + core_predicate: biolink:related_to +LOINC:measured_by: + operation: keep + core_predicate: biolink:related_to +LOINC:measures: + operation: delete +LOINC:member_of: + operation: invert + core_predicate: biolink:has_part +LOINC:method_of: + operation: delete +LOINC:mth_expanded_form_of: + operation: delete +LOINC:mth_has_expanded_form: + operation: keep + core_predicate: biolink:related_to +LOINC:multipart_of: + operation: invert + core_predicate: biolink:has_part +LOINC:parent_group_of: + operation: delete +LOINC:property_of: + operation: keep + core_predicate: biolink:related_to +LOINC:scale_of: + operation: delete +LOINC:suffix_of: + operation: delete +LOINC:supersystem_of: + operation: delete +LOINC:system_of: + operation: delete +LOINC:time_aspect_of: + operation: delete +LOINC:time_modifier_of: + operation: delete +MEDDRA:classified_as: + operation: keep + core_predicate: biolink:close_match +MEDDRA:has_member: + operation: keep + core_predicate: biolink:has_part +MEDDRA:member_of: + operation: invert + core_predicate: biolink:has_part +MESH:AQ: + operation: delete +MESH:QB: + operation: delete +MESH:RO: + operation: keep + core_predicate: biolink:related_to +MESH:SIB: + operation: delete +MESH:has_mapping_qualifier: + operation: keep + core_predicate: biolink:related_to +MESH:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +MESH:isa: + operation: keep + core_predicate: biolink:subclass_of +MESH:mapped_from: + operation: delete +MESH:mapped_to: + operation: keep + core_predicate: biolink:related_to +MESH:mapping_qualifier_of: + operation: delete +MI:0192: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0194: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0195: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0197: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0203: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0204: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0210: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0211: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0212: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0213: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0214: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0216: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0217: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0220: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0403: + operation: keep + core_predicate: biolink:colocalizes_with +MI:0407: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0408: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0414: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0556: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0557: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0559: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0566: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0567: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0569: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0570: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0572: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0844: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0871: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0882: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0883: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0902: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0914: + operation: keep + core_predicate: biolink:interacts_with +MI:0915: + operation: keep + core_predicate: biolink:physically_interacts_with +MI:0945: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1126: + operation: keep + core_predicate: biolink:interacts_with +MI:1127: + operation: keep + core_predicate: biolink:interacts_with +MI:1148: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1237: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1310: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:2252: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:2364: + operation: keep + core_predicate: biolink:colocalizes_with +MONDO:0100332: + operation: invert + core_predicate: biolink:causes +MONDO:0100333: + operation: invert + core_predicate: biolink:causes +MONDO:disease_causes_feature: + operation: keep + core_predicate: biolink:causes +MONDO:disease_has_basis_in_accumulation_of: + operation: keep + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_basis_in_development_of: + operation: keep + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_location: + operation: keep + core_predicate: biolink:disease_has_location +MONDO:disease_has_major_feature: + operation: keep + core_predicate: biolink:has_part +MONDO:disease_responds_to: + operation: invert + core_predicate: biolink:treats +MONDO:disease_shares_features_of: + operation: keep + core_predicate: biolink:related_to +MONDO:disease_triggers: + operation: keep + core_predicate: biolink:causes +MONDO:equivalentTo: + operation: keep + core_predicate: biolink:same_as +MONDO:has_onset: + operation: keep + core_predicate: biolink:related_to +MONDO:has_onset_before: + operation: keep + core_predicate: biolink:related_to +MONDO:has_onset_during_or_after: + operation: keep + core_predicate: biolink:related_to +MONDO:part_of_progression_of_disease: + operation: invert + core_predicate: biolink:has_part +MONDO:predisposes_towards: + operation: keep + core_predicate: biolink:contributes_to +NBO-PROPERTY:by_means: + operation: keep + core_predicate: biolink:actively_involved_in +NBO-PROPERTY:has_participant: + operation: keep + core_predicate: biolink:has_participant +NBO-PROPERTY:in_response_to: + operation: keep + core_predicate: biolink:causes +NBO-PROPERTY:is_about: + operation: keep + core_predicate: biolink:related_to +NCIT:A11: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A14: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A16: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A3: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A7: + operation: keep + core_predicate: biolink:physically_interacts_with +NCIT:Anatomic_Structure_Has_Location_Role: + operation: invert + core_predicate: biolink:located_in +NCIT:C15220: + operation: keep + core_predicate: biolink:diagnoses +NCIT:C16798: + operation: keep + core_predicate: biolink:in_linkage_disequilibrium_with +NCIT:C2861: + operation: keep + core_predicate: biolink:causes_adverse_event +NCIT:C37933: + operation: keep + core_predicate: biolink:contraindicated_for +NCIT:R100: + operation: keep + core_predicate: biolink:affects +NCIT:R101: + operation: keep + core_predicate: biolink:affects +NCIT:R102: + operation: keep + core_predicate: biolink:affects +NCIT:R108: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:R113: + operation: keep + core_predicate: biolink:affects +NCIT:R115: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:R124: + operation: keep + core_predicate: biolink:affects +NCIT:R130: + operation: invert + core_predicate: biolink:has_participant +NCIT:R131: + operation: invert + core_predicate: biolink:has_participant +NCIT:R133: + operation: keep + core_predicate: biolink:affects +NCIT:R145: + operation: keep + core_predicate: biolink:located_in +NCIT:R146: + operation: keep + core_predicate: biolink:affects +NCIT:R150: + operation: keep + core_predicate: biolink:affects +NCIT:R155: + operation: keep + core_predicate: biolink:located_in +NCIT:R156: + operation: keep + core_predicate: biolink:located_in +NCIT:R158: + operation: keep + core_predicate: biolink:affects +NCIT:R160: + operation: keep + core_predicate: biolink:affects +NCIT:R163: + operation: keep + core_predicate: biolink:related_to +NCIT:R165: + operation: keep + core_predicate: biolink:located_in +NCIT:R166: + operation: keep + core_predicate: biolink:located_in +NCIT:R167: + operation: keep + core_predicate: biolink:located_in +NCIT:R168: + operation: keep + core_predicate: biolink:located_in +NCIT:R169: + operation: keep + core_predicate: biolink:located_in +NCIT:R170: + operation: keep + core_predicate: biolink:located_in +NCIT:R171: + operation: keep + core_predicate: biolink:located_in +NCIT:R173: + operation: keep + core_predicate: biolink:affects +NCIT:R175: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R176: + operation: invert + core_predicate: biolink:gene_associated_with_condition +NCIT:R178: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:R23: + operation: keep + core_predicate: biolink:affects +NCIT:R25: + operation: keep + core_predicate: biolink:affects +NCIT:R27: + operation: invert + core_predicate: biolink:has_part +NCIT:R29: + operation: keep + core_predicate: biolink:produces +NCIT:R30: + operation: keep + core_predicate: biolink:affects +NCIT:R36: + operation: keep + core_predicate: biolink:subclass_of +NCIT:R37: + operation: invert + core_predicate: biolink:has_participant +NCIT:R38: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R39: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:R40: + operation: keep + core_predicate: biolink:located_in +NCIT:R42: + operation: keep + core_predicate: biolink:subclass_of +NCIT:R47: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:R48: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R50: + operation: keep + core_predicate: biolink:has_part +NCIT:R51: + operation: invert + core_predicate: biolink:has_participant +NCIT:R52: + operation: keep + core_predicate: biolink:capable_of +NCIT:R53: + operation: invert + core_predicate: biolink:has_participant +NCIT:R72: + operation: keep + core_predicate: biolink:affects +NCIT:R81: + operation: keep + core_predicate: biolink:related_to +NCIT:R82: + operation: invert + core_predicate: biolink:has_part +NCIT:R88: + operation: keep + core_predicate: biolink:related_to +NCIT:R89: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:abnormal_cell_affected_by_chemical_or_drug: + operation: delete +NCIT:abnormality_associated_with_allele: + operation: delete +NCIT:activity_of_allele: + operation: delete +NCIT:allele_absent_from_wild-type_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:allele_has_abnormality: + operation: keep + core_predicate: biolink:causes +NCIT:allele_has_activity: + operation: keep + core_predicate: biolink:has_molecular_consequence +NCIT:allele_in_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:allele_plays_altered_role_in_process: + operation: keep + core_predicate: biolink:affects +NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: + operation: keep + core_predicate: biolink:affects +NCIT:anatomic_structure_has_location: + operation: delete +NCIT:anatomic_structure_is_physical_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:anatomy_originated_from_biological_process: + operation: delete +NCIT:associated_with_malfunction_of_gene_product: + operation: delete +NCIT:biological_process_has_associated_location: + operation: keep + core_predicate: biolink:affects +NCIT:biological_process_has_initiator_chemical_or_drug: + operation: delete +NCIT:biological_process_has_initiator_process: + operation: delete +NCIT:biological_process_has_result_anatomy: + operation: keep + core_predicate: biolink:has_output +NCIT:biological_process_has_result_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:biological_process_has_result_chemical_or_drug: + operation: keep + core_predicate: biolink:produces +NCIT:biological_process_involves_chemical_or_drug: + operation: invert + core_predicate: biolink:actively_involved_in +NCIT:biological_process_involves_gene_product: + operation: delete +NCIT:biological_process_is_part_of_process: + operation: delete +NCIT:biological_process_results_from_biological_process: + operation: delete +NCIT:biomarker_type_includes_gene: + operation: delete +NCIT:biomarker_type_includes_gene_product: + operation: delete +NCIT:cdrh_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cell_type_is_associated_with_eo_disease: + operation: delete +NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: + operation: delete +NCIT:chemical_or_drug_affects_abnormal_cell: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_cell_type_or_tissue: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_gene_product: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_mechanism_of_action: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_physiologic_effect: + operation: keep + core_predicate: biolink:causes +NCIT:chemical_or_drug_initiates_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:chemical_or_drug_is_metabolized_by_enzyme: + operation: delete +NCIT:chemical_or_drug_is_product_of_biological_process: + operation: delete +NCIT:chemical_or_drug_metabolism_is_associated_with_allele: + operation: delete +NCIT:chemical_or_drug_plays_role_in_biological_process: + operation: delete +NCIT:chemotherapy_regimen_has_component: + operation: delete +NCIT:chromosomal_location_of_allele: + operation: delete +NCIT:chromosomal_location_of_wild-type_gene: + operation: delete +NCIT:chromosome_involved_in_cytogenetic_abnormality: + operation: delete +NCIT:chromosome_mapped_to_disease: + operation: keep + core_predicate: biolink:causes +NCIT:completely_excised_anatomy_has_procedure: + operation: delete +NCIT:completely_excised_anatomy_may_have_procedure: + operation: delete +NCIT:complex_has_physical_part: + operation: keep + core_predicate: biolink:has_part +NCIT:concept_in_subset: + operation: delete +NCIT:conceptual_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:ctcae_5_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cytogenetic_abnormality_involves_chromosome: + operation: keep + core_predicate: biolink:affects +NCIT:data_element_of: + operation: delete +NCIT:disease_excludes_abnormal_cell: + operation: delete +NCIT:disease_excludes_cytogenetic_abnormality: + operation: delete +NCIT:disease_excludes_finding: + operation: delete +NCIT:disease_excludes_metastatic_anatomic_site: + operation: delete +NCIT:disease_excludes_molecular_abnormality: + operation: delete +NCIT:disease_excludes_normal_cell_origin: + operation: delete +NCIT:disease_excludes_normal_tissue_origin: + operation: delete +NCIT:disease_excludes_primary_anatomic_site: + operation: delete +NCIT:disease_has_abnormal_cell: + operation: delete +NCIT:disease_has_accepted_treatment_with_regimen: + operation: delete +NCIT:disease_has_associated_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_has_associated_disease: + operation: keep + core_predicate: biolink:has_real_world_evidence_of_association_with +NCIT:disease_has_associated_gene: + operation: delete +NCIT:disease_has_cytogenetic_abnormality: + operation: delete +NCIT:disease_has_finding: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_metastatic_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_has_molecular_abnormality: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_normal_cell_origin: + operation: delete +NCIT:disease_has_normal_tissue_origin: + operation: keep + core_predicate: biolink:causes +NCIT:disease_has_primary_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_is_grade: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_is_marked_by_gene: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_is_stage: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_mapped_to_chromosome: + operation: delete +NCIT:disease_mapped_to_gene: + operation: delete +NCIT:disease_may_have_abnormal_cell: + operation: keep + core_predicate: biolink:affects +NCIT:disease_may_have_associated_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_may_have_cytogenetic_abnormality: + operation: delete +NCIT:disease_may_have_finding: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_molecular_abnormality: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_normal_cell_origin: + operation: delete +NCIT:endogenous_product_related_to: + operation: delete +NCIT:enzyme_metabolizes_chemical_or_drug: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: uptake - - object_direction: decreased -""", - "biolink:increases_uptake_of": """ + - object_aspect: localization + - object_direction: increased +NCIT:eo_anatomy_is_associated_with_eo_disease: + operation: delete +NCIT:eo_disease_has_associated_cell_type: + operation: keep + core_predicate: biolink:affects +NCIT:eo_disease_has_associated_eo_anatomy: + operation: keep + core_predicate: biolink:affects +NCIT:eo_disease_has_property_or_attribute: + operation: keep + core_predicate: biolink:related_to +NCIT:eo_disease_maps_to_human_disease: + operation: delete +NCIT:excised_anatomy_has_procedure: + operation: delete +NCIT:excised_anatomy_may_have_procedure: + operation: delete +NCIT:gene_associated_with_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_encodes_gene_product: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_found_in_organism: + operation: keep + core_predicate: biolink:in_taxon +NCIT:gene_has_abnormality: + operation: delete +NCIT:gene_has_physical_location: + operation: keep + core_predicate: biolink:located_in +NCIT:gene_in_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:gene_involved_in_molecular_abnormality: + operation: keep + core_predicate: biolink:actively_involved_in +NCIT:gene_involved_in_pathogenesis_of_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_is_biomarker_of: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:gene_is_biomarker_type: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_mapped_to_disease: + operation: keep + core_predicate: biolink:affects +NCIT:gene_mutant_encodes_gene_product_sequence_variation: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_plays_role_in_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_affected_by_chemical_or_drug: + operation: delete +NCIT:gene_product_encoded_by_gene: + operation: delete +NCIT:gene_product_expressed_in_tissue: + operation: keep + core_predicate: biolink:expressed_in +NCIT:gene_product_has_abnormality: + operation: keep + core_predicate: biolink:affects +NCIT:gene_product_has_associated_anatomy: + operation: keep + core_predicate: biolink:expressed_in +NCIT:gene_product_has_biochemical_function: + operation: keep + core_predicate: biolink:capable_of +NCIT:gene_product_has_chemical_classification: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_product_has_gene_product_variant: + operation: delete +NCIT:gene_product_has_organism_source: + operation: keep + core_predicate: biolink:in_taxon +NCIT:gene_product_has_structural_domain_or_motif: + operation: keep + core_predicate: biolink:has_part +NCIT:gene_product_is_biomarker_of: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:gene_product_is_biomarker_type: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_product_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_is_physical_part_of: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_malfunction_associated_with_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_product_plays_role_in_biological_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: + operation: keep + core_predicate: biolink:is_sequence_variant_of +NCIT:gene_product_variant_of_gene_product: + operation: keep + core_predicate: biolink:is_sequence_variant_of +NCIT:genetic_biomarker_related_to: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:has_cdrh_parent: + operation: delete +NCIT:has_conceptual_part: + operation: delete +NCIT:has_ctcae_5_parent: + operation: delete +NCIT:has_data_element: + operation: keep + core_predicate: biolink:related_to +NCIT:has_free_acid_or_base_form: + operation: delete +NCIT:has_gene_product_element: + operation: delete +NCIT:has_inc_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:has_nichd_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:has_pharmaceutical_administration_method: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_basic_dose_form: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_intended_site: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_release_characteristics: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_state_of_matter: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_transformation: + operation: keep + core_predicate: biolink:related_to +NCIT:has_physical_part_of_anatomic_structure: + operation: delete +NCIT:has_salt_form: + operation: keep + core_predicate: biolink:chemically_similar_to +NCIT:has_target: + operation: keep + core_predicate: biolink:physically_interacts_with +NCIT:human_disease_maps_to_eo_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:imaged_anatomy_has_procedure: + operation: delete +NCIT:inc_parent_of: + operation: delete +NCIT:is_abnormal_cell_of_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:is_abnormality_of_gene: + operation: delete +NCIT:is_abnormality_of_gene_product: + operation: delete +NCIT:is_associated_anatomic_site_of: + operation: delete +NCIT:is_associated_anatomy_of_gene_product: + operation: delete +NCIT:is_associated_disease_of: + operation: keep + core_predicate: biolink:correlated_with +NCIT:is_biochemical_function_of_gene_product: + operation: delete +NCIT:is_chemical_classification_of_gene_product: + operation: delete +NCIT:is_chromosomal_location_of_gene: + operation: delete +NCIT:is_component_of_chemotherapy_regimen: + operation: invert + core_predicate: biolink:has_part +NCIT:is_cytogenetic_abnormality_of_disease: + operation: invert + core_predicate: biolink:correlated_with +NCIT:is_finding_of_disease: + operation: delete +NCIT:is_grade_of_disease: + operation: delete +NCIT:is_location_of_anatomic_structure: + operation: keep + core_predicate: biolink:located_in +NCIT:is_location_of_biological_process: + operation: delete +NCIT:is_marked_by_gene_product: + operation: delete +NCIT:is_mechanism_of_action_of_chemical_or_drug: + operation: delete +NCIT:is_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_molecular_abnormality_of_disease: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:is_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:is_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_abnormal_cell_of_disease: + operation: delete +NCIT:is_not_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:is_not_finding_of_disease: + operation: delete +NCIT:is_not_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_not_molecular_abnormality_of_disease: + operation: delete +NCIT:is_not_normal_cell_origin_of_disease: + operation: delete +NCIT:is_not_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_organism_source_of_gene_product: + operation: invert + core_predicate: biolink:in_taxon +NCIT:is_physical_location_of_gene: + operation: delete +NCIT:is_physiologic_effect_of_chemical_or_drug: + operation: delete +NCIT:is_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_property_or_attribute_of_eo_disease: + operation: delete +NCIT:is_qualified_by: + operation: keep + core_predicate: biolink:related_to +NCIT:is_related_to_endogenous_product: + operation: keep + core_predicate: biolink:related_to +NCIT:is_stage_of_disease: + operation: delete +NCIT:is_structural_domain_or_motif_of_gene_product: + operation: delete +NCIT:is_target: + operation: delete +NCIT:kind_is_domain_of: + operation: delete +NCIT:kind_is_range_of: + operation: delete +NCIT:may_be_abnormal_cell_of_disease: + operation: delete +NCIT:may_be_associated_disease_of_disease: + operation: delete +NCIT:may_be_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:may_be_finding_of_disease: + operation: delete +NCIT:may_be_molecular_abnormality_of_disease: + operation: delete +NCIT:may_be_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:molecular_abnormality_involves_gene: + operation: delete +NCIT:neoplasm_has_special_category: + operation: keep + core_predicate: biolink:subclass_of +NCIT:nichd_parent_of: + operation: delete +NCIT:organism_has_gene: + operation: invert + core_predicate: biolink:in_taxon +NCIT:partially_excised_anatomy_has_procedure: + operation: delete +NCIT:partially_excised_anatomy_may_have_procedure: + operation: delete +NCIT:pathogenesis_of_disease_involves_gene: + operation: delete +NCIT:pathway_has_gene_element: + operation: keep + core_predicate: biolink:has_participant +NCIT:pharmaceutical_administration_method_of: + operation: delete +NCIT:pharmaceutical_basic_dose_form_of: + operation: delete +NCIT:pharmaceutical_intended_site_of: + operation: delete +NCIT:pharmaceutical_release_characteristics_of: + operation: delete +NCIT:pharmaceutical_state_of_matter_of: + operation: delete +NCIT:pharmaceutical_transformation_of: + operation: delete +NCIT:procedure_has_completely_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_imaged_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_partially_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_target_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_completely_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_partially_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:process_altered_by_allele: + operation: delete +NCIT:process_includes_biological_process: + operation: keep + core_predicate: biolink:has_participant +NCIT:process_initiates_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:process_involves_gene: + operation: keep + core_predicate: biolink:has_participant +NCIT:qualifier_applies_to: + operation: keep + core_predicate: biolink:related_to +NCIT:regimen_has_accepted_use_for_disease: + operation: keep + core_predicate: biolink:treats +NCIT:related_to_genetic_biomarker: + operation: delete +NCIT:role_has_domain: + operation: keep + core_predicate: biolink:related_to +NCIT:role_has_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:role_has_range: + operation: keep + core_predicate: biolink:related_to +NCIT:role_is_parent_of: + operation: delete +NCIT:special_category_includes_neoplasm: + operation: delete +NCIT:subset_includes_concept: + operation: invert + core_predicate: biolink:subclass_of +NCIT:target_anatomy_has_procedure: + operation: delete +NCIT:tissue_is_expression_site_of_gene_product: + operation: delete +NDDF:dose_form_of: + operation: delete +NDDF:has_dose_form: + operation: keep + core_predicate: biolink:subclass_of +NDDF:has_ingredient: + operation: keep + core_predicate: biolink:has_part +NDDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +OBI:0000293: + operation: keep + core_predicate: biolink:has_participant +OBI:0000295: + operation: invert + core_predicate: biolink:has_participant +OBI:0000299: + operation: keep + core_predicate: biolink:has_output +OBI:0000417: + operation: keep + core_predicate: biolink:has_output +OBI:0001927: + operation: invert + core_predicate: biolink:related_to +OBO:INO_0000154: + operation: keep + core_predicate: biolink:related_to +OBO:MF#manifestationOf: + operation: keep + core_predicate: biolink:manifestation_of +OBO:bspo#parallel_to: + operation: keep + core_predicate: biolink:coexists_with +OBO:doid#has_symptom: + operation: keep + core_predicate: biolink:has_phenotype +OBO:envo#has_increased_levels_of: + operation: keep + core_predicate: biolink:related_to +OBO:exo#interacts_with: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_receptor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_stressor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with_an_exposure_receptor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with_an_exposure_stressor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:has_role: + operation: keep + core_predicate: biolink:related_to +OBO:nbo#by_means: + operation: invert + core_predicate: biolink:actively_involved_in +OBO:nbo#has_participant: + operation: keep + core_predicate: biolink:has_participant +OBO:nbo#in_response_to: + operation: invert + core_predicate: biolink:causes +OBO:nbo#is_about: + operation: keep + core_predicate: biolink:related_to +OBO:uo#is_unit_of: + operation: invert + core_predicate: biolink:related_to +OIO:hasDbXref: + operation: keep + core_predicate: biolink:close_match +OMIM:allelic_variant_of: + operation: keep + core_predicate: biolink:is_sequence_variant_of +OMIM:has_allelic_variant: + operation: delete +OMIM:has_inheritance_type: + operation: keep + core_predicate: biolink:related_to +OMIM:has_manifestation: + operation: invert + core_predicate: biolink:subclass_of +OMIM:has_phenotype: + operation: keep + core_predicate: biolink:has_phenotype +OMIM:inheritance_type_of: + operation: delete +OMIM:manifestation_of: + operation: keep + core_predicate: biolink:manifestation_of +OMIM:phenotype_of: + operation: invert + core_predicate: biolink:has_phenotype +ORPHA:317343: + operation: keep + core_predicate: biolink:causes +ORPHA:317344: + operation: keep + core_predicate: biolink:causes +ORPHA:317346: + operation: keep + core_predicate: biolink:causes +ORPHA:317348: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:317349: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:327767: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:410295: + operation: keep + core_predicate: biolink:causes +ORPHA:410296: + operation: keep + core_predicate: biolink:causes +ORPHA:465410: + operation: keep + core_predicate: biolink:biomarker_for +ORPHANET:317343: + operation: keep + core_predicate: biolink:causes +ORPHANET:317344: + operation: keep + core_predicate: biolink:causes +ORPHANET:317345: + operation: keep + core_predicate: biolink:correlated_with +ORPHANET:317346: + operation: keep + core_predicate: biolink:causes +ORPHANET:317348: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:317349: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:327767: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:410295: + operation: keep + core_predicate: biolink:causes +ORPHANET:410296: + operation: keep + core_predicate: biolink:causes +ORPHANET:465410: + operation: keep + core_predicate: biolink:biomarker_for +ORPHANET:C016: + operation: keep + core_predicate: biolink:related_to +ORPHANET:C017: + operation: keep + core_predicate: biolink:related_to +PATO:0000085: + operation: keep + core_predicate: biolink:associated_with_sensitivity_to +PATO:correlates_with: + operation: keep + core_predicate: biolink:correlated_with +PATO:decreased_in_magnitude_relative_to: + operation: keep + core_predicate: biolink:related_to +PATO:has_cross_section: + operation: keep + core_predicate: biolink:related_to +PATO:has_relative_magnitude: + operation: keep + core_predicate: biolink:related_to +PATO:increased_in_magnitude_relative_to: + operation: keep + core_predicate: biolink:related_to +PATO:reciprocal_of: + operation: keep + core_predicate: biolink:related_to +PATO:towards: + operation: invert + core_predicate: biolink:actively_involved_in +PDQ:associated_disease: + operation: keep + core_predicate: biolink:correlated_with +PDQ:associated_genetic_condition: + operation: delete +PDQ:component_of: + operation: invert + core_predicate: biolink:has_part +PDQ:has_component: + operation: keep + core_predicate: biolink:has_part +PHAROS:drug_targets: + operation: keep + core_predicate: biolink:directly_interacts_with +PR:confers_resistance_to: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: uptake + - object_aspect: activity + - object_direction: decreased +PR:has_gene_template: + operation: keep + core_predicate: biolink:gene_product_of +PR:lacks_part: + operation: keep + core_predicate: biolink:lacks_part +PR:non-covalently_bound_to: + operation: keep + core_predicate: biolink:physically_interacts_with +PSY:RB: + operation: invert + core_predicate: biolink:subclass_of +PSY:RO: + operation: keep + core_predicate: biolink:related_to +PSY:use: + operation: keep + core_predicate: biolink:subclass_of +PSY:used_for: + operation: invert + core_predicate: biolink:has_input +PathWhiz:has_bound: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_compound: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_element_collection: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_element_in_bound: + operation: keep + core_predicate: biolink:has_part +PathWhiz:has_enzyme: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_left_element: + operation: keep + core_predicate: biolink:has_input +PathWhiz:has_location: + operation: keep + core_predicate: biolink:occurs_in +PathWhiz:has_nucleic_acid: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_protein: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_protein_in_complex: + operation: keep + core_predicate: biolink:has_part +PathWhiz:has_reaction: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_right_element: + operation: keep + core_predicate: biolink:has_output +PathWhiz:in_species: + operation: keep + core_predicate: biolink:occurs_in +REACT:has_element: + operation: keep + core_predicate: biolink:has_part +REACT:has_event: + operation: keep + core_predicate: biolink:has_participant +REACT:has_input: + operation: keep + core_predicate: biolink:has_input +REACT:has_member: + operation: keep + core_predicate: biolink:has_part +REACT:has_output: + operation: keep + core_predicate: biolink:has_output +REACT:in_species: + operation: keep + core_predicate: biolink:occurs_in +REACT:is_requirement_for: + operation: keep + core_predicate: biolink:entity_regulates_entity +REACT:linked_to_disease: + operation: keep + core_predicate: biolink:related_to +REACT:negatively_regulates: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +REACT:negatively_regulates_gene_expression: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +REACT:positively_regulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +REACT:positively_regulates_gene_expression: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +REACT:related_to: + operation: keep + core_predicate: biolink:related_to +REPODB:clinically_tested_approved_unknown_phase: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_3: + operation: keep + core_predicate: biolink:treats +RO:0000052: + operation: keep + core_predicate: biolink:related_to +RO:0000053: + operation: keep + core_predicate: biolink:related_to +RO:0000056: + operation: invert + core_predicate: biolink:has_participant +RO:0000057: + operation: keep + core_predicate: biolink:has_participant +RO:0000059: + operation: keep + core_predicate: biolink:related_to +RO:0000086: + operation: keep + core_predicate: biolink:related_to +RO:0000087: + operation: keep + core_predicate: biolink:related_to +RO:00002325: + operation: keep + core_predicate: biolink:colocalizes_with +RO:0001000: + operation: invert + core_predicate: biolink:derives_into +RO:0001001: + operation: invert + core_predicate: biolink:derives_from +RO:0001015: + operation: invert + core_predicate: biolink:located_in +RO:0001018: + operation: invert + core_predicate: biolink:has_part +RO:0001019: + operation: keep + core_predicate: biolink:has_part +RO:0001022: + operation: invert + core_predicate: biolink:causes +RO:0001025: + operation: keep + core_predicate: biolink:located_in +RO:0002001: + operation: keep + core_predicate: biolink:related_to +RO:0002002: + operation: keep + core_predicate: biolink:related_to +RO:0002003: + operation: keep + core_predicate: biolink:related_to +RO:0002005: + operation: keep + core_predicate: biolink:related_to +RO:0002007: + operation: invert + core_predicate: biolink:has_part +RO:0002008: + operation: keep + core_predicate: biolink:related_to +RO:0002082: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002083: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002084: + operation: keep + core_predicate: biolink:related_to +RO:0002087: + operation: invert + core_predicate: biolink:precedes +RO:0002090: + operation: keep + core_predicate: biolink:precedes +RO:0002092: + operation: keep + core_predicate: biolink:related_to +RO:0002093: + operation: keep + core_predicate: biolink:related_to +RO:0002100: + operation: keep + core_predicate: biolink:overlaps +RO:0002101: + operation: keep + core_predicate: biolink:overlaps +RO:0002102: + operation: keep + core_predicate: biolink:overlaps +RO:0002103: + operation: keep + core_predicate: biolink:interacts_with +RO:0002104: + operation: keep + core_predicate: biolink:has_part +RO:0002120: + operation: keep + core_predicate: biolink:interacts_with +RO:0002130: + operation: keep + core_predicate: biolink:interacts_with +RO:0002131: + operation: keep + core_predicate: biolink:overlaps +RO:0002134: + operation: keep + core_predicate: biolink:related_to +RO:0002150: + operation: keep + core_predicate: biolink:related_to +RO:0002159: + operation: keep + core_predicate: biolink:related_to +RO:0002160: + operation: keep + core_predicate: biolink:in_taxon +RO:0002162: + operation: keep + core_predicate: biolink:in_taxon +RO:0002170: + operation: keep + core_predicate: biolink:related_to +RO:0002176: + operation: keep + core_predicate: biolink:related_to +RO:0002177: + operation: keep + core_predicate: biolink:related_to +RO:0002178: + operation: keep + core_predicate: biolink:related_to +RO:0002179: + operation: keep + core_predicate: biolink:related_to +RO:0002180: + operation: keep + core_predicate: biolink:has_part +RO:0002200: + operation: keep + core_predicate: biolink:has_phenotype +RO:0002202: + operation: keep + core_predicate: biolink:develops_from +RO:0002203: + operation: keep + core_predicate: biolink:develops_from +RO:0002204: + operation: invert + core_predicate: biolink:has_gene_product +RO:0002205: + operation: invert + core_predicate: biolink:gene_product_of +RO:0002207: + operation: keep + core_predicate: biolink:develops_from +RO:0002211: + operation: keep + core_predicate: biolink:regulates +RO:0002212: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +RO:0002213: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance - object_direction: increased -""", - "biolink:affects_secretion_of": """ +RO:0002215: + operation: keep + core_predicate: biolink:capable_of +RO:0002216: + operation: invert + core_predicate: biolink:has_participant +RO:0002219: + operation: keep + core_predicate: biolink:coexists_with +RO:0002220: + operation: keep + core_predicate: biolink:coexists_with +RO:0002221: + operation: keep + core_predicate: biolink:coexists_with +RO:0002223: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002224: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002225: + operation: keep + core_predicate: biolink:develops_from +RO:0002226: + operation: keep + core_predicate: biolink:develops_from +RO:0002229: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002230: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002231: + operation: keep + core_predicate: biolink:occurs_in +RO:0002232: + operation: keep + core_predicate: biolink:occurs_in +RO:0002233: + operation: keep + core_predicate: biolink:has_input +RO:0002234: + operation: keep + core_predicate: biolink:has_output +RO:0002241: + operation: keep + core_predicate: biolink:related_to +RO:0002254: + operation: keep + core_predicate: biolink:related_to +RO:0002255: + operation: keep + core_predicate: biolink:contributes_to +RO:0002256: + operation: keep + core_predicate: biolink:causes +RO:0002263: + operation: keep + core_predicate: biolink:acts_upstream_of +RO:0002264: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within +RO:0002285: + operation: invert + core_predicate: biolink:precedes +RO:0002292: + operation: invert + core_predicate: biolink:expressed_in +RO:0002295: + operation: keep + core_predicate: biolink:regulates +RO:0002296: + operation: keep + core_predicate: biolink:has_output +RO:0002297: + operation: keep + core_predicate: biolink:has_output +RO:0002298: + operation: keep + core_predicate: biolink:has_output +RO:0002299: + operation: keep + core_predicate: biolink:has_output +RO:0002302: + operation: invert + core_predicate: biolink:treats +RO:0002303: + operation: keep + core_predicate: biolink:located_in +RO:0002309: + operation: keep + core_predicate: biolink:related_to +RO:0002313: + operation: keep core_predicate: biolink:affects qualifiers: - - object_aspect: secretion -""", - "biolink:decreases_secretion_of": """ + - object_aspect: transport +RO:0002314: + operation: keep + core_predicate: biolink:related_to +RO:0002315: + operation: keep + core_predicate: biolink:causes +RO:0002322: + operation: keep + core_predicate: biolink:related_to +RO:0002326: + operation: keep + core_predicate: biolink:contributes_to +RO:0002327: + operation: invert + core_predicate: biolink:enabled_by +RO:0002328: + operation: keep + core_predicate: biolink:related_to +RO:0002331: + operation: keep + core_predicate: biolink:actively_involved_in +RO:0002332: + operation: keep + core_predicate: biolink:related_to +RO:0002333: + operation: invert + core_predicate: biolink:enables +RO:0002334: + operation: invert + core_predicate: biolink:entity_regulates_entity +RO:0002338: + operation: keep + core_predicate: biolink:related_to +RO:0002339: + operation: keep + core_predicate: biolink:related_to +RO:0002340: + operation: keep core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +RO:0002341: + operation: keep + core_predicate: biolink:related_to +RO:0002342: + operation: keep + core_predicate: biolink:related_to +RO:0002343: + operation: keep + core_predicate: biolink:affects +RO:0002344: + operation: keep + core_predicate: biolink:related_to +RO:0002345: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +RO:0002348: + operation: keep + core_predicate: biolink:related_to +RO:0002349: + operation: keep + core_predicate: biolink:related_to +RO:0002350: + operation: invert + core_predicate: biolink:has_part +RO:0002351: + operation: keep + core_predicate: biolink:has_part +RO:0002352: + operation: invert + core_predicate: biolink:has_input +RO:0002353: + operation: invert + core_predicate: biolink:has_output +RO:0002354: + operation: invert + core_predicate: biolink:has_output +RO:0002355: + operation: keep + core_predicate: biolink:affects +RO:0002356: + operation: keep + core_predicate: biolink:related_to +RO:0002371: + operation: keep + core_predicate: biolink:related_to +RO:0002372: + operation: keep + core_predicate: biolink:related_to +RO:0002373: + operation: keep + core_predicate: biolink:related_to +RO:0002374: + operation: keep + core_predicate: biolink:related_to +RO:0002376: + operation: invert + core_predicate: biolink:has_part +RO:0002380: + operation: invert + core_predicate: biolink:has_part +RO:0002385: + operation: keep + core_predicate: biolink:related_to +RO:0002387: + operation: keep + core_predicate: biolink:related_to +RO:0002410: + operation: keep + core_predicate: biolink:causes +RO:0002411: + operation: keep + core_predicate: biolink:precedes +RO:0002412: + operation: keep + core_predicate: biolink:precedes +RO:0002432: + operation: keep + core_predicate: biolink:active_in +RO:0002433: + operation: keep + core_predicate: biolink:overlaps +RO:0002434: + operation: keep + core_predicate: biolink:interacts_with +RO:0002435: + operation: keep + core_predicate: biolink:genetically_interacts_with +RO:0002436: + operation: keep + core_predicate: biolink:molecularly_interacts_with +RO:0002448: + operation: invert + core_predicate: biolink:entity_regulated_by_entity +RO:0002449: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +RO:0002450: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +RO:0002451: + operation: keep + core_predicate: biolink:related_to +RO:0002452: + operation: keep + core_predicate: biolink:has_phenotype +RO:0002470: + operation: keep + core_predicate: biolink:related_to +RO:0002473: + operation: keep + core_predicate: biolink:has_part +RO:0002488: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002489: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002491: + operation: keep + core_predicate: biolink:coexists_with +RO:0002492: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002493: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002494: + operation: keep + core_predicate: biolink:related_to +RO:0002495: + operation: keep + core_predicate: biolink:related_to +RO:0002496: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002497: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002500: + operation: keep + core_predicate: biolink:capable_of +RO:0002503: + operation: keep + core_predicate: biolink:actively_involved_in +RO:0002505: + operation: invert + core_predicate: biolink:has_participant +RO:0002506: + operation: keep + core_predicate: biolink:causes +RO:0002507: + operation: keep + core_predicate: biolink:causes +RO:0002509: + operation: keep + core_predicate: biolink:causes +RO:0002510: + operation: keep + core_predicate: biolink:transcribed_from +RO:0002511: + operation: invert + core_predicate: biolink:transcribed_from +RO:0002524: + operation: keep + core_predicate: biolink:has_part +RO:0002551: + operation: keep + core_predicate: biolink:has_part +RO:0002565: + operation: invert + core_predicate: biolink:has_participant +RO:0002568: + operation: keep + core_predicate: biolink:related_to +RO:0002571: + operation: invert + core_predicate: biolink:has_part +RO:0002572: + operation: invert + core_predicate: biolink:has_part +RO:0002573: + operation: keep + core_predicate: biolink:related_to +RO:0002576: + operation: invert + core_predicate: biolink:has_part +RO:0002578: + operation: keep + core_predicate: biolink:regulates +RO:0002588: + operation: keep + core_predicate: biolink:has_output +RO:0002590: + operation: keep + core_predicate: biolink:has_input +RO:0002591: + operation: keep + core_predicate: biolink:affects +RO:0002592: + operation: keep + core_predicate: biolink:affects +RO:0002599: + operation: keep + core_predicate: biolink:prevents +RO:0002604: + operation: keep + core_predicate: biolink:opposite_of +RO:0002606: + operation: keep + core_predicate: biolink:treats +RO:0002607: + operation: keep + core_predicate: biolink:biomarker_for +RO:0002608: + operation: invert + core_predicate: biolink:causes +RO:0002610: + operation: keep + core_predicate: biolink:correlated_with +RO:0002629: + operation: keep + core_predicate: biolink:regulates qualified_predicate: biolink:causes qualifiers: - - object_aspect: secretion + - object_aspect: activity_or_abundance + - object_direction: increased +RO:0002630: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +RO:0003000: + operation: keep + core_predicate: biolink:produces +RO:0003001: + operation: invert + core_predicate: biolink:produces +RO:0003002: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression - object_direction: decreased -""", - "biolink:increases_secretion_of": """ +RO:0003003: + operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: secretion + - object_aspect: expression - object_direction: increased -""" - } - - -def get_mapped_predicates(): - # Get info from the existing predicate-remap.yaml - # Note yaml.full_load does not retain comments - with open(PREDICATE_REMAP_OLD_FILE_PATH, "r") as fp: - predicate_remap_dict = yaml.full_load(fp) - - for key, value_dict in predicate_remap_dict.items(): - for operation, values in value_dict.items(): - # disregards current "keep" operation, changes "rename" to "keep - if operation == "rename": - new_value = ["keep"] - elif operation in ("invert", "delete"): - new_value = [operation] - - # add biolink predicate to list - if values is not None: - new_value.append(values[1]) - predicate_remap_dict[key] = new_value - - return predicate_remap_dict - - -def get_biolink_predicates(): - with open(BIOLINK_MODEL_FILE_PATH, "r") as fp: - # convert biolink-model.yaml into a dictionary - biolink_dict = yaml.full_load(fp) - - # create a dict for valid predicates - valid_dict = {} - - # create a dictionary for the remapped predicates - predicates_dict = {} - - # iterate over the biolink dictionary to remap predicates - # while also generating a list of predicates - for biolink_key, biolink_value in biolink_dict["slots"].items(): - - deprecated = False - - # build a dictionary of biolink predicates - if biolink_key == "related to": - valid_dict[biolink_key] = "keep" - elif type(biolink_value) == dict and "is_a" in biolink_value.keys() \ - and biolink_value["is_a"] in valid_dict.keys(): - if "inverse" in biolink_value.keys(): - valid_dict[biolink_key] = "invert" - else: - valid_dict[biolink_key] = "keep" - - # Add flag for deprecated - if "deprecated" in biolink_value.keys(): - deprecated = True - - # If key is in valid_dict, add it to `predicates_dict` - if biolink_key in valid_dict.keys(): - for key, value_list in biolink_value.items(): - # Map predicates to `related to` - if key in ("exact_mappings", "broad_mappings", "narrow_mappings") and value_list is not None: - # value_list is a list of predicates - for predicate in value_list: - if predicate not in predicates_dict: - operation = valid_dict[biolink_key] - biolink_predicate = "biolink:" + "_".join(biolink_key.split()) - # Filter out undesired KPs - if predicate.split(":", 1)[0] not in ("SNOMED", "SNOMEDCT", "GAMMA"): - if operation != "invert": - predicates_dict[predicate] = [operation, biolink_predicate] - else: - invert_predicate = "biolink:" + "_".join(biolink_value["inverse"].split()) - predicates_dict[predicate] = [operation, invert_predicate] - - if deprecated: - predicates_dict[predicate].append("deprecated") - - return predicates_dict - - -def remap_predicates(predicates_dict, predicate_map_dict): - # print(predicate_map_dict) - print(predicates_dict) - - # Add data from the old predicate_remap.yaml to the predicates dict - for predicate, value_list in predicate_map_dict.items(): - if predicate not in predicates_dict: - predicates_dict[predicate] = value_list - - ordered_dict = OrderedDict(sorted(predicates_dict.items())) - - with open(OUTPUT_FILE_PATH, "w") as ofp, open("remap.log", "w") as log: - text = "" - for key, value in ordered_dict.items(): - # print(f"{key} {value}") - operation = value[0] - if len(value) > 1: - biolink_predicate = value[1] - ofp.write(f"{key}: \n operation: {operation}") # (key + ":\n operation: keep") - # Check if the predicate is in the qualifiers dict and has a "keep" operation - if operation == "keep" and biolink_predicate in QUALIFIER_MAPPING_DICT.keys(): - text = QUALIFIER_MAPPING_DICT[biolink_predicate] - elif operation == "delete": - text = "\n" - else: - text = "\n core_predicate: " + biolink_predicate + "\n" - - # Write to log predicates that are deprecated but not covered in qualifier map - if len(value) == 3 and value[1] not in QUALIFIER_MAPPING_DICT.keys(): - log.write(f"{key} {value[1]} {operation}\n") - - ofp.write(text) - - print("Completed") - - return - - -if __name__ == "__main__": - predicates = get_biolink_predicates() - mapped_predicates = get_mapped_predicates() - remap_predicates(predicates, mapped_predicates) +RO:0003301: + operation: keep + core_predicate: biolink:model_of +RO:0003303: + operation: keep + core_predicate: biolink:causes +RO:0003304: + operation: keep + core_predicate: biolink:contributes_to +RO:0003307: + operation: keep + core_predicate: biolink:ameliorates +RO:0003309: + operation: keep + core_predicate: biolink:exacerbates +RO:0004001: + operation: keep + core_predicate: biolink:causes +RO:0004007: + operation: keep + core_predicate: biolink:has_participant +RO:0004008: + operation: keep + core_predicate: biolink:has_output +RO:0004009: + operation: keep + core_predicate: biolink:has_input +RO:0004019: + operation: invert + core_predicate: biolink:causes +RO:0004020: + operation: invert + core_predicate: biolink:causes +RO:0004021: + operation: keep + core_predicate: biolink:has_participant +RO:0004022: + operation: keep + core_predicate: biolink:has_phenotype +RO:0004024: + operation: keep + core_predicate: biolink:disrupts +RO:0004025: + operation: keep + core_predicate: biolink:disrupts +RO:0004026: + operation: keep + core_predicate: biolink:related_to +RO:0004027: + operation: keep + core_predicate: biolink:related_to +RO:0004028: + operation: invert + core_predicate: biolink:causes +RO:0004029: + operation: keep + core_predicate: biolink:associated_with +RO:0004030: + operation: invert + core_predicate: biolink:causes +RO:0004032: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within_positive_effect +RO:0004033: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within_negative_effect +RO:0004034: + operation: keep + core_predicate: biolink:acts_upstream_of_positive_effect +RO:0004035: + operation: keep + core_predicate: biolink:acts_upstream_of_negative_effect +RO:0009001: + operation: keep + core_predicate: biolink:related_to +RO:0009004: + operation: keep + core_predicate: biolink:related_to +RO:0009501: + operation: invert + core_predicate: biolink:causes +RO:0012003: + operation: keep + core_predicate: biolink:affects +RO:0012008: + operation: keep + core_predicate: biolink:affects +RO:0013001: + operation: keep + core_predicate: biolink:related_to +RO:0014001: + operation: keep + core_predicate: biolink:related_to +RO:HOM0000000: + operation: keep + core_predicate: biolink:similar_to +RO:has_participant: + operation: keep + core_predicate: biolink:has_participant +RO:participates_in: + operation: invert + core_predicate: biolink:has_participant +RXNORM:consists_of: + operation: keep + core_predicate: biolink:has_part +RXNORM:constitutes: + operation: invert + core_predicate: biolink:has_part +RXNORM:contained_in: + operation: invert + core_predicate: biolink:has_part +RXNORM:contains: + operation: keep + core_predicate: biolink:has_part +RXNORM:dose_form_of: + operation: delete +RXNORM:doseformgroup_of: + operation: delete +RXNORM:form_of: + operation: delete +RXNORM:has_dose_form: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:has_doseformgroup: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:has_form: + operation: keep + core_predicate: biolink:related_to +RXNORM:has_ingredient: + operation: keep + core_predicate: biolink:has_part +RXNORM:has_ingredients: + operation: delete +RXNORM:has_part: + operation: keep + core_predicate: biolink:has_part +RXNORM:has_precise_ingredient: + operation: delete +RXNORM:has_quantified_form: + operation: keep + core_predicate: biolink:close_match +RXNORM:has_tradename: + operation: keep + core_predicate: biolink:related_to +RXNORM:ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:ingredients_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +RXNORM:isa: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:part_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:precise_ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:quantified_form_of: + operation: delete +RXNORM:reformulated_to: + operation: keep + core_predicate: biolink:related_to +RXNORM:reformulation_of: + operation: delete +RXNORM:tradename_of: + operation: delete +SEMMEDDB:1532: + operation: delete +SEMMEDDB:AFFECTS: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:CAUSES: + operation: keep + core_predicate: biolink:causes +SEMMEDDB:COEXISTS_WITH: + operation: keep + core_predicate: biolink:coexists_with +SEMMEDDB:CONVERTS_TO: + operation: invert + core_predicate: biolink:derives_from +SEMMEDDB:DISRUPTS: + operation: keep + core_predicate: biolink:disrupts +SEMMEDDB:INHIBITS: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +SEMMEDDB:IS_A: + operation: keep + core_predicate: biolink:subclass_of +SEMMEDDB:LOCATION_OF: + operation: invert + core_predicate: biolink:located_in +SEMMEDDB:MANIFESTATION_OF: + operation: keep + core_predicate: biolink:manifestation_of +SEMMEDDB:OCCURS_IN: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:PART_OF: + operation: invert + core_predicate: biolink:has_part +SEMMEDDB:PRECEDES: + operation: keep + core_predicate: biolink:precedes +SEMMEDDB:PREVENTS: + operation: keep + core_predicate: biolink:prevents +SEMMEDDB:PROCESS_OF: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:PRODUCES: + operation: keep + core_predicate: biolink:produces +SEMMEDDB:SAME_AS: + operation: keep + core_predicate: biolink:close_match +SEMMEDDB:STIMULATES: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:TREATS: + operation: keep + core_predicate: biolink:treats +SEMMEDDB:administered_to: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:affects: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:associated_with: + operation: keep + core_predicate: biolink:associated_with +SEMMEDDB:augments: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:causes: + operation: keep + core_predicate: biolink:causes +SEMMEDDB:coexists_with: + operation: keep + core_predicate: biolink:coexists_with +SEMMEDDB:compared_with: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:complicates: + operation: keep + core_predicate: biolink:exacerbates +SEMMEDDB:converts_to: + operation: invert + core_predicate: biolink:derives_from +SEMMEDDB:diagnoses: + operation: keep + core_predicate: biolink:diagnoses +SEMMEDDB:disrupts: + operation: keep + core_predicate: biolink:disrupts +SEMMEDDB:higher_than: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:inhibits: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +SEMMEDDB:interacts_with: + operation: keep + core_predicate: biolink:interacts_with +SEMMEDDB:isa: + operation: keep + core_predicate: biolink:subclass_of +SEMMEDDB:location_of: + operation: invert + core_predicate: biolink:located_in +SEMMEDDB:lower_than: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:manifestation_of: + operation: keep + core_predicate: biolink:manifestation_of +SEMMEDDB:measurement_of: + operation: delete +SEMMEDDB:measures: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:method_of: + operation: delete +SEMMEDDB:nom: + operation: delete +SEMMEDDB:occurs_in: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:part_of: + operation: invert + core_predicate: biolink:has_part +SEMMEDDB:precedes: + operation: keep + core_predicate: biolink:precedes +SEMMEDDB:predisposes: + operation: keep + core_predicate: biolink:predisposes +SEMMEDDB:prep: + operation: delete +SEMMEDDB:prevents: + operation: keep + core_predicate: biolink:prevents +SEMMEDDB:process_of: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:produces: + operation: keep + core_predicate: biolink:produces +SEMMEDDB:same_as: + operation: keep + core_predicate: biolink:close_match +SEMMEDDB:stimulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:treats: + operation: keep + core_predicate: biolink:treats +SEMMEDDB:uses: + operation: keep + core_predicate: biolink:has_input +SEMMEDDB:verb: + operation: delete +SEMMEDDB:xref: + operation: keep + core_predicate: biolink:related_to +SIO:000001: + operation: delete +SIO:000203: + operation: keep + core_predicate: biolink:directly_interacts_with +SIO:000628: + operation: keep + core_predicate: biolink:mentions +SIO:000983: + operation: keep + core_predicate: biolink:biomarker_for +SIO:001331: + operation: keep + core_predicate: biolink:diagnoses +SIO:010080: + operation: invert + core_predicate: biolink:transcribed_from +SIO:010081: + operation: keep + core_predicate: biolink:transcribed_from +SIO:010285: + operation: keep + core_predicate: biolink:in_complex_with +SO:0001583: + operation: keep + core_predicate: biolink:is_missense_variant_of +SO:0001589: + operation: keep + core_predicate: biolink:is_frameshift_variant_of +SO:0001629: + operation: keep + core_predicate: biolink:is_splice_site_variant_of +SO:0001819: + operation: keep + core_predicate: biolink:is_synonymous_variant_of +SO:0002054: + operation: keep + core_predicate: biolink:is_nonsense_variant_of +SO:has_origin: + operation: keep + core_predicate: biolink:coexists_with +SO:similar_to: + operation: keep + core_predicate: biolink:similar_to +UBERON:anastomoses_with: + operation: keep + core_predicate: biolink:coexists_with +UBERON:anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channel_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channels_from: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channels_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON:conduit_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:existence_starts_and_ends_during: + operation: keep + core_predicate: biolink:coexists_with +UBERON:extends_fibers_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON:filtered_through: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_central_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_innermost_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_outermost_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:indirectly_supplies: + operation: keep + core_predicate: biolink:coexists_with +UBERON:posteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:protects: + operation: keep + core_predicate: biolink:coexists_with +UBERON:proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:sexually_homologous_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:site_of: + operation: invert + core_predicate: biolink:occurs_in +UBERON:subdivision_of: + operation: invert + core_predicate: biolink:has_part +UBERON:synapsed_by: + operation: keep + core_predicate: biolink:related_to +UBERON_CORE:anastomoses_with: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channel_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channels_from: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channels_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:conduit_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:extends_fibers_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:filtered_through: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:in_central_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:in_innermost_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:in_outermost_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:indirectly_supplies: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:layer_part_of: + operation: invert + core_predicate: biolink:has_part +UBERON_CORE:posteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:protects: + operation: keep + core_predicate: biolink:related_to +UBERON_CORE:proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:sexually_homologous_to: + operation: keep + core_predicate: biolink:homologous_to +UBERON_CORE:site_of: + operation: keep + core_predicate: biolink:occurs_in +UBERON_CORE:subdivision_of: + operation: invert + core_predicate: biolink:has_part +UBERON_CORE:synapsed_by: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:trunk_part_of: + operation: invert + core_predicate: biolink:has_part +UBERON_NONAMESPACE:connected_to: + operation: keep + core_predicate: biolink:related_to +UBERON_NONAMESPACE:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_NONAMESPACE:innervated_by: + operation: keep + core_predicate: biolink:related_to +UBERON_NONAMESPACE:subdivision_of: + operation: keep + core_predicate: biolink:coexists_with +UMLS:RB: + operation: invert + core_predicate: biolink:subclass_of +UMLS:RO: + operation: keep + core_predicate: biolink:related_to +UMLS:RQ: + operation: keep + core_predicate: biolink:related_to +UMLS:SIB: + operation: delete +UMLS:SY: + operation: keep + core_predicate: biolink:close_match +UMLS:class_code_classified_by: + operation: keep + core_predicate: biolink:related_to +UMLS:classifies_class_code: + operation: delete +UMLS:component_of: + operation: invert + core_predicate: biolink:has_part +UMLS:context_binding_of: + operation: delete +UMLS:exhibited_by: + operation: keep + core_predicate: biolink:related_to +UMLS:exhibits: + operation: delete +UMLS:form_of: + operation: delete +UMLS:has_component: + operation: keep + core_predicate: biolink:has_part +UMLS:has_context_binding: + operation: keep + core_predicate: biolink:related_to +UMLS:has_form: + operation: keep + core_predicate: biolink:related_to +UMLS:has_mapping_qualifier: + operation: keep + core_predicate: biolink:related_to +UMLS:has_owning_affiliate: + operation: invert + core_predicate: biolink:has_part +UMLS:has_owning_section: + operation: delete +UMLS:has_owning_subsection: + operation: delete +UMLS:has_physiologic_effect: + operation: keep + core_predicate: biolink:causes +UMLS:has_structural_class: + operation: keep + core_predicate: biolink:related_to +UMLS:has_supported_concept_property: + operation: keep + core_predicate: biolink:related_to +UMLS:has_supported_concept_relationship: + operation: keep + core_predicate: biolink:related_to +UMLS:larger_than: + operation: keep + core_predicate: biolink:related_to +UMLS:mapped_from: + operation: delete +UMLS:mapped_to: + operation: keep + core_predicate: biolink:related_to +UMLS:may_be_qualified_by: + operation: keep + core_predicate: biolink:related_to +UMLS:may_qualify: + operation: delete +UMLS:measured_by: + operation: delete +UMLS:measures: + operation: keep + core_predicate: biolink:related_to +UMLS:owning_affiliate_of: + operation: delete +UMLS:owning_section_of: + operation: keep + core_predicate: biolink:related_to +UMLS:owning_subsection_of: + operation: invert + core_predicate: biolink:has_part +UMLS:related_to: + operation: keep + core_predicate: biolink:related_to +UMLS:supported_concept_property_in: + operation: delete +UMLS:supported_concept_relationship_in: + operation: delete +UO-PROPERTY:is_unit_of: + operation: keep + core_predicate: biolink:related_to +UPHENO:0000001: + operation: keep + core_predicate: biolink:affects +VANDF:has_ingredient: + operation: keep + core_predicate: biolink:has_part +VANDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +VANDF:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +VANDF:isa: + operation: keep + core_predicate: biolink:subclass_of +WIKIDATA:P2888: + operation: keep + core_predicate: biolink:exact_match +WIKIDATA:P3433: + operation: keep + core_predicate: biolink:is_sequence_variant_of +WIKIDATA:Q181394: + operation: keep + core_predicate: biolink:has_nutrient +WIKIDATA:Q39893449: + operation: keep + core_predicate: biolink:exact_match +WIKIDATA:Q39893967: + operation: invert + core_predicate: biolink:broad_match +WIKIDATA:Q39894595: + operation: keep + core_predicate: biolink:broad_match +WIKIDATA:Q66088480: + operation: invert + core_predicate: biolink:subclass_of +WIKIDATA_PROPERTY:P1056: + operation: keep + core_predicate: biolink:produces +WIKIDATA_PROPERTY:P123: + operation: keep + core_predicate: biolink:publisher +WIKIDATA_PROPERTY:P128: + operation: keep + core_predicate: biolink:regulates +WIKIDATA_PROPERTY:P129: + operation: keep + core_predicate: biolink:physically_interacts_with +WIKIDATA_PROPERTY:P1542: + operation: keep + core_predicate: biolink:causes +WIKIDATA_PROPERTY:P1557: + operation: keep + core_predicate: biolink:manifestation_of +WIKIDATA_PROPERTY:P156: + operation: keep + core_predicate: biolink:precedes +WIKIDATA_PROPERTY:P2175: + operation: keep + core_predicate: biolink:treats +WIKIDATA_PROPERTY:P2176: + operation: invert + core_predicate: biolink:treats +WIKIDATA_PROPERTY:P2293: + operation: keep + core_predicate: biolink:genetic_association +WIKIDATA_PROPERTY:P276: + operation: invert + core_predicate: biolink:located_in +WIKIDATA_PROPERTY:P279: + operation: keep + core_predicate: biolink:subclass_of +WIKIDATA_PROPERTY:P361: + operation: invert + core_predicate: biolink:has_part +WIKIDATA_PROPERTY:P50: + operation: keep + core_predicate: biolink:author +WIKIDATA_PROPERTY:P527: + operation: keep + core_predicate: biolink:has_part +WIKIDATA_PROPERTY:P688: + operation: invert + core_predicate: biolink:gene_product_of +WIKIDATA_PROPERTY:P703: + operation: keep + core_predicate: biolink:in_taxon +WIKIDATA_PROPERTY:P828: + operation: invert + core_predicate: biolink:causes +WIKIDATA_PROPERTY:P98: + operation: keep + core_predicate: biolink:editor +biolink:in_taxon: + operation: keep + core_predicate: biolink:subclass_of +biolink:part_of: + operation: invert + core_predicate: biolink:has_part +biolink:subclass_of: + operation: invert + core_predicate: biolink:has_part +dct:contributor: + operation: keep + core_predicate: biolink:contributor +dct:creator: + operation: keep + core_predicate: biolink:author +dct:publisher: + operation: keep + core_predicate: biolink:publisher +faldo:location: + operation: keep + core_predicate: biolink:has_sequence_location +oboFormat:xref: + operation: keep + core_predicate: biolink:close_match +oboformat:xref: + operation: keep + core_predicate: biolink:close_match +owl:inverseOf: + operation: keep + core_predicate: biolink:related_to +owl:sameAs: + operation: keep + core_predicate: biolink:same_as +owl:topObjectProperty: + operation: keep + core_predicate: biolink:related_to +rdf:type: + operation: keep + core_predicate: biolink:related_to +rdfs:subClassOf: + operation: keep + core_predicate: biolink:subclass_of +rdfs:subPropertyOf: + operation: keep + core_predicate: biolink:subclass_of +skos:broadMatch: + operation: keep + core_predicate: biolink:broad_match +skos:closeMatch: + operation: keep + core_predicate: biolink:close_match +skos:exactMatch: + operation: keep + core_predicate: biolink:exact_match +skos:narrowMatch: + operation: invert + core_predicate: biolink:broad_match +skos:relatedMatch: + operation: keep + core_predicate: biolink:related_to From a333a8b4e3121f12af7fdf733efda384cde6b35b Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 9 Aug 2022 08:28:53 -0700 Subject: [PATCH 023/127] #220 Annotate run-simplify.sh --- run-simplify.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/run-simplify.sh b/run-simplify.sh index e48f3b0a..510d308f 100755 --- a/run-simplify.sh +++ b/run-simplify.sh @@ -48,6 +48,7 @@ else echo "*** TEST MODE -- NO INCREMENT ***" fi +# TODO: Update self edge exception list for compliance with Biolink 3.0 ${VENV_DIR}/bin/python3 -u ${CODE_DIR}/filter_kg_and_remap_predicates.py ${test_flag} --dropNegated \ --dropSelfEdgesExcept interacts_with,positively_regulates,inhibits,increase \ ${predicate_mapping_file} ${infores_mapping_file} ${curies_to_urls_file} ${input_json} \ From 12f4b4889f363b24fd39ed2c0a9259ff274d7537 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 9 Aug 2022 09:09:15 -0700 Subject: [PATCH 024/127] #221 Annotate filter_kg_and_remap_predicates.py --- filter_kg_and_remap_predicates.py | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 3b448be9..4a27aa80 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -1,5 +1,6 @@ #!/usr/bin/env python3 '''Filters the RTX "KG2" second-generation knowledge graph, simplifying predicates and removing redundant edges. + Filter out negated edges, merge edges, remap predicates, remap source curies. Usage: filter_kg_and_remap_predicates.py ''' @@ -58,21 +59,26 @@ def make_arg_parser(): if drop_self_edges_except is not None: assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) + # Config files predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) + # ** Not sure about this notation ** [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] graph = kg2_util.load_json(input_file_name) new_edges = dict() + # Create sets to handle knowledge sources original_predicate_curies_not_in_config = set() provided_by_curies_not_in_config_nodes = set() provided_by_curies_not_in_config_edges = set() record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in predicate_remap_config.keys()} + # To Do: Update command set command_set = {'delete', 'keep', 'invert', 'rename'} for original_predicate_curie, command in predicate_remap_config.items(): assert len(command) == 1 assert next(iter(command.keys())) in command_set + # Every predicate curie should get its own node. Otherwise add to this set to complain. original_predicate_curies_not_in_nodes = set() nodes_dict = dict() for node_dict in graph['nodes']: @@ -96,6 +102,7 @@ def make_arg_parser(): predicate_label = original_predicate_label original_predicate_curie = edge_dict['original_predicate'] predicate_curie = original_predicate_curie + # ** Double check meaning ** if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: record_of_original_predicate_curie_occurrences[original_predicate_curie] = True pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) @@ -123,23 +130,28 @@ def make_arg_parser(): get_new_rel_info = True if get_new_rel_info: predicate_label = remap_subinfo[0] - predicate_curie = remap_subinfo[1] + predicate_curie = remap_subinfo[1] # Gets the biolink predicate if invert: edge_dict['relation_label'] = 'INVERTED:' + original_predicate_label new_object = edge_dict['subject'] edge_dict['subject'] = edge_dict['object'] edge_dict['object'] = new_object edge_dict['predicate_label'] = predicate_label + # Delete negated edges and self edges except interacts_with,positively_regulates,inhibits,increase + # as defined in run-simplify.sh + # To Do: verify exception list complies with updates from Biolink 3.0 if drop_self_edges_except is not None and \ edge_dict['subject'] == edge_dict['object'] and \ predicate_label not in drop_self_edges_except: continue # see issue 743 edge_dict['predicate'] = predicate_curie + # Sets biolink curie; remapping if predicate_curie not in nodes_dict: predicate_curie_prefix = predicate_curie.split(':')[0] predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') + # Create list of curies to complain about if not in biolink if predicate_uri_prefix == predicate_curie_prefix: - original_predicate_curies_not_in_nodes.add(predicate_curie) + original_predicate_curies_not_in_nodes.add(predicate_curie) provided_by = edge_dict['knowledge_source'] infores_curie_dict = infores_remap_config.get(provided_by, None) if infores_curie_dict is None: @@ -147,20 +159,24 @@ def make_arg_parser(): else: infores_curie = infores_curie_dict['infores_curie'] edge_dict['knowledge_source'] = [infores_curie] + # TODO: Update with additional properties edge_key = edge_dict['subject'] + ' /// ' + predicate_label + ' /// ' + edge_dict['object'] existing_edge = new_edges.get(edge_key, None) + # TODO: Update merging to handle semantic distinction between qualifiers if existing_edge is not None: existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + edge_dict['knowledge_source']))) existing_edge['publications'] += edge_dict['publications'] existing_edge['publications_info'].update(edge_dict['publications_info']) else: new_edges[edge_key] = edge_dict + # Releasing some memory del graph['edges'] del graph['nodes'] graph['nodes'] = list(nodes_dict.values()) del nodes_dict graph['edges'] = list(new_edges.values()) del new_edges + # Warnings for issues that came up for original_predicate_curie in record_of_original_predicate_curie_occurrences: if not record_of_original_predicate_curie_occurrences[original_predicate_curie]: print('original predicate curie is in the config file but was not used in any edge in the graph: ' + original_predicate_curie, file=sys.stderr) @@ -191,6 +207,7 @@ def make_arg_parser(): update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') build_name = str + # Add node to describe build for line in version_file: test_flag = "" if test_mode: From d6153e8c198d808fcec5fef97ab6fa0614f1caad Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 10 Aug 2022 13:50:02 -0700 Subject: [PATCH 025/127] #220 Changes for Biolink 3.0 compliance --- filter_kg_and_remap_predicates.py | 2 +- filter_kg_and_remap_predicates_new.py | 242 ++++++++++++++++++++++++++ run-simplify.sh | 4 +- 3 files changed, 245 insertions(+), 3 deletions(-) create mode 100644 filter_kg_and_remap_predicates_new.py diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 4a27aa80..c44f8b4b 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -71,6 +71,7 @@ def make_arg_parser(): original_predicate_curies_not_in_config = set() provided_by_curies_not_in_config_nodes = set() provided_by_curies_not_in_config_edges = set() + # ** Double check meaning ** record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in predicate_remap_config.keys()} # To Do: Update command set @@ -102,7 +103,6 @@ def make_arg_parser(): predicate_label = original_predicate_label original_predicate_curie = edge_dict['original_predicate'] predicate_curie = original_predicate_curie - # ** Double check meaning ** if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: record_of_original_predicate_curie_occurrences[original_predicate_curie] = True pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) diff --git a/filter_kg_and_remap_predicates_new.py b/filter_kg_and_remap_predicates_new.py new file mode 100644 index 00000000..124c54de --- /dev/null +++ b/filter_kg_and_remap_predicates_new.py @@ -0,0 +1,242 @@ +#!/usr/bin/env python3 +'''Filters the RTX "KG2" second-generation knowledge graph, simplifying predicates and removing redundant edges. + Filter out negated edges, merge edges, remap predicates, remap source curies. + + Usage: filter_kg_and_remap_predicates.py +''' + +__author__ = 'Stephen Ramsey' +__copyright__ = 'Oregon State University' +__credits__ = ['Stephen Ramsey'] +__license__ = 'MIT' +__version__ = '0.1.0' +__maintainer__ = '' +__email__ = '' +__status__ = 'Prototype' + +import argparse +import kg2_util +import pprint +import sys +from datetime import datetime + +# 1. What is the indicator for negation? +# - It's a prefix in the relation property in the edge... possibly. +# - Negated edges only come from SEMMEDDB, so we look in semmeddb_tuple_list_json_to_kg_json +# - A value on L209, the source relation checks and sets value +# 2. Instruction below "drop any edge if it is in between two SnoMedCT nodes" still needed? No + +# - check for any input relation_labels that occur twice in the predicate-remap.yaml file +# - rename script something like "filter_kg_and_remap_relation_labels.py" +# - need to detect the command "keep" in the YAML file +# - drop edges with 'NEGATION' +# - *don't* merge two edges if at least one of them has nonempty publication_info +# - change 'xref' to skos:closeMatch (skos) +# - drop any edge if it is in between two SnoMedCT nodes (optionally; use command-line option) +# - programmatically generate list of "keep" lines to add to the YAML file so all 1,100 +# distinct relation_labels are represented in the file +# - note (somehow) if a relationship has been inverted, in the "orig_relation_curie" field + + +def make_arg_parser(): + arg_parser = argparse.ArgumentParser(description='filter_kg.py: filters and simplifies the KG2 knowledge grpah for the RTX system') + arg_parser.add_argument('predicateRemapYaml', type=str, help="The YAML file describing how predicates should be remapped to simpler predicates") + arg_parser.add_argument('inforesRemapYaml', type=str, help="The YAML file describing how knowledge_source fields should be remapped to Translator infores curies") + arg_parser.add_argument('curiesToURIFile', type=str, help="The file mapping CURIE prefixes to URI fragments") + arg_parser.add_argument('inputFileJson', type=str, help="The input KG2 graph, in JSON format") + arg_parser.add_argument('outputFileJson', type=str, help="The output KG2 graph, in JSON format") + arg_parser.add_argument('versionFile', type=str, help="The text file storing the KG2 version") + arg_parser.add_argument('--test', dest='test', action='store_true', default=False) + arg_parser.add_argument('--dropSelfEdgesExcept', required=False, dest='drop_self_edges_except', default=None) + arg_parser.add_argument('--dropNegated', dest='drop_negated', action='store_true', default=False) + return arg_parser + + +if __name__ == '__main__': + args = make_arg_parser().parse_args() + predicate_remap_file_name = args.predicateRemapYaml + infores_remap_file_name = args.inforesRemapYaml + curies_to_uri_file_name = args.curiesToURIFile + input_file_name = args.inputFileJson + output_file_name = args.outputFileJson + test_mode = args.test + drop_negated = args.drop_negated + drop_self_edges_except = args.drop_self_edges_except + + if drop_self_edges_except is not None: + assert type(drop_self_edges_except) == str + drop_self_edges_except = set(drop_self_edges_except.split(',')) + + # Config files + # safe load takes a yaml file and returns a dictionary + predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) + infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) + + map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) + + [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] + graph = kg2_util.load_json(input_file_name) + new_edges = dict() + # Create sets to handle knowledge sources + original_predicate_curies_not_in_config = set() + knowledge_source_curies_not_in_config_nodes = set() + knowledge_source_curies_not_in_config_edges = set() + record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in + predicate_remap_config.keys()} + + # To Do: Update everything for rename/keep commands + # Old command set: {'delete', 'keep', 'invert', 'rename'} + command_set = {'delete', 'keep', 'invert'} + + for original_predicate_curie, command in predicate_remap_config.items(): + assert len(command) == 1 + assert next(iter(command.keys())) in command_set + # Every predicate curie should get its own node. Otherwise add to this set to complain. + original_predicate_curies_not_in_nodes = set() + nodes_dict = dict() + for node_dict in graph['nodes']: + node_id = node_dict['id'] + knowledge_source = node_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(knowledge_source, None) + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_nodes.add(knowledge_source) + else: + infores_curie = infores_curie_dict['infores_curie'] + node_dict['knowledge_source'] = infores_curie + nodes_dict[node_id] = node_dict + edge_ctr = 0 + for edge_dict in graph['edges']: + edge_ctr += 1 + if edge_ctr % 1000000 == 0: + print('processing edge ' + str(edge_ctr) + ' out of ' + str(len(graph['edges']))) + # TODO: Add logic to handle "positively_regulates" changed to "regulates/ causes/ activity or abundance/ increased" + if drop_negated and edge_dict['negated']: + continue + original_predicate_label = edge_dict['relation_label'] + predicate_label = original_predicate_label + original_predicate_curie = edge_dict['original_predicate'] + predicate_curie = original_predicate_curie + # ** Double check meaning ** + if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: + record_of_original_predicate_curie_occurrences[original_predicate_curie] = True + pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) + else: + # there is a original predicate CURIE in the graph that is not in the config file + original_predicate_curies_not_in_config.add(original_predicate_curie) + pred_remap_info = {'keep': None} + assert pred_remap_info is not None + invert = False + get_new_rel_info = False + if pred_remap_info is None: + assert original_predicate_curie in original_predicate_curies_not_in_config + else: + if 'delete' in pred_remap_info: + continue + remap_subinfo = pred_remap_info.get('invert', None) + if remap_subinfo is not None: + invert = True + get_new_rel_info = True + else: + remap_subinfo = pred_remap_info.get('rename', None) + if remap_subinfo is None: + assert 'keep' in pred_remap_info + else: + get_new_rel_info = True + if get_new_rel_info: + predicate_label = remap_subinfo[0] + predicate_curie = remap_subinfo[1] # Gets the biolink predicate + if invert: + edge_dict['relation_label'] = 'INVERTED:' + original_predicate_label + new_object = edge_dict['subject'] + edge_dict['subject'] = edge_dict['object'] + edge_dict['object'] = new_object + edge_dict['predicate_label'] = predicate_label + # Delete negated edges and self edges except interacts_with,positively_regulates,inhibits,increase + # as defined in run-simplify.sh + # To Do: verify exception list complies with updates from Biolink 3.0 + if drop_self_edges_except is not None and \ + edge_dict['subject'] == edge_dict['object'] and \ + predicate_label not in drop_self_edges_except: + continue # see issue 743 + edge_dict['predicate'] = predicate_curie + # Sets biolink curie; remapping + if predicate_curie not in nodes_dict: + predicate_curie_prefix = predicate_curie.split(':')[0] + predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') + # Create list of curies to complain about if not in biolink + if predicate_uri_prefix == predicate_curie_prefix: + original_predicate_curies_not_in_nodes.add(predicate_curie) + knowledge_source = edge_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(knowledge_source, None) + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_edges.add(knowledge_source) + else: + infores_curie = infores_curie_dict['infores_curie'] + edge_dict['knowledge_source'] = [infores_curie] + # TODO: Update with additional properties + edge_key = edge_dict['subject'] + ' /// ' + predicate_label + ' /// ' + edge_dict['object'] + existing_edge = new_edges.get(edge_key, None) + # TODO: Update merging to handle semantic distinction between qualifiers + if existing_edge is not None: + existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + edge_dict['knowledge_source']))) + existing_edge['publications'] += edge_dict['publications'] + existing_edge['publications_info'].update(edge_dict['publications_info']) + else: + new_edges[edge_key] = edge_dict + # Releasing some memory + del graph['edges'] + del graph['nodes'] + graph['nodes'] = list(nodes_dict.values()) + del nodes_dict + graph['edges'] = list(new_edges.values()) + del new_edges + # Warnings for issues that came up + for original_predicate_curie in record_of_original_predicate_curie_occurrences: + if not record_of_original_predicate_curie_occurrences[original_predicate_curie]: + print('original predicate curie is in the config file but was not used in any edge in the graph: ' + original_predicate_curie, file=sys.stderr) + for original_predicate_curie in original_predicate_curies_not_in_nodes: + print('could not find a node for original predicate curie: ' + original_predicate_curie) + original_predicate_curies_not_in_config_for_iteration = list(original_predicate_curies_not_in_config) + for original_predicate_curie_not_in_config in original_predicate_curies_not_in_config_for_iteration: + if not original_predicate_curie_not_in_config.startswith(kg2_util.CURIE_PREFIX_BIOLINK + ':'): + print('original predicate curie is missing from the YAML config file: ' + original_predicate_curie_not_in_config, + file=sys.stderr) + else: + original_predicate_curies_not_in_config.remove(original_predicate_curie_not_in_config) + for knowledge_source_curies_not_in_config_node in knowledge_source_curies_not_in_config_nodes: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_node, + file=sys.stderr) + for knowledge_source_curies_not_in_config_edge in knowledge_source_curies_not_in_config_edges: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_edge, + file=sys.stderr) + if len(original_predicate_curies_not_in_config) > 0: + print("There are original predicate curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + exit(1) + if len(knowledge_source_curies_not_in_config_nodes) > 0: + print("There are nodes knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + exit(1) + if len(knowledge_source_curies_not_in_config_edges) > 0: + print("There are edges knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + exit(1) + update_date = datetime.now().strftime("%Y-%m-%d %H:%M") + version_file = open(args.versionFile, 'r') + build_name = str + # Add node to describe build + for line in version_file: + test_flag = "" + if test_mode: + test_flag = "-TEST" + build_name = "RTX KG" + line.rstrip() + test_flag + break + build_node = kg2_util.make_node(kg2_util.CURIE_PREFIX_RTX + ':' + 'KG2', + kg2_util.BASE_URL_RTX + 'KG2', + build_name, + kg2_util.BIOLINK_CATEGORY_INFORMATION_RESOURCE, + update_date, + kg2_util.CURIE_PREFIX_RTX + ':') + build_info = {'version': build_node['name'], 'timestamp_utc': build_node['update_date']} + pprint.pprint(build_info) + graph["build"] = build_info + graph["nodes"].append(build_node) + kg2_util.save_json(graph, output_file_name, test_mode) + del graph diff --git a/run-simplify.sh b/run-simplify.sh index 510d308f..89213c60 100755 --- a/run-simplify.sh +++ b/run-simplify.sh @@ -48,9 +48,9 @@ else echo "*** TEST MODE -- NO INCREMENT ***" fi -# TODO: Update self edge exception list for compliance with Biolink 3.0 +# TODO: Inhibits and increase are not in biolink model anymore - Find out what that should be now ${VENV_DIR}/bin/python3 -u ${CODE_DIR}/filter_kg_and_remap_predicates.py ${test_flag} --dropNegated \ - --dropSelfEdgesExcept interacts_with,positively_regulates,inhibits,increase \ + --dropSelfEdgesExcept interacts_with,regulates,inhibits,increase \ ${predicate_mapping_file} ${infores_mapping_file} ${curies_to_urls_file} ${input_json} \ ${output_json} ${local_version_filename} ${s3_cp_cmd} ${local_version_filename} s3://${s3_bucket_public}/${s3_version_filename} From c57344f9a63c8685a7c00994a88015970600bcf7 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 12 Aug 2022 14:46:29 -0700 Subject: [PATCH 026/127] #221 Changes for biolink 3.0 compliance --- filter_kg_and_remap_predicates.py | 85 ++++++++++++------- ...lter_kg_and_remap_predicates_DEPRECATED.py | 58 +++++-------- kg2_util.py | 9 ++ 3 files changed, 85 insertions(+), 67 deletions(-) rename filter_kg_and_remap_predicates_new.py => filter_kg_and_remap_predicates_DEPRECATED.py (83%) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index c44f8b4b..eb0ec0ad 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -20,10 +20,16 @@ import sys from datetime import datetime +# 1. What is the indicator for negation? +# - It's a prefix in the relation property in the edge... possibly. +# - Negated edges only come from SEMMEDDB, so we look in semmeddb_tuple_list_json_to_kg_json +# - A value on L209, the source relation checks and sets value +# 2. Instruction below "drop any edge if it is in between two SnoMedCT nodes" still needed? No + # - check for any input relation_labels that occur twice in the predicate-remap.yaml file # - rename script something like "filter_kg_and_remap_relation_labels.py" # - need to detect the command "keep" in the YAML file -# - drop edges with 'NEGATION' ? +# - drop edges with 'NEGATION' # - *don't* merge two edges if at least one of them has nonempty publication_info # - change 'xref' to skos:closeMatch (skos) # - drop any edge if it is in between two SnoMedCT nodes (optionally; use command-line option) @@ -35,7 +41,7 @@ def make_arg_parser(): arg_parser = argparse.ArgumentParser(description='filter_kg.py: filters and simplifies the KG2 knowledge grpah for the RTX system') arg_parser.add_argument('predicateRemapYaml', type=str, help="The YAML file describing how predicates should be remapped to simpler predicates") - arg_parser.add_argument('inforesRemapYaml', type=str, help="The YAML file describing how provided_by fields should be remapped to Translator infores curies") + arg_parser.add_argument('inforesRemapYaml', type=str, help="The YAML file describing how knowledge_source fields should be remapped to Translator infores curies") arg_parser.add_argument('curiesToURIFile', type=str, help="The file mapping CURIE prefixes to URI fragments") arg_parser.add_argument('inputFileJson', type=str, help="The input KG2 graph, in JSON format") arg_parser.add_argument('outputFileJson', type=str, help="The output KG2 graph, in JSON format") @@ -56,53 +62,72 @@ def make_arg_parser(): test_mode = args.test drop_negated = args.drop_negated drop_self_edges_except = args.drop_self_edges_except + if drop_self_edges_except is not None: assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) + # Config files + # safe load takes a yaml file and returns a dictionary predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) - map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) - # ** Not sure about this notation ** + + (map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name)) + [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] graph = kg2_util.load_json(input_file_name) new_edges = dict() # Create sets to handle knowledge sources original_predicate_curies_not_in_config = set() - provided_by_curies_not_in_config_nodes = set() - provided_by_curies_not_in_config_edges = set() - # ** Double check meaning ** + knowledge_source_curies_not_in_config_nodes = set() + knowledge_source_curies_not_in_config_edges = set() + + # This should not change because predicate_remap_config.keys() is still just original predicate curies record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in predicate_remap_config.keys()} - # To Do: Update command set - command_set = {'delete', 'keep', 'invert', 'rename'} + + # To Do: Update everything for rename/keep commands + # Old command set: {'delete', 'keep', 'invert', 'rename'} + command_set = {'delete', 'keep', 'invert'} + + # The length of the 'command' could be 1 if it just has the operation, such as with 'delete' + # or up to 4 if there is the operation, core predicate, qualified predicate, and qualifiers + # Verify that the operation is allowed for original_predicate_curie, command in predicate_remap_config.items(): - assert len(command) == 1 - assert next(iter(command.keys())) in command_set + assert len(command) in range(1, 5) + assert command["operation"] in command_set + # Every predicate curie should get its own node. Otherwise add to this set to complain. original_predicate_curies_not_in_nodes = set() nodes_dict = dict() for node_dict in graph['nodes']: node_id = node_dict['id'] - provided_by = node_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(provided_by, None) + knowledge_source = node_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(knowledge_source, None) if infores_curie_dict is None: - provided_by_curies_not_in_config_nodes.add(provided_by) + knowledge_source_curies_not_in_config_nodes.add(knowledge_source) else: infores_curie = infores_curie_dict['infores_curie'] node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict + edge_ctr = 0 + num_edges = len(graph['edges']) for edge_dict in graph['edges']: + # Print progress edge_ctr += 1 if edge_ctr % 1000000 == 0: - print('processing edge ' + str(edge_ctr) + ' out of ' + str(len(graph['edges']))) + print(f'Processing edge {str(edge_ctr)} out of {str(num_edges)}') + + # TODO: Add logic to handle "positively_regulates" changed to "regulates/ causes/ activity or abundance/ increased" if drop_negated and edge_dict['negated']: continue + original_predicate_label = edge_dict['relation_label'] predicate_label = original_predicate_label original_predicate_curie = edge_dict['original_predicate'] predicate_curie = original_predicate_curie + # ** Double check meaning ** if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: record_of_original_predicate_curie_occurrences[original_predicate_curie] = True pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) @@ -116,7 +141,7 @@ def make_arg_parser(): if pred_remap_info is None: assert original_predicate_curie in original_predicate_curies_not_in_config else: - if 'delete' in pred_remap_info: + if pred_remap_info['operation'] == 'delete': continue remap_subinfo = pred_remap_info.get('invert', None) if remap_subinfo is not None: @@ -144,25 +169,23 @@ def make_arg_parser(): edge_dict['subject'] == edge_dict['object'] and \ predicate_label not in drop_self_edges_except: continue # see issue 743 - edge_dict['predicate'] = predicate_curie # Sets biolink curie; remapping + edge_dict['predicate'] = predicate_curie if predicate_curie not in nodes_dict: predicate_curie_prefix = predicate_curie.split(':')[0] predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') # Create list of curies to complain about if not in biolink if predicate_uri_prefix == predicate_curie_prefix: original_predicate_curies_not_in_nodes.add(predicate_curie) - provided_by = edge_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(provided_by, None) + knowledge_source = edge_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(knowledge_source, None) if infores_curie_dict is None: - provided_by_curies_not_in_config_edges.add(provided_by) + knowledge_source_curies_not_in_config_edges.add(knowledge_source) else: infores_curie = infores_curie_dict['infores_curie'] edge_dict['knowledge_source'] = [infores_curie] - # TODO: Update with additional properties - edge_key = edge_dict['subject'] + ' /// ' + predicate_label + ' /// ' + edge_dict['object'] + edge_key = f'{edge_subject} {predicate} {predicate_qualifier} /// {edge_object}' existing_edge = new_edges.get(edge_key, None) - # TODO: Update merging to handle semantic distinction between qualifiers if existing_edge is not None: existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + edge_dict['knowledge_source']))) existing_edge['publications'] += edge_dict['publications'] @@ -189,20 +212,20 @@ def make_arg_parser(): file=sys.stderr) else: original_predicate_curies_not_in_config.remove(original_predicate_curie_not_in_config) - for provided_by_curies_not_in_config_node in provided_by_curies_not_in_config_nodes: - print('knowledge_source node curie is missing from the YAML config file: ' + provided_by_curies_not_in_config_node, + for knowledge_source_curies_not_in_config_node in knowledge_source_curies_not_in_config_nodes: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_node, file=sys.stderr) - for provided_by_curies_not_in_config_edge in provided_by_curies_not_in_config_edges: - print('knowledge_source node curie is missing from the YAML config file: ' + provided_by_curies_not_in_config_edge, + for knowledge_source_curies_not_in_config_edge in knowledge_source_curies_not_in_config_edges: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_edge, file=sys.stderr) if len(original_predicate_curies_not_in_config) > 0: print("There are original predicate curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) - if len(provided_by_curies_not_in_config_nodes) > 0: - print("There are nodes provided_by curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + if len(knowledge_source_curies_not_in_config_nodes) > 0: + print("There are nodes knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) - if len(provided_by_curies_not_in_config_edges) > 0: - print("There are edges provided_by curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + if len(knowledge_source_curies_not_in_config_edges) > 0: + print("There are edges knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') diff --git a/filter_kg_and_remap_predicates_new.py b/filter_kg_and_remap_predicates_DEPRECATED.py similarity index 83% rename from filter_kg_and_remap_predicates_new.py rename to filter_kg_and_remap_predicates_DEPRECATED.py index 124c54de..c44f8b4b 100644 --- a/filter_kg_and_remap_predicates_new.py +++ b/filter_kg_and_remap_predicates_DEPRECATED.py @@ -20,16 +20,10 @@ import sys from datetime import datetime -# 1. What is the indicator for negation? -# - It's a prefix in the relation property in the edge... possibly. -# - Negated edges only come from SEMMEDDB, so we look in semmeddb_tuple_list_json_to_kg_json -# - A value on L209, the source relation checks and sets value -# 2. Instruction below "drop any edge if it is in between two SnoMedCT nodes" still needed? No - # - check for any input relation_labels that occur twice in the predicate-remap.yaml file # - rename script something like "filter_kg_and_remap_relation_labels.py" # - need to detect the command "keep" in the YAML file -# - drop edges with 'NEGATION' +# - drop edges with 'NEGATION' ? # - *don't* merge two edges if at least one of them has nonempty publication_info # - change 'xref' to skos:closeMatch (skos) # - drop any edge if it is in between two SnoMedCT nodes (optionally; use command-line option) @@ -41,7 +35,7 @@ def make_arg_parser(): arg_parser = argparse.ArgumentParser(description='filter_kg.py: filters and simplifies the KG2 knowledge grpah for the RTX system') arg_parser.add_argument('predicateRemapYaml', type=str, help="The YAML file describing how predicates should be remapped to simpler predicates") - arg_parser.add_argument('inforesRemapYaml', type=str, help="The YAML file describing how knowledge_source fields should be remapped to Translator infores curies") + arg_parser.add_argument('inforesRemapYaml', type=str, help="The YAML file describing how provided_by fields should be remapped to Translator infores curies") arg_parser.add_argument('curiesToURIFile', type=str, help="The file mapping CURIE prefixes to URI fragments") arg_parser.add_argument('inputFileJson', type=str, help="The input KG2 graph, in JSON format") arg_parser.add_argument('outputFileJson', type=str, help="The output KG2 graph, in JSON format") @@ -62,32 +56,26 @@ def make_arg_parser(): test_mode = args.test drop_negated = args.drop_negated drop_self_edges_except = args.drop_self_edges_except - if drop_self_edges_except is not None: assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) - # Config files - # safe load takes a yaml file and returns a dictionary predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) - map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) - + # ** Not sure about this notation ** [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] graph = kg2_util.load_json(input_file_name) new_edges = dict() # Create sets to handle knowledge sources original_predicate_curies_not_in_config = set() - knowledge_source_curies_not_in_config_nodes = set() - knowledge_source_curies_not_in_config_edges = set() + provided_by_curies_not_in_config_nodes = set() + provided_by_curies_not_in_config_edges = set() + # ** Double check meaning ** record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in predicate_remap_config.keys()} - - # To Do: Update everything for rename/keep commands - # Old command set: {'delete', 'keep', 'invert', 'rename'} - command_set = {'delete', 'keep', 'invert'} - + # To Do: Update command set + command_set = {'delete', 'keep', 'invert', 'rename'} for original_predicate_curie, command in predicate_remap_config.items(): assert len(command) == 1 assert next(iter(command.keys())) in command_set @@ -96,10 +84,10 @@ def make_arg_parser(): nodes_dict = dict() for node_dict in graph['nodes']: node_id = node_dict['id'] - knowledge_source = node_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(knowledge_source, None) + provided_by = node_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(provided_by, None) if infores_curie_dict is None: - knowledge_source_curies_not_in_config_nodes.add(knowledge_source) + provided_by_curies_not_in_config_nodes.add(provided_by) else: infores_curie = infores_curie_dict['infores_curie'] node_dict['knowledge_source'] = infores_curie @@ -109,14 +97,12 @@ def make_arg_parser(): edge_ctr += 1 if edge_ctr % 1000000 == 0: print('processing edge ' + str(edge_ctr) + ' out of ' + str(len(graph['edges']))) - # TODO: Add logic to handle "positively_regulates" changed to "regulates/ causes/ activity or abundance/ increased" if drop_negated and edge_dict['negated']: continue original_predicate_label = edge_dict['relation_label'] predicate_label = original_predicate_label original_predicate_curie = edge_dict['original_predicate'] predicate_curie = original_predicate_curie - # ** Double check meaning ** if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: record_of_original_predicate_curie_occurrences[original_predicate_curie] = True pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) @@ -166,10 +152,10 @@ def make_arg_parser(): # Create list of curies to complain about if not in biolink if predicate_uri_prefix == predicate_curie_prefix: original_predicate_curies_not_in_nodes.add(predicate_curie) - knowledge_source = edge_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(knowledge_source, None) + provided_by = edge_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(provided_by, None) if infores_curie_dict is None: - knowledge_source_curies_not_in_config_edges.add(knowledge_source) + provided_by_curies_not_in_config_edges.add(provided_by) else: infores_curie = infores_curie_dict['infores_curie'] edge_dict['knowledge_source'] = [infores_curie] @@ -203,20 +189,20 @@ def make_arg_parser(): file=sys.stderr) else: original_predicate_curies_not_in_config.remove(original_predicate_curie_not_in_config) - for knowledge_source_curies_not_in_config_node in knowledge_source_curies_not_in_config_nodes: - print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_node, + for provided_by_curies_not_in_config_node in provided_by_curies_not_in_config_nodes: + print('knowledge_source node curie is missing from the YAML config file: ' + provided_by_curies_not_in_config_node, file=sys.stderr) - for knowledge_source_curies_not_in_config_edge in knowledge_source_curies_not_in_config_edges: - print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_edge, + for provided_by_curies_not_in_config_edge in provided_by_curies_not_in_config_edges: + print('knowledge_source node curie is missing from the YAML config file: ' + provided_by_curies_not_in_config_edge, file=sys.stderr) if len(original_predicate_curies_not_in_config) > 0: print("There are original predicate curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) - if len(knowledge_source_curies_not_in_config_nodes) > 0: - print("There are nodes knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + if len(provided_by_curies_not_in_config_nodes) > 0: + print("There are nodes provided_by curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) - if len(knowledge_source_curies_not_in_config_edges) > 0: - print("There are edges knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) + if len(provided_by_curies_not_in_config_edges) > 0: + print("There are edges provided_by curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) exit(1) update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') diff --git a/kg2_util.py b/kg2_util.py index 20b8a953..cda76525 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -692,6 +692,9 @@ def make_node(id: str, def make_edge_key(edge_dict: dict): return edge_dict['subject'] + '---' + \ edge_dict['original_predicate'] + '---' + \ + edge_dict['qualified_predicate'] + '---' + \ + edge_dict['qualified_object_aspect'] + '---' + \ + edge_dict['qualified_object_direction'] + '---' + \ edge_dict['object'] + '---' + \ edge_dict['knowledge_source'] @@ -700,6 +703,9 @@ def make_edge(subject_id: str, object_id: str, relation_curie: str, relation_label: str, + qualified_predicate: str, + qualified_object_aspect: str, + qualified_object_direction: str, knowledge_source: str, update_date: str = None): @@ -707,6 +713,9 @@ def make_edge(subject_id: str, 'object': object_id, 'relation_label': relation_label, 'original_predicate': relation_curie, + 'qualified_predicate': qualified_predicate, + 'qualified_object_aspect': qualified_object_aspect, + 'qualified_object_direction': qualified_object_direction, 'negated': False, 'publications': [], 'publications_info': {}, From 4b07b8b0aca9da986fe4fc050ac1740d579dd73c Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 12 Aug 2022 14:47:34 -0700 Subject: [PATCH 027/127] #221 Manually set next kg2 version to 2.8.0 --- update_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/update_version.py b/update_version.py index 562e52aa..6e29fb04 100755 --- a/update_version.py +++ b/update_version.py @@ -17,7 +17,7 @@ __email__ = '' __status__ = 'Prototype' -VERSION = '2.7.7' +VERSION = '2.8.0' VERSION_FILE = 'kg2-version.txt' From fe08e9e5bba5ba83e084b9467ac9e151a839ea39 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 12 Aug 2022 15:01:05 -0700 Subject: [PATCH 028/127] #221 Update filter_kg_and_remap_predicates.py --- filter_kg_and_remap_predicates.py | 56 ++++++++++++++++++++++++------- 1 file changed, 44 insertions(+), 12 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index eb0ec0ad..24693581 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -127,40 +127,53 @@ def make_arg_parser(): predicate_label = original_predicate_label original_predicate_curie = edge_dict['original_predicate'] predicate_curie = original_predicate_curie - # ** Double check meaning ** + if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: record_of_original_predicate_curie_occurrences[original_predicate_curie] = True pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) else: # there is a original predicate CURIE in the graph that is not in the config file original_predicate_curies_not_in_config.add(original_predicate_curie) - pred_remap_info = {'keep': None} + assert pred_remap_info is not None + invert = False get_new_rel_info = False + operation_not_allowed = {} + if pred_remap_info is None: assert original_predicate_curie in original_predicate_curies_not_in_config else: if pred_remap_info['operation'] == 'delete': continue - remap_subinfo = pred_remap_info.get('invert', None) - if remap_subinfo is not None: + elif pred_remap_info['operation'] == 'invert': invert = True get_new_rel_info = True + elif pred_remap_info['operation'] == 'keep': + get_new_rel_info = True else: - remap_subinfo = pred_remap_info.get('rename', None) - if remap_subinfo is None: - assert 'keep' in pred_remap_info - else: - get_new_rel_info = True + operation_not_allowed[predicate_curie] = pred_remap_info['operation'] + + qualified_predicate_curie = pred_remap_info.get('qualified_predicate', None) + qualifiers_dict = pred_remap_info.get('qualifiers', None) + + if qualifiers_dict is not None: + edge_dict['qualified_predicate'] = qualified_predicate_curie + qualified_predicate_object_aspect = qualifiers_dict.get('object aspect', None) + qualified_predicate_object_direction = qualifiers_dict.get('object direction', None) + if qualified_predicate_object_aspect is not None: + edge_dict['qualified_object_aspect'] = qualified_predicate_object_aspect + if qualified_predicate_object_direction is not None: + edge_dict['qualified_object_direction'] = qualified_predicate_object_direction if get_new_rel_info: - predicate_label = remap_subinfo[0] - predicate_curie = remap_subinfo[1] # Gets the biolink predicate + predicate_curie = pred_remap_info['core_predicate'] + if invert: edge_dict['relation_label'] = 'INVERTED:' + original_predicate_label new_object = edge_dict['subject'] edge_dict['subject'] = edge_dict['object'] edge_dict['object'] = new_object + edge_dict['predicate_label'] = predicate_label # Delete negated edges and self edges except interacts_with,positively_regulates,inhibits,increase # as defined in run-simplify.sh @@ -169,6 +182,7 @@ def make_arg_parser(): edge_dict['subject'] == edge_dict['object'] and \ predicate_label not in drop_self_edges_except: continue # see issue 743 + # Sets biolink curie; remapping edge_dict['predicate'] = predicate_curie if predicate_curie not in nodes_dict: @@ -177,6 +191,7 @@ def make_arg_parser(): # Create list of curies to complain about if not in biolink if predicate_uri_prefix == predicate_curie_prefix: original_predicate_curies_not_in_nodes.add(predicate_curie) + knowledge_source = edge_dict['knowledge_source'] infores_curie_dict = infores_remap_config.get(knowledge_source, None) if infores_curie_dict is None: @@ -184,10 +199,27 @@ def make_arg_parser(): else: infores_curie = infores_curie_dict['infores_curie'] edge_dict['knowledge_source'] = [infores_curie] + + edge_subject = edge_dict['subject'] + edge_object = edge_dict['object'] + + if qualified_predicate_curie: + predicate = " /// " + qualified_predicate_curie + else: + predicate = " /// " + predicate_curie + + predicate_qualifier = "" + if qualifiers_dict is not None: + if qualified_predicate_object_aspect: + predicate_qualifier = " /// " + qualified_predicate_object_aspect + if qualified_predicate_object_direction: + predicate_qualifier += f" /// {qualified_predicate_object_direction}" edge_key = f'{edge_subject} {predicate} {predicate_qualifier} /// {edge_object}' + existing_edge = new_edges.get(edge_key, None) if existing_edge is not None: - existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + edge_dict['knowledge_source']))) + existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + + edge_dict['knowledge_source']))) existing_edge['publications'] += edge_dict['publications'] existing_edge['publications_info'].update(edge_dict['publications_info']) else: From 21a933ce1863e5ff14ee8f896547267a4d406adb Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 12 Aug 2022 15:15:52 -0700 Subject: [PATCH 029/127] #221 Update biolink version --- master-config.shinc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/master-config.shinc b/master-config.shinc index b03bc52a..e1e20999 100644 --- a/master-config.shinc +++ b/master-config.shinc @@ -18,4 +18,4 @@ infores_mapping_file=${CODE_DIR}/kg2-provided-by-curie-to-infores-curie.yaml ont_load_inventory_file=${CODE_DIR}/ont-load-inventory${test_suffix}.yaml umls2rdf_config_master=${CODE_DIR}/umls2rdf-umls.conf rtx_config_file=RTXConfiguration-config.json -biolink_model_version=2.2.11 +biolink_model_version=3.0.0 From 4c4e786d1ea208a926026113d9d5d464e09a5913 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 09:29:11 -0700 Subject: [PATCH 030/127] #226 #227 Update requirements-kg2-build.txt --- requirements-kg2-build.