Merge pull request #268 from togoid/main

release 2024-10-10

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-09-30
+Datasets last updated: 2024-10-10
 
 ## 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.
@@ -22,7 +22,7 @@ Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya,
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## Statistics (as of 2024-09-30)
+## Statistics (as of 2024-10-10)
 - 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: 2024-09-30
+Datasets last updated: 2024-10-10
 
 ## 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。
@@ -28,7 +28,7 @@ Datasets last updated: 2024-09-30
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## 統計 (2024-09-30)
+## 統計 (2024-10-10)
 - 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

@@ -1,10 +1,16 @@
+# *NOTICE*  
+The TogoID service will be temporarily unavailable due to a system update from 10:00 am to 00:00 pm (JST) on Tuesday, October 15, 2024. We apologize for any incovenience caused.
+
 # 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.
 
+# 2024-10-10
+- Weekly update has been completed.  
+
 # 2024-09-30
 - Weekly update has been completed.  
 - A new pair `chebi-glytoucan` has been added.  

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	216801
-bioproject-pubmed.tsv	278016
+bioproject-geo_series.tsv	217446
+bioproject-pubmed.tsv	278826
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	19849642
-biosample-geo_sample.tsv	9409388
+biosample-bioproject.tsv	19938580
+biosample-geo_sample.tsv	9431518
 cellosaurus-ncit_disease.tsv	75821
 cellosaurus-orphanet_phenotype.tsv	41448
 chebi-glytoucan.tsv	10615
@@ -30,14 +30,17 @@ chembl_target-interpro.tsv	10947
 chembl_target-pdb.tsv	34588
 chembl_target-pfam.tsv	3549
 chembl_target-reactome_pathway.tsv	8047
+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	2937727
-clinvar-hgnc.tsv	3025517
-clinvar-medgen.tsv	4145651
-clinvar-mondo.tsv	1986712
-clinvar-ncbigene.tsv	3025834
-clinvar-omim_phenotype.tsv	1635593
-clinvar-orphanet_phenotype.tsv	1859264
+clinvar-dbsnp.tsv	2937745
+clinvar-hgnc.tsv	3025875
+clinvar-medgen.tsv	4162525
+clinvar-mondo.tsv	1986846
+clinvar-ncbigene.tsv	3026191
+clinvar-omim_phenotype.tsv	1634429
+clinvar-orphanet_phenotype.tsv	1859346
 clinvar-uniprot.tsv	20797
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
@@ -92,14 +95,14 @@ insdc-bioproject.tsv	59409158
 insdc-biosample.tsv	193975949
 insdc_master-bioproject.tsv	1533582
 insdc_master-biosample.tsv	1533178
-interpro-go.tsv	30288
-interpro-pdb.tsv	1615604
-interpro-pfam.tsv	21171
-interpro-prosite.tsv	1283
-interpro-pubmed.tsv	113855
-interpro-reactome_pathway.tsv	473753
+interpro-go.tsv	30282
+interpro-pdb.tsv	1645155
+interpro-pfam.tsv	21310
+interpro-prosite.tsv	1282
+interpro-pubmed.tsv	114937
+interpro-reactome_pathway.tsv	477238
 interpro-smart.tsv	1274
-interpro-uniprot.tsv	759739513
+interpro-uniprot.tsv	770832917
 jga_study-jga_dataset.tsv	199
 jga_study-nbdc_human_db.tsv	305
 jga_study-pubmed.tsv	130
@@ -114,41 +117,41 @@ medgen-mondo.tsv	21567
 medgen-ncbigene.tsv	7229
 medgen-omim_phenotype.tsv	11043
 medgen-orphanet_phenotype.tsv	9063
-mgi_gene-ensembl_gene.tsv	56430
+mgi_gene-ensembl_gene.tsv	56428
 mgi_gene-hgnc.tsv	24587
-mgi_gene-mgi_allele.tsv	110329
