Merge pull request #285 from togoid/main

release 2024-12-30

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-12-23
+Datasets last updated: 2024-12-30
 
 ## 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: 2024-12-23
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-12-23)
+## Statistics (as of 2024-12-30)
 - 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: 2024-12-23
+Datasets last updated: 2024-12-30
 
 ## 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: 2024-12-23
 ## 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 (2024-12-23)
+## 統計 (2024-12-30)
 - 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 @@
+# 2024-12-30
+- Weekly update has been completed.
+
 # 2024-12-23
 - Weekly update has been completed.
 

log/error.log

@@ -1,8 +1,10 @@
+Error: check_remote_file_time(input/glytoucan/glycosmos_ggdbs_pubmed.csv, https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv): no time information in ""
+Error: Remote file is empty
 Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data): no time information in ""
 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%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: <urlopen error [Errno 110] Connection timed out>: 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 0 / 4376 = 0.0 < 0.5

log/pair_count.tsv

@@ -2,12 +2,12 @@ affy_probeset-ncbigene.tsv	19063
 assembly_insdc-bioproject.tsv	2283159
 assembly_insdc-biosample.tsv	2225812
 assembly_insdc-insdc_master.tsv	2150193
-bioproject-biosample.tsv	21326211
-bioproject-geo_series.tsv	222154
-bioproject-pubmed.tsv	283572
+bioproject-biosample.tsv	21398558
+bioproject-geo_series.tsv	222501
+bioproject-pubmed.tsv	283831
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	21326211
-biosample-geo_sample.tsv	9592752
+biosample-bioproject.tsv	21398558
+biosample-geo_sample.tsv	9611986
 cellosaurus-ncit_disease.tsv	76763
 cellosaurus-orphanet_phenotype.tsv	41988
 chebi-glytoucan.tsv	10615
@@ -34,14 +34,14 @@ 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	2937853
-clinvar-hgnc.tsv	3073116
-clinvar-medgen.tsv	4219572
-clinvar-mondo.tsv	2007959
-clinvar-ncbigene.tsv	3073436
-clinvar-omim_phenotype.tsv	1650719
-clinvar-orphanet_phenotype.tsv	1876752
-clinvar-uniprot.tsv	20800
+clinvar-dbsnp.tsv	2936889
+clinvar-hgnc.tsv	3075959
+clinvar-medgen.tsv	4218095
+clinvar-mondo.tsv	2002420
+clinvar-ncbigene.tsv	3076279
+clinvar-omim_phenotype.tsv	1649863
+clinvar-orphanet_phenotype.tsv	1875006
+clinvar-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
 doid-mesh.tsv	4019
@@ -119,7 +119,7 @@ medgen-omim_phenotype.tsv	11369
 medgen-orphanet_phenotype.tsv	9044
 mgi_gene-ensembl_gene.tsv	56426
 mgi_gene-hgnc.tsv	24584
-mgi_gene-mgi_allele.tsv	112305
+mgi_gene-mgi_allele.tsv	112535
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79092
 mgi_genotype-doid.tsv	7844
@@ -132,22 +132,22 @@ mondo-mesh.tsv	8352
 mondo-omim_phenotype.tsv	9693
 mondo-orphanet_phenotype.tsv	10380
 nando-mondo.tsv	2390
-ncbigene-ensembl_gene.tsv	11745187
-ncbigene-ensembl_protein.tsv	13481840
-ncbigene-ensembl_transcript.tsv	14087936
+ncbigene-ensembl_gene.tsv	11736534
+ncbigene-ensembl_protein.tsv	13456249
+ncbigene-ensembl_transcript.tsv	14040414
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	102899249
+ncbigene-go.tsv	103069537
 ncbigene-hgnc.tsv	43859
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18576
-ncbigene-refseq_genomic.tsv	211771
-ncbigene-refseq_protein.tsv	69884551
-ncbigene-refseq_rna.tsv	67904058
+ncbigene-omim_gene.tsv	18583
+ncbigene-refseq_genomic.tsv	211774
+ncbigene-refseq_protein.tsv	70198561
+ncbigene-refseq_rna.tsv	68005494
 ncbigene-rgd.tsv	77241
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	57863025
+ncbigene-taxonomy.tsv	58148816
 ncbigene-vgnc.tsv	112163
 ncbigene-wormbase_gene.tsv	28785
 ncbigene-xenbase_gene.tsv	46840
@@ -170,14 +170,14 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9739099
+pmc-pubmed.tsv	9752727
 prosite-prosite_prorule.tsv	1459
 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	119108895
+pubchem_compound-inchi_key.tsv	119314791
 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	683457
-refseq_protein-uniprot.tsv	175222296
+refseq_protein-uniprot.tsv	175222283
 refseq_rna-dbsnp.tsv	267033326
 refseq_rna-hgnc.tsv	227308
 refseq_rna-ncbigene.tsv	66957414
@@ -209,28 +209,28 @@ rhea-go.tsv	4448
 rhea-pubmed.tsv	142680
 rhea-reactome_reaction.tsv	1511
 rhea-uniprot.tsv	42384671
-sra_accession-bioproject.tsv	543595
-sra_accession-biosample.tsv	32427001
-sra_accession-sra_analysis.tsv	329302
-sra_accession-sra_experiment.tsv	36544800
-sra_accession-sra_project.tsv	632118
-sra_accession-sra_run.tsv	41367694
-sra_accession-sra_sample.tsv	35257303
-sra_experiment-bioproject.tsv	31968733
-sra_experiment-biosample.tsv	32265671
-sra_experiment-sra_project.tsv	32313254
-sra_experiment-sra_sample.tsv	32312977
-sra_project-bioproject.tsv	543614
-sra_run-bioproject.tsv	33855800
-sra_run-biosample.tsv	34166458
-sra_run-sra_experiment.tsv	34222772
-sra_run-sra_project.tsv	34213095
-sra_run-sra_sample.tsv	34213846
-sra_sample-biosample.tsv	32441420
+sra_accession-bioproject.tsv	548585
+sra_accession-biosample.tsv	32682465
+sra_accession-sra_analysis.tsv	329305
+sra_accession-sra_experiment.tsv	36676207
+sra_accession-sra_project.tsv	635025
+sra_accession-sra_run.tsv	41501893
+sra_accession-sra_sample.tsv	35400045
+sra_experiment-bioproject.tsv	32165254
+sra_experiment-biosample.tsv	32503023
+sra_experiment-sra_project.tsv	32509776
+sra_experiment-sra_sample.tsv	32509515
+sra_project-bioproject.tsv	555466
+sra_run-bioproject.tsv	34064543
+sra_run-biosample.tsv	34413756
+sra_run-sra_experiment.tsv	34430861
+sra_run-sra_project.tsv	34421839
+sra_run-sra_sample.tsv	34420323
+sra_sample-biosample.tsv	32710602
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50757
+taxonomy-pubmed.tsv	50753
 togovar-clinvar.tsv	781585
 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	5340075365
+total	5344103538