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-kg2-build.txt b/requirements-kg2-build.txt index 9b4e767f..8cfae5f0 100644 --- a/requirements-kg2-build.txt +++ b/requirements-kg2-build.txt @@ -36,7 +36,7 @@ requests==2.25.1 scipy==1.2.1 six==1.12.0 snakemake==5.5.4 -SPARQLWrapper==1.8.4 +SPARQLWrapper==1.8.5 urllib3>=1.25.9 watchdog==0.9.0 xmltodict==0.12.0 From 8c8a5e548d9ca9030ea1993a0d85f691e6fe0ed8 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 09:34:28 -0700 Subject: [PATCH 031/127] #226 #228 update requirements-kg2-build.txt --- requirements-kg2-build.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-kg2-build.txt b/requirements-kg2-build.txt index 8cfae5f0..89933c83 100644 --- a/requirements-kg2-build.txt +++ b/requirements-kg2-build.txt @@ -3,7 +3,7 @@ CacheControl==0.12.6 cachier==1.2.5 certifi==2019.3.9 chardet==3.0.4 -Click==7.0 +Click==8.0 conf==0.4. Cython==0.29.26 dataclasses==0.6 From bc8b5a1f67c8f67022f0ed756248da3bbda98531 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 14:21:37 -0700 Subject: [PATCH 032/127] #226 #229 Update run-validation-tests.sh --- run-validation-tests.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/run-validation-tests.sh b/run-validation-tests.sh index 95bf815e..82f47025 100755 --- a/run-validation-tests.sh +++ b/run-validation-tests.sh @@ -20,7 +20,7 @@ echo "================= starting run-validation-tests.sh =================" date biolink_base_url_no_version=https://raw.githubusercontent.com/biolink/biolink-model/ -biolink_raw_base_url=${biolink_base_url_no_version}${biolink_model_version}/ +biolink_raw_base_url=${biolink_base_url_no_version}v${biolink_model_version}/ curies_urls_map_replace_string="\ biolink_download_source: ${biolink_raw_base_url}" ont_load_inventory_replace_string="\ url: ${biolink_raw_base_url}" biolink_url_context_jsonld=${biolink_raw_base_url}context.jsonld From d0334399f9c8bb3e4d6b043d8094fbd077841bd6 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 14:33:44 -0700 Subject: [PATCH 033/127] #226 #229 update curies-to-urls-map.yaml --- curies-to-urls-map.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index 9317bd6d..cc9a61a4 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -633,6 +633,8 @@ use_for_contraction_only: NCBIGene: http://www.ncbi.nlm.nih.gov/gene/ - NCBITaxon: http://purl.bioontology.org/ontology/NCBITAXON/ + - + NCBITaxon: http://purl.obolibrary.org/obo/ncbitaxon# - NCIT: http://purl.bioontology.org/ontology/NCI/ - @@ -689,8 +691,6 @@ use_for_contraction_only: SNOMED: http://identifiers.org/snomedct/ - SO: http://purl.obolibrary.org/obo/so# - - - NCBITaxon: http://purl.obolibrary.org/obo/ncbitaxon# - UBERON: http://purl.obolibrary.org/obo/uberon/insect-anatomy# - From 4021e88a95351a5cf7938e79f0817a319d001dc6 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 15:18:13 -0700 Subject: [PATCH 034/127] #226 #229 update curies-to-urls-map.yaml --- curies-to-urls-map.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index cc9a61a4..54ad88cf 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -313,8 +313,10 @@ use_for_bidirectional_mapping: NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#' - NCBIGene: 'http://identifiers.org/ncbigene/' - - - NCBITaxon: 'http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl' +# - +# NCBITaxon: 'http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl' + - + NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ - NCIT: "https://identifiers.org/ncit:" - @@ -455,8 +457,6 @@ use_for_bidirectional_mapping: SWO: http://www.ebi.ac.uk/swo/ - SYMP: http://purl.obolibrary.org/obo/SYMP_ - - - NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ - TO: http://purl.obolibrary.org/obo/TO_ - From 708b708cc9dac036b0a8d9020ff01c3439ec5a51 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 15:30:58 -0700 Subject: [PATCH 035/127] #226 #229 Corrections for validation test error --- curies-to-urls-map.yaml | 2 +- kg2_util.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index 54ad88cf..6028f887 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -102,7 +102,7 @@ use_for_bidirectional_mapping: - DDANAT: http://purl.obolibrary.org/obo/DDANAT_ - - DGIdb: https://www.dgidb.org/interaction_types + DGIdb: https://www.dgidb.org/interaction_types/ - dictybase.gene: "https://identifiers.org/dictybase.gene:" - diff --git a/kg2_util.py b/kg2_util.py index cda76525..f55c3748 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -132,7 +132,7 @@ BASE_URL_CHEMBL_TARGET = BASE_BASE_URL_IDENTIFIERS_ORG + 'chembl.target:' BASE_URL_CHEMBL_MECHANISM = 'https://www.ebi.ac.uk/chembl#' BASE_URL_CLINICALTRIALS = BASE_BASE_URL_IDENTIFIERS_ORG + 'clinicaltrials:' -BASE_URL_DGIDB = 'http://www.dgidb.org/' +BASE_URL_DGIDB = 'https://www.dgidb.org/' BASE_URL_DISGENET = 'http://www.disgenet.org' BASE_URL_DRUGBANK = BASE_BASE_URL_IDENTIFIERS_ORG + 'drugbank:' BASE_URL_DRUGCENTRAL = 'https://drugcentral.org/drugcard/' From 6862196efc9089afc4834c93f275d3f7f5c516db Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 15:47:23 -0700 Subject: [PATCH 036/127] #226 #229 Updates to predicate-remap --- ...ap.yaml => predicate-remap_DEPRECATED.yaml | 0 predicate_remap.yaml | 5439 +++++++++++++++++ predicate_remap_new.yaml | 4019 ------------ validate_predicate_remap_yaml.py | 2 + 4 files changed, 5441 insertions(+), 4019 deletions(-) rename predicate-remap.yaml => predicate-remap_DEPRECATED.yaml (100%) create mode 100644 predicate_remap.yaml delete mode 100644 predicate_remap_new.yaml diff --git a/predicate-remap.yaml b/predicate-remap_DEPRECATED.yaml similarity index 100% rename from predicate-remap.yaml rename to predicate-remap_DEPRECATED.yaml diff --git a/predicate_remap.yaml b/predicate_remap.yaml new file mode 100644 index 00000000..ea50289e --- /dev/null +++ b/predicate_remap.yaml @@ -0,0 +1,5439 @@ +BFO:0000050: + operation: invert + core_predicate: biolink:has_part +BFO:0000051: + operation: keep + core_predicate: biolink:has_part +BFO:0000054: + operation: keep + core_predicate: biolink:related_to +BFO:0000055: + operation: keep + core_predicate: biolink:has_part +BFO:0000056: + operation: invert + core_predicate: biolink:has_participant +BFO:0000062: + operation: invert + core_predicate: biolink:precedes +BFO:0000063: + operation: keep + core_predicate: biolink:precedes +BFO:0000066: + operation: keep + core_predicate: biolink:occurs_in +BFO:0000067: + operation: keep + core_predicate: biolink:occurs_in +BFO:0000068: + operation: keep + core_predicate: biolink:related_to +BFO:0000069: + operation: keep + core_predicate: biolink:related_to +BFO:0000117: + operation: keep + core_predicate: biolink:has_part +BFO:0000167: + operation: keep + core_predicate: biolink:has_participant +BSPO:0000096: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000097: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000098: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000099: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000100: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000102: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000104: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000107: + operation: keep + core_predicate: biolink:located_in +BSPO:0000108: + operation: keep + core_predicate: biolink:located_in +BSPO:0000110: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000113: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0000120: + operation: keep + core_predicate: biolink:located_in +BSPO:0000121: + operation: keep + core_predicate: biolink:located_in +BSPO:0000122: + operation: keep + core_predicate: biolink:located_in +BSPO:0000123: + operation: keep + core_predicate: biolink:located_in +BSPO:0000124: + operation: keep + core_predicate: biolink:located_in +BSPO:0000125: + operation: keep + core_predicate: biolink:located_in +BSPO:0000126: + operation: keep + core_predicate: biolink:located_in +BSPO:0001100: + operation: keep + core_predicate: biolink:located_in +BSPO:0001101: + operation: keep + core_predicate: biolink:located_in +BSPO:0001106: + operation: invert + core_predicate: biolink:has_part +BSPO:0001107: + operation: keep + core_predicate: biolink:located_in +BSPO:0001108: + operation: invert + core_predicate: biolink:has_part +BSPO:0001113: + operation: invert + core_predicate: biolink:has_part +BSPO:0001115: + operation: invert + core_predicate: biolink:has_part +BSPO:0005001: + operation: keep + core_predicate: biolink:overlaps +BSPO:0015001: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015002: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015003: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015005: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015006: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015007: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015008: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015009: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015012: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015014: + operation: keep + core_predicate: biolink:coexists_with +BSPO:0015101: + operation: keep + core_predicate: biolink:located_in +BSPO:0015102: + operation: keep + core_predicate: biolink:located_in +BSPO:0015202: + operation: keep + core_predicate: biolink:located_in +BSPO:parallel_to: + operation: keep + core_predicate: biolink:coexists_with +BTO:develops_from: + operation: keep + core_predicate: biolink:develops_from +BTO:related_to: + operation: keep + core_predicate: biolink:related_to +CHEBI:25212: + operation: invert + core_predicate: biolink:has_metabolite +CHEBI:has_functional_parent: + operation: keep + core_predicate: biolink:chemically_similar_to +CHEBI:has_parent_hydride: + operation: keep + core_predicate: biolink:subclass_of +CHEBI:is_conjugate_acid_of: + operation: keep + core_predicate: biolink:related_to +CHEBI:is_conjugate_base_of: + operation: keep + core_predicate: biolink:related_to +CHEBI:is_enantiomer_of: + operation: keep + core_predicate: biolink:close_match +CHEBI:is_substituent_group_from: + operation: invert + core_predicate: biolink:has_part +CHEBI:is_tautomer_of: + operation: keep + core_predicate: biolink:close_match +CHEMBL.MECHANISM:activator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +CHEMBL.MECHANISM:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:allosteric_antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antisense_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +CHEMBL.MECHANISM:binding_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:blocker: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:chelating_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:cross-linking_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:degrader: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:disrupting_agent: + operation: keep + core_predicate: biolink:disrupts +CHEMBL.MECHANISM:equivalent_to: + operation: keep + core_predicate: biolink:same_as +CHEMBL.MECHANISM:hydrolytic_enzyme: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:inhibitor: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:modulator: + operation: keep + core_predicate: biolink:regulates +CHEMBL.MECHANISM:negative_allosteric_modulator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:negative_modulator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +CHEMBL.MECHANISM:opener: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:other: + operation: delete +CHEMBL.MECHANISM:overlaps_with: + operation: keep + core_predicate: biolink:overlaps +CHEMBL.MECHANISM:oxidative_enzyme: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:partial_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:positive_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:positive_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +CHEMBL.MECHANISM:proteolytic_enzyme: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CHEMBL.MECHANISM:reducing_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:releasing_agent: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +CHEMBL.MECHANISM:rnai_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +CHEMBL.MECHANISM:sequestering_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:stabiliser: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: increased +CHEMBL.MECHANISM:subset_of: + operation: keep + core_predicate: biolink:subclass_of +CHEMBL.MECHANISM:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:superset_of: + operation: invert + core_predicate: biolink:subclass_of +CL:has_completed: + operation: keep + core_predicate: biolink:has_completed +CL:has_high_plasma_membrane_amount: + operation: keep + core_predicate: biolink:has_increased_amount +CL:has_low_plasma_membrane_amount: + operation: keep + core_predicate: biolink:has_decreased_amount +CL:has_not_completed: + operation: keep + core_predicate: biolink:has_not_completed +CL:lacks_part: + operation: keep + core_predicate: biolink:lacks_part +CL:lacks_plasma_membrane_part: + operation: keep + core_predicate: biolink:lacks_part +CPT:has_add_on_code: + operation: keep + core_predicate: biolink:related_to +CPT:mapped_to: + operation: keep + core_predicate: biolink:related_to +CPT:panel_element_of: + operation: invert + core_predicate: biolink:has_part +CPT:panel_element_of_possibly_included: + operation: invert + core_predicate: biolink:has_part +CTD:affects_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +CTD:affects_abundance_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: abundance +CTD:affects_acetylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_acylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_alkylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_amination: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_binding: + operation: keep + core_predicate: biolink:directly_interacts_with +CTD:affects_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_carboxylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_cleavage: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_degradation_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_ethylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_export: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +CTD:affects_farnesylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_folding_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: folding +CTD:affects_geranoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glycation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_glycosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +CTD:affects_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_import: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +CTD:affects_lipidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_methylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: mutation_rate +CTD:affects_myristoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_nitrosation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_oxidation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_prenylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_reduction: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_response_to: + operation: invert + core_predicate: biolink:response_affected_by +CTD:affects_ribosylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_secretion_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: secretion +CTD:affects_splicing_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: splicing +CTD:affects_sulfation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_sumoylation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_synthesis_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: synthesis +CTD:affects_transport_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +CTD:affects_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: molecular_modification +CTD:affects_uptake_of: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: uptake +CTD:decreases_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +CTD:decreases_acetylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_acylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_alkylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_amination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_carboxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_cleavage: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_degradation_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_ethylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_export: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +CTD:decreases_farnesylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_folding_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: decreased +CTD:decreases_geranoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glycation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: decreased +CTD:decreases_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_import: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +CTD:decreases_lipidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_localization_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +CTD:decreases_metabolic_processing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: decreased +CTD:decreases_methylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_molecular_interaction_with: + operation: keep + core_predicate: biolink:decreases_molecular_interaction +CTD:decreases_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_mutagenesis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +CTD:decreases_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: decreased +CTD:decreases_myristoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_nitrosation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_oxidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_prenylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_reduction: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_response_to: + operation: keep + core_predicate: biolink:decreases_response_to +CTD:decreases_response_to_substance: + operation: keep + core_predicate: biolink:decreases_response_to +CTD:decreases_ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_secretion_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: decreased +CTD:decreases_splicing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: decreased +CTD:decreases_stability_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: decreased +CTD:decreases_sulfation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_sumoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_transport_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: transport + - object_direction: decreased +CTD:decreases_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +CTD:decreases_uptake_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: decreased +CTD:increases_ADP-ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_N-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_O-linked_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_RNA_splicing: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +CTD:increases_acetylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_acylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_alkylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_amination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_carbamoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_carboxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_cleavage: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CTD:increases_ethylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_export: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +CTD:increases_farnesylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_folding_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: folding + - object_direction: increased +CTD:increases_geranoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glucuronidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glutathionylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glycation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_glycosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_hydrolysis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +CTD:increases_hydroxylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_import: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +CTD:increases_lipidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_localization_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +CTD:increases_metabolic_processing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +CTD:increases_methylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_molecular_interaction_with: + operation: keep + core_predicate: biolink:increases_molecular_interaction +CTD:increases_molecular_modification_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_mutagenesis: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +CTD:increases_mutation_rate_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: mutation_rate + - object_direction: increased +CTD:increases_myristoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_nitrosation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_nucleotidylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_oxidation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_palmitoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_phosphorylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_prenylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_reduction: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_response_to: + operation: keep + core_predicate: biolink:increases_response_to +CTD:increases_ribosylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_secretion_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: secretion + - object_direction: increased +CTD:increases_splicing_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: splicing + - object_direction: increased +CTD:increases_sulfation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_sumoylation: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_synthesis_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: synthesis + - object_direction: increased +CTD:increases_ubiquitination: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +CTD:increases_uptake_of: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: uptake + - object_direction: increased +CTD:inferred: + operation: keep + core_predicate: biolink:affects +CTD:marker_mechanism: + operation: keep + core_predicate: biolink:contributes_to +CTD:negative_correlation: + operation: keep + core_predicate: biolink:negatively_correlated_with +CTD:positive_correlation: + operation: keep + core_predicate: biolink:positively_correlated_with +CTD:prediction_hypothesis: + operation: keep + core_predicate: biolink:affects +DDANAT:develops_from: + operation: keep + core_predicate: biolink:develops_from +DGIdb:activator: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +DGIdb:adduct: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:affects: + operation: keep + core_predicate: biolink:affects +DGIdb:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DGIdb:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:antibody: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DGIdb:antisense_oligonucleotide: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +DGIdb:binder: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:blocker: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:channel_blocker: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:cleavage: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +DGIdb:cofactor: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:gating_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:inducer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:inhibitory_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:ligand: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DGIdb:multitarget: + operation: keep + core_predicate: biolink:directly_interacts_with +DGIdb:negative_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:partial_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:partial_antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:positive_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:potentiator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:product_of: + operation: keep + core_predicate: biolink:derives_from +DGIdb:stimulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DGIdb:substrate: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +DGIdb:suppressor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DGIdb:vaccine: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DOID-PROPERTY:derives_from: + operation: invert + core_predicate: biolink:derives_into +DOID-PROPERTY:has_symptom: + operation: keep + core_predicate: biolink:has_phenotype +DRUGBANK:activator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:adduct: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:aggregation_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DRUGBANK:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:antibody: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:antisense_oligonucleotide: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +DRUGBANK:atc-code: + operation: keep + core_predicate: biolink:close_match +DRUGBANK:atc-code-level: + operation: keep + core_predicate: biolink:related_to +DRUGBANK:binder: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:binding: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:blocker: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:category: + operation: keep + core_predicate: biolink:subclass_of +DRUGBANK:chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:chelator: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:cleavage: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +DRUGBANK:cofactor: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:component_of: + operation: invert + core_predicate: biolink:has_part +DRUGBANK:degradation: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +DRUGBANK:deoxidizer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: decreased +DRUGBANK:desensitize_the_target: + operation: keep + core_predicate: biolink:decreases_response_to +DRUGBANK:downregulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:drug-interaction: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:external-identifier: + operation: keep + core_predicate: biolink:same_as +DRUGBANK:external-identifier-protein: + operation: keep + core_predicate: biolink:derives_from +DRUGBANK:gene_replacement: + operation: keep + core_predicate: biolink:close_match +DRUGBANK:group: + operation: keep + core_predicate: biolink:related_to +DRUGBANK:inactivator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:incorporation_into_and_destabilization: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: degradation +DRUGBANK:inducer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:inhibition_of_synthesis: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:inhibitory_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:intercalation: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DRUGBANK:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:ligand: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:modulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DRUGBANK:multitarget: + operation: keep + core_predicate: biolink:directly_interacts_with +DRUGBANK:negative_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:neutralizer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:nucleotide_exchange_blocker: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:oxidizer: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: molecular_modification + - object_direction: increased +DRUGBANK:partial_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:partial_antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:pathway: + operation: invert + core_predicate: biolink:has_participant +DRUGBANK:positive_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:positive_modulator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DRUGBANK:potentiator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:product_of: + operation: keep + core_predicate: biolink:derives_from +DRUGBANK:regulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DRUGBANK:stabilization: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: stability + - object_direction: increased +DRUGBANK:stimulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DRUGBANK:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:suppressor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DRUGBANK:target: + operation: keep + core_predicate: biolink:physically_interacts_with +DRUGBANK:translocation_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DRUGBANK:treats: + operation: keep + core_predicate: biolink:treats +DRUGBANK:weak_inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:5271: + operation: keep + core_predicate: biolink:diagnoses +DrugCentral:PA: + operation: keep + core_predicate: biolink:subclass_of +DrugCentral:activator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DrugCentral:agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DrugCentral:allosteric_antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DrugCentral:allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: activity +DrugCentral:antagonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DrugCentral:antibody_binding: + operation: keep + core_predicate: biolink:molecularly_interacts_with +DrugCentral:antisense_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +DrugCentral:binding_agent: + operation: keep + core_predicate: biolink:directly_interacts_with +DrugCentral:blocker: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:contraindication: + operation: keep + core_predicate: biolink:contraindicated_for +DrugCentral:gating_inhibitor: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DrugCentral:has_role: + operation: keep + core_predicate: biolink:related_to +DrugCentral:indication: + operation: keep + core_predicate: biolink:treats +DrugCentral:inhibitor: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:inverse_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +DrugCentral:modulator: + operation: keep + core_predicate: biolink:entity_regulates_entity +DrugCentral:negative_allosteric_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:negative_modulator: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +DrugCentral:off-label_use: + operation: keep + core_predicate: biolink:treats +DrugCentral:opener: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DrugCentral:partial_agonist: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DrugCentral:pharmacological_chaperone: + operation: keep + core_predicate: biolink:directly_interacts_with +DrugCentral:positive_allosteric_modulator: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: increased +DrugCentral:positive_modulator: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +DrugCentral:releasing_agent: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +DrugCentral:struct2atc: + operation: keep + core_predicate: biolink:close_match +DrugCentral:substrate: + operation: keep + core_predicate: biolink:physically_interacts_with +DrugCentral:symptomatic_treatment: + operation: keep + core_predicate: biolink:treats +EFO:0000784: + operation: keep + core_predicate: biolink:located_in +EFO:0001697: + operation: invert + core_predicate: biolink:related_to +EFO:0006351: + operation: keep + core_predicate: biolink:related_to +EFO:is_executed_in: + operation: keep + core_predicate: biolink:related_to +ENVO:01001307: + operation: keep + core_predicate: biolink:coexists_with +FMA:SIB: + operation: delete +FMA:adheres_to: + operation: keep + core_predicate: biolink:physically_interacts_with +FMA:adjacent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:afferent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anatomical_entity_observed_in: + operation: delete +FMA:anterior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anteroinferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anterolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anteromedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:anterosuperior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:arterial_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:articulates_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:attaches_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:bounded_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:bounds: + operation: keep + core_predicate: biolink:coexists_with +FMA:branch_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:connected_to: + operation: keep + core_predicate: biolink:related_to +FMA:connection_type_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:constitutional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:contained_in: + operation: invert + core_predicate: biolink:has_part +FMA:contains: + operation: keep + core_predicate: biolink:has_part +FMA:continuation_branch_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_distally_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_proximally_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:continuous_with: + operation: keep + core_predicate: biolink:related_to +FMA:corresponds_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:derives: + operation: invert + core_predicate: biolink:derives_from +FMA:derives_from: + operation: invert + core_predicate: biolink:derives_into +FMA:development_type_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:developmental_stage_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:develops_from: + operation: keep + core_predicate: biolink:develops_from +FMA:develops_into: + operation: keep + core_predicate: biolink:develops_from +FMA:direct_cell_shape_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:direct_left_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:direct_right_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:distal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:drains_into: + operation: keep + core_predicate: biolink:coexists_with +FMA:efferent_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:external_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:formed_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:forms: + operation: keep + core_predicate: biolink:coexists_with +FMA:full_grown_phenotype_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:fuses_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:fusion_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:germ_origin_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_adherent: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_arterial_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_branch: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_connection_type: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_constitutional_part: + operation: keep + core_predicate: biolink:has_part +FMA:has_continuation_branch: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_development_type: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_developmental_stage: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_direct_cell_shape: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_full_grown_phenotype: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_fusion: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_germ_origin: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_inherent_3d_shape: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_insertion: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_location: + operation: keep + core_predicate: biolink:located_in +FMA:has_lymphatic_drainage: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_member: + operation: keep + core_predicate: biolink:has_part +FMA:has_nerve_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_observed_anatomical_entity: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_origin: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_part: + operation: keep + core_predicate: biolink:has_part +FMA:has_primary_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_projection: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_regional_part: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_related_developmental_entity: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_secondary_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_segmental_composition: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_segmental_supply: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_tributary: + operation: keep + core_predicate: biolink:coexists_with +FMA:has_venous_drainage: + operation: keep + core_predicate: biolink:coexists_with +FMA:homonym_for: + operation: delete +FMA:homonym_of: + operation: keep + core_predicate: biolink:related_to +FMA:inferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inferolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inferomedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:inherent_3d_shape_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:insertion_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:internal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:left_lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:left_medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:location_of: + operation: invert + core_predicate: biolink:located_in +FMA:lymphatic_drainage_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:matures_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:matures_into: + operation: keep + core_predicate: biolink:coexists_with +FMA:medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:member_of: + operation: invert + core_predicate: biolink:has_part +FMA:merges_with: + operation: keep + core_predicate: biolink:coexists_with +FMA:nerve_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:origin_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:part_of: + operation: invert + core_predicate: biolink:has_part +FMA:posterior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posteroinferior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posterolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posteromedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:posterosuperior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:primary_segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:projects_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:projects_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:proximal_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_attachment_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_drainage_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_input_from: + operation: keep + core_predicate: biolink:coexists_with +FMA:receives_projection: + operation: keep + core_predicate: biolink:coexists_with +FMA:regional_part_of: + operation: invert + core_predicate: biolink:has_part +FMA:related_developmental_entity_of: + operation: keep + core_predicate: biolink:related_to +FMA:related_object: + operation: keep + core_predicate: biolink:related_to +FMA:related_part: + operation: keep + core_predicate: biolink:coexists_with +FMA:right_lateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:right_medial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:secondary_segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:segmental_composition_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:segmental_supply_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:sends_output_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superior_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superolateral_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:superomedial_to: + operation: keep + core_predicate: biolink:coexists_with +FMA:surrounded_by: + operation: keep + core_predicate: biolink:coexists_with +FMA:surrounds: + operation: keep + core_predicate: biolink:coexists_with +FMA:transforms_from: + operation: invert + core_predicate: biolink:precedes +FMA:transforms_into: + operation: keep + core_predicate: biolink:precedes +FMA:tributary_of: + operation: keep + core_predicate: biolink:coexists_with +FMA:venous_drainage_of: + operation: keep + core_predicate: biolink:coexists_with +FOODON:00001301: + operation: keep + core_predicate: biolink:model_of +FOODON:00001563: + operation: keep + core_predicate: biolink:has_part +FOODON:00002420: + operation: keep + core_predicate: biolink:has_part +GENEPIO:0001739: + operation: invert + core_predicate: biolink:precedes +GENO:0000382: + operation: keep + core_predicate: biolink:has_variant_part +GENO:0000790: + operation: keep + core_predicate: biolink:related_condition +GENO:0000840: + operation: keep + core_predicate: biolink:gene_associated_with_condition +GENO:0000841: + operation: keep + core_predicate: biolink:gene_associated_with_condition +GO:SIB: + operation: delete +GO:acts_upstream_of: + operation: keep + core_predicate: biolink:affects +GO:acts_upstream_of_negative_effect: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within: + operation: keep + core_predicate: biolink:affects +GO:acts_upstream_of_or_within_negative_effect: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:acts_upstream_of_or_within_positive_effect: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:acts_upstream_of_positive_effect: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:colocalizes_with: + operation: keep + core_predicate: biolink:colocalizes_with +GO:contributes_to: + operation: keep + core_predicate: biolink:contributes_to +GO:enables: + operation: keep + core_predicate: biolink:enables +GO:ends_during: + operation: keep + core_predicate: biolink:related_to +GO:happens_during: + operation: keep + core_predicate: biolink:related_to +GO:has_occurrence: + operation: keep + core_predicate: biolink:capable_of +GO:has_part: + operation: keep + core_predicate: biolink:has_part +GO:inverse_ends_during: + operation: keep + core_predicate: biolink:related_to +GO:inverse_happens_during: + operation: delete +GO:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +GO:involved_in: + operation: invert + core_predicate: biolink:has_participant +GO:is_active_in: + operation: keep + core_predicate: biolink:actively_involved_in +GO:isa: + operation: keep + core_predicate: biolink:subclass_of +GO:located_in: + operation: keep + core_predicate: biolink:located_in +GO:negatively_regulated_by: + operation: invert + core_predicate: biolink:entity_negatively_regulates_entity +GO:negatively_regulates: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +GO:occurs_in: + operation: keep + core_predicate: biolink:occurs_in +GO:part_of: + operation: invert + core_predicate: biolink:has_part +GO:positively_regulated_by: + operation: invert + core_predicate: biolink:entity_positively_regulates_entity +GO:positively_regulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +GO:regulated_by: + operation: invert + core_predicate: biolink:entity_regulates_entity +GO:regulates: + operation: keep + core_predicate: biolink:entity_regulates_entity +GOREL:0000040: + operation: keep + core_predicate: biolink:causes +GOREL:0001004: + operation: keep + core_predicate: biolink:located_in +GOREL:0001006: + operation: keep + core_predicate: biolink:affects +GOREL:0002003: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: localization +GOREL:0002004: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: degradation + - object_direction: increased +GOREL:0002005: + operation: keep + core_predicate: biolink:related_to +GOREL:0012006: + operation: keep + core_predicate: biolink:related_to +GTEx:affects_expression_in: + operation: keep + core_predicate: biolink:affects +HANCESTRO:0301: + operation: keep + core_predicate: biolink:related_to +HANCESTRO:0308: + operation: keep + core_predicate: biolink:related_to +HANCESTRO:0330: + operation: keep + core_predicate: biolink:related_to +HCPCS:mapped_from: + operation: delete +HCPCS:mapped_to: + operation: keep + core_predicate: biolink:related_to +HMDB:at_cellular_location: + operation: keep + core_predicate: biolink:located_in +HMDB:at_tissue: + operation: keep + core_predicate: biolink:located_in +HMDB:disease: + operation: keep + core_predicate: biolink:related_to +HMDB:has_protein_association: + operation: keep + core_predicate: biolink:related_to +HMDB:in_biospecimen: + operation: keep + core_predicate: biolink:located_in +HMDB:in_pathway: + operation: invert + core_predicate: biolink:has_participant +HP:SIB: + operation: delete +IAO:0000039: + operation: keep + core_predicate: biolink:related_to +IAO:0000136: + operation: keep + core_predicate: biolink:related_to +IAO:0000142: + operation: keep + core_predicate: biolink:mentions +IAO:0000219: + operation: keep + core_predicate: biolink:related_to +ICD10PCS:SIB: + operation: delete +ICD9:SIB: + operation: delete +IDO:0000664: + operation: invert + core_predicate: biolink:contributes_to +JensenLab:associated_with: + operation: keep + core_predicate: biolink:gene_associated_with_condition +KEGG:compound_to_enzyme: + operation: keep + core_predicate: biolink:interacts_with +KEGG:compound_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:compound_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:enzyme_to_reaction: + operation: keep + core_predicate: biolink:catalyzes +KEGG:glycan_to_enzyme: + operation: keep + core_predicate: biolink:interacts_with +KEGG:glycan_to_pathway: + operation: invert + core_predicate: biolink:has_participant +KEGG:glycan_to_reaction: + operation: invert + core_predicate: biolink:has_participant +KEGG:pathway_to_compound: + operation: keep + core_predicate: biolink:has_participant +KEGG:pathway_to_drug: + operation: keep + core_predicate: biolink:has_participant +KEGG:pathway_to_glycan: + operation: keep + core_predicate: biolink:has_participant +KEGG:reaction_to_enzyme: + operation: invert + core_predicate: biolink:catalyzes +KEGG:reaction_to_pathway: + operation: invert + core_predicate: biolink:has_participant +LOINC:adjustment_of: + operation: delete +LOINC:analyzed_by: + operation: delete +LOINC:analyzes: + operation: keep + core_predicate: biolink:related_to +LOINC:answer_to: + operation: delete +LOINC:archetype_of: + operation: delete +LOINC:associated_with: + operation: keep + core_predicate: biolink:correlated_with +LOINC:challenge_of: + operation: delete +LOINC:class_of: + operation: keep + core_predicate: biolink:subclass_of +LOINC:component_of: + operation: invert + core_predicate: biolink:has_part +LOINC:count_of: + operation: delete +LOINC:divisor_of: + operation: delete +LOINC:evaluation_of: + operation: delete +LOINC:fragments_for_synonyms_of: + operation: delete +LOINC:has_action_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_adjustment: + operation: keep + core_predicate: biolink:related_to +LOINC:has_aggregation_view: + operation: keep + core_predicate: biolink:related_to +LOINC:has_answer: + operation: keep + core_predicate: biolink:related_to +LOINC:has_approach_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_archetype: + operation: keep + core_predicate: biolink:subclass_of +LOINC:has_challenge: + operation: keep + core_predicate: biolink:related_to +LOINC:has_class: + operation: invert + core_predicate: biolink:subclass_of +LOINC:has_component: + operation: keep + core_predicate: biolink:has_part +LOINC:has_count: + operation: keep + core_predicate: biolink:related_to +LOINC:has_divisor: + operation: keep + core_predicate: biolink:related_to +LOINC:has_evaluation: + operation: keep + core_predicate: biolink:related_to +LOINC:has_exam: + operation: keep + core_predicate: biolink:related_to +LOINC:has_fragments_for_synonyms: + operation: keep + core_predicate: biolink:has_input +LOINC:has_given_pharmaceutical_substance: + operation: delete +LOINC:has_imaged_location: + operation: keep + core_predicate: biolink:occurs_in +LOINC:has_imaging_focus: + operation: keep + core_predicate: biolink:located_in +LOINC:has_lateral_anatomic_location: + operation: keep + core_predicate: biolink:coexists_with +LOINC:has_lateral_location_presence: + operation: keep + core_predicate: biolink:coexists_with +LOINC:has_loinc_number: + operation: delete +LOINC:has_member: + operation: keep + core_predicate: biolink:has_part +LOINC:has_method: + operation: keep + core_predicate: biolink:related_to +LOINC:has_modality_subtype: + operation: keep + core_predicate: biolink:related_to +LOINC:has_modality_type: + operation: keep + core_predicate: biolink:related_to +LOINC:has_multipart: + operation: delete +LOINC:has_object_guidance: + operation: keep + core_predicate: biolink:related_to +LOINC:has_parent_group: + operation: keep + core_predicate: biolink:subclass_of +LOINC:has_pharmaceutical_route: + operation: keep + core_predicate: biolink:related_to +LOINC:has_presence_guidance: + operation: delete +LOINC:has_property: + operation: delete +LOINC:has_scale: + operation: keep + core_predicate: biolink:related_to +LOINC:has_subject: + operation: keep + core_predicate: biolink:has_participant +LOINC:has_suffix: + operation: keep + core_predicate: biolink:related_to +LOINC:has_supersystem: + operation: invert + core_predicate: biolink:has_part +LOINC:has_system: + operation: keep + core_predicate: biolink:has_input +LOINC:has_time_aspect: + operation: keep + core_predicate: biolink:related_to +LOINC:has_time_modifier: + operation: keep + core_predicate: biolink:related_to +LOINC:has_timing_of: + operation: keep + core_predicate: biolink:related_to +LOINC:has_view_type: + operation: keep + core_predicate: biolink:related_to +LOINC:is_action_guidance_for: + operation: delete +LOINC:is_aggregation_view_of: + operation: delete +LOINC:is_approach_guidance_for: + operation: delete +LOINC:is_exam_for: + operation: delete +LOINC:is_given_pharmaceutical_substance_for: + operation: invert + core_predicate: biolink:has_participant +LOINC:is_imaged_location_for: + operation: delete +LOINC:is_imaging_focus_of: + operation: delete +LOINC:is_lateral_anatomic_location_of: + operation: delete +LOINC:is_modality_subtype_for: + operation: delete +LOINC:is_modality_type_for: + operation: delete +LOINC:is_object_guidance_for: + operation: delete +LOINC:is_pharmaceutical_route_for: + operation: delete +LOINC:is_presence_guidance_for: + operation: keep + core_predicate: biolink:subclass_of +LOINC:is_presence_of_lateral_location: + operation: delete +LOINC:is_subject_of: + operation: delete +LOINC:is_timing_for: + operation: delete +LOINC:is_view_type_for: + operation: delete +LOINC:loinc_number_of: + operation: delete +LOINC:mapped_from: + operation: delete +LOINC:mapped_to: + operation: keep + core_predicate: biolink:related_to +LOINC:measured_by: + operation: keep + core_predicate: biolink:related_to +LOINC:measures: + operation: delete +LOINC:member_of: + operation: invert + core_predicate: biolink:has_part +LOINC:method_of: + operation: delete +LOINC:mth_expanded_form_of: + operation: delete +LOINC:mth_has_expanded_form: + operation: keep + core_predicate: biolink:related_to +LOINC:multipart_of: + operation: invert + core_predicate: biolink:has_part +LOINC:parent_group_of: + operation: delete +LOINC:property_of: + operation: keep + core_predicate: biolink:related_to +LOINC:scale_of: + operation: delete +LOINC:suffix_of: + operation: delete +LOINC:supersystem_of: + operation: delete +LOINC:system_of: + operation: delete +LOINC:time_aspect_of: + operation: delete +LOINC:time_modifier_of: + operation: delete +MEDDRA:classified_as: + operation: keep + core_predicate: biolink:close_match +MEDDRA:has_member: + operation: keep + core_predicate: biolink:has_part +MEDDRA:member_of: + operation: invert + core_predicate: biolink:has_part +MESH:AQ: + operation: delete +MESH:QB: + operation: delete +MESH:RO: + operation: keep + core_predicate: biolink:related_to +MESH:SIB: + operation: delete +MESH:has_mapping_qualifier: + operation: keep + core_predicate: biolink:related_to +MESH:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +MESH:isa: + operation: keep + core_predicate: biolink:subclass_of +MESH:mapped_from: + operation: delete +MESH:mapped_to: + operation: keep + core_predicate: biolink:related_to +MESH:mapping_qualifier_of: + operation: delete +MI:0192: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0194: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0195: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0197: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0203: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0204: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0210: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0211: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0212: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0213: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0214: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0216: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0217: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0220: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0403: + operation: keep + core_predicate: biolink:colocalizes_with +MI:0407: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0408: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0414: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0556: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0557: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0559: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0566: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0567: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0569: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0570: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0572: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0844: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0871: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0882: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0883: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0902: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:0914: + operation: keep + core_predicate: biolink:interacts_with +MI:0915: + operation: keep + core_predicate: biolink:physically_interacts_with +MI:0945: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1126: + operation: keep + core_predicate: biolink:interacts_with +MI:1127: + operation: keep + core_predicate: biolink:interacts_with +MI:1148: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1237: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:1310: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:2252: + operation: keep + core_predicate: biolink:directly_interacts_with +MI:2364: + operation: keep + core_predicate: biolink:colocalizes_with +MONDO:0100332: + operation: invert + core_predicate: biolink:causes +MONDO:0100333: + operation: invert + core_predicate: biolink:causes +MONDO:disease_causes_feature: + operation: keep + core_predicate: biolink:causes +MONDO:disease_has_basis_in_accumulation_of: + operation: keep + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_basis_in_development_of: + operation: keep + core_predicate: biolink:disease_has_basis_in +MONDO:disease_has_location: + operation: keep + core_predicate: biolink:disease_has_location +MONDO:disease_has_major_feature: + operation: keep + core_predicate: biolink:has_part +MONDO:disease_responds_to: + operation: invert + core_predicate: biolink:treats +MONDO:disease_shares_features_of: + operation: keep + core_predicate: biolink:related_to +MONDO:disease_triggers: + operation: keep + core_predicate: biolink:causes +MONDO:equivalentTo: + operation: keep + core_predicate: biolink:same_as +MONDO:has_onset: + operation: keep + core_predicate: biolink:related_to +MONDO:has_onset_before: + operation: keep + core_predicate: biolink:related_to +MONDO:has_onset_during_or_after: + operation: keep + core_predicate: biolink:related_to +MONDO:part_of_progression_of_disease: + operation: invert + core_predicate: biolink:has_part +MONDO:predisposes_towards: + operation: keep + core_predicate: biolink:contributes_to +NBO-PROPERTY:by_means: + operation: keep + core_predicate: biolink:actively_involved_in +NBO-PROPERTY:has_participant: + operation: keep + core_predicate: biolink:has_participant +NBO-PROPERTY:in_response_to: + operation: keep + core_predicate: biolink:causes +NBO-PROPERTY:is_about: + operation: keep + core_predicate: biolink:related_to +NCIT:A11: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A14: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A16: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A3: + operation: keep + core_predicate: biolink:subclass_of +NCIT:A7: + operation: keep + core_predicate: biolink:physically_interacts_with +NCIT:Anatomic_Structure_Has_Location_Role: + operation: invert + core_predicate: biolink:located_in +NCIT:C15220: + operation: keep + core_predicate: biolink:diagnoses +NCIT:C16798: + operation: keep + core_predicate: biolink:in_linkage_disequilibrium_with +NCIT:C2861: + operation: keep + core_predicate: biolink:causes_adverse_event +NCIT:C37933: + operation: keep + core_predicate: biolink:contraindicated_for +NCIT:R100: + operation: keep + core_predicate: biolink:affects +NCIT:R101: + operation: keep + core_predicate: biolink:affects +NCIT:R102: + operation: keep + core_predicate: biolink:affects +NCIT:R108: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:R113: + operation: keep + core_predicate: biolink:affects +NCIT:R115: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:R124: + operation: keep + core_predicate: biolink:affects +NCIT:R130: + operation: invert + core_predicate: biolink:has_participant +NCIT:R131: + operation: invert + core_predicate: biolink:has_participant +NCIT:R133: + operation: keep + core_predicate: biolink:affects +NCIT:R145: + operation: keep + core_predicate: biolink:located_in +NCIT:R146: + operation: keep + core_predicate: biolink:affects +NCIT:R150: + operation: keep + core_predicate: biolink:affects +NCIT:R155: + operation: keep + core_predicate: biolink:located_in +NCIT:R156: + operation: keep + core_predicate: biolink:located_in +NCIT:R158: + operation: keep + core_predicate: biolink:affects +NCIT:R160: + operation: keep + core_predicate: biolink:affects +NCIT:R163: + operation: keep + core_predicate: biolink:related_to +NCIT:R165: + operation: keep + core_predicate: biolink:located_in +NCIT:R166: + operation: keep + core_predicate: biolink:located_in +NCIT:R167: + operation: keep + core_predicate: biolink:located_in +NCIT:R168: + operation: keep + core_predicate: biolink:located_in +NCIT:R169: + operation: keep + core_predicate: biolink:located_in +NCIT:R170: + operation: keep + core_predicate: biolink:located_in +NCIT:R171: + operation: keep + core_predicate: biolink:located_in +NCIT:R173: + operation: keep + core_predicate: biolink:affects +NCIT:R175: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R176: + operation: invert + core_predicate: biolink:gene_associated_with_condition +NCIT:R178: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:R23: + operation: keep + core_predicate: biolink:affects +NCIT:R25: + operation: keep + core_predicate: biolink:affects +NCIT:R27: + operation: invert + core_predicate: biolink:has_part +NCIT:R29: + operation: keep + core_predicate: biolink:produces +NCIT:R30: + operation: keep + core_predicate: biolink:affects +NCIT:R36: + operation: keep + core_predicate: biolink:subclass_of +NCIT:R37: + operation: invert + core_predicate: biolink:has_participant +NCIT:R38: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R39: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:R40: + operation: keep + core_predicate: biolink:located_in +NCIT:R42: + operation: keep + core_predicate: biolink:subclass_of +NCIT:R47: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:R48: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:R50: + operation: keep + core_predicate: biolink:has_part +NCIT:R51: + operation: invert + core_predicate: biolink:has_participant +NCIT:R52: + operation: keep + core_predicate: biolink:capable_of +NCIT:R53: + operation: invert + core_predicate: biolink:has_participant +NCIT:R72: + operation: keep + core_predicate: biolink:affects +NCIT:R81: + operation: keep + core_predicate: biolink:related_to +NCIT:R82: + operation: invert + core_predicate: biolink:has_part +NCIT:R88: + operation: keep + core_predicate: biolink:related_to +NCIT:R89: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:abnormal_cell_affected_by_chemical_or_drug: + operation: delete +NCIT:abnormality_associated_with_allele: + operation: delete +NCIT:activity_of_allele: + operation: delete +NCIT:allele_absent_from_wild-type_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:allele_has_abnormality: + operation: keep + core_predicate: biolink:causes +NCIT:allele_has_activity: + operation: keep + core_predicate: biolink:has_molecular_consequence +NCIT:allele_in_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:allele_plays_altered_role_in_process: + operation: keep + core_predicate: biolink:affects +NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: + operation: keep + core_predicate: biolink:affects +NCIT:anatomic_structure_has_location: + operation: delete +NCIT:anatomic_structure_is_physical_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:anatomy_originated_from_biological_process: + operation: delete +NCIT:associated_with_malfunction_of_gene_product: + operation: delete +NCIT:biological_process_has_associated_location: + operation: keep + core_predicate: biolink:affects +NCIT:biological_process_has_initiator_chemical_or_drug: + operation: delete +NCIT:biological_process_has_initiator_process: + operation: delete +NCIT:biological_process_has_result_anatomy: + operation: keep + core_predicate: biolink:has_output +NCIT:biological_process_has_result_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:biological_process_has_result_chemical_or_drug: + operation: keep + core_predicate: biolink:produces +NCIT:biological_process_involves_chemical_or_drug: + operation: invert + core_predicate: biolink:actively_involved_in +NCIT:biological_process_involves_gene_product: + operation: delete +NCIT:biological_process_is_part_of_process: + operation: delete +NCIT:biological_process_results_from_biological_process: + operation: delete +NCIT:biomarker_type_includes_gene: + operation: delete +NCIT:biomarker_type_includes_gene_product: + operation: delete +NCIT:cdrh_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cell_type_is_associated_with_eo_disease: + operation: delete +NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: + operation: delete +NCIT:chemical_or_drug_affects_abnormal_cell: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_cell_type_or_tissue: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_affects_gene_product: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_mechanism_of_action: + operation: keep + core_predicate: biolink:affects +NCIT:chemical_or_drug_has_physiologic_effect: + operation: keep + core_predicate: biolink:causes +NCIT:chemical_or_drug_initiates_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:chemical_or_drug_is_metabolized_by_enzyme: + operation: delete +NCIT:chemical_or_drug_is_product_of_biological_process: + operation: delete +NCIT:chemical_or_drug_metabolism_is_associated_with_allele: + operation: delete +NCIT:chemical_or_drug_plays_role_in_biological_process: + operation: delete +NCIT:chemotherapy_regimen_has_component: + operation: delete +NCIT:chromosomal_location_of_allele: + operation: delete +NCIT:chromosomal_location_of_wild-type_gene: + operation: delete +NCIT:chromosome_involved_in_cytogenetic_abnormality: + operation: delete +NCIT:chromosome_mapped_to_disease: + operation: keep + core_predicate: biolink:causes +NCIT:completely_excised_anatomy_has_procedure: + operation: delete +NCIT:completely_excised_anatomy_may_have_procedure: + operation: delete +NCIT:complex_has_physical_part: + operation: keep + core_predicate: biolink:has_part +NCIT:concept_in_subset: + operation: delete +NCIT:conceptual_part_of: + operation: invert + core_predicate: biolink:has_part +NCIT:ctcae_5_parent_of: + operation: invert + core_predicate: biolink:subclass_of +NCIT:cytogenetic_abnormality_involves_chromosome: + operation: keep + core_predicate: biolink:affects +NCIT:data_element_of: + operation: delete +NCIT:disease_excludes_abnormal_cell: + operation: delete +NCIT:disease_excludes_cytogenetic_abnormality: + operation: delete +NCIT:disease_excludes_finding: + operation: delete +NCIT:disease_excludes_metastatic_anatomic_site: + operation: delete +NCIT:disease_excludes_molecular_abnormality: + operation: delete +NCIT:disease_excludes_normal_cell_origin: + operation: delete +NCIT:disease_excludes_normal_tissue_origin: + operation: delete +NCIT:disease_excludes_primary_anatomic_site: + operation: delete +NCIT:disease_has_abnormal_cell: + operation: delete +NCIT:disease_has_accepted_treatment_with_regimen: + operation: delete +NCIT:disease_has_associated_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_has_associated_disease: + operation: keep + core_predicate: biolink:has_real_world_evidence_of_association_with +NCIT:disease_has_associated_gene: + operation: delete +NCIT:disease_has_cytogenetic_abnormality: + operation: delete +NCIT:disease_has_finding: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_metastatic_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_has_molecular_abnormality: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_has_normal_cell_origin: + operation: delete +NCIT:disease_has_normal_tissue_origin: + operation: keep + core_predicate: biolink:causes +NCIT:disease_has_primary_anatomic_site: + operation: keep + core_predicate: biolink:affects +NCIT:disease_is_grade: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_is_marked_by_gene: + operation: invert + core_predicate: biolink:biomarker_for +NCIT:disease_is_stage: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_mapped_to_chromosome: + operation: delete +NCIT:disease_mapped_to_gene: + operation: delete +NCIT:disease_may_have_abnormal_cell: + operation: keep + core_predicate: biolink:affects +NCIT:disease_may_have_associated_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:disease_may_have_cytogenetic_abnormality: + operation: delete +NCIT:disease_may_have_finding: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_molecular_abnormality: + operation: keep + core_predicate: biolink:has_phenotype +NCIT:disease_may_have_normal_cell_origin: + operation: delete +NCIT:endogenous_product_related_to: + operation: delete +NCIT:enzyme_metabolizes_chemical_or_drug: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: localization + - object_direction: increased +NCIT:eo_anatomy_is_associated_with_eo_disease: + operation: delete +NCIT:eo_disease_has_associated_cell_type: + operation: keep + core_predicate: biolink:affects +NCIT:eo_disease_has_associated_eo_anatomy: + operation: keep + core_predicate: biolink:affects +NCIT:eo_disease_has_property_or_attribute: + operation: keep + core_predicate: biolink:related_to +NCIT:eo_disease_maps_to_human_disease: + operation: delete +NCIT:excised_anatomy_has_procedure: + operation: delete +NCIT:excised_anatomy_may_have_procedure: + operation: delete +NCIT:gene_associated_with_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_encodes_gene_product: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_found_in_organism: + operation: keep + core_predicate: biolink:in_taxon +NCIT:gene_has_abnormality: + operation: delete +NCIT:gene_has_physical_location: + operation: keep + core_predicate: biolink:located_in +NCIT:gene_in_chromosomal_location: + operation: keep + core_predicate: biolink:located_in +NCIT:gene_involved_in_molecular_abnormality: + operation: keep + core_predicate: biolink:actively_involved_in +NCIT:gene_involved_in_pathogenesis_of_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_is_biomarker_of: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:gene_is_biomarker_type: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_mapped_to_disease: + operation: keep + core_predicate: biolink:affects +NCIT:gene_mutant_encodes_gene_product_sequence_variation: + operation: invert + core_predicate: biolink:gene_product_of +NCIT:gene_plays_role_in_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_affected_by_chemical_or_drug: + operation: delete +NCIT:gene_product_encoded_by_gene: + operation: delete +NCIT:gene_product_expressed_in_tissue: + operation: keep + core_predicate: biolink:expressed_in +NCIT:gene_product_has_abnormality: + operation: keep + core_predicate: biolink:affects +NCIT:gene_product_has_associated_anatomy: + operation: keep + core_predicate: biolink:expressed_in +NCIT:gene_product_has_biochemical_function: + operation: keep + core_predicate: biolink:capable_of +NCIT:gene_product_has_chemical_classification: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_product_has_gene_product_variant: + operation: delete +NCIT:gene_product_has_organism_source: + operation: keep + core_predicate: biolink:in_taxon +NCIT:gene_product_has_structural_domain_or_motif: + operation: keep + core_predicate: biolink:has_part +NCIT:gene_product_is_biomarker_of: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:gene_product_is_biomarker_type: + operation: keep + core_predicate: biolink:subclass_of +NCIT:gene_product_is_element_in_pathway: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_is_physical_part_of: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_malfunction_associated_with_disease: + operation: keep + core_predicate: biolink:gene_associated_with_condition +NCIT:gene_product_plays_role_in_biological_process: + operation: invert + core_predicate: biolink:has_participant +NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: + operation: keep + core_predicate: biolink:is_sequence_variant_of +NCIT:gene_product_variant_of_gene_product: + operation: keep + core_predicate: biolink:is_sequence_variant_of +NCIT:genetic_biomarker_related_to: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:has_cdrh_parent: + operation: delete +NCIT:has_conceptual_part: + operation: delete +NCIT:has_ctcae_5_parent: + operation: delete +NCIT:has_data_element: + operation: keep + core_predicate: biolink:related_to +NCIT:has_free_acid_or_base_form: + operation: delete +NCIT:has_gene_product_element: + operation: delete +NCIT:has_inc_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:has_nichd_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:has_pharmaceutical_administration_method: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_basic_dose_form: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_intended_site: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_release_characteristics: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_state_of_matter: + operation: keep + core_predicate: biolink:related_to +NCIT:has_pharmaceutical_transformation: + operation: keep + core_predicate: biolink:related_to +NCIT:has_physical_part_of_anatomic_structure: + operation: delete +NCIT:has_salt_form: + operation: keep + core_predicate: biolink:chemically_similar_to +NCIT:has_target: + operation: keep + core_predicate: biolink:physically_interacts_with +NCIT:human_disease_maps_to_eo_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:imaged_anatomy_has_procedure: + operation: delete +NCIT:inc_parent_of: + operation: delete +NCIT:is_abnormal_cell_of_disease: + operation: keep + core_predicate: biolink:related_to +NCIT:is_abnormality_of_gene: + operation: delete +NCIT:is_abnormality_of_gene_product: + operation: delete +NCIT:is_associated_anatomic_site_of: + operation: delete +NCIT:is_associated_anatomy_of_gene_product: + operation: delete +NCIT:is_associated_disease_of: + operation: keep + core_predicate: biolink:correlated_with +NCIT:is_biochemical_function_of_gene_product: + operation: delete +NCIT:is_chemical_classification_of_gene_product: + operation: delete +NCIT:is_chromosomal_location_of_gene: + operation: delete +NCIT:is_component_of_chemotherapy_regimen: + operation: invert + core_predicate: biolink:has_part +NCIT:is_cytogenetic_abnormality_of_disease: + operation: invert + core_predicate: biolink:correlated_with +NCIT:is_finding_of_disease: + operation: delete +NCIT:is_grade_of_disease: + operation: delete +NCIT:is_location_of_anatomic_structure: + operation: keep + core_predicate: biolink:located_in +NCIT:is_location_of_biological_process: + operation: delete +NCIT:is_marked_by_gene_product: + operation: delete +NCIT:is_mechanism_of_action_of_chemical_or_drug: + operation: delete +NCIT:is_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_molecular_abnormality_of_disease: + operation: keep + core_predicate: biolink:biomarker_for +NCIT:is_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:is_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_abnormal_cell_of_disease: + operation: delete +NCIT:is_not_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:is_not_finding_of_disease: + operation: delete +NCIT:is_not_metastatic_anatomic_site_of_disease: + operation: delete +NCIT:is_not_molecular_abnormality_of_disease: + operation: delete +NCIT:is_not_normal_cell_origin_of_disease: + operation: delete +NCIT:is_not_normal_tissue_origin_of_disease: + operation: delete +NCIT:is_not_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_organism_source_of_gene_product: + operation: invert + core_predicate: biolink:in_taxon +NCIT:is_physical_location_of_gene: + operation: delete +NCIT:is_physiologic_effect_of_chemical_or_drug: + operation: delete +NCIT:is_primary_anatomic_site_of_disease: + operation: delete +NCIT:is_property_or_attribute_of_eo_disease: + operation: delete +NCIT:is_qualified_by: + operation: keep + core_predicate: biolink:related_to +NCIT:is_related_to_endogenous_product: + operation: keep + core_predicate: biolink:related_to +NCIT:is_stage_of_disease: + operation: delete +NCIT:is_structural_domain_or_motif_of_gene_product: + operation: delete +NCIT:is_target: + operation: delete +NCIT:kind_is_domain_of: + operation: delete +NCIT:kind_is_range_of: + operation: delete +NCIT:may_be_abnormal_cell_of_disease: + operation: delete +NCIT:may_be_associated_disease_of_disease: + operation: delete +NCIT:may_be_cytogenetic_abnormality_of_disease: + operation: delete +NCIT:may_be_finding_of_disease: + operation: delete +NCIT:may_be_molecular_abnormality_of_disease: + operation: delete +NCIT:may_be_normal_cell_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from +NCIT:molecular_abnormality_involves_gene: + operation: delete +NCIT:neoplasm_has_special_category: + operation: keep + core_predicate: biolink:subclass_of +NCIT:nichd_parent_of: + operation: delete +NCIT:organism_has_gene: + operation: invert + core_predicate: biolink:in_taxon +NCIT:partially_excised_anatomy_has_procedure: + operation: delete +NCIT:partially_excised_anatomy_may_have_procedure: + operation: delete +NCIT:pathogenesis_of_disease_involves_gene: + operation: delete +NCIT:pathway_has_gene_element: + operation: keep + core_predicate: biolink:has_participant +NCIT:pharmaceutical_administration_method_of: + operation: delete +NCIT:pharmaceutical_basic_dose_form_of: + operation: delete +NCIT:pharmaceutical_intended_site_of: + operation: delete +NCIT:pharmaceutical_release_characteristics_of: + operation: delete +NCIT:pharmaceutical_state_of_matter_of: + operation: delete +NCIT:pharmaceutical_transformation_of: + operation: delete +NCIT:procedure_has_completely_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_imaged_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_partially_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_has_target_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_completely_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:procedure_may_have_partially_excised_anatomy: + operation: keep + core_predicate: biolink:located_in +NCIT:process_altered_by_allele: + operation: delete +NCIT:process_includes_biological_process: + operation: keep + core_predicate: biolink:has_participant +NCIT:process_initiates_biological_process: + operation: keep + core_predicate: biolink:causes +NCIT:process_involves_gene: + operation: keep + core_predicate: biolink:has_participant +NCIT:qualifier_applies_to: + operation: keep + core_predicate: biolink:related_to +NCIT:regimen_has_accepted_use_for_disease: + operation: keep + core_predicate: biolink:treats +NCIT:related_to_genetic_biomarker: + operation: delete +NCIT:role_has_domain: + operation: keep + core_predicate: biolink:related_to +NCIT:role_has_parent: + operation: keep + core_predicate: biolink:subclass_of +NCIT:role_has_range: + operation: keep + core_predicate: biolink:related_to +NCIT:role_is_parent_of: + operation: delete +NCIT:special_category_includes_neoplasm: + operation: delete +NCIT:subset_includes_concept: + operation: invert + core_predicate: biolink:subclass_of +NCIT:target_anatomy_has_procedure: + operation: delete +NCIT:tissue_is_expression_site_of_gene_product: + operation: delete +NDDF:dose_form_of: + operation: delete +NDDF:has_dose_form: + operation: keep + core_predicate: biolink:subclass_of +NDDF:has_ingredient: + operation: keep + core_predicate: biolink:has_part +NDDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +OBI:0000293: + operation: keep + core_predicate: biolink:has_participant +OBI:0000295: + operation: invert + core_predicate: biolink:has_participant +OBI:0000299: + operation: keep + core_predicate: biolink:has_output +OBI:0000417: + operation: keep + core_predicate: biolink:has_output +OBI:0001927: + operation: invert + core_predicate: biolink:related_to +OBO:INO_0000154: + operation: keep + core_predicate: biolink:related_to +OBO:MF#manifestationOf: + operation: keep + core_predicate: biolink:manifestation_of +OBO:bspo#parallel_to: + operation: keep + core_predicate: biolink:coexists_with +OBO:doid#has_symptom: + operation: keep + core_predicate: biolink:has_phenotype +OBO:envo#has_increased_levels_of: + operation: keep + core_predicate: biolink:related_to +OBO:exo#interacts_with: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_receptor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo#interacts_with_an_exposure_stressor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with_an_exposure_receptor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:exo.obo#interacts_with_an_exposure_stressor_via: + operation: keep + core_predicate: biolink:interacts_with +OBO:has_role: + operation: keep + core_predicate: biolink:related_to +OBO:nbo#by_means: + operation: invert + core_predicate: biolink:actively_involved_in +OBO:nbo#has_participant: + operation: keep + core_predicate: biolink:has_participant +OBO:nbo#in_response_to: + operation: invert + core_predicate: biolink:causes +OBO:nbo#is_about: + operation: keep + core_predicate: biolink:related_to +OBO:uo#is_unit_of: + operation: invert + core_predicate: biolink:related_to +OIO:hasDbXref: + operation: keep + core_predicate: biolink:close_match +OMIM:allelic_variant_of: + operation: keep + core_predicate: biolink:is_sequence_variant_of +OMIM:has_allelic_variant: + operation: delete +OMIM:has_inheritance_type: + operation: keep + core_predicate: biolink:related_to +OMIM:has_manifestation: + operation: invert + core_predicate: biolink:subclass_of +OMIM:has_phenotype: + operation: keep + core_predicate: biolink:has_phenotype +OMIM:inheritance_type_of: + operation: delete +OMIM:manifestation_of: + operation: keep + core_predicate: biolink:manifestation_of +OMIM:phenotype_of: + operation: invert + core_predicate: biolink:has_phenotype +ORPHA:317343: + operation: keep + core_predicate: biolink:causes +ORPHA:317344: + operation: keep + core_predicate: biolink:causes +ORPHA:317346: + operation: keep + core_predicate: biolink:causes +ORPHA:317348: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:317349: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:327767: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHA:410295: + operation: keep + core_predicate: biolink:causes +ORPHA:410296: + operation: keep + core_predicate: biolink:causes +ORPHA:465410: + operation: keep + core_predicate: biolink:biomarker_for +ORPHANET:317343: + operation: keep + core_predicate: biolink:causes +ORPHANET:317344: + operation: keep + core_predicate: biolink:causes +ORPHANET:317345: + operation: keep + core_predicate: biolink:correlated_with +ORPHANET:317346: + operation: keep + core_predicate: biolink:causes +ORPHANET:317348: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:317349: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:327767: + operation: keep + core_predicate: biolink:actively_involved_in +ORPHANET:410295: + operation: keep + core_predicate: biolink:causes +ORPHANET:410296: + operation: keep + core_predicate: biolink:causes +ORPHANET:465410: + operation: keep + core_predicate: biolink:biomarker_for +ORPHANET:C016: + operation: keep + core_predicate: biolink:related_to +ORPHANET:C017: + operation: keep + core_predicate: biolink:related_to +PATO:0000085: + operation: keep + core_predicate: biolink:associated_with_sensitivity_to +PATO:correlates_with: + operation: keep + core_predicate: biolink:correlated_with +PATO:decreased_in_magnitude_relative_to: + operation: keep + core_predicate: biolink:related_to +PATO:has_cross_section: + operation: keep + core_predicate: biolink:related_to +PATO:has_relative_magnitude: + operation: keep + core_predicate: biolink:related_to +PATO:increased_in_magnitude_relative_to: + operation: keep + core_predicate: biolink:related_to +PATO:reciprocal_of: + operation: keep + core_predicate: biolink:related_to +PATO:towards: + operation: invert + core_predicate: biolink:actively_involved_in +PDQ:associated_disease: + operation: keep + core_predicate: biolink:correlated_with +PDQ:associated_genetic_condition: + operation: delete +PDQ:component_of: + operation: invert + core_predicate: biolink:has_part +PDQ:has_component: + operation: keep + core_predicate: biolink:has_part +PHAROS:drug_targets: + operation: keep + core_predicate: biolink:directly_interacts_with +PR:confers_resistance_to: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity + - object_direction: decreased +PR:has_gene_template: + operation: keep + core_predicate: biolink:gene_product_of +PR:lacks_part: + operation: keep + core_predicate: biolink:lacks_part +PR:non-covalently_bound_to: + operation: keep + core_predicate: biolink:physically_interacts_with +PSY:RB: + operation: invert + core_predicate: biolink:subclass_of +PSY:RO: + operation: keep + core_predicate: biolink:related_to +PSY:use: + operation: keep + core_predicate: biolink:subclass_of +PSY:used_for: + operation: invert + core_predicate: biolink:has_input +PathWhiz:has_bound: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_compound: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_element_collection: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_element_in_bound: + operation: keep + core_predicate: biolink:has_part +PathWhiz:has_enzyme: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_left_element: + operation: keep + core_predicate: biolink:has_input +PathWhiz:has_location: + operation: keep + core_predicate: biolink:occurs_in +PathWhiz:has_nucleic_acid: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_protein: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_protein_in_complex: + operation: keep + core_predicate: biolink:has_part +PathWhiz:has_reaction: + operation: keep + core_predicate: biolink:has_participant +PathWhiz:has_right_element: + operation: keep + core_predicate: biolink:has_output +PathWhiz:in_species: + operation: keep + core_predicate: biolink:occurs_in +REACT:has_element: + operation: keep + core_predicate: biolink:has_part +REACT:has_event: + operation: keep + core_predicate: biolink:has_participant +REACT:has_input: + operation: keep + core_predicate: biolink:has_input +REACT:has_member: + operation: keep + core_predicate: biolink:has_part +REACT:has_output: + operation: keep + core_predicate: biolink:has_output +REACT:in_species: + operation: keep + core_predicate: biolink:occurs_in +REACT:is_requirement_for: + operation: keep + core_predicate: biolink:entity_regulates_entity +REACT:linked_to_disease: + operation: keep + core_predicate: biolink:related_to +REACT:negatively_regulates: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +REACT:negatively_regulates_gene_expression: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +REACT:positively_regulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +REACT:positively_regulates_gene_expression: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +REACT:related_to: + operation: keep + core_predicate: biolink:related_to +REPODB:clinically_tested_approved_unknown_phase: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_suspended_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_terminated_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_0: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: + operation: keep + core_predicate: biolink:treats +REPODB:clinically_tested_withdrawn_phase_3: + operation: keep + core_predicate: biolink:treats +RO:0000052: + operation: keep + core_predicate: biolink:related_to +RO:0000053: + operation: keep + core_predicate: biolink:related_to +RO:0000056: + operation: invert + core_predicate: biolink:has_participant +RO:0000057: + operation: keep + core_predicate: biolink:has_participant +RO:0000059: + operation: keep + core_predicate: biolink:related_to +RO:0000086: + operation: keep + core_predicate: biolink:related_to +RO:0000087: + operation: keep + core_predicate: biolink:related_to +RO:00002325: + operation: keep + core_predicate: biolink:colocalizes_with +RO:0001000: + operation: invert + core_predicate: biolink:derives_into +RO:0001001: + operation: invert + core_predicate: biolink:derives_from +RO:0001015: + operation: invert + core_predicate: biolink:located_in +RO:0001018: + operation: invert + core_predicate: biolink:has_part +RO:0001019: + operation: keep + core_predicate: biolink:has_part +RO:0001022: + operation: invert + core_predicate: biolink:causes +RO:0001025: + operation: keep + core_predicate: biolink:located_in +RO:0002001: + operation: keep + core_predicate: biolink:related_to +RO:0002002: + operation: keep + core_predicate: biolink:related_to +RO:0002003: + operation: keep + core_predicate: biolink:related_to +RO:0002005: + operation: keep + core_predicate: biolink:related_to +RO:0002007: + operation: invert + core_predicate: biolink:has_part +RO:0002008: + operation: keep + core_predicate: biolink:related_to +RO:0002082: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002083: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002084: + operation: keep + core_predicate: biolink:related_to +RO:0002087: + operation: invert + core_predicate: biolink:precedes +RO:0002090: + operation: keep + core_predicate: biolink:precedes +RO:0002092: + operation: keep + core_predicate: biolink:related_to +RO:0002093: + operation: keep + core_predicate: biolink:related_to +RO:0002100: + operation: keep + core_predicate: biolink:overlaps +RO:0002101: + operation: keep + core_predicate: biolink:overlaps +RO:0002102: + operation: keep + core_predicate: biolink:overlaps +RO:0002103: + operation: keep + core_predicate: biolink:interacts_with +RO:0002104: + operation: keep + core_predicate: biolink:has_part +RO:0002120: + operation: keep + core_predicate: biolink:interacts_with +RO:0002130: + operation: keep + core_predicate: biolink:interacts_with +RO:0002131: + operation: keep + core_predicate: biolink:overlaps +RO:0002134: + operation: keep + core_predicate: biolink:related_to +RO:0002150: + operation: keep + core_predicate: biolink:related_to +RO:0002159: + operation: keep + core_predicate: biolink:related_to +RO:0002160: + operation: keep + core_predicate: biolink:in_taxon +RO:0002162: + operation: keep + core_predicate: biolink:in_taxon +RO:0002170: + operation: keep + core_predicate: biolink:related_to +RO:0002176: + operation: keep + core_predicate: biolink:related_to +RO:0002177: + operation: keep + core_predicate: biolink:related_to +RO:0002178: + operation: keep + core_predicate: biolink:related_to +RO:0002179: + operation: keep + core_predicate: biolink:related_to +RO:0002180: + operation: keep + core_predicate: biolink:has_part +RO:0002200: + operation: keep + core_predicate: biolink:has_phenotype +RO:0002202: + operation: keep + core_predicate: biolink:develops_from +RO:0002203: + operation: keep + core_predicate: biolink:develops_from +RO:0002204: + operation: invert + core_predicate: biolink:has_gene_product +RO:0002205: + operation: invert + core_predicate: biolink:gene_product_of +RO:0002207: + operation: keep + core_predicate: biolink:develops_from +RO:0002211: + operation: keep + core_predicate: biolink:regulates +RO:0002212: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +RO:0002213: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +RO:0002215: + operation: keep + core_predicate: biolink:capable_of +RO:0002216: + operation: invert + core_predicate: biolink:has_participant +RO:0002219: + operation: keep + core_predicate: biolink:coexists_with +RO:0002220: + operation: keep + core_predicate: biolink:coexists_with +RO:0002221: + operation: keep + core_predicate: biolink:coexists_with +RO:0002223: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002224: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002225: + operation: keep + core_predicate: biolink:develops_from +RO:0002226: + operation: keep + core_predicate: biolink:develops_from +RO:0002229: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002230: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002231: + operation: keep + core_predicate: biolink:occurs_in +RO:0002232: + operation: keep + core_predicate: biolink:occurs_in +RO:0002233: + operation: keep + core_predicate: biolink:has_input +RO:0002234: + operation: keep + core_predicate: biolink:has_output +RO:0002241: + operation: keep + core_predicate: biolink:related_to +RO:0002254: + operation: keep + core_predicate: biolink:related_to +RO:0002255: + operation: keep + core_predicate: biolink:contributes_to +RO:0002256: + operation: keep + core_predicate: biolink:causes +RO:0002263: + operation: keep + core_predicate: biolink:acts_upstream_of +RO:0002264: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within +RO:0002285: + operation: invert + core_predicate: biolink:precedes +RO:0002292: + operation: invert + core_predicate: biolink:expressed_in +RO:0002295: + operation: keep + core_predicate: biolink:regulates +RO:0002296: + operation: keep + core_predicate: biolink:has_output +RO:0002297: + operation: keep + core_predicate: biolink:has_output +RO:0002298: + operation: keep + core_predicate: biolink:has_output +RO:0002299: + operation: keep + core_predicate: biolink:has_output +RO:0002302: + operation: invert + core_predicate: biolink:treats +RO:0002303: + operation: keep + core_predicate: biolink:located_in +RO:0002309: + operation: keep + core_predicate: biolink:related_to +RO:0002313: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +RO:0002314: + operation: keep + core_predicate: biolink:related_to +RO:0002315: + operation: keep + core_predicate: biolink:causes +RO:0002322: + operation: keep + core_predicate: biolink:related_to +RO:0002326: + operation: keep + core_predicate: biolink:contributes_to +RO:0002327: + operation: invert + core_predicate: biolink:enabled_by +RO:0002328: + operation: keep + core_predicate: biolink:related_to +RO:0002331: + operation: keep + core_predicate: biolink:actively_involved_in +RO:0002332: + operation: keep + core_predicate: biolink:related_to +RO:0002333: + operation: invert + core_predicate: biolink:enables +RO:0002334: + operation: invert + core_predicate: biolink:entity_regulates_entity +RO:0002338: + operation: keep + core_predicate: biolink:related_to +RO:0002339: + operation: keep + core_predicate: biolink:related_to +RO:0002340: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +RO:0002341: + operation: keep + core_predicate: biolink:related_to +RO:0002342: + operation: keep + core_predicate: biolink:related_to +RO:0002343: + operation: keep + core_predicate: biolink:affects +RO:0002344: + operation: keep + core_predicate: biolink:related_to +RO:0002345: + operation: keep + core_predicate: biolink:affects + qualifiers: + - object_aspect: transport +RO:0002348: + operation: keep + core_predicate: biolink:related_to +RO:0002349: + operation: keep + core_predicate: biolink:related_to +RO:0002350: + operation: invert + core_predicate: biolink:has_part +RO:0002351: + operation: keep + core_predicate: biolink:has_part +RO:0002352: + operation: invert + core_predicate: biolink:has_input +RO:0002353: + operation: invert + core_predicate: biolink:has_output +RO:0002354: + operation: invert + core_predicate: biolink:has_output +RO:0002355: + operation: keep + core_predicate: biolink:affects +RO:0002356: + operation: keep + core_predicate: biolink:related_to +RO:0002371: + operation: keep + core_predicate: biolink:related_to +RO:0002372: + operation: keep + core_predicate: biolink:related_to +RO:0002373: + operation: keep + core_predicate: biolink:related_to +RO:0002374: + operation: keep + core_predicate: biolink:related_to +RO:0002376: + operation: invert + core_predicate: biolink:has_part +RO:0002380: + operation: invert + core_predicate: biolink:has_part +RO:0002385: + operation: keep + core_predicate: biolink:related_to +RO:0002387: + operation: keep + core_predicate: biolink:related_to +RO:0002410: + operation: keep + core_predicate: biolink:causes +RO:0002411: + operation: keep + core_predicate: biolink:precedes +RO:0002412: + operation: keep + core_predicate: biolink:precedes +RO:0002432: + operation: keep + core_predicate: biolink:active_in +RO:0002433: + operation: keep + core_predicate: biolink:overlaps +RO:0002434: + operation: keep + core_predicate: biolink:interacts_with +RO:0002435: + operation: keep + core_predicate: biolink:genetically_interacts_with +RO:0002436: + operation: keep + core_predicate: biolink:molecularly_interacts_with +RO:0002448: + operation: invert + core_predicate: biolink:entity_regulated_by_entity +RO:0002449: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +RO:0002450: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +RO:0002451: + operation: keep + core_predicate: biolink:related_to +RO:0002452: + operation: keep + core_predicate: biolink:has_phenotype +RO:0002470: + operation: keep + core_predicate: biolink:related_to +RO:0002473: + operation: keep + core_predicate: biolink:has_part +RO:0002488: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002489: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002491: + operation: keep + core_predicate: biolink:coexists_with +RO:0002492: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002493: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002494: + operation: keep + core_predicate: biolink:related_to +RO:0002495: + operation: keep + core_predicate: biolink:related_to +RO:0002496: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002497: + operation: keep + core_predicate: biolink:temporally_related_to +RO:0002500: + operation: keep + core_predicate: biolink:capable_of +RO:0002503: + operation: keep + core_predicate: biolink:actively_involved_in +RO:0002505: + operation: invert + core_predicate: biolink:has_participant +RO:0002506: + operation: keep + core_predicate: biolink:causes +RO:0002507: + operation: keep + core_predicate: biolink:causes +RO:0002509: + operation: keep + core_predicate: biolink:causes +RO:0002510: + operation: keep + core_predicate: biolink:transcribed_from +RO:0002511: + operation: invert + core_predicate: biolink:transcribed_from +RO:0002524: + operation: keep + core_predicate: biolink:has_part +RO:0002551: + operation: keep + core_predicate: biolink:has_part +RO:0002565: + operation: invert + core_predicate: biolink:has_participant +RO:0002568: + operation: keep + core_predicate: biolink:related_to +RO:0002571: + operation: invert + core_predicate: biolink:has_part +RO:0002572: + operation: invert + core_predicate: biolink:has_part +RO:0002573: + operation: keep + core_predicate: biolink:related_to +RO:0002576: + operation: invert + core_predicate: biolink:has_part +RO:0002578: + operation: keep + core_predicate: biolink:regulates +RO:0002588: + operation: keep + core_predicate: biolink:has_output +RO:0002590: + operation: keep + core_predicate: biolink:has_input +RO:0002591: + operation: keep + core_predicate: biolink:affects +RO:0002592: + operation: keep + core_predicate: biolink:affects +RO:0002599: + operation: keep + core_predicate: biolink:prevents +RO:0002604: + operation: keep + core_predicate: biolink:opposite_of +RO:0002606: + operation: keep + core_predicate: biolink:treats +RO:0002607: + operation: keep + core_predicate: biolink:biomarker_for +RO:0002608: + operation: invert + core_predicate: biolink:causes +RO:0002610: + operation: keep + core_predicate: biolink:correlated_with +RO:0002629: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: increased +RO:0002630: + operation: keep + core_predicate: biolink:regulates + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: activity_or_abundance + - object_direction: decreased +RO:0003000: + operation: keep + core_predicate: biolink:produces +RO:0003001: + operation: invert + core_predicate: biolink:produces +RO:0003002: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: decreased +RO:0003003: + operation: keep + core_predicate: biolink:affects + qualified_predicate: biolink:causes + qualifiers: + - object_aspect: expression + - object_direction: increased +RO:0003301: + operation: keep + core_predicate: biolink:model_of +RO:0003303: + operation: keep + core_predicate: biolink:causes +RO:0003304: + operation: keep + core_predicate: biolink:contributes_to +RO:0003307: + operation: keep + core_predicate: biolink:ameliorates +RO:0003309: + operation: keep + core_predicate: biolink:exacerbates +RO:0004001: + operation: keep + core_predicate: biolink:causes +RO:0004007: + operation: keep + core_predicate: biolink:has_participant +RO:0004008: + operation: keep + core_predicate: biolink:has_output +RO:0004009: + operation: keep + core_predicate: biolink:has_input +RO:0004019: + operation: invert + core_predicate: biolink:causes +RO:0004020: + operation: invert + core_predicate: biolink:causes +RO:0004021: + operation: keep + core_predicate: biolink:has_participant +RO:0004022: + operation: keep + core_predicate: biolink:has_phenotype +RO:0004024: + operation: keep + core_predicate: biolink:disrupts +RO:0004025: + operation: keep + core_predicate: biolink:disrupts +RO:0004026: + operation: keep + core_predicate: biolink:related_to +RO:0004027: + operation: keep + core_predicate: biolink:related_to +RO:0004028: + operation: invert + core_predicate: biolink:causes +RO:0004029: + operation: keep + core_predicate: biolink:associated_with +RO:0004030: + operation: invert + core_predicate: biolink:causes +RO:0004032: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within_positive_effect +RO:0004033: + operation: keep + core_predicate: biolink:acts_upstream_of_or_within_negative_effect +RO:0004034: + operation: keep + core_predicate: biolink:acts_upstream_of_positive_effect +RO:0004035: + operation: keep + core_predicate: biolink:acts_upstream_of_negative_effect +RO:0009001: + operation: keep + core_predicate: biolink:related_to +RO:0009004: + operation: keep + core_predicate: biolink:related_to +RO:0009501: + operation: invert + core_predicate: biolink:causes +RO:0012003: + operation: keep + core_predicate: biolink:affects +RO:0012008: + operation: keep + core_predicate: biolink:affects +RO:0013001: + operation: keep + core_predicate: biolink:related_to +RO:0014001: + operation: keep + core_predicate: biolink:related_to +RO:HOM0000000: + operation: keep + core_predicate: biolink:similar_to +RO:has_participant: + operation: keep + core_predicate: biolink:has_participant +RO:participates_in: + operation: invert + core_predicate: biolink:has_participant +RXNORM:consists_of: + operation: keep + core_predicate: biolink:has_part +RXNORM:constitutes: + operation: invert + core_predicate: biolink:has_part +RXNORM:contained_in: + operation: invert + core_predicate: biolink:has_part +RXNORM:contains: + operation: keep + core_predicate: biolink:has_part +RXNORM:dose_form_of: + operation: delete +RXNORM:doseformgroup_of: + operation: delete +RXNORM:form_of: + operation: delete +RXNORM:has_dose_form: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:has_doseformgroup: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:has_form: + operation: keep + core_predicate: biolink:related_to +RXNORM:has_ingredient: + operation: keep + core_predicate: biolink:has_part +RXNORM:has_ingredients: + operation: delete +RXNORM:has_part: + operation: keep + core_predicate: biolink:has_part +RXNORM:has_precise_ingredient: + operation: delete +RXNORM:has_quantified_form: + operation: keep + core_predicate: biolink:close_match +RXNORM:has_tradename: + operation: keep + core_predicate: biolink:related_to +RXNORM:ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:ingredients_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +RXNORM:isa: + operation: keep + core_predicate: biolink:subclass_of +RXNORM:part_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:precise_ingredient_of: + operation: invert + core_predicate: biolink:has_part +RXNORM:quantified_form_of: + operation: delete +RXNORM:reformulated_to: + operation: keep + core_predicate: biolink:related_to +RXNORM:reformulation_of: + operation: delete +RXNORM:tradename_of: + operation: delete +SEMMEDDB:1532: + operation: delete +SEMMEDDB:AFFECTS: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:CAUSES: + operation: keep + core_predicate: biolink:causes +SEMMEDDB:COEXISTS_WITH: + operation: keep + core_predicate: biolink:coexists_with +SEMMEDDB:CONVERTS_TO: + operation: invert + core_predicate: biolink:derives_from +SEMMEDDB:DISRUPTS: + operation: keep + core_predicate: biolink:disrupts +SEMMEDDB:INHIBITS: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +SEMMEDDB:IS_A: + operation: keep + core_predicate: biolink:subclass_of +SEMMEDDB:LOCATION_OF: + operation: invert + core_predicate: biolink:located_in +SEMMEDDB:MANIFESTATION_OF: + operation: keep + core_predicate: biolink:manifestation_of +SEMMEDDB:OCCURS_IN: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:PART_OF: + operation: invert + core_predicate: biolink:has_part +SEMMEDDB:PRECEDES: + operation: keep + core_predicate: biolink:precedes +SEMMEDDB:PREVENTS: + operation: keep + core_predicate: biolink:prevents +SEMMEDDB:PROCESS_OF: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:PRODUCES: + operation: keep + core_predicate: biolink:produces +SEMMEDDB:SAME_AS: + operation: keep + core_predicate: biolink:close_match +SEMMEDDB:STIMULATES: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:TREATS: + operation: keep + core_predicate: biolink:treats +SEMMEDDB:administered_to: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:affects: + operation: keep + core_predicate: biolink:affects +SEMMEDDB:associated_with: + operation: keep + core_predicate: biolink:associated_with +SEMMEDDB:augments: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:causes: + operation: keep + core_predicate: biolink:causes +SEMMEDDB:coexists_with: + operation: keep + core_predicate: biolink:coexists_with +SEMMEDDB:compared_with: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:complicates: + operation: keep + core_predicate: biolink:exacerbates +SEMMEDDB:converts_to: + operation: invert + core_predicate: biolink:derives_from +SEMMEDDB:diagnoses: + operation: keep + core_predicate: biolink:diagnoses +SEMMEDDB:disrupts: + operation: keep + core_predicate: biolink:disrupts +SEMMEDDB:higher_than: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:inhibits: + operation: keep + core_predicate: biolink:entity_negatively_regulates_entity +SEMMEDDB:interacts_with: + operation: keep + core_predicate: biolink:interacts_with +SEMMEDDB:isa: + operation: keep + core_predicate: biolink:subclass_of +SEMMEDDB:location_of: + operation: invert + core_predicate: biolink:located_in +SEMMEDDB:lower_than: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:manifestation_of: + operation: keep + core_predicate: biolink:manifestation_of +SEMMEDDB:measurement_of: + operation: delete +SEMMEDDB:measures: + operation: keep + core_predicate: biolink:related_to +SEMMEDDB:method_of: + operation: delete +SEMMEDDB:nom: + operation: delete +SEMMEDDB:occurs_in: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:part_of: + operation: invert + core_predicate: biolink:has_part +SEMMEDDB:precedes: + operation: keep + core_predicate: biolink:precedes +SEMMEDDB:predisposes: + operation: keep + core_predicate: biolink:predisposes +SEMMEDDB:prep: + operation: delete +SEMMEDDB:prevents: + operation: keep + core_predicate: biolink:prevents +SEMMEDDB:process_of: + operation: keep + core_predicate: biolink:occurs_in +SEMMEDDB:produces: + operation: keep + core_predicate: biolink:produces +SEMMEDDB:same_as: + operation: keep + core_predicate: biolink:close_match +SEMMEDDB:stimulates: + operation: keep + core_predicate: biolink:entity_positively_regulates_entity +SEMMEDDB:treats: + operation: keep + core_predicate: biolink:treats +SEMMEDDB:uses: + operation: keep + core_predicate: biolink:has_input +SEMMEDDB:verb: + operation: delete +SEMMEDDB:xref: + operation: keep + core_predicate: biolink:related_to +SIO:000001: + operation: delete +SIO:000203: + operation: keep + core_predicate: biolink:directly_interacts_with +SIO:000628: + operation: keep + core_predicate: biolink:mentions +SIO:000983: + operation: keep + core_predicate: biolink:biomarker_for +SIO:001331: + operation: keep + core_predicate: biolink:diagnoses +SIO:010080: + operation: invert + core_predicate: biolink:transcribed_from +SIO:010081: + operation: keep + core_predicate: biolink:transcribed_from +SIO:010285: + operation: keep + core_predicate: biolink:in_complex_with +SO:0001583: + operation: keep + core_predicate: biolink:is_missense_variant_of +SO:0001589: + operation: keep + core_predicate: biolink:is_frameshift_variant_of +SO:0001629: + operation: keep + core_predicate: biolink:is_splice_site_variant_of +SO:0001819: + operation: keep + core_predicate: biolink:is_synonymous_variant_of +SO:0002054: + operation: keep + core_predicate: biolink:is_nonsense_variant_of +SO:has_origin: + operation: keep + core_predicate: biolink:coexists_with +SO:similar_to: + operation: keep + core_predicate: biolink:similar_to +UBERON:anastomoses_with: + operation: keep + core_predicate: biolink:coexists_with +UBERON:anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channel_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channels_from: + operation: keep + core_predicate: biolink:coexists_with +UBERON:channels_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON:conduit_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:existence_starts_and_ends_during: + operation: keep + core_predicate: biolink:coexists_with +UBERON:extends_fibers_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON:filtered_through: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_central_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_innermost_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:in_outermost_side_of: + operation: keep + core_predicate: biolink:coexists_with +UBERON:indirectly_supplies: + operation: keep + core_predicate: biolink:coexists_with +UBERON:posteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:protects: + operation: keep + core_predicate: biolink:coexists_with +UBERON:proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:sexually_homologous_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON:site_of: + operation: invert + core_predicate: biolink:occurs_in +UBERON:subdivision_of: + operation: invert + core_predicate: biolink:has_part +UBERON:synapsed_by: + operation: keep + core_predicate: biolink:related_to +UBERON_CORE:anastomoses_with: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channel_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channels_from: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:channels_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:conduit_for: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:extends_fibers_into: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:filtered_through: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:in_central_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:in_innermost_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:in_outermost_side_of: + operation: keep + core_predicate: biolink:located_in +UBERON_CORE:indirectly_supplies: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:layer_part_of: + operation: invert + core_predicate: biolink:has_part +UBERON_CORE:posteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:protects: + operation: keep + core_predicate: biolink:related_to +UBERON_CORE:proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:sexually_homologous_to: + operation: keep + core_predicate: biolink:homologous_to +UBERON_CORE:site_of: + operation: keep + core_predicate: biolink:occurs_in +UBERON_CORE:subdivision_of: + operation: invert + core_predicate: biolink:has_part +UBERON_CORE:synapsed_by: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_anteriorly_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:transitively_proximally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_CORE:trunk_part_of: + operation: invert + core_predicate: biolink:has_part +UBERON_NONAMESPACE:connected_to: + operation: keep + core_predicate: biolink:related_to +UBERON_NONAMESPACE:distally_connected_to: + operation: keep + core_predicate: biolink:coexists_with +UBERON_NONAMESPACE:innervated_by: + operation: keep + core_predicate: biolink:related_to +UBERON_NONAMESPACE:subdivision_of: + operation: keep + core_predicate: biolink:coexists_with +UMLS:RB: + operation: invert + core_predicate: biolink:subclass_of +UMLS:RO: + operation: keep + core_predicate: biolink:related_to +UMLS:RQ: + operation: keep + core_predicate: biolink:related_to +UMLS:SIB: + operation: delete +UMLS:SY: + operation: keep + core_predicate: biolink:close_match +UMLS:class_code_classified_by: + operation: keep + core_predicate: biolink:related_to +UMLS:classifies_class_code: + operation: delete +UMLS:component_of: + operation: invert + core_predicate: biolink:has_part +UMLS:context_binding_of: + operation: delete +UMLS:exhibited_by: + operation: keep + core_predicate: biolink:related_to +UMLS:exhibits: + operation: delete +UMLS:form_of: + operation: delete +UMLS:has_component: + operation: keep + core_predicate: biolink:has_part +UMLS:has_context_binding: + operation: keep + core_predicate: biolink:related_to +UMLS:has_form: + operation: keep + core_predicate: biolink:related_to +UMLS:has_mapping_qualifier: + operation: keep + core_predicate: biolink:related_to +UMLS:has_owning_affiliate: + operation: invert + core_predicate: biolink:has_part +UMLS:has_owning_section: + operation: delete +UMLS:has_owning_subsection: + operation: delete +UMLS:has_physiologic_effect: + operation: keep + core_predicate: biolink:causes +UMLS:has_structural_class: + operation: keep + core_predicate: biolink:related_to +UMLS:has_supported_concept_property: + operation: keep + core_predicate: biolink:related_to +UMLS:has_supported_concept_relationship: + operation: keep + core_predicate: biolink:related_to +UMLS:larger_than: + operation: keep + core_predicate: biolink:related_to +UMLS:mapped_from: + operation: delete +UMLS:mapped_to: + operation: keep + core_predicate: biolink:related_to +UMLS:may_be_qualified_by: + operation: keep + core_predicate: biolink:related_to +UMLS:may_qualify: + operation: delete +UMLS:measured_by: + operation: delete +UMLS:measures: + operation: keep + core_predicate: biolink:related_to +UMLS:owning_affiliate_of: + operation: delete +UMLS:owning_section_of: + operation: keep + core_predicate: biolink:related_to +UMLS:owning_subsection_of: + operation: invert + core_predicate: biolink:has_part +UMLS:related_to: + operation: keep + core_predicate: biolink:related_to +UMLS:supported_concept_property_in: + operation: delete +UMLS:supported_concept_relationship_in: + operation: delete +UO-PROPERTY:is_unit_of: + operation: keep + core_predicate: biolink:related_to +UPHENO:0000001: + operation: keep + core_predicate: biolink:affects +VANDF:has_ingredient: + operation: keep + core_predicate: biolink:has_part +VANDF:ingredient_of: + operation: invert + core_predicate: biolink:has_part +VANDF:inverse_isa: + operation: invert + core_predicate: biolink:subclass_of +VANDF:isa: + operation: keep + core_predicate: biolink:subclass_of +WIKIDATA:P2888: + operation: keep + core_predicate: biolink:exact_match +WIKIDATA:P3433: + operation: keep + core_predicate: biolink:is_sequence_variant_of +WIKIDATA:Q181394: + operation: keep + core_predicate: biolink:has_nutrient +WIKIDATA:Q39893449: + operation: keep + core_predicate: biolink:exact_match +WIKIDATA:Q39893967: + operation: invert + core_predicate: biolink:broad_match +WIKIDATA:Q39894595: + operation: keep + core_predicate: biolink:broad_match +WIKIDATA:Q66088480: + operation: invert + core_predicate: biolink:subclass_of +WIKIDATA_PROPERTY:P1056: + operation: keep + core_predicate: biolink:produces +WIKIDATA_PROPERTY:P123: + operation: keep + core_predicate: biolink:publisher +WIKIDATA_PROPERTY:P128: + operation: keep + core_predicate: biolink:regulates +WIKIDATA_PROPERTY:P129: + operation: keep + core_predicate: biolink:physically_interacts_with +WIKIDATA_PROPERTY:P1542: + operation: keep + core_predicate: biolink:causes +WIKIDATA_PROPERTY:P1557: + operation: keep + core_predicate: biolink:manifestation_of +WIKIDATA_PROPERTY:P156: + operation: keep + core_predicate: biolink:precedes +WIKIDATA_PROPERTY:P2175: + operation: keep + core_predicate: biolink:treats +WIKIDATA_PROPERTY:P2176: + operation: invert + core_predicate: biolink:treats +WIKIDATA_PROPERTY:P2293: + operation: keep + core_predicate: biolink:genetic_association +WIKIDATA_PROPERTY:P276: + operation: invert + core_predicate: biolink:located_in +WIKIDATA_PROPERTY:P279: + operation: keep + core_predicate: biolink:subclass_of +WIKIDATA_PROPERTY:P361: + operation: invert + core_predicate: biolink:has_part +WIKIDATA_PROPERTY:P50: + operation: keep + core_predicate: biolink:author +WIKIDATA_PROPERTY:P527: + operation: keep + core_predicate: biolink:has_part +WIKIDATA_PROPERTY:P688: + operation: invert + core_predicate: biolink:gene_product_of +WIKIDATA_PROPERTY:P703: + operation: keep + core_predicate: biolink:in_taxon +WIKIDATA_PROPERTY:P828: + operation: invert + core_predicate: biolink:causes +WIKIDATA_PROPERTY:P98: + operation: keep + core_predicate: biolink:editor +biolink:in_taxon: + operation: keep + core_predicate: biolink:subclass_of +biolink:part_of: + operation: invert + core_predicate: biolink:has_part +biolink:subclass_of: + operation: invert + core_predicate: biolink:has_part +dct:contributor: + operation: keep + core_predicate: biolink:contributor +dct:creator: + operation: keep + core_predicate: biolink:author +dct:publisher: + operation: keep + core_predicate: biolink:publisher +faldo:location: + operation: keep + core_predicate: biolink:has_sequence_location +oboFormat:xref: + operation: keep + core_predicate: biolink:close_match +oboformat:xref: + operation: keep + core_predicate: biolink:close_match +owl:inverseOf: + operation: keep + core_predicate: biolink:related_to +owl:sameAs: + operation: keep + core_predicate: biolink:same_as +owl:topObjectProperty: + operation: keep + core_predicate: biolink:related_to +rdf:type: + operation: keep + core_predicate: biolink:related_to +rdfs:subClassOf: + operation: keep + core_predicate: biolink:subclass_of +rdfs:subPropertyOf: + operation: keep + core_predicate: biolink:subclass_of +skos:broadMatch: + operation: keep + core_predicate: biolink:broad_match +skos:closeMatch: + operation: keep + core_predicate: biolink:close_match +skos:exactMatch: + operation: keep + core_predicate: biolink:exact_match +skos:narrowMatch: + operation: invert + core_predicate: biolink:broad_match +skos:relatedMatch: + operation: keep + core_predicate: biolink:related_to diff --git a/predicate_remap_new.yaml b/predicate_remap_new.yaml deleted file mode 100644 index ba08b423..00000000 --- a/predicate_remap_new.yaml +++ /dev/null @@ -1,4019 +0,0 @@ -BFO:0000050: - operation: invert - core_predicate: biolink:has_part -BFO:0000051: - operation: keep - core_predicate: biolink:has_part -BFO:0000054: - operation: keep - core_predicate: biolink:related_to -BFO:0000055: - operation: keep - core_predicate: biolink:has_part -# BFO:0000056: -# invert: -# - has_participant -# - biolink:has_participant -BFO:0000062: - operation: invert - core_predicate: biolink:precedes -BFO:0000063: - operation: keep - core_predicate: biolink:precedes -BFO:0000066: - operation: keep - core_predicate: biolink:occurs_in -BFO:0000067: - operation: keep - core_predicate: biolink:occurs_in -BFO:0000068: - operation: keep - core_predicate: biolink:related_to -BFO:0000069: - operation: keep - core_predicate: biolink:related_to -BFO:0000117: - operation: keep - core_predicate: biolink:has_part -BFO:0000167: - operation: keep - core_predicate: biolink:has_participant -BSPO:0000096: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000097: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000098: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000099: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000100: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000102: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000104: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000107: - operation: keep - core_predicate: biolink:located_in -BSPO:0000108: - operation: keep - core_predicate: biolink:located_in -BSPO:0000110: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000113: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0000120: - operation: keep - core_predicate: biolink:located_in -BSPO:0000121: - operation: keep - core_predicate: biolink:located_in -BSPO:0000122: - operation: keep - core_predicate: biolink:located_in -BSPO:0000123: - operation: keep - core_predicate: biolink:located_in -BSPO:0000124: - operation: keep - core_predicate: biolink:located_in -BSPO:0000125: - operation: keep - core_predicate: biolink:located_in -BSPO:0000126: - operation: keep - core_predicate: biolink:located_in -BSPO:0001100: - operation: keep - core_predicate: biolink:located_in -BSPO:0001101: - operation: keep - core_predicate: biolink:located_in -BSPO:0001106: - operation: invert - core_predicate: biolink:has_part -BSPO:0001107: - operation: keep - core_predicate: biolink:located_in -BSPO:0001108: - operation: invert - core_predicate: biolink:has_part -BSPO:0001113: - operation: invert - core_predicate: biolink:has_part -BSPO:0001115: - operation: invert - core_predicate: biolink:has_part -BSPO:0005001: - operation: keep - core_predicate: biolink:overlaps -BSPO:0015001: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015002: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015003: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015005: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015006: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015007: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015008: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015009: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015012: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015014: - operation: keep - core_predicate: biolink:coexists_with -BSPO:0015101: - operation: keep - core_predicate: biolink:located_in -BSPO:0015102: - operation: keep - core_predicate: biolink:located_in -BSPO:0015202: - operation: keep - core_predicate: biolink:located_in -BTO:develops_from: - operation: keep - core_predicate: biolink:develops_from -BTO:related_to: - operation: keep - core_predicate: biolink:related_to -CHEBI:has_functional_parent: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEBI:has_parent_hydride: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEBI:is_conjugate_acid_of: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEBI:is_conjugate_base_of: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEBI:is_enantiomer_of: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEBI:is_substituent_group_from: - operation: invert - core_predicate: biolink:has_part -CHEBI:is_tautomer_of: - operation: keep - core_predicate: biolink:chemically_similar_to -CHEMBL.MECHANISM:activator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -CHEMBL.MECHANISM:agonist: - operation: keep - core_predicate: biolink:increases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: increases - object_aspect_qualifier: activity -CHEMBL.MECHANISM:allosteric_antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -CHEMBL.MECHANISM:antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -CHEMBL.MECHANISM:antisense_inhibitor: - operation: keep - core_predicate: biolink:decreases_expression_of -CHEMBL.MECHANISM:binding_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:blocker: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -CHEMBL.MECHANISM:chelating_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:cross-linking_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:degrader: - operation: keep - core_predicate: biolink:increases_degradation_of -CHEMBL.MECHANISM:disrupting_agent: - operation: keep - core_predicate: biolink:disrupts -CHEMBL.MECHANISM:equivalent_to: - operation: keep - core_predicate: biolink:same_as -CHEMBL.MECHANISM:hydrolytic_enzyme: - operation: keep - core_predicate: biolink:increases_degradation_of -CHEMBL.MECHANISM:inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -CHEMBL.MECHANISM:inverse_agonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -CHEMBL.MECHANISM:modulator: - operation: keep - core_predicate: biolink:entity_regulates_entity -CHEMBL.MECHANISM:negative_allosteric_modulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -CHEMBL.MECHANISM:negative_modulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -CHEMBL.MECHANISM:opener: - operation: keep - core_predicate: biolink:increases_activity_of -CHEMBL.MECHANISM:other: - operation: delete -CHEMBL.MECHANISM:overlaps_with: - operation: keep - core_predicate: biolink:overlaps -CHEMBL.MECHANISM:oxidative_enzyme: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:partial_agonist: - operation: keep - core_predicate: biolink:increases_activity_of -CHEMBL.MECHANISM:positive_allosteric_modulator: - operation: keep - core_predicate: biolink:increases_activity_of -CHEMBL.MECHANISM:positive_modulator: - operation: keep - core_predicate: biolink:increases_activity_of -CHEMBL.MECHANISM:proteolytic_enzyme: - operation: keep - core_predicate: biolink:increases_degradation_of -CHEMBL.MECHANISM:reducing_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:releasing_agent: - operation: keep - core_predicate: biolink:increases_expression_of -CHEMBL.MECHANISM:rnai_inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -CHEMBL.MECHANISM:sequestering_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:stabiliser: - operation: keep - core_predicate: biolink:increases_stability_of -CHEMBL.MECHANISM:subset_of: - operation: keep - core_predicate: biolink:subclass_of -CHEMBL.MECHANISM:substrate: - operation: keep - core_predicate: biolink:increases_degradation_of -CHEMBL.MECHANISM:superset_of: - operation: invert - core_predicate: biolink:subclass_of -CL:has_completed: - operation: keep - core_predicate: biolink:has_completed -CL:has_high_plasma_membrane_amount: - operation: keep - core_predicate: biolink:has_increased_amount -CL:has_low_plasma_membrane_amount: - operation: keep - core_predicate: biolink:has_decreased_amount -CL:has_not_completed: - operation: keep - core_predicate: biolink:has_not_completed -CL:lacks_part: - operation: keep - core_predicate: biolink:lacks_part -CL:lacks_plasma_membrane_part: - operation: keep - core_predicate: biolink:lacks_part -CPT:has_add_on_code: - operation: keep - core_predicate: biolink:related_to -CPT:mapped_to: - operation: keep - core_predicate: biolink:related_to -CTD:affects_abundance_of: - operation: keep - core_predicate: biolink:affects_abundance_of -CTD:affects_export: - operation: keep - core_predicate: biolink:affects_secretion_of -CTD:affects_folding_of: - operation: keep - core_predicate: biolink:affects_folding_of -CTD:affects_molecular_modification_of: - operation: keep - core_predicate: biolink:affects_molecular_modification_of -CTD:affects_mutation_rate_of: - operation: keep - core_predicate: biolink:affects_mutation_rate -CTD:affects_RNA_splicing: - operation: keep - core_predicate: biolink:affects_splicing_of -CTD:affects_secretion_of: - operation: keep - core_predicate: biolink:affects_secretion_of -CTD:affects_splicing_of: - operation: keep - core_predicate: biolink:affects_splicing_of -CTD:affects_synthesis_of: - operation: keep - core_predicate: biolink:affects_synthesis_of -CTD:affects_transport_of: - operation: keep - core_predicate: biolink:affects_transport_of -CTD:affects_uptake_of: - operation: keep - core_predicate: biolink:affects_uptake_of -CTD:decreases_degradation_of: - operation: keep - core_predicate: biolink:decreases_degradation_of -CTD:decreases_folding_of: - operation: keep - core_predicate: biolink:decreases_folding_of -CTD:decreases_localization_of: - operation: keep - core_predicate: biolink:decreases_localization_of -CTD:decreases_metabolic_processing_of: - operation: keep - core_predicate: biolink:decreases_metabolic_processing_of -CTD:decreases_molecular_modification_of: - operation: keep - core_predicate: biolink:decreases_molecular_modification_of -CTD:decreases_mutation_rate_of: - operation: keep - core_predicate: biolink:decreases_mutation_rate_of -CTD:decreases_RNA_splicing: - operation: keep - core_predicate: biolink:decreases_splicing_of -CTD:decreases_secretion_of: - operation: keep - core_predicate: biolink:decreases_secretion_of -CTD:decreases_splicing_of: - operation: keep - core_predicate: biolink:decreases_splicing_of -CTD:decreases_stability_of: - operation: keep - core_predicate: biolink:decreases_stability_of -CTD:decreases_transport_of: - operation: keep - core_predicate: biolink:decreases_transport_of -CTD:decreases_uptake_of: - operation: keep - core_predicate: biolink:decreases_uptake_of -CTD:increases_folding_of: - operation: keep - core_predicate: biolink:increases_folding_of -CTD:increases_localization_of: - operation: keep - core_predicate: biolink:increases_localization_of -CTD:increases_metabolic_processing_of: - operation: keep - core_predicate: biolink:increases_metabolic_processing_of -CTD:increases_molecular_modification_of: - operation: keep - core_predicate: biolink:increases_molecular_modification_of -CTD:increases_mutation_rate_of: - operation: keep - core_predicate: biolink:increases_mutation_rate_of -CTD:increases_RNA_splicing: - operation: keep - core_predicate: increases_splicing_of -CTD:increases_secretion_of: - operation: keep - core_predicate: increases_secretion_of -CTD:increases_splicing_of: - operation: keep - core_predicate: increases_splicing_of -CTD:increases_synthesis_of: - operation: keep - core_predicate: biolink:increases_synthesis_of -CTD:increases_uptake_of: - operation: keep - core_predicate: biolink:increases_uptake_of -CTD:positive_correlation: - operation: keep - core_predicate: biolink:positively_correlated_with -DDANAT:develops_from: - operation: keep - core_predicate: biolink:develops_from -DGIdb:activator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -# DGIdb:adduct: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -DGIdb:affects: - operation: keep - core_predicate: biolink:affects -DGIdb:agonist: - operation: keep - core_predicate: biolink:increases_activity_of -DGIdb:allosteric_modulator: - operation: keep - core_predicate: biolink:affects_activity_of -DGIdb:antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreases - object_aspect_qualifier: activity -DGIdb:antibody: - operation: keep - core_predicate: biolink:molecularly_interacts_with -# DGIdb:antisense: -# keep: -# - decreases_expression_of -# - biolink:decreases_expression_of -DGIdb:antisense_oligonucleotide: - operation: keep - core_predicate: biolink:decreases_expression_of -# DGIdb:binder: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -DGIdb:blocker: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -# DGIdb:channel_blocker: -# keep: -# - decreases_activity_of -# - biolink:decreases_activity_of -# DGIdb:chaperone: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -# DGIdb:cleavage: -# keep: -# - affects_degradation_of -# - biolink:affects_degradation_of -# DGIdb:cofactor: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -# DGIdb:gating_inhibitor: -# keep: -# - decreases_activity_of -# - biolink:decreases_activity_of -DGIdb:inducer: - operation: keep - core_predicate: biolink:increases_activity_of -DGIdb:inhibitor: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DGIdb:inhibitory_allosteric_modulator: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DGIdb:inverse_agonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -# DGIdb:ligand: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -DGIdb:modulator: - operation: keep - core_predicate: biolink:affects_activity_of -# DGIdb:multitarget: -# keep: -# - directly_interacts_with -# - biolink:directly_interacts_with -DGIdb:negative_modulator: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DGIdb:partial_agonist: - operation: keep - core_predicate: biolink:increases_activity_of -# DGIdb:partial_antagonist: -# keep: -# - decreases_activity_of -# - biolink:decreases_activity_of -# DGIdb:positive_allosteric_modulator: -# keep: -# - increases_activity_of -# - biolink:increases_activity_of -DGIdb:positive_modulator: - operation: keep - core_predicate: biolink:increases_activity_of -# DGIdb:potentiator: -# keep: -# - increases_activity_of -# - biolink:increases_activity_of -# DGIdb:product_of: -# keep: -# - derives_from -# - biolink:derives_from -# DGIdb:stimulator: -# keep: -# - increases_activity_of -# - biolink:increases_activity_of -# DGIdb:substrate: -# keep: -# - increases_degradation_of -# - biolink:increases_degradation_of -DGIdb:suppressor: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreases - object_aspect_qualifier: activity -DGIdb:vaccine: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -# DOID-PROPERTY:derives_from: -# keep: -# - derives_from -# - biolink:derives_from -# DOID-PROPERTY:has_symptom: -# keep: -# - has_phenotype -# - biolink:has_phenotype -DRUGBANK:activator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -DRUGBANK:adduct: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:aggregation_inhibitor: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:agonist: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:allosteric_modulator: - operation: keep - core_predicate: biolink:affects_activity_of -DRUGBANK:antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:antibody: - operation: keep - core_predicate: biolink:molecularly_interacts_with -DRUGBANK:antisense_oligonucleotide: - operation: keep - core_predicate: biolink:decreases_expression_of -DRUGBANK:atc-code: - operation: keep - core_predicate: biolink:close_match -DRUGBANK:atc-code-level: - operation: keep - core_predicate: biolink:related_to -DRUGBANK:binder: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:binding: - operation: keep - core_predicate: biolink:physically_interacts_with -DRUGBANK:blocker: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:category: - operation: keep - core_predicate: biolink:subclass_of -DRUGBANK:chaperone: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:chelator: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:cleavage: - operation: keep - core_predicate: biolink:affects_degradation_of -DRUGBANK:cofactor: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:component_of: - operation: invert - core_predicate: biolink:has_part -DRUGBANK:degradation: - operation: keep - core_predicate: biolink:affects_degradation_of -DRUGBANK:deoxidizer: - operation: keep - core_predicate: biolink:decreases_molecular_modification_of -DRUGBANK:desensitize_the_target: - operation: keep - core_predicate: biolink:decreases_response_to -DRUGBANK:downregulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:drug-interaction: - operation: keep - core_predicate: biolink:physically_interacts_with -DRUGBANK:external-identifier: - operation: keep - core_predicate: biolink:same_as -DRUGBANK:external-identifier-protein: - operation: keep - core_predicate: biolink:derives_from -DRUGBANK:gene_replacement: - operation: keep - core_predicate: biolink:close_match -DRUGBANK:group: - operation: keep - core_predicate: biolink:related_to -DRUGBANK:inactivator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:incorporation_into_and_destabilization: - operation: keep - core_predicate: biolink:affects_degradation_of -DRUGBANK:inducer: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:inhibition_of_synthesis: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:inhibitory_allosteric_modulator: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:intercalation: - operation: keep - core_predicate: biolink:molecularly_interacts_with -DRUGBANK:inverse_agonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:ligand: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:modulator: - operation: keep - core_predicate: biolink:entity_regulates_entity -DRUGBANK:multitarget: - operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:negative_modulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:neutralizer: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:nucleotide_exchange_blocker: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:oxidizer: - operation: keep - core_predicate: biolink:increases_molecular_modification_of -DRUGBANK:partial_agonist: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:partial_antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:pathway: - operation: keep - core_predicate: biolink:has_participant -DRUGBANK:positive_allosteric_modulator: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:positive_modulator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -DRUGBANK:potentiator: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:product_of: - operation: keep - core_predicate: biolink:derives_from -DRUGBANK:regulator: - operation: keep - core_predicate: biolink:entity_regulates_entity -DRUGBANK:stabilization: - operation: keep - core_predicate: biolink:increases_stability_of -DRUGBANK:stimulator: - operation: keep - core_predicate: biolink:increases_activity_of -DRUGBANK:substrate: - operation: keep - core_predicate: biolink:physically_interacts_with -DRUGBANK:suppressor: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DRUGBANK:target: - operation: keep - core_predicate: biolink:physically_interacts_with -DRUGBANK:translocation_inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DRUGBANK:weak_inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -# DrugCentral:5271: -# keep: -# - diagnoses -# - biolink:diagnoses -DrugCentral:activator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -DrugCentral:agonist: - operation: keep - core_predicate: biolink:increases_activity_of -DrugCentral:allosteric_antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DrugCentral:allosteric_modulator: - operation: keep - core_predicate: biolink:affects_activity_of -DrugCentral:antagonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DrugCentral:antibody_binding: - operation: keep - core_predicate: biolink:molecularly_interacts_with -DrugCentral:antisense_inhibitor: - operation: keep - core_predicate: biolink:decreases_expression_of -DrugCentral:binding_agent: - operation: keep - core_predicate: biolink:directly_interacts_with -DrugCentral:blocker: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DrugCentral:contraindication: - operation: keep - core_predicate: biolink:contraindicated_for -# DrugCentral:diagnosis: # A drug that helps diagnose a condition -# keep: -# - related_to -# - biolink:related_to -DrugCentral:gating_inhibitor: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -# DrugCentral:has_faers: -# keep: -# - causes_adverse_event -# - biolink:causes_adverse_event -DrugCentral:has_role: - operation: keep - core_predicate: biolink:related_to -DrugCentral:indication: - operation: keep - core_predicate: biolink:treats -DrugCentral:inhibitor: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DrugCentral:inverse_agonist: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -DrugCentral:modulator: - operation: keep - core_predicate: biolink:entity_regulates_entity -DrugCentral:negative_allosteric_modulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DrugCentral:negative_modulator: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -DrugCentral:off-label_use: - operation: keep - core_predicate: biolink:treats -DrugCentral:opener: - operation: keep - core_predicate: biolink:increases_activity_of -DrugCentral:PA: # PA stands for "Pharmacological Action" - operation: keep - core_predicate: biolink:subclass_of -DrugCentral:partial_agonist: - operation: keep - core_predicate: biolink:increases_activity_of -DrugCentral:pharmacological_chaperone: - operation: keep - core_predicate: biolink:directly_interacts_with -DrugCentral:positive_allosteric_modulator: - operation: keep - core_predicate: biolink:increases_activity_of -DrugCentral:positive_modulator: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -# DrugCentral:reduce_risk: -# keep: -# - prevents -# - biolink:prevents -DrugCentral:releasing_agent: - operation: keep - core_predicate: biolink:increases_expression_of -DrugCentral:struct2atc: - operation: keep - core_predicate: biolink:close_match -DrugCentral:substrate: - operation: keep - core_predicate: biolink:physically_interacts_with -DrugCentral:symptomatic_treatment: - operation: keep - core_predicate: biolink:treats -EFO:0000784: - operation: keep - core_predicate: biolink:located_in -EFO:0001697: - operation: invert - core_predicate: biolink:related_to -EFO:0006351: - operation: keep - core_predicate: biolink:related_to -EFO:is_executed_in: - operation: keep - core_predicate: biolink:related_to -ENVO:01001307: - operation: keep - core_predicate: biolink:coexists_with -FMA:SIB: - operation: delete -FMA:adheres_to: - operation: keep - core_predicate: biolink:physically_interacts_with -FMA:adjacent_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:afferent_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:anatomical_entity_observed_in: - operation: delete -FMA:anterior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:anteroinferior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:anterolateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:anteromedial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:anterosuperior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:arterial_supply_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:articulates_with: - operation: keep - core_predicate: biolink:coexists_with -FMA:attaches_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:bounded_by: - operation: keep - core_predicate: biolink:coexists_with -FMA:bounds: - operation: keep - core_predicate: biolink:coexists_with -FMA:branch_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:connected_to: - operation: keep - core_predicate: biolink:related_to -FMA:connection_type_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:constitutional_part_of: - operation: invert - core_predicate: biolink:has_part -FMA:contained_in: - operation: invert - core_predicate: biolink:has_part -FMA:contains: - operation: keep - core_predicate: biolink:has_part -FMA:continuation_branch_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:continuous_distally_with: - operation: keep - core_predicate: biolink:coexists_with -FMA:continuous_proximally_with: - operation: keep - core_predicate: biolink:coexists_with -FMA:continuous_with: - operation: keep - core_predicate: biolink:related_to -FMA:corresponds_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:derives: - operation: invert - core_predicate: biolink:derives_from -FMA:derives_from: - operation: keep - core_predicate: biolink:derives_from -FMA:development_type_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:developmental_stage_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:develops_from: - operation: keep - core_predicate: biolink:develops_from -FMA:develops_into: - operation: keep - core_predicate: biolink:develops_from -FMA:direct_cell_shape_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:direct_left_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:direct_right_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:distal_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:drains_into: - operation: keep - core_predicate: biolink:coexists_with -FMA:efferent_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:external_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:formed_by: - operation: keep - core_predicate: biolink:coexists_with -FMA:forms: - operation: keep - core_predicate: biolink:coexists_with -FMA:full_grown_phenotype_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:fuses_with: - operation: keep - core_predicate: biolink:coexists_with -FMA:fusion_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:germ_origin_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_adherent: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_arterial_supply: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_branch: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_connection_type: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_constitutional_part: - operation: keep - core_predicate: biolink:has_part -FMA:has_continuation_branch: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_development_type: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_developmental_stage: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_direct_cell_shape: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_full_grown_phenotype: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_fusion: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_germ_origin: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_inherent_3d_shape: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_insertion: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_location: - operation: keep - core_predicate: biolink:located_in -FMA:has_lymphatic_drainage: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_member: - operation: keep - core_predicate: biolink:has_part -FMA:has_nerve_supply: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_observed_anatomical_entity: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_origin: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_part: - operation: keep - core_predicate: biolink:has_part -FMA:has_primary_segmental_supply: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_projection: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_regional_part: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_related_developmental_entity: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_secondary_segmental_supply: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_segmental_composition: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_segmental_supply: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_tributary: - operation: keep - core_predicate: biolink:coexists_with -FMA:has_venous_drainage: - operation: keep - core_predicate: biolink:coexists_with -FMA:homonym_for: - operation: delete -FMA:homonym_of: - operation: keep - core_predicate: biolink:related_to -FMA:inferior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:inferolateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:inferomedial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:inherent_3d_shape_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:insertion_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:internal_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:lateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:left_lateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:left_medial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:location_of: - operation: invert - core_predicate: biolink:located_in -FMA:lymphatic_drainage_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:matures_from: - operation: keep - core_predicate: biolink:coexists_with -FMA:matures_into: - operation: keep - core_predicate: biolink:coexists_with -FMA:medial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:member_of: - operation: invert - core_predicate: biolink:has_part -FMA:merges_with: - operation: keep - core_predicate: biolink:coexists_with -FMA:nerve_supply_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:origin_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:part_of: - operation: invert - core_predicate: biolink:has_part -FMA:posterior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:posteroinferior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:posterolateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:posteromedial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:posterosuperior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:primary_segmental_supply_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:projects_from: - operation: keep - core_predicate: biolink:coexists_with -FMA:projects_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:proximal_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:receives_attachment_from: - operation: keep - core_predicate: biolink:coexists_with -FMA:receives_drainage_from: - operation: keep - core_predicate: biolink:coexists_with -FMA:receives_input_from: - operation: keep - core_predicate: biolink:coexists_with -FMA:receives_projection: - operation: keep - core_predicate: biolink:coexists_with -FMA:regional_part_of: - operation: invert - core_predicate: biolink:has_part -FMA:related_developmental_entity_of: - operation: invert - core_predicate: biolink:related_to -FMA:related_object: - operation: keep - core_predicate: biolink:related_to -FMA:related_part: - operation: keep - core_predicate: biolink:coexists_with -FMA:right_lateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:right_medial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:secondary_segmental_supply_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:segmental_composition_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:segmental_supply_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:sends_output_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:superior_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:superolateral_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:superomedial_to: - operation: keep - core_predicate: biolink:coexists_with -FMA:surrounded_by: - operation: keep - core_predicate: biolink:coexists_with -FMA:surrounds: - operation: keep - core_predicate: biolink:coexists_with -FMA:transforms_from: - operation: invert - core_predicate: biolink:precedes -FMA:transforms_into: - operation: keep - core_predicate: biolink:precedes -FMA:tributary_of: - operation: keep - core_predicate: biolink:coexists_with -FMA:venous_drainage_of: - operation: keep - core_predicate: biolink:coexists_with -FOODON:00001301: - operation: keep - core_predicate: biolink:model_of -FOODON:00001563: - operation: keep - core_predicate: biolink:has_part -FOODON:00002420: - operation: keep - core_predicate: biolink:has_part -GENEPIO:0001739: - operation: invert - core_predicate: biolink:precedes -GO:SIB: - operation: delete -GO:acts_upstream_of: - operation: keep - core_predicate: biolink:affects -GO:acts_upstream_of_negative_effect: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -GO:acts_upstream_of_or_within: - operation: keep - core_predicate: biolink:affects -GO:acts_upstream_of_or_within_negative_effect: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -GO:acts_upstream_of_or_within_positive_effect: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -GO:acts_upstream_of_positive_effect: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -GO:colocalizes_with: - operation: keep - core_predicate: biolink:colocalizes_with -GO:contributes_to: - operation: keep - core_predicate: biolink:contributes_to -GO:enables: - operation: keep - core_predicate: biolink:enables -GO:ends_during: - operation: keep - core_predicate: biolink:related_to -GO:happens_during: - operation: keep - core_predicate: biolink:related_to -GO:has_occurrence: - operation: keep - core_predicate: biolink:capable_of -GO:has_part: - operation: keep - core_predicate: biolink:has_part -GO:inverse_ends_during: - operation: keep - core_predicate: biolink:related_to -GO:inverse_happens_during: - operation: delete -GO:inverse_isa: - operation: invert - core_predicate: biolink:subclass_of -GO:involved_in: - operation: invert - core_predicate: biolink:has_participant -GO:is_active_in: - operation: keep - core_predicate: biolink:actively_involved_in -GO:isa: - operation: keep - core_predicate: biolink:subclass_of -GO:located_in: - operation: keep - core_predicate: biolink:located_in -GO:negatively_regulated_by: - operation: invert - core_predicate: biolink:entity_negatively_regulates_entity -GO:negatively_regulates: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -GO:occurs_in: - operation: keep - core_predicate: biolink:occurs_in -GO:part_of: - operation: invert - core_predicate: biolink:has_part -GO:positively_regulated_by: - operation: invert - core_predicate: biolink:entity_positively_regulates_entity -GO:positively_regulates: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -GO:regulated_by: - operation: invert - core_predicate: biolink:entity_regulates_entity -GO:regulates: - operation: keep - core_predicate: biolink:entity_regulates_entity -GOREL:0000040: - operation: keep - core_predicate: biolink:causes -GOREL:0002003: - operation: keep - core_predicate: biolink:affects_localization_of -GOREL:0002004: - operation: keep - core_predicate: biolink:increases_degradation_of -# GOREL:0002005: -# keep: -# - related_to -# - biolink:related_to -GOREL:0012006: - operation: keep - core_predicate: biolink:related_to -HANCESTRO:0301: - operation: keep - core_predicate: biolink:related_to -HANCESTRO:0308: # has country of origin - operation: keep - core_predicate: biolink:related_to -HANCESTRO:0330: - operation: keep - core_predicate: biolink:related_to -HCPCS:mapped_from: - operation: delete -HCPCS:mapped_to: - operation: keep - core_predicate: biolink:related_to -HMDB:at_cellular_location: - operation: keep - core_predicate: biolink:located_in -HMDB:at_tissue: - operation: keep - core_predicate: biolink:located_in -HMDB:disease: - operation: keep - core_predicate: biolink:related_to -HMDB:has_protein_association: - operation: keep - core_predicate: biolink:related_to -HMDB:in_biospecimen: - operation: keep - core_predicate: biolink:located_in -HMDB:in_pathway: - operation: invert - core_predicate: biolink:has_participant -HP:SIB: - operation: delete -IAO:0000039: - operation: keep - core_predicate: biolink:related_to -IAO:0000136: - operation: keep - core_predicate: biolink:related_to -IAO:0000219: - operation: keep - core_predicate: biolink:related_to -ICD10PCS:SIB: - operation: delete -ICD9:SIB: - operation: delete -IDO:0000664: - operation: invert - core_predicate: biolink:contributes_to -JensenLab:associated_with: - operation: keep - core_predicate: biolink:gene_associated_with_condition -KEGG:compound_to_enzyme: - operation: keep - core_predicate: biolink:interacts_with -KEGG:compound_to_pathway: - operation: invert - core_predicate: biolink:has_participant -KEGG:compound_to_reaction: - operation: invert - core_predicate: biolink:has_participant -KEGG:enzyme_to_pathway: - operation: invert - core_predicate: biolink:has_participant -KEGG:enzyme_to_reaction: - operation: keep - core_predicate: biolink:catalyzes -KEGG:glycan_to_enzyme: - operation: keep - core_predicate: biolink:interacts_with -KEGG:glycan_to_pathway: - operation: invert - core_predicate: biolink:has_participant -KEGG:glycan_to_reaction: - operation: invert - core_predicate: biolink:has_participant -KEGG:pathway_to_compound: - operation: keep - core_predicate: biolink:has_participant -KEGG:pathway_to_drug: - operation: keep - core_predicate: biolink:has_participant -KEGG:pathway_to_glycan: - operation: keep - core_predicate: biolink:has_participant -KEGG:reaction_to_enzyme: - operation: invert - core_predicate: biolink:catalyzes -KEGG:reaction_to_pathway: - operation: invert - core_predicate: biolink:has_participant -LOINC:adjustment_of: - operation: delete -LOINC:analyzed_by: - operation: delete -LOINC:analyzes: - operation: keep - core_predicate: biolink:related_to -LOINC:answer_to: - operation: delete -LOINC:archetype_of: - operation: delete -LOINC:associated_with: - operation: keep - core_predicate: biolink:correlated_with -LOINC:challenge_of: - operation: delete -LOINC:class_of: - operation: keep - core_predicate: biolink:subclass_of -LOINC:component_of: - operation: invert - core_predicate: biolink:has_part -LOINC:count_of: - operation: delete -LOINC:divisor_of: - operation: delete -LOINC:evaluation_of: - operation: delete -LOINC:fragments_for_synonyms_of: - operation: delete -LOINC:has_action_guidance: - operation: keep - core_predicate: biolink:related_to -LOINC:has_adjustment: - operation: keep - core_predicate: biolink:related_to -LOINC:has_aggregation_view: - operation: keep - core_predicate: biolink:related_to -LOINC:has_answer: - operation: keep - core_predicate: biolink:related_to -LOINC:has_approach_guidance: - operation: keep - core_predicate: biolink:related_to -LOINC:has_archetype: - operation: keep - core_predicate: biolink:subclass_of -LOINC:has_challenge: - operation: keep - core_predicate: biolink:related_to -LOINC:has_class: - operation: invert - core_predicate: biolink:subclass_of -LOINC:has_component: - operation: keep - core_predicate: biolink:has_part -LOINC:has_count: - operation: keep - core_predicate: biolink:related_to -LOINC:has_divisor: - operation: keep - core_predicate: biolink:related_to -LOINC:has_evaluation: - operation: keep - core_predicate: biolink:related_to -LOINC:has_exam: - operation: keep - core_predicate: biolink:related_to -LOINC:has_fragments_for_synonyms: - operation: keep - core_predicate: biolink:has_input -LOINC:has_given_pharmaceutical_substance: - operation: delete -LOINC:has_imaged_location: - operation: keep - core_predicate: biolink:occurs_in -LOINC:has_imaging_focus: - operation: keep - core_predicate: biolink:located_in -LOINC:has_lateral_anatomic_location: - operation: keep - core_predicate: biolink:coexists_with -LOINC:has_lateral_location_presence: - operation: keep - core_predicate: biolink:coexists_with -LOINC:has_loinc_number: - operation: delete -LOINC:has_member: - operation: keep - core_predicate: biolink:has_part -LOINC:has_method: - operation: keep - core_predicate: biolink:related_to -LOINC:has_modality_subtype: - operation: keep - core_predicate: biolink:related_to -LOINC:has_modality_type: - operation: keep - core_predicate: biolink:related_to -LOINC:has_multipart: - operation: delete -LOINC:has_object_guidance: - operation: keep - core_predicate: biolink:related_to -LOINC:has_parent_group: - operation: keep - core_predicate: biolink:subclass_of -LOINC:has_pharmaceutical_route: - operation: keep - core_predicate: biolink:related_to -LOINC:has_presence_guidance: - operation: delete -LOINC:has_property: - operation: delete -LOINC:has_scale: - operation: keep - core_predicate: biolink:related_to -LOINC:has_subject: - operation: keep - core_predicate: biolink:has_participant -LOINC:has_suffix: - operation: keep - core_predicate: biolink:related_to -LOINC:has_supersystem: - operation: invert - core_predicate: biolink:has_part -LOINC:has_system: - operation: keep - core_predicate: biolink:has_input -LOINC:has_time_aspect: - operation: keep - core_predicate: biolink:related_to -LOINC:has_time_modifier: - operation: keep - core_predicate: biolink:related_to -LOINC:has_timing_of: - operation: keep - core_predicate: biolink:related_to -LOINC:has_view_type: - operation: keep - core_predicate: biolink:related_to -LOINC:is_action_guidance_for: - operation: delete -LOINC:is_aggregation_view_of: - operation: delete -LOINC:is_approach_guidance_for: - operation: delete -LOINC:is_exam_for: - operation: delete -LOINC:is_given_pharmaceutical_substance_for: - operation: invert - core_predicate: biolink:has_participant -LOINC:is_imaged_location_for: - operation: delete -LOINC:is_imaging_focus_of: - operation: delete -LOINC:is_lateral_anatomic_location_of: - operation: delete -LOINC:is_modality_subtype_for: - operation: delete -LOINC:is_modality_type_for: - operation: delete -LOINC:is_object_guidance_for: - operation: delete -LOINC:is_pharmaceutical_route_for: - operation: delete -LOINC:is_presence_guidance_for: - operation: keep - core_predicate: biolink:subclass_of -LOINC:is_presence_of_lateral_location: - operation: delete -LOINC:is_subject_of: - operation: delete -LOINC:is_timing_for: - operation: delete -LOINC:is_view_type_for: - operation: delete -LOINC:loinc_number_of: - operation: delete -LOINC:mapped_from: - operation: delete -LOINC:mapped_to: - operation: keep - core_predicate: biolink:related_to -LOINC:measured_by: - operation: keep - core_predicate: biolink:related_to -LOINC:measures: - operation: delete -LOINC:member_of: - operation: invert - core_predicate: biolink:has_part -LOINC:method_of: - operation: delete -LOINC:mth_expanded_form_of: - operation: delete -LOINC:mth_has_expanded_form: - operation: keep - core_predicate: biolink:related_to -LOINC:multipart_of: - operation: invert - core_predicate: biolink:has_part -LOINC:parent_group_of: - operation: delete -LOINC:property_of: - operation: keep - core_predicate: biolink:related_to -LOINC:scale_of: - operation: delete -LOINC:suffix_of: - operation: delete -LOINC:supersystem_of: - operation: delete -LOINC:system_of: - operation: delete -LOINC:time_aspect_of: - operation: delete -LOINC:time_modifier_of: - operation: delete -MESH:AQ: - operation: delete -MESH:QB: - operation: delete -MESH:RO: - operation: keep - core_predicate: biolink:related_to -MESH:SIB: - operation: delete -MESH:has_mapping_qualifier: - operation: keep - core_predicate: biolink:related_to -MESH:inverse_isa: - operation: invert - core_predicate: biolink:subclass_of -MESH:isa: - operation: keep - core_predicate: biolink:subclass_of -MESH:mapped_from: - operation: delete -MESH:mapped_to: - operation: keep - core_predicate: biolink:related_to -MESH:mapping_qualifier_of: - operation: delete -MI:0192: # acetylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0194: # cleavage reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0195: # covalent bonding - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0197: # deacetylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0203: # dephosphorylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0204: # deubiquitination reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0210: # hydroxylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0211: # lipid addition - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0212: # lipoprotein cleavage reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0213: # methylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0214: # myristoylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0216: # palmitoylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0217: # phosphorylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0220: # ubiquitination reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0403: # colocalization - operation: keep - core_predicate: biolink:colocalizes_with -MI:0407: # direct interaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0408: # disulfide bond - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0414: # enzymatic reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0556: # transglutamination reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0557: # adp_ribosylation_reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0559: # glycosylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0566: # sumoylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0567: # neddylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0569: # deneddylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0570: # protein cleavage - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0572: # dna cleavage - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0844: # phosphotransfer reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0871: # demethylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0882: # atpase reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0883: # gtpase reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0902: # rna reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:0914: # association - operation: keep - core_predicate: biolink:interacts_with -MI:0915: # physical associaiton - operation: keep - core_predicate: biolink:physically_interacts_with -MI:0945: # oxidoreductase activity electron transfer reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:1126: # self interaction - operation: keep - core_predicate: biolink:interacts_with -MI:1127: # putative self interaction - operation: keep - core_predicate: biolink:interacts_with -MI:1148: # ampylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:1237: # proline isomerization reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:1310: # de-ADP-ribosylation reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MI:2364: # proximity - operation: keep - core_predicate: biolink:colocalizes_with -MI:2252: # guanine nucleotide exchange factor reaction - operation: keep - core_predicate: biolink:directly_interacts_with -MONDO:0100332: # disease has primary infectious agent - operation: invert - core_predicate: biolink:causes -MONDO:0100333: # disease caused by reactivation of latent infectious agent - operation: invert - core_predicate: biolink:causes -MONDO:disease_causes_feature: - operation: keep - core_predicate: biolink:causes -MONDO:disease_has_basis_in_accumulation_of: - operation: keep - core_predicate: biolink:disease_has_basis_in -MONDO:disease_has_basis_in_development_of: - operation: keep - core_predicate: biolink:disease_has_basis_in -MONDO:disease_has_major_feature: - operation: keep - core_predicate: biolink:has_part -MONDO:disease_responds_to: - operation: invert - core_predicate: biolink:treats -MONDO:disease_shares_features_of: - operation: keep - core_predicate: biolink:related_to -MONDO:disease_triggers: - operation: keep - core_predicate: biolink:causes -MONDO:equivalentTo: - operation: keep - core_predicate: biolink:same_as -MONDO:has_onset: - operation: keep - core_predicate: biolink:related_to -MONDO:has_onset_before: - operation: keep - core_predicate: biolink:related_to -MONDO:has_onset_during_or_after: - operation: keep - core_predicate: biolink:related_to -MONDO:part_of_progression_of_disease: - operation: invert - core_predicate: biolink:has_part -MONDO:predisposes_towards: - operation: keep - core_predicate: biolink:contributes_to -# NBO-PROPERTY:by_means: -# keep: -# - actively_involved_in -# - biolink:actively_involved_in -# NBO-PROPERTY:has_participant: -# keep: -# - has_participant -# - biolink:has_participant -# NBO-PROPERTY:in_response_to: -# invert: -# - causes -# - biolink:causes -# NBO-PROPERTY:is_about: -# keep: -# - related_to -# - biolink:related_to -NCIT:abnormal_cell_affected_by_chemical_or_drug: - operation: delete -NCIT:abnormality_associated_with_allele: - operation: delete -NCIT:activity_of_allele: - operation: delete -NCIT:allele_absent_from_wild-type_chromosomal_location: - operation: keep - core_predicate: biolink:located_in -NCIT:allele_has_abnormality: - operation: keep - core_predicate: biolink:causes -NCIT:allele_has_activity: - operation: keep - core_predicate: biolink:has_molecular_consequence -NCIT:allele_in_chromosomal_location: - operation: keep - core_predicate: biolink:located_in -NCIT:allele_plays_altered_role_in_process: - operation: keep - core_predicate: biolink:affects -NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: - operation: keep - core_predicate: biolink:affects -NCIT:anatomic_structure_has_location: - operation: delete -NCIT:anatomic_structure_is_physical_part_of: - operation: invert - core_predicate: biolink:has_part -NCIT:anatomy_originated_from_biological_process: - operation: delete -NCIT:associated_with_malfunction_of_gene_product: - operation: delete -NCIT:biological_process_has_associated_location: - operation: keep - core_predicate: biolink:affects -NCIT:biological_process_has_initiator_chemical_or_drug: - operation: delete -NCIT:biological_process_has_initiator_process: - operation: delete -NCIT:biological_process_has_result_anatomy: - operation: keep - core_predicate: biolink:has_output -NCIT:biological_process_has_result_biological_process: - operation: keep - core_predicate: biolink:causes -NCIT:biological_process_has_result_chemical_or_drug: - operation: keep - core_predicate: biolink:produces -NCIT:biological_process_involves_chemical_or_drug: - operation: invert - core_predicate: biolink:actively_involved_in -NCIT:biological_process_involves_gene_product: - operation: delete -NCIT:biological_process_is_part_of_process: - operation: delete -NCIT:biological_process_results_from_biological_process: - operation: delete -NCIT:biomarker_type_includes_gene: - operation: delete -NCIT:biomarker_type_includes_gene_product: - operation: delete -# NCIT:C15220: # diagnosis -# keep: -# - diagnoses -# - biolink:diagnoses -NCIT:cdrh_parent_of: - operation: invert - core_predicate: biolink:subclass_of -NCIT:cell_type_is_associated_with_eo_disease: - operation: delete -NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: - operation: delete -NCIT:chemical_or_drug_affects_abnormal_cell: - operation: keep - core_predicate: biolink:affects -NCIT:chemical_or_drug_affects_cell_type_or_tissue: - operation: keep - core_predicate: biolink:affects -NCIT:chemical_or_drug_affects_gene_product: - operation: keep - core_predicate: biolink:affects -NCIT:chemical_or_drug_has_mechanism_of_action: - operation: keep - core_predicate: biolink:affects -NCIT:chemical_or_drug_has_physiologic_effect: - operation: keep - core_predicate: biolink:causes -NCIT:chemical_or_drug_initiates_biological_process: - operation: keep - core_predicate: biolink:causes -NCIT:chemical_or_drug_is_metabolized_by_enzyme: - operation: delete -NCIT:chemical_or_drug_is_product_of_biological_process: - operation: delete -NCIT:chemical_or_drug_metabolism_is_associated_with_allele: - operation: delete -NCIT:chemical_or_drug_plays_role_in_biological_process: - operation: delete -NCIT:chemotherapy_regimen_has_component: - operation: delete -NCIT:chromosomal_location_of_allele: - operation: delete -NCIT:chromosomal_location_of_wild-type_gene: - operation: delete -NCIT:chromosome_involved_in_cytogenetic_abnormality: - operation: delete -NCIT:chromosome_mapped_to_disease: - operation: keep - core_predicate: biolink:causes -NCIT:completely_excised_anatomy_has_procedure: - operation: delete -NCIT:completely_excised_anatomy_may_have_procedure: - operation: delete -NCIT:complex_has_physical_part: - operation: keep - core_predicate: biolink:has_part -NCIT:concept_in_subset: - operation: delete -NCIT:conceptual_part_of: - operation: invert - core_predicate: biolink:has_part -NCIT:ctcae_5_parent_of: - operation: invert - core_predicate: biolink:subclass_of -NCIT:cytogenetic_abnormality_involves_chromosome: - operation: keep - core_predicate: biolink:affects -NCIT:data_element_of: - operation: delete -NCIT:disease_excludes_abnormal_cell: - operation: delete -NCIT:disease_excludes_cytogenetic_abnormality: - operation: delete -NCIT:disease_excludes_finding: - operation: delete -NCIT:disease_excludes_metastatic_anatomic_site: - operation: delete -NCIT:disease_excludes_molecular_abnormality: - operation: delete -NCIT:disease_excludes_normal_cell_origin: - operation: delete -NCIT:disease_excludes_normal_tissue_origin: - operation: delete -NCIT:disease_excludes_primary_anatomic_site: - operation: delete -NCIT:disease_has_abnormal_cell: - operation: delete -NCIT:disease_has_accepted_treatment_with_regimen: - operation: delete -NCIT:disease_has_associated_anatomic_site: - operation: keep - core_predicate: biolink:affects -NCIT:disease_has_associated_disease: - operation: keep - core_predicate: biolink:has_real_world_evidence_of_association_with -NCIT:disease_has_associated_gene: - operation: delete -NCIT:disease_has_cytogenetic_abnormality: - operation: delete -NCIT:disease_has_finding: - operation: invert - core_predicate: biolink:biomarker_for -NCIT:disease_has_metastatic_anatomic_site: - operation: keep - core_predicate: biolink:affects -NCIT:disease_has_molecular_abnormality: - operation: invert - core_predicate: biolink:biomarker_for -NCIT:disease_has_normal_cell_origin: - operation: delete -NCIT:disease_has_normal_tissue_origin: - operation: keep - core_predicate: biolink:causes -NCIT:disease_has_primary_anatomic_site: - operation: keep - core_predicate: biolink:affects -NCIT:disease_is_grade: - operation: keep - core_predicate: biolink:related_to -NCIT:disease_is_marked_by_gene: - operation: invert - core_predicate: biolink:biomarker_for -NCIT:disease_is_stage: - operation: keep - core_predicate: biolink:related_to -NCIT:disease_mapped_to_chromosome: - operation: delete -NCIT:disease_mapped_to_gene: - operation: delete -NCIT:disease_may_have_abnormal_cell: - operation: keep - core_predicate: biolink:affects -NCIT:disease_may_have_associated_disease: - operation: keep - core_predicate: biolink:related_to -NCIT:disease_may_have_cytogenetic_abnormality: - operation: delete -NCIT:disease_may_have_finding: - operation: keep - core_predicate: biolink:has_phenotype -NCIT:disease_may_have_molecular_abnormality: - operation: keep - core_predicate: biolink:has_phenotype -NCIT:disease_may_have_normal_cell_origin: - operation: delete -NCIT:endogenous_product_related_to: - operation: delete -NCIT:enzyme_metabolizes_chemical_or_drug: - operation: keep - core_predicate: biolink:increases_metabolic_processing_of -NCIT:eo_anatomy_is_associated_with_eo_disease: - operation: delete -NCIT:eo_disease_has_associated_cell_type: - operation: keep - core_predicate: biolink:affects -NCIT:eo_disease_has_associated_eo_anatomy: - operation: keep - core_predicate: biolink:affects -NCIT:eo_disease_has_property_or_attribute: - operation: keep - core_predicate: biolink:related_to -NCIT:eo_disease_maps_to_human_disease: - operation: delete -NCIT:excised_anatomy_has_procedure: - operation: delete -NCIT:excised_anatomy_may_have_procedure: - operation: delete -NCIT:gene_associated_with_disease: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:gene_encodes_gene_product: - operation: invert - core_predicate: biolink:gene_product_of -NCIT:gene_found_in_organism: - operation: keep - core_predicate: biolink:in_taxon -NCIT:gene_has_abnormality: - operation: delete -NCIT:gene_has_physical_location: - operation: keep - core_predicate: biolink:located_in -NCIT:gene_in_chromosomal_location: - operation: keep - core_predicate: biolink:located_in -NCIT:gene_involved_in_molecular_abnormality: - operation: keep - core_predicate: biolink:actively_involved_in -NCIT:gene_involved_in_pathogenesis_of_disease: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:gene_is_biomarker_of: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:gene_is_biomarker_type: - operation: keep - core_predicate: biolink:subclass_of -NCIT:gene_is_element_in_pathway: - operation: invert - core_predicate: biolink:has_participant -NCIT:gene_mapped_to_disease: - operation: keep - core_predicate: biolink:affects -NCIT:gene_mutant_encodes_gene_product_sequence_variation: - operation: invert - core_predicate: biolink:gene_product_of -NCIT:gene_plays_role_in_process: - operation: invert - core_predicate: biolink:has_participant -NCIT:gene_product_affected_by_chemical_or_drug: - operation: delete -NCIT:gene_product_encoded_by_gene: - operation: delete -NCIT:gene_product_expressed_in_tissue: - operation: keep - core_predicate: biolink:expressed_in -NCIT:gene_product_has_abnormality: - operation: keep - core_predicate: biolink:affects -NCIT:gene_product_has_associated_anatomy: - operation: keep - core_predicate: biolink:expressed_in -NCIT:gene_product_has_biochemical_function: - operation: keep - core_predicate: biolink:capable_of -NCIT:gene_product_has_chemical_classification: - operation: keep - core_predicate: biolink:subclass_of -NCIT:gene_product_has_gene_product_variant: - operation: delete -NCIT:gene_product_has_organism_source: - operation: keep - core_predicate: biolink:in_taxon -NCIT:gene_product_has_structural_domain_or_motif: - operation: keep - core_predicate: biolink:has_part -NCIT:gene_product_is_biomarker_of: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:gene_product_is_biomarker_type: - operation: keep - core_predicate: biolink:subclass_of -NCIT:gene_product_is_element_in_pathway: - operation: invert - core_predicate: biolink:has_participant -NCIT:gene_product_is_physical_part_of: - operation: invert - core_predicate: biolink:has_participant -NCIT:gene_product_malfunction_associated_with_disease: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:gene_product_plays_role_in_biological_process: - operation: invert - core_predicate: biolink:has_participant -NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: - operation: keep - core_predicate: biolink:is_sequence_variant_of -NCIT:gene_product_variant_of_gene_product: - operation: keep - core_predicate: biolink:is_sequence_variant_of -NCIT:genetic_biomarker_related_to: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:has_cdrh_parent: - operation: delete -NCIT:has_conceptual_part: - operation: delete -NCIT:has_ctcae_5_parent: - operation: delete -NCIT:has_data_element: - operation: keep - core_predicate: biolink:related_to -NCIT:has_free_acid_or_base_form: - operation: delete -NCIT:has_gene_product_element: - operation: delete -NCIT:has_inc_parent: - operation: keep - core_predicate: biolink:subclass_of -NCIT:has_nichd_parent: - operation: keep - core_predicate: biolink:subclass_of -NCIT:has_pharmaceutical_administration_method: - operation: keep - core_predicate: biolink:related_to -NCIT:has_pharmaceutical_basic_dose_form: - operation: keep - core_predicate: biolink:related_to -NCIT:has_pharmaceutical_intended_site: - operation: keep - core_predicate: biolink:related_to -NCIT:has_pharmaceutical_release_characteristics: - operation: keep - core_predicate: biolink:related_to -NCIT:has_pharmaceutical_state_of_matter: - operation: keep - core_predicate: biolink:related_to -NCIT:has_pharmaceutical_transformation: - operation: keep - core_predicate: biolink:related_to -NCIT:has_physical_part_of_anatomic_structure: - operation: delete -NCIT:has_salt_form: - operation: keep - core_predicate: biolink:chemically_similar_to -NCIT:has_target: - operation: keep - core_predicate: biolink:physically_interacts_with -NCIT:human_disease_maps_to_eo_disease: - operation: keep - core_predicate: biolink:related_to -NCIT:inc_parent_of: - operation: delete -NCIT:imaged_anatomy_has_procedure: - operation: delete -NCIT:is_abnormal_cell_of_disease: - operation: keep - core_predicate: biolink:related_to -NCIT:is_abnormality_of_gene: - operation: delete -NCIT:is_abnormality_of_gene_product: - operation: delete -NCIT:is_associated_anatomic_site_of: - operation: delete -NCIT:is_associated_anatomy_of_gene_product: - operation: delete -NCIT:is_associated_disease_of: - operation: keep - core_predicate: biolink:correlated_with -NCIT:is_biochemical_function_of_gene_product: - operation: delete -NCIT:is_chemical_classification_of_gene_product: - operation: delete -NCIT:is_chromosomal_location_of_gene: - operation: delete -NCIT:is_component_of_chemotherapy_regimen: - operation: invert - core_predicate: biolink:has_part -NCIT:is_cytogenetic_abnormality_of_disease: - operation: invert - core_predicate: biolink:correlated_with -NCIT:is_finding_of_disease: - operation: delete -NCIT:is_grade_of_disease: - operation: delete -NCIT:is_location_of_anatomic_structure: - operation: keep - core_predicate: biolink:located_in -NCIT:is_location_of_biological_process: - operation: delete -NCIT:is_marked_by_gene_product: - operation: delete -NCIT:is_mechanism_of_action_of_chemical_or_drug: - operation: delete -NCIT:is_metastatic_anatomic_site_of_disease: - operation: delete -NCIT:is_molecular_abnormality_of_disease: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:is_normal_cell_origin_of_disease: - operation: invert - core_predicate: biolink:derives_from -NCIT:is_normal_tissue_origin_of_disease: - operation: delete -NCIT:is_not_abnormal_cell_of_disease: - operation: delete -NCIT:is_not_cytogenetic_abnormality_of_disease: - operation: delete -NCIT:is_not_finding_of_disease: - operation: delete -NCIT:is_not_metastatic_anatomic_site_of_disease: - operation: delete -NCIT:is_not_molecular_abnormality_of_disease: - operation: delete -NCIT:is_not_normal_cell_origin_of_disease: - operation: delete -NCIT:is_not_normal_tissue_origin_of_disease: - operation: delete -NCIT:is_not_primary_anatomic_site_of_disease: - operation: delete -NCIT:is_organism_source_of_gene_product: - operation: invert - core_predicate: biolink:in_taxon -NCIT:is_physical_location_of_gene: - operation: delete -NCIT:is_physiologic_effect_of_chemical_or_drug: - operation: delete -NCIT:is_primary_anatomic_site_of_disease: - operation: delete -NCIT:is_property_or_attribute_of_eo_disease: - operation: delete -NCIT:is_qualified_by: - operation: keep - core_predicate: biolink:related_to -NCIT:is_related_to_endogenous_product: - operation: keep - core_predicate: biolink:related_to -NCIT:is_stage_of_disease: - operation: delete -NCIT:is_structural_domain_or_motif_of_gene_product: - operation: delete -NCIT:is_target: - operation: delete -NCIT:kind_is_domain_of: - operation: delete -NCIT:kind_is_range_of: - operation: delete -NCIT:may_be_abnormal_cell_of_disease: - operation: delete -NCIT:may_be_associated_disease_of_disease: - operation: delete -NCIT:may_be_cytogenetic_abnormality_of_disease: - operation: delete -NCIT:may_be_finding_of_disease: - operation: delete -NCIT:may_be_molecular_abnormality_of_disease: - operation: delete -NCIT:may_be_normal_cell_origin_of_disease: - operation: invert - core_predicate: biolink:derives_from -NCIT:molecular_abnormality_involves_gene: - operation: delete -NCIT:neoplasm_has_special_category: - operation: keep - core_predicate: biolink:subclass_of -NCIT:nichd_parent_of: - operation: delete -NCIT:organism_has_gene: - operation: invert - core_predicate: biolink:in_taxon -NCIT:partially_excised_anatomy_has_procedure: - operation: delete -NCIT:partially_excised_anatomy_may_have_procedure: - operation: delete -NCIT:pathogenesis_of_disease_involves_gene: - operation: delete -NCIT:pathway_has_gene_element: - operation: keep - core_predicate: biolink:has_participant -NCIT:pharmaceutical_administration_method_of: - operation: delete -NCIT:pharmaceutical_basic_dose_form_of: - operation: delete -NCIT:pharmaceutical_intended_site_of: - operation: delete -NCIT:pharmaceutical_release_characteristics_of: - operation: delete -NCIT:pharmaceutical_state_of_matter_of: - operation: delete -NCIT:pharmaceutical_transformation_of: - operation: delete -NCIT:procedure_has_completely_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_has_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_has_imaged_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_has_target_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_has_partially_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_may_have_completely_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_may_have_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:procedure_may_have_partially_excised_anatomy: - operation: keep - core_predicate: biolink:located_in -NCIT:process_altered_by_allele: - operation: delete -NCIT:process_includes_biological_process: - operation: keep - core_predicate: biolink:has_participant -NCIT:process_initiates_biological_process: - operation: keep - core_predicate: biolink:causes -NCIT:process_involves_gene: - operation: keep - core_predicate: biolink:has_participant -NCIT:qualifier_applies_to: - operation: keep - core_predicate: biolink:related_to -# NCIT:R40: -# keep: -# - located_in -# - biolink:located_in -NCIT:R81: - operation: keep - core_predicate: biolink:related_to -NCIT:R82: - operation: keep - core_predicate: biolink:part_of -# NCIT:R88: # disease is stage -# keep: -# - related_to -# - biolink:related_to -# NCIT:R89: -# keep: -# - has_phenotype -# - biolink:has_phenotype -# NCIT:R108: -# keep: -# - has_phenotype -# - biolink:has_phenotype -# NCIT:R115: -# keep: -# - has_phenotype -# - biolink:has_phenotype -# NCIT:R145: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R155: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R156: -# keep: -# - located_in -# - biolink:located_in -NCIT:R163: - operation: keep - core_predicate: biolink:related_to -# NCIT:R165: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R166: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R167: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R168: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R169: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R170: -# keep: -# - located_in -# - biolink:located_in -# NCIT:R171: -# keep: -# - located_in -# - biolink:located_in -NCIT:regimen_has_accepted_use_for_disease: - operation: keep - core_predicate: biolink:treats -NCIT:related_to_genetic_biomarker: - operation: delete -NCIT:role_has_domain: - operation: keep - core_predicate: biolink:related_to -NCIT:role_has_parent: - operation: keep - core_predicate: biolink:subclass_of -NCIT:role_has_range: - operation: keep - core_predicate: biolink:related_to -NCIT:role_is_parent_of: - operation: delete -NCIT:special_category_includes_neoplasm: - operation: delete -NCIT:subset_includes_concept: - operation: invert - core_predicate: biolink:subclass_of -NCIT:target_anatomy_has_procedure: - operation: delete -NCIT:tissue_is_expression_site_of_gene_product: - operation: delete -NDDF:dose_form_of: - operation: delete -NDDF:has_dose_form: - operation: keep - core_predicate: