Merge pull request #274 from togoid/main

release 2024-10-28
togoid · Oct 28, 2024 · ba9f219 · ba9f219
2 parents 8cdc18e + 3178e0a
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diff --git a/docs/help.md b/docs/help.md
@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-10-21
+Datasets last updated: 2024-10-28
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) is an ID conversion service implementing unique features with an intuitive web interface and an API for programmatic access. TogoID supports datasets from various biological categories such as gene, protein, chemical compound, pathway, disease, etc. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an [ontology](https://togoid.dbcls.jp/ontology) that defines the semantics of the dataset relations.
@@ -10,7 +10,7 @@ Datasets last updated: 2024-10-21
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-10-21)
+## Statistics (as of 2024-10-28)
 - Number of target datasets 
     - 105 (from 73 databases)
 - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. 

diff --git a/docs/help_ja.md b/docs/help_ja.md
@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-10-21
+Datasets last updated: 2024-10-28
 
 ## About
 - [TogoID](https://togoid.dbcls.jp/) は、直感的なインターフェースにより生命科学系データベース(DB)間のつながりを探索的に確認しながらID変換を行うことができるウェブアプリケーションです。同一の実体を指すID間の変換だけでなく、関連する別のカテゴリーのIDへの変換も可能です。また、直接リンクされていないDBのID間でも、他のDBを経由した変換を探索することができます。
@@ -10,7 +10,7 @@ Datasets last updated: 2024-10-21
 ## 動画マニュアル
 - [TogoIDを使って生命科学系データベースのさまざまなIDを探索的に変換する](https://youtu.be/gXnvm6Fn4R8)
 
-## 統計 (2024-10-21)
+## 統計 (2024-10-28)
 - 対象データセット数 
     - 105 (73 のデータベースに由来)
 - 対象DBの詳細やID例については、"DATASETS" タブ からご覧いただけます。 

diff --git a/docs/news.md b/docs/news.md
@@ -1,9 +1,7 @@
-# 2024-09-06
-*New features released!*  
-- You can now display labels for IDs by toggling the "Show labels" switch in the results table.  
-- In the LABEL2ID tab, you can convert labels into IDs (e.g., gene symbols to NCBI Gene IDs or disease names to MONDO IDs).  
-- TogoID now supports handling multiple semantic relations between the same dataset pair (e.g., try converting between GlyTouCan and UniProt).  
-A detailed document is currently being prepared.
+
+# 2024-10-28
+- Weekly update has been completed.  
+- The documentation has been updated. Please see the DOCUMENTS tab to learn about TogoID's features including recent developments.
 
 # 2024-10-21
 - Weekly update has been completed.
@@ -28,6 +26,12 @@ A detailed document is currently being prepared.
 # 2024-09-09
 - Weekly update has been completed.
 
+# 2024-09-06
+*New features released!*  
+- You can now display labels for IDs by toggling the "Show labels" switch in the results table.  
+- In the LABEL2ID tab, you can convert labels into IDs (e.g., gene symbols to NCBI Gene IDs or disease names to MONDO IDs).  
+- TogoID now supports handling multiple semantic relations between the same dataset pair (e.g., try converting between GlyTouCan and UniProt).  
+
 # 2024-09-05
 - Weekly update has been completed.
 

