Merge pull request #276 from togoid/main

release 2024-11-14

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-05
+Datasets last updated: 2024-11-14
 
 ## 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: 2024-11-05
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-11-05)
+## Statistics (as of 2024-11-14)
 - 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: 2024-11-05
+Datasets last updated: 2024-11-14
 
 ## 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: 2024-11-05
 ## 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 (2024-11-05)
+## 統計 (2024-11-14)
 - 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 +1,5 @@
+# 2024-11-14
+- Weekly update has been completed.
 
 # 2024-11-05
 - 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 502: Bad Gateway: 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: 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	219155
-bioproject-pubmed.tsv	280897
+bioproject-geo_series.tsv	219632
+bioproject-pubmed.tsv	281330
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	20158980
-biosample-geo_sample.tsv	9499972
+biosample-bioproject.tsv	20225455
+biosample-geo_sample.tsv	9517180
 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	2937819
-clinvar-hgnc.tsv	3052664
-clinvar-medgen.tsv	4183498
-clinvar-mondo.tsv	1991311
-clinvar-ncbigene.tsv	3052984
-clinvar-omim_phenotype.tsv	1637518
-clinvar-orphanet_phenotype.tsv	1862716
+clinvar-dbsnp.tsv	2937837
+clinvar-hgnc.tsv	3055902
+clinvar-medgen.tsv	4188105
+clinvar-mondo.tsv	1991707
+clinvar-ncbigene.tsv	3056222
+clinvar-omim_phenotype.tsv	1637694
+clinvar-orphanet_phenotype.tsv	1862922
 clinvar-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
@@ -118,40 +118,40 @@ medgen-ncbigene.tsv	7229
 medgen-omim_phenotype.tsv	11043
 medgen-orphanet_phenotype.tsv	9063
 mgi_gene-ensembl_gene.tsv	56426
-mgi_gene-hgnc.tsv	24587
-mgi_gene-mgi_allele.tsv	110999
+mgi_gene-hgnc.tsv	24584
+mgi_gene-mgi_allele.tsv	111129
 mgi_gene-ncbigene.tsv	90618
-mgi_gene-uniprot.tsv	79034
-mgi_genotype-doid.tsv	7838
-mgi_genotype-mgi_allele.tsv	124731
-mgi_genotype-mp.tsv	401241
+mgi_gene-uniprot.tsv	79070
+mgi_genotype-doid.tsv	7839
+mgi_genotype-mgi_allele.tsv	124777
+mgi_genotype-mp.tsv	401337
 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	11648014
-ncbigene-ensembl_protein.tsv	13414145
-ncbigene-ensembl_transcript.tsv	14101829
+ncbigene-ensembl_gene.tsv	11671126
+ncbigene-ensembl_protein.tsv	13442166
+ncbigene-ensembl_transcript.tsv	14133624
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	101701291
+ncbigene-go.tsv	102174808
 ncbigene-hgnc.tsv	43833
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18541
-ncbigene-refseq_genomic.tsv	211762
-ncbigene-refseq_protein.tsv	69118246
-ncbigene-refseq_rna.tsv	67171889
-ncbigene-rgd.tsv	47288
+ncbigene-omim_gene.tsv	18544
+ncbigene-refseq_genomic.tsv	211764
+ncbigene-refseq_protein.tsv	69154949
+ncbigene-refseq_rna.tsv	67173056
+ncbigene-rgd.tsv	47289
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	57206436
+ncbigene-taxonomy.tsv	57240175
 ncbigene-vgnc.tsv	112162
 ncbigene-wormbase_gene.tsv	28785
-ncbigene-xenbase_gene.tsv	46842
-ncbigene-zfin_gene.tsv	27169
+ncbigene-xenbase_gene.tsv	46841
+ncbigene-zfin_gene.tsv	27171
 ncit_disease-ncit_tissue.tsv	27199
 oma_protein-ensembl_gene.tsv	2533621
 oma_protein-ensembl_transcript.tsv	2925554
@@ -170,14 +170,14 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9614170
+pmc-pubmed.tsv	9629383
 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	118730900
+pubchem_compound-inchi_key.tsv	119084186
 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	154618873
+refseq_protein-uniprot.tsv	154618104
 refseq_rna-dbsnp.tsv	267059416
 refseq_rna-hgnc.tsv	227230
 refseq_rna-ncbigene.tsv	65546825
@@ -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	536535
-sra_accession-biosample.tsv	31958980
-sra_accession-sra_analysis.tsv	329255
-sra_accession-sra_experiment.tsv	35876479
-sra_accession-sra_project.tsv	621556
-sra_accession-sra_run.tsv	40676738
-sra_accession-sra_sample.tsv	34592184
-sra_experiment-bioproject.tsv	31454530
-sra_experiment-biosample.tsv	31789122
-sra_experiment-sra_project.tsv	31799051
-sra_experiment-sra_sample.tsv	31798774
-sra_project-bioproject.tsv	536554
-sra_run-bioproject.tsv	33327693
-sra_run-biosample.tsv	33673989
-sra_run-sra_experiment.tsv	33691490
-sra_run-sra_project.tsv	33684988
-sra_run-sra_sample.tsv	33683705
-sra_sample-biosample.tsv	31973248
+sra_accession-bioproject.tsv	537052
+sra_accession-biosample.tsv	32023315
+sra_accession-sra_analysis.tsv	329284
+sra_accession-sra_experiment.tsv	35985315
+sra_accession-sra_project.tsv	623349
+sra_accession-sra_run.tsv	40790046
+sra_accession-sra_sample.tsv	34699841
+sra_experiment-bioproject.tsv	31502359
+sra_experiment-biosample.tsv	31834873
+sra_experiment-sra_project.tsv	31846880
+sra_experiment-sra_sample.tsv	31846603
+sra_project-bioproject.tsv	537071
+sra_run-bioproject.tsv	33386528
+sra_run-biosample.tsv	33719878
+sra_run-sra_experiment.tsv	33751992
+sra_run-sra_project.tsv	33743823
+sra_run-sra_sample.tsv	33731672
+sra_sample-biosample.tsv	32037734
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50467
+taxonomy-pubmed.tsv	50581
 togovar-clinvar.tsv	745335
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -270,4 +270,4 @@ wikipathways-hmdb.tsv	4125
 wikipathways-lipidmaps.tsv	1398
 wikipathways-ncbigene.tsv	30268
 wikipathways-uniprot.tsv	33518
-total	5190192279
+total	5192207706

log/pair_count_history.tsv

@@ -63,3 +63,4 @@ Date	affy_probeset-ncbigene	assembly_insdc-bioproject	assembly_insdc-biosample	a
 2024-10-19	19063	2283159	2225812	2150193		2546485	218318	280110	104586	20027457	9463924	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	2937807	3048112	4176542	1989799	3048432	1636833	1861412	20798	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	110465	90618	79034	7837	124623	400910	10712	574	1486	8352	9693		10380	2390	11654277	13449374	14177749	25078	101431326	43828		71683	17541	18530	211763	68719760	66732541	47288	6471	32835	56873692	112162	28779	46842	27163	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9575886	1455	4965	174843	2372556	10789	69203	118727283	33861	69387	1253395	2877	623594	1267	270070	13144	41304	348	393545	868219	203666	3318	14709	194	679876	154618423	267059416	227230	65546825	190869	6191600	56922967	65576846	216654	7719	4435	142680	1511	41448659	529783	31699855	329243	35659853	617870	40455586	34436063	31083409	31394401	31427930	31427737	533225	32951299	33259254	33317034	33308594	33294197	31720969	4276	26026	593209	50481	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	5184078473
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