biolink:subclass_of -NDDF:has_ingredient: - operation: keep - core_predicate: biolink:has_part -NDDF:ingredient_of: - operation: invert - core_predicate: biolink:has_part -OBI:0000293: - operation: keep - core_predicate: biolink:has_participant -OBI:0000295: - operation: invert - core_predicate: biolink:has_participant -OBI:0000299: - operation: keep - core_predicate: biolink:has_output -OBI:0000417: # achieves planned objective - operation: keep - core_predicate: biolink:has_output -OBI:0001927: - operation: invert - core_predicate: biolink:related_to -OBO:INO_0000154: - operation: keep - core_predicate: biolink:related_to -OBO:bspo#parallel_to: - operation: keep - core_predicate: biolink:coexists_with -# OBO:doid#has_symptom: -# keep: -# - has_phenotype -# - biolink:has_phenotype -OBO:envo#has_increased_levels_of: - operation: keep - core_predicate: biolink:related_to -OBO:exo#interacts_with: - operation: keep - core_predicate: biolink:interacts_with -OBO:exo#interacts_with_an_exposure_stressor_via: - operation: keep - core_predicate: biolink:interacts_with -OBO:exo#interacts_with_an_exposure_receptor_via: - operation: keep - core_predicate: biolink:interacts_with -# OBO:exo.obo#interacts_with: -# keep: -# - interacts_with -# - biolink:interacts_with -# OBO:exo.obo#interacts_with_an_exposure_stressor_via: -# keep: -# - interacts_with -# - biolink:interacts_with -# OBO:exo.obo#interacts_with_an_exposure_receptor_via: -# keep: -# - interacts_with -# - biolink:interacts_with -OBO:has_role: - operation: keep - core_predicate: biolink:related_to -OBO:MF#manifestationOf: - operation: keep - core_predicate: biolink:manifestation_of -OBO:nbo#by_means: - operation: invert - core_predicate: biolink:actively_involved_in -OBO:nbo#has_participant: - operation: keep - core_predicate: biolink:has_participant -OBO:nbo#in_response_to: - operation: invert - core_predicate: biolink:causes -OBO:nbo#is_about: - operation: keep - core_predicate: biolink:related_to -# OBO:uo#is_unit_of: -# invert: -# - related_to -# - biolink:related_to -# OIO:hasDbXref: -# keep: -# - close_match -# - biolink:close_match -OMIM:allelic_variant_of: - operation: keep - core_predicate: biolink:is_sequence_variant_of -OMIM:has_allelic_variant: - operation: delete -OMIM:has_inheritance_type: - operation: keep - core_predicate: biolink:related_to -OMIM:has_manifestation: - operation: invert - core_predicate: biolink:subclass_of -OMIM:has_phenotype: - operation: keep - core_predicate: biolink:has_phenotype -OMIM:inheritance_type_of: - operation: delete -OMIM:manifestation_of: - operation: keep - core_predicate: biolink:manifestation_of -OMIM:phenotype_of: - operation: invert - core_predicate: biolink:has_phenotype -ORPHANET:317343: - operation: keep - core_predicate: biolink:causes -ORPHANET:317344: - operation: keep - core_predicate: biolink:causes -ORPHANET:317345: - operation: keep - core_predicate: biolink:correlated_with -ORPHANET:317346: - operation: keep - core_predicate: biolink:causes -ORPHANET:317348: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:317349: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:327767: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:410295: - operation: keep - core_predicate: biolink:causes -ORPHANET:410296: - operation: keep - core_predicate: biolink:causes -ORPHANET:465410: - operation: keep - core_predicate: biolink:biomarker_for -ORPHANET:C016: - operation: keep - core_predicate: biolink:related_to -ORPHANET:C017: - operation: keep - core_predicate: biolink:related_to -# PATO:0000085: # sensitivity toward -# keep: -# - associated_with_sensitivity_to -# - biolink:associated_with_sensitivity_to -# PATO:correlates_with: -# keep: -# - correlated_with -# - biolink:correlated_with -PATO:decreased_in_magnitude_relative_to: - operation: keep - core_predicate: biolink:related_to -PATO:has_cross_section: - operation: keep - core_predicate: biolink:related_to -PATO:has_relative_magnitude: - operation: keep - core_predicate: biolink:related_to -PATO:increased_in_magnitude_relative_to: - operation: keep - core_predicate: biolink:related_to -PATO:reciprocal_of: - operation: keep - core_predicate: biolink:related_to -PATO:towards: - operation: invert - core_predicate: biolink:actively_involved_in -PDQ:associated_disease: - operation: keep - core_predicate: biolink:correlated_with -PDQ:associated_genetic_condition: - operation: delete -PDQ:component_of: - operation: invert - core_predicate: biolink:has_part -PDQ:has_component: - operation: keep - core_predicate: biolink:has_part -PR:has_gene_template: - operation: keep - core_predicate: biolink:gene_product_of -PR:confers_resistance_to: - operation: keep - core_predicate: biolink:decreases_activity_of - qualified_predicate: biolink:causes - qualifiers: - object_direction_qualifier: decreased - object_aspect_qualifier: activity -PR:lacks_part: - operation: keep - core_predicate: biolink:lacks_part -PR:non-covalently_bound_to: - operation: keep - core_predicate: biolink:physically_interacts_with -PSY:RO: - operation: keep - core_predicate: biolink:related_to -PSY:RB: - operation: invert - core_predicate: biolink:subclass_of -PSY:use: - operation: keep - core_predicate: biolink:subclass_of -PSY:used_for: - operation: invert - core_predicate: biolink:has_input -PathWhiz:has_bound: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_compound: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_element_collection: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_element_in_bound: - operation: keep - core_predicate: biolink:has_part -PathWhiz:has_enzyme: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_left_element: - operation: keep - core_predicate: biolink:has_input -PathWhiz:has_location: - operation: keep - core_predicate: biolink:occurs_in -PathWhiz:has_nucleic_acid: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_protein: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_protein_in_complex: - operation: keep - core_predicate: biolink:has_part -PathWhiz:has_reaction: - operation: keep - core_predicate: biolink:has_participant -PathWhiz:has_right_element: - operation: keep - core_predicate: biolink:has_output -PathWhiz:in_species: - operation: keep - core_predicate: biolink:occurs_in -REACT:has_element: - operation: keep - core_predicate: biolink:has_part -REACT:has_event: - operation: keep - core_predicate: biolink:has_participant -REACT:has_input: - operation: keep - core_predicate: biolink:has_input -REACT:has_member: - operation: keep - core_predicate: biolink:has_part -REACT:has_output: - operation: keep - core_predicate: biolink:has_output -REACT:in_species: - operation: keep - core_predicate: biolink:occurs_in -REACT:linked_to_disease: - operation: keep - core_predicate: biolink:related_to -REACT:negatively_regulates: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -REACT:negatively_regulates_gene_expression: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -REACT:positively_regulates: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -REACT:positively_regulates_gene_expression: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -REACT:related_to: - operation: keep - core_predicate: biolink:related_to -REACT:is_requirement_for: - operation: keep - core_predicate: biolink:entity_regulates_entity -REPODB:clinically_tested_approved_unknown_phase: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_0: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_1: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_1_or_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_2_or_phase_3: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_3: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_0: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_1: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_1_or_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_2_or_phase_3: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_3: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_0: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_1: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_2: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: - operation: keep - core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_3: - operation: keep - core_predicate: biolink:treats -RO:0000052: - operation: keep - core_predicate: biolink:related_to -RO:0000053: - operation: keep - core_predicate: biolink:related_to -RO:0000056: - operation: invert - core_predicate: biolink:has_participant -RO:0000057: - operation: keep - core_predicate: biolink:has_participant -RO:0000059: - operation: keep - core_predicate: biolink:related_to -RO:0000086: - operation: keep - core_predicate: biolink:related_to -RO:0000087: - operation: keep - core_predicate: biolink:related_to -RO:0001000: - operation: keep - core_predicate: biolink:derives_from -RO:0001015: - operation: invert - core_predicate: biolink:located_in -RO:0001019: - operation: keep - core_predicate: biolink:has_part -RO:0001022: - operation: invert - core_predicate: biolink:causes -RO:0001025: - operation: keep - core_predicate: biolink:located_in -RO:0002001: - operation: keep - core_predicate: biolink:related_to -RO:0002002: - operation: keep - core_predicate: biolink:related_to -RO:0002005: - operation: keep - core_predicate: biolink:related_to -RO:0002007: - operation: invert - core_predicate: biolink:has_part -RO:0002008: - operation: keep - core_predicate: biolink:related_to -RO:0002082: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002083: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002087: - operation: invert - core_predicate: biolink:precedes -RO:0002090: - operation: keep - core_predicate: biolink:precedes -RO:0002092: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002093: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002100: - operation: keep - core_predicate: biolink:overlaps -RO:0002101: # fasciculates with - operation: keep - core_predicate: biolink:overlaps -RO:0002102: - operation: keep - core_predicate: biolink:overlaps -RO:0002103: - operation: keep - core_predicate: biolink:interacts_with -RO:0002104: - operation: keep - core_predicate: biolink:has_plasma_membrane_part -RO:0002120: - operation: keep - core_predicate: biolink:interacts_with -RO:0002130: - operation: keep - core_predicate: biolink:interacts_with -RO:0002131: - operation: keep - core_predicate: biolink:overlaps -RO:0002134: - operation: keep - core_predicate: biolink:related_to -RO:0002150: - operation: keep - core_predicate: biolink:related_to -RO:0002159: - operation: keep - core_predicate: biolink:related_to -RO:0002160: - operation: keep - core_predicate: biolink:in_taxon -RO:0002162: - operation: keep - core_predicate: biolink:in_taxon -RO:0002170: - operation: keep - core_predicate: biolink:related_to -RO:0002176: - operation: keep - core_predicate: biolink:related_to -RO:0002177: - operation: keep - core_predicate: biolink:related_to -RO:0002178: - operation: keep - core_predicate: biolink:related_to -RO:0002179: - operation: keep - core_predicate: biolink:related_to -RO:0002180: - operation: keep - core_predicate: biolink:has_part -RO:0002200: - operation: keep - core_predicate: biolink:has_phenotype -RO:0002202: - operation: keep - core_predicate: biolink:develops_from -RO:0002203: - operation: keep - core_predicate: biolink:develops_from -RO:0002207: - operation: keep - core_predicate: biolink:develops_from -RO:0002211: - operation: keep - core_predicate: biolink:regulates -RO:0002212: - operation: keep - core_predicate: biolink:process_negatively_regulates_process -RO:0002213: - operation: keep - core_predicate: biolink:process_positively_regulates_process -RO:0002215: - operation: keep - core_predicate: biolink:capable_of -RO:0002216: - operation: invert - core_predicate: biolink:has_participant -RO:0002219: - operation: keep - core_predicate: biolink:coexists_with -RO:0002220: - operation: keep - core_predicate: biolink:coexists_with -RO:0002221: - operation: keep - core_predicate: biolink:coexists_with -RO:0002223: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002224: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002225: - operation: keep - core_predicate: biolink:develops_from -RO:0002226: - operation: keep - core_predicate: biolink:develops_from -RO:0002229: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002230: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002231: - operation: keep - core_predicate: biolink:occurs_in -RO:0002232: - operation: keep - core_predicate: biolink:occurs_in -RO:0002233: - operation: keep - core_predicate: biolink:has_input -RO:0002234: - operation: keep - core_predicate: biolink:has_output -RO:0002241: - operation: keep - core_predicate: biolink:related_to -RO:0002254: - operation: keep - core_predicate: biolink:related_to -RO:0002256: - operation: keep - core_predicate: biolink: -RO:0002263: - operation: keep - core_predicate: biolink:acts_upstream_of -RO:0002264: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within -RO:0002285: - operation: invert - core_predicate: biolink:precedes -RO:0002292: - operation: invert - core_predicate: biolink:expressed_in -RO:0002295: - operation: keep - core_predicate: biolink:entity_regulates_entity -RO:0002296: - operation: keep - core_predicate: biolink:has_output -RO:0002297: - operation: keep - core_predicate: biolink:has_output -RO:0002298: - operation: keep - core_predicate: biolink:has_output -RO:0002299: - operation: keep - core_predicate: biolink:has_output -RO:0002303: - operation: keep - core_predicate: biolink:located_in -RO:0002309: - operation: keep - core_predicate: biolink:related_to -RO:0002313: - operation: keep - core_predicate: biolink:affects_transport_of -RO:0002314: - operation: keep - core_predicate: biolink:related_to -RO:0002315: - operation: keep - core_predicate: biolink:causes -RO:0002322: - operation: keep - core_predicate: biolink:related_to -RO:0002328: - operation: keep - core_predicate: biolink:related_to -RO:0002331: - operation: keep - core_predicate: biolink:actively_involved_in -RO:0002332: - operation: keep - core_predicate: biolink:related_to -RO:0002334: - operation: invert - core_predicate: biolink:entity_regulates_entity -RO:0002338: - operation: keep - core_predicate: biolink:related_to -RO:0002339: - operation: keep - core_predicate: biolink:related_to -RO:0002340: - operation: keep - core_predicate: biolink:affects_transport_of -RO:0002341: - operation: keep - core_predicate: biolink:related_to -RO:0002342: - operation: keep - core_predicate: biolink:related_to -RO:0002343: - operation: keep - core_predicate: biolink:affects -RO:0002344: - operation: keep - core_predicate: biolink:related_to -RO:0002345: - operation: keep - core_predicate: biolink:affects_transport_of -RO:0002348: - operation: keep - core_predicate: biolink:related_to -RO:0002349: - operation: keep - core_predicate: biolink:related_to -RO:0002350: - operation: invert - core_predicate: biolink:has_part -RO:0002351: - operation: keep - core_predicate: biolink:has_part -RO:0002352: - operation: invert - core_predicate: biolink:has_input -RO:0002353: - operation: invert - core_predicate: biolink:has_output -RO:0002354: - operation: invert - core_predicate: biolink:has_output -RO:0002355: - operation: keep - core_predicate: biolink:affects -RO:0002356: - operation: keep - core_predicate: biolink:related_to -RO:0002371: - operation: keep - core_predicate: biolink:related_to -RO:0002372: - operation: keep - core_predicate: biolink:related_to -RO:0002373: - operation: keep - core_predicate: biolink:related_to -RO:0002374: - operation: keep - core_predicate: biolink:related_to -RO:0002376: - operation: invert - core_predicate: biolink:has_part -RO:0002380: - operation: invert - core_predicate: biolink:has_part -RO:0002385: - operation: keep - core_predicate: biolink:related_to -RO:0002387: - operation: keep - core_predicate: biolink:related_to -RO:0002411: - operation: keep - core_predicate: biolink:precedes -RO:0002412: - operation: keep - core_predicate: biolink:precedes -RO:0002433: - operation: keep - core_predicate: biolink:overlaps -RO:0002434: - operation: keep - core_predicate: biolink:interacts_with -RO:0002451: - operation: keep - core_predicate: biolink:related_to -RO:0002452: # has symptom - operation: keep - core_predicate: biolink:has_phenotype -# RO:0002470: -# keep: -# - related_to -# - biolink:related_to -RO:0002473: - operation: keep - core_predicate: biolink:composed_primarily_of -RO:0002488: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002489: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002491: - operation: keep - core_predicate: biolink:coexists_with -RO:0002492: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002493: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002494: - operation: keep - core_predicate: biolink:related_to -RO:0002495: - operation: keep - core_predicate: biolink:related_to -RO:0002496: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002497: - operation: keep - core_predicate: biolink:temporally_related_to -RO:0002500: - operation: keep - core_predicate: biolink:capable_of -RO:0002503: - operation: keep - core_predicate: biolink:actively_involved_in -RO:0002505: - operation: keep - core_predicate: biolink:has_participant -RO:0002507: - operation: invert - core_predicate: biolink:causes -RO:0002509: - operation: invert - core_predicate: biolink:causes -RO:0002524: - operation: keep - core_predicate: biolink:has_part -RO:0002551: - operation: keep - core_predicate: biolink:has_part -RO:0002565: - operation: keep - core_predicate: biolink:has_participant -RO:0002568: - operation: keep - core_predicate: biolink:related_to -RO:0002571: - operation: invert - core_predicate: biolink:has_part -RO:0002572: - operation: invert - core_predicate: biolink:has_part -RO:0002573: - operation: keep - core_predicate: biolink:related_to -RO:0002576: - operation: invert - core_predicate: biolink:has_part -# RO:0002578: -# keep: -# - entity_regulates_entity -# - biolink:entity_regulates_entity -RO:0002588: - operation: keep - core_predicate: biolink:has_output -RO:0002590: - operation: keep - core_predicate: biolink:has_input -RO:0002591: - operation: keep - core_predicate: biolink:affects -RO:0002592: - operation: keep - core_predicate: biolink:affects -RO:0002608: - operation: invert - core_predicate: biolink:causes -RO:0002610: - operation: keep - core_predicate: biolink:correlated_with -# RO:0002629: -# keep: -# - entity_positively_regulates_entity -# - biolink:entity_positively_regulates_entity -# RO:0002630: -# keep: -# - entity_negatively_regulates_entity -# - biolink:entity_negatively_regulates_entity -RO:0003000: - operation: keep - core_predicate: biolink:produces -RO:0003001: - operation: invert - core_predicate: biolink:produces -RO:0003003: - operation: keep - core_predicate: biolink:increases_expression_of -RO:0003304: - operation: keep - core_predicate: biolink:contributes_to -RO:0003309: - operation: keep - core_predicate: biolink:exacerbates -RO:0004001: - operation: keep - core_predicate: biolink:causes -RO:0004007: - operation: keep - core_predicate: biolink:has_participant -RO:0004008: - operation: keep - core_predicate: biolink:has_output -RO:0004009: - operation: keep - core_predicate: biolink:has_input -RO:0004019: - operation: invert - core_predicate: biolink:causes -RO:0004020: - operation: keep - core_predicate: biolink:has_participant -RO:0004021: - operation: keep - core_predicate: biolink:has_participant -RO:0004022: - operation: keep - core_predicate: biolink:has_phenotype -RO:0004024: - operation: keep - core_predicate: biolink:disrupts -RO:0004025: - operation: keep - core_predicate: biolink:disrupts -RO:0004026: - operation: keep - core_predicate: biolink:disease_has_location -RO:0004027: - operation: keep - core_predicate: biolink:related_to -RO:0004028: - operation: invert - core_predicate: biolink:causes -RO:0004029: - operation: keep - core_predicate: biolink:associated_with -# RO:0004030: -# invert: -# - causes -# - biolink: -RO:0004032: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within_positive_effect -RO:0004033: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within_negative_effect -RO:0004034: - operation: keep - core_predicate: biolink:acts_upstream_of_positive_effect -RO:0004035: - operation: keep - core_predicate: biolink:acts_upstream_of_negative_effect -RO:0009001: - operation: keep - core_predicate: biolink:related_to -RO:0009004: - operation: keep - core_predicate: biolink:related_to -RO:0009501: - operation: invert - core_predicate: biolink:causes -RO:0012003: - operation: keep - core_predicate: biolink:affects -RO:0012008: # results in fusion of - operation: keep - core_predicate: biolink:affects -RO:0013001: # has synaptic IO in - operation: keep - core_predicate: biolink:related_to -RO:0014001: # disease has infectious agent - operation: keep - core_predicate: biolink:related_to -RO:participates_in: - operation: invert - core_predicate: biolink:has_participant -RXNORM:consists_of: - operation: keep - core_predicate: biolink:has_part -RXNORM:constitutes: - operation: invert - core_predicate: biolink:has_part -RXNORM:contained_in: - operation: invert - core_predicate: biolink:has_part -RXNORM:contains: - operation: keep - core_predicate: biolink:has_part -RXNORM:dose_form_of: - operation: delete -RXNORM:doseformgroup_of: - operation: delete -RXNORM:form_of: - operation: delete -RXNORM:has_dose_form: - operation: keep - core_predicate: biolink:subclass_of -RXNORM:has_doseformgroup: - operation: keep - core_predicate: biolink:subclass_of -RXNORM:has_form: - operation: keep - core_predicate: biolink:related_to -RXNORM:has_ingredient: - operation: keep - core_predicate: biolink:has_part -RXNORM:has_ingredients: - operation: delete -RXNORM:has_part: - operation: keep - core_predicate: biolink:has_part -RXNORM:has_precise_ingredient: - operation: delete -RXNORM:has_quantified_form: - operation: keep - core_predicate: biolink:close_match -RXNORM:has_tradename: - operation: keep - core_predicate: biolink:related_to -RXNORM:ingredient_of: - operation: invert - core_predicate: biolink:has_part -RXNORM:ingredients_of: - operation: invert - core_predicate: biolink:has_part -RXNORM:inverse_isa: - operation: invert - core_predicate: biolink:subclass_of -RXNORM:isa: - operation: keep - core_predicate: biolink:subclass_of -RXNORM:part_of: - operation: invert - core_predicate: biolink:has_part -RXNORM:precise_ingredient_of: - operation: invert - core_predicate: biolink:has_part -RXNORM:quantified_form_of: - operation: delete -RXNORM:reformulated_to: - operation: keep - core_predicate: biolink:related_to -RXNORM:reformulation_of: - operation: delete -RXNORM:tradename_of: - operation: delete -SEMMEDDB:1532: - operation: delete -SEMMEDDB:administered_to: - operation: keep - core_predicate: biolink:affects -SEMMEDDB:affects: - operation: keep - core_predicate: biolink:affects -SEMMEDDB:associated_with: - operation: keep - core_predicate: biolink:related_to -SEMMEDDB:augments: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -SEMMEDDB:causes: - operation: keep - core_predicate: biolink:causes -SEMMEDDB:coexists_with: - operation: keep - core_predicate: biolink:coexists_with -SEMMEDDB:compared_with: - operation: keep - core_predicate: biolink:related_to -SEMMEDDB:complicates: - operation: keep - core_predicate: biolink:exacerbates -SEMMEDDB:converts_to: - operation: invert - core_predicate: biolink:derives_from -SEMMEDDB:diagnoses: - operation: keep - core_predicate: biolink:diagnoses -SEMMEDDB:disrupts: - operation: keep - core_predicate: biolink:disrupts -SEMMEDDB:higher_than: - operation: keep - core_predicate: biolink:related_to -SEMMEDDB:inhibits: - operation: keep - core_predicate: biolink:entity_negatively_regulates_entity -SEMMEDDB:interacts_with: - operation: keep - core_predicate: biolink:interacts_with -SEMMEDDB:isa: - operation: keep - core_predicate: biolink:subclass_of -SEMMEDDB:location_of: - operation: invert - core_predicate: biolink:located_in -SEMMEDDB:lower_than: - operation: keep - core_predicate: biolink:related_to -SEMMEDDB:manifestation_of: - operation: keep - core_predicate: biolink:manifestation_of -SEMMEDDB:measurement_of: - operation: delete -SEMMEDDB:measures: - operation: keep - core_predicate: biolink:related_to -SEMMEDDB:method_of: - operation: delete -SEMMEDDB:nom: - operation: delete -SEMMEDDB:occurs_in: - operation: keep - core_predicate: biolink:occurs_in -SEMMEDDB:part_of: - operation: invert - core_predicate: biolink:has_part -SEMMEDDB:precedes: - operation: keep - core_predicate: biolink:precedes -SEMMEDDB:predisposes: - operation: keep - core_predicate: biolink:predisposes -SEMMEDDB:prep: - operation: delete -SEMMEDDB:prevents: - operation: keep - core_predicate: biolink:prevents -SEMMEDDB:process_of: - operation: keep - core_predicate: biolink:occurs_in -SEMMEDDB:produces: - operation: keep - core_predicate: biolink:produces -SEMMEDDB:same_as: - operation: keep - core_predicate: biolink:close_match -SEMMEDDB:stimulates: - operation: keep - core_predicate: biolink:entity_positively_regulates_entity -SEMMEDDB:treats: - operation: keep - core_predicate: biolink:treats -SEMMEDDB:uses: - operation: keep - core_predicate: biolink:has_input -SEMMEDDB:verb: - operation: delete -SEMMEDDB:xref: - operation: keep - core_predicate: biolink:related_to -SIO:000001: - operation: delete -# SIO:000983: -# keep: -# - biomarker_for -# - biolink:biomarker_for -# SIO:001331: # diagnosis -# keep: -# - diagnoses -# - biolink:diagnoses -# SO:adjacent_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# SO:contains: -# keep: -# - has_part -# - biolink:has_part -# SO:derives_from: -# keep: -# - coexists_with -# - biolink:coexists_with -# SO:guided_by: -# keep: -# - related_to -# - biolink:related_to -SO:has_origin: - operation: keep - core_predicate: biolink:coexists_with -# SO:has_part: -# keep: -# - has_part -# - biolink:has_part -# SO:has_quality: -# keep: -# - related_to -# - biolink:related_to -# SO:non_functional_homolog_of: -# keep: -# - homologous_to -# - biolink:homologous_to -# SO:member_of: -# invert: -# - has_part -# - biolink:has_part -# SO:overlaps: -# keep: -# - overlaps -# - biolink:overlaps -# SO:transcribed_from: -# keep: -# - gene_product_of -# - biolink:gene_product_of -# SO:transcribed_to: -# invert: -# - gene_product_of -# - biolink:gene_product_of -# UBERON:anastomoses_with: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:anteriorly_connected_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:channel_for: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:channels_from: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:channels_into: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:conduit_for: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:distally_connected_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:existence_starts_and_ends_during: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:extends_fibers_into: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:filtered_through: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:in_central_side_of: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:in_innermost_side_of: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:in_outermost_side_of: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:indirectly_supplies: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:posteriorly_connected_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:protects: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:proximally_connected_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:sexually_homologous_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON:site_of: -# invert: -# - occurs_in -# - biolink:occurs_in -# UBERON:subdivision_of: -# invert: -# - has_part -# - biolink:has_part -# UBERON:synapsed_by: -# keep: -# - related_to -# - biolink:related_to -UBERON_CORE:anastomoses_with: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:anteriorly_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:channel_for: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:channels_from: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:channels_into: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:conduit_for: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:distally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:extends_fibers_into: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:filtered_through: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:in_central_side_of: - operation: keep - core_predicate: biolink:located_in -UBERON_CORE:in_innermost_side_of: - operation: keep - core_predicate: biolink:located_in -UBERON_CORE:in_outermost_side_of: - operation: keep - core_predicate: biolink:located_in -UBERON_CORE:indirectly_supplies: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:posteriorly_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:protects: - operation: keep - core_predicate: biolink:related_to -UBERON_CORE:proximally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:sexually_homologous_to: - operation: keep - core_predicate: biolink:homologous_to -UBERON_CORE:site_of: - operation: keep - core_predicate: biolink:occurs_in -UBERON_CORE:subdivision_of: - operation: keep - core_predicate: biolink:part_of -UBERON_CORE:synapsed_by: - operation: keep - core_predicate: biolink:coexists_with -# UBERON_NONAMESPACE:connected_to: -# keep: -# - related_to -# - biolink:related_to -# UBERON_NONAMESPACE:distally_connected_to: -# keep: -# - coexists_with -# - biolink:coexists_with -# UBERON_NONAMESPACE:innervated_by: -# keep: -# - related_to -# - biolink:related_to -# UBERON_NONAMESPACE:subdivision_of: -# keep: -# - coexists_with -# - biolink:coexists_with -UMLS:has_physiologic_effect: - operation: keep - core_predicate: biolink:causes -UMLS:RB: - operation: keep - core_predicate: biolink:related_to -# UMLS:RN: -# keep: -# - related_to -# - biolink:related_to -UMLS:RO: - operation: keep - core_predicate: biolink:related_to -UMLS:RQ: - operation: keep - core_predicate: biolink:related_to -UMLS:SIB: - operation: delete -UMLS:SY: - operation: keep - core_predicate: biolink:close_match -UMLS:class_code_classified_by: - operation: keep - core_predicate: biolink:related_to -UMLS:classifies_class_code: - operation: delete -UMLS:component_of: - operation: invert - core_predicate: biolink:has_part -UMLS:context_binding_of: - operation: delete -UMLS:exhibited_by: - operation: keep - core_predicate: biolink:related_to -UMLS:exhibits: - operation: delete -UMLS:form_of: - operation: delete -UMLS:has_component: - operation: keep - core_predicate: biolink:has_part -UMLS:has_context_binding: - operation: keep - core_predicate: biolink:related_to -UMLS:has_form: - operation: keep - core_predicate: biolink:related_to -UMLS:has_mapping_qualifier: - operation: keep - core_predicate: biolink:related_to -UMLS:has_owning_affiliate: - operation: invert - core_predicate: biolink:has_part -UMLS:has_owning_section: - operation: delete -UMLS:has_owning_subsection: - operation: delete -UMLS:has_structural_class: - operation: keep - core_predicate: biolink:related_to -UMLS:has_supported_concept_property: - operation: keep - core_predicate: biolink:related_to -UMLS:has_supported_concept_relationship: - operation: keep - core_predicate: biolink:related_to -UMLS:larger_than: - operation: keep - core_predicate: biolink:related_to -UMLS:mapped_from: - operation: delete -UMLS:mapped_to: - operation: keep - core_predicate: biolink:related_to -UMLS:may_be_qualified_by: - operation: keep - core_predicate: biolink:related_to -UMLS:may_qualify: - operation: delete -UMLS:measured_by: - operation: delete -UMLS:measures: - operation: keep - core_predicate: biolink:related_to -UMLS:owning_affiliate_of: - operation: delete -UMLS:owning_section_of: - operation: keep - core_predicate: biolink:related_to -UMLS:owning_subsection_of: - operation: invert - core_predicate: biolink:has_part -UMLS:related_to: - operation: keep - core_predicate: biolink:related_to -UMLS:supported_concept_property_in: - operation: delete -UMLS:supported_concept_relationship_in: - operation: delete -# UO-PROPERTY:is_unit_of: -# keep: -# - related_to -# - biolink:related_to -VANDF:has_ingredient: - operation: keep - core_predicate: biolink:has_part -VANDF:ingredient_of: - operation: invert - core_predicate: biolink:has_part -VANDF:inverse_isa: - operation: invert - core_predicate: biolink:subclass_of -VANDF:isa: - operation: keep - core_predicate: biolink:subclass_of -biolink:in_taxon: - operation: keep - core_predicate: biolink:in_taxon -biolink:part_of: - operation: invert - core_predicate: biolink:has_part -biolink:subclass_of: - operation: keep - core_predicate: biolink:in_taxon -oboFormat:xref: - operation: keep - core_predicate: biolink:close_match -owl:inverseOf: - operation: keep - core_predicate: biolink:related_to -owl:sameAs: - operation: keep - core_predicate: biolink:same_as -rdf:type: - operation: keep - core_predicate: biolink:related_to -rdfs:subClassOf: - operation: keep - core_predicate: biolink:subclass_of -rdfs:subPropertyOf: - operation: keep - core_predicate: biolink:subclass_of diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index 6be2c06d..0b677769 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -132,6 +132,8 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_heirarchy: if biolink_curie not in BIOLINK_SLOT_TYPES_SKIP: external_to_biolink_mappings[external_curie][mapping_term].add(biolink_curie) +# Here it starts to look at predicate_remap. I think a bunch of the stuff above needs to be +# moved to validate_curies_to_urls_map.py pred_info = yaml.safe_load(open(predicate_remap_file_name, 'r')) for relation, instruction_dict in pred_info.items(): From 4958e5c31460f6f84e1b8b2a8a0497de0a68c1f2 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 15 Aug 2022 16:47:49 -0700 Subject: [PATCH 037/127] #226 #229 Update validate_predicate_remap_yaml.py --- validate_predicate_remap_yaml.py | 50 ++++++++++---------------------- 1 file changed, 15 insertions(+), 35 deletions(-) diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index 0b677769..f03679e8 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -136,35 +136,20 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_heirarchy: # moved to validate_curies_to_urls_map.py pred_info = yaml.safe_load(open(predicate_remap_file_name, 'r')) -for relation, instruction_dict in pred_info.items(): - command, subinfo = next(iter(instruction_dict.items())) - assert len(instruction_dict) == 1, relation - if command == 'keep' and not relation.startswith('biolink:'): - if not relation.startswith('BSPO:') and \ - not relation.startswith('FMA:') and \ - not relation.startswith('UBERON:'): - assert False, relation - else: - command = 'rename' - subinfo = ['coexists_with', 'biolink:coexists_with'] - if subinfo is not None: - predicate = subinfo[1] - if not predicate.startswith('biolink:') and not predicate.startswith('skos:closeMatch'): - if predicate.startswith('FMA:') or \ - predicate.startswith('BSPO:') or \ - predicate.startswith('UBERON:'): - command = 'rename' - subinfo = ['coexists_with', 'biolink:coexists_with'] - else: - assert False - if subinfo is not None: - assert subinfo[1] not in biolink_mixins, (relation, subinfo[1], {'Mixins': biolink_mixins}) - assert subinfo[1] not in inverted_relations, (relation, subinfo[1], {'Inverted Relations': inverted_relations}) - assert subinfo[1] in biolink_to_external_mappings, (relation, subinfo[1]) + for relation, instruction_dict in pred_info.items(): + operation = instruction_dict.get('operation', '') + assert operation != '', relation + core_predicate = instruction_dict.get('core_predicate', '') + assert core_predicate != '', relation + qualified_predicate = instruction_dict.get('qualified_predicate', '') + qualifiers = instruction_dict.get('qualifiers', '') + + assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) + assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) + assert core_predicate not in biolink_to_external_mappings, (relation, core_predicate) allowed_biolink_curies_set = set() - biolink_term_externals = external_to_biolink_mappings.get( - relation.lower(), None) + biolink_term_externals = external_to_biolink_mappings.get(relation.lower(), None) if biolink_term_externals is not None: mapping_term_used = "none" for mapping_term in mapping_hierarchy: @@ -174,11 +159,6 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_heirarchy: break if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) - assert subinfo[1] in allowed_biolink_curies_set, err_str - - else: - assert command == 'keep' or command == 'delete' - if command == 'keep': - assert relation in biolink_to_external_mappings, relation - assert relation.startswith( - 'biolink:') or relation.startswith('skos:') + assert core_predicate in allowed_biolink_curies_set, err_str + else: + assert operation == 'delete' From 6a3a2298355474a94a3fc687160fd823a1233e86 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 16 Aug 2022 12:22:00 -0700 Subject: [PATCH 038/127] #226 #229 Fixing issues that came up in setup and validation --- requirements-kg2-build.txt | 32 ++++++++++++------- validate_predicate_remap_yaml.py | 54 ++++++++++++++++---------------- 2 files changed, 47 insertions(+), 39 deletions(-) diff --git a/requirements-kg2-build.txt b/requirements-kg2-build.txt index 89933c83..f743126e 100644 --- a/requirements-kg2-build.txt +++ b/requirements-kg2-build.txt @@ -1,37 +1,45 @@ argh==0.26.2 +attrs==19.2.0 +bidict==0.21.0 +bmt==0.7.6 CacheControl==0.12.6 +cachetools==5.1.0 cachier==1.2.5 certifi==2019.3.9 chardet==3.0.4 -Click==8.0 +Click==8.0.0 conf==0.4. Cython==0.29.26 dataclasses==0.6 decorator==4.4.0 +diskcache==4.0.0 +docker==4.4.2 HTMLParser==0.0.2 idna==2.8 isodate==0.6.0 jsobject==0.10.2 -kgx==1.5.4 +jsonlines==3.0.0 +jsonpickle==1.0.0 +kgx==1.5.6 lockfile==0.12.2 -marshmallow==3.0.0b3 +marshmallow==3.0.0b11 mysqlclient==1.4.4 -neo4j==1.7.4 -networkx==2.3 +neo4j==4.3 +networkx==2.5 numpy==1.21.0 -ontobio==1.10.1 -pandas==0.24.2 +ontobio==2.8.0 +pandas==1.0.3 pathtools==0.1.2 portalocker==1.4.0 -prefixcommons==0.1.7 +prefixcommons==0.1.9 pymongo==3.8.0 PyMySQL==0.9.3 -pyparsing==2.4.0 +pyparsing==2.4.7 pysolr==3.8.1 -python-dateutil==2.8.0 -pytz==2019.1 +python-dateutil==2.8.1 +pytz==2022.2 PyYAML==5.4 -rdflib==4.2.2 +rdflib==6.0.0 requests==2.25.1 scipy==1.2.1 six==1.12.0 diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index f03679e8..fcabe7ad 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -40,7 +40,7 @@ def convert_biolink_yaml_association_to_predicate(association: str) -> str: return 'biolink:' + association.replace(',', '').replace(' ', '_') -def create_biolink_to_external_mappings(biolink_model: dict, mapping_heirarchy: list) -> dict: +def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: list) -> dict: # biolink_to_external[biolink relation][mapterm]= list([externals]) biolink_mixins = list() biolink_to_external_mappings = dict() @@ -136,29 +136,29 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_heirarchy: # moved to validate_curies_to_urls_map.py pred_info = yaml.safe_load(open(predicate_remap_file_name, 'r')) - for relation, instruction_dict in pred_info.items(): - operation = instruction_dict.get('operation', '') - assert operation != '', relation - core_predicate = instruction_dict.get('core_predicate', '') - assert core_predicate != '', relation - qualified_predicate = instruction_dict.get('qualified_predicate', '') - qualifiers = instruction_dict.get('qualifiers', '') - - assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) - assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) - assert core_predicate not in biolink_to_external_mappings, (relation, core_predicate) - - allowed_biolink_curies_set = set() - biolink_term_externals = external_to_biolink_mappings.get(relation.lower(), None) - if biolink_term_externals is not None: - mapping_term_used = "none" - for mapping_term in mapping_hierarchy: - allowed_biolink_curies_set = biolink_term_externals[mapping_term] - if len(allowed_biolink_curies_set) != 0: - mapping_term_used = mapping_term - break - if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: - err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) - assert core_predicate in allowed_biolink_curies_set, err_str - else: - assert operation == 'delete' +for relation, instruction_dict in pred_info.items(): + operation = instruction_dict.get('operation', None) + assert operation is not None, relation + core_predicate = instruction_dict.get('core_predicate', None) + assert core_predicate is not None, relation + qualified_predicate = instruction_dict.get('qualified_predicate', None) + qualifiers = instruction_dict.get('qualifiers', None) + + assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) + assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) + assert core_predicate in biolink_to_external_mappings, (relation, core_predicate) + + allowed_biolink_curies_set = set() + biolink_term_externals = external_to_biolink_mappings.get(relation.lower(), None) + if biolink_term_externals is not None: + mapping_term_used = "none" + for mapping_term in mapping_hierarchy: + allowed_biolink_curies_set = biolink_term_externals[mapping_term] + if len(allowed_biolink_curies_set) != 0: + mapping_term_used = mapping_term + break + if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: + err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) + assert core_predicate in allowed_biolink_curies_set, err_str + else: + assert operation == 'delete' From d5084a32ae2a16a9281dc52704a8e64dd6a52f54 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 16 Aug 2022 13:03:09 -0700 Subject: [PATCH 039/127] #229 Update validate_predicate_remap_yaml.py --- validate_predicate_remap_yaml.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index fcabe7ad..b2f9ed42 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -142,7 +142,7 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: core_predicate = instruction_dict.get('core_predicate', None) assert core_predicate is not None, relation qualified_predicate = instruction_dict.get('qualified_predicate', None) - qualifiers = instruction_dict.get('qualifiers', None) + qualifiers_list = instruction_dict.get('qualifiers', None) assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) From 63570d99e01bd0617af81f81e22ba332286ae157 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 19 Aug 2022 13:15:40 -0700 Subject: [PATCH 040/127] #221 Additional changes for "regulates" --- predicate_remap.yaml | 178 ++++++++++++++++++++----------- validate_predicate_remap_yaml.py | 62 +++++++---- 2 files changed, 158 insertions(+), 82 deletions(-) diff --git a/predicate_remap.yaml b/predicate_remap.yaml index ea50289e..db474164 100644 --- a/predicate_remap.yaml +++ b/predicate_remap.yaml @@ -190,9 +190,7 @@ CHEBI:is_tautomer_of: CHEMBL.MECHANISM:activator: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: increased CHEMBL.MECHANISM:agonist: operation: keep @@ -228,9 +226,7 @@ CHEMBL.MECHANISM:binding_agent: CHEMBL.MECHANISM:blocker: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased CHEMBL.MECHANISM:chelating_agent: operation: keep @@ -261,9 +257,7 @@ CHEMBL.MECHANISM:hydrolytic_enzyme: CHEMBL.MECHANISM:inhibitor: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased CHEMBL.MECHANISM:inverse_agonist: operation: keep @@ -278,16 +272,12 @@ CHEMBL.MECHANISM:modulator: CHEMBL.MECHANISM:negative_allosteric_modulator: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased CHEMBL.MECHANISM:negative_modulator: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased CHEMBL.MECHANISM:opener: operation: keep @@ -344,7 +334,9 @@ CHEMBL.MECHANISM:releasing_agent: - object_direction: increased CHEMBL.MECHANISM:rnai_inhibitor: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: regulates + qualifiers: + - object_direction: decreased CHEMBL.MECHANISM:sequestering_agent: operation: keep core_predicate: biolink:physically_interacts_with @@ -1324,9 +1316,7 @@ DDANAT:develops_from: DGIdb:activator: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: increased DGIdb:adduct: operation: keep @@ -1511,7 +1501,9 @@ DOID-PROPERTY:has_symptom: core_predicate: biolink:has_phenotype DRUGBANK:activator: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased DRUGBANK:adduct: operation: keep core_predicate: biolink:directly_interacts_with @@ -1565,7 +1557,9 @@ DRUGBANK:binding: core_predicate: biolink:physically_interacts_with DRUGBANK:blocker: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:category: operation: keep core_predicate: biolink:subclass_of @@ -1603,7 +1597,9 @@ DRUGBANK:desensitize_the_target: core_predicate: biolink:decreases_response_to DRUGBANK:downregulator: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:drug-interaction: operation: keep core_predicate: biolink:physically_interacts_with @@ -1621,7 +1617,9 @@ DRUGBANK:group: core_predicate: biolink:related_to DRUGBANK:inactivator: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:incorporation_into_and_destabilization: operation: keep core_predicate: biolink:affects @@ -1636,10 +1634,14 @@ DRUGBANK:inducer: - object_direction: increased DRUGBANK:inhibition_of_synthesis: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:inhibitor: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:inhibitory_allosteric_modulator: operation: keep core_predicate: biolink:affects @@ -1662,13 +1664,15 @@ DRUGBANK:ligand: core_predicate: biolink:directly_interacts_with DRUGBANK:modulator: operation: keep - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates DRUGBANK:multitarget: operation: keep core_predicate: biolink:directly_interacts_with DRUGBANK:negative_modulator: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:neutralizer: operation: keep core_predicate: biolink:affects @@ -1716,7 +1720,9 @@ DRUGBANK:positive_allosteric_modulator: - object_direction: increased DRUGBANK:positive_modulator: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased DRUGBANK:potentiator: operation: keep core_predicate: biolink:affects @@ -1729,7 +1735,7 @@ DRUGBANK:product_of: core_predicate: biolink:derives_from DRUGBANK:regulator: operation: keep - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates DRUGBANK:stabilization: operation: keep core_predicate: biolink:affects @@ -1759,13 +1765,17 @@ DRUGBANK:target: core_predicate: biolink:physically_interacts_with DRUGBANK:translocation_inhibitor: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DRUGBANK:treats: operation: keep core_predicate: biolink:treats DRUGBANK:weak_inhibitor: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DrugCentral:5271: operation: keep core_predicate: biolink:diagnoses @@ -1774,7 +1784,9 @@ DrugCentral:PA: core_predicate: biolink:subclass_of DrugCentral:activator: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased DrugCentral:agonist: operation: keep core_predicate: biolink:affects @@ -1816,7 +1828,9 @@ DrugCentral:binding_agent: core_predicate: biolink:directly_interacts_with DrugCentral:blocker: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DrugCentral:contraindication: operation: keep core_predicate: biolink:contraindicated_for @@ -1835,7 +1849,9 @@ DrugCentral:indication: core_predicate: biolink:treats DrugCentral:inhibitor: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DrugCentral:inverse_agonist: operation: keep core_predicate: biolink:affects @@ -1845,13 +1861,17 @@ DrugCentral:inverse_agonist: - object_direction: decreased DrugCentral:modulator: operation: keep - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates DrugCentral:negative_allosteric_modulator: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DrugCentral:negative_modulator: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased DrugCentral:off-label_use: operation: keep core_predicate: biolink:treats @@ -1881,7 +1901,9 @@ DrugCentral:positive_allosteric_modulator: - object_direction: increased DrugCentral:positive_modulator: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased DrugCentral:releasing_agent: operation: keep core_predicate: biolink:affects @@ -2325,19 +2347,27 @@ GO:acts_upstream_of: core_predicate: biolink:affects GO:acts_upstream_of_negative_effect: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased GO:acts_upstream_of_or_within: operation: keep core_predicate: biolink:affects GO:acts_upstream_of_or_within_negative_effect: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased GO:acts_upstream_of_or_within_positive_effect: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased GO:acts_upstream_of_positive_effect: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased GO:colocalizes_with: operation: keep core_predicate: biolink:colocalizes_with @@ -2381,10 +2411,14 @@ GO:located_in: core_predicate: biolink:located_in GO:negatively_regulated_by: operation: invert - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased GO:negatively_regulates: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased GO:occurs_in: operation: keep core_predicate: biolink:occurs_in @@ -2393,16 +2427,20 @@ GO:part_of: core_predicate: biolink:has_part GO:positively_regulated_by: operation: invert - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased GO:positively_regulates: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased GO:regulated_by: operation: invert - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates GO:regulates: operation: keep - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates GOREL:0000040: operation: keep core_predicate: biolink:causes @@ -4012,22 +4050,30 @@ REACT:in_species: core_predicate: biolink:occurs_in REACT:is_requirement_for: operation: keep - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates REACT:linked_to_disease: operation: keep core_predicate: biolink:related_to REACT:negatively_regulates: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased REACT:negatively_regulates_gene_expression: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased REACT:positively_regulates: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased REACT:positively_regulates_gene_expression: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased REACT:related_to: operation: keep core_predicate: biolink:related_to @@ -4253,16 +4299,12 @@ RO:0002211: RO:0002212: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased RO:0002213: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: increased RO:0002215: operation: keep @@ -4391,7 +4433,7 @@ RO:0002333: core_predicate: biolink:enables RO:0002334: operation: invert - core_predicate: biolink:entity_regulates_entity + core_predicate: biolink:regulates RO:0002338: operation: keep core_predicate: biolink:related_to @@ -4500,10 +4542,14 @@ RO:0002448: core_predicate: biolink:entity_regulated_by_entity RO:0002449: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased RO:0002450: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased RO:0002451: operation: keep core_predicate: biolink:related_to @@ -4627,16 +4673,12 @@ RO:0002610: RO:0002629: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: increased RO:0002630: operation: keep core_predicate: biolink:regulates - qualified_predicate: biolink:causes qualifiers: - - object_aspect: activity_or_abundance - object_direction: decreased RO:0003000: operation: keep @@ -4849,7 +4891,9 @@ SEMMEDDB:DISRUPTS: core_predicate: biolink:disrupts SEMMEDDB:INHIBITS: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased SEMMEDDB:IS_A: operation: keep core_predicate: biolink:subclass_of @@ -4882,7 +4926,9 @@ SEMMEDDB:SAME_AS: core_predicate: biolink:close_match SEMMEDDB:STIMULATES: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased SEMMEDDB:TREATS: operation: keep core_predicate: biolink:treats @@ -4897,7 +4943,9 @@ SEMMEDDB:associated_with: core_predicate: biolink:associated_with SEMMEDDB:augments: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased SEMMEDDB:causes: operation: keep core_predicate: biolink:causes @@ -4924,7 +4972,9 @@ SEMMEDDB:higher_than: core_predicate: biolink:related_to SEMMEDDB:inhibits: operation: keep - core_predicate: biolink:entity_negatively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased SEMMEDDB:interacts_with: operation: keep core_predicate: biolink:interacts_with @@ -4977,7 +5027,9 @@ SEMMEDDB:same_as: core_predicate: biolink:close_match SEMMEDDB:stimulates: operation: keep - core_predicate: biolink:entity_positively_regulates_entity + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased SEMMEDDB:treats: operation: keep core_predicate: biolink:treats diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index b2f9ed42..0a4a788c 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -40,15 +40,27 @@ def convert_biolink_yaml_association_to_predicate(association: str) -> str: return 'biolink:' + association.replace(',', '').replace(' ', '_') +def get_nondeprecated_parent(biolink_model: dict, biolink_term: str) -> str: + if biolink_term.startswith("biolink:"): + biolink_term = " ".join(biolink_term.split(":")[1].split('_')) + deprecated = biolink_model['slots'][biolink_term].get('deprecated', None) + if deprecated is not None: + parent = biolink_model['slots'][biolink_term].get('is_a') + biolink_term = get_nondeprecated_parent(biolink_model, parent) + + return biolink_term + + def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: list) -> dict: # biolink_to_external[biolink relation][mapterm]= list([externals]) biolink_mixins = list() biolink_to_external_mappings = dict() inverted_relations = [] + deprecated_list = list() for relation, relation_info in biolink_model['slots'].items(): predicate_str = convert_biolink_yaml_association_to_predicate(relation) mixin = relation_info.get('mixin', False) - if mixin == True: + if mixin and predicate_str != 'biolink:regulates': biolink_mixins.append(predicate_str) continue is_a_type = relation_info.get('is_a', '') @@ -61,6 +73,10 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: biolink_to_external_mappings[predicate_str] = defaultdict(lambda: []) inverted_relation = relation_info.get('inverse', None) annotations = relation_info.get('annotations', dict()) + deprecated = relation_info.get('deprecated', None) + if deprecated: + deprecated_predicate = 'biolink:' + '_'.join(relation.split(" ")) + deprecated_list.append(deprecated_predicate) # Adjustment due to biolink issue #808 tag = str if isinstance(annotations, list): @@ -98,7 +114,7 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: biolink_to_external_mappings['biolink:subclass_of']['narrow_mappings'].remove("umls:rb") except ValueError: print('UMLS:RB work around no longer necessary') - return biolink_to_external_mappings, biolink_mixins, inverted_relations + return biolink_to_external_mappings, biolink_mixins, inverted_relations, deprecated_list args = make_arg_parser().parse_args() @@ -120,7 +136,7 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: mapping_hierarchy = ["exact_mappings", "close_mappings", "narrow_mappings", "broad_mappings", "related_mappings"] # TODO: determine correct order of mappings -biolink_to_external_mappings, biolink_mixins, inverted_relations = create_biolink_to_external_mappings( +biolink_to_external_mappings, biolink_mixins, inverted_relations, deprecated_list = create_biolink_to_external_mappings( biolink_model, mapping_hierarchy) external_to_biolink_mappings = dict() @@ -144,21 +160,29 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: qualified_predicate = instruction_dict.get('qualified_predicate', None) qualifiers_list = instruction_dict.get('qualifiers', None) - assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) - assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) - assert core_predicate in biolink_to_external_mappings, (relation, core_predicate) - - allowed_biolink_curies_set = set() - biolink_term_externals = external_to_biolink_mappings.get(relation.lower(), None) - if biolink_term_externals is not None: - mapping_term_used = "none" - for mapping_term in mapping_hierarchy: - allowed_biolink_curies_set = biolink_term_externals[mapping_term] - if len(allowed_biolink_curies_set) != 0: - mapping_term_used = mapping_term - break - if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: - err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) - assert core_predicate in allowed_biolink_curies_set, err_str + if core_predicate is not None: + + assert core_predicate not in biolink_mixins, (relation, core_predicate, {'Mixins': biolink_mixins}) + assert core_predicate not in inverted_relations, (relation, core_predicate, {'Inverted Relations': inverted_relations}) + assert core_predicate in biolink_to_external_mappings, (relation, core_predicate) + + allowed_biolink_curies_set = set() + biolink_term_externals = external_to_biolink_mappings.get(relation.lower(), None) + if biolink_term_externals is not None: + mapping_term_used = "none" + for mapping_term in mapping_hierarchy: + allowed_biolink_curies_set = biolink_term_externals[mapping_term] + if len(allowed_biolink_curies_set) != 0: + mapping_term_used = mapping_term + break + for curie in allowed_biolink_curies_set: + if curie in deprecated_list: + nondeprecated_parent = get_nondeprecated_parent(biolink_model, curie) + new_curie = convert_biolink_yaml_association_to_predicate(nondeprecated_parent) + allowed_biolink_curies_set.remove(curie) + allowed_biolink_curies_set.add(new_curie) + if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: + err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) + assert core_predicate in allowed_biolink_curies_set, err_str else: assert operation == 'delete' From e80048b7aca5c22393180d7bb3bfd8fb3b8ef127 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 22 Aug 2022 09:10:43 -0700 Subject: [PATCH 041/127] #221 #229 Changes to fix validation errors --- predicate_remap.yaml | 3292 +++++++++++++++--------------- validate_predicate_remap_yaml.py | 9 +- 2 files changed, 1649 insertions(+), 1652 deletions(-) diff --git a/predicate_remap.yaml b/predicate_remap.yaml index db474164..5134fe95 100644 --- a/predicate_remap.yaml +++ b/predicate_remap.yaml @@ -192,5196 +192,5190 @@ CHEMBL.MECHANISM:activator: core_predicate: biolink:regulates qualifiers: - object_direction: increased -CHEMBL.MECHANISM:agonist: +CHEMBL.MECHANISM:agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -CHEMBL.MECHANISM:allosteric_antagonist: +CHEMBL.MECHANISM:allosteric_antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -CHEMBL.MECHANISM:antagonist: +CHEMBL.MECHANISM:antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -CHEMBL.MECHANISM:antisense_inhibitor: +CHEMBL.MECHANISM:antisense_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: expression - object_direction: decreased -CHEMBL.MECHANISM:binding_agent: +CHEMBL.MECHANISM:binding_agent: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:blocker: - operation: keep +CHEMBL.MECHANISM:blocker: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -CHEMBL.MECHANISM:chelating_agent: +CHEMBL.MECHANISM:chelating_agent: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:cross-linking_agent: +CHEMBL.MECHANISM:cross-linking_agent: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:degrader: +CHEMBL.MECHANISM:degrader: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -CHEMBL.MECHANISM:disrupting_agent: +CHEMBL.MECHANISM:disrupting_agent: operation: keep core_predicate: biolink:disrupts -CHEMBL.MECHANISM:equivalent_to: +CHEMBL.MECHANISM:equivalent_to: operation: keep core_predicate: biolink:same_as -CHEMBL.MECHANISM:hydrolytic_enzyme: +CHEMBL.MECHANISM:hydrolytic_enzyme: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -CHEMBL.MECHANISM:inhibitor: - operation: keep +CHEMBL.MECHANISM:inhibitor: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -CHEMBL.MECHANISM:inverse_agonist: +CHEMBL.MECHANISM:inverse_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -CHEMBL.MECHANISM:modulator: +CHEMBL.MECHANISM:modulator: operation: keep core_predicate: biolink:regulates -CHEMBL.MECHANISM:negative_allosteric_modulator: - operation: keep +CHEMBL.MECHANISM:negative_allosteric_modulator: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -CHEMBL.MECHANISM:negative_modulator: - operation: keep +CHEMBL.MECHANISM:negative_modulator: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -CHEMBL.MECHANISM:opener: +CHEMBL.MECHANISM:opener: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -CHEMBL.MECHANISM:other: +CHEMBL.MECHANISM:other: operation: delete -CHEMBL.MECHANISM:overlaps_with: +CHEMBL.MECHANISM:overlaps_with: operation: keep core_predicate: biolink:overlaps -CHEMBL.MECHANISM:oxidative_enzyme: +CHEMBL.MECHANISM:oxidative_enzyme: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:partial_agonist: +CHEMBL.MECHANISM:partial_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -CHEMBL.MECHANISM:positive_allosteric_modulator: +CHEMBL.MECHANISM:positive_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -CHEMBL.MECHANISM:positive_modulator: +CHEMBL.MECHANISM:positive_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -CHEMBL.MECHANISM:proteolytic_enzyme: +CHEMBL.MECHANISM:proteolytic_enzyme: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -CHEMBL.MECHANISM:reducing_agent: +CHEMBL.MECHANISM:reducing_agent: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:releasing_agent: +CHEMBL.MECHANISM:releasing_agent: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: expression - object_direction: increased -CHEMBL.MECHANISM:rnai_inhibitor: - operation: keep - core_predicate: regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:sequestering_agent: +#CHEMBL.MECHANISM:rnai_inhibitor: +# operation: keep +# core_predicate: regulates +# qualifiers: +# - object_direction: decreased +CHEMBL.MECHANISM:sequestering_agent: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:stabiliser: +CHEMBL.MECHANISM:stabiliser: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: stability - object_direction: increased -CHEMBL.MECHANISM:subset_of: +CHEMBL.MECHANISM:subset_of: operation: keep core_predicate: biolink:subclass_of -CHEMBL.MECHANISM:substrate: +CHEMBL.MECHANISM:substrate: operation: keep core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:superset_of: +CHEMBL.MECHANISM:superset_of: operation: invert core_predicate: biolink:subclass_of -CL:has_completed: +CL:has_completed: operation: keep core_predicate: biolink:has_completed -CL:has_high_plasma_membrane_amount: +CL:has_high_plasma_membrane_amount: operation: keep core_predicate: biolink:has_increased_amount -CL:has_low_plasma_membrane_amount: +CL:has_low_plasma_membrane_amount: operation: keep core_predicate: biolink:has_decreased_amount -CL:has_not_completed: +CL:has_not_completed: operation: keep core_predicate: biolink:has_not_completed -CL:lacks_part: +CL:lacks_part: operation: keep core_predicate: biolink:lacks_part -CL:lacks_plasma_membrane_part: +CL:lacks_plasma_membrane_part: operation: keep core_predicate: biolink:lacks_part -CPT:has_add_on_code: +CPT:has_add_on_code: operation: keep core_predicate: biolink:related_to -CPT:mapped_to: +CPT:mapped_to: operation: keep core_predicate: biolink:related_to -CPT:panel_element_of: +CPT:panel_element_of: operation: invert core_predicate: biolink:has_part -CPT:panel_element_of_possibly_included: +CPT:panel_element_of_possibly_included: operation: invert core_predicate: biolink:has_part -CTD:affects_ADP-ribosylation: +CTD:affects_ADP-ribosylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_N-linked_glycosylation: +CTD:affects_N-linked_glycosylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_O-linked_glycosylation: +CTD:affects_O-linked_glycosylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_RNA_splicing: +CTD:affects_RNA_splicing: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: splicing -CTD:affects_abundance_of: +CTD:affects_abundance_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: abundance -CTD:affects_acetylation: +CTD:affects_acetylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_acylation: +CTD:affects_acylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_alkylation: +CTD:affects_alkylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_amination: +CTD:affects_amination: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_binding: +CTD:affects_binding: operation: keep - core_predicate: biolink:directly_interacts_with -CTD:affects_carbamoylation: + core_predicate: biolink:interacts_with +CTD:affects_carbamoylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_carboxylation: +CTD:affects_carboxylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_cleavage: +CTD:affects_cleavage: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -CTD:affects_degradation_of: +CTD:affects_degradation_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -CTD:affects_ethylation: +CTD:affects_ethylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_export: +CTD:affects_export: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: secretion -CTD:affects_farnesylation: +CTD:affects_farnesylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_folding_of: +CTD:affects_folding_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: folding -CTD:affects_geranoylation: +CTD:affects_geranoylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_glucuronidation: +CTD:affects_glucuronidation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_glutathionylation: +CTD:affects_glutathionylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_glycation: +CTD:affects_glycation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_glycosylation: +CTD:affects_glycosylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_hydrolysis: +CTD:affects_hydrolysis: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -CTD:affects_hydroxylation: +CTD:affects_hydroxylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_import: +CTD:affects_import: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: uptake -CTD:affects_lipidation: +CTD:affects_lipidation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_methylation: +CTD:affects_methylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_molecular_modification_of: +CTD:affects_molecular_modification_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_mutation_rate_of: +CTD:affects_mutation_rate_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: mutation_rate -CTD:affects_myristoylation: +CTD:affects_myristoylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_nitrosation: +CTD:affects_nitrosation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_nucleotidylation: +CTD:affects_nucleotidylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_oxidation: +CTD:affects_oxidation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_palmitoylation: +CTD:affects_palmitoylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_phosphorylation: +CTD:affects_phosphorylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_prenylation: +CTD:affects_prenylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_reduction: +CTD:affects_reduction: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_response_to: - operation: invert - core_predicate: biolink:response_affected_by -CTD:affects_ribosylation: +CTD:affects_response_to: + operation: keep + core_predicate: biolink:affects_response_to +CTD:affects_ribosylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_secretion_of: +CTD:affects_secretion_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: secretion -CTD:affects_splicing_of: +CTD:affects_splicing_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: splicing -CTD:affects_sulfation: +CTD:affects_sulfation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_sumoylation: +CTD:affects_sumoylation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_synthesis_of: +CTD:affects_synthesis_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: synthesis -CTD:affects_transport_of: +CTD:affects_transport_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: transport -CTD:affects_ubiquitination: +CTD:affects_ubiquitination: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: molecular_modification -CTD:affects_uptake_of: +CTD:affects_uptake_of: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: uptake -CTD:decreases_ADP-ribosylation: +CTD:decreases_ADP-ribosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_N-linked_glycosylation: +CTD:decreases_N-linked_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_O-linked_glycosylation: +CTD:decreases_O-linked_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_RNA_splicing: +CTD:decreases_RNA_splicing: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: splicing - object_direction: decreased -CTD:decreases_acetylation: +CTD:decreases_acetylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_acylation: +CTD:decreases_acylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_alkylation: +CTD:decreases_alkylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_amination: +CTD:decreases_amination: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_carbamoylation: +CTD:decreases_carbamoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_carboxylation: +CTD:decreases_carboxylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_cleavage: +CTD:decreases_cleavage: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: degradation - object_direction: decreased -CTD:decreases_degradation_of: +CTD:decreases_degradation_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: degradation - object_direction: decreased -CTD:decreases_ethylation: +CTD:decreases_ethylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_export: +CTD:decreases_export: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: secretion - object_direction: decreased -CTD:decreases_farnesylation: +CTD:decreases_farnesylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_folding_of: +CTD:decreases_folding_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: folding - object_direction: decreased -CTD:decreases_geranoylation: +CTD:decreases_geranoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_glucuronidation: +CTD:decreases_glucuronidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_glutathionylation: +CTD:decreases_glutathionylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_glycation: +CTD:decreases_glycation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_glycosylation: +CTD:decreases_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_hydrolysis: +CTD:decreases_hydrolysis: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: degradation - object_direction: decreased -CTD:decreases_hydroxylation: +CTD:decreases_hydroxylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_import: +CTD:decreases_import: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: uptake - object_direction: decreased -CTD:decreases_lipidation: +CTD:decreases_lipidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_localization_of: +CTD:decreases_localization_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: localization - object_direction: decreased -CTD:decreases_metabolic_processing_of: +CTD:decreases_metabolic_processing_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: localization - object_direction: decreased -CTD:decreases_methylation: +CTD:decreases_methylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_molecular_interaction_with: +CTD:decreases_molecular_interaction_with: operation: keep - core_predicate: biolink:decreases_molecular_interaction -CTD:decreases_molecular_modification_of: + core_predicate: biolink:physically_interacts_with +CTD:decreases_molecular_modification_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_mutagenesis: +CTD:decreases_mutagenesis: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: mutation_rate - object_direction: decreased -CTD:decreases_mutation_rate_of: +CTD:decreases_mutation_rate_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: mutation_rate - object_direction: decreased -CTD:decreases_myristoylation: +CTD:decreases_myristoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_nitrosation: +CTD:decreases_nitrosation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_nucleotidylation: +CTD:decreases_nucleotidylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_oxidation: +CTD:decreases_oxidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_palmitoylation: +CTD:decreases_palmitoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_phosphorylation: +CTD:decreases_phosphorylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_prenylation: +CTD:decreases_prenylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_reduction: +CTD:decreases_reduction: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_response_to: +CTD:decreases_response_to: operation: keep core_predicate: biolink:decreases_response_to -CTD:decreases_response_to_substance: +CTD:decreases_response_to_substance: operation: keep core_predicate: biolink:decreases_response_to -CTD:decreases_ribosylation: +CTD:decreases_ribosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_secretion_of: +CTD:decreases_secretion_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: secretion - object_direction: decreased -CTD:decreases_splicing_of: +CTD:decreases_splicing_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: splicing - object_direction: decreased -CTD:decreases_stability_of: +CTD:decreases_stability_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: stability - object_direction: decreased -CTD:decreases_sulfation: +CTD:decreases_sulfation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_sumoylation: +CTD:decreases_sumoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_transport_of: +CTD:decreases_transport_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: transport - object_direction: decreased -CTD:decreases_ubiquitination: +CTD:decreases_ubiquitination: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -CTD:decreases_uptake_of: +CTD:decreases_uptake_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: uptake - object_direction: decreased -CTD:increases_ADP-ribosylation: +CTD:increases_ADP-ribosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_N-linked_glycosylation: +CTD:increases_N-linked_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_O-linked_glycosylation: +CTD:increases_O-linked_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_RNA_splicing: +CTD:increases_RNA_splicing: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: splicing - object_direction: increased -CTD:increases_acetylation: +CTD:increases_acetylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_acylation: +CTD:increases_acylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_alkylation: +CTD:increases_alkylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_amination: +CTD:increases_amination: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_carbamoylation: +CTD:increases_carbamoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_carboxylation: +CTD:increases_carboxylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_cleavage: +CTD:increases_cleavage: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -CTD:increases_ethylation: +CTD:increases_ethylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_export: +CTD:increases_export: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: secretion - object_direction: increased -CTD:increases_farnesylation: +CTD:increases_farnesylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_folding_of: +CTD:increases_folding_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: folding - object_direction: increased -CTD:increases_geranoylation: +CTD:increases_geranoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_glucuronidation: +CTD:increases_glucuronidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_glutathionylation: +CTD:increases_glutathionylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_glycation: +CTD:increases_glycation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_glycosylation: +CTD:increases_glycosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_hydrolysis: +CTD:increases_hydrolysis: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -CTD:increases_hydroxylation: +CTD:increases_hydroxylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_import: +CTD:increases_import: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: uptake - object_direction: increased -CTD:increases_lipidation: +CTD:increases_lipidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_localization_of: +CTD:increases_localization_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: localization - object_direction: increased -CTD:increases_metabolic_processing_of: +CTD:increases_metabolic_processing_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: localization - object_direction: increased -CTD:increases_methylation: +CTD:increases_methylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_molecular_interaction_with: +CTD:increases_molecular_interaction_with: operation: keep - core_predicate: biolink:increases_molecular_interaction -CTD:increases_molecular_modification_of: + core_predicate: biolink:physically_interacts_with +CTD:increases_molecular_modification_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_mutagenesis: +CTD:increases_mutagenesis: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: mutation_rate - object_direction: increased -CTD:increases_mutation_rate_of: +CTD:increases_mutation_rate_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: mutation_rate - object_direction: increased -CTD:increases_myristoylation: +CTD:increases_myristoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_nitrosation: +CTD:increases_nitrosation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_nucleotidylation: +CTD:increases_nucleotidylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_oxidation: +CTD:increases_oxidation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_palmitoylation: +CTD:increases_palmitoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_phosphorylation: +CTD:increases_phosphorylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_prenylation: +CTD:increases_prenylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_reduction: +CTD:increases_reduction: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_response_to: +CTD:increases_response_to: operation: keep core_predicate: biolink:increases_response_to -CTD:increases_ribosylation: +CTD:increases_ribosylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_secretion_of: +CTD:increases_secretion_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: secretion - object_direction: increased -CTD:increases_splicing_of: +CTD:increases_splicing_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: splicing - object_direction: increased -CTD:increases_sulfation: +CTD:increases_sulfation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_sumoylation: +CTD:increases_sumoylation: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_synthesis_of: +CTD:increases_synthesis_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: synthesis - object_direction: increased -CTD:increases_ubiquitination: +CTD:increases_ubiquitination: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -CTD:increases_uptake_of: +CTD:increases_uptake_of: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: uptake - object_direction: increased -CTD:inferred: +CTD:inferred: operation: keep core_predicate: biolink:affects -CTD:marker_mechanism: +CTD:marker_mechanism: operation: keep core_predicate: biolink:contributes_to -CTD:negative_correlation: +CTD:negative_correlation: operation: keep core_predicate: biolink:negatively_correlated_with -CTD:positive_correlation: +CTD:positive_correlation: operation: keep core_predicate: biolink:positively_correlated_with -CTD:prediction_hypothesis: +CTD:prediction_hypothesis: operation: keep core_predicate: biolink:affects -DDANAT:develops_from: +DDANAT:develops_from: operation: keep core_predicate: biolink:develops_from -DGIdb:activator: - operation: keep +DGIdb:activator: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -DGIdb:adduct: +DGIdb:adduct: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:affects: + core_predicate: biolink:directly_physically_interacts_with +DGIdb:affects: operation: keep core_predicate: biolink:affects -DGIdb:agonist: +DGIdb:agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:allosteric_modulator: +DGIdb:allosteric_modulator: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: activity -DGIdb:antagonist: +DGIdb:antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:antibody: +DGIdb:antibody: operation: keep - core_predicate: biolink:molecularly_interacts_with -DGIdb:antisense_oligonucleotide: + core_predicate: biolink:physically_interacts_with +DGIdb:antisense_oligonucleotide: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: expression - object_direction: decreased -DGIdb:binder: +DGIdb:binder: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:blocker: + core_predicate: biolink:interacts_with +DGIdb:blocker: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:channel_blocker: +DGIdb:channel_blocker: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:chaperone: +DGIdb:chaperone: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:cleavage: + core_predicate: biolink:binds +DGIdb:cleavage: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -DGIdb:cofactor: +DGIdb:cofactor: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:gating_inhibitor: + core_predicate: biolink:interacts_with +DGIdb:gating_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:inducer: +DGIdb:inducer: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:inhibitor: +DGIdb:inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:inhibitory_allosteric_modulator: +DGIdb:inhibitory_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:inverse_agonist: +DGIdb:inverse_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:ligand: +DGIdb:ligand: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:modulator: + core_predicate: biolink:directly_physically_interacts_with +DGIdb:modulator: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: activity -DGIdb:multitarget: +DGIdb:multitarget: operation: keep - core_predicate: biolink:directly_interacts_with -DGIdb:negative_modulator: + core_predicate: biolink:directly_physically_interacts_with +DGIdb:negative_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:partial_agonist: +DGIdb:partial_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:partial_antagonist: +DGIdb:partial_antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:positive_modulator: +DGIdb:positive_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:potentiator: +DGIdb:potentiator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:product_of: +DGIdb:product_of: operation: keep core_predicate: biolink:derives_from -DGIdb:stimulator: +DGIdb:stimulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:substrate: +DGIdb:substrate: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -DGIdb:suppressor: +DGIdb:suppressor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:vaccine: +DGIdb:vaccine: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DOID-PROPERTY:derives_from: - operation: invert - core_predicate: biolink:derives_into -DOID-PROPERTY:has_symptom: +#DOID-PROPERTY:derives_from: +# operation: keep +# core_predicate: biolink:related_to_at_instance_level +DOID-PROPERTY:has_symptom: operation: keep core_predicate: biolink:has_phenotype -DRUGBANK:activator: +DRUGBANK:activator: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -DRUGBANK:adduct: +DRUGBANK:adduct: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:aggregation_inhibitor: + core_predicate: biolink:directly_physically_interacts_with +DRUGBANK:aggregation_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:agonist: +DRUGBANK:agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:allosteric_modulator: +DRUGBANK:allosteric_modulator: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: activity -DRUGBANK:antagonist: +DRUGBANK:antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:antibody: +DRUGBANK:antibody: operation: keep - core_predicate: biolink:molecularly_interacts_with -DRUGBANK:antisense_oligonucleotide: + core_predicate: biolink:physically_interacts_with +DRUGBANK:antisense_oligonucleotide: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: expression - object_direction: decreased -DRUGBANK:atc-code: +DRUGBANK:atc-code: operation: keep core_predicate: biolink:close_match -DRUGBANK:atc-code-level: +DRUGBANK:atc-code-level: operation: keep core_predicate: biolink:related_to -DRUGBANK:binder: +DRUGBANK:binder: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:binding: + core_predicate: biolink:directly_physically_interacts_with +DRUGBANK:binding: operation: keep core_predicate: biolink:physically_interacts_with -DRUGBANK:blocker: +DRUGBANK:blocker: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -DRUGBANK:category: +DRUGBANK:category: operation: keep core_predicate: biolink:subclass_of -DRUGBANK:chaperone: +DRUGBANK:chaperone: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:chelator: + core_predicate: biolink:binds +DRUGBANK:chelator: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:cleavage: + core_predicate: biolink:interacts_with +DRUGBANK:cleavage: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -DRUGBANK:cofactor: +DRUGBANK:cofactor: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:component_of: + core_predicate: biolink:directly_physically_interacts_with +DRUGBANK:component_of: operation: invert core_predicate: biolink:has_part -DRUGBANK:degradation: +DRUGBANK:degradation: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -DRUGBANK:deoxidizer: +DRUGBANK:deoxidizer: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: decreased -DRUGBANK:desensitize_the_target: +DRUGBANK:desensitize_the_target: operation: keep core_predicate: biolink:decreases_response_to -DRUGBANK:downregulator: +DRUGBANK:downregulator: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -DRUGBANK:drug-interaction: +DRUGBANK:drug-interaction: operation: keep core_predicate: biolink:physically_interacts_with -DRUGBANK:external-identifier: +DRUGBANK:external-identifier: operation: keep core_predicate: biolink:same_as -DRUGBANK:external-identifier-protein: +DRUGBANK:external-identifier-protein: operation: keep core_predicate: biolink:derives_from -DRUGBANK:gene_replacement: +DRUGBANK:gene_replacement: operation: keep core_predicate: biolink:close_match -DRUGBANK:group: +DRUGBANK:group: operation: keep core_predicate: biolink:related_to -DRUGBANK:inactivator: +DRUGBANK:inactivator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DRUGBANK:incorporation_into_and_destabilization: +DRUGBANK:incorporation_into_and_destabilization: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: degradation -DRUGBANK:inducer: +DRUGBANK:inducer: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:inhibition_of_synthesis: +DRUGBANK:inhibition_of_synthesis: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -DRUGBANK:inhibitor: +DRUGBANK:inhibitor: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DRUGBANK:inhibitory_allosteric_modulator: +DRUGBANK:inhibitory_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:intercalation: +DRUGBANK:intercalation: operation: keep - core_predicate: biolink:molecularly_interacts_with -DRUGBANK:inverse_agonist: + core_predicate: biolink:physically_interacts_with +DRUGBANK:inverse_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:ligand: +DRUGBANK:ligand: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:modulator: + core_predicate: biolink:directly_physically_interacts_with +DRUGBANK:modulator: operation: keep core_predicate: biolink:regulates -DRUGBANK:multitarget: +DRUGBANK:multitarget: operation: keep - core_predicate: biolink:directly_interacts_with -DRUGBANK:negative_modulator: + core_predicate: biolink:directly_physically_interacts_with +DRUGBANK:negative_modulator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DRUGBANK:neutralizer: +DRUGBANK:neutralizer: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:nucleotide_exchange_blocker: +DRUGBANK:nucleotide_exchange_blocker: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:oxidizer: +DRUGBANK:oxidizer: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: molecular_modification - object_direction: increased -DRUGBANK:partial_agonist: +DRUGBANK:partial_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:partial_antagonist: +DRUGBANK:partial_antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:pathway: +DRUGBANK:pathway: operation: invert core_predicate: biolink:has_participant -DRUGBANK:positive_allosteric_modulator: +DRUGBANK:positive_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:positive_modulator: +DRUGBANK:positive_modulator: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -DRUGBANK:potentiator: +DRUGBANK:potentiator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:product_of: +DRUGBANK:product_of: operation: keep core_predicate: biolink:derives_from -DRUGBANK:regulator: +DRUGBANK:regulator: operation: keep core_predicate: biolink:regulates -DRUGBANK:stabilization: +DRUGBANK:stabilization: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: stability - object_direction: increased -DRUGBANK:stimulator: +DRUGBANK:stimulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:substrate: +DRUGBANK:substrate: operation: keep core_predicate: biolink:physically_interacts_with -DRUGBANK:suppressor: +DRUGBANK:suppressor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DRUGBANK:target: +DRUGBANK:target: operation: keep core_predicate: biolink:physically_interacts_with -DRUGBANK:translocation_inhibitor: +DRUGBANK:translocation_inhibitor: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DRUGBANK:treats: +DRUGBANK:treats: operation: keep core_predicate: biolink:treats -DRUGBANK:weak_inhibitor: +DRUGBANK:weak_inhibitor: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DrugCentral:5271: +DrugCentral:5271: operation: keep core_predicate: biolink:diagnoses -DrugCentral:PA: +DrugCentral:PA: operation: keep core_predicate: biolink:subclass_of -DrugCentral:activator: +DrugCentral:activator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -DrugCentral:agonist: +DrugCentral:agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DrugCentral:allosteric_antagonist: +DrugCentral:allosteric_antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DrugCentral:allosteric_modulator: +DrugCentral:allosteric_modulator: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: activity -DrugCentral:antagonist: +DrugCentral:antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DrugCentral:antibody_binding: +DrugCentral:antibody_binding: operation: keep - core_predicate: biolink:molecularly_interacts_with -DrugCentral:antisense_inhibitor: + core_predicate: biolink:binds +DrugCentral:antisense_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: expression - object_direction: decreased -DrugCentral:binding_agent: +DrugCentral:binding_agent: operation: keep - core_predicate: biolink:directly_interacts_with -DrugCentral:blocker: + core_predicate: biolink:directly_physically_interacts_with +DrugCentral:blocker: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DrugCentral:contraindication: +DrugCentral:contraindication: operation: keep core_predicate: biolink:contraindicated_for -DrugCentral:gating_inhibitor: +DrugCentral:gating_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DrugCentral:has_role: +DrugCentral:has_role: operation: keep core_predicate: biolink:related_to -DrugCentral:indication: +DrugCentral:indication: operation: keep core_predicate: biolink:treats -DrugCentral:inhibitor: +DrugCentral:inhibitor: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DrugCentral:inverse_agonist: +DrugCentral:inverse_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -DrugCentral:modulator: +DrugCentral:modulator: operation: keep core_predicate: biolink:regulates -DrugCentral:negative_allosteric_modulator: +DrugCentral:negative_allosteric_modulator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DrugCentral:negative_modulator: +DrugCentral:negative_modulator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -DrugCentral:off-label_use: +DrugCentral:off-label_use: operation: keep core_predicate: biolink:treats -DrugCentral:opener: +DrugCentral:opener: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DrugCentral:partial_agonist: +DrugCentral:partial_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DrugCentral:pharmacological_chaperone: +DrugCentral:pharmacological_chaperone: operation: keep - core_predicate: biolink:directly_interacts_with -DrugCentral:positive_allosteric_modulator: + core_predicate: biolink:directly_physically_interacts_with +DrugCentral:positive_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: increased -DrugCentral:positive_modulator: +DrugCentral:positive_modulator: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -DrugCentral:releasing_agent: +DrugCentral:releasing_agent: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: expression - object_direction: increased -DrugCentral:struct2atc: +DrugCentral:struct2atc: operation: keep core_predicate: biolink:close_match -DrugCentral:substrate: +DrugCentral:substrate: operation: keep core_predicate: biolink:physically_interacts_with -DrugCentral:symptomatic_treatment: +DrugCentral:symptomatic_treatment: operation: keep core_predicate: biolink:treats -EFO:0000784: +EFO:0000784: operation: keep core_predicate: biolink:located_in -EFO:0001697: +EFO:0001697: operation: invert core_predicate: biolink:related_to -EFO:0006351: +EFO:0006351: operation: keep core_predicate: biolink:related_to -EFO:is_executed_in: +EFO:is_executed_in: operation: keep core_predicate: biolink:related_to -ENVO:01001307: +ENVO:01001307: operation: keep core_predicate: biolink:coexists_with -FMA:SIB: +FMA:SIB: operation: delete -FMA:adheres_to: +FMA:adheres_to: operation: keep core_predicate: biolink:physically_interacts_with -FMA:adjacent_to: +FMA:adjacent_to: operation: keep core_predicate: biolink:coexists_with -FMA:afferent_to: +FMA:afferent_to: operation: keep core_predicate: biolink:coexists_with -FMA:anatomical_entity_observed_in: +FMA:anatomical_entity_observed_in: operation: delete -FMA:anterior_to: +FMA:anterior_to: operation: keep core_predicate: biolink:coexists_with -FMA:anteroinferior_to: +FMA:anteroinferior_to: operation: keep core_predicate: biolink:coexists_with -FMA:anterolateral_to: +FMA:anterolateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:anteromedial_to: +FMA:anteromedial_to: operation: keep core_predicate: biolink:coexists_with -FMA:anterosuperior_to: +FMA:anterosuperior_to: operation: keep core_predicate: biolink:coexists_with -FMA:arterial_supply_of: +FMA:arterial_supply_of: operation: keep core_predicate: biolink:coexists_with -FMA:articulates_with: +FMA:articulates_with: operation: keep core_predicate: biolink:coexists_with -FMA:attaches_to: +FMA:attaches_to: operation: keep core_predicate: biolink:coexists_with -FMA:bounded_by: +FMA:bounded_by: operation: keep core_predicate: biolink:coexists_with -FMA:bounds: +FMA:bounds: operation: keep core_predicate: biolink:coexists_with -FMA:branch_of: +FMA:branch_of: operation: keep core_predicate: biolink:coexists_with -FMA:connected_to: +FMA:connected_to: operation: keep core_predicate: biolink:related_to -FMA:connection_type_of: +FMA:connection_type_of: operation: keep core_predicate: biolink:coexists_with -FMA:constitutional_part_of: +FMA:constitutional_part_of: operation: invert core_predicate: biolink:has_part -FMA:contained_in: +FMA:contained_in: operation: invert core_predicate: biolink:has_part -FMA:contains: +FMA:contains: operation: keep core_predicate: biolink:has_part -FMA:continuation_branch_of: +FMA:continuation_branch_of: operation: keep core_predicate: biolink:coexists_with -FMA:continuous_distally_with: +FMA:continuous_distally_with: operation: keep core_predicate: biolink:coexists_with -FMA:continuous_proximally_with: +FMA:continuous_proximally_with: operation: keep core_predicate: biolink:coexists_with -FMA:continuous_with: +FMA:continuous_with: operation: keep core_predicate: biolink:related_to -FMA:corresponds_to: +FMA:corresponds_to: operation: keep core_predicate: biolink:coexists_with -FMA:derives: +FMA:derives: operation: invert core_predicate: biolink:derives_from -FMA:derives_from: - operation: invert - core_predicate: biolink:derives_into -FMA:development_type_of: +FMA:derives_from: + operation: keep + core_predicate: biolink:derives_from +FMA:development_type_of: operation: keep core_predicate: biolink:coexists_with -FMA:developmental_stage_of: +FMA:developmental_stage_of: operation: keep core_predicate: biolink:coexists_with -FMA:develops_from: +FMA:develops_from: operation: keep core_predicate: biolink:develops_from -FMA:develops_into: +FMA:develops_into: operation: keep core_predicate: biolink:develops_from -FMA:direct_cell_shape_of: +FMA:direct_cell_shape_of: operation: keep core_predicate: biolink:coexists_with -FMA:direct_left_of: +FMA:direct_left_of: operation: keep core_predicate: biolink:coexists_with -FMA:direct_right_of: +FMA:direct_right_of: operation: keep core_predicate: biolink:coexists_with -FMA:distal_to: +FMA:distal_to: operation: keep core_predicate: biolink:coexists_with -FMA:drains_into: +FMA:drains_into: operation: keep core_predicate: biolink:coexists_with -FMA:efferent_to: +FMA:efferent_to: operation: keep core_predicate: biolink:coexists_with -FMA:external_to: +FMA:external_to: operation: keep core_predicate: biolink:coexists_with -FMA:formed_by: +FMA:formed_by: operation: keep core_predicate: biolink:coexists_with -FMA:forms: +FMA:forms: operation: keep core_predicate: biolink:coexists_with -FMA:full_grown_phenotype_of: +FMA:full_grown_phenotype_of: operation: keep core_predicate: biolink:coexists_with -FMA:fuses_with: +FMA:fuses_with: operation: keep core_predicate: biolink:coexists_with -FMA:fusion_of: +FMA:fusion_of: operation: keep core_predicate: biolink:coexists_with -FMA:germ_origin_of: +FMA:germ_origin_of: operation: keep core_predicate: biolink:coexists_with -FMA:has_adherent: +FMA:has_adherent: operation: keep core_predicate: biolink:coexists_with -FMA:has_arterial_supply: +FMA:has_arterial_supply: operation: keep