Merge pull request #278 from togoid/main

release 2024-11-26

bin/sparql/mondo_labels.rq

@@ -14,7 +14,7 @@ WHERE {
     oboInOwl:hasBroadSynonym
   }
   ?mondo a owl:Class ;
-    rdfs:label ?label ;
+    ?p ?label ;
     oboInOwl:id ?mondo_id .
 
   BIND (strafter(str(?mondo_id), 'MONDO:') AS ?id)

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-18
+Datasets last updated: 2024-11-26
 
 ## 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: 2024-11-18
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-11-18)
+## Statistics (as of 2024-11-26)
 - Number of target datasets 
     - 105 (from 73 databases)
 - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. 

docs/help_ja.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-18
+Datasets last updated: 2024-11-26
 
 ## 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: 2024-11-18
 ## 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 (2024-11-18)
+## 統計 (2024-11-26)
 - 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。 

docs/news.md

@@ -1,3 +1,6 @@
+# 2024-11-26
+- Weekly update has been completed.
+
 # 2024-11-18
 - Weekly update has been completed.
 

log/error.log

@@ -3,7 +3,7 @@ Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi
 Error: Remote file is empty
 # Error: output/tsv/chembl_target-ensembl_gene.tsv new file size per old 0 / 61845 = 0.0 < 0.5
 # Error: Failed to create output/tsv/chembl_target-ensembl_gene.tsv or created file was empty
-Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C10%2C9%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5BAad21122h-2a_2-6_5%2ANCC%2F3%3DO%5D%5Ba2112h-1b_1-5_2%2ANCC%2F3%3DO%5D%2F1-2-3-3-3-4-2-3-3-3%2Fa4-b1_b3-c2_b4-f1_c8-d2_d8-e2_f3-g1_f6-j2_g3-h2_h8-i2&rootnode=true G14091MR
+Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C11%2C10%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5Ba2122h-1b_1-5_2%2ANCC%2F3%3DO%5D%5Ba1221m-1a_1-5%5D%2F1-2-3-2-3-2-3-4-2-3-2%2Fa4-b1_b3-c1_c4-d1_d3-e1_e4-f1_f3-g1_g3-h1_g4-i1_i3-j1_j4-k1&rootnode=true G64227KZ
 # 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

