Merge pull request #275 from togoid/main

release 2024-11-05

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-10-28
+Datasets last updated: 2024-11-05
 
 ## 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: 2024-10-28
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-10-28)
+## Statistics (as of 2024-11-05)
 - 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: 2024-10-28
+Datasets last updated: 2024-11-05
 
 ## 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: 2024-10-28
 ## 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 (2024-10-28)
+## 統計 (2024-11-05)
 - 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

@@ -1,4 +1,7 @@
 
+# 2024-11-05
+- Weekly update has been completed.
+
 # 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.

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%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 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: 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	218653
-bioproject-pubmed.tsv	280373
+bioproject-geo_series.tsv	219155
+bioproject-pubmed.tsv	280897
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	20082284
-biosample-geo_sample.tsv	9478410
+biosample-bioproject.tsv	20158980
+biosample-geo_sample.tsv	9499972
 cellosaurus-ncit_disease.tsv	75821
 cellosaurus-orphanet_phenotype.tsv	41448
 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	2937807
-clinvar-hgnc.tsv	3048477
-clinvar-medgen.tsv	4177072
-clinvar-mondo.tsv	1990261
-clinvar-ncbigene.tsv	3048797
-clinvar-omim_phenotype.tsv	1637242
-clinvar-orphanet_phenotype.tsv	1861848
-clinvar-uniprot.tsv	20798
+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-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
 doid-mesh.tsv	4019
@@ -119,39 +119,39 @@ 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	110480
+mgi_gene-mgi_allele.tsv	110999
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79034
 mgi_genotype-doid.tsv	7838
-mgi_genotype-mgi_allele.tsv	124681
-mgi_genotype-mp.tsv	401152
+mgi_genotype-mgi_allele.tsv	124731
+mgi_genotype-mp.tsv	401241
 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	11638524
-ncbigene-ensembl_protein.tsv	13403395
-ncbigene-ensembl_transcript.tsv	14090731
+ncbigene-ensembl_gene.tsv	11648014
+ncbigene-ensembl_protein.tsv	13414145
+ncbigene-ensembl_transcript.tsv	14101829
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	101708425
-ncbigene-hgnc.tsv	43830
+ncbigene-go.tsv	101701291
+ncbigene-hgnc.tsv	43833
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18536
-ncbigene-refseq_genomic.tsv	211761
-ncbigene-refseq_protein.tsv	69014178
-ncbigene-refseq_rna.tsv	67056457
+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-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	57139197
+ncbigene-taxonomy.tsv	57206436
 ncbigene-vgnc.tsv	112162
-ncbigene-wormbase_gene.tsv	28779
+ncbigene-wormbase_gene.tsv	28785
 ncbigene-xenbase_gene.tsv	46842
-ncbigene-zfin_gene.tsv	27161
+ncbigene-zfin_gene.tsv	27169
 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	9593110
+pmc-pubmed.tsv	9614170
 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	118728820
+pubchem_compound-inchi_key.tsv	118730900
 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	154618874
+refseq_protein-uniprot.tsv	154618873
 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	535765
-sra_accession-biosample.tsv	31924194
+sra_accession-bioproject.tsv	536535
+sra_accession-biosample.tsv	31958980
 sra_accession-sra_analysis.tsv	329255
-sra_accession-sra_experiment.tsv	35778526
-sra_accession-sra_project.tsv	619680
-sra_accession-sra_run.tsv	40578279
-sra_accession-sra_sample.tsv	34520229
-sra_experiment-bioproject.tsv	31409027
-sra_experiment-biosample.tsv	31744486
-sra_experiment-sra_project.tsv	31753548
-sra_experiment-sra_sample.tsv	31753271
-sra_project-bioproject.tsv	535784
-sra_run-bioproject.tsv	33277499
-sra_run-biosample.tsv	33629100
-sra_run-sra_experiment.tsv	33641296
-sra_run-sra_project.tsv	33634794
-sra_run-sra_sample.tsv	33637946
-sra_sample-biosample.tsv	31938462
+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
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50461
+taxonomy-pubmed.tsv	50467
 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	5188977489
+total	5190192279

log/pair_count_history.tsv

@@ -62,3 +62,4 @@ Date	affy_probeset-ncbigene	assembly_insdc-bioproject	assembly_insdc-biosample	a
 2024-10-12	19063	2283159	2225812	2150193		2546485	217809	279413	104586	19988521	9447146	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	2937791	3044255	4171173	1988452	3044575	1635664	1860371	20798	115826	3340026	4019	4849	5671	54855	12969337	15910019	47792	14749031	5546630	12969340	224377	55211171	241612	40165483	141	5046	155799	290	1270	82906	82906	402	310	35510	2049	41234	43873	21166	1325		24071	1912	43815	17277	34911	13531	28774	18940	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	110437	90618	79034	7837	124623	400910	10712	574	1486	8352	9693		10380	2390	11654277	13449374	14177749	25078	101041913	43827		71684	17541	18527	211762	68217911	66619410	47288	6471	32835	56353463	112162	28779	46842	27163	27199	2533621	2925554	5849918	14432954				4319	4337	4316	4298	1192	1798	7832	8040	1685211	726658	530587	339565	341431	9561234	1455	4965	174843	2372556	10789	69203	118680448	33861	69387	1253395	2877	623594	1267	270070	13144	41304	348	393545	868219	203666	3318	14709	194	679876	154618594	267059416	227230	65546825	190869	6191600	56922967	65576846	216654	7719	4435	142680	1511	41448659	529462	31680248	329243	35570093	616586	40350221	34372201	31035975	31352287	31380496	31380303	532904	32903026	33216964	33268661	33260321	33246345	31701362	4276	26026	593209	50493	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	4119	1398	30258	33518	5181681751
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