log/pair_count_history.tsv

@@ -70,3 +70,4 @@ Date	affy_probeset-ncbigene	assembly_insdc-bioproject	assembly_insdc-biosample	a
 2024-12-07	19063	2283159	2225812	2150193		2546485	221334	282694	104586	20439564	9573846	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	2937889	3068652	4210198	2001160	3068972	1646702	1871572	20800	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	2121	41201	43839	21140	1325		24077	1912	43753	17348	35052	13532	28712	18945	20374	13701	217899	522	104230	275237	8814	220065	137689		113135	59409158	193975949	1533582	1533178	30269	1679206	22308	1282	116156	479226	1274	787874156	199	305	130	12929	48152	12349	137319849	6318	18747	17044	22699	7334	11369		9044	56426	24584	112132	90618	79070	7844	125076	401601	10712	574	1486	8352	9693		10380	2390	11788732	13562026	14257155	25078	102596805	43859		71682	17541	18559	211769	69806245	67710490	77241	6471	32835	57866358	112163	28785	46840	27178	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9703036	1459	4965	174843	2372556	10789	69203	119107534	33861	69387	1253395	2877	623594	1267	270070	13144	41304	348	393545	868219	203666	3318	14709	194	679876	159946382	267033326	227308	66957414	190999	6311722	58133044	66987567	216654	7719	4448	142680	1511	42384671	543090	32388968	329302	36430485	629932	41251239	35118028	31918768	32226084	32263289	32263012	543109	33803917	34126791	34170279	34161212	34163744	32403387	4276	26026	593209	50709	781585	66877211	72473309	287277970	60732887	935843	60001809	692119	173346179	2578	10340	66728	41313492	9647701	9863257	9863257	590661858	82519	269942826	237103	13525491	7583382	16357	7263		7996	400528	282944	46026396	254254987	254254987	733559	190	790497				5929	1153	4131	1429	30267	33518	5303878533
 2024-12-16	19063	2283159	2225812	2150193		2546485	221856	283298	104586	20508479	9590138	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	2937893	3069553	4211502	2001782	3069873	1647115	1872043	20800	115826	3340026	4019	4849	5671	55423	12969337	15910019	47792	14749031	5546630	12969340	241195	55211171	241612	40165483	141	5046	155799	290	1270	70216	82906	402	310	35510	2121	41201	43839	21140	1325		24078	1912	43753	17350	35060	13532	28712	18945	20374	13701	217899	522	104230	275237	8823	220065	139028		114066	59409158	193975949	1533582	1533178	30269	1679206	22308	1282	116156	479226	1274	787874156	199	305	130	12929	48152	12349	137319849	6318	18747	17044	22699	7334	11369		9044	56426	24584	112260	90618	79070	7844	125076	401601	10712	574	1486	8352	9693		10380	2390	11755401	13509818	14158040	25078	102800883	43859		71682	17541	18562	211772	69891186	67763645	77241	6471	32835	57932960	112163	28785	46840	27181	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9722361	1459	4965	174843	2372556	10789	69203	119108895	33861	69387	1253395	2877	623594	1267	270398	13144	41304	348	393545	871849	204183	3318	14709	194	683457	175209073	267033326	227308	66957414	190999	6311722	58133044	66987567	216654	7719	4448	142680	1511	42384671	543595	32427001	329302	36544800	632118	41367694	35257303	31968733	32265671	32313254	32312977	543614	33855800	34166458	34222772	34213095	34213846	32441420	4276	26026	593209	50715	781585	66877211	72473309	287277970	60732887	935843	60001809	692119	173346179	2578	10340	66728	41313492	9647701	9863257	9863257	590661858	82519	269942826	237103	13525491	7583382	16357	7263		7996	400528	282944	46026396	254254987	254254987	733559	190	790497				5929	1153	4131	1429	30267	33518	5320359597