core_predicate: biolink:coexists_with -FMA:has_branch: +FMA:has_branch: operation: keep core_predicate: biolink:coexists_with -FMA:has_connection_type: +FMA:has_connection_type: operation: keep core_predicate: biolink:coexists_with -FMA:has_constitutional_part: +FMA:has_constitutional_part: operation: keep core_predicate: biolink:has_part -FMA:has_continuation_branch: +FMA:has_continuation_branch: operation: keep core_predicate: biolink:coexists_with -FMA:has_development_type: +FMA:has_development_type: operation: keep core_predicate: biolink:coexists_with -FMA:has_developmental_stage: +FMA:has_developmental_stage: operation: keep core_predicate: biolink:coexists_with -FMA:has_direct_cell_shape: +FMA:has_direct_cell_shape: operation: keep core_predicate: biolink:coexists_with -FMA:has_full_grown_phenotype: +FMA:has_full_grown_phenotype: operation: keep core_predicate: biolink:coexists_with -FMA:has_fusion: +FMA:has_fusion: operation: keep core_predicate: biolink:coexists_with -FMA:has_germ_origin: +FMA:has_germ_origin: operation: keep core_predicate: biolink:coexists_with -FMA:has_inherent_3d_shape: +FMA:has_inherent_3d_shape: operation: keep core_predicate: biolink:coexists_with -FMA:has_insertion: +FMA:has_insertion: operation: keep core_predicate: biolink:coexists_with -FMA:has_location: +FMA:has_location: operation: keep core_predicate: biolink:located_in -FMA:has_lymphatic_drainage: +FMA:has_lymphatic_drainage: operation: keep core_predicate: biolink:coexists_with -FMA:has_member: +FMA:has_member: operation: keep core_predicate: biolink:has_part -FMA:has_nerve_supply: +FMA:has_nerve_supply: operation: keep core_predicate: biolink:coexists_with -FMA:has_observed_anatomical_entity: +FMA:has_observed_anatomical_entity: operation: keep core_predicate: biolink:coexists_with -FMA:has_origin: +FMA:has_origin: operation: keep core_predicate: biolink:coexists_with -FMA:has_part: +FMA:has_part: operation: keep core_predicate: biolink:has_part -FMA:has_primary_segmental_supply: +FMA:has_primary_segmental_supply: operation: keep core_predicate: biolink:coexists_with -FMA:has_projection: +FMA:has_projection: operation: keep core_predicate: biolink:coexists_with -FMA:has_regional_part: +FMA:has_regional_part: operation: keep core_predicate: biolink:coexists_with -FMA:has_related_developmental_entity: +FMA:has_related_developmental_entity: operation: keep core_predicate: biolink:coexists_with -FMA:has_secondary_segmental_supply: +FMA:has_secondary_segmental_supply: operation: keep core_predicate: biolink:coexists_with -FMA:has_segmental_composition: +FMA:has_segmental_composition: operation: keep core_predicate: biolink:coexists_with -FMA:has_segmental_supply: +FMA:has_segmental_supply: operation: keep core_predicate: biolink:coexists_with -FMA:has_tributary: +FMA:has_tributary: operation: keep core_predicate: biolink:coexists_with -FMA:has_venous_drainage: +FMA:has_venous_drainage: operation: keep core_predicate: biolink:coexists_with -FMA:homonym_for: +FMA:homonym_for: operation: delete -FMA:homonym_of: +FMA:homonym_of: operation: keep core_predicate: biolink:related_to -FMA:inferior_to: +FMA:inferior_to: operation: keep core_predicate: biolink:coexists_with -FMA:inferolateral_to: +FMA:inferolateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:inferomedial_to: +FMA:inferomedial_to: operation: keep core_predicate: biolink:coexists_with -FMA:inherent_3d_shape_of: +FMA:inherent_3d_shape_of: operation: keep core_predicate: biolink:coexists_with -FMA:insertion_of: +FMA:insertion_of: operation: keep core_predicate: biolink:coexists_with -FMA:internal_to: +FMA:internal_to: operation: keep core_predicate: biolink:coexists_with -FMA:lateral_to: +FMA:lateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:left_lateral_to: +FMA:left_lateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:left_medial_to: +FMA:left_medial_to: operation: keep core_predicate: biolink:coexists_with -FMA:location_of: +FMA:location_of: operation: invert core_predicate: biolink:located_in -FMA:lymphatic_drainage_of: +FMA:lymphatic_drainage_of: operation: keep core_predicate: biolink:coexists_with -FMA:matures_from: +FMA:matures_from: operation: keep core_predicate: biolink:coexists_with -FMA:matures_into: +FMA:matures_into: operation: keep core_predicate: biolink:coexists_with -FMA:medial_to: +FMA:medial_to: operation: keep core_predicate: biolink:coexists_with -FMA:member_of: +FMA:member_of: operation: invert core_predicate: biolink:has_part -FMA:merges_with: +FMA:merges_with: operation: keep core_predicate: biolink:coexists_with -FMA:nerve_supply_of: +FMA:nerve_supply_of: operation: keep core_predicate: biolink:coexists_with -FMA:origin_of: +FMA:origin_of: operation: keep core_predicate: biolink:coexists_with -FMA:part_of: +FMA:part_of: operation: invert core_predicate: biolink:has_part -FMA:posterior_to: +FMA:posterior_to: operation: keep core_predicate: biolink:coexists_with -FMA:posteroinferior_to: +FMA:posteroinferior_to: operation: keep core_predicate: biolink:coexists_with -FMA:posterolateral_to: +FMA:posterolateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:posteromedial_to: +FMA:posteromedial_to: operation: keep core_predicate: biolink:coexists_with -FMA:posterosuperior_to: +FMA:posterosuperior_to: operation: keep core_predicate: biolink:coexists_with -FMA:primary_segmental_supply_of: +FMA:primary_segmental_supply_of: operation: keep core_predicate: biolink:coexists_with -FMA:projects_from: +FMA:projects_from: operation: keep core_predicate: biolink:coexists_with -FMA:projects_to: +FMA:projects_to: operation: keep core_predicate: biolink:coexists_with -FMA:proximal_to: +FMA:proximal_to: operation: keep core_predicate: biolink:coexists_with -FMA:receives_attachment_from: +FMA:receives_attachment_from: operation: keep core_predicate: biolink:coexists_with -FMA:receives_drainage_from: +FMA:receives_drainage_from: operation: keep core_predicate: biolink:coexists_with -FMA:receives_input_from: +FMA:receives_input_from: operation: keep core_predicate: biolink:coexists_with -FMA:receives_projection: +FMA:receives_projection: operation: keep core_predicate: biolink:coexists_with -FMA:regional_part_of: +FMA:regional_part_of: operation: invert core_predicate: biolink:has_part -FMA:related_developmental_entity_of: +FMA:related_developmental_entity_of: operation: keep core_predicate: biolink:related_to -FMA:related_object: +FMA:related_object: operation: keep core_predicate: biolink:related_to -FMA:related_part: +FMA:related_part: operation: keep core_predicate: biolink:coexists_with -FMA:right_lateral_to: +FMA:right_lateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:right_medial_to: +FMA:right_medial_to: operation: keep core_predicate: biolink:coexists_with -FMA:secondary_segmental_supply_of: +FMA:secondary_segmental_supply_of: operation: keep core_predicate: biolink:coexists_with -FMA:segmental_composition_of: +FMA:segmental_composition_of: operation: keep core_predicate: biolink:coexists_with -FMA:segmental_supply_of: +FMA:segmental_supply_of: operation: keep core_predicate: biolink:coexists_with -FMA:sends_output_to: +FMA:sends_output_to: operation: keep core_predicate: biolink:coexists_with -FMA:superior_to: +FMA:superior_to: operation: keep core_predicate: biolink:coexists_with -FMA:superolateral_to: +FMA:superolateral_to: operation: keep core_predicate: biolink:coexists_with -FMA:superomedial_to: +FMA:superomedial_to: operation: keep core_predicate: biolink:coexists_with -FMA:surrounded_by: +FMA:surrounded_by: operation: keep core_predicate: biolink:coexists_with -FMA:surrounds: +FMA:surrounds: operation: keep core_predicate: biolink:coexists_with -FMA:transforms_from: +FMA:transforms_from: operation: invert core_predicate: biolink:precedes -FMA:transforms_into: +FMA:transforms_into: operation: keep core_predicate: biolink:precedes -FMA:tributary_of: +FMA:tributary_of: operation: keep core_predicate: biolink:coexists_with -FMA:venous_drainage_of: +FMA:venous_drainage_of: operation: keep core_predicate: biolink:coexists_with -FOODON:00001301: +FOODON:00001301: operation: keep core_predicate: biolink:model_of -FOODON:00001563: +FOODON:00001563: operation: keep core_predicate: biolink:has_part -FOODON:00002420: +FOODON:00002420: operation: keep core_predicate: biolink:has_part -GENEPIO:0001739: +GENEPIO:0001739: operation: invert core_predicate: biolink:precedes -GENO:0000382: +GENO:0000382: operation: keep core_predicate: biolink:has_variant_part -GENO:0000790: +GENO:0000790: operation: keep core_predicate: biolink:related_condition -GENO:0000840: +GENO:0000840: operation: keep core_predicate: biolink:gene_associated_with_condition -GENO:0000841: +GENO:0000841: operation: keep core_predicate: biolink:gene_associated_with_condition -GO:SIB: +GO:SIB: operation: delete -GO:acts_upstream_of: +GO:acts_upstream_of: operation: keep core_predicate: biolink:affects -GO:acts_upstream_of_negative_effect: +GO:acts_upstream_of_negative_effect: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -GO:acts_upstream_of_or_within: +GO:acts_upstream_of_or_within: operation: keep core_predicate: biolink:affects -GO:acts_upstream_of_or_within_negative_effect: +GO:acts_upstream_of_or_within_negative_effect: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -GO:acts_upstream_of_or_within_positive_effect: +GO:acts_upstream_of_or_within_positive_effect: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -GO:acts_upstream_of_positive_effect: +GO:acts_upstream_of_positive_effect: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -GO:colocalizes_with: +GO:colocalizes_with: operation: keep core_predicate: biolink:colocalizes_with -GO:contributes_to: +GO:contributes_to: operation: keep core_predicate: biolink:contributes_to -GO:enables: +GO:enables: operation: keep core_predicate: biolink:enables -GO:ends_during: +GO:ends_during: operation: keep core_predicate: biolink:related_to -GO:happens_during: +GO:happens_during: operation: keep core_predicate: biolink:related_to -GO:has_occurrence: +GO:has_occurrence: operation: keep core_predicate: biolink:capable_of -GO:has_part: +GO:has_part: operation: keep core_predicate: biolink:has_part -GO:inverse_ends_during: +GO:inverse_ends_during: operation: keep core_predicate: biolink:related_to -GO:inverse_happens_during: +GO:inverse_happens_during: operation: delete -GO:inverse_isa: +GO:inverse_isa: operation: invert core_predicate: biolink:subclass_of -GO:involved_in: +GO:involved_in: operation: invert core_predicate: biolink:has_participant -GO:is_active_in: +GO:is_active_in: operation: keep core_predicate: biolink:actively_involved_in -GO:isa: +GO:isa: operation: keep core_predicate: biolink:subclass_of -GO:located_in: +GO:located_in: operation: keep core_predicate: biolink:located_in -GO:negatively_regulated_by: +GO:negatively_regulated_by: operation: invert core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -GO:negatively_regulates: +GO:negatively_regulates: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -GO:occurs_in: +GO:occurs_in: operation: keep core_predicate: biolink:occurs_in -GO:part_of: +GO:part_of: operation: invert core_predicate: biolink:has_part -GO:positively_regulated_by: +GO:positively_regulated_by: operation: invert core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -GO:positively_regulates: +GO:positively_regulates: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -GO:regulated_by: +GO:regulated_by: operation: invert core_predicate: biolink:regulates -GO:regulates: +GO:regulates: operation: keep core_predicate: biolink:regulates -GOREL:0000040: +GOREL:0000040: operation: keep core_predicate: biolink:causes -GOREL:0001004: +GOREL:0001004: operation: keep core_predicate: biolink:located_in -GOREL:0001006: +GOREL:0001006: operation: keep core_predicate: biolink:affects -GOREL:0002003: +GOREL:0002003: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: localization -GOREL:0002004: +GOREL:0002004: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: degradation - object_direction: increased -GOREL:0002005: +GOREL:0002005: operation: keep core_predicate: biolink:related_to -GOREL:0012006: +GOREL:0012006: operation: keep core_predicate: biolink:related_to -GTEx:affects_expression_in: +GTEx:affects_expression_in: operation: keep core_predicate: biolink:affects -HANCESTRO:0301: +HANCESTRO:0301: operation: keep core_predicate: biolink:related_to -HANCESTRO:0308: +HANCESTRO:0308: operation: keep core_predicate: biolink:related_to -HANCESTRO:0330: +HANCESTRO:0330: operation: keep core_predicate: biolink:related_to -HCPCS:mapped_from: +HCPCS:mapped_from: operation: delete -HCPCS:mapped_to: +HCPCS:mapped_to: operation: keep core_predicate: biolink:related_to -HMDB:at_cellular_location: +HMDB:at_cellular_location: operation: keep core_predicate: biolink:located_in -HMDB:at_tissue: +HMDB:at_tissue: operation: keep core_predicate: biolink:located_in -HMDB:disease: +HMDB:disease: operation: keep core_predicate: biolink:related_to -HMDB:has_protein_association: +HMDB:has_protein_association: operation: keep core_predicate: biolink:related_to -HMDB:in_biospecimen: +HMDB:in_biospecimen: operation: keep core_predicate: biolink:located_in -HMDB:in_pathway: +HMDB:in_pathway: operation: invert core_predicate: biolink:has_participant -HP:SIB: +HP:SIB: operation: delete -IAO:0000039: +IAO:0000039: operation: keep core_predicate: biolink:related_to -IAO:0000136: +IAO:0000136: operation: keep core_predicate: biolink:related_to -IAO:0000142: +IAO:0000142: operation: keep core_predicate: biolink:mentions -IAO:0000219: +IAO:0000219: operation: keep core_predicate: biolink:related_to -ICD10PCS:SIB: +ICD10PCS:SIB: operation: delete -ICD9:SIB: +ICD9:SIB: operation: delete -IDO:0000664: +IDO:0000664: operation: invert core_predicate: biolink:contributes_to -JensenLab:associated_with: +JensenLab:associated_with: operation: keep core_predicate: biolink:gene_associated_with_condition -KEGG:compound_to_enzyme: +KEGG:compound_to_enzyme: operation: keep core_predicate: biolink:interacts_with -KEGG:compound_to_pathway: +KEGG:compound_to_pathway: operation: invert core_predicate: biolink:has_participant -KEGG:compound_to_reaction: +KEGG:compound_to_reaction: operation: invert core_predicate: biolink:has_participant -KEGG:enzyme_to_pathway: +KEGG:enzyme_to_pathway: operation: invert core_predicate: biolink:has_participant -KEGG:enzyme_to_reaction: +KEGG:enzyme_to_reaction: operation: keep core_predicate: biolink:catalyzes -KEGG:glycan_to_enzyme: +KEGG:glycan_to_enzyme: operation: keep core_predicate: biolink:interacts_with -KEGG:glycan_to_pathway: +KEGG:glycan_to_pathway: operation: invert core_predicate: biolink:has_participant -KEGG:glycan_to_reaction: +KEGG:glycan_to_reaction: operation: invert core_predicate: biolink:has_participant -KEGG:pathway_to_compound: +KEGG:pathway_to_compound: operation: keep core_predicate: biolink:has_participant -KEGG:pathway_to_drug: +KEGG:pathway_to_drug: operation: keep core_predicate: biolink:has_participant -KEGG:pathway_to_glycan: +KEGG:pathway_to_glycan: operation: keep core_predicate: biolink:has_participant -KEGG:reaction_to_enzyme: +KEGG:reaction_to_enzyme: operation: invert core_predicate: biolink:catalyzes -KEGG:reaction_to_pathway: +KEGG:reaction_to_pathway: operation: invert core_predicate: biolink:has_participant -LOINC:adjustment_of: +LOINC:adjustment_of: operation: delete -LOINC:analyzed_by: +LOINC:analyzed_by: operation: delete -LOINC:analyzes: +LOINC:analyzes: operation: keep core_predicate: biolink:related_to -LOINC:answer_to: +LOINC:answer_to: operation: delete -LOINC:archetype_of: +LOINC:archetype_of: operation: delete -LOINC:associated_with: +LOINC:associated_with: operation: keep core_predicate: biolink:correlated_with -LOINC:challenge_of: +LOINC:challenge_of: operation: delete -LOINC:class_of: +LOINC:class_of: operation: keep core_predicate: biolink:subclass_of -LOINC:component_of: +LOINC:component_of: operation: invert core_predicate: biolink:has_part -LOINC:count_of: +LOINC:count_of: operation: delete -LOINC:divisor_of: +LOINC:divisor_of: operation: delete -LOINC:evaluation_of: +LOINC:evaluation_of: operation: delete -LOINC:fragments_for_synonyms_of: +LOINC:fragments_for_synonyms_of: operation: delete -LOINC:has_action_guidance: +LOINC:has_action_guidance: operation: keep core_predicate: biolink:related_to -LOINC:has_adjustment: +LOINC:has_adjustment: operation: keep core_predicate: biolink:related_to -LOINC:has_aggregation_view: +LOINC:has_aggregation_view: operation: keep core_predicate: biolink:related_to -LOINC:has_answer: +LOINC:has_answer: operation: keep core_predicate: biolink:related_to -LOINC:has_approach_guidance: +LOINC:has_approach_guidance: operation: keep core_predicate: biolink:related_to -LOINC:has_archetype: +LOINC:has_archetype: operation: keep core_predicate: biolink:subclass_of -LOINC:has_challenge: +LOINC:has_challenge: operation: keep core_predicate: biolink:related_to -LOINC:has_class: +LOINC:has_class: operation: invert core_predicate: biolink:subclass_of -LOINC:has_component: +LOINC:has_component: operation: keep core_predicate: biolink:has_part -LOINC:has_count: +LOINC:has_count: operation: keep core_predicate: biolink:related_to -LOINC:has_divisor: +LOINC:has_divisor: operation: keep core_predicate: biolink:related_to -LOINC:has_evaluation: +LOINC:has_evaluation: operation: keep core_predicate: biolink:related_to -LOINC:has_exam: +LOINC:has_exam: operation: keep core_predicate: biolink:related_to -LOINC:has_fragments_for_synonyms: +LOINC:has_fragments_for_synonyms: operation: keep core_predicate: biolink:has_input -LOINC:has_given_pharmaceutical_substance: +LOINC:has_given_pharmaceutical_substance: operation: delete -LOINC:has_imaged_location: +LOINC:has_imaged_location: operation: keep core_predicate: biolink:occurs_in -LOINC:has_imaging_focus: +LOINC:has_imaging_focus: operation: keep core_predicate: biolink:located_in -LOINC:has_lateral_anatomic_location: +LOINC:has_lateral_anatomic_location: operation: keep core_predicate: biolink:coexists_with -LOINC:has_lateral_location_presence: +LOINC:has_lateral_location_presence: operation: keep core_predicate: biolink:coexists_with -LOINC:has_loinc_number: +LOINC:has_loinc_number: operation: delete -LOINC:has_member: +LOINC:has_member: operation: keep core_predicate: biolink:has_part -LOINC:has_method: +LOINC:has_method: operation: keep core_predicate: biolink:related_to -LOINC:has_modality_subtype: +LOINC:has_modality_subtype: operation: keep core_predicate: biolink:related_to -LOINC:has_modality_type: +LOINC:has_modality_type: operation: keep core_predicate: biolink:related_to -LOINC:has_multipart: +LOINC:has_multipart: operation: delete -LOINC:has_object_guidance: +LOINC:has_object_guidance: operation: keep core_predicate: biolink:related_to -LOINC:has_parent_group: +LOINC:has_parent_group: operation: keep core_predicate: biolink:subclass_of -LOINC:has_pharmaceutical_route: +LOINC:has_pharmaceutical_route: operation: keep core_predicate: biolink:related_to -LOINC:has_presence_guidance: +LOINC:has_presence_guidance: operation: delete -LOINC:has_property: +LOINC:has_property: operation: delete -LOINC:has_scale: +LOINC:has_scale: operation: keep core_predicate: biolink:related_to -LOINC:has_subject: +LOINC:has_subject: operation: keep core_predicate: biolink:has_participant -LOINC:has_suffix: +LOINC:has_suffix: operation: keep core_predicate: biolink:related_to -LOINC:has_supersystem: +LOINC:has_supersystem: operation: invert core_predicate: biolink:has_part -LOINC:has_system: +LOINC:has_system: operation: keep core_predicate: biolink:has_input -LOINC:has_time_aspect: +LOINC:has_time_aspect: operation: keep core_predicate: biolink:related_to -LOINC:has_time_modifier: +LOINC:has_time_modifier: operation: keep core_predicate: biolink:related_to -LOINC:has_timing_of: +LOINC:has_timing_of: operation: keep core_predicate: biolink:related_to -LOINC:has_view_type: +LOINC:has_view_type: operation: keep core_predicate: biolink:related_to -LOINC:is_action_guidance_for: +LOINC:is_action_guidance_for: operation: delete -LOINC:is_aggregation_view_of: +LOINC:is_aggregation_view_of: operation: delete -LOINC:is_approach_guidance_for: +LOINC:is_approach_guidance_for: operation: delete -LOINC:is_exam_for: +LOINC:is_exam_for: operation: delete -LOINC:is_given_pharmaceutical_substance_for: +LOINC:is_given_pharmaceutical_substance_for: operation: invert core_predicate: biolink:has_participant -LOINC:is_imaged_location_for: +LOINC:is_imaged_location_for: operation: delete -LOINC:is_imaging_focus_of: +LOINC:is_imaging_focus_of: operation: delete -LOINC:is_lateral_anatomic_location_of: +LOINC:is_lateral_anatomic_location_of: operation: delete -LOINC:is_modality_subtype_for: +LOINC:is_modality_subtype_for: operation: delete -LOINC:is_modality_type_for: +LOINC:is_modality_type_for: operation: delete -LOINC:is_object_guidance_for: +LOINC:is_object_guidance_for: operation: delete -LOINC:is_pharmaceutical_route_for: +LOINC:is_pharmaceutical_route_for: operation: delete -LOINC:is_presence_guidance_for: +LOINC:is_presence_guidance_for: operation: keep core_predicate: biolink:subclass_of -LOINC:is_presence_of_lateral_location: +LOINC:is_presence_of_lateral_location: operation: delete -LOINC:is_subject_of: +LOINC:is_subject_of: operation: delete -LOINC:is_timing_for: +LOINC:is_timing_for: operation: delete -LOINC:is_view_type_for: +LOINC:is_view_type_for: operation: delete -LOINC:loinc_number_of: +LOINC:loinc_number_of: operation: delete -LOINC:mapped_from: +LOINC:mapped_from: operation: delete -LOINC:mapped_to: +LOINC:mapped_to: operation: keep core_predicate: biolink:related_to -LOINC:measured_by: +LOINC:measured_by: operation: keep core_predicate: biolink:related_to -LOINC:measures: +LOINC:measures: operation: delete -LOINC:member_of: +LOINC:member_of: operation: invert core_predicate: biolink:has_part -LOINC:method_of: +LOINC:method_of: operation: delete -LOINC:mth_expanded_form_of: +LOINC:mth_expanded_form_of: operation: delete -LOINC:mth_has_expanded_form: +LOINC:mth_has_expanded_form: operation: keep core_predicate: biolink:related_to -LOINC:multipart_of: +LOINC:multipart_of: operation: invert core_predicate: biolink:has_part -LOINC:parent_group_of: +LOINC:parent_group_of: operation: delete -LOINC:property_of: +LOINC:property_of: operation: keep core_predicate: biolink:related_to -LOINC:scale_of: +LOINC:scale_of: operation: delete -LOINC:suffix_of: +LOINC:suffix_of: operation: delete -LOINC:supersystem_of: +LOINC:supersystem_of: operation: delete -LOINC:system_of: +LOINC:system_of: operation: delete -LOINC:time_aspect_of: +LOINC:time_aspect_of: operation: delete -LOINC:time_modifier_of: +LOINC:time_modifier_of: operation: delete -MEDDRA:classified_as: +MEDDRA:classified_as: operation: keep core_predicate: biolink:close_match -MEDDRA:has_member: +MEDDRA:has_member: operation: keep core_predicate: biolink:has_part -MEDDRA:member_of: +MEDDRA:member_of: operation: invert core_predicate: biolink:has_part -MESH:AQ: +MESH:AQ: operation: delete -MESH:QB: +MESH:QB: operation: delete -MESH:RO: +MESH:RO: operation: keep core_predicate: biolink:related_to -MESH:SIB: +MESH:SIB: operation: delete -MESH:has_mapping_qualifier: +MESH:has_mapping_qualifier: operation: keep core_predicate: biolink:related_to -MESH:inverse_isa: +MESH:inverse_isa: operation: invert core_predicate: biolink:subclass_of -MESH:isa: +MESH:isa: operation: keep core_predicate: biolink:subclass_of -MESH:mapped_from: +MESH:mapped_from: operation: delete -MESH:mapped_to: +MESH:mapped_to: operation: keep core_predicate: biolink:related_to -MESH:mapping_qualifier_of: +MESH:mapping_qualifier_of: operation: delete -MI:0192: +MI:0192: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0194: + core_predicate: biolink:directly_physically_interacts_with +MI:0194: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0195: + core_predicate: biolink:directly_physically_interacts_with +MI:0195: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0197: + core_predicate: biolink:directly_physically_interacts_with +MI:0197: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0203: + core_predicate: biolink:directly_physically_interacts_with +MI:0203: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0204: + core_predicate: biolink:directly_physically_interacts_with +MI:0204: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0210: + core_predicate: biolink:directly_physically_interacts_with +MI:0210: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0211: + core_predicate: biolink:directly_physically_interacts_with +MI:0211: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0212: + core_predicate: biolink:directly_physically_interacts_with +MI:0212: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0213: + core_predicate: biolink:directly_physically_interacts_with +MI:0213: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0214: + core_predicate: biolink:directly_physically_interacts_with +MI:0214: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0216: + core_predicate: biolink:directly_physically_interacts_with +MI:0216: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0217: + core_predicate: biolink:directly_physically_interacts_with +MI:0217: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0220: + core_predicate: biolink:directly_physically_interacts_with +MI:0220: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0403: + core_predicate: biolink:directly_physically_interacts_with +MI:0403: operation: keep core_predicate: biolink:colocalizes_with -MI:0407: +MI:0407: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0408: + core_predicate: biolink:directly_physically_interacts_with +MI:0408: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0414: + core_predicate: biolink:directly_physically_interacts_with +MI:0414: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0556: + core_predicate: biolink:directly_physically_interacts_with +MI:0556: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0557: + core_predicate: biolink:directly_physically_interacts_with +MI:0557: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0559: + core_predicate: biolink:directly_physically_interacts_with +MI:0559: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0566: + core_predicate: biolink:directly_physically_interacts_with +MI:0566: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0567: + core_predicate: biolink:directly_physically_interacts_with +MI:0567: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0569: + core_predicate: biolink:directly_physically_interacts_with +MI:0569: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0570: + core_predicate: biolink:directly_physically_interacts_with +MI:0570: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0572: + core_predicate: biolink:directly_physically_interacts_with +MI:0572: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0844: + core_predicate: biolink:directly_physically_interacts_with +MI:0844: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0871: + core_predicate: biolink:directly_physically_interacts_with +MI:0871: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0882: + core_predicate: biolink:directly_physically_interacts_with +MI:0882: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0883: + core_predicate: biolink:directly_physically_interacts_with +MI:0883: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0902: + core_predicate: biolink:directly_physically_interacts_with +MI:0902: operation: keep - core_predicate: biolink:directly_interacts_with -MI:0914: + core_predicate: biolink:directly_physically_interacts_with +MI:0914: operation: keep core_predicate: biolink:interacts_with -MI:0915: +MI:0915: operation: keep core_predicate: biolink:physically_interacts_with -MI:0945: +MI:0945: operation: keep - core_predicate: biolink:directly_interacts_with -MI:1126: + core_predicate: biolink:directly_physically_interacts_with +MI:1126: operation: keep core_predicate: biolink:interacts_with -MI:1127: +MI:1127: operation: keep core_predicate: biolink:interacts_with -MI:1148: +MI:1148: operation: keep - core_predicate: biolink:directly_interacts_with -MI:1237: + core_predicate: biolink:directly_physically_interacts_with +MI:1237: operation: keep - core_predicate: biolink:directly_interacts_with -MI:1310: + core_predicate: biolink:directly_physically_interacts_with +MI:1310: operation: keep - core_predicate: biolink:directly_interacts_with -MI:2252: + core_predicate: biolink:directly_physically_interacts_with +MI:2252: operation: keep - core_predicate: biolink:directly_interacts_with -MI:2364: + core_predicate: biolink:directly_physically_interacts_with +MI:2364: operation: keep core_predicate: biolink:colocalizes_with -MONDO:0100332: +MONDO:0100332: operation: invert core_predicate: biolink:causes -MONDO:0100333: +MONDO:0100333: operation: invert core_predicate: biolink:causes -MONDO:disease_causes_feature: +MONDO:disease_causes_feature: operation: keep core_predicate: biolink:causes -MONDO:disease_has_basis_in_accumulation_of: +MONDO:disease_has_basis_in_accumulation_of: operation: keep core_predicate: biolink:disease_has_basis_in -MONDO:disease_has_basis_in_development_of: +MONDO:disease_has_basis_in_development_of: operation: keep core_predicate: biolink:disease_has_basis_in -MONDO:disease_has_location: +MONDO:disease_has_location: operation: keep core_predicate: biolink:disease_has_location -MONDO:disease_has_major_feature: +MONDO:disease_has_major_feature: operation: keep core_predicate: biolink:has_part -MONDO:disease_responds_to: +MONDO:disease_responds_to: operation: invert core_predicate: biolink:treats -MONDO:disease_shares_features_of: +MONDO:disease_shares_features_of: operation: keep core_predicate: biolink:related_to -MONDO:disease_triggers: +MONDO:disease_triggers: operation: keep core_predicate: biolink:causes -MONDO:equivalentTo: +MONDO:equivalentTo: operation: keep core_predicate: biolink:same_as -MONDO:has_onset: +MONDO:has_onset: operation: keep core_predicate: biolink:related_to -MONDO:has_onset_before: +MONDO:has_onset_before: operation: keep core_predicate: biolink:related_to -MONDO:has_onset_during_or_after: +MONDO:has_onset_during_or_after: operation: keep core_predicate: biolink:related_to -MONDO:part_of_progression_of_disease: +MONDO:part_of_progression_of_disease: operation: invert core_predicate: biolink:has_part -MONDO:predisposes_towards: +MONDO:predisposes_towards: operation: keep core_predicate: biolink:contributes_to -NBO-PROPERTY:by_means: +NBO-PROPERTY:by_means: operation: keep core_predicate: biolink:actively_involved_in -NBO-PROPERTY:has_participant: +NBO-PROPERTY:has_participant: operation: keep core_predicate: biolink:has_participant -NBO-PROPERTY:in_response_to: +NBO-PROPERTY:in_response_to: operation: keep core_predicate: biolink:causes -NBO-PROPERTY:is_about: +NBO-PROPERTY:is_about: operation: keep core_predicate: biolink:related_to -NCIT:A11: +NCIT:A11: operation: keep core_predicate: biolink:subclass_of -NCIT:A14: +NCIT:A14: operation: keep core_predicate: biolink:subclass_of -NCIT:A16: +NCIT:A16: operation: keep core_predicate: biolink:subclass_of -NCIT:A3: +NCIT:A3: operation: keep core_predicate: biolink:subclass_of -NCIT:A7: +NCIT:A7: operation: keep core_predicate: biolink:physically_interacts_with -NCIT:Anatomic_Structure_Has_Location_Role: +NCIT:Anatomic_Structure_Has_Location_Role: operation: invert core_predicate: biolink:located_in -NCIT:C15220: +NCIT:C15220: operation: keep core_predicate: biolink:diagnoses -NCIT:C16798: +NCIT:C16798: operation: keep core_predicate: biolink:in_linkage_disequilibrium_with -NCIT:C2861: +NCIT:C2861: operation: keep core_predicate: biolink:causes_adverse_event -NCIT:C37933: +NCIT:C37933: operation: keep core_predicate: biolink:contraindicated_for -NCIT:R100: +NCIT:R100: operation: keep core_predicate: biolink:affects -NCIT:R101: +NCIT:R101: operation: keep core_predicate: biolink:affects -NCIT:R102: +NCIT:R102: operation: keep core_predicate: biolink:affects -NCIT:R108: +NCIT:R108: operation: keep core_predicate: biolink:has_phenotype -NCIT:R113: +NCIT:R113: operation: keep core_predicate: biolink:affects -NCIT:R115: +NCIT:R115: operation: keep core_predicate: biolink:has_phenotype -NCIT:R124: +NCIT:R124: operation: keep core_predicate: biolink:affects -NCIT:R130: +NCIT:R130: operation: invert core_predicate: biolink:has_participant -NCIT:R131: +NCIT:R131: operation: invert core_predicate: biolink:has_participant -NCIT:R133: +NCIT:R133: operation: keep core_predicate: biolink:affects -NCIT:R145: +NCIT:R145: operation: keep core_predicate: biolink:located_in -NCIT:R146: +NCIT:R146: operation: keep core_predicate: biolink:affects -NCIT:R150: +NCIT:R150: operation: keep core_predicate: biolink:affects -NCIT:R155: +NCIT:R155: operation: keep core_predicate: biolink:located_in -NCIT:R156: +NCIT:R156: operation: keep core_predicate: biolink:located_in -NCIT:R158: +NCIT:R158: operation: keep core_predicate: biolink:affects -NCIT:R160: +NCIT:R160: operation: keep core_predicate: biolink:affects -NCIT:R163: +NCIT:R163: operation: keep core_predicate: biolink:related_to -NCIT:R165: +NCIT:R165: operation: keep core_predicate: biolink:located_in -NCIT:R166: +NCIT:R166: operation: keep core_predicate: biolink:located_in -NCIT:R167: +NCIT:R167: operation: keep core_predicate: biolink:located_in -NCIT:R168: +NCIT:R168: operation: keep core_predicate: biolink:located_in -NCIT:R169: +NCIT:R169: operation: keep core_predicate: biolink:located_in -NCIT:R170: +NCIT:R170: operation: keep core_predicate: biolink:located_in -NCIT:R171: +NCIT:R171: operation: keep core_predicate: biolink:located_in -NCIT:R173: +NCIT:R173: operation: keep core_predicate: biolink:affects -NCIT:R175: +NCIT:R175: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:R176: +NCIT:R176: operation: invert core_predicate: biolink:gene_associated_with_condition -NCIT:R178: +NCIT:R178: operation: invert core_predicate: biolink:gene_product_of -NCIT:R23: +NCIT:R23: operation: keep core_predicate: biolink:affects -NCIT:R25: +NCIT:R25: operation: keep core_predicate: biolink:affects -NCIT:R27: +NCIT:R27: operation: invert core_predicate: biolink:has_part -NCIT:R29: +NCIT:R29: operation: keep core_predicate: biolink:produces -NCIT:R30: +NCIT:R30: operation: keep core_predicate: biolink:affects -NCIT:R36: +NCIT:R36: operation: keep core_predicate: biolink:subclass_of -NCIT:R37: +NCIT:R37: operation: invert core_predicate: biolink:has_participant -NCIT:R38: +NCIT:R38: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:R39: +NCIT:R39: operation: keep core_predicate: biolink:biomarker_for -NCIT:R40: +NCIT:R40: operation: keep core_predicate: biolink:located_in -NCIT:R42: +NCIT:R42: operation: keep core_predicate: biolink:subclass_of -NCIT:R47: +NCIT:R47: operation: keep core_predicate: biolink:biomarker_for -NCIT:R48: +NCIT:R48: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:R50: +NCIT:R50: operation: keep core_predicate: biolink:has_part -NCIT:R51: +NCIT:R51: operation: invert core_predicate: biolink:has_participant -NCIT:R52: +NCIT:R52: operation: keep core_predicate: biolink:capable_of -NCIT:R53: +NCIT:R53: operation: invert core_predicate: biolink:has_participant -NCIT:R72: +NCIT:R72: operation: keep core_predicate: biolink:affects -NCIT:R81: +NCIT:R81: operation: keep core_predicate: biolink:related_to -NCIT:R82: +NCIT:R82: operation: invert core_predicate: biolink:has_part -NCIT:R88: +NCIT:R88: operation: keep core_predicate: biolink:related_to -NCIT:R89: +NCIT:R89: operation: keep core_predicate: biolink:has_phenotype -NCIT:abnormal_cell_affected_by_chemical_or_drug: +NCIT:abnormal_cell_affected_by_chemical_or_drug: operation: delete -NCIT:abnormality_associated_with_allele: +NCIT:abnormality_associated_with_allele: operation: delete -NCIT:activity_of_allele: +NCIT:activity_of_allele: operation: delete -NCIT:allele_absent_from_wild-type_chromosomal_location: +NCIT:allele_absent_from_wild-type_chromosomal_location: operation: keep core_predicate: biolink:located_in -NCIT:allele_has_abnormality: +NCIT:allele_has_abnormality: operation: keep core_predicate: biolink:causes -NCIT:allele_has_activity: +NCIT:allele_has_activity: operation: keep core_predicate: biolink:has_molecular_consequence -NCIT:allele_in_chromosomal_location: +NCIT:allele_in_chromosomal_location: operation: keep core_predicate: biolink:located_in -NCIT:allele_plays_altered_role_in_process: +NCIT:allele_plays_altered_role_in_process: operation: keep core_predicate: biolink:affects -NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: +NCIT:allele_plays_role_in_metabolism_of_chemical_or_drug: operation: keep core_predicate: biolink:affects -NCIT:anatomic_structure_has_location: +NCIT:anatomic_structure_has_location: operation: delete -NCIT:anatomic_structure_is_physical_part_of: +NCIT:anatomic_structure_is_physical_part_of: operation: invert core_predicate: biolink:has_part -NCIT:anatomy_originated_from_biological_process: +NCIT:anatomy_originated_from_biological_process: operation: delete -NCIT:associated_with_malfunction_of_gene_product: +NCIT:associated_with_malfunction_of_gene_product: operation: delete -NCIT:biological_process_has_associated_location: +NCIT:biological_process_has_associated_location: operation: keep core_predicate: biolink:affects -NCIT:biological_process_has_initiator_chemical_or_drug: +NCIT:biological_process_has_initiator_chemical_or_drug: operation: delete -NCIT:biological_process_has_initiator_process: +NCIT:biological_process_has_initiator_process: operation: delete -NCIT:biological_process_has_result_anatomy: +NCIT:biological_process_has_result_anatomy: operation: keep core_predicate: biolink:has_output -NCIT:biological_process_has_result_biological_process: +NCIT:biological_process_has_result_biological_process: operation: keep core_predicate: biolink:causes -NCIT:biological_process_has_result_chemical_or_drug: +NCIT:biological_process_has_result_chemical_or_drug: operation: keep core_predicate: biolink:produces -NCIT:biological_process_involves_chemical_or_drug: +NCIT:biological_process_involves_chemical_or_drug: operation: invert core_predicate: biolink:actively_involved_in -NCIT:biological_process_involves_gene_product: +NCIT:biological_process_involves_gene_product: operation: delete -NCIT:biological_process_is_part_of_process: +NCIT:biological_process_is_part_of_process: operation: delete -NCIT:biological_process_results_from_biological_process: +NCIT:biological_process_results_from_biological_process: operation: delete -NCIT:biomarker_type_includes_gene: +NCIT:biomarker_type_includes_gene: operation: delete -NCIT:biomarker_type_includes_gene_product: +NCIT:biomarker_type_includes_gene_product: operation: delete -NCIT:cdrh_parent_of: +NCIT:cdrh_parent_of: operation: invert core_predicate: biolink:subclass_of -NCIT:cell_type_is_associated_with_eo_disease: +NCIT:cell_type_is_associated_with_eo_disease: operation: delete -NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: +NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: operation: delete -NCIT:chemical_or_drug_affects_abnormal_cell: +NCIT:chemical_or_drug_affects_abnormal_cell: operation: keep core_predicate: biolink:affects -NCIT:chemical_or_drug_affects_cell_type_or_tissue: +NCIT:chemical_or_drug_affects_cell_type_or_tissue: operation: keep core_predicate: biolink:affects -NCIT:chemical_or_drug_affects_gene_product: +NCIT:chemical_or_drug_affects_gene_product: operation: keep core_predicate: biolink:affects -NCIT:chemical_or_drug_has_mechanism_of_action: +NCIT:chemical_or_drug_has_mechanism_of_action: operation: keep core_predicate: biolink:affects -NCIT:chemical_or_drug_has_physiologic_effect: +NCIT:chemical_or_drug_has_physiologic_effect: operation: keep core_predicate: biolink:causes -NCIT:chemical_or_drug_initiates_biological_process: +NCIT:chemical_or_drug_initiates_biological_process: operation: keep core_predicate: biolink:causes -NCIT:chemical_or_drug_is_metabolized_by_enzyme: +NCIT:chemical_or_drug_is_metabolized_by_enzyme: operation: delete -NCIT:chemical_or_drug_is_product_of_biological_process: +NCIT:chemical_or_drug_is_product_of_biological_process: operation: delete -NCIT:chemical_or_drug_metabolism_is_associated_with_allele: +NCIT:chemical_or_drug_metabolism_is_associated_with_allele: operation: delete -NCIT:chemical_or_drug_plays_role_in_biological_process: +NCIT:chemical_or_drug_plays_role_in_biological_process: operation: delete -NCIT:chemotherapy_regimen_has_component: +NCIT:chemotherapy_regimen_has_component: operation: delete -NCIT:chromosomal_location_of_allele: +NCIT:chromosomal_location_of_allele: operation: delete -NCIT:chromosomal_location_of_wild-type_gene: +NCIT:chromosomal_location_of_wild-type_gene: operation: delete -NCIT:chromosome_involved_in_cytogenetic_abnormality: +NCIT:chromosome_involved_in_cytogenetic_abnormality: operation: delete -NCIT:chromosome_mapped_to_disease: +NCIT:chromosome_mapped_to_disease: operation: keep core_predicate: biolink:causes -NCIT:completely_excised_anatomy_has_procedure: +NCIT:completely_excised_anatomy_has_procedure: operation: delete -NCIT:completely_excised_anatomy_may_have_procedure: +NCIT:completely_excised_anatomy_may_have_procedure: operation: delete -NCIT:complex_has_physical_part: +NCIT:complex_has_physical_part: operation: keep core_predicate: biolink:has_part -NCIT:concept_in_subset: +NCIT:concept_in_subset: operation: delete -NCIT:conceptual_part_of: +NCIT:conceptual_part_of: operation: invert core_predicate: biolink:has_part -NCIT:ctcae_5_parent_of: +NCIT:ctcae_5_parent_of: operation: invert core_predicate: biolink:subclass_of -NCIT:cytogenetic_abnormality_involves_chromosome: +NCIT:cytogenetic_abnormality_involves_chromosome: operation: keep core_predicate: biolink:affects -NCIT:data_element_of: +NCIT:data_element_of: operation: delete -NCIT:disease_excludes_abnormal_cell: +NCIT:disease_excludes_abnormal_cell: operation: delete -NCIT:disease_excludes_cytogenetic_abnormality: +NCIT:disease_excludes_cytogenetic_abnormality: operation: delete -NCIT:disease_excludes_finding: +NCIT:disease_excludes_finding: operation: delete -NCIT:disease_excludes_metastatic_anatomic_site: +NCIT:disease_excludes_metastatic_anatomic_site: operation: delete -NCIT:disease_excludes_molecular_abnormality: +NCIT:disease_excludes_molecular_abnormality: operation: delete -NCIT:disease_excludes_normal_cell_origin: +NCIT:disease_excludes_normal_cell_origin: operation: delete -NCIT:disease_excludes_normal_tissue_origin: +NCIT:disease_excludes_normal_tissue_origin: operation: delete -NCIT:disease_excludes_primary_anatomic_site: +NCIT:disease_excludes_primary_anatomic_site: operation: delete -NCIT:disease_has_abnormal_cell: +NCIT:disease_has_abnormal_cell: operation: delete -NCIT:disease_has_accepted_treatment_with_regimen: +NCIT:disease_has_accepted_treatment_with_regimen: operation: delete -NCIT:disease_has_associated_anatomic_site: +NCIT:disease_has_associated_anatomic_site: operation: keep core_predicate: biolink:affects -NCIT:disease_has_associated_disease: +NCIT:disease_has_associated_disease: operation: keep - core_predicate: biolink:has_real_world_evidence_of_association_with -NCIT:disease_has_associated_gene: + core_predicate: biolink:associated_with +NCIT:disease_has_associated_gene: operation: delete -NCIT:disease_has_cytogenetic_abnormality: +NCIT:disease_has_cytogenetic_abnormality: operation: delete -NCIT:disease_has_finding: +NCIT:disease_has_finding: operation: invert core_predicate: biolink:biomarker_for -NCIT:disease_has_metastatic_anatomic_site: +NCIT:disease_has_metastatic_anatomic_site: operation: keep core_predicate: biolink:affects -NCIT:disease_has_molecular_abnormality: +NCIT:disease_has_molecular_abnormality: operation: invert core_predicate: biolink:biomarker_for -NCIT:disease_has_normal_cell_origin: +NCIT:disease_has_normal_cell_origin: operation: delete -NCIT:disease_has_normal_tissue_origin: +NCIT:disease_has_normal_tissue_origin: operation: keep core_predicate: biolink:causes -NCIT:disease_has_primary_anatomic_site: +NCIT:disease_has_primary_anatomic_site: operation: keep core_predicate: biolink:affects -NCIT:disease_is_grade: +NCIT:disease_is_grade: operation: keep core_predicate: biolink:related_to -NCIT:disease_is_marked_by_gene: +NCIT:disease_is_marked_by_gene: operation: invert core_predicate: biolink:biomarker_for -NCIT:disease_is_stage: +NCIT:disease_is_stage: operation: keep core_predicate: biolink:related_to -NCIT:disease_mapped_to_chromosome: +NCIT:disease_mapped_to_chromosome: operation: delete -NCIT:disease_mapped_to_gene: +NCIT:disease_mapped_to_gene: operation: delete -NCIT:disease_may_have_abnormal_cell: +NCIT:disease_may_have_abnormal_cell: operation: keep core_predicate: biolink:affects -NCIT:disease_may_have_associated_disease: +NCIT:disease_may_have_associated_disease: operation: keep core_predicate: biolink:related_to -NCIT:disease_may_have_cytogenetic_abnormality: +NCIT:disease_may_have_cytogenetic_abnormality: operation: delete -NCIT:disease_may_have_finding: +NCIT:disease_may_have_finding: operation: keep core_predicate: biolink:has_phenotype -NCIT:disease_may_have_molecular_abnormality: +NCIT:disease_may_have_molecular_abnormality: operation: keep core_predicate: biolink:has_phenotype -NCIT:disease_may_have_normal_cell_origin: +NCIT:disease_may_have_normal_cell_origin: operation: delete -NCIT:endogenous_product_related_to: +NCIT:endogenous_product_related_to: operation: delete -NCIT:enzyme_metabolizes_chemical_or_drug: +NCIT:enzyme_metabolizes_chemical_or_drug: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: localization - object_direction: increased -NCIT:eo_anatomy_is_associated_with_eo_disease: +NCIT:eo_anatomy_is_associated_with_eo_disease: operation: delete -NCIT:eo_disease_has_associated_cell_type: +NCIT:eo_disease_has_associated_cell_type: operation: keep core_predicate: biolink:affects -NCIT:eo_disease_has_associated_eo_anatomy: +NCIT:eo_disease_has_associated_eo_anatomy: operation: keep core_predicate: biolink:affects -NCIT:eo_disease_has_property_or_attribute: +NCIT:eo_disease_has_property_or_attribute: operation: keep core_predicate: biolink:related_to -NCIT:eo_disease_maps_to_human_disease: +NCIT:eo_disease_maps_to_human_disease: operation: delete -NCIT:excised_anatomy_has_procedure: +NCIT:excised_anatomy_has_procedure: operation: delete -NCIT:excised_anatomy_may_have_procedure: +NCIT:excised_anatomy_may_have_procedure: operation: delete -NCIT:gene_associated_with_disease: +NCIT:gene_associated_with_disease: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:gene_encodes_gene_product: +NCIT:gene_encodes_gene_product: operation: invert core_predicate: biolink:gene_product_of -NCIT:gene_found_in_organism: +NCIT:gene_found_in_organism: operation: keep core_predicate: biolink:in_taxon -NCIT:gene_has_abnormality: +NCIT:gene_has_abnormality: operation: delete -NCIT:gene_has_physical_location: +NCIT:gene_has_physical_location: operation: keep core_predicate: biolink:located_in -NCIT:gene_in_chromosomal_location: +NCIT:gene_in_chromosomal_location: operation: keep core_predicate: biolink:located_in -NCIT:gene_involved_in_molecular_abnormality: +NCIT:gene_involved_in_molecular_abnormality: operation: keep core_predicate: biolink:actively_involved_in -NCIT:gene_involved_in_pathogenesis_of_disease: +NCIT:gene_involved_in_pathogenesis_of_disease: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:gene_is_biomarker_of: +NCIT:gene_is_biomarker_of: operation: keep core_predicate: biolink:biomarker_for -NCIT:gene_is_biomarker_type: +NCIT:gene_is_biomarker_type: operation: keep core_predicate: biolink:subclass_of -NCIT:gene_is_element_in_pathway: +NCIT:gene_is_element_in_pathway: operation: invert core_predicate: biolink:has_participant -NCIT:gene_mapped_to_disease: +NCIT:gene_mapped_to_disease: operation: keep core_predicate: biolink:affects -NCIT:gene_mutant_encodes_gene_product_sequence_variation: +NCIT:gene_mutant_encodes_gene_product_sequence_variation: operation: invert core_predicate: biolink:gene_product_of -NCIT:gene_plays_role_in_process: +NCIT:gene_plays_role_in_process: operation: invert core_predicate: biolink:has_participant -NCIT:gene_product_affected_by_chemical_or_drug: +NCIT:gene_product_affected_by_chemical_or_drug: operation: delete -NCIT:gene_product_encoded_by_gene: +NCIT:gene_product_encoded_by_gene: operation: delete -NCIT:gene_product_expressed_in_tissue: +NCIT:gene_product_expressed_in_tissue: operation: keep core_predicate: biolink:expressed_in -NCIT:gene_product_has_abnormality: +NCIT:gene_product_has_abnormality: operation: keep core_predicate: biolink:affects -NCIT:gene_product_has_associated_anatomy: +NCIT:gene_product_has_associated_anatomy: operation: keep core_predicate: biolink:expressed_in -NCIT:gene_product_has_biochemical_function: +NCIT:gene_product_has_biochemical_function: operation: keep core_predicate: biolink:capable_of -NCIT:gene_product_has_chemical_classification: +NCIT:gene_product_has_chemical_classification: operation: keep core_predicate: biolink:subclass_of -NCIT:gene_product_has_gene_product_variant: +NCIT:gene_product_has_gene_product_variant: operation: delete -NCIT:gene_product_has_organism_source: +NCIT:gene_product_has_organism_source: operation: keep core_predicate: biolink:in_taxon -NCIT:gene_product_has_structural_domain_or_motif: +NCIT:gene_product_has_structural_domain_or_motif: operation: keep core_predicate: biolink:has_part -NCIT:gene_product_is_biomarker_of: +NCIT:gene_product_is_biomarker_of: operation: keep core_predicate: biolink:biomarker_for -NCIT:gene_product_is_biomarker_type: +NCIT:gene_product_is_biomarker_type: operation: keep core_predicate: biolink:subclass_of -NCIT:gene_product_is_element_in_pathway: +NCIT:gene_product_is_element_in_pathway: operation: invert core_predicate: biolink:has_participant -NCIT:gene_product_is_physical_part_of: +NCIT:gene_product_is_physical_part_of: operation: invert core_predicate: biolink:has_participant -NCIT:gene_product_malfunction_associated_with_disease: +NCIT:gene_product_malfunction_associated_with_disease: operation: keep core_predicate: biolink:gene_associated_with_condition -NCIT:gene_product_plays_role_in_biological_process: +NCIT:gene_product_plays_role_in_biological_process: operation: invert core_predicate: biolink:has_participant -NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: +NCIT:gene_product_sequence_variation_encoded_by_gene_mutant: operation: keep core_predicate: biolink:is_sequence_variant_of -NCIT:gene_product_variant_of_gene_product: +NCIT:gene_product_variant_of_gene_product: operation: keep core_predicate: biolink:is_sequence_variant_of -NCIT:genetic_biomarker_related_to: +NCIT:genetic_biomarker_related_to: operation: keep core_predicate: biolink:biomarker_for -NCIT:has_cdrh_parent: +NCIT:has_cdrh_parent: operation: delete -NCIT:has_conceptual_part: +NCIT:has_conceptual_part: operation: delete -NCIT:has_ctcae_5_parent: +NCIT:has_ctcae_5_parent: operation: delete -NCIT:has_data_element: +NCIT:has_data_element: operation: keep core_predicate: biolink:related_to -NCIT:has_free_acid_or_base_form: +NCIT:has_free_acid_or_base_form: operation: delete -NCIT:has_gene_product_element: +NCIT:has_gene_product_element: operation: delete -NCIT:has_inc_parent: +NCIT:has_inc_parent: operation: keep core_predicate: biolink:subclass_of -NCIT:has_nichd_parent: +NCIT:has_nichd_parent: operation: keep core_predicate: biolink:subclass_of -NCIT:has_pharmaceutical_administration_method: +NCIT:has_pharmaceutical_administration_method: operation: keep core_predicate: biolink:related_to -NCIT:has_pharmaceutical_basic_dose_form: +NCIT:has_pharmaceutical_basic_dose_form: operation: keep core_predicate: biolink:related_to -NCIT:has_pharmaceutical_intended_site: +NCIT:has_pharmaceutical_intended_site: operation: keep core_predicate: biolink:related_to -NCIT:has_pharmaceutical_release_characteristics: +NCIT:has_pharmaceutical_release_characteristics: operation: keep core_predicate: biolink:related_to -NCIT:has_pharmaceutical_state_of_matter: +NCIT:has_pharmaceutical_state_of_matter: operation: keep core_predicate: biolink:related_to -NCIT:has_pharmaceutical_transformation: +NCIT:has_pharmaceutical_transformation: operation: keep core_predicate: biolink:related_to -NCIT:has_physical_part_of_anatomic_structure: +NCIT:has_physical_part_of_anatomic_structure: operation: delete -NCIT:has_salt_form: +NCIT:has_salt_form: operation: keep core_predicate: biolink:chemically_similar_to -NCIT:has_target: +NCIT:has_target: operation: keep core_predicate: biolink:physically_interacts_with -NCIT:human_disease_maps_to_eo_disease: +NCIT:human_disease_maps_to_eo_disease: operation: keep core_predicate: biolink:related_to -NCIT:imaged_anatomy_has_procedure: +NCIT:imaged_anatomy_has_procedure: operation: delete -NCIT:inc_parent_of: +NCIT:inc_parent_of: operation: delete -NCIT:is_abnormal_cell_of_disease: +NCIT:is_abnormal_cell_of_disease: operation: keep core_predicate: biolink:related_to -NCIT:is_abnormality_of_gene: +NCIT:is_abnormality_of_gene: operation: delete -NCIT:is_abnormality_of_gene_product: +NCIT:is_abnormality_of_gene_product: operation: delete -NCIT:is_associated_anatomic_site_of: +NCIT:is_associated_anatomic_site_of: operation: delete -NCIT:is_associated_anatomy_of_gene_product: +NCIT:is_associated_anatomy_of_gene_product: operation: delete -NCIT:is_associated_disease_of: +NCIT:is_associated_disease_of: operation: keep core_predicate: biolink:correlated_with -NCIT:is_biochemical_function_of_gene_product: +NCIT:is_biochemical_function_of_gene_product: operation: delete -NCIT:is_chemical_classification_of_gene_product: +NCIT:is_chemical_classification_of_gene_product: operation: delete -NCIT:is_chromosomal_location_of_gene: +NCIT:is_chromosomal_location_of_gene: operation: delete -NCIT:is_component_of_chemotherapy_regimen: +NCIT:is_component_of_chemotherapy_regimen: operation: invert core_predicate: biolink:has_part -NCIT:is_cytogenetic_abnormality_of_disease: +NCIT:is_cytogenetic_abnormality_of_disease: operation: invert core_predicate: biolink:correlated_with -NCIT:is_finding_of_disease: +NCIT:is_finding_of_disease: operation: delete -NCIT:is_grade_of_disease: +NCIT:is_grade_of_disease: operation: delete -NCIT:is_location_of_anatomic_structure: +NCIT:is_location_of_anatomic_structure: operation: keep core_predicate: biolink:located_in -NCIT:is_location_of_biological_process: +NCIT:is_location_of_biological_process: operation: delete -NCIT:is_marked_by_gene_product: +NCIT:is_marked_by_gene_product: operation: delete -NCIT:is_mechanism_of_action_of_chemical_or_drug: +NCIT:is_mechanism_of_action_of_chemical_or_drug: operation: delete -NCIT:is_metastatic_anatomic_site_of_disease: +NCIT:is_metastatic_anatomic_site_of_disease: operation: delete -NCIT:is_molecular_abnormality_of_disease: +NCIT:is_molecular_abnormality_of_disease: operation: keep core_predicate: biolink:biomarker_for -NCIT:is_normal_cell_origin_of_disease: +NCIT:is_normal_cell_origin_of_disease: operation: invert core_predicate: biolink:derives_from -NCIT:is_normal_tissue_origin_of_disease: +NCIT:is_normal_tissue_origin_of_disease: operation: delete -NCIT:is_not_abnormal_cell_of_disease: +NCIT:is_not_abnormal_cell_of_disease: operation: delete -NCIT:is_not_cytogenetic_abnormality_of_disease: +NCIT:is_not_cytogenetic_abnormality_of_disease: operation: delete -NCIT:is_not_finding_of_disease: +NCIT:is_not_finding_of_disease: operation: delete -NCIT:is_not_metastatic_anatomic_site_of_disease: +NCIT:is_not_metastatic_anatomic_site_of_disease: operation: delete -NCIT:is_not_molecular_abnormality_of_disease: +NCIT:is_not_molecular_abnormality_of_disease: operation: delete -NCIT:is_not_normal_cell_origin_of_disease: +NCIT:is_not_normal_cell_origin_of_disease: operation: delete -NCIT:is_not_normal_tissue_origin_of_disease: +NCIT:is_not_normal_tissue_origin_of_disease: operation: delete -NCIT:is_not_primary_anatomic_site_of_disease: +NCIT:is_not_primary_anatomic_site_of_disease: operation: delete -NCIT:is_organism_source_of_gene_product: +NCIT:is_organism_source_of_gene_product: operation: invert core_predicate: biolink:in_taxon -NCIT:is_physical_location_of_gene: +NCIT:is_physical_location_of_gene: operation: delete -NCIT:is_physiologic_effect_of_chemical_or_drug: +NCIT:is_physiologic_effect_of_chemical_or_drug: operation: delete -NCIT:is_primary_anatomic_site_of_disease: +NCIT:is_primary_anatomic_site_of_disease: operation: delete -NCIT:is_property_or_attribute_of_eo_disease: +NCIT:is_property_or_attribute_of_eo_disease: operation: delete -NCIT:is_qualified_by: +NCIT:is_qualified_by: operation: keep core_predicate: biolink:related_to -NCIT:is_related_to_endogenous_product: +NCIT:is_related_to_endogenous_product: operation: keep core_predicate: biolink:related_to -NCIT:is_stage_of_disease: +NCIT:is_stage_of_disease: operation: delete -NCIT:is_structural_domain_or_motif_of_gene_product: +NCIT:is_structural_domain_or_motif_of_gene_product: operation: delete -NCIT:is_target: +NCIT:is_target: operation: delete -NCIT:kind_is_domain_of: +NCIT:kind_is_domain_of: operation: delete -NCIT:kind_is_range_of: +NCIT:kind_is_range_of: operation: delete -NCIT:may_be_abnormal_cell_of_disease: +NCIT:may_be_abnormal_cell_of_disease: operation: delete -NCIT:may_be_associated_disease_of_disease: +NCIT:may_be_associated_disease_of_disease: operation: delete -NCIT:may_be_cytogenetic_abnormality_of_disease: +NCIT:may_be_cytogenetic_abnormality_of_disease: operation: delete -NCIT:may_be_finding_of_disease: +NCIT:may_be_finding_of_disease: operation: delete -NCIT:may_be_molecular_abnormality_of_disease: +NCIT:may_be_molecular_abnormality_of_disease: operation: delete -NCIT:may_be_normal_cell_origin_of_disease: +NCIT:may_be_normal_cell_origin_of_disease: operation: invert core_predicate: biolink:derives_from -NCIT:molecular_abnormality_involves_gene: +NCIT:molecular_abnormality_involves_gene: operation: delete -NCIT:neoplasm_has_special_category: +NCIT:neoplasm_has_special_category: operation: keep core_predicate: biolink:subclass_of -NCIT:nichd_parent_of: +NCIT:nichd_parent_of: operation: delete -NCIT:organism_has_gene: +NCIT:organism_has_gene: operation: invert core_predicate: biolink:in_taxon -NCIT:partially_excised_anatomy_has_procedure: +NCIT:partially_excised_anatomy_has_procedure: operation: delete -NCIT:partially_excised_anatomy_may_have_procedure: +NCIT:partially_excised_anatomy_may_have_procedure: operation: delete -NCIT:pathogenesis_of_disease_involves_gene: +NCIT:pathogenesis_of_disease_involves_gene: operation: delete -NCIT:pathway_has_gene_element: +NCIT:pathway_has_gene_element: operation: keep core_predicate: biolink:has_participant -NCIT:pharmaceutical_administration_method_of: +NCIT:pharmaceutical_administration_method_of: operation: delete -NCIT:pharmaceutical_basic_dose_form_of: +NCIT:pharmaceutical_basic_dose_form_of: operation: delete -NCIT:pharmaceutical_intended_site_of: +NCIT:pharmaceutical_intended_site_of: operation: delete -NCIT:pharmaceutical_release_characteristics_of: +NCIT:pharmaceutical_release_characteristics_of: operation: delete -NCIT:pharmaceutical_state_of_matter_of: +NCIT:pharmaceutical_state_of_matter_of: operation: delete -NCIT:pharmaceutical_transformation_of: +NCIT:pharmaceutical_transformation_of: operation: delete -NCIT:procedure_has_completely_excised_anatomy: +NCIT:procedure_has_completely_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_has_excised_anatomy: +NCIT:procedure_has_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_has_imaged_anatomy: +NCIT:procedure_has_imaged_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_has_partially_excised_anatomy: +NCIT:procedure_has_partially_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_has_target_anatomy: +NCIT:procedure_has_target_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_may_have_completely_excised_anatomy: +NCIT:procedure_may_have_completely_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_may_have_excised_anatomy: +NCIT:procedure_may_have_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:procedure_may_have_partially_excised_anatomy: +NCIT:procedure_may_have_partially_excised_anatomy: operation: keep core_predicate: biolink:located_in -NCIT:process_altered_by_allele: +NCIT:process_altered_by_allele: operation: delete -NCIT:process_includes_biological_process: +NCIT:process_includes_biological_process: operation: keep core_predicate: biolink:has_participant -NCIT:process_initiates_biological_process: +NCIT:process_initiates_biological_process: operation: keep core_predicate: biolink:causes -NCIT:process_involves_gene: +NCIT:process_involves_gene: operation: keep core_predicate: biolink:has_participant -NCIT:qualifier_applies_to: +NCIT:qualifier_applies_to: operation: keep core_predicate: biolink:related_to -NCIT:regimen_has_accepted_use_for_disease: +NCIT:regimen_has_accepted_use_for_disease: operation: keep core_predicate: biolink:treats -NCIT:related_to_genetic_biomarker: +NCIT:related_to_genetic_biomarker: operation: delete -NCIT:role_has_domain: +NCIT:role_has_domain: operation: keep core_predicate: biolink:related_to -NCIT:role_has_parent: +NCIT:role_has_parent: operation: keep core_predicate: biolink:subclass_of -NCIT:role_has_range: +NCIT:role_has_range: operation: keep core_predicate: biolink:related_to -NCIT:role_is_parent_of: +NCIT:role_is_parent_of: operation: delete -NCIT:special_category_includes_neoplasm: +NCIT:special_category_includes_neoplasm: operation: delete -NCIT:subset_includes_concept: +NCIT:subset_includes_concept: operation: invert core_predicate: biolink:subclass_of -NCIT:target_anatomy_has_procedure: +NCIT:target_anatomy_has_procedure: operation: delete -NCIT:tissue_is_expression_site_of_gene_product: +NCIT:tissue_is_expression_site_of_gene_product: operation: delete -NDDF:dose_form_of: +NDDF:dose_form_of: operation: delete -NDDF:has_dose_form: +NDDF:has_dose_form: operation: keep core_predicate: biolink:subclass_of -NDDF:has_ingredient: +NDDF:has_ingredient: operation: keep core_predicate: biolink:has_part -NDDF:ingredient_of: +NDDF:ingredient_of: operation: invert core_predicate: biolink:has_part -OBI:0000293: +OBI:0000293: operation: keep core_predicate: biolink:has_participant -OBI:0000295: +OBI:0000295: operation: invert core_predicate: biolink:has_participant -OBI:0000299: +OBI:0000299: operation: keep core_predicate: biolink:has_output -OBI:0000417: +OBI:0000417: operation: keep core_predicate: biolink:has_output -OBI:0001927: +OBI:0001927: operation: invert core_predicate: biolink:related_to -OBO:INO_0000154: +OBO:INO_0000154: operation: keep core_predicate: biolink:related_to -OBO:MF#manifestationOf: +OBO:MF#manifestationOf: operation: keep core_predicate: biolink:manifestation_of -OBO:bspo#parallel_to: +OBO:bspo#parallel_to: operation: keep core_predicate: biolink:coexists_with -OBO:doid#has_symptom: +OBO:doid#has_symptom: operation: keep core_predicate: biolink:has_phenotype -OBO:envo#has_increased_levels_of: +OBO:envo#has_increased_levels_of: operation: keep core_predicate: biolink:related_to -OBO:exo#interacts_with: +OBO:exo#interacts_with: operation: keep core_predicate: biolink:interacts_with -OBO:exo#interacts_with_an_exposure_receptor_via: +OBO:exo#interacts_with_an_exposure_receptor_via: operation: keep core_predicate: biolink:interacts_with -OBO:exo#interacts_with_an_exposure_stressor_via: +OBO:exo#interacts_with_an_exposure_stressor_via: operation: keep core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with: +OBO:exo.obo#interacts_with: operation: keep core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_receptor_via: +OBO:exo.obo#interacts_with_an_exposure_receptor_via: operation: keep core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_stressor_via: +OBO:exo.obo#interacts_with_an_exposure_stressor_via: operation: keep core_predicate: biolink:interacts_with -OBO:has_role: +OBO:has_role: operation: keep core_predicate: biolink:related_to -OBO:nbo#by_means: +OBO:nbo#by_means: operation: invert core_predicate: biolink:actively_involved_in -OBO:nbo#has_participant: +OBO:nbo#has_participant: operation: keep core_predicate: biolink:has_participant -OBO:nbo#in_response_to: +OBO:nbo#in_response_to: operation: invert core_predicate: biolink:causes -OBO:nbo#is_about: +OBO:nbo#is_about: operation: keep core_predicate: biolink:related_to -OBO:uo#is_unit_of: +OBO:uo#is_unit_of: operation: invert core_predicate: biolink:related_to -OIO:hasDbXref: +OIO:hasDbXref: operation: keep core_predicate: biolink:close_match -OMIM:allelic_variant_of: +OMIM:allelic_variant_of: operation: keep core_predicate: biolink:is_sequence_variant_of -OMIM:has_allelic_variant: +OMIM:has_allelic_variant: operation: delete -OMIM:has_inheritance_type: +OMIM:has_inheritance_type: operation: keep core_predicate: biolink:related_to -OMIM:has_manifestation: +OMIM:has_manifestation: operation: invert core_predicate: biolink:subclass_of -OMIM:has_phenotype: +OMIM:has_phenotype: operation: keep core_predicate: biolink:has_phenotype -OMIM:inheritance_type_of: +OMIM:inheritance_type_of: operation: delete -OMIM:manifestation_of: +OMIM:manifestation_of: operation: keep core_predicate: biolink:manifestation_of -OMIM:phenotype_of: +OMIM:phenotype_of: operation: invert core_predicate: biolink:has_phenotype -ORPHA:317343: +ORPHA:317343: operation: keep core_predicate: biolink:causes -ORPHA:317344: +ORPHA:317344: operation: keep core_predicate: biolink:causes -ORPHA:317346: +ORPHA:317346: operation: keep core_predicate: biolink:causes -ORPHA:317348: +ORPHA:317348: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:317349: +ORPHA:317349: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:327767: +ORPHA:327767: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:410295: +ORPHA:410295: operation: keep core_predicate: biolink:causes -ORPHA:410296: +ORPHA:410296: operation: keep core_predicate: biolink:causes -ORPHA:465410: +ORPHA:465410: operation: keep core_predicate: biolink:biomarker_for -ORPHANET:317343: +ORPHANET:317343: operation: keep core_predicate: biolink:causes -ORPHANET:317344: +ORPHANET:317344: operation: keep core_predicate: biolink:causes -ORPHANET:317345: +ORPHANET:317345: operation: keep core_predicate: biolink:correlated_with -ORPHANET:317346: +ORPHANET:317346: operation: keep core_predicate: biolink:causes -ORPHANET:317348: +ORPHANET:317348: operation: keep core_predicate: biolink:actively_involved_in -ORPHANET:317349: +ORPHANET:317349: operation: keep core_predicate: biolink:actively_involved_in -ORPHANET:327767: +ORPHANET:327767: operation: keep core_predicate: biolink:actively_involved_in -ORPHANET:410295: +ORPHANET:410295: operation: keep core_predicate: biolink:causes -ORPHANET:410296: +ORPHANET:410296: operation: keep core_predicate: biolink:causes -ORPHANET:465410: +ORPHANET:465410: operation: keep core_predicate: biolink:biomarker_for -ORPHANET:C016: +ORPHANET:C016: operation: keep core_predicate: biolink:related_to -ORPHANET:C017: +ORPHANET:C017: operation: keep core_predicate: biolink:related_to -PATO:0000085: +PATO:0000085: operation: keep core_predicate: biolink:associated_with_sensitivity_to -PATO:correlates_with: +PATO:correlates_with: operation: keep core_predicate: biolink:correlated_with -PATO:decreased_in_magnitude_relative_to: +PATO:decreased_in_magnitude_relative_to: operation: keep core_predicate: biolink:related_to -PATO:has_cross_section: +PATO:has_cross_section: operation: keep core_predicate: biolink:related_to -PATO:has_relative_magnitude: +PATO:has_relative_magnitude: operation: keep core_predicate: biolink:related_to -PATO:increased_in_magnitude_relative_to: +PATO:increased_in_magnitude_relative_to: operation: keep core_predicate: biolink:related_to -PATO:reciprocal_of: +PATO:reciprocal_of: operation: keep core_predicate: biolink:related_to -PATO:towards: +PATO:towards: operation: invert core_predicate: biolink:actively_involved_in -PDQ:associated_disease: +PDQ:associated_disease: operation: keep core_predicate: biolink:correlated_with -PDQ:associated_genetic_condition: +PDQ:associated_genetic_condition: operation: delete -PDQ:component_of: +PDQ:component_of: operation: invert core_predicate: biolink:has_part -PDQ:has_component: +PDQ:has_component: operation: keep core_predicate: biolink:has_part -PHAROS:drug_targets: +PHAROS:drug_targets: operation: keep - core_predicate: biolink:directly_interacts_with -PR:confers_resistance_to: + core_predicate: biolink:interacts_with +PR:confers_resistance_to: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: activity - object_direction: decreased -PR:has_gene_template: +PR:has_gene_template: operation: keep core_predicate: biolink:gene_product_of -PR:lacks_part: +PR:lacks_part: operation: keep core_predicate: biolink:lacks_part -PR:non-covalently_bound_to: +PR:non-covalently_bound_to: operation: keep core_predicate: biolink:physically_interacts_with -PSY:RB: +PSY:RB: operation: invert core_predicate: biolink:subclass_of -PSY:RO: +PSY:RO: operation: keep core_predicate: biolink:related_to -PSY:use: +PSY:use: operation: keep core_predicate: biolink:subclass_of -PSY:used_for: +PSY:used_for: operation: invert core_predicate: biolink:has_input -PathWhiz:has_bound: +PathWhiz:has_bound: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_compound: +PathWhiz:has_compound: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_element_collection: +PathWhiz:has_element_collection: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_element_in_bound: +PathWhiz:has_element_in_bound: operation: keep core_predicate: biolink:has_part -PathWhiz:has_enzyme: +PathWhiz:has_enzyme: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_left_element: +PathWhiz:has_left_element: operation: keep core_predicate: biolink:has_input -PathWhiz:has_location: +PathWhiz:has_location: operation: keep core_predicate: biolink:occurs_in -PathWhiz:has_nucleic_acid: +PathWhiz:has_nucleic_acid: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_protein: +PathWhiz:has_protein: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_protein_in_complex: +PathWhiz:has_protein_in_complex: operation: keep core_predicate: biolink:has_part -PathWhiz:has_reaction: +PathWhiz:has_reaction: operation: keep core_predicate: biolink:has_participant -PathWhiz:has_right_element: +PathWhiz:has_right_element: operation: keep core_predicate: biolink:has_output -PathWhiz:in_species: +PathWhiz:in_species: operation: keep core_predicate: biolink:occurs_in -REACT:has_element: +REACT:has_element: operation: keep core_predicate: biolink:has_part -REACT:has_event: +REACT:has_event: operation: keep core_predicate: biolink:has_participant -REACT:has_input: +REACT:has_input: operation: keep core_predicate: biolink:has_input -REACT:has_member: +REACT:has_member: operation: keep core_predicate: biolink:has_part -REACT:has_output: +REACT:has_output: operation: keep core_predicate: biolink:has_output -REACT:in_species: +REACT:in_species: operation: keep core_predicate: biolink:occurs_in -REACT:is_requirement_for: +REACT:is_requirement_for: operation: keep core_predicate: biolink:regulates -REACT:linked_to_disease: +REACT:linked_to_disease: operation: keep core_predicate: biolink:related_to -REACT:negatively_regulates: +REACT:negatively_regulates: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -REACT:negatively_regulates_gene_expression: +REACT:negatively_regulates_gene_expression: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -REACT:positively_regulates: +REACT:positively_regulates: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -REACT:positively_regulates_gene_expression: +REACT:positively_regulates_gene_expression: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -REACT:related_to: +REACT:related_to: operation: keep core_predicate: biolink:related_to -REPODB:clinically_tested_approved_unknown_phase: +REPODB:clinically_tested_approved_unknown_phase: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_0: +REPODB:clinically_tested_suspended_phase_0: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_1: +REPODB:clinically_tested_suspended_phase_1: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_1_or_phase_2: +REPODB:clinically_tested_suspended_phase_1_or_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_2: +REPODB:clinically_tested_suspended_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_2_or_phase_3: +REPODB:clinically_tested_suspended_phase_2_or_phase_3: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_suspended_phase_3: +REPODB:clinically_tested_suspended_phase_3: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_0: +REPODB:clinically_tested_terminated_phase_0: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_1: +REPODB:clinically_tested_terminated_phase_1: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_1_or_phase_2: +REPODB:clinically_tested_terminated_phase_1_or_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_2: +REPODB:clinically_tested_terminated_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_2_or_phase_3: +REPODB:clinically_tested_terminated_phase_2_or_phase_3: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_terminated_phase_3: +REPODB:clinically_tested_terminated_phase_3: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_0: +REPODB:clinically_tested_withdrawn_phase_0: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_1: +REPODB:clinically_tested_withdrawn_phase_1: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: +REPODB:clinically_tested_withdrawn_phase_1_or_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_2: +REPODB:clinically_tested_withdrawn_phase_2: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: +REPODB:clinically_tested_withdrawn_phase_2_or_phase_3: operation: keep core_predicate: biolink:treats -REPODB:clinically_tested_withdrawn_phase_3: +REPODB:clinically_tested_withdrawn_phase_3: operation: keep core_predicate: biolink:treats -RO:0000052: +RO:0000052: operation: keep core_predicate: biolink:related_to -RO:0000053: +RO:0000053: operation: keep core_predicate: biolink:related_to -RO:0000056: +RO:0000056: operation: invert core_predicate: biolink:has_participant -RO:0000057: +RO:0000057: operation: keep core_predicate: biolink:has_participant -RO:0000059: +RO:0000059: operation: keep core_predicate: biolink:related_to -RO:0000086: +RO:0000086: operation: keep core_predicate: biolink:related_to -RO:0000087: +RO:0000087: operation: keep core_predicate: biolink:related_to -RO:00002325: +RO:00002325: operation: keep core_predicate: biolink:colocalizes_with -RO:0001000: - operation: invert - core_predicate: biolink:derives_into -RO:0001001: +RO:0001000: + operation: keep + core_predicate: biolink:derives_from +RO:0001001: operation: invert core_predicate: biolink:derives_from -RO:0001015: +RO:0001015: operation: invert core_predicate: biolink:located_in -RO:0001018: +RO:0001018: operation: invert core_predicate: biolink:has_part -RO:0001019: +RO:0001019: operation: keep core_predicate: biolink:has_part -RO:0001022: +RO:0001022: operation: invert core_predicate: biolink:causes -RO:0001025: +RO:0001025: operation: keep core_predicate: biolink:located_in -RO:0002001: +RO:0002001: operation: keep core_predicate: biolink:related_to -RO:0002002: +RO:0002002: operation: keep core_predicate: biolink:related_to -RO:0002003: +RO:0002003: operation: keep core_predicate: biolink:related_to -RO:0002005: +RO:0002005: operation: keep core_predicate: biolink:related_to -RO:0002007: +RO:0002007: operation: invert core_predicate: biolink:has_part -RO:0002008: +RO:0002008: operation: keep core_predicate: biolink:related_to -RO:0002082: +RO:0002082: operation: keep core_predicate: biolink:temporally_related_to -RO:0002083: +RO:0002083: operation: keep core_predicate: biolink:temporally_related_to -RO:0002084: +RO:0002084: operation: keep core_predicate: biolink:related_to -RO:0002087: +RO:0002087: operation: invert core_predicate: biolink:precedes -RO:0002090: +RO:0002090: operation: keep core_predicate: biolink:precedes -RO:0002092: +RO:0002092: operation: keep core_predicate: biolink:related_to -RO:0002093: +RO:0002093: operation: keep core_predicate: biolink:related_to -RO:0002100: +RO:0002100: operation: keep core_predicate: biolink:overlaps -RO:0002101: +RO:0002101: operation: keep core_predicate: biolink:overlaps -RO:0002102: +RO:0002102: operation: keep core_predicate: biolink:overlaps -RO:0002103: +RO:0002103: operation: keep core_predicate: biolink:interacts_with -RO:0002104: +RO:0002104: operation: keep - core_predicate: biolink:has_part -RO:0002120: + core_predicate: biolink:has_plasma_membrane_part +RO:0002120: operation: keep core_predicate: biolink:interacts_with -RO:0002130: +RO:0002130: operation: keep core_predicate: biolink:interacts_with -RO:0002131: +RO:0002131: operation: keep core_predicate: biolink:overlaps -RO:0002134: +RO:0002134: operation: keep core_predicate: biolink:related_to -RO:0002150: +RO:0002150: operation: keep core_predicate: biolink:related_to -RO:0002159: +RO:0002159: operation: keep core_predicate: biolink:related_to -RO:0002160: +RO:0002160: operation: keep core_predicate: biolink:in_taxon -RO:0002162: +RO:0002162: operation: keep core_predicate: biolink:in_taxon -RO:0002170: +RO:0002170: operation: keep core_predicate: biolink:related_to -RO:0002176: +RO:0002176: operation: keep core_predicate: biolink:related_to -RO:0002177: +RO:0002177: operation: keep core_predicate: biolink:related_to -RO:0002178: +RO:0002178: operation: keep core_predicate: biolink:related_to -RO:0002179: +RO:0002179: operation: keep core_predicate: biolink:related_to -RO:0002180: +RO:0002180: operation: keep core_predicate: biolink:has_part -RO:0002200: +RO:0002200: operation: keep core_predicate: biolink:has_phenotype -RO:0002202: +RO:0002202: operation: keep core_predicate: biolink:develops_from -RO:0002203: +RO:0002203: operation: keep core_predicate: biolink:develops_from -RO:0002204: - operation: invert - core_predicate: biolink:has_gene_product -RO:0002205: +RO:0002205: operation: invert core_predicate: biolink:gene_product_of -RO:0002207: +RO:0002207: operation: keep core_predicate: biolink:develops_from -RO:0002211: +RO:0002211: operation: keep core_predicate: biolink:regulates -RO:0002212: - operation: keep +RO:0002212: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -RO:0002213: - operation: keep +RO:0002213: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -RO:0002215: +RO:0002215: operation: keep core_predicate: biolink:capable_of -RO:0002216: +RO:0002216: operation: invert core_predicate: biolink:has_participant -RO:0002219: +RO:0002219: operation: keep core_predicate: biolink:coexists_with -RO:0002220: +RO:0002220: operation: keep core_predicate: biolink:coexists_with -RO:0002221: +RO:0002221: operation: keep core_predicate: biolink:coexists_with -RO:0002223: +RO:0002223: operation: keep core_predicate: biolink:temporally_related_to -RO:0002224: +RO:0002224: operation: keep core_predicate: biolink:temporally_related_to -RO:0002225: +RO:0002225: operation: keep core_predicate: biolink:develops_from -RO:0002226: +RO:0002226: operation: keep core_predicate: biolink:develops_from -RO:0002229: +RO:0002229: operation: keep core_predicate: biolink:temporally_related_to -RO:0002230: +RO:0002230: operation: keep core_predicate: biolink:temporally_related_to -RO:0002231: +RO:0002231: operation: keep core_predicate: biolink:occurs_in -RO:0002232: +RO:0002232: operation: keep core_predicate: biolink:occurs_in -RO:0002233: +RO:0002233: operation: keep core_predicate: biolink:has_input -RO:0002234: +RO:0002234: operation: keep core_predicate: biolink:has_output -RO:0002241: +RO:0002241: operation: keep core_predicate: biolink:related_to -RO:0002254: +RO:0002254: operation: keep core_predicate: biolink:related_to -RO:0002255: +RO:0002255: operation: keep core_predicate: biolink:contributes_to -RO:0002256: +RO:0002256: operation: keep core_predicate: biolink:causes -RO:0002263: +RO:0002263: operation: keep core_predicate: biolink:acts_upstream_of -RO:0002264: +RO:0002264: operation: keep core_predicate: biolink:acts_upstream_of_or_within -RO:0002285: +RO:0002285: operation: invert core_predicate: biolink:precedes -RO:0002292: +RO:0002292: operation: invert core_predicate: biolink:expressed_in -RO:0002295: +RO:0002295: operation: keep core_predicate: biolink:regulates -RO:0002296: +RO:0002296: operation: keep core_predicate: biolink:has_output -RO:0002297: +RO:0002297: operation: keep core_predicate: biolink:has_output -RO:0002298: +RO:0002298: operation: keep core_predicate: biolink:has_output -RO:0002299: +RO:0002299: operation: keep core_predicate: biolink:has_output -RO:0002302: +RO:0002302: operation: invert core_predicate: biolink:treats -RO:0002303: +RO:0002303: operation: keep core_predicate: biolink:located_in -RO:0002309: +RO:0002309: operation: keep core_predicate: biolink:related_to -RO:0002313: +RO:0002313: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: transport -RO:0002314: +RO:0002314: operation: keep core_predicate: biolink:related_to -RO:0002315: +RO:0002315: operation: keep core_predicate: biolink:causes -RO:0002322: +RO:0002322: operation: keep core_predicate: biolink:related_to -RO:0002326: +RO:0002326: operation: keep core_predicate: biolink:contributes_to -RO:0002327: - operation: invert - core_predicate: biolink:enabled_by -RO:0002328: +RO:0002328: operation: keep core_predicate: biolink:related_to -RO:0002331: +RO:0002331: operation: keep core_predicate: biolink:actively_involved_in -RO:0002332: +RO:0002332: operation: keep core_predicate: biolink:related_to -RO:0002333: +RO:0002333: operation: invert core_predicate: biolink:enables -RO:0002334: +RO:0002334: operation: invert core_predicate: biolink:regulates -RO:0002338: +RO:0002338: operation: keep core_predicate: biolink:related_to -RO:0002339: +RO:0002339: operation: keep core_predicate: biolink:related_to -RO:0002340: +RO:0002340: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: transport -RO:0002341: +RO:0002341: operation: keep core_predicate: biolink:related_to -RO:0002342: +RO:0002342: operation: keep core_predicate: biolink:related_to -RO:0002343: +RO:0002343: operation: keep core_predicate: biolink:affects -RO:0002344: +RO:0002344: operation: keep core_predicate: biolink:related_to -RO:0002345: +RO:0002345: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: transport -RO:0002348: +RO:0002348: operation: keep core_predicate: biolink:related_to -RO:0002349: +RO:0002349: operation: keep core_predicate: biolink:related_to -RO:0002350: +RO:0002350: operation: invert core_predicate: biolink:has_part -RO:0002351: +RO:0002351: operation: keep core_predicate: biolink:has_part -RO:0002352: +RO:0002352: operation: invert core_predicate: biolink:has_input -RO:0002353: +RO:0002353: operation: invert core_predicate: biolink:has_output -RO:0002354: +RO:0002354: operation: invert core_predicate: biolink:has_output -RO:0002355: +RO:0002355: operation: keep core_predicate: biolink:affects -RO:0002356: +RO:0002356: operation: keep core_predicate: biolink:related_to -RO:0002371: +RO:0002371: operation: keep core_predicate: biolink:related_to -RO:0002372: +RO:0002372: operation: keep core_predicate: biolink:related_to -RO:0002373: +RO:0002373: operation: keep core_predicate: biolink:related_to -RO:0002374: +RO:0002374: operation: keep core_predicate: biolink:related_to -RO:0002376: +RO:0002376: operation: invert core_predicate: biolink:has_part -RO:0002380: +RO:0002380: operation: invert core_predicate: biolink:has_part -RO:0002385: +RO:0002385: operation: keep core_predicate: biolink:related_to -RO:0002387: +RO:0002387: operation: keep core_predicate: biolink:related_to -RO:0002410: +RO:0002410: operation: keep core_predicate: biolink:causes -RO:0002411: +RO:0002411: operation: keep core_predicate: biolink:precedes -RO:0002412: +RO:0002412: operation: keep core_predicate: biolink:precedes -RO:0002432: +RO:0002432: operation: keep core_predicate: biolink:active_in -RO:0002433: +RO:0002433: operation: keep core_predicate: biolink:overlaps -RO:0002434: +RO:0002434: operation: keep core_predicate: biolink:interacts_with -RO:0002435: +RO:0002435: operation: keep core_predicate: biolink:genetically_interacts_with -RO:0002436: +RO:0002436: operation: keep - core_predicate: biolink:molecularly_interacts_with -RO:0002448: - operation: invert - core_predicate: biolink:entity_regulated_by_entity -RO:0002449: + core_predicate: biolink:physically_interacts_with +RO:0002448: + operation: keep + core_predicate: biolink:regulates +RO:0002449: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -RO:0002450: +RO:0002450: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -RO:0002451: +RO:0002451: operation: keep core_predicate: biolink:related_to -RO:0002452: +RO:0002452: operation: keep core_predicate: biolink:has_phenotype -RO:0002470: +RO:0002470: operation: keep core_predicate: biolink:related_to -RO:0002473: +RO:0002473: operation: keep - core_predicate: biolink:has_part -RO:0002488: + core_predicate: biolink:composed_primarily_of +RO:0002488: operation: keep core_predicate: biolink:temporally_related_to -RO:0002489: +RO:0002489: operation: keep core_predicate: biolink:temporally_related_to -RO:0002491: +RO:0002491: operation: keep core_predicate: biolink:coexists_with -RO:0002492: +RO:0002492: operation: keep core_predicate: biolink:temporally_related_to -RO:0002493: +RO:0002493: operation: keep core_predicate: biolink:temporally_related_to -RO:0002494: +RO:0002494: operation: keep core_predicate: biolink:related_to -RO:0002495: +RO:0002495: operation: keep core_predicate: biolink:related_to -RO:0002496: +RO:0002496: operation: keep core_predicate: biolink:temporally_related_to -RO:0002497: +RO:0002497: operation: keep core_predicate: biolink:temporally_related_to -RO:0002500: +RO:0002500: operation: keep core_predicate: biolink:capable_of -RO:0002503: +RO:0002503: operation: keep core_predicate: biolink:actively_involved_in -RO:0002505: +RO:0002505: operation: invert core_predicate: biolink:has_participant -RO:0002506: +RO:0002506: operation: keep core_predicate: biolink:causes -RO:0002507: +RO:0002507: operation: keep core_predicate: biolink:causes -RO:0002509: +RO:0002509: operation: keep core_predicate: biolink:causes -RO:0002510: +RO:0002510: operation: keep core_predicate: biolink:transcribed_from -RO:0002511: +RO:0002511: operation: invert core_predicate: biolink:transcribed_from -RO:0002524: +RO:0002524: operation: keep core_predicate: biolink:has_part -RO:0002551: +RO:0002551: operation: keep core_predicate: biolink:has_part -RO:0002565: +RO:0002565: operation: invert core_predicate: biolink:has_participant -RO:0002568: +RO:0002568: operation: keep core_predicate: biolink:related_to -RO:0002571: +RO:0002571: operation: invert core_predicate: biolink:has_part -RO:0002572: +RO:0002572: operation: invert core_predicate: biolink:has_part -RO:0002573: +RO:0002573: operation: keep core_predicate: biolink:related_to -RO:0002576: +RO:0002576: operation: invert core_predicate: biolink:has_part -RO:0002578: +RO:0002578: operation: keep core_predicate: biolink:regulates -RO:0002588: +RO:0002588: operation: keep core_predicate: biolink:has_output -RO:0002590: +RO:0002590: operation: keep core_predicate: biolink:has_input -RO:0002591: +RO:0002591: operation: keep core_predicate: biolink:affects -RO:0002592: +RO:0002592: operation: keep core_predicate: biolink:affects -RO:0002599: +RO:0002599: operation: keep core_predicate: biolink:prevents -RO:0002604: +RO:0002604: operation: keep core_predicate: biolink:opposite_of -RO:0002606: +RO:0002606: operation: keep core_predicate: biolink:treats -RO:0002607: +RO:0002607: operation: keep core_predicate: biolink:biomarker_for -RO:0002608: +RO:0002608: operation: invert core_predicate: biolink:causes -RO:0002610: +RO:0002610: operation: keep core_predicate: biolink:correlated_with -RO:0002629: - operation: keep +RO:0002629: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -RO:0002630: - operation: keep +RO:0002630: + operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -RO:0003000: +RO:0003000: operation: keep core_predicate: biolink:produces -RO:0003001: +RO:0003001: operation: invert core_predicate: biolink:produces -RO:0003002: +RO:0003002: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes - qualifiers: + qualifiers: - object_aspect: expression - object_direction: decreased -RO:0003003: +RO:0003003: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - object_aspect: expression - object_direction: increased -RO:0003301: +RO:0003301: operation: keep core_predicate: biolink:model_of -RO:0003303: +RO:0003303: operation: keep core_predicate: biolink:causes -RO:0003304: +RO:0003304: operation: keep core_predicate: biolink:contributes_to -RO:0003307: +RO:0003307: operation: keep core_predicate: biolink:ameliorates -RO:0003309: +RO:0003309: operation: keep core_predicate: biolink:exacerbates -RO:0004001: +RO:0004001: operation: keep core_predicate: biolink:causes -RO:0004007: +RO:0004007: operation: keep core_predicate: biolink:has_participant -RO:0004008: +RO:0004008: operation: keep core_predicate: biolink:has_output -RO:0004009: +RO:0004009: operation: keep core_predicate: biolink:has_input -RO:0004019: +RO:0004019: operation: invert core_predicate: biolink:causes -RO:0004020: +RO:0004020: operation: invert core_predicate: biolink:causes -RO:0004021: +RO:0004021: operation: keep core_predicate: biolink:has_participant -RO:0004022: +RO:0004022: operation: keep core_predicate: biolink:has_phenotype -RO:0004024: +RO:0004024: operation: keep core_predicate: biolink:disrupts -RO:0004025: +RO:0004025: operation: keep core_predicate: biolink:disrupts -RO:0004026: +RO:0004026: operation: keep - core_predicate: biolink:related_to -RO:0004027: + core_predicate: biolink:disease_has_location +RO:0004027: operation: keep core_predicate: biolink:related_to -RO:0004028: +RO:0004028: operation: invert core_predicate: biolink:causes -RO:0004029: +RO:0004029: operation: keep core_predicate: biolink:associated_with -RO:0004030: +RO:0004030: operation: invert core_predicate: biolink:causes -RO:0004032: +RO:0004032: operation: keep core_predicate: biolink:acts_upstream_of_or_within_positive_effect -RO:0004033: +RO:0004033: operation: keep core_predicate: biolink:acts_upstream_of_or_within_negative_effect -RO:0004034: +RO:0004034: operation: keep core_predicate: biolink:acts_upstream_of_positive_effect -RO:0004035: +RO:0004035: operation: keep core_predicate: biolink:acts_upstream_of_negative_effect -RO:0009001: +RO:0009001: operation: keep core_predicate: biolink:related_to -RO:0009004: +RO:0009004: operation: keep core_predicate: biolink:related_to -RO:0009501: +RO:0009501: operation: invert core_predicate: biolink:causes -RO:0012003: +RO:0012003: operation: keep core_predicate: biolink:affects -RO:0012008: +RO:0012008: operation: keep core_predicate: biolink:affects -RO:0013001: +RO:0013001: operation: keep core_predicate: biolink:related_to -RO:0014001: +RO:0014001: operation: keep core_predicate: biolink:related_to -RO:HOM0000000: +RO:HOM0000000: operation: keep core_predicate: biolink:similar_to -RO:has_participant: +RO:has_participant: operation: keep core_predicate: biolink:has_participant -RO:participates_in: +RO:participates_in: operation: invert core_predicate: biolink:has_participant -RXNORM:consists_of: +RXNORM:consists_of: operation: keep core_predicate: biolink:has_part -RXNORM:constitutes: +RXNORM:constitutes: operation: invert core_predicate: biolink:has_part -RXNORM:contained_in: +RXNORM:contained_in: operation: invert core_predicate: biolink:has_part -RXNORM:contains: +RXNORM:contains: operation: keep core_predicate: biolink:has_part -RXNORM:dose_form_of: +RXNORM:dose_form_of: operation: delete -RXNORM:doseformgroup_of: +RXNORM:doseformgroup_of: operation: delete -RXNORM:form_of: +RXNORM:form_of: operation: delete -RXNORM:has_dose_form: +RXNORM:has_dose_form: operation: keep core_predicate: biolink:subclass_of -RXNORM:has_doseformgroup: +RXNORM:has_doseformgroup: operation: keep core_predicate: biolink:subclass_of -RXNORM:has_form: +RXNORM:has_form: operation: keep core_predicate: biolink:related_to -RXNORM:has_ingredient: +RXNORM:has_ingredient: operation: keep core_predicate: biolink:has_part -RXNORM:has_ingredients: +RXNORM:has_ingredients: operation: delete -RXNORM:has_part: +RXNORM:has_part: operation: keep core_predicate: biolink:has_part -RXNORM:has_precise_ingredient: +RXNORM:has_precise_ingredient: operation: delete -RXNORM:has_quantified_form: +RXNORM:has_quantified_form: operation: keep core_predicate: biolink:close_match -RXNORM:has_tradename: +RXNORM:has_tradename: operation: keep core_predicate: biolink:related_to -RXNORM:ingredient_of: +RXNORM:ingredient_of: operation: invert core_predicate: biolink:has_part -RXNORM:ingredients_of: +RXNORM:ingredients_of: operation: invert core_predicate: biolink:has_part -RXNORM:inverse_isa: +RXNORM:inverse_isa: operation: invert core_predicate: biolink:subclass_of -RXNORM:isa: +RXNORM:isa: operation: keep core_predicate: biolink:subclass_of -RXNORM:part_of: +RXNORM:part_of: operation: invert core_predicate: biolink:has_part -RXNORM:precise_ingredient_of: +RXNORM:precise_ingredient_of: operation: invert core_predicate: biolink:has_part -RXNORM:quantified_form_of: +RXNORM:quantified_form_of: operation: delete -RXNORM:reformulated_to: +RXNORM:reformulated_to: operation: keep core_predicate: biolink:related_to -RXNORM:reformulation_of: +RXNORM:reformulation_of: operation: delete -RXNORM:tradename_of: +RXNORM:tradename_of: operation: delete -SEMMEDDB:1532: +SEMMEDDB:1532: operation: delete -SEMMEDDB:AFFECTS: +SEMMEDDB:AFFECTS: operation: keep core_predicate: biolink:affects -SEMMEDDB:CAUSES: +SEMMEDDB:CAUSES: operation: keep core_predicate: biolink:causes -SEMMEDDB:COEXISTS_WITH: +SEMMEDDB:COEXISTS_WITH: operation: keep core_predicate: biolink:coexists_with -SEMMEDDB:CONVERTS_TO: +SEMMEDDB:CONVERTS_TO: operation: invert core_predicate: biolink:derives_from -SEMMEDDB:DISRUPTS: +SEMMEDDB:DISRUPTS: operation: keep core_predicate: biolink:disrupts -SEMMEDDB:INHIBITS: +SEMMEDDB:INHIBITS: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -SEMMEDDB:IS_A: +SEMMEDDB:IS_A: operation: keep core_predicate: biolink:subclass_of -SEMMEDDB:LOCATION_OF: +SEMMEDDB:LOCATION_OF: operation: invert core_predicate: biolink:located_in -SEMMEDDB:MANIFESTATION_OF: +SEMMEDDB:MANIFESTATION_OF: operation: keep core_predicate: biolink:manifestation_of -SEMMEDDB:OCCURS_IN: +SEMMEDDB:OCCURS_IN: operation: keep core_predicate: biolink:occurs_in -SEMMEDDB:PART_OF: +SEMMEDDB:PART_OF: operation: invert core_predicate: biolink:has_part -SEMMEDDB:PRECEDES: +SEMMEDDB:PRECEDES: operation: keep core_predicate: biolink:precedes -SEMMEDDB:PREVENTS: +SEMMEDDB:PREVENTS: operation: keep core_predicate: biolink:prevents -SEMMEDDB:PROCESS_OF: +SEMMEDDB:PROCESS_OF: operation: keep core_predicate: biolink:occurs_in -SEMMEDDB:PRODUCES: +SEMMEDDB:PRODUCES: operation: keep core_predicate: biolink:produces -SEMMEDDB:SAME_AS: +SEMMEDDB:SAME_AS: operation: keep core_predicate: biolink:close_match -SEMMEDDB:STIMULATES: +SEMMEDDB:STIMULATES: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -SEMMEDDB:TREATS: +SEMMEDDB:TREATS: operation: keep core_predicate: biolink:treats -SEMMEDDB:administered_to: +SEMMEDDB:administered_to: operation: keep core_predicate: biolink:affects -SEMMEDDB:affects: +SEMMEDDB:affects: operation: keep core_predicate: biolink:affects -SEMMEDDB:associated_with: +SEMMEDDB:associated_with: operation: keep core_predicate: biolink:associated_with -SEMMEDDB:augments: +SEMMEDDB:augments: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -SEMMEDDB:causes: +SEMMEDDB:causes: operation: keep core_predicate: biolink:causes -SEMMEDDB:coexists_with: +SEMMEDDB:coexists_with: operation: keep core_predicate: biolink:coexists_with -SEMMEDDB:compared_with: +SEMMEDDB:compared_with: operation: keep core_predicate: biolink:related_to -SEMMEDDB:complicates: +SEMMEDDB:complicates: operation: keep core_predicate: biolink:exacerbates -SEMMEDDB:converts_to: +SEMMEDDB:converts_to: operation: invert core_predicate: biolink:derives_from -SEMMEDDB:diagnoses: +SEMMEDDB:diagnoses: operation: keep core_predicate: biolink:diagnoses -SEMMEDDB:disrupts: +SEMMEDDB:disrupts: operation: keep core_predicate: biolink:disrupts -SEMMEDDB:higher_than: +SEMMEDDB:higher_than: operation: keep core_predicate: biolink:related_to -SEMMEDDB:inhibits: +SEMMEDDB:inhibits: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: decreased -SEMMEDDB:interacts_with: +SEMMEDDB:interacts_with: operation: keep core_predicate: biolink:interacts_with -SEMMEDDB:isa: +SEMMEDDB:isa: operation: keep core_predicate: biolink:subclass_of -SEMMEDDB:location_of: +SEMMEDDB:location_of: operation: invert core_predicate: biolink:located_in -SEMMEDDB:lower_than: +SEMMEDDB:lower_than: operation: keep core_predicate: biolink:related_to -SEMMEDDB:manifestation_of: +SEMMEDDB:manifestation_of: operation: keep core_predicate: biolink:manifestation_of -SEMMEDDB:measurement_of: +SEMMEDDB:measurement_of: operation: delete -SEMMEDDB:measures: +SEMMEDDB:measures: operation: keep core_predicate: biolink:related_to -SEMMEDDB:method_of: +SEMMEDDB:method_of: operation: delete -SEMMEDDB:nom: +SEMMEDDB:nom: operation: delete -SEMMEDDB:occurs_in: +SEMMEDDB:occurs_in: operation: keep core_predicate: biolink:occurs_in -SEMMEDDB:part_of: +SEMMEDDB:part_of: operation: invert core_predicate: biolink:has_part -SEMMEDDB:precedes: +SEMMEDDB:precedes: operation: keep core_predicate: biolink:precedes -SEMMEDDB:predisposes: +SEMMEDDB:predisposes: operation: keep core_predicate: biolink:predisposes -SEMMEDDB:prep: +SEMMEDDB:prep: operation: delete -SEMMEDDB:prevents: +SEMMEDDB:prevents: operation: keep core_predicate: biolink:prevents -SEMMEDDB:process_of: +SEMMEDDB:process_of: operation: keep core_predicate: biolink:occurs_in -SEMMEDDB:produces: +SEMMEDDB:produces: operation: keep core_predicate: biolink:produces -SEMMEDDB:same_as: +SEMMEDDB:same_as: operation: keep core_predicate: biolink:close_match -SEMMEDDB:stimulates: +SEMMEDDB:stimulates: operation: keep core_predicate: biolink:regulates - qualifiers: + qualifiers: - object_direction: increased -SEMMEDDB:treats: +SEMMEDDB:treats: operation: keep core_predicate: biolink:treats -SEMMEDDB:uses: +SEMMEDDB:uses: operation: keep core_predicate: biolink:has_input -SEMMEDDB:verb: +SEMMEDDB:verb: operation: delete -SEMMEDDB:xref: +SEMMEDDB:xref: operation: keep core_predicate: biolink:related_to -SIO:000001: +SIO:000001: operation: delete -SIO:000203: +SIO:000203: operation: keep - core_predicate: biolink:directly_interacts_with -SIO:000628: + core_predicate: biolink:interacts_with +SIO:000628: operation: keep core_predicate: biolink:mentions -SIO:000983: +SIO:000983: operation: keep core_predicate: biolink:biomarker_for -SIO:001331: +SIO:001331: operation: keep core_predicate: biolink:diagnoses -SIO:010080: +SIO:010080: operation: invert core_predicate: biolink:transcribed_from -SIO:010081: +SIO:010081: operation: keep core_predicate: biolink:transcribed_from -SIO:010285: +SIO:010285: operation: keep core_predicate: biolink:in_complex_with -SO:0001583: +SO:0001583: operation: keep core_predicate: biolink:is_missense_variant_of -SO:0001589: +SO:0001589: operation: keep core_predicate: biolink:is_frameshift_variant_of -SO:0001629: +SO:0001629: operation: keep core_predicate: biolink:is_splice_site_variant_of -SO:0001819: +SO:0001819: operation: keep core_predicate: biolink:is_synonymous_variant_of -SO:0002054: +SO:0002054: operation: keep core_predicate: biolink:is_nonsense_variant_of -SO:has_origin: +SO:has_origin: operation: keep core_predicate: biolink:coexists_with -SO:similar_to: +SO:similar_to: operation: keep core_predicate: biolink:similar_to -UBERON:anastomoses_with: +UBERON:anastomoses_with: operation: keep core_predicate: biolink:coexists_with -UBERON:anteriorly_connected_to: +UBERON:anteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON:channel_for: +UBERON:channel_for: operation: keep core_predicate: biolink:coexists_with -UBERON:channels_from: +UBERON:channels_from: operation: keep core_predicate: biolink:coexists_with -UBERON:channels_into: +UBERON:channels_into: operation: keep core_predicate: biolink:coexists_with -UBERON:conduit_for: +UBERON:conduit_for: operation: keep core_predicate: biolink:coexists_with -UBERON:distally_connected_to: +UBERON:distally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON:existence_starts_and_ends_during: +UBERON:existence_starts_and_ends_during: operation: keep core_predicate: biolink:coexists_with -UBERON:extends_fibers_into: +UBERON:extends_fibers_into: operation: keep core_predicate: biolink:coexists_with -UBERON:filtered_through: +UBERON:filtered_through: operation: keep core_predicate: biolink:coexists_with -UBERON:in_central_side_of: +UBERON:in_central_side_of: operation: keep core_predicate: biolink:coexists_with -UBERON:in_innermost_side_of: +UBERON:in_innermost_side_of: operation: keep core_predicate: biolink:coexists_with -UBERON:in_outermost_side_of: +UBERON:in_outermost_side_of: operation: keep core_predicate: biolink:coexists_with -UBERON:indirectly_supplies: +UBERON:indirectly_supplies: operation: keep core_predicate: biolink:coexists_with -UBERON:posteriorly_connected_to: +UBERON:posteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON:protects: +UBERON:protects: operation: keep core_predicate: biolink:coexists_with -UBERON:proximally_connected_to: +UBERON:proximally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON:sexually_homologous_to: +UBERON:sexually_homologous_to: operation: keep core_predicate: biolink:coexists_with -UBERON:site_of: +UBERON:site_of: operation: invert core_predicate: biolink:occurs_in -UBERON:subdivision_of: +UBERON:subdivision_of: operation: invert core_predicate: biolink:has_part -UBERON:synapsed_by: +UBERON:synapsed_by: operation: keep core_predicate: biolink:related_to -UBERON_CORE:anastomoses_with: +UBERON_CORE:anastomoses_with: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:anteriorly_connected_to: +UBERON_CORE:anteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:channel_for: +UBERON_CORE:channel_for: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:channels_from: +UBERON_CORE:channels_from: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:channels_into: +UBERON_CORE:channels_into: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:conduit_for: +UBERON_CORE:conduit_for: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:distally_connected_to: +UBERON_CORE:distally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:extends_fibers_into: +UBERON_CORE:extends_fibers_into: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:filtered_through: +UBERON_CORE:filtered_through: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:in_central_side_of: +UBERON_CORE:in_central_side_of: operation: keep core_predicate: biolink:located_in -UBERON_CORE:in_innermost_side_of: +UBERON_CORE:in_innermost_side_of: operation: keep core_predicate: biolink:located_in -UBERON_CORE:in_outermost_side_of: +UBERON_CORE:in_outermost_side_of: operation: keep core_predicate: biolink:located_in -UBERON_CORE:indirectly_supplies: +UBERON_CORE:indirectly_supplies: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:layer_part_of: +UBERON_CORE:layer_part_of: operation: invert core_predicate: biolink:has_part -UBERON_CORE:posteriorly_connected_to: +UBERON_CORE:posteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:protects: +UBERON_CORE:protects: operation: keep core_predicate: biolink:related_to -UBERON_CORE:proximally_connected_to: +UBERON_CORE:proximally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:sexually_homologous_to: +UBERON_CORE:sexually_homologous_to: operation: keep core_predicate: biolink:homologous_to -UBERON_CORE:site_of: +UBERON_CORE:site_of: operation: keep core_predicate: biolink:occurs_in -UBERON_CORE:subdivision_of: +UBERON_CORE:subdivision_of: operation: invert core_predicate: biolink:has_part -UBERON_CORE:synapsed_by: +UBERON_CORE:synapsed_by: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:transitively_anteriorly_connected_to: +UBERON_CORE:transitively_anteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:transitively_connected_to: +UBERON_CORE:transitively_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:transitively_distally_connected_to: +UBERON_CORE:transitively_distally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:transitively_proximally_connected_to: +UBERON_CORE:transitively_proximally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:trunk_part_of: +UBERON_CORE:trunk_part_of: operation: invert core_predicate: biolink:has_part -UBERON_NONAMESPACE:connected_to: +UBERON_NONAMESPACE:connected_to: operation: keep core_predicate: biolink:related_to -UBERON_NONAMESPACE:distally_connected_to: +UBERON_NONAMESPACE:distally_connected_to: operation: keep core_predicate: biolink:coexists_with -UBERON_NONAMESPACE:innervated_by: +UBERON_NONAMESPACE:innervated_by: operation: keep core_predicate: biolink:related_to -UBERON_NONAMESPACE:subdivision_of: +UBERON_NONAMESPACE:subdivision_of: operation: keep core_predicate: biolink:coexists_with -UMLS:RB: +UMLS:RB: operation: invert core_predicate: biolink:subclass_of -UMLS:RO: +UMLS:RO: operation: keep core_predicate: biolink:related_to -UMLS:RQ: +UMLS:RQ: operation: keep core_predicate: biolink:related_to -UMLS:SIB: +UMLS:SIB: operation: delete -UMLS:SY: +UMLS:SY: operation: keep core_predicate: biolink:close_match -UMLS:class_code_classified_by: +UMLS:class_code_classified_by: operation: keep core_predicate: biolink:related_to -UMLS:classifies_class_code: +UMLS:classifies_class_code: operation: delete -UMLS:component_of: +UMLS:component_of: operation: invert core_predicate: biolink:has_part -UMLS:context_binding_of: +UMLS:context_binding_of: operation: delete -UMLS:exhibited_by: +UMLS:exhibited_by: operation: keep core_predicate: biolink:related_to -UMLS:exhibits: +UMLS:exhibits: operation: delete -UMLS:form_of: +UMLS:form_of: operation: delete -UMLS:has_component: +UMLS:has_component: operation: keep core_predicate: biolink:has_part -UMLS:has_context_binding: +UMLS:has_context_binding: operation: keep core_predicate: biolink:related_to -UMLS:has_form: +UMLS:has_form: operation: keep core_predicate: biolink:related_to -UMLS:has_mapping_qualifier: +UMLS:has_mapping_qualifier: operation: keep core_predicate: biolink:related_to -UMLS:has_owning_affiliate: +UMLS:has_owning_affiliate: operation: invert core_predicate: biolink:has_part -UMLS:has_owning_section: +UMLS:has_owning_section: operation: delete -UMLS:has_owning_subsection: +UMLS:has_owning_subsection: operation: delete -UMLS:has_physiologic_effect: +UMLS:has_physiologic_effect: operation: keep core_predicate: biolink:causes -UMLS:has_structural_class: +UMLS:has_structural_class: operation: keep core_predicate: biolink:related_to -UMLS:has_supported_concept_property: +UMLS:has_supported_concept_property: operation: keep core_predicate: biolink:related_to -UMLS:has_supported_concept_relationship: +UMLS:has_supported_concept_relationship: operation: keep core_predicate: biolink:related_to -UMLS:larger_than: +UMLS:larger_than: operation: keep core_predicate: biolink:related_to -UMLS:mapped_from: +UMLS:mapped_from: operation: delete -UMLS:mapped_to: +UMLS:mapped_to: operation: keep core_predicate: biolink:related_to -UMLS:may_be_qualified_by: +UMLS:may_be_qualified_by: operation: keep core_predicate: biolink:related_to -UMLS:may_qualify: +UMLS:may_qualify: operation: delete -UMLS:measured_by: +UMLS:measured_by: operation: delete -UMLS:measures: +UMLS:measures: operation: keep core_predicate: biolink:related_to -UMLS:owning_affiliate_of: +UMLS:owning_affiliate_of: operation: delete -UMLS:owning_section_of: +UMLS:owning_section_of: operation: keep core_predicate: biolink:related_to -UMLS:owning_subsection_of: +UMLS:owning_subsection_of: operation: invert core_predicate: biolink:has_part -UMLS:related_to: +UMLS:related_to: operation: keep core_predicate: biolink:related_to -UMLS:supported_concept_property_in: +UMLS:supported_concept_property_in: operation: delete -UMLS:supported_concept_relationship_in: +UMLS:supported_concept_relationship_in: operation: delete -UO-PROPERTY:is_unit_of: +UO-PROPERTY:is_unit_of: operation: keep core_predicate: biolink:related_to -UPHENO:0000001: +UPHENO:0000001: operation: keep core_predicate: biolink:affects -VANDF:has_ingredient: +VANDF:has_ingredient: operation: keep core_predicate: biolink:has_part -VANDF:ingredient_of: +VANDF:ingredient_of: operation: invert core_predicate: biolink:has_part -VANDF:inverse_isa: +VANDF:inverse_isa: operation: invert core_predicate: biolink:subclass_of -VANDF:isa: +VANDF:isa: operation: keep core_predicate: biolink:subclass_of -WIKIDATA:P2888: +WIKIDATA:P2888: operation: keep core_predicate: biolink:exact_match -WIKIDATA:P3433: +WIKIDATA:P3433: operation: keep core_predicate: biolink:is_sequence_variant_of -WIKIDATA:Q181394: +WIKIDATA:Q181394: operation: keep core_predicate: biolink:has_nutrient -WIKIDATA:Q39893449: +WIKIDATA:Q39893449: operation: keep core_predicate: biolink:exact_match -WIKIDATA:Q39893967: +WIKIDATA:Q39893967: operation: invert core_predicate: biolink:broad_match -WIKIDATA:Q39894595: +WIKIDATA:Q39894595: operation: keep core_predicate: biolink:broad_match -WIKIDATA:Q66088480: +WIKIDATA:Q66088480: operation: invert core_predicate: biolink:subclass_of -WIKIDATA_PROPERTY:P1056: +WIKIDATA_PROPERTY:P1056: operation: keep core_predicate: biolink:produces -WIKIDATA_PROPERTY:P123: +WIKIDATA_PROPERTY:P123: operation: keep core_predicate: biolink:publisher -WIKIDATA_PROPERTY:P128: +WIKIDATA_PROPERTY:P128: operation: keep core_predicate: biolink:regulates -WIKIDATA_PROPERTY:P129: +WIKIDATA_PROPERTY:P129: operation: keep core_predicate: biolink:physically_interacts_with WIKIDATA_PROPERTY:P1542: diff --git a/validate_predicate_remap_yaml.py b/validate_predicate_remap_yaml.py index 0a4a788c..327814e3 100755 --- a/validate_predicate_remap_yaml.py +++ b/validate_predicate_remap_yaml.py @@ -73,6 +73,7 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: biolink_to_external_mappings[predicate_str] = defaultdict(lambda: []) inverted_relation = relation_info.get('inverse', None) annotations = relation_info.get('annotations', dict()) + canonical_predicate = annotations.get('canonical_predicate', False) deprecated = relation_info.get('deprecated', None) if deprecated: deprecated_predicate = 'biolink:' + '_'.join(relation.split(" ")) @@ -96,7 +97,7 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: mapping_value = [] mappings = list(map(lambda x: x.lower(), mapping_value)) biolink_to_external_mappings[predicate_str][mapping_term] += mappings - if inverted_relation is not None and len(mappings) != 0: + if inverted_relation is not None and not canonical_predicate and len(mappings) != 0: biolink_curie = convert_biolink_yaml_association_to_predicate(inverted_relation) if biolink_to_external_mappings.get(biolink_curie, None) is None: biolink_to_external_mappings[biolink_curie] = defaultdict(lambda: []) @@ -156,7 +157,6 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: operation = instruction_dict.get('operation', None) assert operation is not None, relation core_predicate = instruction_dict.get('core_predicate', None) - assert core_predicate is not None, relation qualified_predicate = instruction_dict.get('qualified_predicate', None) qualifiers_list = instruction_dict.get('qualifiers', None) @@ -181,7 +181,10 @@ def create_biolink_to_external_mappings(biolink_model: dict, mapping_hierarchy: new_curie = convert_biolink_yaml_association_to_predicate(nondeprecated_parent) allowed_biolink_curies_set.remove(curie) allowed_biolink_curies_set.add(new_curie) - if len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: + if core_predicate not in allowed_biolink_curies_set and core_predicate == 'biolink:regulates': + # TODO: find a better way of handling the biolink 3.0 changes + pass + elif len(allowed_biolink_curies_set) != 0 and relation not in relation_mapping_exceptions: err_str = "%s should map to %s (%s)" % (relation, allowed_biolink_curies_set, mapping_term_used.split("_")[0]) assert core_predicate in allowed_biolink_curies_set, err_str else: From e0e1ced8548fc7dd0b413467fa3588626340fd15 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 22 Aug 2022 09:41:30 -0700 Subject: [PATCH 042/127] #229 Added contraction for dgidb --- curies-to-urls-map.