diff --git a/log/config-summary.tsv b/log/config-summary.tsv
@@ -60,21 +60,21 @@ glycomotif-glytoucan	FIXME	Glycan	GlycoMotif	http://glycomotif.glyomics.org/glyc
 glytoucan-doid	nbdc01535	Glycan	GlyTouCan	http://identifiers.org/glytoucan/	nbdc00261	Phenotype	Disease ontology	http://purl.obolibrary.org/obo/DOID_	tio:TIO_000010	has related phenotype	has related phenotype	tio:TIO_000011	phenotype is related with	is related with	threeTimesAYear	"sh retrieve.sh"
 glytoucan-ncbigene	nbdc01535	Glycan	GlyTouCan	http://identifiers.org/glytoucan/	nbdc00073	Gene	NCBI Gene	http://identifiers.org/ncbigene/	tio:TIO_000099	glycan is processed by protein coded by gene	is processed by protein coded by gene	tio:TIO_000098	gene codes protein to process glycan	codes protein to process glycan	threeTimesAYear	"sparql_csv2tsv.sh query.rq https://ts.glycosmos.org/sparql"
 glytoucan-uniprot	nbdc01535	Glycan	GlyTouCan	http://identifiers.org/glytoucan/	nbdc00221	Protein	UniProt	http://purl.uniprot.org/uniprot/	tio:TIO_000060	glycan is attached to protein	is attached to	tio:TIO_000061	protein is modified with glycan	is modified with	threeTimesAYear	"sparql_csv2tsv.sh query.rq https://ts.glycosmos.org/sparql"
-hgnc-ccds	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00023	Gene	Consensus CDS	http://identifiers.org/ccds/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$25{gsub(\"\\\"\",\"\",$25); split($25,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-ec	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc01883	Function	Enzyme nomenclature	http://identifiers.org/ec-code/	tio:TIO_000028	sequence has EC number	has EC number	tio:TIO_000029	is EC number of sequence	is EC number of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$47{gsub(\"\\\"\",\"\",$47); split($47,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-ensembl_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00054	Gene	Ensembl gene	http://identifiers.org/ensembl/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$20{gsub(\"\\\"\",\"\",$20); split($20,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-hgnc_symbol	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc01774	Gene	HGNC gene symbol	http://identifiers.org/hgnc.symbol/	tio:TIO_000022	has synonym	has synonym	tio:TIO_000023	is synonym of	is synonym of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$2{print substr($1,6) \"\\t\" $2}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-insdc	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc02567	Gene	GenBank/ENA/DDBJ	http://identifiers.org/insdc/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$23{gsub(\"\\\"\",\"\",$23); split($23,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-lrg	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc02566	Gene	LRG	http://identifiers.org/lrg/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$30{gsub(\"\\\"\",\"\",$30); split($30,a,\"|\"); for(k in a){if(a[k]~/^LRG_[0-9]+$/) print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-mgi_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00135	Gene	MGI gene	http://identifiers.org/mgi/MGI:	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$28{gsub(\"\\\"\",\"\",$28); split($28,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-mirbase	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00136	Transcript	miRBase	http://identifiers.org/mirbase/	tio:TIO_000035	gene is transcribed to transcript	is transcribed to	tio:TIO_000034	transcript is transcribed from gene	is transcribed from	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$33{gsub(\"\\\"\",\"\",$33); split($33,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-ncbigene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00073	Gene	NCBI Gene	http://identifiers.org/ncbigene/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$19{gsub(\"\\\"\",\"\",$19); split($19,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-omim_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00154	Gene	OMIM gene	http://identifiers.org/mim/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$32{gsub(\"\\\"\",\"\",$32); split($32,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-pubmed	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00179	Literature	PubMed	http://rdf.ncbi.nlm.nih.gov/pubmed/	tio:TIO_000032	has reference	has reference	tio:TIO_000033	is reference of	is reference of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$27{gsub(\"\\\"\",\"\",$27); split($27,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-refseq_genomic	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00187	Gene	RefSeq genomic	http://identifiers.org/refseq/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-refseq_rna	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00187	Transcript	RefSeq RNA	http://identifiers.org/refseq/	tio:TIO_000035	gene is transcribed to transcript	is transcribed to	tio:TIO_000034	transcript is transcribed from gene	is transcribed from	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-rgd	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00188	Gene	RGD	http://identifiers.org/rgd/	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$29{gsub(\"\\\"\",\"\",$29); split($29,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
-hgnc-uniprot	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00221	Protein	UniProt	http://purl.uniprot.org/uniprot/	tio:TIO_000025	gene has protein as product	has gene product	tio:TIO_000024	protein is product of gene	is product of gene	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$26{gsub(\"\\\"\",\"\",$26); split($26,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv"
+hgnc-ccds	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00023	Gene	Consensus CDS	http://identifiers.org/ccds/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$25{gsub(\"\\\"\",\"\",$25); split($25,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-ec	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc01883	Function	Enzyme nomenclature	http://identifiers.org/ec-code/	tio:TIO_000028	sequence has EC number	has EC number	tio:TIO_000029	is EC number of sequence	is EC number of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$47{gsub(\"\\\"\",\"\",$47); split($47,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-ensembl_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00054	Gene	Ensembl gene	http://identifiers.org/ensembl/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$20{gsub(\"\\\"\",\"\",$20); split($20,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-hgnc_symbol	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc01774	Gene	HGNC gene symbol	http://identifiers.org/hgnc.symbol/	tio:TIO_000022	has synonym	has synonym	tio:TIO_000023	is synonym of	is synonym of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$2{print substr($1,6) \"\\t\" $2}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-insdc	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc02567	Gene	GenBank/ENA/DDBJ	http://identifiers.org/insdc/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$23{gsub(\"\\\"\",\"\",$23); split($23,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-lrg	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc02566	Gene	LRG	http://identifiers.org/lrg/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$30{gsub(\"\\\"\",\"\",$30); split($30,a,\"|\"); for(k in a){if(a[k]~/^LRG_[0-9]+$/) print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-mgi_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00135	Gene	MGI gene	http://identifiers.org/mgi/MGI:	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$28{gsub(\"\\\"\",\"\",$28); split($28,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-mirbase	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00136	Transcript	miRBase	http://identifiers.org/mirbase/	tio:TIO_000035	gene is transcribed to transcript	is transcribed to	tio:TIO_000034	transcript is transcribed from gene	is transcribed from	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$33{gsub(\"\\\"\",\"\",$33); split($33,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-ncbigene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00073	Gene	NCBI Gene	http://identifiers.org/ncbigene/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$19{gsub(\"\\\"\",\"\",$19); split($19,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-omim_gene	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00154	Gene	OMIM gene	http://identifiers.org/mim/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$32{gsub(\"\\\"\",\"\",$32); split($32,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-pubmed	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00179	Literature	PubMed	http://rdf.ncbi.nlm.nih.gov/pubmed/	tio:TIO_000032	has reference	has reference	tio:TIO_000033	is reference of	is reference of	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$27{gsub(\"\\\"\",\"\",$27); split($27,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-refseq_genomic	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00187	Gene	RefSeq genomic	http://identifiers.org/refseq/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-refseq_rna	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00187	Transcript	RefSeq RNA	http://identifiers.org/refseq/	tio:TIO_000035	gene is transcribed to transcript	is transcribed to	tio:TIO_000034	transcript is transcribed from gene	is transcribed from	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$24{gsub(\"\\\"\",\"\",$24); split($24,a,\"|\"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) \"\\t\" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-rgd	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00188	Gene	RGD	http://identifiers.org/rgd/	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	tio:TIO_000017	sequence is orthologous to sequence	is orthologous to	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$29{gsub(\"\\\"\",\"\",$29); split($29,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
+hgnc-uniprot	nbdc01774	Gene	HGNC	http://identifiers.org/hgnc/	nbdc00221	Protein	UniProt	http://purl.uniprot.org/uniprot/	tio:TIO_000025	gene has protein as product	has gene product	tio:TIO_000024	protein is product of gene	is product of gene	Bimonthly	"awk -F \"\\t\" 'FNR>=2&&$26{gsub(\"\\\"\",\"\",$26); split($26,a,\"|\"); for(k in a)print substr($1,6) \"\\t\" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt"
 hmdb-chebi	nbdc00909	Compound	HMDB	http://identifiers.org/hmdb/	nbdc00027	Compound	ChEBI compound	http://purl.obolibrary.org/obo/CHEBI_	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Triennial	"awk -F \"\\t\" '$2==\"chebi_id\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/hmdb/hmdb_metabolites.tsv"
 hmdb-inchi_key	nbdc00909	Compound	HMDB	http://identifiers.org/hmdb/	FIXME	Compound	InChIKey	http://identifiers.org/inchikey/	tio:TIO_000020	compound is represented as InChIKey	is represented as	tio:TIO_000021	InChIKey represents compound	represents	Triennial	"awk -F \"\\t\" '$2==\"inchikey\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/hmdb/hmdb_metabolites.tsv"
 hmdb-pdb_ccd	nbdc00909	Compound	HMDB	http://identifiers.org/hmdb/	nbdc01766	Compound	PDB CCD	http://identifiers.org/pdb-ccd/	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	tio:TIO_000001	is nearly equivalent to	is nearly equivalent to	Triennial	"awk -F \"\\t\" '$2==\"pdb_id\"{print $1 \"\\t\" $3}' $TOGOID_ROOT/input/hmdb/hmdb_metabolites.tsv"

