Merge pull request #286 from togoid/main

release 2025-01-13

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-12-30
+Datasets last updated: 2025-01-13
 
 ## 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.
@@ -8,9 +8,9 @@ Datasets last updated: 2024-12-30
 - See the "DATASETS" tab for a list of supported datasets.
 
 ## Video tutorial
-- [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
+- [How to use TogoID ver 2.0: an exploratory ID converter to bridge biological datasets](https://youtu.be/ORW1GGIaJsY)
 
-## Statistics (as of 2024-12-30)
+## Statistics (as of 2025-01-13)
 - Number of target datasets 
     - 105 (from 73 databases)
 - For details on the target DBs and ID examples, please refer to the "DATASETS" tab. 
@@ -132,4 +132,6 @@ For LABEL2ID, TogoID uses [PubDictionaries](https://pubdictionaries.org/). [The
 e.g. [Retrieve human gene symbols including synonyms and convert them to NCBI Gene IDs](https://pubdictionaries.org/find_ids.json?labels=ACE2%7CHIF2A&dictionaries=togoid_ncbigene_symbol,togoid_ncbigene_synonym&tags=9606&threshold=1&verbose=true)
 
 ## Publication
-Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya, Shuichi Kawashima, Yasunori Yamamoto, Shinobu Okamoto, Susumu Goto, Toshiaki Katayama, TogoID: an exploratory ID converter to bridge biological datasets, _Bioinformatics_, 2022;, btac491, [https://doi.org/10.1093/bioinformatics/btac491](https://doi.org/10.1093/bioinformatics/btac491)
+- Shuya Ikeda, Kiyoko F Aoki-Kinoshita, Hirokazu Chiba, Susumu Goto, Masae Hosoda, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Tazro Ohta, Hiromasa Ono, Terue Takatsuki, Yasunori Yamamoto, Toshiaki Katayama, Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features, J Biomed Semantics. 2025 Jan 8;16(1):1. [doi:10.1186/s13326-024-00322-1](https://doi.org/10.1186/s13326-024-00322-1).
+
+- Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya, Shuichi Kawashima, Yasunori Yamamoto, Shinobu Okamoto, Susumu Goto, Toshiaki Katayama, TogoID: an exploratory ID converter to bridge biological datasets, _Bioinformatics_, 2022;, btac491, [https://doi.org/10.1093/bioinformatics/btac491](https://doi.org/10.1093/bioinformatics/btac491)

docs/help_ja.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-12-30
+Datasets last updated: 2025-01-13
 
 ## 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。
@@ -8,9 +8,9 @@ Datasets last updated: 2024-12-30
 - TogoIDに収載されているデータセットの詳細については、"DATASETS"タブからご覧いただけます。
 
 ## 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)
+- [TogoID ver. 2.0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/ORW1GGIaJsY)
 
-## 統計 (2024-12-30)
+## 統計 (2025-01-13)
 - 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。 
@@ -128,6 +128,8 @@ TogoID が対象としているデータセットの詳細を閲覧できます
 例: [シノニムを含めてヒトの遺伝子シンボルを検索し NCBI Gene ID に変換する](https://pubdictionaries.org/find_ids.json?labels=ACE2%7CHIF2A&dictionaries=togoid_ncbigene_symbol,togoid_ncbigene_synonym&tags=9606&threshold=1&verbose=true)
 
 ## 論文
+- Shuya Ikeda, Kiyoko F Aoki-Kinoshita, Hirokazu Chiba, Susumu Goto, Masae Hosoda, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Tazro Ohta, Hiromasa Ono, Terue Takatsuki, Yasunori Yamamoto, Toshiaki Katayama, Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features, J Biomed Semantics. 2025 Jan 8;16(1):1. [doi:10.1186/s13326-024-00322-1](https://doi.org/10.1186/s13326-024-00322-1).
+
 - Shuya Ikeda, Hiromasa Ono, Tazro Ohta, Hirokazu Chiba, Yuki Naito, Yuki Moriya, Shuichi Kawashima, Yasunori Yamamoto, Shinobu Okamoto, Susumu Goto, Toshiaki Katayama, TogoID: an exploratory ID converter to bridge biological datasets, _Bioinformatics_, 2022;, btac491, [https://doi.org/10.1093/bioinformatics/btac491](https://doi.org/10.1093/bioinformatics/btac491)
 