+mgi_gene-mgi_allele.tsv	110373
 mgi_gene-ncbigene.tsv	90619
 mgi_gene-uniprot.tsv	79034
-mgi_genotype-doid.tsv	7836
-mgi_genotype-mgi_allele.tsv	124600
-mgi_genotype-mp.tsv	400728
+mgi_genotype-doid.tsv	7837
+mgi_genotype-mgi_allele.tsv	124602
+mgi_genotype-mp.tsv	400771
 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	11640889
-ncbigene-ensembl_protein.tsv	13437484
-ncbigene-ensembl_transcript.tsv	14165019
+ncbigene-ensembl_gene.tsv	11660930
+ncbigene-ensembl_protein.tsv	13459019
+ncbigene-ensembl_transcript.tsv	14189546
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	100805649
-ncbigene-hgnc.tsv	43830
+ncbigene-go.tsv	101043576
+ncbigene-hgnc.tsv	43829
 ncbigene-mgi_gene.tsv	71684
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18530
+ncbigene-omim_gene.tsv	18526
 ncbigene-refseq_genomic.tsv	211759
-ncbigene-refseq_protein.tsv	67906210
-ncbigene-refseq_rna.tsv	66278052
+ncbigene-refseq_protein.tsv	68060620
+ncbigene-refseq_rna.tsv	66432148
 ncbigene-rgd.tsv	47288
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	56097873
+ncbigene-taxonomy.tsv	56251350
 ncbigene-vgnc.tsv	112162
 ncbigene-wormbase_gene.tsv	28779
-ncbigene-xenbase_gene.tsv	46840
-ncbigene-zfin_gene.tsv	27162
+ncbigene-xenbase_gene.tsv	46842
+ncbigene-zfin_gene.tsv	27163
 ncit_disease-ncit_tissue.tsv	27199
 oma_protein-ensembl_gene.tsv	2533621
 oma_protein-ensembl_transcript.tsv	2925554
@@ -167,67 +170,67 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9522934
-prosite-prosite_prorule.tsv	1453
+pmc-pubmed.tsv	9547208
+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	118657562
+pubchem_compound-inchi_key.tsv	118680448
 pubchem_pathway-ncbigene.tsv	33861
 pubchem_pathway-pathbank.tsv	69387
 pubchem_pathway-pubchem_compound.tsv	1253395
 pubchem_pathway-reactome_pathway.tsv	2877
 pubchem_pathway-uniprot.tsv	623594
 pubchem_pathway-wikipathways.tsv	1267
-reactome_pathway-chebi.tsv	268044
+reactome_pathway-chebi.tsv	270070
 reactome_pathway-go.tsv	13144
-reactome_pathway-iuphar_ligand.tsv	40633
+reactome_pathway-iuphar_ligand.tsv	41304
 reactome_pathway-mirbase.tsv	348
 reactome_pathway-reactome_reaction.tsv	393545
-reactome_pathway-uniprot.tsv	868078
-reactome_reaction-chebi.tsv	201371
+reactome_pathway-uniprot.tsv	868219
+reactome_reaction-chebi.tsv	203666
 reactome_reaction-go.tsv	3318
-reactome_reaction-iuphar_ligand.tsv	14387
+reactome_reaction-iuphar_ligand.tsv	14709
 reactome_reaction-mirbase.tsv	194
-reactome_reaction-uniprot.tsv	672687
-refseq_protein-uniprot.tsv	168636138
+reactome_reaction-uniprot.tsv	679876
+refseq_protein-uniprot.tsv	168636384
 refseq_rna-dbsnp.tsv	267059416
 refseq_rna-hgnc.tsv	227230
 refseq_rna-ncbigene.tsv	65546825
 refseq_rna-omim_gene.tsv	190869
 refseq_rna-pubmed.tsv	6191600
 refseq_rna-refseq_protein.tsv	56922967
 refseq_rna-taxonomy.tsv	65576846
-rhea-chebi.tsv	206037
-rhea-ec.tsv	7598
-rhea-go.tsv	4447
-rhea-pubmed.tsv	138072
-rhea-reactome_reaction.tsv	1480
-rhea-uniprot.tsv	41203851
-sra_accession-bioproject.tsv	528400
-sra_accession-biosample.tsv	31608624
+rhea-chebi.tsv	216654
+rhea-ec.tsv	7719
+rhea-go.tsv	4435
+rhea-pubmed.tsv	142680
+rhea-reactome_reaction.tsv	1511
+rhea-uniprot.tsv	41448659
+sra_accession-bioproject.tsv	529030
+sra_accession-biosample.tsv	31645689