diff --git a/log/error.log b/log/error.log
@@ -7,7 +7,7 @@ Error: HTTP Error 502: Bad Gateway: https://api.alpha.glycosmos.org/partialmatch
 # Error: output/tsv/glycomotif-glytoucan.tsv new file size per old 0 / 2804382 = 0.0 < 0.5
 # Error: Failed to create output/tsv/glycomotif-glytoucan.tsv or created file was empty
 # Error: output/tsv/glytoucan-doid.tsv new file size per old 1538 / 4376 = 0.35146252285191953 < 0.5
-# Error: output/tsv/hgnc-ccds.tsv new file size per old 260816 / 544502 = 0.47899915886443023 < 0.5
+# Error: output/tsv/hgnc-ccds.tsv new file size per old 252491 / 544502 = 0.46370995882476096 < 0.5
 # Error: output/tsv/lipidmaps-chebi.tsv new file size per old 248 / 253350 = 0.0009788829682257747 < 0.5
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <html><head>
 # Error: output/tsv/lipidmaps-chebi.tsv seems to contain HTML <title>503 Service Unavailable</title>
@@ -59,6 +59,10 @@ Error: HTTP Error 502: Bad Gateway: https://api.alpha.glycosmos.org/partialmatch
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to be malformed request due to maintenance downtime or capacity
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML problems. Please try again later.</p>
 # Error: output/tsv/lipidmaps-swisslipids.tsv seems to contain HTML </body></html>
+# Error: output/tsv/mbgd_gene-uniprot.tsv new file size per old 0 / 4017692184 = 0.0 < 0.5
+# Error: Failed to create output/tsv/mbgd_gene-uniprot.tsv or created file was empty
+# Error: output/tsv/mbgd_organism-taxonomy.tsv new file size per old 0 / 81445 = 0.0 < 0.5
+# Error: Failed to create output/tsv/mbgd_organism-taxonomy.tsv or created file was empty
 # Error: output/tsv/mondo-doid.tsv new file size per old 0 / 155460 = 0.0 < 0.5
 # Error: Failed to create output/tsv/mondo-doid.tsv or created file was empty
 # Error: output/tsv/mondo-hp_phenotype.tsv new file size per old 0 / 9184 = 0.0 < 0.5