 2024-12-20	19063	2283159	2225812	2150193		21326211	222154	283572	104586	21326211	9592752	76763		41988	10615	175447	34347	3101919	3101919	4931	8211	11771	1915184	47707	14012	1878399	433145	1449263	2126	11847	10947	34588	3549	8047	9094	9094	1533	1434	2937853	3073116	4219572	2007959	3073436	1650719	1876752	20800	115826	3340026	4019	4849	5671	55423	12969337	15910019	47792	14749031	5546630	12969340	241195	55211171	241612	40165483	141	5046	155799	290	1270	70216	82906	402	310	35510	2121	41201	43839	21140	1325		24078	1912	43753	17350	35060	13532	28712	18945	20374	13701	217899	522	104230	275237	8823	220065	139028		114066	59409158	193975949	1533582	1533178	30269	1679206	22308	1282	116156	479226	1274	787874156	199	305	130	12929	48152	12349	137319849	6318	18747	17044	22699	7334	11369		9044	56426	24584	112305	90618	79092	7844	125076	401601	10712	574	1486	8352	9693		10380	2390	11745187	13481840	14087936	25078	102899249	43859		71682	17541	18576	211771	69884551	67904058	77241	6471	32835	57863025	112163	28785	46840	27181	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9739099	1459	4965	174843	2372556	10789	69203	119108895	33861	69387	1253395	2877	623594	1267	270398	13144	41304	348	393545	871849	204183	3318	14709	194	683457	175222296	267033326	227308	66957414	190999	6311722	58133044	66987567	216654	7719	4448	142680	1511	42384671	543595	32427001	329302	36544800	632118	41367694	35257303	31968733	32265671	32313254	32312977	543614	33855800	34166458	34222772	34213095	34213846	32441420	4276	26026	593209	50757	781585	66877211	72473309	287277970	60732887	935843	60001809	692119	173346179	2578	10340	66728	41313492	9647701	9863257	9863257	590661858	82519	269942826	237103	13525491	7583382	16357	7263		7996	400528	282944	46026396	254254987	254254987	733559	190	790497				5929	1153	4131	1429	30267	33518	5340075365
+2024-12-27	19063	2283159	2225812	2150193		21398558	222501	283831	104586	21398558	9611986	76763		41988	10615	175447	34347	3101919	3101919	4931	8211	11771	1915184	47707	14012	1878399	433145	1449263	2126	11847	10947	34588	3549	8047	9094	9094	1533	1434	2936889	3075959	4218095	2002420	3076279	1649863	1875006	20799	115826	3340026	4019	4849	5671	55423	12969337	15910019	47792	14749031	5546630	12969340	241195	55211171	241612	40165483	141	5046	155799	290	1270	70216	82906	402	310	35510	2121	41201	43839	21140	1325		24078	1912	43753	17350	35060	13532	28712	18945	20374	13701	217899	522	104230	275237	8823	220065	139028		114066	59409158	193975949	1533582	1533178	30269	1679206	22308	1282	116156	479226	1274	787874156	199	305	130	12929	48152	12349	137319849	6318	18747	17044	22699	7334	11369		9044	56426	24584	112535	90618	79092	7844	125076	401601	10712	574	1486	8352	9693		10380	2390	11736534	13456249	14040414	25078	103069537	43859		71682	17541	18583	211774	70198561	68005494	77241	6471	32835	58148816	112163	28785	46840	27181	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9752727	1459	4965	174843	2372556	10789	69203	119314791	33861	69387	1253395	2877	623594	1267	270398	13144	41304	348	393545	871849	204183	3318	14709	194	683457	175222283	267033326	227308	66957414	190999	6311722	58133044	66987567	216654	7719	4448	142680	1511	42384671	548585	32682465	329305	36676207	635025	41501893	35400045	32165254	32503023	32509776	32509515	555466	34064543	34413756	34430861	34421839	34420323	32710602	4276	26026	593209	50753	781585	66877211	72473309	287277970	60732887	935843	60001809	692119	173346179	2578	10340	66728	41313492	9647701	9863257	9863257	590661858	82519	269942826	237103	13525491	7583382	16357	7263		7996	400528	282944	46026396	254254987	254254987	733559	190	790497				5929	1153	4131	1429	30267	33518	5344103538