log/pair_count.tsv

@@ -3,11 +3,11 @@ assembly_insdc-bioproject.tsv	2283159
 assembly_insdc-biosample.tsv	2225812
 assembly_insdc-insdc_master.tsv	2150193
 bioproject-biosample.tsv	2546485
-bioproject-geo_series.tsv	220020
-bioproject-pubmed.tsv	281552
+bioproject-geo_series.tsv	220473
+bioproject-pubmed.tsv	281950
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	20274353
-biosample-geo_sample.tsv	9528638
+biosample-bioproject.tsv	20329479
+biosample-geo_sample.tsv	9540054
 cellosaurus-ncit_disease.tsv	75821
 cellosaurus-orphanet_phenotype.tsv	41448
 chebi-glytoucan.tsv	10615
@@ -34,13 +34,13 @@ chembl_target-uniprot-TIO_000002.tsv	9094
 chembl_target-uniprot-TIO_000130.tsv	1533
 chembl_target-uniprot-TIO_000132.tsv	1434
 chembl_target-uniprot.tsv	9094
-clinvar-dbsnp.tsv	2937845
-clinvar-hgnc.tsv	3060210
-clinvar-medgen.tsv	4193666
-clinvar-mondo.tsv	1992996
-clinvar-ncbigene.tsv	3060530
-clinvar-omim_phenotype.tsv	1638969
-clinvar-orphanet_phenotype.tsv	1865227
+clinvar-dbsnp.tsv	2937841
+clinvar-hgnc.tsv	3061979
+clinvar-medgen.tsv	4196850
+clinvar-mondo.tsv	1993860
+clinvar-ncbigene.tsv	3062299
+clinvar-omim_phenotype.tsv	1639794
+clinvar-orphanet_phenotype.tsv	1865790
 clinvar-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
@@ -68,20 +68,20 @@ glytoucan-uniprot-TIO_000126.tsv	402
 glytoucan-uniprot-TIO_000128.tsv	310
 glytoucan-uniprot.tsv	82906
 hgnc-ccds.tsv	35510
-hgnc-ec.tsv	2083
-hgnc-ensembl_gene.tsv	41244
-hgnc-hgnc_symbol.tsv	43882
-hgnc-insdc.tsv	21162
+hgnc-ec.tsv	2118
+hgnc-ensembl_gene.tsv	41199
+hgnc-hgnc_symbol.tsv	43838
+hgnc-insdc.tsv	21140
 hgnc-lrg.tsv	1325
 hgnc-mgi_gene.tsv	24072
 hgnc-mirbase.tsv	1912
-hgnc-ncbigene.tsv	43813
-hgnc-omim_gene.tsv	17320
-hgnc-pubmed.tsv	34994
+hgnc-ncbigene.tsv	43753
+hgnc-omim_gene.tsv	17339
+hgnc-pubmed.tsv	35030
 hgnc-refseq_genomic.tsv	13532
-hgnc-refseq_rna.tsv	28776
+hgnc-refseq_rna.tsv	28712
 hgnc-rgd.tsv	18945
-hgnc-uniprot.tsv	20379
+hgnc-uniprot.tsv	20374
 hmdb-chebi.tsv	13701
 hmdb-inchi_key.tsv	217899
 hmdb-pdb_ccd.tsv	522
@@ -119,38 +119,38 @@ medgen-omim_phenotype.tsv	11043
 medgen-orphanet_phenotype.tsv	9063
 mgi_gene-ensembl_gene.tsv	56426
 mgi_gene-hgnc.tsv	24584
-mgi_gene-mgi_allele.tsv	111987
+mgi_gene-mgi_allele.tsv	112050
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79070
-mgi_genotype-doid.tsv	7839
-mgi_genotype-mgi_allele.tsv	124809
-mgi_genotype-mp.tsv	401409
+mgi_genotype-doid.tsv	7840
+mgi_genotype-mgi_allele.tsv	125052
+mgi_genotype-mp.tsv	401482
 mondo-doid.tsv	10712
 mondo-hp_phenotype.tsv	574
 mondo-meddra.tsv	1486
 mondo-mesh.tsv	8352
 mondo-omim_phenotype.tsv	9693
 mondo-orphanet_phenotype.tsv	10380
 nando-mondo.tsv	2390
-ncbigene-ensembl_gene.tsv	11671120
-ncbigene-ensembl_protein.tsv	13442158
-ncbigene-ensembl_transcript.tsv	14133616
+ncbigene-ensembl_gene.tsv	11681986
+ncbigene-ensembl_protein.tsv	13454144
+ncbigene-ensembl_transcript.tsv	14146143
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	102174797
-ncbigene-hgnc.tsv	43838
+ncbigene-go.tsv	102598546
+ncbigene-hgnc.tsv	43845
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18546
-ncbigene-refseq_genomic.tsv	211768
-ncbigene-refseq_protein.tsv	69217894
-ncbigene-refseq_rna.tsv	67173120
-ncbigene-rgd.tsv	47289
+ncbigene-omim_gene.tsv	18551
+ncbigene-refseq_genomic.tsv	211770
+ncbigene-refseq_protein.tsv	69690608
+ncbigene-refseq_rna.tsv	67642626
+ncbigene-rgd.tsv	77241
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	57305467
+ncbigene-taxonomy.tsv	57768578
 ncbigene-vgnc.tsv	112162
 ncbigene-wormbase_gene.tsv	28785
-ncbigene-xenbase_gene.tsv	46841
+ncbigene-xenbase_gene.tsv	46840
 ncbigene-zfin_gene.tsv	27177
 ncit_disease-ncit_tissue.tsv	27199
 oma_protein-ensembl_gene.tsv	2533621
@@ -170,14 +170,14 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9638140
+pmc-pubmed.tsv	9664384
 prosite-prosite_prorule.tsv	1455
 pubchem_compound-atc.tsv	4965
 pubchem_compound-chebi.tsv	174843
 pubchem_compound-chembl_compound.tsv	2372556
 pubchem_compound-drugbank.tsv	10789
 pubchem_compound-glytoucan.tsv	69203
-pubchem_compound-inchi_key.tsv	119096080
+pubchem_compound-inchi_key.tsv	119096713
 pubchem_pathway-ncbigene.tsv	33861
 pubchem_pathway-pathbank.tsv	69387
 pubchem_pathway-pubchem_compound.tsv	1253395
@@ -195,7 +195,7 @@ reactome_reaction-go.tsv	3318
 reactome_reaction-iuphar_ligand.tsv	14709
 reactome_reaction-mirbase.tsv	194
 reactome_reaction-uniprot.tsv	679876
-refseq_protein-uniprot.tsv	154617878
+refseq_protein-uniprot.tsv	154617876
 refseq_rna-dbsnp.tsv	267033326
 refseq_rna-hgnc.tsv	227308
 refseq_rna-ncbigene.tsv	66957414
@@ -209,28 +209,28 @@ rhea-go.tsv	4435
 rhea-pubmed.tsv	142680
 rhea-reactome_reaction.tsv	1511
 rhea-uniprot.tsv	41448659
-sra_accession-bioproject.tsv	537477
-sra_accession-biosample.tsv	32055914
+sra_accession-bioproject.tsv	537619
+sra_accession-biosample.tsv	32063559
 sra_accession-sra_analysis.tsv	329284
-sra_accession-sra_experiment.tsv	36095148
-sra_accession-sra_project.tsv	624977
-sra_accession-sra_run.tsv	40902883
-sra_accession-sra_sample.tsv	34804828
-sra_experiment-bioproject.tsv	31554967
-sra_experiment-biosample.tsv	31873477
-sra_experiment-sra_project.tsv	31899488
-sra_experiment-sra_sample.tsv	31899211
-sra_project-bioproject.tsv	537496
-sra_run-bioproject.tsv	33441595
-sra_run-biosample.tsv	33758531
-sra_run-sra_experiment.tsv	33817349
-sra_run-sra_project.tsv	33798890
-sra_run-sra_sample.tsv	33786315
-sra_sample-biosample.tsv	32070333
+sra_accession-sra_experiment.tsv	36134714
+sra_accession-sra_project.tsv	625496
+sra_accession-sra_run.tsv	40945774
+sra_accession-sra_sample.tsv	34837349
+sra_experiment-bioproject.tsv	31577033
+sra_experiment-biosample.tsv	31881755
+sra_experiment-sra_project.tsv	31921554
+sra_experiment-sra_sample.tsv	31921277
+sra_project-bioproject.tsv	537638
+sra_run-bioproject.tsv	33463976
+sra_run-biosample.tsv	33772350
+sra_run-sra_experiment.tsv	33847764
+sra_run-sra_project.tsv	33821271
+sra_run-sra_sample.tsv	33813940
+sra_sample-biosample.tsv	32077978
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50609
+taxonomy-pubmed.tsv	50616
 togovar-clinvar.tsv	745335
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -270,4 +270,4 @@ wikipathways-hmdb.tsv	4131
 wikipathways-lipidmaps.tsv	1429
 wikipathways-ncbigene.tsv	30267
 wikipathways-uniprot.tsv	33518
-total	5197418100
+total	5199738167