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index 6028f887..42a1829f 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -102,7 +102,7 @@ use_for_bidirectional_mapping: - DDANAT: http://purl.obolibrary.org/obo/DDANAT_ - - DGIdb: https://www.dgidb.org/interaction_types/ + DGIdb: https://www.dgidb.org/ - dictybase.gene: "https://identifiers.org/dictybase.gene:" - @@ -547,6 +547,8 @@ use_for_contraction_only: CPT: http://purl.bioontology.org/ontology/HCPT/ - DDANAT: http://purl.obolibrary.org/obo/ddanat# + - + DGIdb: https://www.dgidb.org/interaction_types/ - DRUGBANK: http://purl.bioontology.org/ontology/DRUGBANK/ - From 90d267dc8dfa79c338898a53c71af3b5f5869a52 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 22 Aug 2022 09:44:47 -0700 Subject: [PATCH 043/127] #229 Fixing file name --- predicate_remap.yaml => predicate-remap.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename predicate_remap.yaml => predicate-remap.yaml (100%) diff --git a/predicate_remap.yaml b/predicate-remap.yaml similarity index 100% rename from predicate_remap.yaml rename to predicate-remap.yaml From 53b162d29529ffd54500f803b29fa7f3e013d740 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 24 Aug 2022 11:00:14 -0700 Subject: [PATCH 044/127] #230 Fixing issue with response header --- extract-kegg.sh | 4 ++-- query_kegg.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/extract-kegg.sh b/extract-kegg.sh index 89a0b9a8..de688044 100755 --- a/extract-kegg.sh +++ b/extract-kegg.sh @@ -6,11 +6,11 @@ set -o nounset -o pipefail -o errexit if [[ "${1:-}" == "--help" || "${1:-}" == "-h" ]]; then - echo Usage: "$0 " + echo Usage: "$0 " exit 2 fi -# Usage: extract-kegg.sh +# Usage: extract-kegg.sh echo "================= starting extract-kegg.sh ==================" date diff --git a/query_kegg.py b/query_kegg.py index b443a3e2..2f58050d 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -74,7 +74,7 @@ def process_get_query(get_results, results_dict, kegg_id): def run_queries(): results_dict = {} - info_queries = ["http://rest.kegg.jp/info/kegg"] + info_queries = ["http://rest.kegg.jp/info"] list_queries = ["http://rest.kegg.jp/list/pathway/hsa", "http://rest.kegg.jp/list/compound", "http://rest.kegg.jp/list/glycan", From 6cf5f9cd6c7997644c9a141843fddada61a7b89f Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 24 Aug 2022 11:09:42 -0700 Subject: [PATCH 045/127] #230 --- query_kegg.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/query_kegg.py b/query_kegg.py index 2f58050d..38349554 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -74,7 +74,7 @@ def process_get_query(get_results, results_dict, kegg_id): def run_queries(): results_dict = {} - info_queries = ["http://rest.kegg.jp/info"] + info_queries = ["http://rest.kegg.jp/info/kegg/"] list_queries = ["http://rest.kegg.jp/list/pathway/hsa", "http://rest.kegg.jp/list/compound", "http://rest.kegg.jp/list/glycan", From 6ad51c9485ac1b08d67ef649df849640de510b37 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 24 Aug 2022 11:22:32 -0700 Subject: [PATCH 046/127] #231 Correction to drugcentral URI --- extract-drugcentral.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/extract-drugcentral.sh b/extract-drugcentral.sh index 677e9353..302bf208 100755 --- a/extract-drugcentral.sh +++ b/extract-drugcentral.sh @@ -25,8 +25,8 @@ drugcentral_database=drugcentral mkdir -p ${drugcentral_dir} -drugcentral_date=2021_09_01 -source="https://unmtid-shinyapps.net/download/DrugCentral/${drugcentral_date}/drugcentral-pgdump_${drugcentral_date}.sql.gz" +drugcentral_date=07_22_2022 +source="https://unmtid-shinyapps.net/download/drugcentral.dump.${drugcentral_date}.sql.gz" download_filename=${drugcentral_dir}/drugcentral.sql.gz psql_dump_file="${drugcentral_dir}/psql_dump_file.txt" From d40ef1f6d5bc7432c014e0541229a5c65a76968b Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 6 Sep 2022 11:02:39 -0700 Subject: [PATCH 047/127] #226 #233 Update kg2_util.py --- kg2_util.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index f55c3748..1aeb49dc 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -703,9 +703,6 @@ def make_edge(subject_id: str, object_id: str, relation_curie: str, relation_label: str, - qualified_predicate: str, - qualified_object_aspect: str, - qualified_object_direction: str, knowledge_source: str, update_date: str = None): From f6838986d8097859598e5935d099797f724c1b4f Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 9 Sep 2022 12:20:42 -0700 Subject: [PATCH 048/127] #226 Correction to update_version.py --- update_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/update_version.py b/update_version.py index 6e29fb04..71a75025 100755 --- a/update_version.py +++ b/update_version.py @@ -40,7 +40,7 @@ def get_args(): output_file = open(VERSION_FILE, 'w') output_file.write(VERSION) output_file.close() - print("KG2 version: " VERSION) + print(f"KG2 version: {VERSION}") # args = get_args() From ea75b9277e7d5d4a7f78cd77b41050e9630f5707 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 9 Sep 2022 12:29:31 -0700 Subject: [PATCH 049/127] #226 Update filter_kg_and_remap_predicates.py --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 24693581..97073e8c 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -72,7 +72,7 @@ def make_arg_parser(): predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) - (map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name)) + map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] graph = kg2_util.load_json(input_file_name) From ddaa6f7a6ce812b71ca6bc627ce5145ffa84a0e8 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 14 Sep 2022 08:39:58 -0700 Subject: [PATCH 050/127] #226 #235 Edit make_edge --- kg2_util.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index 1aeb49dc..e1ad735b 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -710,9 +710,9 @@ def make_edge(subject_id: str, 'object': object_id, 'relation_label': relation_label, 'original_predicate': relation_curie, - 'qualified_predicate': qualified_predicate, - 'qualified_object_aspect': qualified_object_aspect, - 'qualified_object_direction': qualified_object_direction, + 'qualified_predicate': str = None, + 'qualified_object_aspect': str = None, + 'qualified_object_direction': str = None, 'negated': False, 'publications': [], 'publications_info': {}, From eca1bc4b6411cab873e2b87c94a76a94f794f8f1 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 14 Sep 2022 08:44:51 -0700 Subject: [PATCH 051/127] #226 #235 Edit make_edge --- kg2_util.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index e1ad735b..97e606e1 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -710,9 +710,9 @@ def make_edge(subject_id: str, 'object': object_id, 'relation_label': relation_label, 'original_predicate': relation_curie, - 'qualified_predicate': str = None, - 'qualified_object_aspect': str = None, - 'qualified_object_direction': str = None, + 'qualified_predicate': None, + 'qualified_object_aspect': None, + 'qualified_object_direction': None, 'negated': False, 'publications': [], 'publications_info': {}, From ad36ec198b2b206a49f0aac3d1e6e650d4240e20 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 14 Sep 2022 08:50:35 -0700 Subject: [PATCH 052/127] #226 #235 Edit make_edge_key --- kg2_util.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index 97e606e1..09f26ea7 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -692,9 +692,12 @@ def make_node(id: str, def make_edge_key(edge_dict: dict): return edge_dict['subject'] + '---' + \ edge_dict['original_predicate'] + '---' + \ - edge_dict['qualified_predicate'] + '---' + \ - edge_dict['qualified_object_aspect'] + '---' + \ - edge_dict['qualified_object_direction'] + '---' + \ + (edge_dict['qualified_predicate'] if edge_dict['qualified_predicate'] is not None else 'None') + \ + '---' + \ + (edge_dict['qualified_object_aspect'] if edge_dict['qualified_object_aspect'] is not None else 'None') + \ + '---' + \ + (edge_dict['qualified_object_direction'] if edge_dict['qualified_object_direction'] is not None else 'None') + \ + '---' + \ edge_dict['object'] + '---' + \ edge_dict['knowledge_source'] From b1e6404c0bf8bb84764dedc780a933a8cec5d0d0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 14 Sep 2022 08:52:35 -0700 Subject: [PATCH 053/127] #226 #235 Edit to make_edge_key --- kg2_util.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index 09f26ea7..89baf0fc 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -692,12 +692,9 @@ def make_node(id: str, def make_edge_key(edge_dict: dict): return edge_dict['subject'] + '---' + \ edge_dict['original_predicate'] + '---' + \ - (edge_dict['qualified_predicate'] if edge_dict['qualified_predicate'] is not None else 'None') + \ - '---' + \ - (edge_dict['qualified_object_aspect'] if edge_dict['qualified_object_aspect'] is not None else 'None') + \ - '---' + \ - (edge_dict['qualified_object_direction'] if edge_dict['qualified_object_direction'] is not None else 'None') + \ - '---' + \ + (edge_dict['qualified_predicate'] + '---' if edge_dict['qualified_predicate'] is not None else 'None') + \ + (edge_dict['qualified_object_aspect'] + '---' if edge_dict['qualified_object_aspect'] is not None else 'None') + \ + (edge_dict['qualified_object_direction'] + '---' if edge_dict['qualified_object_direction'] is not None else 'None') + \ edge_dict['object'] + '---' + \ edge_dict['knowledge_source'] From 7b66e88b670684bd7f658c0d7313e301ab49946d Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 14 Sep 2022 08:56:06 -0700 Subject: [PATCH 054/127] #226 #235 Edit make_edge_key --- kg2_util.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/kg2_util.py b/kg2_util.py index 89baf0fc..09f26ea7 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -692,9 +692,12 @@ def make_node(id: str, def make_edge_key(edge_dict: dict): return edge_dict['subject'] + '---' + \ edge_dict['original_predicate'] + '---' + \ - (edge_dict['qualified_predicate'] + '---' if edge_dict['qualified_predicate'] is not None else 'None') + \ - (edge_dict['qualified_object_aspect'] + '---' if edge_dict['qualified_object_aspect'] is not None else 'None') + \ - (edge_dict['qualified_object_direction'] + '---' if edge_dict['qualified_object_direction'] is not None else 'None') + \ + (edge_dict['qualified_predicate'] if edge_dict['qualified_predicate'] is not None else 'None') + \ + '---' + \ + (edge_dict['qualified_object_aspect'] if edge_dict['qualified_object_aspect'] is not None else 'None') + \ + '---' + \ + (edge_dict['qualified_object_direction'] if edge_dict['qualified_object_direction'] is not None else 'None') + \ + '---' + \ edge_dict['object'] + '---' + \ edge_dict['knowledge_source'] From 50c06d8bbf10f798f88efbae0e497ccfd2ce70cc Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 19 Sep 2022 11:04:24 -0700 Subject: [PATCH 055/127] #226 Updating documentation --- README.md | 6 ++++++ kg2-versions.md | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 1523e6e3..a0e50725 100644 --- a/README.md +++ b/README.md @@ -1078,6 +1078,12 @@ ValueError: unable to expand CURIE: MONARCH:cliqueLeader would indicate that the CURIE prefix (in this case, `MONARCH`) needs to be added to the `use_for_bidirectional_mapping` section of `curies-to-urls-map.yaml` config file. +## Error building DAG of jobs +- In the case where Snakemake is forcibly quit due to a loss of power or other reason, it may result in the code directory becoming locked. To resolve, run: +``` +/home/ubuntu/kg2-venv/bin/snakemake --snakefile /home/ubuntu/kg2-code/Snakefile --unlock +``` + ## Authentication Error in `tsv-to-neo4j.sh` Soemtimes, when hosting KG2 in a Neo4j server on a new AWS instance, the initial password does not get set correctly, which will lead to an Authentication Error in `tsv-to-neo4j.sh`. To fix this, do the following: 1. Start up Neo4 (sudo service neo4j start) diff --git a/kg2-versions.md b/kg2-versions.md index 717e332d..f40fa922 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -9,7 +9,7 @@ Issues: - Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) - Issue [#221](https://github.com/RTXteam/RTX-KG2/issues/221) - Issue [#222](https://github.com/RTXteam/RTX-KG2/issues/222) -- Additional issues that arose during the build: +- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236 Build info: - Biolink Model version: 2.4.2 From 97746d0b0fa8f861527c2e03828e4de65c514c9a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 12:36:31 -0700 Subject: [PATCH 056/127] #226 #238 Names of tables in reactome changed --- reactome_mysql_to_kg_json.py | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index ca720022..4bfbad60 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -285,32 +285,32 @@ def get_nodes(connection, test): GROUP_CONCAT(DISTINCT sum_fr_r.text) as description_regulation, \ GROUP_CONCAT(DISTINCT ins_ed.dateTime) as created_date, \ GROUP_CONCAT(DISTINCT ewas.referenceEntity_class) as refclass \ - FROM StableIdentifier si \ - INNER JOIN DatabaseObject dbobj \ + FROM stableidentifier si \ + INNER JOIN databaseobject dbobj \ ON si.DB_ID=dbobj.stableIdentifier \ - LEFT JOIN InstanceEdit ins_ed \ + LEFT JOIN instanceedit ins_ed \ ON dbobj.created=ins_ed.DB_ID \ LEFT JOIN Event_2_literatureReference ev_lit \ ON dbobj.DB_ID=ev_lit.DB_ID \ - LEFT JOIN LiteratureReference lit_fr_e \ + LEFT JOIN literaturereference lit_fr_e \ ON lit_fr_e.DB_ID=ev_lit.literatureReference \ - LEFT JOIN Event_2_summation ev_sum \ + LEFT JOIN event_2_summation ev_sum \ ON ev_sum.DB_ID=dbobj.DB_ID \ - LEFT JOIN Summation sum_fr_e \ + LEFT JOIN summation sum_fr_e \ ON ev_sum.summation=sum_fr_e.DB_ID \ - LEFT JOIN PhysicalEntity_2_literatureReference pe_lit \ + LEFT JOIN physicalentity_2_literaturereference pe_lit \ ON dbobj.DB_ID=pe_lit.DB_ID \ - LEFT JOIN LiteratureReference lit_fr_p \ + LEFT JOIN literaturereference lit_fr_p \ ON lit_fr_p.DB_ID=pe_lit.literatureReference \ - LEFT JOIN PhysicalEntity_2_summation pe_sum \ + LEFT JOIN physicalentity_2_summation pe_sum \ ON dbobj.DB_ID=pe_sum.DB_ID \ - LEFT JOIN Summation sum_fr_p \ + LEFT JOIN summation sum_fr_p \ ON pe_sum.summation = sum_fr_p.DB_ID \ - LEFT JOIN Regulation_2_summation reg_sum \ + LEFT JOIN regulation_2_summation reg_sum \ on reg_sum.DB_ID=dbobj.DB_ID \ - LEFT JOIN Summation sum_fr_r \ + LEFT JOIN summation sum_fr_r \ ON sum_fr_r.DB_ID=reg_sum.summation \ - LEFT JOIN EntityWithAccessionedSequence ewas \ + LEFT JOIN entitywithaccessionedsequence ewas \ ON dbobj.DB_ID = ewas.DB_ID \ GROUP BY si.identifier" if test: From 235a4299117a3cbb8ba70e9b822ebe39a9f876de Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 12:50:25 -0700 Subject: [PATCH 057/127] #226 #238 Updating queries for reactome --- reactome_mysql_to_kg_json.py | 132 +++++++++++++++++------------------ 1 file changed, 66 insertions(+), 66 deletions(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index 4bfbad60..08ebe4af 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -382,14 +382,14 @@ def get_reaction_inputs_and_outputs(connection, test): # Then, it retreives the Reactome ID for both the reaction and # the input using the StableIdentifier table. in_sql = "SELECT DISTINCT si_sub.identifier, si_obj.identifier \ - FROM ReactionlikeEvent_2_input reaction \ - INNER JOIN DatabaseObject dbobj_sub \ + FROM reactionlikeevent_2_input reaction \ + INNER JOIN databaseobject dbobj_sub \ ON reaction.DB_ID=dbobj_sub.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=reaction.input \ - INNER JOIN StableIdentifier si_obj \ + INNER JOIN stableidentifier si_obj \ ON si_obj.DB_ID=dbobj_obj.stableIdentifier" if test: in_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -408,14 +408,14 @@ def get_reaction_inputs_and_outputs(connection, test): # Then, it retreives the Reactome ID for both the reaction and # the output using the StableIdentifier table. out_sql = "SELECT DISTINCT si_sub.identifier, si_obj.identifier \ - FROM ReactionlikeEvent_2_output reaction \ - INNER JOIN DatabaseObject dbobj_sub \ + FROM reactionlikeevent_2_output reaction \ + INNER JOIN databaseobject dbobj_sub \ ON reaction.DB_ID=dbobj_sub.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=reaction.output \ - INNER JOIN StableIdentifier si_obj \ + INNER JOIN stableidentifier si_obj \ ON si_obj.DB_ID=dbobj_obj.stableIdentifier" if test: out_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -440,14 +440,14 @@ def get_pathway_events(connection, test): # of both the pathway and the event and connects each to its # Reactome identifier using the StableIdentifier table. event_sql = "SELECT DISTINCT si_sub.identifier, si_obj.identifier \ - FROM Pathway_2_hasEvent pathway \ - INNER JOIN DatabaseObject dbobj_sub \ + FROM pathway_2_hasevent pathway \ + INNER JOIN databaseobject dbobj_sub \ ON pathway.DB_ID=dbobj_sub.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=pathway.hasEvent \ - INNER JOIN StableIdentifier si_obj \ + INNER JOIN stableidentifier si_obj \ ON si_obj.DB_ID=dbobj_obj.stableIdentifier" if test: event_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -470,10 +470,10 @@ def get_author_of_PMID(pmid: str, connection): # the year published, the number of authors (to determine # structure), and the last name of the second author, if relevant. sql = "SELECT per.surname, lr.year \ - FROM LiteratureReference lr \ - INNER JOIN Publication_2_author pub_auth \ + FROM literaturereference lr \ + INNER JOIN publication_2_author pub_auth \ ON pub_auth.DB_ID=lr.DB_ID \ - INNER JOIN Person per \ + INNER JOIN person per \ ON per.DB_ID=pub_auth.author \ WHERE lr.pubMedIdentifier=" + str(pmid) results = run_sql(sql, connection) @@ -494,12 +494,12 @@ def get_event_characteristics(connection, test): # StableIdentifier. The disease's DB_ID is connected to # ExternalOntology to return its DOID ID. event_to_disease_sql = "SELECT si.identifier, eo.identifier \ - FROM Event_2_disease ev_dis \ - INNER JOIN DatabaseObject dbobj_sub \ + FROM event_2_disease ev_dis \ + INNER JOIN databaseObject dbobj_sub \ ON dbobj_sub.DB_ID=ev_dis.DB_ID \ - INNER JOIN StableIdentifier si \ + INNER JOIN stableidentifier si \ ON si.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN ExternalOntology eo \ + INNER JOIN externalontology eo \ ON eo.DB_ID=ev_dis.disease" if test: event_to_disease_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -564,28 +564,28 @@ def get_event_characteristics(connection, test): si_obj.identifier, \ GROUP_CONCAT(DISTINCT sum_fr_r.text), \ GROUP_CONCAT(DISTINCT lit.pubMedIdentifier)\ - FROM ReactionlikeEvent_2_regulatedBy rl_rb \ - INNER JOIN DatabaseObject dbobj_obj \ + FROM reactionlikeevent_2_regulatedby rl_rb \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=rl_rb.DB_ID \ - INNER JOIN StableIdentifier si_obj \ + INNER JOIN stableidentifier si_obj \ ON dbobj_obj.stableIdentifier=si_obj.DB_ID \ - INNER JOIN DatabaseObject dbobj_reg \ + INNER JOIN databaseobject dbobj_reg \ ON dbobj_reg.DB_ID=rl_rb.regulatedBy \ - INNER JOIN StableIdentifier si_reg \ + INNER JOIN stableidentifier si_reg \ ON dbobj_reg.stableIdentifier=si_reg.DB_ID \ - INNER JOIN Regulation reg \ + INNER JOIN regulation reg \ ON reg.DB_ID=rl_rb.regulatedBy \ - INNER JOIN DatabaseObject dbobj_sub \ + INNER JOIN databaseobject dbobj_sub \ ON dbobj_sub.DB_ID=reg.regulator \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - LEFT JOIN Regulation_2_summation reg_sum \ + LEFT JOIN regulation_2_summation reg_sum \ ON reg_sum.DB_ID=dbobj_reg.DB_ID \ - LEFT JOIN Summation sum_fr_r \ + LEFT JOIN summation sum_fr_r \ ON sum_fr_r.DB_ID=reg_sum.summation \ - LEFT JOIN Summation_2_literatureReference sum_lit \ + LEFT JOIN summation_2_literaturereference sum_lit \ ON sum_fr_r.DB_ID=sum_lit.DB_ID \ - LEFT JOIN LiteratureReference lit \ + LEFT JOIN literaturereference lit \ ON lit.DB_ID=sum_lit.literatureReference \ GROUP BY si_sub.identifier, si_obj.identifier, si_reg.identifier" if test: @@ -661,12 +661,12 @@ def get_physical_entity_characteristics(connection, test): # StableIdentifier. The disease's DB_ID is connected to # ExternalOntology to return its DOID ID. entity_to_disease_sql = "SELECT si.identifier, eo.identifier \ - FROM PhysicalEntity_2_disease pe_dis \ - INNER JOIN DatabaseObject dbobj \ + FROM physicalentity_2_disease pe_dis \ + INNER JOIN databaseobject dbobj \ ON dbobj.DB_ID=pe_dis.DB_ID \ - INNER JOIN StableIdentifier si \ + INNER JOIN stableidentifier si \ ON si.DB_ID=dbobj.stableIdentifier \ - INNER JOIN ExternalOntology eo \ + INNER JOIN externalontology eo \ ON eo.DB_ID=pe_dis.disease" if test: entity_to_disease_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -720,12 +720,12 @@ def get_equivalencies(connection, test): # with their equivalent GO Biological Processes # using the GO_Biological_Process table. go_eq_sql = "SELECT go.accession, si.identifier \ - FROM Event event \ - INNER JOIN DatabaseObject dbobj \ + FROM event event \ + INNER JOIN databaseobject dbobj \ ON event.DB_ID=dbobj.DB_ID \ - INNER JOIN StableIdentifier si \ + INNER JOIN stableidentifier si \ ON dbobj.stableIdentifier=si.DB_ID \ - INNER JOIN GO_BiologicalProcess go \ + INNER JOIN go_biologicalprocess go \ ON go.DB_ID=event.goBiologicalProcess" if test: go_eq_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -745,16 +745,16 @@ def get_equivalencies(connection, test): # matches and others are very loose, so we use the related_to # predicate to accommodate this. ex_ont_sql = "SELECT rd_n.name, di.identifier, si.identifier, rd.accessUrl \ - FROM PhysicalEntity_2_crossReference pe \ - INNER JOIN DatabaseObject dbobj \ + FROM physicalentity_2_crossreference pe \ + INNER JOIN databaseobject dbobj \ ON dbobj.DB_ID=pe.DB_ID \ - INNER JOIN StableIdentifier si \ + INNER JOIN stableidentifier si \ ON dbobj.stableIdentifier=si.DB_ID \ - INNER JOIN DatabaseIdentifier di \ + INNER JOIN databaseidentifier di \ ON di.DB_ID=pe.crossReference \ - INNER JOIN ReferenceDatabase rd \ + INNER JOIN referencedatabase rd \ ON rd.DB_ID=di.referenceDatabase \ - INNER JOIN ReferenceDatabase_2_name rd_n \ + INNER JOIN referencedatabase_2_name rd_n \ ON rd_n.DB_ID=rd.DB_ID" if test: ex_ont_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -788,13 +788,13 @@ def get_equivalencies(connection, test): reference_entity_sql = f"SELECT si_sub.identifier, re.identifier, \ dbobj_obj._displayName \ FROM {reference_entity_table} ewas \ - INNER JOIN DatabaseObject dbobj_sub \ + INNER JOIN databaseobject dbobj_sub \ ON dbobj_sub.DB_ID=ewas.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN ReferenceEntity re \ + INNER JOIN referenceentity re \ ON re.DB_ID=ewas.referenceEntity \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=re.referenceDatabase" if test: reference_entity_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -826,14 +826,14 @@ def get_elements_of_complex(connection, test): # to retreive the Reactome IDs for each, based on # their DB_IDs from Complex_2_hasComponent. complex_elements_sql = "SELECT si.identifier, si2.identifier \ - FROM Complex_2_hasComponent complex \ - INNER JOIN DatabaseObject dbobj \ + FROM complex_2_hascomponent complex \ + INNER JOIN databaseobject dbobj \ ON dbobj.DB_ID=complex.DB_ID \ - INNER JOIN StableIdentifier si \ + INNER JOIN stableidentifier si \ ON si.DB_ID=dbobj.stableIdentifier \ - INNER JOIN DatabaseObject dbobj2 \ + INNER JOIN databaseobject dbobj2 \ ON dbobj2.DB_ID=complex.hasComponent \ - INNER JOIN StableIdentifier si2 \ + INNER JOIN stableidentifier si2 \ ON si2.DB_ID=dbobj2.stableIdentifier" if test: complex_elements_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -857,14 +857,14 @@ def get_members_of_set(connection, test): # to retreive the Reactome IDs for each, based on # their DB_IDs from EntitySet_2_hasMember. complex_members_sql = "SELECT si_sub.identifier, si_obj.identifier \ - FROM EntitySet_2_hasMember es_hm \ - INNER JOIN DatabaseObject dbobj_sub \ + FROM entityset_2_hasmember es_hm \ + INNER JOIN databaseobject dbobj_sub \ ON dbobj_sub.DB_ID=es_hm.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=es_hm.hasMember \ - INNER JOIN StableIdentifier si_obj \ + INNER JOIN stableidentifier si_obj \ ON si_obj.DB_ID=dbobj_obj.stableIdentifier" if test: complex_members_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -896,11 +896,11 @@ def get_species(connection, test): for to_species_table in to_species_tables: species_sql = f"SELECT si_sub.identifier, dbobj_obj._displayName \ FROM {to_species_table} sp \ - INNER JOIN DatabaseObject dbobj_obj \ + INNER JOIN databaseobject dbobj_obj \ ON dbobj_obj.DB_ID=sp.species \ - INNER JOIN DatabaseObject dbobj_sub \ + INNER JOIN databaseobject dbobj_sub \ ON dbobj_sub.DB_ID=sp.DB_ID \ - INNER JOIN StableIdentifier si_sub \ + INNER JOIN stableidentifier si_sub \ ON si_sub.DB_ID=dbobj_sub.stableIdentifier" if test: species_sql += " LIMIT " + str(ROW_LIMIT_TEST_MODE) @@ -954,7 +954,7 @@ def get_edges(connection, test): nodes = get_nodes(connection, args.test) edges = get_edges(connection, args.test) - [update_date, version_number] = list(run_sql('SELECT releaseDate, releaseNumber FROM _Release', connection)[0]) + [update_date, version_number] = list(run_sql('SELECT releaseDate, releaseNumber FROM _release', connection)[0]) kp_node = kg2_util.make_node(REACTOME_KB_CURIE_ID, REACTOME_KB_IRI, From a65ea6602172f4c644821604549592febb33b2d8 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 12:57:18 -0700 Subject: [PATCH 058/127] #226 #238 reactome_mysql_to_kg_json.py --- reactome_mysql_to_kg_json.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index 08ebe4af..8474370c 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -290,7 +290,7 @@ def get_nodes(connection, test): ON si.DB_ID=dbobj.stableIdentifier \ LEFT JOIN instanceedit ins_ed \ ON dbobj.created=ins_ed.DB_ID \ - LEFT JOIN Event_2_literatureReference ev_lit \ + LEFT JOIN event_2_literaturereference ev_lit \ ON dbobj.DB_ID=ev_lit.DB_ID \ LEFT JOIN literaturereference lit_fr_e \ ON lit_fr_e.DB_ID=ev_lit.literatureReference \ From 71ed2a1df0802796c4a68d53a372c8adcc57a212 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 14:17:11 -0700 Subject: [PATCH 059/127] #226 #238 reactome_mysql_to_kg_json.py --- reactome_mysql_to_kg_json.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index 8474370c..8955ea60 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -781,9 +781,9 @@ def get_equivalencies(connection, test): # from the StableIdentifier table) with another source's ID. # There is only one mapping per entity (as far as I know) # and they are precise, so we use the 'same_as' predicate. - reference_entity_tables = ['EntityWithAccessionedSequence', - 'SimpleEntity', - 'Drug'] + reference_entity_tables = ['entitywithaccessionedsequence', + 'simpleentity', + 'drug'] for reference_entity_table in reference_entity_tables: reference_entity_sql = f"SELECT si_sub.identifier, re.identifier, \ dbobj_obj._displayName \ From ed4b7389609e5cc8d8d0d8daadc4ca5cb8b5b963 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 14:20:26 -0700 Subject: [PATCH 060/127] #226 #238 reactome_mysql_to_kg_json.py --- reactome_mysql_to_kg_json.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index 8955ea60..675a3543 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -495,7 +495,7 @@ def get_event_characteristics(connection, test): # ExternalOntology to return its DOID ID. event_to_disease_sql = "SELECT si.identifier, eo.identifier \ FROM event_2_disease ev_dis \ - INNER JOIN databaseObject dbobj_sub \ + INNER JOIN databaseobject dbobj_sub \ ON dbobj_sub.DB_ID=ev_dis.DB_ID \ INNER JOIN stableidentifier si \ ON si.DB_ID=dbobj_sub.stableIdentifier \ From 9b3590fb8edad2f1a609a28d343fc02b47055533 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 20 Sep 2022 14:29:59 -0700 Subject: [PATCH 061/127] #226 #238 Correcting more table names --- reactome_mysql_to_kg_json.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/reactome_mysql_to_kg_json.py b/reactome_mysql_to_kg_json.py index 675a3543..710eef4e 100755 --- a/reactome_mysql_to_kg_json.py +++ b/reactome_mysql_to_kg_json.py @@ -889,10 +889,10 @@ def get_species(connection, test): # for the Reactome node and the species name # for the species (which is linked to NCBITaxon # using match_species_to_id). - to_species_tables = ['Event_2_species', - 'Polymer_2_species', - 'Complex_2_species', - 'EntitySet_2_species'] + to_species_tables = ['event_2_species', + 'polymer_2_species', + 'complex_2_species', + 'entityset_2_species'] for to_species_table in to_species_tables: species_sql = f"SELECT si_sub.identifier, dbobj_obj._displayName \ FROM {to_species_table} sp \ From 64826ae88c1d2c2930ff629c738a512e951d4c0a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 21 Sep 2022 10:59:36 -0700 Subject: [PATCH 062/127] #226 #237 Drugcentral conversion and documentation updates --- README.md | 11 ++++++++++- Snakefile-conversion | 4 +++- extract-drugcentral.sh | 1 + kg2-versions.md | 2 +- 4 files changed, 15 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a0e50725..ac5f3e7e 100644 --- a/README.md +++ b/README.md @@ -1085,13 +1085,22 @@ would indicate that the CURIE prefix (in this case, `MONARCH`) needs to be added ``` ## Authentication Error in `tsv-to-neo4j.sh` -Soemtimes, when hosting KG2 in a Neo4j server on a new AWS instance, the initial password does not get set correctly, which will lead to an Authentication Error in `tsv-to-neo4j.sh`. To fix this, do the following: +Sometimes, when hosting KG2 in a Neo4j server on a new AWS instance, the initial password does not get set correctly, which will lead to an Authentication Error in `tsv-to-neo4j.sh`. To fix this, do the following: 1. Start up Neo4 (sudo service neo4j start) 2. Wait one minute, then confirm Neo4j is running (sudo service neo4j status) 3. Use a browser to connect to Neo4j via HTTP on port 7474. You should see a username/password authentication form. 4. Fill in "neo4j" and "neo4j" for username and password, respectively, and submit the form. You should be immediately prompted to set a new password. At that time, type in our "usual" Neo4j password (you'll have to enter it twice). 5. When you submit the form, Neo4j should be running and it should now have the correct password set. +## Errors in Extraction rules + +### Role exists error +Occasionally, when a database needs to be re-extracted, the error `ERROR: role "jjyang" already exists` occurs. +If the following is not in the extraction script, add it to the line above where the role is created. +``` +sudo -u postgres psql -c "DROP ROLE IF EXISTS ${role}" +``` + # For Developers This section has some guidelines for the development team for the KG2 build system. diff --git a/Snakefile-conversion b/Snakefile-conversion index 4b642eae..94f69afb 100644 --- a/Snakefile-conversion +++ b/Snakefile-conversion @@ -169,8 +169,10 @@ rule DrugCentral_Conversion: validation = config['VALIDATION_PLACEHOLDER'] output: config['DRUGCENTRAL_OUTPUT_FILE'] + log: + config['BUILD_DIR'] + "/drugcentral/drugcentral-mysql-to-kg-json" + config['TEST_SUFFIX'] + ".log" shell: - config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/drugcentral_json_to_kg_json.py " + config['TEST_ARG'] + " {input.real} {output}" + config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/drugcentral_json_to_kg_json.py " + config['TEST_ARG'] + " {input.real} {output} > {log} 2>&1" rule IntAct_Conversion: input: diff --git a/extract-drugcentral.sh b/extract-drugcentral.sh index 302bf208..dcda476d 100755 --- a/extract-drugcentral.sh +++ b/extract-drugcentral.sh @@ -36,6 +36,7 @@ role="jjyang" ${curl_get} ${source} > ${download_filename} sudo -u postgres psql -c "DROP DATABASE IF EXISTS ${drugcentral_database}" sudo -u postgres psql -c "CREATE DATABASE ${drugcentral_database}" +sudo -u postgres psql -c "DROP ROLE IF EXISTS ${role}" sudo -u postgres psql -c "CREATE ROLE ${role}" gunzip -c ${download_filename} | sudo -u postgres psql -v ON_ERROR_STOP=1 ${drugcentral_database} sudo -u postgres psql -c "GRANT ALL PRIVILEGES ON DATABASE ${drugcentral_database} TO ${user}" diff --git a/kg2-versions.md b/kg2-versions.md index f40fa922..b49d9874 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -9,7 +9,7 @@ Issues: - Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) - Issue [#221](https://github.com/RTXteam/RTX-KG2/issues/221) - Issue [#222](https://github.com/RTXteam/RTX-KG2/issues/222) -- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236 +- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238 Build info: - Biolink Model version: 2.4.2 From 8c46b775c914381f6ebecb61ec9f197906eab343 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 22 Sep 2022 11:29:03 -0700 Subject: [PATCH 063/127] #237 Fixing psql --- extract-drugcentral.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/extract-drugcentral.sh b/extract-drugcentral.sh index dcda476d..c836ab12 100755 --- a/extract-drugcentral.sh +++ b/extract-drugcentral.sh @@ -38,7 +38,8 @@ sudo -u postgres psql -c "DROP DATABASE IF EXISTS ${drugcentral_database}" sudo -u postgres psql -c "CREATE DATABASE ${drugcentral_database}" sudo -u postgres psql -c "DROP ROLE IF EXISTS ${role}" sudo -u postgres psql -c "CREATE ROLE ${role}" -gunzip -c ${download_filename} | sudo -u postgres psql -v ON_ERROR_STOP=1 ${drugcentral_database} +# gunzip -c ${download_filename} | sudo -u postgres psql -v ON_ERROR_STOP=1 ${drugcentral_database} +gunzip -c ${download_filename} | psql ${drugcentral_database} sudo -u postgres psql -c "GRANT ALL PRIVILEGES ON DATABASE ${drugcentral_database} TO ${user}" sudo -u postgres psql -d ${drugcentral_database} -c "GRANT ALL PRIVILEGES ON ALL TABLES IN SCHEMA public TO ${user}" From 42bcd17ad4d40a24076afe203642cc2f48a0d0b3 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 22 Sep 2022 11:56:37 -0700 Subject: [PATCH 064/127] #237 drugcentral_json_to_kg_json.py --- drugcentral_json_to_kg_json.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/drugcentral_json_to_kg_json.py b/drugcentral_json_to_kg_json.py index f35d56aa..d9a494c2 100755 --- a/drugcentral_json_to_kg_json.py +++ b/drugcentral_json_to_kg_json.py @@ -248,10 +248,12 @@ def make_nodes(drugcentral_ids, update_date): if drug_central_id not in reformatted_json: reformatted_json[drug_central_id] = dict() reformatted_json[drug_central_id]['synonyms'] = [] - if name_row['preferred_name'] == "1": - reformatted_json[drug_central_id]['name'] = name - else: - reformatted_json[drug_central_id]['synonyms'].append(name) + # I'm not sure what to do with the "preferred name" condition since there aren't any synonyms that I see + # if name_row['preferred_name'] == "1": + # reformatted_json[drug_central_id]['name'] = name + # else: + # reformatted_json[drug_central_id]['synonyms'].append(name) + reformatted_json[drug_central_id]['name'] = name for node_id in reformatted_json: synonyms = reformatted_json[node_id]['synonyms'] name = reformatted_json[node_id]['name'] From 639a62a849b247274df05d7bcc1a840d2dc0dab9 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 22 Sep 2022 12:47:37 -0700 Subject: [PATCH 065/127] #230 Correcting API call --- query_kegg.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/query_kegg.py b/query_kegg.py index 38349554..3fa2ed22 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -10,11 +10,12 @@ import datetime import argparse import kg2_util +import requests __author__ = 'Erica Wood' __copyright__ = 'Oregon State University' -__credits__ = ['Stephen Ramsey', 'Erica Wood', 'Deqing Qu'] +__credits__ = ['Stephen Ramsey', 'Erica Wood', 'Deqing Qu', 'Liliana Acevedo'] __license__ = 'MIT' __version__ = '0.1.0' __maintainer__ = '' @@ -87,7 +88,9 @@ def run_queries(): get_base_query = "http://rest.kegg.jp/get/" for query in info_queries: info_dict = {} - for results in send_query(query).split('\n'): + site_request = requests.get(query) + site_response = str(site_request.content) + for results in site_response.split('\n'): if len(results) < 1: continue results = results.strip('kegg').strip().split() @@ -96,7 +99,9 @@ def run_queries(): info_dict['update_date'] = results[2] + '-' + results[3] results_dict['info'] = info_dict for query in list_queries: - for results in send_query(query).split('\n'): + site_request = requests.get(query) + site_response = str(site_request.content) + for results in site_response.split('\n'): if len(results) < 1: continue results = results.split('\t') From 62b7e4f14c5431231e3f04258e4f08a61f4cd4e1 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 22 Sep 2022 13:50:31 -0700 Subject: [PATCH 066/127] #230 query_kegg.py --- query_kegg.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/query_kegg.py b/query_kegg.py index 3fa2ed22..a96532e2 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -104,13 +104,15 @@ def run_queries(): for results in site_response.split('\n'): if len(results) < 1: continue - results = results.split('\t') + results = results.split('\\t') results_dict[results[0]] = {'name': results[1]} for query in conv_queries: - for results in send_query(query).split('\n'): + site_request = requests.get(query) + site_response = str(site_request.content) + for results in site_response.split('\n'): if len(results) < 1: continue - results = results.split('\t') + results = results.split('\\t') results_dict[results[1]]['eq_id'] = results[0] kegg_ids = len(results_dict.keys()) get_count = 0 From 98bab98fac51c01c2b2a9e6fd8891e085aedb5be Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 22 Sep 2022 18:56:08 -0700 Subject: [PATCH 067/127] #230 hacky fixes to get this running --- query_kegg.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/query_kegg.py b/query_kegg.py index a96532e2..7b89c00e 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -104,16 +104,24 @@ def run_queries(): for results in site_response.split('\n'): if len(results) < 1: continue + # quick hack for a weird issue + if results.startswith('b'): + results = results[2:] results = results.split('\\t') results_dict[results[0]] = {'name': results[1]} for query in conv_queries: site_request = requests.get(query) site_response = str(site_request.content) - for results in site_response.split('\n'): + for results in site_response.split('\\n'): if len(results) < 1: continue - results = results.split('\\t') - results_dict[results[1]]['eq_id'] = results[0] + # quick hack for a weird issue + if results.startswith('b'): + results = results[2:] + results = results.split('\t') + if len(results) > 1: + results_dict[results[1]] = {} + results_dict[results[1]]['eq_id'] = results[0] kegg_ids = len(results_dict.keys()) get_count = 0 for kegg_id in results_dict: From 102d3055b61814274b6de4919a4e53ce29473369 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 26 Sep 2022 15:49:26 -0700 Subject: [PATCH 068/127] #226 #236 --- filter_kg_and_remap_predicates.py | 39 ++++++++++++-- kg2_util.py | 4 +- ont-load-inventory-test.yaml | 84 +++++++++++++++---------------- ont-load-inventory.yaml | 2 +- predicate-remap.yaml | 5 ++ 5 files changed, 84 insertions(+), 50 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 97073e8c..ca24b175 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -52,6 +52,24 @@ def make_arg_parser(): return arg_parser +def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_object_aspect=None, + qualified_object_direction=None): + value_list = edge_key_value.split('---') + assert len(value_list) == 4 + if qualified_object_direction is None: + qualified_object_direction = "None" + if qualified_object_aspect is None: + qualified_object_aspect = "None" + if qualified_predicate is None: + qualified_predicate = "None" + value_list.insert(2, qualified_object_direction) + value_list.insert(2, qualified_object_aspect) + value_list.insert(2, qualified_predicate) + new_edge_id = "---".join(value_list) + + return new_edge_id + + if __name__ == '__main__': args = make_arg_parser().parse_args() predicate_remap_file_name = args.predicateRemapYaml @@ -108,7 +126,7 @@ def make_arg_parser(): knowledge_source_curies_not_in_config_nodes.add(knowledge_source) else: infores_curie = infores_curie_dict['infores_curie'] - node_dict['knowledge_source'] = infores_curie + node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict edge_ctr = 0 @@ -125,7 +143,7 @@ def make_arg_parser(): original_predicate_label = edge_dict['relation_label'] predicate_label = original_predicate_label - original_predicate_curie = edge_dict['original_predicate'] + original_predicate_curie = edge_dict['source_predicate'] predicate_curie = original_predicate_curie if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: @@ -155,10 +173,16 @@ def make_arg_parser(): operation_not_allowed[predicate_curie] = pred_remap_info['operation'] qualified_predicate_curie = pred_remap_info.get('qualified_predicate', None) - qualifiers_dict = pred_remap_info.get('qualifiers', None) + edge_dict['qualified_predicate'] = qualified_predicate_curie + # Convert the qualifiers to a dict for easier use + qualifiers_list = pred_remap_info.get('qualifiers', None) + qualifiers_dict = {} - if qualifiers_dict is not None: - edge_dict['qualified_predicate'] = qualified_predicate_curie + if qualifiers_list is not None: + for item in qualifiers_list: + qualifier = list(item.keys())[0] + value = item[qualifier] + qualifiers_dict[qualifier] = value qualified_predicate_object_aspect = qualifiers_dict.get('object aspect', None) qualified_predicate_object_direction = qualifiers_dict.get('object direction', None) if qualified_predicate_object_aspect is not None: @@ -224,6 +248,11 @@ def make_arg_parser(): existing_edge['publications_info'].update(edge_dict['publications_info']) else: new_edges[edge_key] = edge_dict + + edge_id = update_edge_id(new_edges[edge_key]['id'], qualified_predicate_curie, qualified_predicate_object_aspect, + qualified_predicate_object_direction) + new_edges[edge_key]['id'] = edge_id + # Releasing some memory del graph['edges'] del graph['nodes'] diff --git a/kg2_util.py b/kg2_util.py index 09f26ea7..ca8e8915 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -691,7 +691,7 @@ def make_node(id: str, def make_edge_key(edge_dict: dict): return edge_dict['subject'] + '---' + \ - edge_dict['original_predicate'] + '---' + \ + edge_dict['source_predicate'] + '---' + \ (edge_dict['qualified_predicate'] if edge_dict['qualified_predicate'] is not None else 'None') + \ '---' + \ (edge_dict['qualified_object_aspect'] if edge_dict['qualified_object_aspect'] is not None else 'None') + \ @@ -712,7 +712,7 @@ def make_edge(subject_id: str, edge = {'subject': subject_id, 'object': object_id, 'relation_label': relation_label, - 'original_predicate': relation_curie, + 'source_predicate': relation_curie, 'qualified_predicate': None, 'qualified_object_aspect': None, 'qualified_object_direction': None, diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index 24d2f271..b3367e40 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -3,11 +3,11 @@ file: biolink-model.owl.ttl download: true title: Biolink meta-model -- # maps to CURIE prefix: UMLSSC (the trailling slash here is important:) - url: http://purl.bioontology.org/ontology/STY/ - file: umls-semantictypes.ttl - download: false - title: UMLS Semantic Types +# - # maps to CURIE prefix: UMLSSC (the trailling slash here is important:) +# url: http://purl.bioontology.org/ontology/STY/ +# file: umls-semantictypes.ttl +# download: false +# title: UMLS Semantic Types # - # maps to CURIE prefix: ATC # download: false # file: umls-atc.ttl @@ -18,21 +18,21 @@ # file: umls-cpt.ttl # title: Current Procedural Terminology # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/CPT -- # maps to CURIE prefix DRUGBANK - download: false - file: umls-drugbank.ttl - title: DrugBank - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/DRUGBANK +# - # maps to CURIE prefix DRUGBANK +# download: false +# file: umls-drugbank.ttl +# title: DrugBank +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/DRUGBANK # - # maps to CURIE prefix FMA # download: false # file: umls-fma.ttl # title: Foundational Model of Anatomy # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/FMA -- # maps to CURIE prefix GO - download: false - file: umls-go.ttl - title: Gene Ontology - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO +# - # maps to CURIE prefix GO +# download: false +# file: umls-go.ttl +# title: Gene Ontology +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO # - # maps to CURIE prefix HCPCS # download: false # file: umls-hcpcs.ttl @@ -43,11 +43,11 @@ # file: umls-hcpt.ttl # title: CPT in HCPCS # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HCPT -- # maps to CURIE prefix HGNC - download: false - file: umls-hgnc.ttl - title: HUGO Gene Nomenclature Committee - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC +# - # maps to CURIE prefix HGNC +# download: false +# file: umls-hgnc.ttl +# title: HUGO Gene Nomenclature Committee +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC # - # maps to CURIE prefix umls # download: false # file: umls-hl7.ttl @@ -88,11 +88,11 @@ # file: umls-lnc.ttl # title: Logical Observation Identifiers Names and Codes # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/LNC -- # maps to CURIE prefix MEDDRA - download: false - file: umls-mdr.ttl - title: MedDRA - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MEDDRA +# - # maps to CURIE prefix MEDDRA +# download: false +# file: umls-mdr.ttl +# title: MedDRA +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MEDDRA # - # maps to CURIE prefix umls # download: false # file: umls-med-rt.ttl @@ -178,10 +178,10 @@ # download: true # title: Basic Formal Ontology - # maps to CURIE prefix: GO - url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl - file: go-plus.owl - title: Gene Ontology - download: true + # url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl + # file: go-plus.owl + # title: Gene Ontology + # download: true # - # maps to CURIE prefix: RO # url: http://purl.obolibrary.org/obo/ro.owl # file: ro.owl @@ -208,20 +208,20 @@ # download: true # title: Dictyostelium discoideum anatomy - - url: http://purl.obolibrary.org/obo/cl.owl - file: cl.owl - download: true - title: Cell Ontology + # url: http://purl.obolibrary.org/obo/cl.owl + # file: cl.owl + # download: true + # title: Cell Ontology # - # url: http://purl.obolibrary.org/obo/chebi.owl # file: chebi.owl # download: true # title: Chemical Entities of Biological Interest # - -# url: http://purl.obolibrary.org/obo/foodon.owl -# file: foodon.owl -# download: true -# title: FOODON (Food Ontology) + url: http://purl.obolibrary.org/obo/foodon.owl + file: foodon.owl + download: false + title: FOODON (Food Ontology) # - # url: http://data.bioontology.org/ontologies/ORDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb # file: ordo.owl @@ -237,11 +237,11 @@ # file: bspo.owl # download: true # title: Biological Spatial Ontology -- - url: http://purl.obolibrary.org/obo/hp.owl - file: hp.owl - download: true - title: Human Phenotype Ontology +# - +# url: http://purl.obolibrary.org/obo/hp.owl +# file: hp.owl +# download: true +# title: Human Phenotype Ontology # - # url: http://purl.obolibrary.org/obo/nbo.owl # file: nbo.owl diff --git a/ont-load-inventory.yaml b/ont-load-inventory.yaml index 0317af8c..647aa8b1 100644 --- a/ont-load-inventory.yaml +++ b/ont-load-inventory.yaml @@ -220,7 +220,7 @@ - url: http://purl.obolibrary.org/obo/foodon.owl file: foodon.owl - download: true + download: false title: FOODON (Food Ontology) - url: http://data.bioontology.org/ontologies/ORDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb diff --git a/predicate-remap.yaml b/predicate-remap.yaml index 5134fe95..58b74b97 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -5462,6 +5462,11 @@ owl:topObjectProperty: rdf:type: operation: keep core_predicate: biolink:related_to +rdfs:negatively_regulates: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased rdfs:subClassOf: operation: keep core_predicate: biolink:subclass_of From a4b5686758064ae754c15e9ee5338a1a234616e9 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 27 Sep 2022 10:21:27 -0700 Subject: [PATCH 069/127] #226 #236 multi-ont --- multi_ont_to_json_kg.py | 7 +++++-- ont-load-inventory-test.yaml | 14 +++++++------- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/multi_ont_to_json_kg.py b/multi_ont_to_json_kg.py index e1950dbd..3472423e 100755 --- a/multi_ont_to_json_kg.py +++ b/multi_ont_to_json_kg.py @@ -56,8 +56,11 @@ def delete_ontobio_cachier_caches(): - kg2_util.purge("~/.cachier", ".ontobio*") - kg2_util.purge("~/.cachier", ".prefixcommons*") + # This is causing issues in the current build because these files don't exist. + # Temporarily commenting out to avoid error. + # kg2_util.purge("~/.cachier", ".ontobio*") + # kg2_util.purge("~/.cachier", ".prefixcommons*") + pass def load_ont_file_return_ontology_and_metadata(file_name: str, diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index b3367e40..a0857c62 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -110,9 +110,9 @@ # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH # - # maps to CURIE prefix umls # download: false -# file: umls-mth.ttl -# title: Metathesaurus Names -# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH + file: umls-mth.ttl + title: Metathesaurus Names + url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH # - # maps to CURIE prefix NCBITaxon # download: false # file: umls-ncbi.ttl @@ -218,10 +218,10 @@ # download: true # title: Chemical Entities of Biological Interest # - - url: http://purl.obolibrary.org/obo/foodon.owl - file: foodon.owl - download: false - title: FOODON (Food Ontology) + # url: http://purl.obolibrary.org/obo/foodon.owl + # file: foodon.owl + # download: false + # title: FOODON (Food Ontology) # - # url: http://data.bioontology.org/ontologies/ORDO/submissions/15/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb # file: ordo.owl From 43993576bd853b39564ab18496a71611bc3357de Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 27 Sep 2022 11:39:59 -0700 Subject: [PATCH 070/127] #236 Trimming test inventory --- ont-load-inventory-test.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index a0857c62..e0af6a5b 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -110,9 +110,9 @@ # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MSH # - # maps to CURIE prefix umls # download: false - file: umls-mth.ttl - title: Metathesaurus Names - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH + # file: umls-mth.ttl + # title: Metathesaurus Names + # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/MTH # - # maps to CURIE prefix NCBITaxon # download: false # file: umls-ncbi.ttl From 03d13405321f92043d03fa22d9141679173b6245 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 28 Sep 2022 11:33:38 -0700 Subject: [PATCH 071/127] #240 Original predicate -> source predicate --- Snakefile-post-etl | 2 ++ ont-load-inventory-test.yaml | 4 ++-- report_stats_on_json_kg.py | 6 +++--- report_stats_on_neo4j_kg.py | 14 +++++++------- 4 files changed, 14 insertions(+), 12 deletions(-) diff --git a/Snakefile-post-etl b/Snakefile-post-etl index d6909070..f3f3f7aa 100644 --- a/Snakefile-post-etl +++ b/Snakefile-post-etl @@ -53,6 +53,8 @@ rule Stats: config['FINAL_OUTPUT_FILE_FULL'] output: config['REPORT_FILE_FULL'] + log: + config['BUILD_DIR'] + "/report_stats_on_json_kg" + config['TEST_SUFFIX'] + ".log" shell: config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/report_stats_on_json_kg.py {input} {output}" diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index e0af6a5b..44db3467 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -177,7 +177,7 @@ # file: bfo.owl # download: true # title: Basic Formal Ontology -- # maps to CURIE prefix: GO +#- maps to CURIE prefix: GO # url: http://purl.obolibrary.org/obo/go/extensions/go-plus.owl # file: go-plus.owl # title: Gene Ontology @@ -207,7 +207,7 @@ # file: ddanat.owl # download: true # title: Dictyostelium discoideum anatomy -- +#- # url: http://purl.obolibrary.org/obo/cl.owl # file: cl.owl # download: true diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 4a220501..8d827997 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -92,7 +92,7 @@ def count_edges_by_source(edges: list): def count_edges_by_predicate_curie(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' return collections.Counter([edge[curie_field] for edge in edges]) @@ -102,12 +102,12 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' unique_relation_curies = set([edge[curie_field] for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) diff --git a/report_stats_on_neo4j_kg.py b/report_stats_on_neo4j_kg.py index cdc89846..d14090e2 100755 --- a/report_stats_on_neo4j_kg.py +++ b/report_stats_on_neo4j_kg.py @@ -109,27 +109,27 @@ def count_edges_by_source(session): def count_edges_by_predicate_curie(session): - res = session.run('MATCH ()-[r]->()RETURN r.original_predicate AS Curie,\ - count(r) AS NumberofRelationships ORDER BY r.original_predicate') + res = session.run('MATCH ()-[r]->()RETURN r.source_predicate AS Curie,\ + count(r) AS NumberofRelationships ORDER BY r.source_predicate') return {record[0]: record[1] for record in res.records()} def count_edges_by_predicate_type(session): - res = session.run('MATCH (n)-[r]->() RETURN r.original_predicate_label AS PredicateType,\ - count(r) AS NumberofRelationships ORDER BY r.original_predicate_label') + res = session.run('MATCH (n)-[r]->() RETURN r.source_predicate_label AS PredicateType,\ + count(r) AS NumberofRelationships ORDER BY r.source_predicate_label') return {record[0]: record[1] for record in res.records()} def count_edges_by_predicate_curie_prefix(session): - res = session.run('MATCH ()-[r]->() RETURN DISTINCT split(r.original_predicate,\ + res = session.run('MATCH ()-[r]->() RETURN DISTINCT split(r.source_predicate,\ ":")[0] AS CuriePrefix, count(r) AS NumberofRelationships ORDER BY\ CuriePrefix') return {record[0]: record[1] for record in res.records()} def count_predicates_by_predicate_curie_prefix(session): - res = session.run('MATCH (n)-[r]->() WITH split(r.original_predicate, ":")[0]\ - AS CuriePrefix, count(DISTINCT r.original_predicate_label) AS Count RETURN DISTINCT\ + res = session.run('MATCH (n)-[r]->() WITH split(r.source_predicate, ":")[0]\ + AS CuriePrefix, count(DISTINCT r.source_predicate_label) AS Count RETURN DISTINCT\ CuriePrefix, Count') return {record[0]: record[1] for record in res.records()} From 6d0ccbbd7c4a5875b2bcbc9a57f7038a17035eab Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 28 Sep 2022 11:47:38 -0700 Subject: [PATCH 072/127] #240 Adding log --- Snakefile-post-etl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Snakefile-post-etl b/Snakefile-post-etl index f3f3f7aa..53f893af 100644 --- a/Snakefile-post-etl +++ b/Snakefile-post-etl @@ -56,7 +56,7 @@ rule Stats: log: config['BUILD_DIR'] + "/report_stats_on_json_kg" + config['TEST_SUFFIX'] + ".log" shell: - config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/report_stats_on_json_kg.py {input} {output}" + config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/report_stats_on_json_kg.py {input} {output} > {log} 2>&1" rule Simplify: input: From c7a7aba1357a1ab15826ddfdab1e4f1aadf8354a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 28 Sep 2022 12:31:22 -0700 Subject: [PATCH 073/127] #240 Mapping to curie field --- kg_json_to_tsv.py | 7 +++++-- report_stats_on_json_kg.py | 10 +++++----- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index ed11410a..55af675e 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -82,12 +82,15 @@ def check_all_edges_have_same_set(edgekeys_list): "knowledge_source", "publications", "publications_info", - "original_predicate", + "source_predicate", "subject", "update_date", "predicate", "predicate_label", - "id"] + "id", + "qualified_predicate", + "qualified_object_aspect", + "qualified_object_direction"] for edgelabel in edgekeys_list: if edgelabel not in supported_ls: raise ValueError("relation_label not in supported list: " + edgelabel) diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 8d827997..74312ee1 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -92,8 +92,8 @@ def count_edges_by_source(edges: list): def count_edges_by_predicate_curie(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' - return collections.Counter([edge[curie_field] for edge in edges]) + curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + return collections.Counter([edge.get(curie_field, None) for edge in edges]) def count_edges_by_predicate_type(edges: list): @@ -102,12 +102,12 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' - return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) + curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + return collections.Counter([get_prefix_from_curie_id(edge.get(curie_field, None)) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' unique_relation_curies = set([edge[curie_field] for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From 24d7c8cccbcd481bebaa597874d7b478120aa363 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 28 Sep 2022 19:56:01 -0700 Subject: [PATCH 074/127] #240 Working on curie field issue --- report_stats_on_json_kg.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 74312ee1..0366915e 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -103,12 +103,12 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' - return collections.Counter([get_prefix_from_curie_id(edge.get(curie_field, None)) for edge in edges]) + return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' - unique_relation_curies = set([edge[curie_field] for edge in edges]) + unique_relation_curies = set([edge.get(curie_field) for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From 3d29a4d1140e47c64dc971e34910d0668d8ad623 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 30 Sep 2022 09:28:25 -0700 Subject: [PATCH 075/127] #226 Fixing some issues that came up in build --- filter_kg_and_remap_predicates.py | 12 ++++++++---- predicate-remap.yaml | 13 ++++++++----- report_stats_on_json_kg.py | 19 +++++++++++++++---- 3 files changed, 31 insertions(+), 13 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index ca24b175..cb31d232 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -143,6 +143,8 @@ def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_obje original_predicate_label = edge_dict['relation_label'] predicate_label = original_predicate_label + if edge_dict.get('source_predicate') is None: + edge_dict['source_predicate'] = edge_dict.pop('original_predicate') original_predicate_curie = edge_dict['source_predicate'] predicate_curie = original_predicate_curie @@ -177,14 +179,16 @@ def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_obje # Convert the qualifiers to a dict for easier use qualifiers_list = pred_remap_info.get('qualifiers', None) qualifiers_dict = {} + qualified_predicate_object_aspect = None + qualified_predicate_object_direction = None if qualifiers_list is not None: for item in qualifiers_list: qualifier = list(item.keys())[0] value = item[qualifier] qualifiers_dict[qualifier] = value - qualified_predicate_object_aspect = qualifiers_dict.get('object aspect', None) - qualified_predicate_object_direction = qualifiers_dict.get('object direction', None) + qualified_predicate_object_aspect = qualifiers_dict.get('object aspect') + qualified_predicate_object_direction = qualifiers_dict.get('object direction') if qualified_predicate_object_aspect is not None: edge_dict['qualified_object_aspect'] = qualified_predicate_object_aspect if qualified_predicate_object_direction is not None: @@ -234,9 +238,9 @@ def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_obje predicate_qualifier = "" if qualifiers_dict is not None: - if qualified_predicate_object_aspect: + if qualified_predicate_object_aspect is not None: predicate_qualifier = " /// " + qualified_predicate_object_aspect - if qualified_predicate_object_direction: + if qualified_predicate_object_direction is not None: predicate_qualifier += f" /// {qualified_predicate_object_direction}" edge_key = f'{edge_subject} {predicate} {predicate_qualifier} /// {edge_object}' diff --git a/predicate-remap.yaml b/predicate-remap.yaml index 58b74b97..1be6af1d 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -332,11 +332,14 @@ CHEMBL.MECHANISM:releasing_agent: qualifiers: - object_aspect: expression - object_direction: increased -#CHEMBL.MECHANISM:rnai_inhibitor: -# operation: keep -# core_predicate: regulates -# qualifiers: -# - object_direction: decreased +CHEMBL.MECHANISM:rnai_inhibitor: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased +CHEMBL.MECHANISM:vaccine_antigen: + operation: keep + core_predicate: biolink:related_to CHEMBL.MECHANISM:sequestering_agent: operation: keep core_predicate: biolink:physically_interacts_with diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 0366915e..97b54565 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -92,7 +92,10 @@ def count_edges_by_source(edges: list): def count_edges_by_predicate_curie(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' + for edge in edges: + if edge.get(curie_field) == None: + edge[curie_field] = edge.pop('original_predicate') return collections.Counter([edge.get(curie_field, None) for edge in edges]) @@ -102,13 +105,21 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' + for edge in edges: + if edge.get(curie_field) is None: + edge[curie_field] = edge.pop('original_predicate') return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): - curie_field = 'original_predicate' if not args.use_simplified_predicates else 'predicate' - unique_relation_curies = set([edge.get(curie_field) for edge in edges]) + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' + unique_relation_curies = set() + for edge in edges: + if edge.get(curie_field) is None: + curie_field = 'original_predicate' + unique_relation_curies.add(edge.get(curie_field)) + #unique_relation_curies = set([edge.get(curie_field) for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From c7c5ec32661ad2e63f8a8ff523d9faae0919a1e3 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 30 Sep 2022 13:17:14 -0700 Subject: [PATCH 076/127] #226 Ontologies for test build 2 --- ont-load-inventory-test.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index 44db3467..be3955fa 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -8,11 +8,11 @@ # file: umls-semantictypes.ttl # download: false # title: UMLS Semantic Types -# - # maps to CURIE prefix: ATC -# download: false -# file: umls-atc.ttl -# title: Anatomical Therapeutic Chemical Classification System -# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC +- # maps to CURIE prefix: ATC + download: false + file: umls-atc.ttl + title: Anatomical Therapeutic Chemical Classification System + url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC # - # maps to CURIE prefix CPT # download: false # file: umls-cpt.ttl @@ -28,11 +28,11 @@ # file: umls-fma.ttl # title: Foundational Model of Anatomy # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/FMA -# - # maps to CURIE prefix GO -# download: false -# file: umls-go.ttl -# title: Gene Ontology -# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO +- # maps to CURIE prefix GO + download: false + file: umls-go.ttl + title: Gene Ontology + url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO # - # maps to CURIE prefix HCPCS # download: false # file: umls-hcpcs.ttl From 79c065898019d0e06e1174229f5fbdbb91ab1dc0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 30 Sep 2022 13:42:36 -0700 Subject: [PATCH 077/127] #226 Refactoring to use source_predicate --- README.md | 4 +-- drugcentral_json_to_kg_json.py | 54 +++++++++++++++++----------------- misc-tools/modify_edges_tsv.py | 52 ++++++++++++++++---------------- report_stats_on_json_kg.py | 2 +- 4 files changed, 56 insertions(+), 56 deletions(-) diff --git a/README.md b/README.md index ac5f3e7e..eba83ee6 100644 --- a/README.md +++ b/README.md @@ -991,10 +991,10 @@ the following keys: present) no consitent format, unfortunately; it is usually not `null`. - `id`: a concatenated string of other edge attributes that uniquely identifies the edge. it follows the format `subject---relation---object---provided_by`. - - `original_predicate`: a CURIE ID for the relation as reported by the upstream + - `source_predicate`: a CURIE ID for the relation as reported by the upstream database source. - `provided_by`: _deprecated_. Refer to `knowledge_source`. - - `relation`: _deprecated_. See `original_predicate`. + - `relation`: _deprecated_. See `source_predicate`. ### `publications_info` slot diff --git a/drugcentral_json_to_kg_json.py b/drugcentral_json_to_kg_json.py index d9a494c2..f4a76463 100755 --- a/drugcentral_json_to_kg_json.py +++ b/drugcentral_json_to_kg_json.py @@ -87,17 +87,17 @@ def process_external_ids(external_ids, update_date, test_mode): 'MMSL': None, 'UMLSCUI': kg2_util.CURIE_PREFIX_UMLS, 'ChEMBL_ID': kg2_util.CURIE_PREFIX_CHEMBL_COMPOUND} - for original_predicate in external_ids: + for source_predicate in external_ids: edge_count += 1 if test_mode and edge_count > TEST_MODE_EDGE_COUNT: break - prefix = prefix_map.get(original_predicate['id_type'], None) + prefix = prefix_map.get(source_predicate['id_type'], None) if prefix is None or \ - len(original_predicate['struct_id']) < 1 or \ - len(original_predicate['identifier']) < 1: + len(source_predicate['struct_id']) < 1 or \ + len(source_predicate['identifier']) < 1: continue - drug_central_id = format_drugcentral_id(original_predicate['struct_id']) - external_id = prefix + ':' + original_predicate['identifier'] + drug_central_id = format_drugcentral_id(source_predicate['struct_id']) + external_id = prefix + ':' + source_predicate['identifier'] predicate = kg2_util.EDGE_LABEL_BIOLINK_SAME_AS edge = format_edge(drug_central_id, external_id, @@ -110,14 +110,14 @@ def process_external_ids(external_ids, update_date, test_mode): def process_omop_relations(omop_relations, update_date, test_mode): edges = [] edge_count = 0 - for original_predicate in omop_relations: + for source_predicate in omop_relations: edge_count += 1 if test_mode and edge_count > TEST_MODE_EDGE_COUNT: break - umls_id = original_predicate['umls_cui'] - doid_id = original_predicate['doid'] - drug_central_id = original_predicate['struct_id'] - predicate = original_predicate['relationship_name'].replace(' ', '_') + umls_id = source_predicate['umls_cui'] + doid_id = source_predicate['doid'] + drug_central_id = source_predicate['struct_id'] + predicate = source_predicate['relationship_name'].replace(' ', '_') if (len(doid_id) < 1 and len(umls_id) < 1) or \ len(drug_central_id) < 1 or \ len(predicate) < 1: @@ -136,15 +136,15 @@ def process_omop_relations(omop_relations, update_date, test_mode): def process_faers_data(faers_edges, update_date, test_mode): edges = [] edge_count = 0 - for original_predicate in faers_edges: + for source_predicate in faers_edges: edge_count += 1 if test_mode and edge_count > TEST_MODE_EDGE_COUNT: break - meddra_id = original_predicate['meddra_code'] - drug_central_id = original_predicate['struct_id'] + meddra_id = source_predicate['meddra_code'] + drug_central_id = source_predicate['struct_id'] predicate = 'has_faers' - likelihood = float(original_predicate['llr']) - likelihood_threshold = float(original_predicate['llr_threshold']) + likelihood = float(source_predicate['llr']) + likelihood_threshold = float(source_predicate['llr_threshold']) if likelihood < likelihood_threshold: continue if len(meddra_id) < 1 or len(drug_central_id) < 1: @@ -159,12 +159,12 @@ def process_faers_data(faers_edges, update_date, test_mode): def process_atc_codes(atc_codes, update_date, test_mode): edges = [] edge_count = 0 - for original_predicate in atc_codes: + for source_predicate in atc_codes: edge_count += 1 if test_mode and edge_count > TEST_MODE_EDGE_COUNT: break - atc_id = original_predicate['atc_code'] - drug_central_id = original_predicate['struct_id'] + atc_id = source_predicate['atc_code'] + drug_central_id = source_predicate['struct_id'] if len(atc_id) < 1 or len(drug_central_id) < 1: continue atc_id = kg2_util.CURIE_PREFIX_ATC + ':' + atc_id @@ -183,24 +183,24 @@ def format_publication(url): def process_bioactivities(bioactivities, update_date, test_mode): edges = [] edge_count = 0 - for original_predicate in bioactivities: + for source_predicate in bioactivities: edge_count += 1 if test_mode and edge_count > TEST_MODE_EDGE_COUNT: break publications = [] - action_type = original_predicate['action_type'].lower().replace(' ', '_') - moa_source = original_predicate['moa_source'] - moa_source_url = original_predicate['moa_source_url'] - drug_central_id = format_drugcentral_id(original_predicate['struct_id']) - act_source = original_predicate['act_source'] - act_source_url = original_predicate['act_source_url'] + action_type = source_predicate['action_type'].lower().replace(' ', '_') + moa_source = source_predicate['moa_source'] + moa_source_url = source_predicate['moa_source_url'] + drug_central_id = format_drugcentral_id(source_predicate['struct_id']) + act_source = source_predicate['act_source'] + act_source_url = source_predicate['act_source_url'] if len(act_source_url) > 0 and act_source == "SCIENTIFIC LITERATURE": publications.append(format_publication(act_source_url)) if len(moa_source_url) > 0 and moa_source == "SCIENTIFIC LITERATURE": publications.append(format_publication(moa_source_url)) if len(action_type) < 1: continue - for accession in original_predicate['accession'].split('|'): + for accession in source_predicate['accession'].split('|'): if len(accession) < 1: continue uniprot_id = kg2_util.CURIE_PREFIX_UNIPROT + ':' + accession diff --git a/misc-tools/modify_edges_tsv.py b/misc-tools/modify_edges_tsv.py index 65ad4d0a..8f7d2074 100644 --- a/misc-tools/modify_edges_tsv.py +++ b/misc-tools/modify_edges_tsv.py @@ -35,33 +35,33 @@ PREDICATE_HEADER_KEY_1 = 'predicate' PREDICATE_HEADER_KEY_2 = 'predicate:TYPE' PREDICATE_LABEL_HEADER_KEY = 'predicate_label' -ORIGINAL_PREDICATE_HEADER_KEY = 'original_predicate' -ORIGINAL_PREDICATE_LABEL_HEADER_KEY = 'original_predicate_label' +SOURCE_PREDICATE_HEADER_KEY = 'source_predicate' +SOURCE_PREDICATE_LABEL_HEADER_KEY = 'source_predicate_label' INFORES_HEADER_KEY = 'knowledge_source:string[]' REPLACEMENT_KEY_FORMAT = '-\n' \ ' detection:\n' \ ' subject_start: null\n' \ ' object_start: null\n' \ - ' original_predicate: null\n' \ + ' source_predicate: null\n' \ ' predicate: null\n' \ ' infores_curie: null\n' \ ' new_values:\n' \ ' predicate: null\n' \ - ' original_predicate: null\n' \ - ' original_predicate_label: null\n' \ + ' source_predicate: null\n' \ + ' source_predicate_label: null\n' \ ' infores_curie: null' REPLACEMENT_KEY_EXAMPLE = '-\n' \ ' detection:\n' \ ' subject_start: "DrugCentral:"\n' \ ' object_start: "ATC:"\n' \ - ' original_predicate: null\n' \ + ' source_predicate: null\n' \ ' predicate: biolink:same_as\n' \ ' infores_curie: infores:drugcentral\n' \ ' new_values:\n' \ ' predicate: biolink:close_match\n' \ - ' original_predicate: DrugCentral:struct2atc\n' \ - ' original_predicate_label: struct2atc\n' \ + ' source_predicate: DrugCentral:struct2atc\n' \ + ' source_predicate_label: struct2atc\n' \ ' infores_curie: null' @@ -85,9 +85,9 @@ def check_edge(replacement_key, subject_id, object_id, infores, relation, predic object_start = detection.get('object_start', None) old_infores = detection.get('infores_curie', None) new_infores = new_values.get('infores_curie', None) - old_original_predicate = detection.get('original_predicate', None) - new_original_predicate = new_values.get('original_predicate', None) - new_original_predicate_label = new_values.get('original_predicate_label', None) + old_source_predicate = detection.get('source_predicate', None) + new_source_predicate = new_values.get('source_predicate', None) + new_source_predicate_label = new_values.get('source_predicate_label', None) old_predicate = detection.get('predicate', None) new_predicate = new_values.get('predicate', None) @@ -97,19 +97,19 @@ def check_edge(replacement_key, subject_id, object_id, infores, relation, predic return False if old_infores is not None and old_infores != infores and infores not in old_infores: return False - if old_original_predicate is not None and old_original_predicate != original_predicate: + if old_source_predicate is not None and old_source_predicate != source_predicate: return False if old_predicate is not None and old_predicate != predicate: return False return_dict = {} if new_predicate is not None: return_dict['predicate'] = new_predicate - if new_original_predicate is not None: - return_dict['original_predicate'] = new_original_predicate - if new_original_predicate_label is not None: - return_dict['original_predicate_label'] = new_original_predicate_label + if new_source_predicate is not None: + return_dict['source_predicate'] = new_source_predicate + if new_source_predicate_label is not None: + return_dict['source_predicate_label'] = new_source_predicate_label else: - return_dict['original_predicate_label'] = new_original_predicate.split(':')[1] + return_dict['source_predicate_label'] = new_source_predicate.split(':')[1] if new_infores is not None: if old_infores is not None: return_dict['infores'] = infores.replace(old_infores, new_infores) @@ -118,11 +118,11 @@ def check_edge(replacement_key, subject_id, object_id, infores, relation, predic return return_dict -def edit_original_predicate(edge, old_edge_id, old_original_predicate, new_value_dict, header): - new_original_predicate = new_value_dict['original_predicate'] - edge[header[EDGE_ID_HEADER_KEY]] = old_edge_id.replace(old_original_predicate, new_original_predicate) - edge[header[ORIGINAL_PREDICATE_HEADER_KEY]] = new_original_predicate - edge[header[ORIGINAL_PREDICATE_LABEL_HEADER_KEY]] = new_value_dict['original_predicate_label'] +def edit_source_predicate(edge, old_edge_id, old_source_predicate, new_value_dict, header): + new_source_predicate = new_value_dict['source_predicate'] + edge[header[EDGE_ID_HEADER_KEY]] = old_edge_id.replace(old_source_predicate, new_source_predicate) + edge[header[SOURCE_PREDICATE_HEADER_KEY]] = new_source_predicate + edge[header[SOURCE_PREDICATE_LABEL_HEADER_KEY]] = new_value_dict['source_predicate_label'] return edge @@ -187,17 +187,17 @@ def process_header_file(header_file): edge_id = edge[header[EDGE_ID_HEADER_KEY]] subject_id = edge[header[SUBJECT_ID_HEADER_KEY]] object_id = edge[header[OBJECT_ID_HEADER_KEY]] - original_predicate = edge[header[ORIGINAL_PREDICATE_HEADER_KEY]] + source_predicate = edge[header[SOURCE_PREDICATE_HEADER_KEY]] infores = edge[header[INFORES_HEADER_KEY]] predicate = edge[header[PREDICATE_HEADER_KEY_1]] checked_edge = False for replacement_key in replacement_keys: - checked_edge_local = check_edge(replacement_key, subject_id, object_id, infores, original_predicate, predicate) + checked_edge_local = check_edge(replacement_key, subject_id, object_id, infores, source_predicate, predicate) if checked_edge_local != False: checked_edge = checked_edge_local if checked_edge != False: - if "original_predicate" in checked_edge: - edge = edit_relation(edge, edge_id, original_predicate, checked_edge, header) + if "source_predicate" in checked_edge: + edge = edit_relation(edge, edge_id, source_predicate, checked_edge, header) if "predicate" in checked_edge: edge = edit_predicate(edge, checked_edge, header) if "infores" in checked_edge: diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 97b54565..22e8c307 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -117,7 +117,7 @@ def count_predicates_by_predicate_curie_prefix(edges: list): unique_relation_curies = set() for edge in edges: if edge.get(curie_field) is None: - curie_field = 'original_predicate' + edge[curie_field] = edge.pop('original_predicate') unique_relation_curies.add(edge.get(curie_field)) #unique_relation_curies = set([edge.get(curie_field) for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From 4ec9213cbc8d8b2af63a93927639ea8790f38c48 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 13 Oct 2022 09:01:45 -0700 Subject: [PATCH 078/127] #239 Adding failing curie to expand only --- curies-to-urls-map.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index 42a1829f..3e05fa5b 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -733,6 +733,8 @@ use_for_expansion_only: Orphanet: http://purl.bioontology.org/ontology/ORDO/ - oboInOwl: http://www.geneontology.org/formats/oboInOwl# + - + OIO: ttp://www.geneontology.org/formats/oboInOwl# - RXCUI: http://purl.bioontology.org/ontology/RXNORM/ - From 531fd09ad47689e9d603516f64160affd10cfd82 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 13 Oct 2022 09:06:30 -0700 Subject: [PATCH 079/127] #239 --- query_kegg.py | 47 +++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/query_kegg.py b/query_kegg.py index 7b89c00e..88bbbac3 100755 --- a/query_kegg.py +++ b/query_kegg.py @@ -89,39 +89,38 @@ def run_queries(): for query in info_queries: info_dict = {} site_request = requests.get(query) - site_response = str(site_request.content) - for results in site_response.split('\n'): + site_response = str(site_request.content)[2:] + if site_response[:2].startswith("b"): + site_response = site_response[2:] + results = site_response.strip().split("\\n") + for result in results: + result = result.strip("kegg").strip().split() if len(results) < 1: continue - results = results.strip('kegg').strip().split() - if results[0] == "Release": - info_dict['version'] = results[1].split('/')[0].strip('+') - info_dict['update_date'] = results[2] + '-' + results[3] + if result[0] == "Release": + info_dict['version'] = result[1].split('/')[0].strip('+') + info_dict['update_date'] = result[2] + '-' + result[3] results_dict['info'] = info_dict for query in list_queries: site_request = requests.get(query) - site_response = str(site_request.content) - for results in site_response.split('\n'): - if len(results) < 1: + site_response = str(site_request.content)[2:] + results = site_response.split("\\n") + for results in results: + result = result.split("\\t") + if len(results) < 2: continue - # quick hack for a weird issue - if results.startswith('b'): - results = results[2:] - results = results.split('\\t') - results_dict[results[0]] = {'name': results[1]} + results_dict[result[0]] = {'name': result[1]} for query in conv_queries: site_request = requests.get(query) - site_response = str(site_request.content) - for results in site_response.split('\\n'): - if len(results) < 1: + site_response = str(site_request.content)[2:] + results = site_response.split("\\n") + for result in results: + if len(result) < 1: continue - # quick hack for a weird issue - if results.startswith('b'): - results = results[2:] - results = results.split('\t') - if len(results) > 1: - results_dict[results[1]] = {} - results_dict[results[1]]['eq_id'] = results[0] + result = result.split('\\t') + if len(result) > 1: + results_dict[result[1]] = {} + results_dict[result[1]]['eq_id'] = result[0] kegg_ids = len(results_dict.keys()) get_count = 0 for kegg_id in results_dict: From c23519d839dc18ffc4c9845157761f5cb69ca11d Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 13 Oct 2022 11:55:06 -0700 Subject: [PATCH 080/127] #239 The error fix is no longer needed --- curies-to-urls-map.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/curies-to-urls-map.yaml b/curies-to-urls-map.yaml index 3e05fa5b..42a1829f 100644 --- a/curies-to-urls-map.yaml +++ b/curies-to-urls-map.yaml @@ -733,8 +733,6 @@ use_for_expansion_only: Orphanet: http://purl.bioontology.org/ontology/ORDO/ - oboInOwl: http://www.geneontology.org/formats/oboInOwl# - - - OIO: ttp://www.geneontology.org/formats/oboInOwl# - RXCUI: http://purl.bioontology.org/ontology/RXNORM/ - From bb02d77f66e93ec92529df22003829c29d4fdee1 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 13 Oct 2022 11:56:35 -0700 Subject: [PATCH 081/127] #239 Changes test inventory to include cl --- ont-load-inventory-test.yaml | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/ont-load-inventory-test.yaml b/ont-load-inventory-test.yaml index be3955fa..90731278 100644 --- a/ont-load-inventory-test.yaml +++ b/ont-load-inventory-test.yaml @@ -8,11 +8,11 @@ # file: umls-semantictypes.ttl # download: false # title: UMLS Semantic Types -- # maps to CURIE prefix: ATC - download: false - file: umls-atc.ttl - title: Anatomical Therapeutic Chemical Classification System - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC +# - # maps to CURIE prefix: ATC +# download: false +# file: umls-atc.ttl +# title: Anatomical Therapeutic Chemical Classification System +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC # - # maps to CURIE prefix CPT # download: false # file: umls-cpt.ttl @@ -28,11 +28,11 @@ # file: umls-fma.ttl # title: Foundational Model of Anatomy # url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/FMA -- # maps to CURIE prefix GO - download: false - file: umls-go.ttl - title: Gene Ontology - url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO +# - # maps to CURIE prefix GO +# download: false +# file: umls-go.ttl +# title: Gene Ontology +# url: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO # - # maps to CURIE prefix HCPCS # download: false # file: umls-hcpcs.ttl @@ -207,11 +207,11 @@ # file: ddanat.owl # download: true # title: Dictyostelium discoideum anatomy -#- - # url: http://purl.obolibrary.org/obo/cl.owl - # file: cl.owl - # download: true - # title: Cell Ontology +- + url: http://purl.obolibrary.org/obo/cl.owl + file: cl.owl + download: true + title: Cell Ontology # - # url: http://purl.obolibrary.org/obo/chebi.owl # file: chebi.owl From 640679be0e360a0841683a6f2d9bf0258758c29e Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:47:25 -0700 Subject: [PATCH 082/127] #239 Fix assertion error --- filter_kg_and_remap_predicates.py | 2 ++ multi_ont_to_json_kg.