 sra_accession-sra_analysis.tsv	329141
-sra_accession-sra_experiment.tsv	35358694
-sra_accession-sra_project.tsv	613078
-sra_accession-sra_run.tsv	40139217
-sra_accession-sra_sample.tsv	34193817
-sra_experiment-bioproject.tsv	30937045
-sra_experiment-biosample.tsv	31262333
-sra_experiment-sra_project.tsv	31281566
-sra_experiment-sra_sample.tsv	31281373
-sra_project-bioproject.tsv	531842
-sra_run-bioproject.tsv	32784770
-sra_run-biosample.tsv	33125990
-sra_run-sra_experiment.tsv	33149472
-sra_run-sra_project.tsv	33142065
-sra_run-sra_sample.tsv	33145755
-sra_sample-biosample.tsv	31629738
+sra_accession-sra_experiment.tsv	35486202
+sra_accession-sra_project.tsv	615018
+sra_accession-sra_run.tsv	40263951
+sra_accession-sra_sample.tsv	34290431
+sra_experiment-bioproject.tsv	30997361
+sra_experiment-biosample.tsv	31319829
+sra_experiment-sra_project.tsv	31341882
+sra_experiment-sra_sample.tsv	31341689
+sra_project-bioproject.tsv	532472
+sra_run-bioproject.tsv	32860319
+sra_run-biosample.tsv	33183885
+sra_run-sra_experiment.tsv	33225215
+sra_run-sra_project.tsv	33217614
+sra_run-sra_sample.tsv	33206609
+sra_sample-biosample.tsv	31666803
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50502
+taxonomy-pubmed.tsv	50523
 togovar-clinvar.tsv	745335
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -238,33 +241,33 @@ togovar-ncbigene.tsv	60001809
 togovar-pubmed.tsv	692119
 togovar-refseq_rna.tsv	173346179
 uberon-ncit_tissue.tsv	2578
-uniprot-chembl_target.tsv	10144
-uniprot-dbsnp.tsv	65716
-uniprot-ec.tsv	39722925
-uniprot-ensembl_gene.tsv	9498084
-uniprot-ensembl_protein.tsv	9712712
-uniprot-ensembl_transcript.tsv	9712712
-uniprot-go.tsv	604164314
-uniprot-hgnc.tsv	81986
-uniprot-insdc.tsv	260978721
-uniprot-intact.tsv	230595
-uniprot-ncbigene.tsv	12687882
-uniprot-oma_group.tsv	7653121
-uniprot-omim_gene.tsv	16188
-uniprot-omim_phenotype.tsv	7077
-uniprot-orphanet_phenotype.tsv	8227
-uniprot-pdb.tsv	384047
-uniprot-reactome_pathway.tsv	281259
-uniprot_reference_proteome-assembly_insdc.tsv	588007
-uniprot_reference_proteome-assembly_refseq.tsv	190
-uniprot_reference_proteome-taxonomy.tsv	656198
-uniprot-refseq_protein.tsv	45015597
-uniprot-taxonomy.tsv	245896766
-uniprot-uniprot_mnemonic.tsv	245896766
+uniprot-chembl_target.tsv	10336
+uniprot-dbsnp.tsv	66728
+uniprot-ec.tsv	41313492
+uniprot-ensembl_gene.tsv	9613808
+uniprot-ensembl_protein.tsv	9834392
+uniprot-ensembl_transcript.tsv	9834392
+uniprot-go.tsv	532822218
+uniprot-hgnc.tsv	82524
+uniprot-insdc.tsv	264947440
+uniprot-intact.tsv	237103
+uniprot-ncbigene.tsv	12855457
+uniprot-oma_group.tsv	7617387
+uniprot-omim_gene.tsv	16357
+uniprot-omim_phenotype.tsv	7263
+uniprot-orphanet_phenotype.tsv	7981
+uniprot-pdb.tsv	390829
+uniprot-reactome_pathway.tsv	282944
+uniprot_reference_proteome-assembly_insdc.tsv	641755
+uniprot_reference_proteome-assembly_refseq.tsv	191
+uniprot_reference_proteome-taxonomy.tsv	698680
+uniprot-refseq_protein.tsv	45329880
+uniprot-taxonomy.tsv	248838887
+uniprot-uniprot_mnemonic.tsv	248838887
 wikipathways-chebi.tsv	11471
 wikipathways-doid.tsv	1148
 wikipathways-hmdb.tsv	4119
 wikipathways-lipidmaps.tsv	1398
 wikipathways-ncbigene.tsv	30258
 wikipathways-uniprot.tsv	33518
-total	5240093853
+total	5194479012