log/pair_count_history.tsv

@@ -65,3 +65,4 @@ Date	affy_probeset-ncbigene	assembly_insdc-bioproject	assembly_insdc-biosample	a
 2024-11-02	19063	2283159	2225812	2150193		2546485	219155	280897	104586	20158980	9499972	75821		41448	10615	175447	34347	3101919	3101919	4931	8211	11771	1915184	47707	14012	1878399	433145	1449263	2126	11847	10947	34588	3549	8047	9094	9094	1533	1434	2937819	3052664	4183498	1991311	3052984	1637518	1862716	20799	115826	3340026	4019	4849	5671	55423	12969337	15910019	47792	14749031	5546630	12969340	241195	55211171	241612	40165483	141	5046	155799	290	1270	82906	82906	402	310	35510	2083	41244	43882	21162	1325		24072	1912	43813	17320	34994	13532	28776	18945	20379	13701	217899	522	104230	275237	8814	220065	137689		113135	59409158	193975949	1533582	1533178	30282	1645155	21310	1282	114937	477238	1274	770832917	199	305	130	12929	48152	12349	137319849	6318	16674	16849	21567	7229	11043		9063	56426	24587	110999	90618	79034	7838	124731	401241	10712	574	1486	8352	9693		10380	2390	11648014	13414145	14101829	25078	101701291	43833		71682	17541	18541	211762	69118246	67171889	47288	6471	32835	57206436	112162	28785	46842	27169	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9614170	1455	4965	174843	2372556	10789	69203	118730900	33861	69387	1253395	2877	623594	1267	270070	13144	41304	348	393545	868219	203666	3318	14709	194	679876	154618873	267059416	227230	65546825	190869	6191600	56922967	65576846	216654	7719	4435	142680	1511	41448659	536535	31958980	329255	35876479	621556	40676738	34592184	31454530	31789122	31799051	31798774	536554	33327693	33673989	33691490	33684988	33683705	31973248	4276	26026	593209	50467	745335	66877211	72473309	287277970	60732887	935843	60001809	692119	173346179	2578	10336	66728	41313492	9613808	9834392	9834392	532822218	82524	264947440	237103	12855457	7617387	16357	7263		7981	390829	282944	45329880	248838887	248838887	641755	191	698680	11471	1148	4125	1398	30268	33518	5190192279
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