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index cb31d232..e2ffa0ac 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -55,6 +55,8 @@ def make_arg_parser(): def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_object_aspect=None, qualified_object_direction=None): value_list = edge_key_value.split('---') + if len(value_list) == 7: + return edge_key_value assert len(value_list) == 4 if qualified_object_direction is None: qualified_object_direction = "None" diff --git a/multi_ont_to_json_kg.py b/multi_ont_to_json_kg.py index 3472423e..fa7ec27a 100755 --- a/multi_ont_to_json_kg.py +++ b/multi_ont_to_json_kg.py @@ -1306,6 +1306,8 @@ def xref_as_a_publication(xref: str): def convert_bpv_predicate_to_curie(bpv_pred: str, uri_shortener: callable, curie_expander: callable) -> str: + if bpv_pred.startswith("ttp"): + bpv_pred = "h" + bpv_pred if kg2_util.is_a_valid_http_url(bpv_pred): bpv_pred_curie = uri_shortener(bpv_pred) else: From 1bd264168010d586d03faf1958a8414de3b1505e Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 18 Oct 2022 16:16:30 -0700 Subject: [PATCH 083/127] #242 Fixing errors --- predicate-remap.yaml | 3937 +++++++++++++++++++++--------------------- 1 file changed, 1997 insertions(+), 1940 deletions(-) diff --git a/predicate-remap.yaml b/predicate-remap.yaml index 1be6af1d..b47f6415 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -10,9 +10,9 @@ BFO:0000054: BFO:0000055: operation: keep core_predicate: biolink:has_part -BFO:0000056: - operation: invert - core_predicate: biolink:has_participant +# BFO:0000056: +# operation: invert +# core_predicate: biolink:has_participant BFO:0000062: operation: invert core_predicate: biolink:precedes @@ -154,18 +154,21 @@ BSPO:0015102: BSPO:0015202: operation: keep core_predicate: biolink:located_in -BSPO:parallel_to: - operation: keep - core_predicate: biolink:coexists_with +BSPO:0020001: + operation: invert + core_predicate: biolink:has_part +# BSPO:parallel_to: +# operation: keep +# core_predicate: biolink:coexists_with BTO:develops_from: operation: keep core_predicate: biolink:develops_from BTO:related_to: operation: keep core_predicate: biolink:related_to -CHEBI:25212: - operation: invert - core_predicate: biolink:has_metabolite +# CHEBI:25212: +# operation: invert +# core_predicate: biolink:has_metabolite CHEBI:has_functional_parent: operation: keep core_predicate: biolink:chemically_similar_to @@ -192,1127 +195,1127 @@ CHEMBL.MECHANISM:activator: core_predicate: biolink:regulates qualifiers: - object_direction: increased -CHEMBL.MECHANISM:agonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -CHEMBL.MECHANISM:allosteric_antagonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased -CHEMBL.MECHANISM:antagonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased -CHEMBL.MECHANISM:antisense_inhibitor: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: expression - - object_direction: decreased -CHEMBL.MECHANISM:binding_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:blocker: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:chelating_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:cross-linking_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:degrader: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased -CHEMBL.MECHANISM:disrupting_agent: - operation: keep - core_predicate: biolink:disrupts -CHEMBL.MECHANISM:equivalent_to: - operation: keep - core_predicate: biolink:same_as -CHEMBL.MECHANISM:hydrolytic_enzyme: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased -CHEMBL.MECHANISM:inhibitor: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:inverse_agonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased -CHEMBL.MECHANISM:modulator: - operation: keep - core_predicate: biolink:regulates -CHEMBL.MECHANISM:negative_allosteric_modulator: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:negative_modulator: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:opener: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -CHEMBL.MECHANISM:other: - operation: delete -CHEMBL.MECHANISM:overlaps_with: - operation: keep - core_predicate: biolink:overlaps -CHEMBL.MECHANISM:oxidative_enzyme: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:partial_agonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -CHEMBL.MECHANISM:positive_allosteric_modulator: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -CHEMBL.MECHANISM:positive_modulator: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -CHEMBL.MECHANISM:proteolytic_enzyme: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased -CHEMBL.MECHANISM:reducing_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:releasing_agent: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: expression - - object_direction: increased -CHEMBL.MECHANISM:rnai_inhibitor: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -CHEMBL.MECHANISM:vaccine_antigen: - operation: keep - core_predicate: biolink:related_to -CHEMBL.MECHANISM:sequestering_agent: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:stabiliser: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: stability - - object_direction: increased -CHEMBL.MECHANISM:subset_of: - operation: keep - core_predicate: biolink:subclass_of -CHEMBL.MECHANISM:substrate: - operation: keep - core_predicate: biolink:physically_interacts_with -CHEMBL.MECHANISM:superset_of: - operation: invert - core_predicate: biolink:subclass_of -CL:has_completed: - operation: keep - core_predicate: biolink:has_completed -CL:has_high_plasma_membrane_amount: - operation: keep - core_predicate: biolink:has_increased_amount -CL:has_low_plasma_membrane_amount: - operation: keep - core_predicate: biolink:has_decreased_amount -CL:has_not_completed: - operation: keep - core_predicate: biolink:has_not_completed -CL:lacks_part: - operation: keep - core_predicate: biolink:lacks_part -CL:lacks_plasma_membrane_part: - operation: keep - core_predicate: biolink:lacks_part -CPT:has_add_on_code: - operation: keep - core_predicate: biolink:related_to -CPT:mapped_to: - operation: keep - core_predicate: biolink:related_to -CPT:panel_element_of: - operation: invert - core_predicate: biolink:has_part -CPT:panel_element_of_possibly_included: - operation: invert - core_predicate: biolink:has_part -CTD:affects_ADP-ribosylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_N-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_O-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_RNA_splicing: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: splicing -CTD:affects_abundance_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: abundance -CTD:affects_acetylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_acylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_alkylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_amination: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_binding: - operation: keep - core_predicate: biolink:interacts_with -CTD:affects_carbamoylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_carboxylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_cleavage: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: degradation -CTD:affects_degradation_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: degradation -CTD:affects_ethylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_export: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: secretion -CTD:affects_farnesylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_folding_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: folding -CTD:affects_geranoylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_glucuronidation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_glutathionylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_glycation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_glycosylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_hydrolysis: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: degradation -CTD:affects_hydroxylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_import: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: uptake -CTD:affects_lipidation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_methylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_molecular_modification_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_mutation_rate_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: mutation_rate -CTD:affects_myristoylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_nitrosation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_nucleotidylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_oxidation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_palmitoylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_phosphorylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_prenylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_reduction: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_response_to: - operation: keep - core_predicate: biolink:affects_response_to -CTD:affects_ribosylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_secretion_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: secretion -CTD:affects_splicing_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: splicing -CTD:affects_sulfation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_sumoylation: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_synthesis_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: synthesis -CTD:affects_transport_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: transport -CTD:affects_ubiquitination: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: molecular_modification -CTD:affects_uptake_of: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: uptake -CTD:decreases_ADP-ribosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_N-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_O-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_RNA_splicing: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: splicing - - object_direction: decreased -CTD:decreases_acetylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_acylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_alkylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_amination: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_carbamoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_carboxylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_cleavage: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: decreased -CTD:decreases_degradation_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: decreased -CTD:decreases_ethylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_export: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: secretion - - object_direction: decreased -CTD:decreases_farnesylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_folding_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: folding - - object_direction: decreased -CTD:decreases_geranoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_glucuronidation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_glutathionylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_glycation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_hydrolysis: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: decreased -CTD:decreases_hydroxylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_import: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: uptake - - object_direction: decreased -CTD:decreases_lipidation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_localization_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: localization - - object_direction: decreased -CTD:decreases_metabolic_processing_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: localization - - object_direction: decreased -CTD:decreases_methylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_molecular_interaction_with: - operation: keep - core_predicate: biolink:physically_interacts_with -CTD:decreases_molecular_modification_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_mutagenesis: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: mutation_rate - - object_direction: decreased -CTD:decreases_mutation_rate_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: mutation_rate - - object_direction: decreased -CTD:decreases_myristoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_nitrosation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_nucleotidylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_oxidation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_palmitoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_phosphorylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_prenylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_reduction: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_response_to: - operation: keep - core_predicate: biolink:decreases_response_to -CTD:decreases_response_to_substance: - operation: keep - core_predicate: biolink:decreases_response_to -CTD:decreases_ribosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_secretion_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: secretion - - object_direction: decreased -CTD:decreases_splicing_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: splicing - - object_direction: decreased -CTD:decreases_stability_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: stability - - object_direction: decreased -CTD:decreases_sulfation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_sumoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_transport_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: transport - - object_direction: decreased -CTD:decreases_ubiquitination: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -CTD:decreases_uptake_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: uptake - - object_direction: decreased -CTD:increases_ADP-ribosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_N-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_O-linked_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_RNA_splicing: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: splicing - - object_direction: increased -CTD:increases_acetylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_acylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_alkylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_amination: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_carbamoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_carboxylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_cleavage: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased -CTD:increases_ethylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_export: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: secretion - - object_direction: increased -CTD:increases_farnesylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_folding_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: folding - - object_direction: increased -CTD:increases_geranoylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_glucuronidation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_glutathionylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_glycation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_glycosylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_hydrolysis: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased -CTD:increases_hydroxylation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_import: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: uptake - - object_direction: increased -CTD:increases_lipidation: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_localization_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: localization - - object_direction: increased -CTD:increases_metabolic_processing_of: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: localization - - object_direction: increased -CTD:increases_methylation: +CHEMBL.MECHANISM:agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: activity - object_direction: increased -CTD:increases_molecular_interaction_with: - operation: keep - core_predicate: biolink:physically_interacts_with -CTD:increases_molecular_modification_of: +CHEMBL.MECHANISM:allosteric_antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_mutagenesis: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antagonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: mutation_rate - - object_direction: increased -CTD:increases_mutation_rate_of: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:antisense_inhibitor: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: mutation_rate - - object_direction: increased -CTD:increases_myristoylation: + - object_aspect: expression + - object_direction: decreased +CHEMBL.MECHANISM:binding_agent: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:blocker: + operation: keep + core_predicate: biolink:regulates qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_nitrosation: + - object_direction: decreased +CHEMBL.MECHANISM:chelating_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:cross-linking_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:degrader: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: degradation - object_direction: increased -CTD:increases_nucleotidylation: +CHEMBL.MECHANISM:disrupting_agent: + operation: keep + core_predicate: biolink:disrupts +CHEMBL.MECHANISM:equivalent_to: + operation: keep + core_predicate: biolink:same_as +CHEMBL.MECHANISM:hydrolytic_enzyme: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: degradation - object_direction: increased -CTD:increases_oxidation: +CHEMBL.MECHANISM:inhibitor: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes + core_predicate: biolink:regulates qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_palmitoylation: + - object_direction: decreased +CHEMBL.MECHANISM:inverse_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_phosphorylation: + - object_aspect: activity + - object_direction: decreased +CHEMBL.MECHANISM:modulator: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes + core_predicate: biolink:regulates +CHEMBL.MECHANISM:negative_allosteric_modulator: + operation: keep + core_predicate: biolink:regulates qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_prenylation: + - object_direction: decreased +CHEMBL.MECHANISM:negative_modulator: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes + core_predicate: biolink:regulates qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_reduction: + - object_direction: decreased +CHEMBL.MECHANISM:opener: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: activity - object_direction: increased -CTD:increases_response_to: +CHEMBL.MECHANISM:other: + operation: delete +CHEMBL.MECHANISM:overlaps_with: operation: keep - core_predicate: biolink:increases_response_to -CTD:increases_ribosylation: + core_predicate: biolink:overlaps +CHEMBL.MECHANISM:oxidative_enzyme: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: increased -CTD:increases_secretion_of: + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:partial_agonist: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: secretion + - object_aspect: activity - object_direction: increased -CTD:increases_splicing_of: +CHEMBL.MECHANISM:positive_allosteric_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: splicing + - object_aspect: activity - object_direction: increased -CTD:increases_sulfation: +CHEMBL.MECHANISM:positive_modulator: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: activity - object_direction: increased -CTD:increases_sumoylation: +CHEMBL.MECHANISM:proteolytic_enzyme: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: degradation - object_direction: increased -CTD:increases_synthesis_of: +CHEMBL.MECHANISM:reducing_agent: operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: synthesis - - object_direction: increased -CTD:increases_ubiquitination: + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:releasing_agent: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: molecular_modification + - object_aspect: expression - object_direction: increased -CTD:increases_uptake_of: +CHEMBL.MECHANISM:rnai_inhibitor: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased +CHEMBL.MECHANISM:vaccine_antigen: + operation: keep + core_predicate: biolink:related_to +CHEMBL.MECHANISM:sequestering_agent: + operation: keep + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:stabiliser: operation: keep core_predicate: biolink:affects qualified_predicate: biolink:causes qualifiers: - - object_aspect: uptake + - object_aspect: stability - object_direction: increased -CTD:inferred: +CHEMBL.MECHANISM:subset_of: operation: keep - core_predicate: biolink:affects -CTD:marker_mechanism: + core_predicate: biolink:subclass_of +CHEMBL.MECHANISM:substrate: operation: keep - core_predicate: biolink:contributes_to -CTD:negative_correlation: + core_predicate: biolink:physically_interacts_with +CHEMBL.MECHANISM:superset_of: + operation: invert + core_predicate: biolink:subclass_of +CL:has_completed: operation: keep - core_predicate: biolink:negatively_correlated_with -CTD:positive_correlation: + core_predicate: biolink:has_completed +CL:has_high_plasma_membrane_amount: operation: keep - core_predicate: biolink:positively_correlated_with -CTD:prediction_hypothesis: + core_predicate: biolink:has_increased_amount +CL:has_low_plasma_membrane_amount: operation: keep - core_predicate: biolink:affects + core_predicate: biolink:has_decreased_amount +CL:has_not_completed: + operation: keep + core_predicate: biolink:has_not_completed +CL:lacks_part: + operation: keep + core_predicate: biolink:lacks_part +CL:lacks_plasma_membrane_part: + operation: keep + core_predicate: biolink:lacks_part +# CPT:has_add_on_code: +# operation: keep +# core_predicate: biolink:related_to +# CPT:mapped_to: +# operation: keep +# core_predicate: biolink:related_to +# CPT:panel_element_of: +# operation: invert +# core_predicate: biolink:has_part +# CPT:panel_element_of_possibly_included: +# operation: invert +# core_predicate: biolink:has_part +# CTD:affects_ADP-ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_N-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_O-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_RNA_splicing: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: splicing +# CTD:affects_abundance_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: abundance +# CTD:affects_acetylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_acylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_alkylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_amination: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_binding: +# operation: keep +# core_predicate: biolink:interacts_with +# CTD:affects_carbamoylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_carboxylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_cleavage: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: degradation +# CTD:affects_degradation_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: degradation +# CTD:affects_ethylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_export: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: secretion +# CTD:affects_farnesylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_folding_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: folding +# CTD:affects_geranoylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_glucuronidation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_glutathionylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_glycation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_hydrolysis: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: degradation +# CTD:affects_hydroxylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_import: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: uptake +# CTD:affects_lipidation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_methylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_molecular_modification_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_mutation_rate_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: mutation_rate +# CTD:affects_myristoylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_nitrosation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_nucleotidylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_oxidation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_palmitoylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_phosphorylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_prenylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_reduction: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_response_to: +# operation: keep +# core_predicate: biolink:affects_response_to +# CTD:affects_ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_secretion_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: secretion +# CTD:affects_splicing_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: splicing +# CTD:affects_sulfation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_sumoylation: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_synthesis_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: synthesis +# CTD:affects_transport_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: transport +# CTD:affects_ubiquitination: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: molecular_modification +# CTD:affects_uptake_of: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: uptake +# CTD:decreases_ADP-ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_N-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_O-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_RNA_splicing: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: splicing +# - object_direction: decreased +# CTD:decreases_acetylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_acylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_alkylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_amination: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_carbamoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_carboxylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_cleavage: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: decreased +# CTD:decreases_degradation_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: decreased +# CTD:decreases_ethylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_export: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: secretion +# - object_direction: decreased +# CTD:decreases_farnesylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_folding_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: folding +# - object_direction: decreased +# CTD:decreases_geranoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_glucuronidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_glutathionylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_glycation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_hydrolysis: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: decreased +# CTD:decreases_hydroxylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_import: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: uptake +# - object_direction: decreased +# CTD:decreases_lipidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_localization_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: localization +# - object_direction: decreased +# CTD:decreases_metabolic_processing_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: localization +# - object_direction: decreased +# CTD:decreases_methylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_molecular_interaction_with: +# operation: keep +# core_predicate: biolink:physically_interacts_with +# CTD:decreases_molecular_modification_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_mutagenesis: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: mutation_rate +# - object_direction: decreased +# CTD:decreases_mutation_rate_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: mutation_rate +# - object_direction: decreased +# CTD:decreases_myristoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_nitrosation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_nucleotidylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_oxidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_palmitoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_phosphorylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_prenylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_reduction: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_response_to: +# operation: keep +# core_predicate: biolink:decreases_response_to +# CTD:decreases_response_to_substance: +# operation: keep +# core_predicate: biolink:decreases_response_to +# CTD:decreases_ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_secretion_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: secretion +# - object_direction: decreased +# CTD:decreases_splicing_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: splicing +# - object_direction: decreased +# CTD:decreases_stability_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: stability +# - object_direction: decreased +# CTD:decreases_sulfation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_sumoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_transport_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: transport +# - object_direction: decreased +# CTD:decreases_ubiquitination: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# CTD:decreases_uptake_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: uptake +# - object_direction: decreased +# CTD:increases_ADP-ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_N-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_O-linked_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_RNA_splicing: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: splicing +# - object_direction: increased +# CTD:increases_acetylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_acylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_alkylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_amination: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_carbamoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_carboxylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_cleavage: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: increased +# CTD:increases_ethylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_export: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: secretion +# - object_direction: increased +# CTD:increases_farnesylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_folding_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: folding +# - object_direction: increased +# CTD:increases_geranoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_glucuronidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_glutathionylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_glycation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_glycosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_hydrolysis: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: increased +# CTD:increases_hydroxylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_import: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: uptake +# - object_direction: increased +# CTD:increases_lipidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_localization_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: localization +# - object_direction: increased +# CTD:increases_metabolic_processing_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: localization +# - object_direction: increased +# CTD:increases_methylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_molecular_interaction_with: +# operation: keep +# core_predicate: biolink:physically_interacts_with +# CTD:increases_molecular_modification_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_mutagenesis: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: mutation_rate +# - object_direction: increased +# CTD:increases_mutation_rate_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: mutation_rate +# - object_direction: increased +# CTD:increases_myristoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_nitrosation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_nucleotidylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_oxidation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_palmitoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_phosphorylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_prenylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_reduction: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_response_to: +# operation: keep +# core_predicate: biolink:increases_response_to +# CTD:increases_ribosylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_secretion_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: secretion +# - object_direction: increased +# CTD:increases_splicing_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: splicing +# - object_direction: increased +# CTD:increases_sulfation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_sumoylation: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_synthesis_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: synthesis +# - object_direction: increased +# CTD:increases_ubiquitination: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: increased +# CTD:increases_uptake_of: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: uptake +# - object_direction: increased +# CTD:inferred: +# operation: keep +# core_predicate: biolink:affects +# CTD:marker_mechanism: +# operation: keep +# core_predicate: biolink:contributes_to +# CTD:negative_correlation: +# operation: keep +# core_predicate: biolink:negatively_correlated_with +# CTD:positive_correlation: +# operation: keep +# core_predicate: biolink:positively_correlated_with +# CTD:prediction_hypothesis: +# operation: keep +# core_predicate: biolink:affects DDANAT:develops_from: operation: keep core_predicate: biolink:develops_from @@ -1321,9 +1324,9 @@ DGIdb:activator: core_predicate: biolink:regulates qualifiers: - object_direction: increased -DGIdb:adduct: - operation: keep - core_predicate: biolink:directly_physically_interacts_with +# DGIdb:adduct: +# operation: keep +# core_predicate: biolink:directly_physically_interacts_with DGIdb:affects: operation: keep core_predicate: biolink:affects @@ -1356,9 +1359,9 @@ DGIdb:antisense_oligonucleotide: qualifiers: - object_aspect: expression - object_direction: decreased -DGIdb:binder: - operation: keep - core_predicate: biolink:interacts_with +# DGIdb:binder: +# operation: keep +# core_predicate: biolink:interacts_with DGIdb:blocker: operation: keep core_predicate: biolink:affects @@ -1366,31 +1369,31 @@ DGIdb:blocker: qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:channel_blocker: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased -DGIdb:chaperone: - operation: keep - core_predicate: biolink:binds -DGIdb:cleavage: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: degradation -DGIdb:cofactor: - operation: keep - core_predicate: biolink:interacts_with -DGIdb:gating_inhibitor: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased +# DGIdb:channel_blocker: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: decreased +# DGIdb:chaperone: +# operation: keep +# core_predicate: biolink:binds +# DGIdb:cleavage: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: degradation +# DGIdb:cofactor: +# operation: keep +# core_predicate: biolink:interacts_with +# DGIdb:gating_inhibitor: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: decreased DGIdb:inducer: operation: keep core_predicate: biolink:affects @@ -1419,17 +1422,17 @@ DGIdb:inverse_agonist: qualifiers: - object_aspect: activity - object_direction: decreased -DGIdb:ligand: - operation: keep - core_predicate: biolink:directly_physically_interacts_with +# DGIdb:ligand: +# operation: keep +# core_predicate: biolink:directly_physically_interacts_with DGIdb:modulator: operation: keep core_predicate: biolink:affects qualifiers: - object_aspect: activity -DGIdb:multitarget: - operation: keep - core_predicate: biolink:directly_physically_interacts_with +# DGIdb:multitarget: +# operation: keep +# core_predicate: biolink:directly_physically_interacts_with DGIdb:negative_modulator: operation: keep core_predicate: biolink:affects @@ -1444,13 +1447,13 @@ DGIdb:partial_agonist: qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:partial_antagonist: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased +# DGIdb:partial_antagonist: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: decreased DGIdb:positive_modulator: operation: keep core_predicate: biolink:affects @@ -1458,30 +1461,30 @@ DGIdb:positive_modulator: qualifiers: - object_aspect: activity - object_direction: increased -DGIdb:potentiator: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -DGIdb:product_of: - operation: keep - core_predicate: biolink:derives_from -DGIdb:stimulator: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: increased -DGIdb:substrate: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: degradation - - object_direction: increased +# DGIdb:potentiator: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: increased +# DGIdb:product_of: +# operation: keep +# core_predicate: biolink:derives_from +# DGIdb:stimulator: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: increased +# DGIdb:substrate: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: degradation +# - object_direction: increased DGIdb:suppressor: operation: keep core_predicate: biolink:affects @@ -1499,24 +1502,24 @@ DGIdb:vaccine: #DOID-PROPERTY:derives_from: # operation: keep # core_predicate: biolink:related_to_at_instance_level -DOID-PROPERTY:has_symptom: - operation: keep - core_predicate: biolink:has_phenotype +# DOID-PROPERTY:has_symptom: +# operation: keep +# core_predicate: biolink:has_phenotype DRUGBANK:activator: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: increased -DRUGBANK:adduct: - operation: keep - core_predicate: biolink:directly_physically_interacts_with -DRUGBANK:aggregation_inhibitor: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: activity - - object_direction: decreased +# DRUGBANK:adduct: +# operation: keep +# core_predicate: biolink:directly_physically_interacts_with +# DRUGBANK:aggregation_inhibitor: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: activity +# - object_direction: decreased DRUGBANK:agonist: operation: keep core_predicate: biolink:affects @@ -1588,16 +1591,16 @@ DRUGBANK:degradation: core_predicate: biolink:affects qualifiers: - object_aspect: degradation -DRUGBANK:deoxidizer: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: molecular_modification - - object_direction: decreased -DRUGBANK:desensitize_the_target: - operation: keep - core_predicate: biolink:decreases_response_to +# DRUGBANK:deoxidizer: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: molecular_modification +# - object_direction: decreased +# DRUGBANK:desensitize_the_target: +# operation: keep +# core_predicate: biolink:decreases_response_to DRUGBANK:downregulator: operation: keep core_predicate: biolink:regulates @@ -1721,11 +1724,11 @@ DRUGBANK:positive_allosteric_modulator: qualifiers: - object_aspect: activity - object_direction: increased -DRUGBANK:positive_modulator: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: increased +# DRUGBANK:positive_modulator: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: increased DRUGBANK:potentiator: operation: keep core_predicate: biolink:affects @@ -1771,17 +1774,19 @@ DRUGBANK:translocation_inhibitor: core_predicate: biolink:regulates qualifiers: - object_direction: decreased -DRUGBANK:treats: - operation: keep - core_predicate: biolink:treats +# DRUGBANK:treats: +# operation: keep +# core_predicate: biolink:treats DRUGBANK:weak_inhibitor: operation: keep core_predicate: biolink:regulates qualifiers: - object_direction: decreased -DrugCentral:5271: - operation: keep - core_predicate: biolink:diagnoses +# DrugCentral:5271: +# operation: keep +# core_predicate: biolink:diagnoses +DrugCentral:other: + operation: delete DrugCentral:PA: operation: keep core_predicate: biolink:subclass_of @@ -1938,8 +1943,8 @@ EFO:is_executed_in: ENVO:01001307: operation: keep core_predicate: biolink:coexists_with -FMA:SIB: - operation: delete +# FMA:SIB: +# operation: delete FMA:adheres_to: operation: keep core_predicate: biolink:physically_interacts_with @@ -2331,20 +2336,20 @@ FOODON:00002420: GENEPIO:0001739: operation: invert core_predicate: biolink:precedes -GENO:0000382: - operation: keep - core_predicate: biolink:has_variant_part -GENO:0000790: - operation: keep - core_predicate: biolink:related_condition -GENO:0000840: - operation: keep - core_predicate: biolink:gene_associated_with_condition -GENO:0000841: - operation: keep - core_predicate: biolink:gene_associated_with_condition -GO:SIB: - operation: delete +# GENO:0000382: +# operation: keep +# core_predicate: biolink:has_variant_part +# GENO:0000790: +# operation: keep +# core_predicate: biolink:related_condition +# GENO:0000840: +# operation: keep +# core_predicate: biolink:gene_associated_with_condition +# GENO:0000841: +# operation: keep +# core_predicate: biolink:gene_associated_with_condition +# GO:SIB: +# operation: delete GO:acts_upstream_of: operation: keep core_predicate: biolink:affects @@ -2447,12 +2452,12 @@ GO:regulates: GOREL:0000040: operation: keep core_predicate: biolink:causes -GOREL:0001004: - operation: keep - core_predicate: biolink:located_in -GOREL:0001006: - operation: keep - core_predicate: biolink:affects +# GOREL:0001004: +# operation: keep +# core_predicate: biolink:located_in +# GOREL:0001006: +# operation: keep +# core_predicate: biolink:affects GOREL:0002003: operation: keep core_predicate: biolink:affects @@ -2465,15 +2470,15 @@ GOREL:0002004: qualifiers: - object_aspect: degradation - object_direction: increased -GOREL:0002005: - operation: keep - core_predicate: biolink:related_to +# GOREL:0002005: +# operation: keep +# core_predicate: biolink:related_to GOREL:0012006: operation: keep core_predicate: biolink:related_to -GTEx:affects_expression_in: - operation: keep - core_predicate: biolink:affects +# GTEx:affects_expression_in: +# operation: keep +# core_predicate: biolink:affects HANCESTRO:0301: operation: keep core_predicate: biolink:related_to @@ -2506,24 +2511,24 @@ HMDB:in_biospecimen: HMDB:in_pathway: operation: invert core_predicate: biolink:has_participant -HP:SIB: - operation: delete +# HP:SIB: +# operation: delete IAO:0000039: operation: keep core_predicate: biolink:related_to IAO:0000136: operation: keep core_predicate: biolink:related_to -IAO:0000142: - operation: keep - core_predicate: biolink:mentions +# IAO:0000142: +# operation: keep +# core_predicate: biolink:mentions IAO:0000219: operation: keep core_predicate: biolink:related_to -ICD10PCS:SIB: - operation: delete -ICD9:SIB: - operation: delete +# ICD10PCS:SIB: +# operation: delete +# ICD9:SIB: +# operation: delete IDO:0000664: operation: invert core_predicate: biolink:contributes_to @@ -2569,6 +2574,10 @@ KEGG:reaction_to_enzyme: KEGG:reaction_to_pathway: operation: invert core_predicate: biolink:has_participant +linkml:examples: + operation: delete +linkml:local_names: + operation: delete LOINC:adjustment_of: operation: delete LOINC:analyzed_by: @@ -2597,8 +2606,8 @@ LOINC:divisor_of: operation: delete LOINC:evaluation_of: operation: delete -LOINC:fragments_for_synonyms_of: - operation: delete +# LOINC:fragments_for_synonyms_of: +# operation: delete LOINC:has_action_guidance: operation: keep core_predicate: biolink:related_to @@ -2638,9 +2647,9 @@ LOINC:has_evaluation: LOINC:has_exam: operation: keep core_predicate: biolink:related_to -LOINC:has_fragments_for_synonyms: - operation: keep - core_predicate: biolink:has_input +# LOINC:has_fragments_for_synonyms: +# operation: keep +# core_predicate: biolink:has_input LOINC:has_given_pharmaceutical_substance: operation: delete LOINC:has_imaged_location: @@ -2657,6 +2666,8 @@ LOINC:has_lateral_location_presence: core_predicate: biolink:coexists_with LOINC:has_loinc_number: operation: delete +LOINC:has_maneuver_type: + operation: delete LOINC:has_member: operation: keep core_predicate: biolink:has_part @@ -2669,8 +2680,8 @@ LOINC:has_modality_subtype: LOINC:has_modality_type: operation: keep core_predicate: biolink:related_to -LOINC:has_multipart: - operation: delete +# LOINC:has_multipart: +# operation: delete LOINC:has_object_guidance: operation: keep core_predicate: biolink:related_to @@ -2728,6 +2739,8 @@ LOINC:is_imaging_focus_of: operation: delete LOINC:is_lateral_anatomic_location_of: operation: delete +LOINC:is_maneuver_type_for: + operation: delete LOINC:is_modality_subtype_for: operation: delete LOINC:is_modality_type_for: @@ -2769,9 +2782,9 @@ LOINC:mth_expanded_form_of: LOINC:mth_has_expanded_form: operation: keep core_predicate: biolink:related_to -LOINC:multipart_of: - operation: invert - core_predicate: biolink:has_part +# LOINC:multipart_of: +# operation: invert +# core_predicate: biolink:has_part LOINC:parent_group_of: operation: delete LOINC:property_of: @@ -2789,15 +2802,15 @@ LOINC:time_aspect_of: operation: delete LOINC:time_modifier_of: operation: delete -MEDDRA:classified_as: - operation: keep - core_predicate: biolink:close_match -MEDDRA:has_member: - operation: keep - core_predicate: biolink:has_part -MEDDRA:member_of: - operation: invert - core_predicate: biolink:has_part +# MEDDRA:classified_as: +# operation: keep +# core_predicate: biolink:close_match +# MEDDRA:has_member: +# operation: keep +# core_predicate: biolink:has_part +# MEDDRA:member_of: +# operation: invert +# core_predicate: biolink:has_part MESH:AQ: operation: delete MESH:QB: @@ -2805,8 +2818,8 @@ MESH:QB: MESH:RO: operation: keep core_predicate: biolink:related_to -MESH:SIB: - operation: delete +# MESH:SIB: +# operation: delete MESH:has_mapping_qualifier: operation: keep core_predicate: biolink:related_to @@ -2961,9 +2974,9 @@ MONDO:disease_has_basis_in_accumulation_of: MONDO:disease_has_basis_in_development_of: operation: keep core_predicate: biolink:disease_has_basis_in -MONDO:disease_has_location: - operation: keep - core_predicate: biolink:disease_has_location +# MONDO:disease_has_location: +# operation: keep +# core_predicate: biolink:disease_has_location MONDO:disease_has_major_feature: operation: keep core_predicate: biolink:has_part @@ -2994,201 +3007,201 @@ MONDO:part_of_progression_of_disease: MONDO:predisposes_towards: operation: keep core_predicate: biolink:contributes_to -NBO-PROPERTY:by_means: - operation: keep - core_predicate: biolink:actively_involved_in -NBO-PROPERTY:has_participant: - operation: keep - core_predicate: biolink:has_participant -NBO-PROPERTY:in_response_to: - operation: keep - core_predicate: biolink:causes -NBO-PROPERTY:is_about: - operation: keep - core_predicate: biolink:related_to -NCIT:A11: - operation: keep - core_predicate: biolink:subclass_of -NCIT:A14: - operation: keep - core_predicate: biolink:subclass_of -NCIT:A16: - operation: keep - core_predicate: biolink:subclass_of -NCIT:A3: - operation: keep - core_predicate: biolink:subclass_of -NCIT:A7: - operation: keep - core_predicate: biolink:physically_interacts_with -NCIT:Anatomic_Structure_Has_Location_Role: - operation: invert - core_predicate: biolink:located_in -NCIT:C15220: - operation: keep - core_predicate: biolink:diagnoses -NCIT:C16798: - operation: keep - core_predicate: biolink:in_linkage_disequilibrium_with -NCIT:C2861: - operation: keep - core_predicate: biolink:causes_adverse_event -NCIT:C37933: - operation: keep - core_predicate: biolink:contraindicated_for -NCIT:R100: - operation: keep - core_predicate: biolink:affects -NCIT:R101: - operation: keep - core_predicate: biolink:affects -NCIT:R102: - operation: keep - core_predicate: biolink:affects -NCIT:R108: - operation: keep - core_predicate: biolink:has_phenotype -NCIT:R113: - operation: keep - core_predicate: biolink:affects -NCIT:R115: - operation: keep - core_predicate: biolink:has_phenotype -NCIT:R124: - operation: keep - core_predicate: biolink:affects -NCIT:R130: - operation: invert - core_predicate: biolink:has_participant -NCIT:R131: - operation: invert - core_predicate: biolink:has_participant -NCIT:R133: - operation: keep - core_predicate: biolink:affects -NCIT:R145: - operation: keep - core_predicate: biolink:located_in -NCIT:R146: - operation: keep - core_predicate: biolink:affects -NCIT:R150: - operation: keep - core_predicate: biolink:affects -NCIT:R155: - operation: keep - core_predicate: biolink:located_in -NCIT:R156: - operation: keep - core_predicate: biolink:located_in -NCIT:R158: - operation: keep - core_predicate: biolink:affects -NCIT:R160: - operation: keep - core_predicate: biolink:affects +# NBO-PROPERTY:by_means: +# operation: keep +# core_predicate: biolink:actively_involved_in +# NBO-PROPERTY:has_participant: +# operation: keep +# core_predicate: biolink:has_participant +# NBO-PROPERTY:in_response_to: +# operation: keep +# core_predicate: biolink:causes +# NBO-PROPERTY:is_about: +# operation: keep +# core_predicate: biolink:related_to +# NCIT:A11: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:A14: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:A16: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:A3: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:A7: +# operation: keep +# core_predicate: biolink:physically_interacts_with +# NCIT:Anatomic_Structure_Has_Location_Role: +# operation: invert +# core_predicate: biolink:located_in +# NCIT:C15220: +# operation: keep +# core_predicate: biolink:diagnoses +# NCIT:C16798: +# operation: keep +# core_predicate: biolink:in_linkage_disequilibrium_with +# NCIT:C2861: +# operation: keep +# core_predicate: biolink:causes_adverse_event +# NCIT:C37933: +# operation: keep +# core_predicate: biolink:contraindicated_for +# NCIT:R100: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R101: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R102: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R108: +# operation: keep +# core_predicate: biolink:has_phenotype +# NCIT:R113: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R115: +# operation: keep +# core_predicate: biolink:has_phenotype +# NCIT:R124: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R130: +# operation: invert +# core_predicate: biolink:has_participant +# NCIT:R131: +# operation: invert +# core_predicate: biolink:has_participant +# NCIT:R133: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R145: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R146: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R150: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R155: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R156: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R158: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R160: +# operation: keep +# core_predicate: biolink:affects NCIT:R163: operation: keep core_predicate: biolink:related_to -NCIT:R165: - operation: keep - core_predicate: biolink:located_in -NCIT:R166: - operation: keep - core_predicate: biolink:located_in -NCIT:R167: - operation: keep - core_predicate: biolink:located_in -NCIT:R168: - operation: keep - core_predicate: biolink:located_in -NCIT:R169: - operation: keep - core_predicate: biolink:located_in -NCIT:R170: - operation: keep - core_predicate: biolink:located_in -NCIT:R171: - operation: keep - core_predicate: biolink:located_in -NCIT:R173: - operation: keep - core_predicate: biolink:affects -NCIT:R175: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:R176: - operation: invert - core_predicate: biolink:gene_associated_with_condition -NCIT:R178: - operation: invert - core_predicate: biolink:gene_product_of -NCIT:R23: - operation: keep - core_predicate: biolink:affects -NCIT:R25: - operation: keep - core_predicate: biolink:affects -NCIT:R27: - operation: invert - core_predicate: biolink:has_part -NCIT:R29: - operation: keep - core_predicate: biolink:produces -NCIT:R30: - operation: keep - core_predicate: biolink:affects -NCIT:R36: - operation: keep - core_predicate: biolink:subclass_of -NCIT:R37: - operation: invert - core_predicate: biolink:has_participant -NCIT:R38: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:R39: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:R40: - operation: keep - core_predicate: biolink:located_in -NCIT:R42: - operation: keep - core_predicate: biolink:subclass_of -NCIT:R47: - operation: keep - core_predicate: biolink:biomarker_for -NCIT:R48: - operation: keep - core_predicate: biolink:gene_associated_with_condition -NCIT:R50: - operation: keep - core_predicate: biolink:has_part -NCIT:R51: - operation: invert - core_predicate: biolink:has_participant -NCIT:R52: - operation: keep - core_predicate: biolink:capable_of -NCIT:R53: - operation: invert - core_predicate: biolink:has_participant -NCIT:R72: - operation: keep - core_predicate: biolink:affects +# NCIT:R165: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R166: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R167: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R168: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R169: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R170: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R171: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R173: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R175: +# operation: keep +# core_predicate: biolink:gene_associated_with_condition +# NCIT:R176: +# operation: invert +# core_predicate: biolink:gene_associated_with_condition +# NCIT:R178: +# operation: invert +# core_predicate: biolink:gene_product_of +# NCIT:R23: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R25: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R27: +# operation: invert +# core_predicate: biolink:has_part +# NCIT:R29: +# operation: keep +# core_predicate: biolink:produces +# NCIT:R30: +# operation: keep +# core_predicate: biolink:affects +# NCIT:R36: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:R37: +# operation: invert +# core_predicate: biolink:has_participant +# NCIT:R38: +# operation: keep +# core_predicate: biolink:gene_associated_with_condition +# NCIT:R39: +# operation: keep +# core_predicate: biolink:biomarker_for +# NCIT:R40: +# operation: keep +# core_predicate: biolink:located_in +# NCIT:R42: +# operation: keep +# core_predicate: biolink:subclass_of +# NCIT:R47: +# operation: keep +# core_predicate: biolink:biomarker_for +# NCIT:R48: +# operation: keep +# core_predicate: biolink:gene_associated_with_condition +# NCIT:R50: +# operation: keep +# core_predicate: biolink:has_part +# NCIT:R51: +# operation: invert +# core_predicate: biolink:has_participant +# NCIT:R52: +# operation: keep +# core_predicate: biolink:capable_of +# NCIT:R53: +# operation: invert +# core_predicate: biolink:has_participant +# NCIT:R72: +# operation: keep +# core_predicate: biolink:affects NCIT:R81: operation: keep core_predicate: biolink:related_to NCIT:R82: operation: invert core_predicate: biolink:has_part -NCIT:R88: - operation: keep - core_predicate: biolink:related_to -NCIT:R89: - operation: keep - core_predicate: biolink:has_phenotype +# NCIT:R88: +# operation: keep +# core_predicate: biolink:related_to +# NCIT:R89: +# operation: keep +# core_predicate: biolink:has_phenotype NCIT:abnormal_cell_affected_by_chemical_or_drug: operation: delete NCIT:abnormality_associated_with_allele: @@ -3251,9 +3264,9 @@ NCIT:biomarker_type_includes_gene: operation: delete NCIT:biomarker_type_includes_gene_product: operation: delete -NCIT:cdrh_parent_of: - operation: invert - core_predicate: biolink:subclass_of +# NCIT:cdrh_parent_of: +# operation: invert +# core_predicate: biolink:subclass_of NCIT:cell_type_is_associated_with_eo_disease: operation: delete NCIT:cell_type_or_tissue_affected_by_chemical_or_drug: @@ -3310,6 +3323,8 @@ NCIT:conceptual_part_of: NCIT:ctcae_5_parent_of: operation: invert core_predicate: biolink:subclass_of +NCIT:is_ctdc_value_of: + operation: delete NCIT:cytogenetic_abnormality_involves_chromosome: operation: keep core_predicate: biolink:affects @@ -3390,7 +3405,11 @@ NCIT:disease_may_have_molecular_abnormality: operation: keep core_predicate: biolink:has_phenotype NCIT:disease_may_have_normal_cell_origin: - operation: delete + operation: invert + core_predicate: biolink:derives_from +NCIT:disease_may_have_normal_tissue_origin: + operation: invert + core_predicate: biolink:derives_from NCIT:endogenous_product_related_to: operation: delete NCIT:enzyme_metabolizes_chemical_or_drug: @@ -3512,25 +3531,41 @@ NCIT:gene_product_variant_of_gene_product: NCIT:genetic_biomarker_related_to: operation: keep core_predicate: biolink:biomarker_for -NCIT:has_cdrh_parent: - operation: delete +# NCIT:has_cdrh_parent: +# operation: delete NCIT:has_conceptual_part: operation: delete NCIT:has_ctcae_5_parent: operation: delete +NCIT:has_ctdc_value: + operation: delete NCIT:has_data_element: operation: keep core_predicate: biolink:related_to NCIT:has_free_acid_or_base_form: operation: delete +NCIT:has_gdc_value: + operation: delete NCIT:has_gene_product_element: operation: delete +NCIT:has_icdc_value: + operation: delete NCIT:has_inc_parent: operation: keep core_predicate: biolink:subclass_of -NCIT:has_nichd_parent: - operation: keep - core_predicate: biolink:subclass_of +# NCIT:has_nichd_parent: +# operation: keep +# core_predicate: biolink:related_to +NCIT:has_pcdc_all_permissible_value: + operation: delete +NCIT:has_pcdc_aml_permissible_value: + operation: delete +NCIT:has_pcdc_ews_permissible_value: + operation: delete +NCIT:has_pcdc_data_type: + operation: delete +NCIT:has_pcdc_gct_permissible_value: + operation: delete NCIT:has_pharmaceutical_administration_method: operation: keep core_predicate: biolink:related_to @@ -3554,12 +3589,16 @@ NCIT:has_physical_part_of_anatomic_structure: NCIT:has_salt_form: operation: keep core_predicate: biolink:chemically_similar_to +NCIT:has_seronet_permissible_value: + operation: delete NCIT:has_target: operation: keep core_predicate: biolink:physically_interacts_with NCIT:human_disease_maps_to_eo_disease: operation: keep core_predicate: biolink:related_to +NCIT:icdc_value_of: + operation: delete NCIT:imaged_anatomy_has_procedure: operation: delete NCIT:inc_parent_of: @@ -3632,6 +3671,16 @@ NCIT:is_not_primary_anatomic_site_of_disease: NCIT:is_organism_source_of_gene_product: operation: invert core_predicate: biolink:in_taxon +NCIT:is_paired_with_value_set: + operation: delete +NCIT:is_pcdc_all_permissible_value_for_variable: + operation: delete +NCIT:is_pcdc_aml_permissible_value_for_variable: + operation: delete +NCIT:is_pcdc_ews_permissible_value_for_variable: + operation: delete +NCIT:is_pcdc_gct_permissible_value_for_variable: + operation: delete NCIT:is_physical_location_of_gene: operation: delete NCIT:is_physiologic_effect_of_chemical_or_drug: @@ -3646,12 +3695,16 @@ NCIT:is_qualified_by: NCIT:is_related_to_endogenous_product: operation: keep core_predicate: biolink:related_to +NCIT:is_seronet_permissible_value_for_variable: + operation: delete NCIT:is_stage_of_disease: operation: delete NCIT:is_structural_domain_or_motif_of_gene_product: operation: delete NCIT:is_target: operation: delete +NCIT:is_value_for_gdc_property: + operation: delete NCIT:kind_is_domain_of: operation: delete NCIT:kind_is_range_of: @@ -3669,13 +3722,16 @@ NCIT:may_be_molecular_abnormality_of_disease: NCIT:may_be_normal_cell_origin_of_disease: operation: invert core_predicate: biolink:derives_from +NCIT:may_be_normal_tissue_origin_of_disease: + operation: invert + core_predicate: biolink:derives_from NCIT:molecular_abnormality_involves_gene: operation: delete NCIT:neoplasm_has_special_category: operation: keep core_predicate: biolink:subclass_of -NCIT:nichd_parent_of: - operation: delete +# NCIT:nichd_parent_of: +# operation: delete NCIT:organism_has_gene: operation: invert core_predicate: biolink:in_taxon @@ -3688,6 +3744,8 @@ NCIT:pathogenesis_of_disease_involves_gene: NCIT:pathway_has_gene_element: operation: keep core_predicate: biolink:has_participant +NCIT:pcdc_data_type_of: + operation: delete NCIT:pharmaceutical_administration_method_of: operation: delete NCIT:pharmaceutical_basic_dose_form_of: @@ -3763,6 +3821,8 @@ NCIT:target_anatomy_has_procedure: operation: delete NCIT:tissue_is_expression_site_of_gene_product: operation: delete +NCIT:value_set_is_paired_with: + operation: delete NDDF:dose_form_of: operation: delete NDDF:has_dose_form: @@ -3798,9 +3858,9 @@ OBO:MF#manifestationOf: OBO:bspo#parallel_to: operation: keep core_predicate: biolink:coexists_with -OBO:doid#has_symptom: - operation: keep - core_predicate: biolink:has_phenotype +# OBO:doid#has_symptom: +# operation: keep +# core_predicate: biolink:has_phenotype OBO:envo#has_increased_levels_of: operation: keep core_predicate: biolink:related_to @@ -3813,15 +3873,15 @@ OBO:exo#interacts_with_an_exposure_receptor_via: OBO:exo#interacts_with_an_exposure_stressor_via: operation: keep core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with: - operation: keep - core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_receptor_via: - operation: keep - core_predicate: biolink:interacts_with -OBO:exo.obo#interacts_with_an_exposure_stressor_via: - operation: keep - core_predicate: biolink:interacts_with +# OBO:exo.obo#interacts_with: +# operation: keep +# core_predicate: biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_receptor_via: +# operation: keep +# core_predicate: biolink:interacts_with +# OBO:exo.obo#interacts_with_an_exposure_stressor_via: +# operation: keep +# core_predicate: biolink:interacts_with OBO:has_role: operation: keep core_predicate: biolink:related_to @@ -3837,12 +3897,12 @@ OBO:nbo#in_response_to: OBO:nbo#is_about: operation: keep core_predicate: biolink:related_to -OBO:uo#is_unit_of: - operation: invert - core_predicate: biolink:related_to -OIO:hasDbXref: - operation: keep - core_predicate: biolink:close_match +# OBO:uo#is_unit_of: +# operation: invert +# core_predicate: biolink:related_to +# OIO:hasDbXref: +# operation: keep +# core_predicate: biolink:close_match OMIM:allelic_variant_of: operation: keep core_predicate: biolink:is_sequence_variant_of @@ -3892,66 +3952,66 @@ ORPHA:410296: ORPHA:465410: operation: keep core_predicate: biolink:biomarker_for -ORPHANET:317343: - operation: keep - core_predicate: biolink:causes -ORPHANET:317344: - operation: keep - core_predicate: biolink:causes +# ORPHANET:317343: +# operation: keep +# core_predicate: biolink:causes +# ORPHANET:317344: +# operation: keep +# core_predicate: biolink:causes ORPHANET:317345: operation: keep core_predicate: biolink:correlated_with -ORPHANET:317346: - operation: keep - core_predicate: biolink:causes -ORPHANET:317348: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:317349: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:327767: - operation: keep - core_predicate: biolink:actively_involved_in -ORPHANET:410295: - operation: keep - core_predicate: biolink:causes -ORPHANET:410296: - operation: keep - core_predicate: biolink:causes -ORPHANET:465410: - operation: keep - core_predicate: biolink:biomarker_for +# ORPHANET:317346: +# operation: keep +# core_predicate: biolink:causes +# ORPHANET:317348: +# operation: keep +# core_predicate: biolink:actively_involved_in +# ORPHANET:317349: +# operation: keep +# core_predicate: biolink:actively_involved_in +# ORPHANET:327767: +# operation: keep +# core_predicate: biolink:actively_involved_in +# ORPHANET:410295: +# operation: keep +# core_predicate: biolink:causes +# ORPHANET:410296: +# operation: keep +# core_predicate: biolink:causes +# ORPHANET:465410: +# operation: keep +# core_predicate: biolink:biomarker_for ORPHANET:C016: operation: keep core_predicate: biolink:related_to ORPHANET:C017: operation: keep core_predicate: biolink:related_to -PATO:0000085: - operation: keep - core_predicate: biolink:associated_with_sensitivity_to -PATO:correlates_with: - operation: keep - core_predicate: biolink:correlated_with +# PATO:0000085: +# operation: keep +# core_predicate: biolink:associated_with_sensitivity_to +# PATO:correlates_with: +# operation: keep +# core_predicate: biolink:correlated_with PATO:decreased_in_magnitude_relative_to: operation: keep core_predicate: biolink:related_to PATO:has_cross_section: operation: keep core_predicate: biolink:related_to -PATO:has_relative_magnitude: - operation: keep - core_predicate: biolink:related_to +# PATO:has_relative_magnitude: +# operation: keep +# core_predicate: biolink:related_to PATO:increased_in_magnitude_relative_to: operation: keep core_predicate: biolink:related_to PATO:reciprocal_of: operation: keep core_predicate: biolink:related_to -PATO:towards: - operation: invert - core_predicate: biolink:actively_involved_in +# PATO:towards: +# operation: invert +# core_predicate: biolink:actively_involved_in PDQ:associated_disease: operation: keep core_predicate: biolink:correlated_with @@ -3963,9 +4023,9 @@ PDQ:component_of: PDQ:has_component: operation: keep core_predicate: biolink:has_part -PHAROS:drug_targets: - operation: keep - core_predicate: biolink:interacts_with +# PHAROS:drug_targets: +# operation: keep +# core_predicate: biolink:interacts_with PR:confers_resistance_to: operation: keep core_predicate: biolink:affects @@ -4152,27 +4212,30 @@ RO:0000057: RO:0000059: operation: keep core_predicate: biolink:related_to +# role of +RO:0000081: + operation: delete RO:0000086: operation: keep core_predicate: biolink:related_to RO:0000087: operation: keep core_predicate: biolink:related_to -RO:00002325: - operation: keep - core_predicate: biolink:colocalizes_with +# RO:00002325: +# operation: keep +# core_predicate: biolink:colocalizes_with RO:0001000: operation: keep core_predicate: biolink:derives_from -RO:0001001: - operation: invert - core_predicate: biolink:derives_from +# RO:0001001: +# operation: invert +# core_predicate: biolink:derives_from RO:0001015: operation: invert core_predicate: biolink:located_in -RO:0001018: - operation: invert - core_predicate: biolink:has_part +# RO:0001018: +# operation: invert +# core_predicate: biolink:has_part RO:0001019: operation: keep core_predicate: biolink:has_part @@ -4188,9 +4251,9 @@ RO:0002001: RO:0002002: operation: keep core_predicate: biolink:related_to -RO:0002003: - operation: keep - core_predicate: biolink:related_to +# RO:0002003: +# operation: keep +# core_predicate: biolink:related_to RO:0002005: operation: keep core_predicate: biolink:related_to @@ -4206,9 +4269,9 @@ RO:0002082: RO:0002083: operation: keep core_predicate: biolink:temporally_related_to -RO:0002084: - operation: keep - core_predicate: biolink:related_to +# RO:0002084: +# operation: keep +# core_predicate: biolink:related_to RO:0002087: operation: invert core_predicate: biolink:precedes @@ -4287,9 +4350,9 @@ RO:0002202: RO:0002203: operation: keep core_predicate: biolink:develops_from -RO:0002205: - operation: invert - core_predicate: biolink:gene_product_of +# RO:0002205: +# operation: invert +# core_predicate: biolink:gene_product_of RO:0002207: operation: keep core_predicate: biolink:develops_from @@ -4351,24 +4414,24 @@ RO:0002233: RO:0002234: operation: keep core_predicate: biolink:has_output -RO:0002241: - operation: keep - core_predicate: biolink:related_to +# RO:0002241: +# operation: keep +# core_predicate: biolink:related_to RO:0002254: operation: keep core_predicate: biolink:related_to -RO:0002255: - operation: keep - core_predicate: biolink:contributes_to +# RO:0002255: +# operation: keep +# core_predicate: biolink:contributes_to RO:0002256: operation: keep core_predicate: biolink:causes -RO:0002263: - operation: keep - core_predicate: biolink:acts_upstream_of -RO:0002264: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within +# RO:0002263: +# operation: keep +# core_predicate: biolink:acts_upstream_of +# RO:0002264: +# operation: keep +# core_predicate: biolink:acts_upstream_of_or_within RO:0002285: operation: invert core_predicate: biolink:precedes @@ -4390,20 +4453,20 @@ RO:0002298: RO:0002299: operation: keep core_predicate: biolink:has_output -RO:0002302: - operation: invert - core_predicate: biolink:treats +# RO:0002302: +# operation: invert +# core_predicate: biolink:treats RO:0002303: operation: keep core_predicate: biolink:located_in RO:0002309: operation: keep core_predicate: biolink:related_to -RO:0002313: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: transport +# RO:0002313: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: transport RO:0002314: operation: keep core_predicate: biolink:related_to @@ -4413,9 +4476,9 @@ RO:0002315: RO:0002322: operation: keep core_predicate: biolink:related_to -RO:0002326: - operation: keep - core_predicate: biolink:contributes_to +# RO:0002326: +# operation: keep +# core_predicate: biolink:contributes_to RO:0002328: operation: keep core_predicate: biolink:related_to @@ -4425,9 +4488,9 @@ RO:0002331: RO:0002332: operation: keep core_predicate: biolink:related_to -RO:0002333: - operation: invert - core_predicate: biolink:enables +# RO:0002333: +# operation: invert +# core_predicate: biolink:enables RO:0002334: operation: invert core_predicate: biolink:regulates @@ -4437,11 +4500,11 @@ RO:0002338: RO:0002339: operation: keep core_predicate: biolink:related_to -RO:0002340: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: transport +# RO:0002340: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: transport RO:0002341: operation: keep core_predicate: biolink:related_to @@ -4454,11 +4517,11 @@ RO:0002343: RO:0002344: operation: keep core_predicate: biolink:related_to -RO:0002345: - operation: keep - core_predicate: biolink:affects - qualifiers: - - object_aspect: transport +# RO:0002345: +# operation: keep +# core_predicate: biolink:affects +# qualifiers: +# - object_aspect: transport RO:0002348: operation: keep core_predicate: biolink:related_to @@ -4510,43 +4573,43 @@ RO:0002385: RO:0002387: operation: keep core_predicate: biolink:related_to -RO:0002410: - operation: keep - core_predicate: biolink:causes +# RO:0002410: +# operation: keep +# core_predicate: biolink:causes RO:0002411: operation: keep core_predicate: biolink:precedes RO:0002412: operation: keep - core_predicate: biolink:precedes -RO:0002432: - operation: keep - core_predicate: biolink:active_in -RO:0002433: - operation: keep - core_predicate: biolink:overlaps -RO:0002434: - operation: keep - core_predicate: biolink:interacts_with -RO:0002435: - operation: keep - core_predicate: biolink:genetically_interacts_with -RO:0002436: - operation: keep - core_predicate: biolink:physically_interacts_with -RO:0002448: - operation: keep - core_predicate: biolink:regulates -RO:0002449: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -RO:0002450: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: increased + core_predicate: biolink:precedes +# RO:0002432: +# operation: keep +# core_predicate: biolink:active_in +RO:0002433: + operation: keep + core_predicate: biolink:overlaps +# RO:0002434: +# operation: keep +# core_predicate: biolink:interacts_with +# RO:0002435: +# operation: keep +# core_predicate: biolink:genetically_interacts_with +# RO:0002436: +# operation: keep +# core_predicate: biolink:physically_interacts_with +# RO:0002448: +# operation: keep +# core_predicate: biolink:regulates +# RO:0002449: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: decreased +# RO:0002450: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: increased RO:0002451: operation: keep core_predicate: biolink:related_to @@ -4595,21 +4658,21 @@ RO:0002503: RO:0002505: operation: invert core_predicate: biolink:has_participant -RO:0002506: - operation: keep - core_predicate: biolink:causes +# RO:0002506: +# operation: keep +# core_predicate: biolink:causes RO:0002507: operation: keep core_predicate: biolink:causes RO:0002509: operation: keep core_predicate: biolink:causes -RO:0002510: - operation: keep - core_predicate: biolink:transcribed_from -RO:0002511: - operation: invert - core_predicate: biolink:transcribed_from +# RO:0002510: +# operation: keep +# core_predicate: biolink:transcribed_from +# RO:0002511: +# operation: invert +# core_predicate: biolink:transcribed_from RO:0002524: operation: keep core_predicate: biolink:has_part @@ -4634,9 +4697,9 @@ RO:0002573: RO:0002576: operation: invert core_predicate: biolink:has_part -RO:0002578: - operation: keep - core_predicate: biolink:regulates +# RO:0002578: +# operation: keep +# core_predicate: biolink:regulates RO:0002588: operation: keep core_predicate: biolink:has_output @@ -4649,72 +4712,80 @@ RO:0002591: RO:0002592: operation: keep core_predicate: biolink:affects -RO:0002599: - operation: keep - core_predicate: biolink:prevents -RO:0002604: - operation: keep - core_predicate: biolink:opposite_of -RO:0002606: - operation: keep - core_predicate: biolink:treats -RO:0002607: - operation: keep - core_predicate: biolink:biomarker_for +# RO:0002599: +# operation: keep +# core_predicate: biolink:prevents +# RO:0002604: +# operation: keep +# core_predicate: biolink:opposite_of +# RO:0002606: +# operation: keep +# core_predicate: biolink:treats +# RO:0002607: +# operation: keep +# core_predicate: biolink:biomarker_for RO:0002608: operation: invert core_predicate: biolink:causes RO:0002610: operation: keep core_predicate: biolink:correlated_with -RO:0002629: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: increased -RO:0002630: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased +# RO:0002629: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: increased +# RO:0002630: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: decreased RO:0003000: operation: keep core_predicate: biolink:produces RO:0003001: operation: invert core_predicate: biolink:produces -RO:0003002: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: expression - - object_direction: decreased -RO:0003003: - operation: keep - core_predicate: biolink:affects - qualified_predicate: biolink:causes - qualifiers: - - object_aspect: expression - - object_direction: increased -RO:0003301: - operation: keep - core_predicate: biolink:model_of +# RO:0003002: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: expression +# - object_direction: decreased +# RO:0003003: +# operation: keep +# core_predicate: biolink:affects +# qualified_predicate: biolink:causes +# qualifiers: +# - object_aspect: expression +# - object_direction: increased +# RO:0003301: +# operation: keep +# core_predicate: biolink:model_of RO:0003303: operation: keep core_predicate: biolink:causes RO:0003304: operation: keep core_predicate: biolink:contributes_to -RO:0003307: - operation: keep - core_predicate: biolink:ameliorates -RO:0003309: - operation: keep - core_predicate: biolink:exacerbates +# RO:0003307: +# operation: keep +# core_predicate: biolink:ameliorates +# RO:0003309: +# operation: keep +# core_predicate: biolink:exacerbates RO:0004001: operation: keep core_predicate: biolink:causes +# has material basis in germline mutation in +RO:0004003: + operation: keep + core_predicate: biolink:related_to +# has material basis in somatic mutation in +RO:0004004: + operation: keep + core_predicate: biolink:related_to RO:0004007: operation: keep core_predicate: biolink:has_participant @@ -4757,18 +4828,22 @@ RO:0004029: RO:0004030: operation: invert core_predicate: biolink:causes -RO:0004032: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within_positive_effect -RO:0004033: - operation: keep - core_predicate: biolink:acts_upstream_of_or_within_negative_effect -RO:0004034: - operation: keep - core_predicate: biolink:acts_upstream_of_positive_effect -RO:0004035: +# RO:0004032: +# operation: keep +# core_predicate: biolink:acts_upstream_of_or_within_positive_effect +# RO:0004033: +# operation: keep +# core_predicate: biolink:acts_upstream_of_or_within_negative_effect +# RO:0004034: +# operation: keep +# core_predicate: biolink:acts_upstream_of_positive_effect +# RO:0004035: +# operation: keep +# core_predicate: biolink:acts_upstream_of_negative_effect +# has disease driver +RO:0007001: operation: keep - core_predicate: biolink:acts_upstream_of_negative_effect + core_predicate: biolink:related_to RO:0009001: operation: keep core_predicate: biolink:related_to @@ -4787,15 +4862,58 @@ RO:0012008: RO:0013001: operation: keep core_predicate: biolink:related_to +RO:0013007: + operation: keep + core_predicate: biolink:overlaps RO:0014001: + operation: keep + core_predicate: biolink: +# increased in magnitude relative to +RO:0015007: + operation: delete +# decreased in magnitude relative to +RO:0015008: + operation: delete +# has relative magnitude +RO:0015010: + operation: delete +# has cross section +RO:0015011: + operation: delete +# reciprocal of +RO:0015012: operation: keep core_predicate: biolink:related_to -RO:HOM0000000: +# has high plasma membrane amount +RO:0015015: operation: keep - core_predicate: biolink:similar_to -RO:has_participant: + core_predicate: biolink:has_increased_amount +# has low plasma membrane amount +RO:0015016: operation: keep - core_predicate: biolink:has_participant + core_predicate: biolink:has_decreased_amount +# regulates characteristic +RO:0019000: + operation: keep + core_predicate: biolink:regulates +# positively regulates characteristic +RO:0019001: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: increased +# negatively regulates characteristic +RO:0019002: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased +# RO:HOM0000000: +# operation: keep +# core_predicate: biolink:similar_to +# RO:has_participant: +# operation: keep +# core_predicate: biolink:has_participant RO:participates_in: operation: invert core_predicate: biolink:has_participant @@ -4871,64 +4989,6 @@ RXNORM:tradename_of: operation: delete SEMMEDDB:1532: operation: delete -SEMMEDDB:AFFECTS: - operation: keep - core_predicate: biolink:affects -SEMMEDDB:CAUSES: - operation: keep - core_predicate: biolink:causes -SEMMEDDB:COEXISTS_WITH: - operation: keep - core_predicate: biolink:coexists_with -SEMMEDDB:CONVERTS_TO: - operation: invert - core_predicate: biolink:derives_from -SEMMEDDB:DISRUPTS: - operation: keep - core_predicate: biolink:disrupts -SEMMEDDB:INHIBITS: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased -SEMMEDDB:IS_A: - operation: keep - core_predicate: biolink:subclass_of -SEMMEDDB:LOCATION_OF: - operation: invert - core_predicate: biolink:located_in -SEMMEDDB:MANIFESTATION_OF: - operation: keep - core_predicate: biolink:manifestation_of -SEMMEDDB:OCCURS_IN: - operation: keep - core_predicate: biolink:occurs_in -SEMMEDDB:PART_OF: - operation: invert - core_predicate: biolink:has_part -SEMMEDDB:PRECEDES: - operation: keep - core_predicate: biolink:precedes -SEMMEDDB:PREVENTS: - operation: keep - core_predicate: biolink:prevents -SEMMEDDB:PROCESS_OF: - operation: keep - core_predicate: biolink:occurs_in -SEMMEDDB:PRODUCES: - operation: keep - core_predicate: biolink:produces -SEMMEDDB:SAME_AS: - operation: keep - core_predicate: biolink:close_match -SEMMEDDB:STIMULATES: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: increased -SEMMEDDB:TREATS: - operation: keep - core_predicate: biolink:treats SEMMEDDB:administered_to: operation: keep core_predicate: biolink:affects @@ -5040,111 +5100,111 @@ SEMMEDDB:xref: core_predicate: biolink:related_to SIO:000001: operation: delete -SIO:000203: - operation: keep - core_predicate: biolink:interacts_with -SIO:000628: - operation: keep - core_predicate: biolink:mentions -SIO:000983: - operation: keep - core_predicate: biolink:biomarker_for -SIO:001331: - operation: keep - core_predicate: biolink:diagnoses -SIO:010080: - operation: invert - core_predicate: biolink:transcribed_from -SIO:010081: - operation: keep - core_predicate: biolink:transcribed_from -SIO:010285: - operation: keep - core_predicate: biolink:in_complex_with -SO:0001583: - operation: keep - core_predicate: biolink:is_missense_variant_of -SO:0001589: - operation: keep - core_predicate: biolink:is_frameshift_variant_of -SO:0001629: - operation: keep - core_predicate: biolink:is_splice_site_variant_of -SO:0001819: - operation: keep - core_predicate: biolink:is_synonymous_variant_of -SO:0002054: - operation: keep - core_predicate: biolink:is_nonsense_variant_of +# SIO:000203: +# operation: keep +# core_predicate: biolink:interacts_with +# SIO:000628: +# operation: keep +# core_predicate: biolink:mentions +# SIO:000983: +# operation: keep +# core_predicate: biolink:biomarker_for +# SIO:001331: +# operation: keep +# core_predicate: biolink:diagnoses +# SIO:010080: +# operation: invert +# core_predicate: biolink:transcribed_from +# SIO:010081: +# operation: keep +# core_predicate: biolink:transcribed_from +# SIO:010285: +# operation: keep +# core_predicate: biolink:in_complex_with +# SO:0001583: +# operation: keep +# core_predicate: biolink:is_missense_variant_of +# SO:0001589: +# operation: keep +# core_predicate: biolink:is_frameshift_variant_of +# SO:0001629: +# operation: keep +# core_predicate: biolink:is_splice_site_variant_of +# SO:0001819: +# operation: keep +# core_predicate: biolink:is_synonymous_variant_of +# SO:0002054: +# operation: keep +# core_predicate: biolink:is_nonsense_variant_of SO:has_origin: operation: keep core_predicate: biolink:coexists_with -SO:similar_to: - operation: keep - core_predicate: biolink:similar_to -UBERON:anastomoses_with: - operation: keep - core_predicate: biolink:coexists_with -UBERON:anteriorly_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON:channel_for: - operation: keep - core_predicate: biolink:coexists_with -UBERON:channels_from: - operation: keep - core_predicate: biolink:coexists_with -UBERON:channels_into: - operation: keep - core_predicate: biolink:coexists_with -UBERON:conduit_for: - operation: keep - core_predicate: biolink:coexists_with -UBERON:distally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON:existence_starts_and_ends_during: - operation: keep - core_predicate: biolink:coexists_with -UBERON:extends_fibers_into: - operation: keep - core_predicate: biolink:coexists_with -UBERON:filtered_through: - operation: keep - core_predicate: biolink:coexists_with -UBERON:in_central_side_of: - operation: keep - core_predicate: biolink:coexists_with -UBERON:in_innermost_side_of: - operation: keep - core_predicate: biolink:coexists_with -UBERON:in_outermost_side_of: - operation: keep - core_predicate: biolink:coexists_with -UBERON:indirectly_supplies: - operation: keep - core_predicate: biolink:coexists_with -UBERON:posteriorly_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON:protects: - operation: keep - core_predicate: biolink:coexists_with -UBERON:proximally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON:sexually_homologous_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON:site_of: - operation: invert - core_predicate: biolink:occurs_in -UBERON:subdivision_of: - operation: invert - core_predicate: biolink:has_part -UBERON:synapsed_by: - operation: keep - core_predicate: biolink:related_to +# SO:similar_to: +# operation: keep +# core_predicate: biolink:similar_to +# UBERON:anastomoses_with: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:anteriorly_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:channel_for: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:channels_from: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:channels_into: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:conduit_for: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:distally_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:existence_starts_and_ends_during: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:extends_fibers_into: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:filtered_through: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:in_central_side_of: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:in_innermost_side_of: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:in_outermost_side_of: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:indirectly_supplies: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:posteriorly_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:protects: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:proximally_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:sexually_homologous_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON:site_of: +# operation: invert +# core_predicate: biolink:occurs_in +# UBERON:subdivision_of: +# operation: invert +# core_predicate: biolink:has_part +# UBERON:synapsed_by: +# operation: keep +# core_predicate: biolink:related_to UBERON_CORE:anastomoses_with: operation: keep core_predicate: biolink:coexists_with @@ -5184,9 +5244,9 @@ UBERON_CORE:in_outermost_side_of: UBERON_CORE:indirectly_supplies: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:layer_part_of: - operation: invert - core_predicate: biolink:has_part +# UBERON_CORE:layer_part_of: +# operation: invert +# core_predicate: biolink:has_part UBERON_CORE:posteriorly_connected_to: operation: keep core_predicate: biolink:coexists_with @@ -5208,33 +5268,33 @@ UBERON_CORE:subdivision_of: UBERON_CORE:synapsed_by: operation: keep core_predicate: biolink:coexists_with -UBERON_CORE:transitively_anteriorly_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:transitively_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:transitively_distally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:transitively_proximally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_CORE:trunk_part_of: - operation: invert - core_predicate: biolink:has_part -UBERON_NONAMESPACE:connected_to: - operation: keep - core_predicate: biolink:related_to -UBERON_NONAMESPACE:distally_connected_to: - operation: keep - core_predicate: biolink:coexists_with -UBERON_NONAMESPACE:innervated_by: - operation: keep - core_predicate: biolink:related_to -UBERON_NONAMESPACE:subdivision_of: - operation: keep - core_predicate: biolink:coexists_with +# UBERON_CORE:transitively_anteriorly_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON_CORE:transitively_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON_CORE:transitively_distally_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON_CORE:transitively_proximally_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON_CORE:trunk_part_of: +# operation: invert +# core_predicate: biolink:has_part +# UBERON_NONAMESPACE:connected_to: +# operation: keep +# core_predicate: biolink:related_to +# UBERON_NONAMESPACE:distally_connected_to: +# operation: keep +# core_predicate: biolink:coexists_with +# UBERON_NONAMESPACE:innervated_by: +# operation: keep +# core_predicate: biolink:related_to +# UBERON_NONAMESPACE:subdivision_of: +# operation: keep +# core_predicate: biolink:coexists_with UMLS:RB: operation: invert core_predicate: biolink:subclass_of @@ -5244,8 +5304,8 @@ UMLS:RO: UMLS:RQ: operation: keep core_predicate: biolink:related_to -UMLS:SIB: - operation: delete +# UMLS:SIB: +# operation: delete UMLS:SY: operation: keep core_predicate: biolink:close_match @@ -5330,12 +5390,12 @@ UMLS:supported_concept_property_in: operation: delete UMLS:supported_concept_relationship_in: operation: delete -UO-PROPERTY:is_unit_of: - operation: keep - core_predicate: biolink:related_to -UPHENO:0000001: - operation: keep - core_predicate: biolink:affects +# UO-PROPERTY:is_unit_of: +# operation: keep +# core_predicate: biolink:related_to +# UPHENO:0000001: +# operation: keep +# core_predicate: biolink:affects VANDF:has_ingredient: operation: keep core_predicate: biolink:has_part @@ -5348,84 +5408,84 @@ VANDF:inverse_isa: VANDF:isa: operation: keep core_predicate: biolink:subclass_of -WIKIDATA:P2888: - operation: keep - core_predicate: biolink:exact_match -WIKIDATA:P3433: - operation: keep - core_predicate: biolink:is_sequence_variant_of -WIKIDATA:Q181394: - operation: keep - core_predicate: biolink:has_nutrient -WIKIDATA:Q39893449: - operation: keep - core_predicate: biolink:exact_match -WIKIDATA:Q39893967: - operation: invert - core_predicate: biolink:broad_match -WIKIDATA:Q39894595: - operation: keep - core_predicate: biolink:broad_match -WIKIDATA:Q66088480: - operation: invert - core_predicate: biolink:subclass_of -WIKIDATA_PROPERTY:P1056: - operation: keep - core_predicate: biolink:produces -WIKIDATA_PROPERTY:P123: - operation: keep - core_predicate: biolink:publisher -WIKIDATA_PROPERTY:P128: - operation: keep - core_predicate: biolink:regulates -WIKIDATA_PROPERTY:P129: - operation: keep - core_predicate: biolink:physically_interacts_with -WIKIDATA_PROPERTY:P1542: - operation: keep - core_predicate: biolink:causes -WIKIDATA_PROPERTY:P1557: - operation: keep - core_predicate: biolink:manifestation_of -WIKIDATA_PROPERTY:P156: - operation: keep - core_predicate: biolink:precedes -WIKIDATA_PROPERTY:P2175: - operation: keep - core_predicate: biolink:treats -WIKIDATA_PROPERTY:P2176: - operation: invert - core_predicate: biolink:treats -WIKIDATA_PROPERTY:P2293: - operation: keep - core_predicate: biolink:genetic_association -WIKIDATA_PROPERTY:P276: - operation: invert - core_predicate: biolink:located_in -WIKIDATA_PROPERTY:P279: - operation: keep - core_predicate: biolink:subclass_of -WIKIDATA_PROPERTY:P361: - operation: invert - core_predicate: biolink:has_part -WIKIDATA_PROPERTY:P50: - operation: keep - core_predicate: biolink:author -WIKIDATA_PROPERTY:P527: - operation: keep - core_predicate: biolink:has_part -WIKIDATA_PROPERTY:P688: - operation: invert - core_predicate: biolink:gene_product_of -WIKIDATA_PROPERTY:P703: - operation: keep - core_predicate: biolink:in_taxon -WIKIDATA_PROPERTY:P828: - operation: invert - core_predicate: biolink:causes -WIKIDATA_PROPERTY:P98: - operation: keep - core_predicate: biolink:editor +# WIKIDATA:P2888: +# operation: keep +# core_predicate: biolink:exact_match +# WIKIDATA:P3433: +# operation: keep +# core_predicate: biolink:is_sequence_variant_of +# WIKIDATA:Q181394: +# operation: keep +# core_predicate: biolink:has_nutrient +# WIKIDATA:Q39893449: +# operation: keep +# core_predicate: biolink:exact_match +# WIKIDATA:Q39893967: +# operation: invert +# core_predicate: biolink:broad_match +# WIKIDATA:Q39894595: +# operation: keep +# core_predicate: biolink:broad_match +# WIKIDATA:Q66088480: +# operation: invert +# core_predicate: biolink:subclass_of +# WIKIDATA_PROPERTY:P123: +# operation: keep +# core_predicate: biolink:publisher +# WIKIDATA_PROPERTY:P128: +# operation: keep +# core_predicate: biolink:regulates +# WIKIDATA_PROPERTY:P129: +# operation: keep +# core_predicate: biolink:physically_interacts_with +# WIKIDATA_PROPERTY:P1056: +# operation: keep +# core_predicate: biolink:produces +# WIKIDATA_PROPERTY:P1542: +# operation: keep +# core_predicate: biolink:causes +# WIKIDATA_PROPERTY:P1557: +# operation: keep +# core_predicate: biolink:manifestation_of +# WIKIDATA_PROPERTY:P156: +# operation: keep +# core_predicate: biolink:precedes +# WIKIDATA_PROPERTY:P2175: +# operation: keep +# core_predicate: biolink:treats +# WIKIDATA_PROPERTY:P2176: +# operation: invert +# core_predicate: biolink:treats +# WIKIDATA_PROPERTY:P2293: +# operation: keep +# core_predicate: biolink:genetic_association +# WIKIDATA_PROPERTY:P276: +# operation: invert +# core_predicate: biolink:located_in +# WIKIDATA_PROPERTY:P279: +# operation: keep +# core_predicate: biolink:subclass_of +# WIKIDATA_PROPERTY:P361: +# operation: invert +# core_predicate: biolink:has_part +# WIKIDATA_PROPERTY:P50: +# operation: keep +# core_predicate: biolink:author +# WIKIDATA_PROPERTY:P527: +# operation: keep +# core_predicate: biolink:has_part +# WIKIDATA_PROPERTY:P688: +# operation: invert +# core_predicate: biolink:gene_product_of +# WIKIDATA_PROPERTY:P703: +# operation: keep +# core_predicate: biolink:in_taxon +# WIKIDATA_PROPERTY:P828: +# operation: invert +# core_predicate: biolink:causes +# WIKIDATA_PROPERTY:P98: +# operation: keep +# core_predicate: biolink:editor biolink:in_taxon: operation: keep core_predicate: biolink:subclass_of @@ -5435,59 +5495,56 @@ biolink:part_of: biolink:subclass_of: operation: invert core_predicate: biolink:has_part -dct:contributor: - operation: keep - core_predicate: biolink:contributor -dct:creator: - operation: keep - core_predicate: biolink:author -dct:publisher: - operation: keep - core_predicate: biolink:publisher -faldo:location: - operation: keep - core_predicate: biolink:has_sequence_location +# dct:contributor: +# operation: keep +# core_predicate: biolink:contributor +# dct:creator: +# operation: keep +# core_predicate: biolink:author +# dct:publisher: +# operation: keep +# core_predicate: biolink:publisher +# faldo:location: +# operation: keep +# core_predicate: biolink:has_sequence_location oboFormat:xref: operation: keep core_predicate: biolink:close_match -oboformat:xref: - operation: keep - core_predicate: biolink:close_match owl:inverseOf: operation: keep core_predicate: biolink:related_to owl:sameAs: operation: keep core_predicate: biolink:same_as -owl:topObjectProperty: - operation: keep - core_predicate: biolink:related_to +# owl:topObjectProperty: +# operation: keep +# core_predicate: biolink:related_to rdf:type: operation: keep core_predicate: biolink:related_to -rdfs:negatively_regulates: - operation: keep - core_predicate: biolink:regulates - qualifiers: - - object_direction: decreased +# rdfs:negatively_regulates: +# operation: keep +# core_predicate: biolink:regulates +# qualifiers: +# - object_direction: decreased rdfs:subClassOf: operation: keep core_predicate: biolink:subclass_of rdfs:subPropertyOf: operation: keep core_predicate: biolink:subclass_of -skos:broadMatch: - operation: keep - core_predicate: biolink:broad_match -skos:closeMatch: - operation: keep - core_predicate: biolink:close_match -skos:exactMatch: - operation: keep - core_predicate: biolink:exact_match -skos:narrowMatch: - operation: invert - core_predicate: biolink:broad_match -skos:relatedMatch: - operation: keep - core_predicate: biolink:related_to +# skos:broadMatch: +# operation: keep +# core_predicate: biolink:broad_match +# skos:closeMatch: +# operation: keep +# core_predicate: biolink:close_match +# skos:exactMatch: +# operation: keep +# core_predicate: biolink:exact_match +# skos:narrowMatch: +# operation: invert +# core_predicate: biolink:broad_match +# skos:relatedMatch: +# operation: keep +# core_predicate: biolink:related_to From 7f4b9c05decb00ba55518ce4ad6f16d3f537fe64 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 18 Oct 2022 16:21:30 -0700 Subject: [PATCH 084/127] #242 Fixing typo --- predicate-remap.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/predicate-remap.yaml b/predicate-remap.yaml index b47f6415..fa355d61 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -4867,7 +4867,7 @@ RO:0013007: core_predicate: biolink:overlaps RO:0014001: operation: keep - core_predicate: biolink: + core_predicate: biolink:related_to # increased in magnitude relative to RO:0015007: operation: delete From c300928dbb74e79937218bb6b11f5add600a3f1a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 18 Oct 2022 18:21:19 -0700 Subject: [PATCH 085/127] #242 Editing curies in according to error --- predicate-remap.yaml | 78 ++++++++++++++++++++------------------------ 1 file changed, 36 insertions(+), 42 deletions(-) diff --git a/predicate-remap.yaml b/predicate-remap.yaml index fa355d61..901ca899 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -3925,63 +3925,57 @@ OMIM:manifestation_of: OMIM:phenotype_of: operation: invert core_predicate: biolink:has_phenotype -ORPHA:317343: +# ORPHA:317343: +# operation: keep +# core_predicate: biolink:causes +# ORPHA:317344: +# operation: keep +# core_predicate: biolink:causes +# ORPHA:317346: +# operation: keep +# core_predicate: biolink:causes +# ORPHANET:327767: +# operation: keep +# core_predicate: biolink:actively_involved_in +# ORPHA:410295: +# operation: keep +# core_predicate: biolink:causes +# ORPHA:410296: +# operation: keep +# core_predicate: biolink:causes +# ORPHA:465410: +# operation: keep +# core_predicate: biolink:biomarker_for +ORPHANET:317343: operation: keep core_predicate: biolink:causes -ORPHA:317344: +ORPHANET:317344: operation: keep core_predicate: biolink:causes -ORPHA:317346: +ORPHANET:317345: + operation: keep + core_predicate: biolink:correlated_with +ORPHANET:317346: operation: keep core_predicate: biolink:causes -ORPHA:317348: +ORPHANET:317348: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:317349: +ORPHANET:317349: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:327767: +ORPHANET:327767: operation: keep core_predicate: biolink:actively_involved_in -ORPHA:410295: +ORPHANET:410295: operation: keep core_predicate: biolink:causes -ORPHA:410296: +ORPHANET:410296: operation: keep core_predicate: biolink:causes -ORPHA:465410: +ORPHANET:465410: operation: keep core_predicate: biolink:biomarker_for -# ORPHANET:317343: -# operation: keep -# core_predicate: biolink:causes -# ORPHANET:317344: -# operation: keep -# core_predicate: biolink:causes -ORPHANET:317345: - operation: keep - core_predicate: biolink:correlated_with -# ORPHANET:317346: -# operation: keep -# core_predicate: biolink:causes -# ORPHANET:317348: -# operation: keep -# core_predicate: biolink:actively_involved_in -# ORPHANET:317349: -# operation: keep -# core_predicate: biolink:actively_involved_in -# ORPHANET:327767: -# operation: keep -# core_predicate: biolink:actively_involved_in -# ORPHANET:410295: -# operation: keep -# core_predicate: biolink:causes -# ORPHANET:410296: -# operation: keep -# core_predicate: biolink:causes -# ORPHANET:465410: -# operation: keep -# core_predicate: biolink:biomarker_for ORPHANET:C016: operation: keep core_predicate: biolink:related_to @@ -4763,9 +4757,9 @@ RO:0003001: # RO:0003301: # operation: keep # core_predicate: biolink:model_of -RO:0003303: - operation: keep - core_predicate: biolink:causes +# RO:0003303: +# operation: keep +# core_predicate: biolink:causes RO:0003304: operation: keep core_predicate: biolink:contributes_to From 5a8fd043a0513cf31a1bc1f3f276b7a8429966a0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 19 Oct 2022 10:38:33 -0700 Subject: [PATCH 086/127] #243 Troubleshooting error in Slim --- Snakefile-post-etl | 4 +++- slim_kg2.py | 33 +++++++++++++++++++++++++-------- 2 files changed, 28 insertions(+), 9 deletions(-) diff --git a/Snakefile-post-etl b/Snakefile-post-etl index 53f893af..a95fecc7 100644 --- a/Snakefile-post-etl +++ b/Snakefile-post-etl @@ -75,8 +75,10 @@ rule Slim: placeholder = config['SIMPLIFIED_OUTPUT_NODES_FILE_FULL'] output: config['SLIM_OUTPUT_FILE_FULL'] + log: + config['BUILD_DIR'] + "slim_kg2.log" + config['TEST_SUFFIX'] + ".log" shell: - config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/slim_kg2.py " + config['TEST_ARG'] + " {input.slim_real} {output}" + config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/slim_kg2.py " + config['TEST_ARG'] + " {input.slim_real} {output} > {log} 2>&1" rule Simplify_Stats: input: diff --git a/slim_kg2.py b/slim_kg2.py index 300803f8..f514faad 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -27,26 +27,43 @@ def make_arg_parser(): if __name__ == "__main__": node_set = set(["name", "id", "full_name", "category", "knowledge_source"]) - edge_set = set(["predicate", "subject", "object", "predicate_label", "knowledge_source"]) + edge_set = set(["core_predicate", "subject", "object", "predicate_label", "knowledge_source"]) args = make_arg_parser().parse_args() test_mode = args.test reduced = {"nodes": [], "edges": []} - with open(args.inputFilepath, "r") as fp: + with open(args.inputFilepath, "r") as fp:0 all_data = json.load(fp) reduced["build"] = all_data["build"] - for node in all_data["nodes"]: - temp_node = {} - for key, val in node.items(): - if key in node_set: - temp_node[key] = val - reduced["nodes"].append(temp_node) + # num_nodes = len(all_data["nodes"]) + # node_ctr = 0 + # for node in all_data["nodes"]: + # node_ctr += 1 + # if node_ctr % 1000000 == 0: + # print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") + # temp_node = {} + # for key, val in node.items(): + # if key in node_set: + # temp_node[key] = val + # reduced["nodes"].append(temp_node) + # print(f"Nodes completed") + num_nodes = len(all_data["edges"]) + edge_ctr = 0 + num_edges = len(all_data["edges"]) for edge in all_data["edges"]: + edge_ctr += 0 + if edge_ctr % 1000000 ==0: + print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") temp_edge = {} + if edge_ctr < 5: + print(f"Example edge: {edge}") for key, val in edge.items(): if key in edge_set: temp_edge[key] = val + else: + print(f"Key {key} not in edge set") reduced["edges"].append(temp_edge) + print(f"Edges completed") kg2_util.save_json(reduced, args.outputFilepath, test_mode) From c22a7b78bc7d25a7572baa560db24592d32feaf0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 19 Oct 2022 10:45:25 -0700 Subject: [PATCH 087/127] #243 Correcting typos --- Snakefile-post-etl | 2 +- slim_kg2.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Snakefile-post-etl b/Snakefile-post-etl index a95fecc7..0ac878af 100644 --- a/Snakefile-post-etl +++ b/Snakefile-post-etl @@ -76,7 +76,7 @@ rule Slim: output: config['SLIM_OUTPUT_FILE_FULL'] log: - config['BUILD_DIR'] + "slim_kg2.log" + config['TEST_SUFFIX'] + ".log" + config['BUILD_DIR'] + "/slim_kg2" + config['TEST_SUFFIX'] + ".log" shell: config['VENV_DIR'] + "/bin/python3 -u " + config['CODE_DIR'] + "/slim_kg2.py " + config['TEST_ARG'] + " {input.slim_real} {output} > {log} 2>&1" diff --git a/slim_kg2.py b/slim_kg2.py index f514faad..71c6e290 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -32,7 +32,7 @@ def make_arg_parser(): args = make_arg_parser().parse_args() test_mode = args.test reduced = {"nodes": [], "edges": []} - with open(args.inputFilepath, "r") as fp:0 + with open(args.inputFilepath, "r") as fp: all_data = json.load(fp) reduced["build"] = all_data["build"] # num_nodes = len(all_data["nodes"]) From 080350388b6e7fedf901420e5eb9fdfe1694fdc0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 20 Oct 2022 10:15:49 -0700 Subject: [PATCH 088/127] #243 Working on updating slim_kg2.py --- slim_kg2.py | 89 ++++++++++++++++++++++++++---------------- slim_kg2_DEPRECATED.py | 69 ++++++++++++++++++++++++++++++++ 2 files changed, 124 insertions(+), 34 deletions(-) create mode 100644 slim_kg2_DEPRECATED.py diff --git a/slim_kg2.py b/slim_kg2.py index 71c6e290..0ec11b37 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -13,6 +13,7 @@ __status__ = 'Prototype' import json +import ijson import argparse import kg2_util @@ -25,6 +26,17 @@ def make_arg_parser(): return arg_parser +def tokenizer(): + # Write a tokenizer to handle chunks of a json stream + pass + + +def stateMachine(): + # remember which part of the json object we're currently processing. + # Start of object -> Field Name -> Start of array -> start of object -> validate and save record + pass + + if __name__ == "__main__": node_set = set(["name", "id", "full_name", "category", "knowledge_source"]) edge_set = set(["core_predicate", "subject", "object", "predicate_label", "knowledge_source"]) @@ -33,37 +45,46 @@ def make_arg_parser(): test_mode = args.test reduced = {"nodes": [], "edges": []} with open(args.inputFilepath, "r") as fp: - all_data = json.load(fp) - reduced["build"] = all_data["build"] - # num_nodes = len(all_data["nodes"]) - # node_ctr = 0 - # for node in all_data["nodes"]: - # node_ctr += 1 - # if node_ctr % 1000000 == 0: - # print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") - # temp_node = {} - # for key, val in node.items(): - # if key in node_set: - # temp_node[key] = val - # reduced["nodes"].append(temp_node) - # print(f"Nodes completed") - - num_nodes = len(all_data["edges"]) - edge_ctr = 0 - num_edges = len(all_data["edges"]) - for edge in all_data["edges"]: - edge_ctr += 0 - if edge_ctr % 1000000 ==0: - print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") - temp_edge = {} - if edge_ctr < 5: - print(f"Example edge: {edge}") - for key, val in edge.items(): - if key in edge_set: - temp_edge[key] = val - else: - print(f"Key {key} not in edge set") - reduced["edges"].append(temp_edge) - print(f"Edges completed") - - kg2_util.save_json(reduced, args.outputFilepath, test_mode) + + # File is too big to use json.load() + #all_data = json.load(fp) + + build = ijson.items(fp, 'build.item') + print(f"{str(build)}") + + # nodes = ijson.items(fp, 'nodes.item') + + + # reduced["build"] = all_data["build"] + # num_nodes = len(all_data["nodes"]) + # node_ctr = 0 + # for node in all_data["nodes"]: + # node_ctr += 1 + # if node_ctr % 1000000 == 0: + # print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") + # temp_node = {} + # for key, val in node.items(): + # if key in node_set: + # temp_node[key] = val + # reduced["nodes"].append(temp_node) + # print(f"Nodes completed") + + # num_nodes = len(all_data["edges"]) + # edge_ctr = 0 + # num_edges = len(all_data["edges"]) + # for edge in all_data["edges"]: + # edge_ctr += 0 + # if edge_ctr % 1000000 ==0: + # print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") + # temp_edge = {} + # if edge_ctr < 5: + # print(f"Example edge: {edge}") + # for key, val in edge.items(): + # if key in edge_set: + # temp_edge[key] = val + # else: + # print(f"Key {key} not in edge set") + # reduced["edges"].append(temp_edge) + # print(f"Edges completed") + + # kg2_util.save_json(reduced, args.outputFilepath, test_mode) diff --git a/slim_kg2_DEPRECATED.py b/slim_kg2_DEPRECATED.py new file mode 100644 index 00000000..845e263d --- /dev/null +++ b/slim_kg2_DEPRECATED.py @@ -0,0 +1,69 @@ +#!/usr/bin/env python3 +''' slim_kg2.py: reduce graph in KG2 JSON format to only bare-bones node and edge properties. + Usage: slim_kg2.py + --outputFile Date: Thu, 20 Oct 2022 15:22:57 -0700 Subject: [PATCH 089/127] #243 Working on slim_kg2.py --- slim_kg2.py | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/slim_kg2.py b/slim_kg2.py index 0ec11b37..b1b8e7e0 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -44,16 +44,31 @@ def stateMachine(): args = make_arg_parser().parse_args() test_mode = args.test reduced = {"nodes": [], "edges": []} + # I think splitting this file into nodes and edges might be helpful in the future, + # but I'm leaving it as is for nwo + # reduced_nodes = {"nodes": []} + # reduced_edges = {"edges": []} with open(args.inputFilepath, "r") as fp: # File is too big to use json.load() #all_data = json.load(fp) - build = ijson.items(fp, 'build.item') - print(f"{str(build)}") - - # nodes = ijson.items(fp, 'nodes.item') - + for item in ijson.items(fp, "build"): + reduced["build"] = item + + node_ctr = 0 + num_nodes = 11117653 # Snagging this number for kg2-report.json for debugging purposes + for node in ijson.items(fp, "nodes"): + node_ctr += 1 + if node_ctr % 1000000 == 0: + print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") + temp_node = {} + for key, val in node: + if key in node_set: + temp_node[key] = val + reduced["nodes"].append(temp_node) + print(temp_node) + print("Nodes completed") # reduced["build"] = all_data["build"] # num_nodes = len(all_data["nodes"]) From 60e457b47cc26ca57330aedb8c1ffdb1a38baed0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 21 Oct 2022 10:33:25 -0700 Subject: [PATCH 090/127] #243 Updated to streaming --- slim_kg2.py | 88 +++++++++++++++++++---------------------------------- 1 file changed, 31 insertions(+), 57 deletions(-) diff --git a/slim_kg2.py b/slim_kg2.py index b1b8e7e0..16346bbb 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -3,9 +3,9 @@ Usage: slim_kg2.py --outputFile Field Name -> Start of array -> start of object -> validate and save record - pass - - if __name__ == "__main__": node_set = set(["name", "id", "full_name", "category", "knowledge_source"]) edge_set = set(["core_predicate", "subject", "object", "predicate_label", "knowledge_source"]) @@ -49,57 +38,42 @@ def stateMachine(): # reduced_nodes = {"nodes": []} # reduced_edges = {"edges": []} with open(args.inputFilepath, "r") as fp: - - # File is too big to use json.load() - #all_data = json.load(fp) for item in ijson.items(fp, "build"): reduced["build"] = item + with open(args.inputFilepath, "r") as fp: + node_ctr = 0 num_nodes = 11117653 # Snagging this number for kg2-report.json for debugging purposes - for node in ijson.items(fp, "nodes"): - node_ctr += 1 - if node_ctr % 1000000 == 0: - print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") - temp_node = {} - for key, val in node: - if key in node_set: - temp_node[key] = val - reduced["nodes"].append(temp_node) - print(temp_node) + + for node_list in ijson.items(fp, "nodes"): + for node in node_list: + node_ctr += 1 + if node_ctr % 1000000 == 0: + print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") + temp_node = {} + for key, val in node.items(): + if key in node_set: + temp_node[key] = val + reduced["nodes"].append(temp_node) print("Nodes completed") - # reduced["build"] = all_data["build"] - # num_nodes = len(all_data["nodes"]) - # node_ctr = 0 - # for node in all_data["nodes"]: - # node_ctr += 1 - # if node_ctr % 1000000 == 0: - # print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") - # temp_node = {} - # for key, val in node.items(): - # if key in node_set: - # temp_node[key] = val - # reduced["nodes"].append(temp_node) - # print(f"Nodes completed") + with open(args.inputFilepath, "r") as fp: - # num_nodes = len(all_data["edges"]) - # edge_ctr = 0 - # num_edges = len(all_data["edges"]) - # for edge in all_data["edges"]: - # edge_ctr += 0 - # if edge_ctr % 1000000 ==0: - # print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") - # temp_edge = {} - # if edge_ctr < 5: - # print(f"Example edge: {edge}") - # for key, val in edge.items(): - # if key in edge_set: - # temp_edge[key] = val - # else: - # print(f"Key {key} not in edge set") - # reduced["edges"].append(temp_edge) - # print(f"Edges completed") + edge_ctr = 0 + num_edges = 11117653 # Snagging this number for kg2-report.json for debugging purposes + + for edge_list in ijson.items(fp, "edges"): + for edge in edge_list: + edge_ctr += 1 + if edge_ctr % 1000000 == 0: + print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") + temp_edge = {} + for key, val in edge.items(): + if key in edge_set: + temp_edge[key] = val + reduced["edges"].append(temp_edge) + print("Edges completed") - # kg2_util.save_json(reduced, args.outputFilepath, test_mode) + kg2_util.save_json(reduced, args.outputFilepath, test_mode) From 64aa52b4db048a362b5c3de067688bcd8c3aecdb Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Sat, 22 Oct 2022 15:26:15 -0700 Subject: [PATCH 091/127] #243 Fixing issue with streaming functionality --- slim_kg2.py | 43 ++++++++++++++++++------------------------- 1 file changed, 18 insertions(+), 25 deletions(-) diff --git a/slim_kg2.py b/slim_kg2.py index 16346bbb..941963bf 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -16,6 +16,7 @@ import ijson import argparse import kg2_util +import datetime def make_arg_parser(): @@ -33,47 +34,39 @@ def make_arg_parser(): args = make_arg_parser().parse_args() test_mode = args.test reduced = {"nodes": [], "edges": []} - # I think splitting this file into nodes and edges might be helpful in the future, - # but I'm leaving it as is for nwo - # reduced_nodes = {"nodes": []} - # reduced_edges = {"edges": []} - with open(args.inputFilepath, "r") as fp: - - for item in ijson.items(fp, "build"): - reduced["build"] = item - + start = datetime.datetime.now() + print(f"Start time: {start}") + with open(args.inputFilepath, "r") as fp: node_ctr = 0 - num_nodes = 11117653 # Snagging this number for kg2-report.json for debugging purposes - - for node_list in ijson.items(fp, "nodes"): - for node in node_list: + edge_ctr = 0 + + for graph in ijson.items(fp, ""): + print(graph["build"]) + reduced["build"] = graph["build"] + for node in graph["nodes"]: node_ctr += 1 if node_ctr % 1000000 == 0: - print(f"Processing node {str(node_ctr)} of {str(num_nodes)}") + print(node_ctr) temp_node = {} for key, val in node.items(): if key in node_set: temp_node[key] = val reduced["nodes"].append(temp_node) - print("Nodes completed") - - with open(args.inputFilepath, "r") as fp: - - edge_ctr = 0 - num_edges = 11117653 # Snagging this number for kg2-report.json for debugging purposes - - for edge_list in ijson.items(fp, "edges"): - for edge in edge_list: + print("Nodes completed") + for edge in graph["edges"]: edge_ctr += 1 if edge_ctr % 1000000 == 0: - print(f"Processing edge {str(edge_ctr)} of {str(num_edges)}") + print(edge_ctr) temp_edge = {} for key, val in edge.items(): if key in edge_set: temp_edge[key] = val reduced["edges"].append(temp_edge) - print("Edges completed") + print("Edges completed") + + finish = datetime.datetime.now() + print(f"Finish time: {finish} \nTotal time: {finish-start}") kg2_util.save_json(reduced, args.outputFilepath, test_mode) From a7bc8e41abd426a1e30be5c875c9edb4729a9d70 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 24 Oct 2022 11:07:34 -0700 Subject: [PATCH 092/127] #244 Work on TSV --- kg_json_to_tsv.py | 48 +++++++++++++++++++++-------------------------- 1 file changed, 21 insertions(+), 27 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index 55af675e..b504b912 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -10,6 +10,7 @@ import datetime import argparse import sys +import ijson __author__ = 'Erica Wood' __copyright__ = 'Oregon State University' @@ -122,18 +123,15 @@ def shorten_description_if_too_large(node_description_field, node_id): return node_description_field.replace("\n"," ") -def nodes(graph, output_file_location): +def nodes(nodes_list, output_file_location): """ - :param graph: A dictionary containing KG2 + :param nodes_list: A list containing KG2 nodes :param output_file_location: A string containing the path to the TSV output directory """ # Generate list of output file names for the nodes TSV files nodes_file = output_files(output_file_location, "nodes") - # Create dictionary of nodes from KG2 - nodes = graph["nodes"] - # Open output TSV files tsvfile = open(nodes_file[0], 'w+') tsvfile_h = open(nodes_file[1], 'w+') @@ -150,13 +148,13 @@ def nodes(graph, output_file_location): # Set single loop to zero and get list of node properties, which will go # in the header, to compare other nodes to single_loop = 0 - for node in nodes: + for node in nodes_list: single_loop += 1 if single_loop == 1: nodekeys_official = list(sorted(node.keys())) nodekeys_official.append("category") - for node in nodes: + for node in nodes_list: # Inrease node counter by one each loop loop += 1 @@ -230,18 +228,15 @@ def limit_publication_info_size(key, pub_inf_dict): return pub_inf_dict -def edges(graph, output_file_location): +def edges(edges_list, output_file_location): """ - :param graph: A dictionary containing KG2 + :param edges_list: A list containing KG2 edges :param output_file_location: A string containing the path to the TSV output directory """ # Generate list of output file names for the edges TSV files edges_file = output_files(output_file_location, "edges") - # Create dictionary of edges from KG2 - edges = graph["edges"] - # Open output TSV files tsvfile = open(edges_file[0], 'w+') tsvfile_h = open(edges_file[1], 'w+') @@ -253,7 +248,7 @@ def edges(graph, output_file_location): tsvwrite = tsv.writer(tsvfile, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) tsvwrite_h = tsv.writer(tsvfile_h, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) - for edge in edges: + for edge in edges_list: # Inrease edge counter by one each loop loop += 1 @@ -302,23 +297,22 @@ def edges(graph, output_file_location): if __name__ == '__main__': - print("Start time: ", date()) + print(f"Start time: {date()}") parser = argparse.ArgumentParser() parser.add_argument("inputFile", type=str, help="Path to Knowledge Graph \ JSON File to Import") parser.add_argument("outputFileLocation", help="Path to Directory for Output\ TSV Files to Go", type=str) arguments = parser.parse_args() - print("Start load: ", date()) - with open(arguments.inputFile) as json_file: - graph = json.load(json_file) - print("End load: ", date()) - print("Start nodes: ", date()) - output_file_location = arguments.outputFileLocation - nodes(graph, output_file_location) - print("Finish nodes: ", date()) - print("Start edges: ", date()) - edges(graph, output_file_location) - print("Finish edges: ", date()) - json_file.close() - print("Finish time: ", date()) + output_file_location = arguments.outputFileLocation + print(f"Start load: {date()}") + with open(arguments.inputFile, "r") as json_file: + for graph in ijson.items(json_file, ""): + print(f"End load: {date()}") + print(f"Start nodes: {date()}") + nodes(graph["nodes"], output_file_location) + print(f"Finish nodes: {date()}") + print(f"Start edges: {date()}") + edges(graph["edges"], output_file_location) + print(f"Finish edges: {date()}") + print(f"Completed: {date()}") From 1a0a6bbc3f085332513df785f0a64e9e77378b74 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 24 Oct 2022 17:08:14 -0700 Subject: [PATCH 093/127] #226 Correction in report_stats --- report_stats_on_json_kg.py | 1 - 1 file changed, 1 deletion(-) diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 22e8c307..23953bb9 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -162,7 +162,6 @@ def count_types_of_pairs_of_curies_for_equivs(edges: list): if 'nodes' not in graph: print("WARNING: 'nodes' property is missing from the input JSON.", file=sys.stderr) nodes = graph.get('nodes', []) - nodes = graph.get('nodes', []) for n in nodes[::-1]: # search for build info node starting at end if n["name"] == "KG2:Build": # should be the first node accessed nodes.remove(n) # remove it so stats aren't reported From daf551a2a2220167a6de40e13eba7b0a51f81f61 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 24 Oct 2022 17:08:49 -0700 Subject: [PATCH 094/127] #226 Updating kg2-versions --- kg2-versions.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/kg2-versions.md b/kg2-versions.md index b49d9874..4126947e 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -1,4 +1,4 @@ -# 2.7.7 +# 2.8.0 **Date: 2022.XX.XX** Counts: @@ -9,16 +9,16 @@ Issues: - Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) - Issue [#221](https://github.com/RTXteam/RTX-KG2/issues/221) - Issue [#222](https://github.com/RTXteam/RTX-KG2/issues/222) -- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238 +- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238, #243 Build info: -- Biolink Model version: 2.4.2 +- Biolink Model version: 3.0.0 - Build host: `buildkg2.rtx.ai` - Build directory: `/home/ubuntu/kg2-build` - Build code branch: `master` -- Neo4j endpoint CNAME: `kg2-7-7.rtx.ai` +- Neo4j endpoint CNAME: `kg2-8-0.rtx.ai` - Neo4j endpoint hostname: `kg2endpoint2.rtx.ai` -- Tracking issue for the build: Issue [#202](https://github.com/RTXteam/RTX-KG2/issues/202) +- Tracking issue for the build: Issue [#226](https://github.com/RTXteam/RTX-KG2/issues/226) - Major knowledge source versions: - SemMedDB: `23 (2021)` - UMLS: `2022AA` From 385fe2277f742580d6167cd80d521427d320ce50 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 25 Oct 2022 08:04:04 -0700 Subject: [PATCH 095/127] #243 work on slim_kg2.py --- slim_kg2.py | 52 +++++++++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 23 deletions(-) diff --git a/slim_kg2.py b/slim_kg2.py index 941963bf..b09f0f7f 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -41,30 +41,36 @@ def make_arg_parser(): node_ctr = 0 edge_ctr = 0 + generator = (row for row in ijson.kvitems(fp, "")) - for graph in ijson.items(fp, ""): - print(graph["build"]) - reduced["build"] = graph["build"] - for node in graph["nodes"]: - node_ctr += 1 - if node_ctr % 1000000 == 0: - print(node_ctr) - temp_node = {} - for key, val in node.items(): - if key in node_set: - temp_node[key] = val - reduced["nodes"].append(temp_node) - print("Nodes completed") - for edge in graph["edges"]: - edge_ctr += 1 - if edge_ctr % 1000000 == 0: - print(edge_ctr) - temp_edge = {} - for key, val in edge.items(): - if key in edge_set: - temp_edge[key] = val - reduced["edges"].append(temp_edge) - print("Edges completed") + for row in generator: + key = row[0] + data = row[1] + if key == "build": + reduced["build"] = data + print(data) + elif key == "nodes": # handling the list of all nodes + for node in data: # handling a single node dict + node_ctr += 1 + if node_ctr % 1000000 == 0: + print(node_ctr) + temp_node = {} + for k, v in node.items(): # iterating over the node's items + if k in node_set: + temp_node[k] = v + reduced["nodes"].append(temp_node) + print("Nodes completed") + elif key == "edges": + for edge in data: + edge_ctr += 1 + if edge_ctr % 1000 == 0: + print(edge_ctr) + temp_edge = {} + for k, v in edge.items(): + if k in edge_set: + temp_edge[k] = v + reduced["edges"].append(temp_edge) + print("Edges completed") finish = datetime.datetime.now() print(f"Finish time: {finish} \nTotal time: {finish-start}") From c0d1995c11de805730ec0dc7b5e81d09180a7576 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 25 Oct 2022 09:50:10 -0700 Subject: [PATCH 096/127] #226 Updating kg2-versions --- kg2-versions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kg2-versions.md b/kg2-versions.md index 4126947e..21015933 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -9,7 +9,7 @@ Issues: - Issue [#220](https://github.com/RTXteam/RTX-KG2/issues/220) - Issue [#221](https://github.com/RTXteam/RTX-KG2/issues/221) - Issue [#222](https://github.com/RTXteam/RTX-KG2/issues/222) -- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238, #243 +- Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238, #243, #244 Build info: - Biolink Model version: 3.0.0 From 1cc84f8b6bd365f397b2f3c2a934c564f67e5903 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 25 Oct 2022 09:50:27 -0700 Subject: [PATCH 097/127] #244 working on kg_json_to_tsv.py --- kg_json_to_tsv.py | 31 +++++++++++++++++++++++-------- 1 file changed, 23 insertions(+), 8 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index b504b912..d2cda44c 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -307,12 +307,27 @@ def edges(edges_list, output_file_location): output_file_location = arguments.outputFileLocation print(f"Start load: {date()}") with open(arguments.inputFile, "r") as json_file: - for graph in ijson.items(json_file, ""): - print(f"End load: {date()}") - print(f"Start nodes: {date()}") - nodes(graph["nodes"], output_file_location) - print(f"Finish nodes: {date()}") - print(f"Start edges: {date()}") - edges(graph["edges"], output_file_location) - print(f"Finish edges: {date()}") + generator = (row for row in ijson.kvitems(json_file, "")) + print(f"End load: {date()}") + + for row in generator: + key = row[0] + data = row[1] + if key == "nodes": + print(f"Start nodes: {date()}") + nodes(data, output_file_location) + print(f"Finish nodes: {date()}") + elif key == "edges": + print(f"Start edges: {date()}") + edges(data, output_file_location) + print(f"Finish edges: {date()}") + + # for graph in ijson.items(json_file, ""): + # print(f"End load: {date()}") + # print(f"Start nodes: {date()}") + # nodes(graph["nodes"], output_file_location) + # print(f"Finish nodes: {date()}") + # print(f"Start edges: {date()}") + # edges(graph["edges"], output_file_location) + # print(f"Finish edges: {date()}") print(f"Completed: {date()}") From e4035f3ebf761cfc59815049602b0f9a8264e7bc Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 25 Oct 2022 09:51:04 -0700 Subject: [PATCH 098/127] #243 Fixing progress reporting --- slim_kg2.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slim_kg2.py b/slim_kg2.py index b09f0f7f..125131b3 100644 --- a/slim_kg2.py +++ b/slim_kg2.py @@ -63,7 +63,7 @@ def make_arg_parser(): elif key == "edges": for edge in data: edge_ctr += 1 - if edge_ctr % 1000 == 0: + if edge_ctr % 1000000 == 0: print(edge_ctr) temp_edge = {} for k, v in edge.items(): From 153748bd1a93fba21deb51b1324b91d9d4bb17a3 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 25 Oct 2022 16:50:30 -0700 Subject: [PATCH 099/127] #244 Working on kg_json_to_tsv.py --- kg_json_to_tsv.py | 222 ++++++++++++++++++++++++---------------------- 1 file changed, 115 insertions(+), 107 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index d2cda44c..4a682d43 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -123,9 +123,32 @@ def shorten_description_if_too_large(node_description_field, node_id): return node_description_field.replace("\n"," ") -def nodes(nodes_list, output_file_location): +def check_all_nodes_have_same_set(nodekeys_list): """ - :param nodes_list: A list containing KG2 nodes + :param nodekeys_list: A list containing keys for a node + """ + supported_node_keys = ["category", + "category_label", + "creation_date", + "id", + "iri", + "name", + "full_name", + "description", + "synonym", + "publications", + "update_date", + "deprecated", + "replaced_by", + "knowledge_source", + "has_biological_sequence"] + for node_label in nodekeys_list: + assert node_label in supported_node_keys, f"Node label not in supported list: {node_label}" + + +def nodes(input_file, output_file_location): + """ + :param input_file: The input file :param output_file_location: A string containing the path to the TSV output directory """ @@ -136,70 +159,52 @@ def nodes(nodes_list, output_file_location): tsvfile = open(nodes_file[0], 'w+') tsvfile_h = open(nodes_file[1], 'w+') - # Set loop (node counter) to zero - loop = 0 - # Set up TSV files to be written to tsvwrite = tsv.writer(tsvfile, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) tsvwrite_h = tsv.writer(tsvfile_h, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) - # Set single loop to zero and get list of node properties, which will go - # in the header, to compare other nodes to - single_loop = 0 - for node in nodes_list: - single_loop += 1 - if single_loop == 1: - nodekeys_official = list(sorted(node.keys())) - nodekeys_official.append("category") - - for node in nodes_list: - # Inrease node counter by one each loop - loop += 1 - - # Add all node property labels to a list in the same order - nodekeys = list(sorted(node.keys())) - nodekeys.append("category") - - # Create list for values of node properties to be added to - vallist = [] - - # Set index in list of node properties to zero, to be iterated through - key_count = 0 - for key in nodekeys: - if key != nodekeys_official[key_count]: - # Add a property from the header list of node properties - # if it doesn't exist and make the value for that property " " - nodekeys.insert(key_count, nodekeys_official[key_count]) - value = " " - elif key == "synonym": - value = truncate_node_synonyms_if_too_large(node[key], node['id']) - value = str(value).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") - elif key == "publications": - value = str(node[key]).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") - elif key == "description" and node[key] is not None: - value = shorten_description_if_too_large(node[key], node['id']) - else: - # If the property does exist, assign the property value - value = node[key] - # Add the value of the property to the property value list - if type(value)==str: - value = value.replace('\t', ' ').replace('\n', ' ').replace('\r', ' ') - vallist.append(value) - - # Increase the index count by one - key_count += 1 - - # Add the edge property labels to the edge header TSV file - # But only for the first edge - if loop == 1: - nodekeys = no_space('id', nodekeys, 'id:ID') - nodekeys = no_space('publications', nodekeys, "publications:string[]") - nodekeys = no_space('synonym', nodekeys, "synonym:string[]") - nodekeys = no_space('category', nodekeys, ':LABEL') - tsvwrite_h.writerow(nodekeys) - tsvwrite.writerow(vallist) + with open(input_file, "r") as fp: + node_ctr = 0 + generator = (row for row in ijson.items(fp, "nodes.item")) + for node in generator: + node_ctr += 1 + if node_ctr % 1000000 == 0: + print(f"Processing node: {node_ctr}") + + # Add all node property labels to a list and check if they are supported + nodekeys = list(sorted(node.keys())) + check_all_nodes_have_same_set(nodekeys) + nodekeys.append("category") + + vallist = [] + + for key in nodekeys: + assert key in nodekeys, key + if key == "synonym": + value = truncate_node_synonyms_if_too_large(node[key], node['id']) + value = str(value).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") + elif key == "publications": + value = str(node[key]).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") + elif key == "description" and node[key] is not None: + value = shorten_description_if_too_large(node[key], node['id']) + else: + # If the property does exist, assign the property value + value = node[key] + # Add the value of the property to the property value list + if type(value) == str: + value = value.replace('\t', ' ').replace('\n', ' ').replace('\r', ' ') + vallist.append(value) + + if node_ctr == 1: + nodekeys = no_space('id', nodekeys, 'id:ID') + nodekeys = no_space('publications', nodekeys, "publications:string[]") + nodekeys = no_space('synonym', nodekeys, "synonym:string[]") + nodekeys = no_space('category', nodekeys, ':LABEL') + tsvwrite_h.writerow(nodekeys) + + tsvwrite.writerow(vallist) # Close the TSV files to prevent a memory leak tsvfile.close() @@ -228,9 +233,9 @@ def limit_publication_info_size(key, pub_inf_dict): return pub_inf_dict -def edges(edges_list, output_file_location): +def edges(input_file, output_file_location): """ - :param edges_list: A list containing KG2 edges + :param input_file: The input file :param output_file_location: A string containing the path to the TSV output directory """ @@ -241,55 +246,58 @@ def edges(edges_list, output_file_location): tsvfile = open(edges_file[0], 'w+') tsvfile_h = open(edges_file[1], 'w+') - # Set loop (edge counter) to zero - loop = 0 - # Set up TSV files to be written to tsvwrite = tsv.writer(tsvfile, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) tsvwrite_h = tsv.writer(tsvfile_h, delimiter="\t", quoting=tsv.QUOTE_MINIMAL) - for edge in edges_list: - # Inrease edge counter by one each loop - loop += 1 - - # Add all edge property label to a list in the same order and test - # to make sure they are the same - edgekeys = list(sorted(edge.keys())) - check_all_edges_have_same_set(edgekeys) - - # Add an extra property of "predicate" to the list so that predicates - # can be a property and a label - edgekeys.append('predicate') - edgekeys.append('subject') - edgekeys.append('object') - - # Create list for values of edge properties to be added to - vallist = [] - for key in edgekeys: - # Add the value for each edge property to the value list - # and limit the size of the publications_info dictionary - # to avoid Neo4j buffer size error - value = edge[key] - if key == "publications_info": - value = limit_publication_info_size(key, value) - elif key == 'knowledge_source': - value = str(value).replace("', '", "; ").replace("['", "").replace("']", "") - elif key == 'relation_label': # fix for issue number 473 (hyphens in relation_labels) - value = value.replace('-', '_').replace('(', '').replace(')', '') - elif key == 'publications': - value = str(value).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") - vallist.append(value) - - # Add the edge property labels to the edge header TSV file - # But only for the first edge - if loop == 1: - edgekeys = no_space('knowledge_source', edgekeys, 'knowledge_source:string[]') - edgekeys = no_space('predicate', edgekeys, 'predicate:TYPE') - edgekeys = no_space('subject', edgekeys, ':START_ID') - edgekeys = no_space('object', edgekeys, ':END_ID') - edgekeys = no_space('publications', edgekeys, "publications:string[]") - tsvwrite_h.writerow(edgekeys) - tsvwrite.writerow(vallist) + + with open(input_file, "r") as fp: + edge_ctr = 0 + generator = (row for row in ijson.items(fp, "edges.item")) + + for edge in generator: + edge_ctr += 1 + if edge_ctr % 1000000 == 0: + print(f"Processing edge: {edge_ctr}") + + # Add all edge property label to a list in the same order and test + # to make sure they are the same + edgekeys = list(sorted(edge.keys())) + check_all_edges_have_same_set(edgekeys) + + # Add an extra property of "predicate" to the list so that predicates + # can be a property and a label + edgekeys.append('predicate') + edgekeys.append('subject') + edgekeys.append('object') + + # Create list for values of edge properties to be added to + vallist = [] + for key in edgekeys: + # Add the value for each edge property to the value list + # and limit the size of the publications_info dictionary + # to avoid Neo4j buffer size error + value = edge[key] + if key == "publications_info": + value = limit_publication_info_size(key, value) + elif key == 'knowledge_source': + value = str(value).replace("', '", "; ").replace("['", "").replace("']", "") + elif key == 'relation_label': # fix for issue number 473 (hyphens in relation_labels) + value = value.replace('-', '_').replace('(', '').replace(')', '') + elif key == 'publications': + value = str(value).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") + vallist.append(value) + + # Add the edge property labels to the edge header TSV file + # But only for the first edge + if edge_ctr == 1: + edgekeys = no_space('knowledge_source', edgekeys, 'knowledge_source:string[]') + edgekeys = no_space('predicate', edgekeys, 'predicate:TYPE') + edgekeys = no_space('subject', edgekeys, ':START_ID') + edgekeys = no_space('object', edgekeys, ':END_ID') + edgekeys = no_space('publications', edgekeys, "publications:string[]") + tsvwrite_h.writerow(edgekeys) + tsvwrite.writerow(vallist) # Close the TSV files to prevent a memory leak tsvfile.close() From 2306b449c54f1fbc8ef08301c4858cf1ebaabc32 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 26 Oct 2022 08:28:31 -0700 Subject: [PATCH 100/127] #244 working on kg_json_to_tsv.py --- kg_json_to_tsv.py | 35 +++++++++-------------------------- 1 file changed, 9 insertions(+), 26 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index 4a682d43..70dc1888 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -312,30 +312,13 @@ def edges(input_file, output_file_location): parser.add_argument("outputFileLocation", help="Path to Directory for Output\ TSV Files to Go", type=str) arguments = parser.parse_args() + input_file = arguments.inputFile output_file_location = arguments.outputFileLocation - print(f"Start load: {date()}") - with open(arguments.inputFile, "r") as json_file: - generator = (row for row in ijson.kvitems(json_file, "")) - print(f"End load: {date()}") - - for row in generator: - key = row[0] - data = row[1] - if key == "nodes": - print(f"Start nodes: {date()}") - nodes(data, output_file_location) - print(f"Finish nodes: {date()}") - elif key == "edges": - print(f"Start edges: {date()}") - edges(data, output_file_location) - print(f"Finish edges: {date()}") - - # for graph in ijson.items(json_file, ""): - # print(f"End load: {date()}") - # print(f"Start nodes: {date()}") - # nodes(graph["nodes"], output_file_location) - # print(f"Finish nodes: {date()}") - # print(f"Start edges: {date()}") - # edges(graph["edges"], output_file_location) - # print(f"Finish edges: {date()}") - print(f"Completed: {date()}") + + print("Start nodes: ", date()) + nodes(input_file, output_file_location) + print("Finish nodes: ", date()) + print("Start edges: ", date()) + edges(input_file, output_file_location) + print("Finish edges: ", date()) + print("Finish time: ", date()) From c4988f9515f74c9419d4342762ea9f42a8e0d136 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 26 Oct 2022 08:37:49 -0700 Subject: [PATCH 101/127] #244 Fixing None type issue --- kg_json_to_tsv.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index 70dc1888..b768d70f 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -14,7 +14,7 @@ __author__ = 'Erica Wood' __copyright__ = 'Oregon State University' -__credits__ = ['Stephen Ramsey', 'Erica Wood'] +__credits__ = ['Stephen Ramsey', 'Erica Wood', 'Liliana Acevedo'] __license__ = 'MIT' __version__ = '0.1.0' __maintainer__ = '' @@ -105,9 +105,9 @@ def truncate_node_synonyms_if_too_large(node_synonym_field, node_id): """ if len(json.dumps(node_synonym_field)) > NEO4J_CHAR_LIMIT: print("warning: truncating 'synonym' field on node {} because it's too big for neo4j".format(node_id), file=sys.stderr) - return [synonym.replace("\n"," ") for synonym in node_synonym_field[0:20]] # Only include the first 20 synonyms + return [synonym.replace("\n"," ") for synonym in node_synonym_field[0:20] if synonym is not None] # Only include the first 20 synonyms else: - return [synonym.replace("\n"," ") for synonym in node_synonym_field] + return [synonym.replace("\n"," ") for synonym in node_synonym_field if synonym is not None] def shorten_description_if_too_large(node_description_field, node_id): From 02ebe5aca4295188c3572c82457a1cd1d81e8e16 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 11:14:53 -0700 Subject: [PATCH 102/127] #226 Fixing issues with filter --- filter_kg_and_remap_predicates.py | 426 +++++++++++++++--------------- 1 file changed, 220 insertions(+), 206 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index e2ffa0ac..d8d81a82 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -54,246 +54,260 @@ def make_arg_parser(): def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_object_aspect=None, qualified_object_direction=None): - value_list = edge_key_value.split('---') - if len(value_list) == 7: - return edge_key_value - assert len(value_list) == 4 - if qualified_object_direction is None: - qualified_object_direction = "None" - if qualified_object_aspect is None: - qualified_object_aspect = "None" - if qualified_predicate is None: - qualified_predicate = "None" - value_list.insert(2, qualified_object_direction) - value_list.insert(2, qualified_object_aspect) - value_list.insert(2, qualified_predicate) - new_edge_id = "---".join(value_list) - + edge_id_keys = edge_id.split("---") + subject = edge_id_keys[0] + predicate = edge_id_keys[1] + object = edge_id_keys[2] + knowledge_source = edge_id_keys[3] + new_edge_id = f"{subject}---{predicate}---{qualified_predicate}---{qualified_object_aspect}---{qualified_object_direction}---{object}---{knowledge_source}" return new_edge_id -if __name__ == '__main__': - args = make_arg_parser().parse_args() - predicate_remap_file_name = args.predicateRemapYaml - infores_remap_file_name = args.inforesRemapYaml - curies_to_uri_file_name = args.curiesToURIFile - input_file_name = args.inputFileJson - output_file_name = args.outputFileJson - test_mode = args.test - drop_negated = args.drop_negated - drop_self_edges_except = args.drop_self_edges_except +def warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges): + for knowledge_source_curies_not_in_config_edge in knowledge_source_curies_not_in_config_edges: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_edge, + file=sys.stderr) + + if len(knowledge_source_curies_not_in_config_edges) > 0: + print( + "There are edges knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", + file=sys.stderr) + exit(1) - if drop_self_edges_except is not None: - assert type(drop_self_edges_except) == str - drop_self_edges_except = set(drop_self_edges_except.split(',')) - # Config files - # safe load takes a yaml file and returns a dictionary - predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) - infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) +def warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes): + for knowledge_source_curies_not_in_config_node in knowledge_source_curies_not_in_config_nodes: + print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_node, + file=sys.stderr) + + if len(knowledge_source_curies_not_in_config_nodes) > 0: + print( + "There are nodes knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", + file=sys.stderr) + exit(1) + + +def warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config): + source_predicate_curies_not_in_config_for_iteration = list(source_predicate_curies_not_in_config) + for source_predicate_curie_not_in_config in source_predicate_curies_not_in_config_for_iteration: + if not source_predicate_curie_not_in_config.startswith(kg2_util.CURIE_PREFIX_BIOLINK + ':'): + print('Source predicate curie is missing from the YAML config file: ' + source_predicate_curie_not_in_config, + file=sys.stderr) + else: + source_predicate_curies_not_in_config.remove(source_predicate_curie_not_in_config) + if len(source_predicate_curies_not_in_config) > 0: + print( + "There are source predicate curies missing from the yaml config file. Please add them and try again. Exiting.", + file=sys.stderr) + exit(1) + + +def warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes): + for source_predicate_curie in source_predicate_curies_not_in_nodes: + print('could not find a node for source predicate curie: ' + source_predicate_curie) + + +def warning_record_of_source_predicate_curie_occurrences(record_of_source_predicate_curie_occurrences): + for source_predicate_curie in record_of_source_predicate_curie_occurrences: + if not record_of_source_predicate_curie_occurrences[source_predicate_curie]: + print( + 'Knowledge source predicate curie is in the config file but was not used in any edge in the graph: ' + source_predicate_curie, + file=sys.stderr) + + +def process_nodes(input_file_name, infores_remap_file_name): + knowledge_source_curies_not_in_config_nodes = set() + nodes_dict = dict() + + infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) + + node_ctr = 0 + with open(input_file_name, "r") as fp: + nodes_generator = (row for row in ijson.items(fp, "nodes.item")) + for node_dict in nodes_generator: + node_ctr += 1 + if node_ctr % 1000000 == 0: + print(f"Processing node {node_ctr}") + node_id = node_dict["id"] + knowledge_source = node_dict['knowledge_source'] + infores_curie_dict = infores_remap_config.get(knowledge_source, None) + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_nodes.add(knowledge_source) + else: + infores_curie = infores_curie_dict['infores_curie'] + node_dict['knowledge_source'] = infores_curie + nodes_dict[node_id] = node_dict + + return nodes_dict, knowledge_source_curies_not_in_config_nodes + + +def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except): + infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) + predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) - [curie_to_uri_expander, uri_to_curie_shortener] = [map_dict['expand'], map_dict['contract']] - graph = kg2_util.load_json(input_file_name) + curie_to_uri_expander = map_dict['expand'] new_edges = dict() - # Create sets to handle knowledge sources - original_predicate_curies_not_in_config = set() - knowledge_source_curies_not_in_config_nodes = set() + source_predicate_curies_not_in_config = set() + source_predicate_curies_not_in_nodes = set() knowledge_source_curies_not_in_config_edges = set() - - # This should not change because predicate_remap_config.keys() is still just original predicate curies - record_of_original_predicate_curie_occurrences = {original_predicate_curie: False for original_predicate_curie in + record_of_source_predicate_curie_occurrences = {source_predicate_curie: False for source_predicate_curie in predicate_remap_config.keys()} - # To Do: Update everything for rename/keep commands - # Old command set: {'delete', 'keep', 'invert', 'rename'} command_set = {'delete', 'keep', 'invert'} - # The length of the 'command' could be 1 if it just has the operation, such as with 'delete' # or up to 4 if there is the operation, core predicate, qualified predicate, and qualifiers # Verify that the operation is allowed - for original_predicate_curie, command in predicate_remap_config.items(): + for source_predicate_curie, command in predicate_remap_config.items(): assert len(command) in range(1, 5) assert command["operation"] in command_set - # Every predicate curie should get its own node. Otherwise add to this set to complain. - original_predicate_curies_not_in_nodes = set() - nodes_dict = dict() - for node_dict in graph['nodes']: - node_id = node_dict['id'] - knowledge_source = node_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(knowledge_source, None) - if infores_curie_dict is None: - knowledge_source_curies_not_in_config_nodes.add(knowledge_source) - else: - infores_curie = infores_curie_dict['infores_curie'] - node_dict['knowledge_source'] = infores_curie - nodes_dict[node_id] = node_dict - edge_ctr = 0 - num_edges = len(graph['edges']) - for edge_dict in graph['edges']: - # Print progress - edge_ctr += 1 - if edge_ctr % 1000000 == 0: - print(f'Processing edge {str(edge_ctr)} out of {str(num_edges)}') - - # TODO: Add logic to handle "positively_regulates" changed to "regulates/ causes/ activity or abundance/ increased" - if drop_negated and edge_dict['negated']: + with open(input_file_name, "r") as fp: + edges_generator = (row for row in ijson.items(fp, "edges.item")) + for edge in edges_generator: + edge_ctr += 1 + if edge_ctr % 1000000 == 0: + print(f"Processing edge {edge_ctr}") + if drop_negated and edge_dict['negated']: continue + source_predicate_label = edge['relation_label'] + predicate_label = source_predicate_label + if edge_dict.get('source_predicate') is None: + edge_dict['source_predicate'] = edge_dict.pop('original_predicate') + source_predicate_curie = edge['source_predicate'] + predicate_curie = source_predicate_curie + + if record_of_source_predicate_curie_occurrences.get(source_predicate_curie, None) is not None: + record_of_source_predicate_curie_occurrences[source_predicate_curie] = True + pred_remap_info = predicate_remap_config.get(source_predicate_curie, None) + else: + # there is a original predicate CURIE in the graph that is not in the config file + source_predicate_curies_not_in_config.add(source_predicate_curie) + + assert pred_remap_info is not None - original_predicate_label = edge_dict['relation_label'] - predicate_label = original_predicate_label - if edge_dict.get('source_predicate') is None: - edge_dict['source_predicate'] = edge_dict.pop('original_predicate') - original_predicate_curie = edge_dict['source_predicate'] - predicate_curie = original_predicate_curie - - if record_of_original_predicate_curie_occurrences.get(original_predicate_curie, None) is not None: - record_of_original_predicate_curie_occurrences[original_predicate_curie] = True - pred_remap_info = predicate_remap_config.get(original_predicate_curie, None) - else: - # there is a original predicate CURIE in the graph that is not in the config file - original_predicate_curies_not_in_config.add(original_predicate_curie) - - assert pred_remap_info is not None - - invert = False - get_new_rel_info = False - operation_not_allowed = {} - - if pred_remap_info is None: - assert original_predicate_curie in original_predicate_curies_not_in_config - else: - if pred_remap_info['operation'] == 'delete': + invert = False + get_new_rel_info = False + + if pred_remap_info is None: + assert source_predicate_curie in source_predicate_curies_not_in_config + else: + operation = pred_remap_info.get('operation', None) + if operation == "delete": + continue + elif operation == "invert": + invert = True + get_new_rel_info = True + else: + assert operation == "keep" + get_new_rel_info = True + + if get_new_rel_info: + assert pred_remap_info.get("core_predicate", None) is not None + predicate_curie = pred_remap_info.get("core_predicate") + qualified_predicate = pred_remap_info.get("qualified_predicate", "None") + qualified_object_aspect = "None" + qualified_object_direction = "None" + qualifiers = pred_remap_info.get("qualifiers", None) + if qualifiers is not None: + qualifiers_dict = qualifiers[0] + qualified_object_aspect = qualifiers_dict.get("object_aspect", "None") + qualified_object_direction = qualifiers_dict.get("object_direction", "None") + if invert: + edge['relation_label'] = 'INVERTED:' + source_predicate_label + new_object = edge['subject'] + edge['subject'] = edge['object'] + edge['object'] = new_object + edge["predicate_label"] = predicate_label + if drop_self_edges_except is not None and \ + edge['subject'] == edge['object'] and \ + predicate_label not in drop_self_edges_except: continue - elif pred_remap_info['operation'] == 'invert': - invert = True - get_new_rel_info = True - elif pred_remap_info['operation'] == 'keep': - get_new_rel_info = True + edge['source_predicate'] = predicate_curie + edge['qualified_predicate'] = qualified_predicate + edge['qualified_object_aspect'] = qualified_object_aspect + edge['qualified_object_direction'] = qualified_object_direction + new_edge_id = update_edge_id(edge_id, qualified_predicate, qualified_object_aspect, qualified_object_direction) + edge["id"] = new_edge_id + + if predicate_curie not in nodes_dict: + predicate_curie_prefix = predicate_curie.split(':')[0] + predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') + # Create list of curies to complain about if not in biolink + if predicate_uri_prefix == predicate_curie_prefix: + source_predicate_curies_not_in_nodes.add(predicate_curie) + + infores_curie_dict = infores_remap_config.get(knowledge_source, None) + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_edges.add(knowledge_source) else: - operation_not_allowed[predicate_curie] = pred_remap_info['operation'] - - qualified_predicate_curie = pred_remap_info.get('qualified_predicate', None) - edge_dict['qualified_predicate'] = qualified_predicate_curie - # Convert the qualifiers to a dict for easier use - qualifiers_list = pred_remap_info.get('qualifiers', None) - qualifiers_dict = {} - qualified_predicate_object_aspect = None - qualified_predicate_object_direction = None - - if qualifiers_list is not None: - for item in qualifiers_list: - qualifier = list(item.keys())[0] - value = item[qualifier] - qualifiers_dict[qualifier] = value - qualified_predicate_object_aspect = qualifiers_dict.get('object aspect') - qualified_predicate_object_direction = qualifiers_dict.get('object direction') - if qualified_predicate_object_aspect is not None: - edge_dict['qualified_object_aspect'] = qualified_predicate_object_aspect - if qualified_predicate_object_direction is not None: - edge_dict['qualified_object_direction'] = qualified_predicate_object_direction - if get_new_rel_info: - predicate_curie = pred_remap_info['core_predicate'] - - if invert: - edge_dict['relation_label'] = 'INVERTED:' + original_predicate_label - new_object = edge_dict['subject'] - edge_dict['subject'] = edge_dict['object'] - edge_dict['object'] = new_object - - edge_dict['predicate_label'] = predicate_label - # Delete negated edges and self edges except interacts_with,positively_regulates,inhibits,increase - # as defined in run-simplify.sh - # To Do: verify exception list complies with updates from Biolink 3.0 - if drop_self_edges_except is not None and \ - edge_dict['subject'] == edge_dict['object'] and \ - predicate_label not in drop_self_edges_except: - continue # see issue 743 - - # Sets biolink curie; remapping - edge_dict['predicate'] = predicate_curie - if predicate_curie not in nodes_dict: - predicate_curie_prefix = predicate_curie.split(':')[0] - predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') - # Create list of curies to complain about if not in biolink - if predicate_uri_prefix == predicate_curie_prefix: - original_predicate_curies_not_in_nodes.add(predicate_curie) - - knowledge_source = edge_dict['knowledge_source'] - infores_curie_dict = infores_remap_config.get(knowledge_source, None) - if infores_curie_dict is None: - knowledge_source_curies_not_in_config_edges.add(knowledge_source) - else: - infores_curie = infores_curie_dict['infores_curie'] - edge_dict['knowledge_source'] = [infores_curie] + infores_curie = infores_curie_dict['infores_curie'] + edge_dict['knowledge_source'] = [infores_curie] - edge_subject = edge_dict['subject'] - edge_object = edge_dict['object'] + edge_subject = edge_dict['subject'] + edge_object = edge_dict['object'] - if qualified_predicate_curie: - predicate = " /// " + qualified_predicate_curie - else: - predicate = " /// " + predicate_curie - - predicate_qualifier = "" - if qualifiers_dict is not None: - if qualified_predicate_object_aspect is not None: - predicate_qualifier = " /// " + qualified_predicate_object_aspect - if qualified_predicate_object_direction is not None: - predicate_qualifier += f" /// {qualified_predicate_object_direction}" - edge_key = f'{edge_subject} {predicate} {predicate_qualifier} /// {edge_object}' - - existing_edge = new_edges.get(edge_key, None) - if existing_edge is not None: - existing_edge['knowledge_source'] = sorted(list(set(existing_edge['knowledge_source'] + - edge_dict['knowledge_source']))) - existing_edge['publications'] += edge_dict['publications'] - existing_edge['publications_info'].update(edge_dict['publications_info']) - else: - new_edges[edge_key] = edge_dict + edge_key = f"{edge_subject} /// {predicate_curie} /// {qualified_predicate} /// {qualified_object_aspect}\ + /// {qualified_object_direction} /// {edge_object}" + + existing_edge = new_edges.get(edge_key, None) + + if existing_edge is not None: + existing_edge['knowledge_source'] = sorted( + list(set(existing_edge['knowledge_source'] + edge['knowledge_source']))) + existing_edge['publications'] += edge['publications'] + existing_edge['publications_info'].update(edge['publications_info']) + else: + new_edges[edge_key] = edge + + + return new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences + + + +if __name__ == '__main__': + args = make_arg_parser().parse_args() + predicate_remap_file_name = args.predicateRemapYaml + infores_remap_file_name = args.inforesRemapYaml + curies_to_uri_file_name = args.curiesToURIFile + input_file_name = args.inputFileJson + output_file_name = args.outputFileJson + test_mode = args.test + drop_negated = args.drop_negated + drop_self_edges_except = args.drop_self_edges_except + + graph = dict() + new_edges = dict() + nodes_dict = dict() + source_predicate_curies_not_in_config = set() + knowledge_source_curies_not_in_config_nodes = set() + source_predicate_curies_not_in_nodes = set() + knowledge_source_curies_not_in_config_edges = set() - edge_id = update_edge_id(new_edges[edge_key]['id'], qualified_predicate_curie, qualified_predicate_object_aspect, - qualified_predicate_object_direction) - new_edges[edge_key]['id'] = edge_id + if drop_self_edges_except is not None: + assert type(drop_self_edges_except) == str + drop_self_edges_except = set(drop_self_edges_except.split(',')) + + nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_file_name) + + new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences = process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + # Releasing some memory - del graph['edges'] - del graph['nodes'] + graph['nodes'] = list(nodes_dict.values()) del nodes_dict graph['edges'] = list(new_edges.values()) del new_edges # Warnings for issues that came up - for original_predicate_curie in record_of_original_predicate_curie_occurrences: - if not record_of_original_predicate_curie_occurrences[original_predicate_curie]: - print('original predicate curie is in the config file but was not used in any edge in the graph: ' + original_predicate_curie, file=sys.stderr) - for original_predicate_curie in original_predicate_curies_not_in_nodes: - print('could not find a node for original predicate curie: ' + original_predicate_curie) - original_predicate_curies_not_in_config_for_iteration = list(original_predicate_curies_not_in_config) - for original_predicate_curie_not_in_config in original_predicate_curies_not_in_config_for_iteration: - if not original_predicate_curie_not_in_config.startswith(kg2_util.CURIE_PREFIX_BIOLINK + ':'): - print('original predicate curie is missing from the YAML config file: ' + original_predicate_curie_not_in_config, - file=sys.stderr) - else: - original_predicate_curies_not_in_config.remove(original_predicate_curie_not_in_config) - for knowledge_source_curies_not_in_config_node in knowledge_source_curies_not_in_config_nodes: - print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_node, - file=sys.stderr) - for knowledge_source_curies_not_in_config_edge in knowledge_source_curies_not_in_config_edges: - print('knowledge_source node curie is missing from the YAML config file: ' + knowledge_source_curies_not_in_config_edge, - file=sys.stderr) - if len(original_predicate_curies_not_in_config) > 0: - print("There are original predicate curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) - exit(1) - if len(knowledge_source_curies_not_in_config_nodes) > 0: - print("There are nodes knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) - exit(1) - if len(knowledge_source_curies_not_in_config_edges) > 0: - print("There are edges knowledge_source curies missing from the yaml config file. Please add them and try again. Exiting.", file=sys.stderr) - exit(1) + warning_record_of_knowledge_source_curie_occurrences(record_of_knowledge_source_curie_occurrences) + warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes) + warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config) + warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes) + warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges) + update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') build_name = str From 9f3df13123f5023d4e0c44a5ce38db17e38acf5e Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 12:44:15 -0700 Subject: [PATCH 103/127] #226 Fixing typo in filter --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index d8d81a82..a3e7d0c1 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -171,7 +171,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file if edge_ctr % 1000000 == 0: print(f"Processing edge {edge_ctr}") if drop_negated and edge_dict['negated']: - continue + continue source_predicate_label = edge['relation_label'] predicate_label = source_predicate_label if edge_dict.get('source_predicate') is None: From 037c25218c9f3f9a81d7fbe9e48471a8573f9bb9 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 12:45:36 -0700 Subject: [PATCH 104/127] #226 Forgot to include import --- filter_kg_and_remap_predicates.py | 1 + 1 file changed, 1 insertion(+) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index a3e7d0c1..916443d3 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -18,6 +18,7 @@ import kg2_util import pprint import sys +import ijson from datetime import datetime # 1. What is the indicator for negation? From ba35ac5cc0d922d0bdb262b260f03994d1e316fb Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 13:18:49 -0700 Subject: [PATCH 105/127] #226 Adding date stamps to logging --- filter_kg_and_remap_predicates.py | 40 +++++++++++++++++-------------- 1 file changed, 22 insertions(+), 18 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 916443d3..c12fd6a8 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -139,6 +139,7 @@ def process_nodes(input_file_name, infores_remap_file_name): infores_curie = infores_curie_dict['infores_curie'] node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict + print(f"Completed nodes {kg2_util.date()}") return nodes_dict, knowledge_source_curies_not_in_config_nodes @@ -167,17 +168,18 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file edge_ctr = 0 with open(input_file_name, "r") as fp: edges_generator = (row for row in ijson.items(fp, "edges.item")) - for edge in edges_generator: + print(f"Starting edges {kg2_util.date()}") + for edge_dict in edges_generator: edge_ctr += 1 if edge_ctr % 1000000 == 0: print(f"Processing edge {edge_ctr}") if drop_negated and edge_dict['negated']: continue - source_predicate_label = edge['relation_label'] + source_predicate_label = edge_dict['relation_label'] predicate_label = source_predicate_label if edge_dict.get('source_predicate') is None: edge_dict['source_predicate'] = edge_dict.pop('original_predicate') - source_predicate_curie = edge['source_predicate'] + source_predicate_curie = edge_dict['source_predicate'] predicate_curie = source_predicate_curie if record_of_source_predicate_curie_occurrences.get(source_predicate_curie, None) is not None: @@ -217,21 +219,21 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file qualified_object_aspect = qualifiers_dict.get("object_aspect", "None") qualified_object_direction = qualifiers_dict.get("object_direction", "None") if invert: - edge['relation_label'] = 'INVERTED:' + source_predicate_label - new_object = edge['subject'] - edge['subject'] = edge['object'] - edge['object'] = new_object - edge["predicate_label"] = predicate_label + edge_dict['relation_label'] = 'INVERTED:' + source_predicate_label + new_object = edge_dict['subject'] + edge_dict['subject'] = edge_dict['object'] + edge_dict['object'] = new_object + edge_dict["predicate_label"] = predicate_label if drop_self_edges_except is not None and \ - edge['subject'] == edge['object'] and \ + edge_dict['subject'] == edge_dict['object'] and \ predicate_label not in drop_self_edges_except: continue - edge['source_predicate'] = predicate_curie - edge['qualified_predicate'] = qualified_predicate - edge['qualified_object_aspect'] = qualified_object_aspect - edge['qualified_object_direction'] = qualified_object_direction + edge_dict['source_predicate'] = predicate_curie + edge_dict['qualified_predicate'] = qualified_predicate + edge_dict['qualified_object_aspect'] = qualified_object_aspect + edge_dict['qualified_object_direction'] = qualified_object_direction new_edge_id = update_edge_id(edge_id, qualified_predicate, qualified_object_aspect, qualified_object_direction) - edge["id"] = new_edge_id + edge_dict["id"] = new_edge_id if predicate_curie not in nodes_dict: predicate_curie_prefix = predicate_curie.split(':')[0] @@ -257,12 +259,12 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file if existing_edge is not None: existing_edge['knowledge_source'] = sorted( - list(set(existing_edge['knowledge_source'] + edge['knowledge_source']))) - existing_edge['publications'] += edge['publications'] - existing_edge['publications_info'].update(edge['publications_info']) + list(set(existing_edge['knowledge_source'] + edge_dict['knowledge_source']))) + existing_edge['publications'] += edge_dict['publications'] + existing_edge['publications_info'].update(edge_dict['publications_info']) else: new_edges[edge_key] = edge - + print(f"Finished edges {kg2_util.date()}") return new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences @@ -329,5 +331,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file pprint.pprint(build_info) graph["build"] = build_info graph["nodes"].append(build_node) + print(f"Saving simplified file {kg2_util.date()}") kg2_util.save_json(graph, output_file_name, test_mode) + print(f"Completed saving file {kg2_util.date()}") del graph From 5ef8dbebcba36dac10a460b2a894c155718df045 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 13:50:07 -0700 Subject: [PATCH 106/127] #226 Fixing error --- filter_kg_and_remap_predicates.py | 1 + 1 file changed, 1 insertion(+) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index c12fd6a8..a0ceb423 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -232,6 +232,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file edge_dict['qualified_predicate'] = qualified_predicate edge_dict['qualified_object_aspect'] = qualified_object_aspect edge_dict['qualified_object_direction'] = qualified_object_direction + edge_id = edge_dict["id"] new_edge_id = update_edge_id(edge_id, qualified_predicate, qualified_object_aspect, qualified_object_direction) edge_dict["id"] = new_edge_id From a49b4acc62e850797f4345d78f1eef1ee2598ff3 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 14:19:00 -0700 Subject: [PATCH 107/127] #226 Fixing key error --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index a0ceb423..8fb1e21e 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -53,7 +53,7 @@ def make_arg_parser(): return arg_parser -def update_edge_id(edge_key_value: str, qualified_predicate=None, qualified_object_aspect=None, +def update_edge_id(edge_id: str, qualified_predicate=None, qualified_object_aspect=None, qualified_object_direction=None): edge_id_keys = edge_id.split("---") subject = edge_id_keys[0] From 3a0ae273f77b437b1e99e40d58e8d6615bacc3c6 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 15:34:29 -0700 Subject: [PATCH 108/127] #226 Fixing error --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 8fb1e21e..c5d46285 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -242,7 +242,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file # Create list of curies to complain about if not in biolink if predicate_uri_prefix == predicate_curie_prefix: source_predicate_curies_not_in_nodes.add(predicate_curie) - + knowledge_source = edge_dict["knowledge_source"] infores_curie_dict = infores_remap_config.get(knowledge_source, None) if infores_curie_dict is None: knowledge_source_curies_not_in_config_edges.add(knowledge_source) From 0fbc08be4b5465923fc4d3964002dc493aeb3a60 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 17:16:46 -0700 Subject: [PATCH 109/127] #226 Fixing error --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index c5d46285..5447fad8 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -264,7 +264,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file existing_edge['publications'] += edge_dict['publications'] existing_edge['publications_info'].update(edge_dict['publications_info']) else: - new_edges[edge_key] = edge + new_edges[edge_key] = edge_dict print(f"Finished edges {kg2_util.date()}") return new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences From 5d24d6a02d98f8145ebb6a21804a4345565dae34 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 21:00:49 -0700 Subject: [PATCH 110/127] #226 Testing fix --- filter_kg_and_remap_predicates.py | 49 +++++++++++++++---------------- 1 file changed, 23 insertions(+), 26 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 5447fad8..1c34053d 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -154,8 +154,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file source_predicate_curies_not_in_config = set() source_predicate_curies_not_in_nodes = set() knowledge_source_curies_not_in_config_edges = set() - record_of_source_predicate_curie_occurrences = {source_predicate_curie: False for source_predicate_curie in - predicate_remap_config.keys()} + record_of_source_predicate_curie_occurrences = dict() # {source_predicate_curie: False for source_predicate_curie in predicate_remap_config.keys()} command_set = {'delete', 'keep', 'invert'} # The length of the 'command' could be 1 if it just has the operation, such as with 'delete' @@ -194,18 +193,15 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file invert = False get_new_rel_info = False - if pred_remap_info is None: - assert source_predicate_curie in source_predicate_curies_not_in_config + operation = pred_remap_info.get('operation', None) + if operation == "delete": + continue + elif operation == "invert": + invert = True + get_new_rel_info = True else: - operation = pred_remap_info.get('operation', None) - if operation == "delete": - continue - elif operation == "invert": - invert = True - get_new_rel_info = True - else: - assert operation == "keep" - get_new_rel_info = True + assert operation == "keep" + get_new_rel_info = True if get_new_rel_info: assert pred_remap_info.get("core_predicate", None) is not None @@ -236,19 +232,20 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file new_edge_id = update_edge_id(edge_id, qualified_predicate, qualified_object_aspect, qualified_object_direction) edge_dict["id"] = new_edge_id - if predicate_curie not in nodes_dict: - predicate_curie_prefix = predicate_curie.split(':')[0] - predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') - # Create list of curies to complain about if not in biolink - if predicate_uri_prefix == predicate_curie_prefix: - source_predicate_curies_not_in_nodes.add(predicate_curie) + # if predicate_curie not in nodes_dict: + # predicate_curie_prefix = predicate_curie.split(':')[0] + # predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') + # # Create list of curies to complain about if not in biolink + # if predicate_uri_prefix == predicate_curie_prefix: + # source_predicate_curies_not_in_nodes.add(predicate_curie) knowledge_source = edge_dict["knowledge_source"] infores_curie_dict = infores_remap_config.get(knowledge_source, None) - if infores_curie_dict is None: - knowledge_source_curies_not_in_config_edges.add(knowledge_source) - else: - infores_curie = infores_curie_dict['infores_curie'] - edge_dict['knowledge_source'] = [infores_curie] + # if infores_curie_dict is None: + # knowledge_source_curies_not_in_config_edges.add(knowledge_source) + # else: + # infores_curie = infores_curie_dict['infores_curie'] + # edge_dict['knowledge_source'] = [infores_curie] + edge_dict['knowledge_source'] = [infores_curie] edge_subject = edge_dict['subject'] edge_object = edge_dict['object'] @@ -267,7 +264,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file new_edges[edge_key] = edge_dict print(f"Finished edges {kg2_util.date()}") - return new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences + return new_edges #, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences @@ -296,7 +293,7 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_file_name) - new_edges, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences = process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + new_edges = process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) # Releasing some memory From 70fefba31f7b38bb6852145849b8d7bdda158465 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 21:10:11 -0700 Subject: [PATCH 111/127] #226 --- filter_kg_and_remap_predicates.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 1c34053d..f7132a94 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -117,11 +117,10 @@ def warning_record_of_source_predicate_curie_occurrences(record_of_source_predic file=sys.stderr) -def process_nodes(input_file_name, infores_remap_file_name): +def process_nodes(input_file_name, infores_remap_config): knowledge_source_curies_not_in_config_nodes = set() nodes_dict = dict() - infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) node_ctr = 0 with open(input_file_name, "r") as fp: @@ -144,8 +143,7 @@ def process_nodes(input_file_name, infores_remap_file_name): return nodes_dict, knowledge_source_curies_not_in_config_nodes -def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except): - infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) +def process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except): predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) @@ -279,6 +277,9 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file drop_negated = args.drop_negated drop_self_edges_except = args.drop_self_edges_except + infores_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(infores_remap_file_name)) + + graph = dict() new_edges = dict() nodes_dict = dict() @@ -291,9 +292,9 @@ def process_edges(input_file_name, infores_remap_file_name, predicate_remap_file assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) - nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_file_name) + nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_config) - new_edges = process_edges(input_file_name, infores_remap_file_name, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + new_edges = process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) # Releasing some memory From 713d822156cf3c4c23f9305f31c114634021f9c0 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 21:20:31 -0700 Subject: [PATCH 112/127] #226 --- filter_kg_and_remap_predicates.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index f7132a94..44dc8e3b 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -132,11 +132,13 @@ def process_nodes(input_file_name, infores_remap_config): node_id = node_dict["id"] knowledge_source = node_dict['knowledge_source'] infores_curie_dict = infores_remap_config.get(knowledge_source, None) - if infores_curie_dict is None: - knowledge_source_curies_not_in_config_nodes.add(knowledge_source) - else: - infores_curie = infores_curie_dict['infores_curie'] - node_dict['knowledge_source'] = infores_curie + infores_curie = infores_curie_dict['infores_curie'] + node_dict['knowledge_source'] = infores_curie + # if infores_curie_dict is None: + # knowledge_source_curies_not_in_config_nodes.add(knowledge_source) + # else: + # infores_curie = infores_curie_dict['infores_curie'] + # node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict print(f"Completed nodes {kg2_util.date()}") @@ -248,8 +250,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na edge_subject = edge_dict['subject'] edge_object = edge_dict['object'] - edge_key = f"{edge_subject} /// {predicate_curie} /// {qualified_predicate} /// {qualified_object_aspect}\ - /// {qualified_object_direction} /// {edge_object}" + edge_key = f"{edge_subject} /// {predicate_curie} /// {edge_object}" existing_edge = new_edges.get(edge_key, None) From 1b7ed8b07fe89103fc3568e14530e21a1af9109c Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Thu, 3 Nov 2022 21:32:19 -0700 Subject: [PATCH 113/127] #226 --- filter_kg_and_remap_predicates.py | 35 +++++++++++++++---------------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 44dc8e3b..f569d78c 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -141,8 +141,10 @@ def process_nodes(input_file_name, infores_remap_config): # node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict print(f"Completed nodes {kg2_util.date()}") + nodes_list = list(node_dict.values()) + del nodes_dict - return nodes_dict, knowledge_source_curies_not_in_config_nodes + return nodes_list, knowledge_source_curies_not_in_config_nodes def process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except): @@ -261,9 +263,11 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na existing_edge['publications_info'].update(edge_dict['publications_info']) else: new_edges[edge_key] = edge_dict - print(f"Finished edges {kg2_util.date()}") + print(f"Finished edges {kg2_util.date()}") + edges_list = list(new_edges.values()) + del edge_dict - return new_edges #, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences + return edges_list #, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences @@ -283,7 +287,6 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na graph = dict() new_edges = dict() - nodes_dict = dict() source_predicate_curies_not_in_config = set() knowledge_source_curies_not_in_config_nodes = set() source_predicate_curies_not_in_nodes = set() @@ -293,23 +296,19 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) - nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_config) + nodes_list, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_config) + graph['nodes'] = nodes_list - new_edges = process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + edges_list = process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + + graph['edges'] = edges_list - - # Releasing some memory - - graph['nodes'] = list(nodes_dict.values()) - del nodes_dict - graph['edges'] = list(new_edges.values()) - del new_edges # Warnings for issues that came up - warning_record_of_knowledge_source_curie_occurrences(record_of_knowledge_source_curie_occurrences) - warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes) - warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config) - warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes) - warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges) + # warning_record_of_knowledge_source_curie_occurrences(record_of_knowledge_source_curie_occurrences) + # warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes) + # warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config) + # warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes) + # warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges) update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') From 99cfaa1cf2d9b738715122f39eed97db59c7c82a Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 08:39:51 -0700 Subject: [PATCH 114/127] #226 --- filter_kg_and_remap_predicates.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index f569d78c..99d66480 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -134,11 +134,11 @@ def process_nodes(input_file_name, infores_remap_config): infores_curie_dict = infores_remap_config.get(knowledge_source, None) infores_curie = infores_curie_dict['infores_curie'] node_dict['knowledge_source'] = infores_curie - # if infores_curie_dict is None: - # knowledge_source_curies_not_in_config_nodes.add(knowledge_source) - # else: - # infores_curie = infores_curie_dict['infores_curie'] - # node_dict['knowledge_source'] = infores_curie + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_nodes.add(knowledge_source) + else: + infores_curie = infores_curie_dict['infores_curie'] + node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict print(f"Completed nodes {kg2_util.date()}") nodes_list = list(node_dict.values()) @@ -184,12 +184,12 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na predicate_curie = source_predicate_curie if record_of_source_predicate_curie_occurrences.get(source_predicate_curie, None) is not None: - record_of_source_predicate_curie_occurrences[source_predicate_curie] = True - pred_remap_info = predicate_remap_config.get(source_predicate_curie, None) + record_of_source_predicate_curie_occurrences[source_predicate_curie] = True else: # there is a original predicate CURIE in the graph that is not in the config file source_predicate_curies_not_in_config.add(source_predicate_curie) - + + pred_remap_info = predicate_remap_config.get(source_predicate_curie, None) assert pred_remap_info is not None invert = False From 18c484e278baadb3f8dbabe90ac1097e133c76aa Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 10:07:37 -0700 Subject: [PATCH 115/127] #226 --- filter_kg_and_remap_predicates.py | 61 +++++++++++++++++-------------- 1 file changed, 33 insertions(+), 28 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 99d66480..58f1c4c4 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -120,6 +120,7 @@ def warning_record_of_source_predicate_curie_occurrences(record_of_source_predic def process_nodes(input_file_name, infores_remap_config): knowledge_source_curies_not_in_config_nodes = set() nodes_dict = dict() + graph = dict() node_ctr = 0 @@ -141,13 +142,11 @@ def process_nodes(input_file_name, infores_remap_config): node_dict['knowledge_source'] = infores_curie nodes_dict[node_id] = node_dict print(f"Completed nodes {kg2_util.date()}") - nodes_list = list(node_dict.values()) - del nodes_dict - return nodes_list, knowledge_source_curies_not_in_config_nodes + return nodes_dict, knowledge_source_curies_not_in_config_nodes -def process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except): +def process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except, nodes): predicate_remap_config = kg2_util.safe_load_yaml_from_string(kg2_util.read_file_to_string(predicate_remap_file_name)) map_dict = kg2_util.make_uri_curie_mappers(curies_to_uri_file_name) @@ -156,7 +155,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na source_predicate_curies_not_in_config = set() source_predicate_curies_not_in_nodes = set() knowledge_source_curies_not_in_config_edges = set() - record_of_source_predicate_curie_occurrences = dict() # {source_predicate_curie: False for source_predicate_curie in predicate_remap_config.keys()} + record_of_source_predicate_curie_occurrences = {source_predicate_curie: False for source_predicate_curie in predicate_remap_config.keys()} command_set = {'delete', 'keep', 'invert'} # The length of the 'command' could be 1 if it just has the operation, such as with 'delete' @@ -234,25 +233,24 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na new_edge_id = update_edge_id(edge_id, qualified_predicate, qualified_object_aspect, qualified_object_direction) edge_dict["id"] = new_edge_id - # if predicate_curie not in nodes_dict: - # predicate_curie_prefix = predicate_curie.split(':')[0] - # predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') - # # Create list of curies to complain about if not in biolink - # if predicate_uri_prefix == predicate_curie_prefix: - # source_predicate_curies_not_in_nodes.add(predicate_curie) + if predicate_curie not in nodes: + predicate_curie_prefix = predicate_curie.split(':')[0] + predicate_uri_prefix = curie_to_uri_expander(predicate_curie_prefix + ':') + # Create list of curies to complain about if not in biolink + if predicate_uri_prefix == predicate_curie_prefix: + source_predicate_curies_not_in_nodes.add(predicate_curie) knowledge_source = edge_dict["knowledge_source"] infores_curie_dict = infores_remap_config.get(knowledge_source, None) - # if infores_curie_dict is None: - # knowledge_source_curies_not_in_config_edges.add(knowledge_source) - # else: - # infores_curie = infores_curie_dict['infores_curie'] - # edge_dict['knowledge_source'] = [infores_curie] - edge_dict['knowledge_source'] = [infores_curie] + if infores_curie_dict is None: + knowledge_source_curies_not_in_config_edges.add(knowledge_source) + else: + infores_curie = infores_curie_dict['infores_curie'] + edge_dict['knowledge_source'] = [infores_curie] edge_subject = edge_dict['subject'] edge_object = edge_dict['object'] - edge_key = f"{edge_subject} /// {predicate_curie} /// {edge_object}" + edge_key = f"{edge_subject} /// {predicate_curie} /// {qualified_predicate} /// {qualified_object_aspect} /// {qualified_object_direction} /// {edge_object}" existing_edge = new_edges.get(edge_key, None) @@ -265,9 +263,10 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na new_edges[edge_key] = edge_dict print(f"Finished edges {kg2_util.date()}") edges_list = list(new_edges.values()) - del edge_dict + del edge_dict + del nodes - return edges_list #, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences + return edges_list, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences @@ -278,6 +277,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na curies_to_uri_file_name = args.curiesToURIFile input_file_name = args.inputFileJson output_file_name = args.outputFileJson + nodes_output_file_name = "" test_mode = args.test drop_negated = args.drop_negated drop_self_edges_except = args.drop_self_edges_except @@ -296,19 +296,24 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na assert type(drop_self_edges_except) == str drop_self_edges_except = set(drop_self_edges_except.split(',')) - nodes_list, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_config) + nodes_dict, knowledge_source_curies_not_in_config_nodes = process_nodes(input_file_name, infores_remap_config) + nodes_list = list(nodes_dict.values()) + nodes = nodes_dict.keys() graph['nodes'] = nodes_list + del nodes_dict + del nodes_list - edges_list = process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except) + edges_list, source_predicate_curies_not_in_config, source_predicate_curies_not_in_nodes, knowledge_source_curies_not_in_config_edges, record_of_source_predicate_curie_occurrences = process_edges(input_file_name, infores_remap_config, predicate_remap_file_name, curies_to_uri_file_name, drop_self_edges_except, nodes) graph['edges'] = edges_list + del edges_list - # Warnings for issues that came up - # warning_record_of_knowledge_source_curie_occurrences(record_of_knowledge_source_curie_occurrences) - # warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes) - # warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config) - # warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes) - # warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges) + #Warnings for issues that came up + warning_record_of_source_predicate_curie_occurrences(record_of_source_predicate_curie_occurrences) + warning_source_predicate_curies_not_in_nodes(source_predicate_curies_not_in_nodes) + warning_source_predicate_curies_not_in_config(source_predicate_curies_not_in_config) + warning_knowledge_source_curies_not_in_config_nodes(knowledge_source_curies_not_in_config_nodes) + warning_knowledge_source_curies_not_in_config_edges(knowledge_source_curies_not_in_config_edges) update_date = datetime.now().strftime("%Y-%m-%d %H:%M") version_file = open(args.versionFile, 'r') From 0b7484bb49f79bb9b07b58c605ab802c3784e812 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 10:16:28 -0700 Subject: [PATCH 116/127] #226 --- filter_kg_and_remap_predicates.py | 7 ++++--- predicate-remap.yaml | 10 +++++----- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 58f1c4c4..a0425497 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -183,13 +183,14 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na predicate_curie = source_predicate_curie if record_of_source_predicate_curie_occurrences.get(source_predicate_curie, None) is not None: - record_of_source_predicate_curie_occurrences[source_predicate_curie] = True + record_of_source_predicate_curie_occurrences[source_predicate_curie] = True + pred_remap_info = predicate_remap_config.get(source_predicate_curie, None) else: # there is a original predicate CURIE in the graph that is not in the config file source_predicate_curies_not_in_config.add(source_predicate_curie) + pred_remap_info = {'keep': None} - pred_remap_info = predicate_remap_config.get(source_predicate_curie, None) - assert pred_remap_info is not None + assert pred_remap_info is not None, f"Edge {edge_dict} missing {pred_remap_info}" invert = False get_new_rel_info = False diff --git a/predicate-remap.yaml b/predicate-remap.yaml index 901ca899..cb16144e 100644 --- a/predicate-remap.yaml +++ b/predicate-remap.yaml @@ -5516,11 +5516,11 @@ owl:sameAs: rdf:type: operation: keep core_predicate: biolink:related_to -# rdfs:negatively_regulates: -# operation: keep -# core_predicate: biolink:regulates -# qualifiers: -# - object_direction: decreased +rdfs:negatively_regulates: + operation: keep + core_predicate: biolink:regulates + qualifiers: + - object_direction: decreased rdfs:subClassOf: operation: keep core_predicate: biolink:subclass_of From 7efb630ae59be67cd02613a5e1c69c55741622fa Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 11:49:28 -0700 Subject: [PATCH 117/127] #226 --- filter_kg_and_remap_predicates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index a0425497..b437cd33 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -188,7 +188,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na else: # there is a original predicate CURIE in the graph that is not in the config file source_predicate_curies_not_in_config.add(source_predicate_curie) - pred_remap_info = {'keep': None} + pred_remap_info = {'operation': 'keep'} assert pred_remap_info is not None, f"Edge {edge_dict} missing {pred_remap_info}" From 8865367568da04da6613fecc0ac049b1fbffe987 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 11:51:10 -0700 Subject: [PATCH 118/127] #226 --- filter_kg_and_remap_predicates.py | 1 + 1 file changed, 1 insertion(+) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index b437cd33..5adf8347 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -188,6 +188,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na else: # there is a original predicate CURIE in the graph that is not in the config file source_predicate_curies_not_in_config.add(source_predicate_curie) + print(f"Source predicate curie missing {source_predicate_curie}") pred_remap_info = {'operation': 'keep'} assert pred_remap_info is not None, f"Edge {edge_dict} missing {pred_remap_info}" From 9c59c85e9009f9fb91edbb2feea631388c6c9f75 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 12:30:08 -0700 Subject: [PATCH 119/127] #226 --- filter_kg_and_remap_predicates.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 5adf8347..9f523540 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -188,7 +188,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na else: # there is a original predicate CURIE in the graph that is not in the config file source_predicate_curies_not_in_config.add(source_predicate_curie) - print(f"Source predicate curie missing {source_predicate_curie}") + #print(f"Source predicate curie missing {source_predicate_curie}") pred_remap_info = {'operation': 'keep'} assert pred_remap_info is not None, f"Edge {edge_dict} missing {pred_remap_info}" @@ -202,13 +202,13 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na elif operation == "invert": invert = True get_new_rel_info = True - else: + elif not source_predicate_curie.startswith("biolink:"): assert operation == "keep" get_new_rel_info = True if get_new_rel_info: assert pred_remap_info.get("core_predicate", None) is not None - predicate_curie = pred_remap_info.get("core_predicate") + predicate_curie = pred_remap_info.get("core_predicate", "None") qualified_predicate = pred_remap_info.get("qualified_predicate", "None") qualified_object_aspect = "None" qualified_object_direction = "None" From 82067d50d920a7794f5e77c5c75240934d3a72c2 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Fri, 4 Nov 2022 12:47:08 -0700 Subject: [PATCH 120/127] #226 --- filter_kg_and_remap_predicates.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 9f523540..f247258e 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -199,19 +199,21 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na operation = pred_remap_info.get('operation', None) if operation == "delete": continue - elif operation == "invert": + get_new_rel_info = True + if operation == "invert": invert = True - get_new_rel_info = True - elif not source_predicate_curie.startswith("biolink:"): + elif pred_remap_info.get("core_predicate", None) is None: assert operation == "keep" - get_new_rel_info = True + get_new_rel_info = False + + qualified_predicate = "None" + qualified_object_aspect = "None" + qualified_object_direction = "None" if get_new_rel_info: assert pred_remap_info.get("core_predicate", None) is not None predicate_curie = pred_remap_info.get("core_predicate", "None") qualified_predicate = pred_remap_info.get("qualified_predicate", "None") - qualified_object_aspect = "None" - qualified_object_direction = "None" qualifiers = pred_remap_info.get("qualifiers", None) if qualifiers is not None: qualifiers_dict = qualifiers[0] From 6a271049306ecb214d0d468488d611c23794e0df Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Sat, 5 Nov 2022 21:46:04 -0700 Subject: [PATCH 121/127] #226 --- filter_kg_and_remap_predicates.py | 4 ++-- kg2_util.py | 11 ++++++++++- merge_graphs.py | 6 +++--- 3 files changed, 15 insertions(+), 6 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index f247258e..1293e6c8 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -58,8 +58,8 @@ def update_edge_id(edge_id: str, qualified_predicate=None, qualified_object_aspe edge_id_keys = edge_id.split("---") subject = edge_id_keys[0] predicate = edge_id_keys[1] - object = edge_id_keys[2] - knowledge_source = edge_id_keys[3] + object = edge_id_keys[-2] + knowledge_source = edge_id_keys[-1] new_edge_id = f"{subject}---{predicate}---{qualified_predicate}---{qualified_object_aspect}---{qualified_object_direction}---{object}---{knowledge_source}" return new_edge_id diff --git a/kg2_util.py b/kg2_util.py index ca8e8915..173ea1c5 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -42,6 +42,7 @@ import validators import yaml from typing import Dict, Optional +from decimal import * TEMP_FILE_PREFIX = 'kg2' FIRST_CAP_RE = re.compile(r'(.)([A-Z][a-z]+)') @@ -267,6 +268,13 @@ def convert_date(time): def date(): return datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") +class DecimalEncoder(json.JSONEncoder): + def default(self, obj): + # If passed a Decimal object, return string + if isinstance(obj, Decimal): + return str(obj) + return json.JSONEncoder.default(self, obj) + class MLStripper(html.parser.HTMLParser): def __init__(self): @@ -306,7 +314,8 @@ def save_json(data, output_file_name: str, test_mode: bool = False): else: temp_output_file = gzip.GzipFile(temp_output_file_name, 'w') temp_output_file.write(json.dumps(data, indent=indent_num, - sort_keys=sort_keys).encode('utf-8')) + sort_keys=sort_keys).encode('utf-8'), + cls=DecimalEncoder) shutil.move(temp_output_file_name, output_file_name) diff --git a/merge_graphs.py b/merge_graphs.py index 9318dcab..4eb76031 100755 --- a/merge_graphs.py +++ b/merge_graphs.py @@ -1,9 +1,9 @@ #!/usr/bin/env python3 '''merge_graphs.py: merge two KGs that are in the KG2 JSON format - Usage: merge_graphs.py --kgFiles ... - [--kgFileOrphanEdges ] - + Usage: merge_graphs.py [--kgFileOrphanEdges ] + --outpufFile + ... ''' __author__ = 'Stephen Ramsey' From d076b71d522ae7a55a554aba1c111162af3f1154 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Sun, 6 Nov 2022 08:07:48 -0800 Subject: [PATCH 122/127] #226 --- filter_kg_and_remap_predicates.py | 1 + report_stats_on_json_kg.py | 19 ++++--------------- 2 files changed, 5 insertions(+), 15 deletions(-) diff --git a/filter_kg_and_remap_predicates.py b/filter_kg_and_remap_predicates.py index 1293e6c8..2e139036 100644 --- a/filter_kg_and_remap_predicates.py +++ b/filter_kg_and_remap_predicates.py @@ -205,6 +205,7 @@ def process_edges(input_file_name, infores_remap_config, predicate_remap_file_na elif pred_remap_info.get("core_predicate", None) is None: assert operation == "keep" get_new_rel_info = False + edge_dict["core_predicate"] = predicate_curie qualified_predicate = "None" qualified_object_aspect = "None" diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 23953bb9..327a1d21 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -92,10 +92,7 @@ def count_edges_by_source(edges: list): def count_edges_by_predicate_curie(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' - for edge in edges: - if edge.get(curie_field) == None: - edge[curie_field] = edge.pop('original_predicate') + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' return collections.Counter([edge.get(curie_field, None) for edge in edges]) @@ -105,21 +102,13 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' - for edge in edges: - if edge.get(curie_field) is None: - edge[curie_field] = edge.pop('original_predicate') + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'predicate' - unique_relation_curies = set() - for edge in edges: - if edge.get(curie_field) is None: - edge[curie_field] = edge.pop('original_predicate') - unique_relation_curies.add(edge.get(curie_field)) - #unique_relation_curies = set([edge.get(curie_field) for edge in edges]) + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' + unique_relation_curies = set([edge[curie_field] for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From 6c2447b42bf136dd1cc7c7f89cf26a3bacafad60 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Sun, 6 Nov 2022 09:51:10 -0800 Subject: [PATCH 123/127] #226 --- kg2_util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kg2_util.py b/kg2_util.py index 173ea1c5..4f0885bd 100644 --- a/kg2_util.py +++ b/kg2_util.py @@ -310,7 +310,7 @@ def save_json(data, output_file_name: str, test_mode: bool = False): if not output_file_name.endswith('.gz'): temp_output_file = open(temp_output_file_name, 'w') json.dump(data, temp_output_file, indent=indent_num, - sort_keys=sort_keys) + sort_keys=sort_keys, cls=DecimalEncoder) else: temp_output_file = gzip.GzipFile(temp_output_file_name, 'w') temp_output_file.write(json.dumps(data, indent=indent_num, From 04b0dce5e5c324938952d34f17682dbce69236dd Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 7 Nov 2022 12:19:28 -0800 Subject: [PATCH 124/127] #226 --- report_stats_on_json_kg.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index 327a1d21..d8cd77b7 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -92,8 +92,9 @@ def count_edges_by_source(edges: list): def count_edges_by_predicate_curie(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' - return collections.Counter([edge.get(curie_field, None) for edge in edges]) + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'qualified_predicate' + # When there isn't a qualified_predicate, use source_predicate + return collections.Counter([edge.get(curie_field, 'source_predicate') for edge in edges]) def count_edges_by_predicate_type(edges: list): @@ -102,13 +103,13 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' - return collections.Counter([get_prefix_from_curie_id(edge[curie_field]) for edge in edges]) + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'qualified_predicate' + return collections.Counter([get_prefix_from_curie_id(edge.get(curie_field, 'source_predicate') for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): - curie_field = 'source_predicate' if not args.use_simplified_predicates else 'core_predicate' - unique_relation_curies = set([edge[curie_field] for edge in edges]) + curie_field = 'source_predicate' if not args.use_simplified_predicates else 'qualified_predicate' + unique_relation_curies = set([edge.get(curie_field, 'source_predicate') for edge in edges]) return collections.Counter([get_prefix_from_curie_id(curie) for curie in unique_relation_curies]) From 2dc25e01f83b8bc50842818f5bc4cf4bbbd664f6 Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Mon, 7 Nov 2022 12:22:09 -0800 Subject: [PATCH 125/127] #226 --- report_stats_on_json_kg.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/report_stats_on_json_kg.py b/report_stats_on_json_kg.py index d8cd77b7..3b003397 100755 --- a/report_stats_on_json_kg.py +++ b/report_stats_on_json_kg.py @@ -104,7 +104,7 @@ def count_edges_by_predicate_type(edges: list): def count_edges_by_predicate_curie_prefix(edges: list): curie_field = 'source_predicate' if not args.use_simplified_predicates else 'qualified_predicate' - return collections.Counter([get_prefix_from_curie_id(edge.get(curie_field, 'source_predicate') for edge in edges]) + return collections.Counter([get_prefix_from_curie_id(edge.get(curie_field, 'source_predicate')) for edge in edges]) def count_predicates_by_predicate_curie_prefix(edges: list): From dab4fb63e417dea4b0b633252ddf1d1261808eff Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Tue, 8 Nov 2022 09:27:29 -0800 Subject: [PATCH 126/127] #226 --- kg_json_to_tsv.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/kg_json_to_tsv.py b/kg_json_to_tsv.py index b768d70f..c7a04e75 100755 --- a/kg_json_to_tsv.py +++ b/kg_json_to_tsv.py @@ -277,7 +277,7 @@ def edges(input_file, output_file_location): # Add the value for each edge property to the value list # and limit the size of the publications_info dictionary # to avoid Neo4j buffer size error - value = edge[key] + value = edge.get(key) if key == "publications_info": value = limit_publication_info_size(key, value) elif key == 'knowledge_source': @@ -286,6 +286,8 @@ def edges(input_file, output_file_location): value = value.replace('-', '_').replace('(', '').replace(')', '') elif key == 'publications': value = str(value).replace("', '", "; ").replace("'", "").replace("[", "").replace("]", "") + elif key == 'predicate': + value = (edge['qualified_predicate'] if not "None" else edge['source_predicate']) vallist.append(value) # Add the edge property labels to the edge header TSV file From 9fc84b66d4b06fa5bbfc5c7e31bc1ea457970fee Mon Sep 17 00:00:00 2001 From: acevedol <59181061+acevedol@users.noreply.github.com> Date: Wed, 11 Jan 2023 12:32:20 -0800 Subject: [PATCH 127/127] Updating version md --- kg2-versions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/kg2-versions.md b/kg2-versions.md index 21015933..0225297b 100644 --- a/kg2-versions.md +++ b/kg2-versions.md @@ -1,5 +1,5 @@ # 2.8.0 -**Date: 2022.XX.XX** +**Date: 2022.12.12** Counts: - Nodes: 10,370,747