 ## 紹介PDF･記事

docs/news.md

@@ -1,3 +1,7 @@
+# 2025-01-13
+- [Our new publication](https://link.springer.com/article/10.1186/s13326-024-00322-1) has been published.
+- Weekly update has been completed.
+
 # 2024-12-30
 - Weekly update has been completed.
 

log/error.log

@@ -1,9 +1,11 @@
-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: output/tsv/ensembl_gene-affy_probeset.tsv new file size per old 0 / 1493051 = 0.0 < 0.5
+# Error: Failed to create output/tsv/ensembl_gene-affy_probeset.tsv or created file was empty
+# Error: output/tsv/ensembl_transcript-affy_probeset.tsv new file size per old 0 / 6536965 = 0.0 < 0.5
+# Error: Failed to create output/tsv/ensembl_transcript-affy_probeset.tsv or created file was empty
 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
@@ -65,4 +67,17 @@ Error: <urlopen error [Errno 110] Connection timed out>: https://api.alpha.glyco
 # Error: Failed to create output/tsv/mondo-omim_phenotype.tsv or created file was empty
 # Error: output/tsv/mondo-orphanet_phenotype.tsv new file size per old 0 / 146923 = 0.0 < 0.5
 # Error: Failed to create output/tsv/mondo-orphanet_phenotype.tsv or created file was empty
+# Error: output/tsv/togovar-clinvar.tsv new file size per old 139 / 15732849 = 8.835017738999466e-06 < 0.5
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <head><title>404 Not Found</title></head>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <body>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <center><h1>404 Not Found</h1></center>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <hr><center>nginx/1.27.3</center>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML </body>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML </html>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <head><title>404 Not Found</title></head>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <body>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <center><h1>404 Not Found</h1></center>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML <hr><center>nginx/1.27.3</center>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML </body>
+# Error: output/tsv/togovar-clinvar.tsv seems to contain HTML </html>
 # Error: output/tsv/wikipathways-uniprot.tsv new file size per old 60240 / 470542 = 0.12802257821830995 < 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	21398558
-bioproject-geo_series.tsv	222501
-bioproject-pubmed.tsv	283831
+bioproject-biosample.tsv	21586980
+bioproject-geo_series.tsv	223885
+bioproject-pubmed.tsv	284644
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	21398558
-biosample-geo_sample.tsv	9611986
+biosample-bioproject.tsv	21586980
+biosample-geo_sample.tsv	9667148
 cellosaurus-ncit_disease.tsv	76763
 cellosaurus-orphanet_phenotype.tsv	41988
 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	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-dbsnp.tsv	2936911
+clinvar-hgnc.tsv	3079438
+clinvar-medgen.tsv	4225793
+clinvar-mondo.tsv	2008296
+clinvar-ncbigene.tsv	3079758
+clinvar-omim_phenotype.tsv	1651151
+clinvar-orphanet_phenotype.tsv	1880128
 clinvar-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
@@ -69,17 +69,17 @@ glytoucan-uniprot-TIO_000128.tsv	310
 glytoucan-uniprot.tsv	70216
 hgnc-ccds.tsv	35510
 hgnc-ec.tsv	2121
-hgnc-ensembl_gene.tsv	41201
-hgnc-hgnc_symbol.tsv	43839
+hgnc-ensembl_gene.tsv	41215
+hgnc-hgnc_symbol.tsv	43853
 hgnc-insdc.tsv	21140
 hgnc-lrg.tsv	1325
 hgnc-mgi_gene.tsv	24078
 hgnc-mirbase.tsv	1912
-hgnc-ncbigene.tsv	43753
-hgnc-omim_gene.tsv	17350
-hgnc-pubmed.tsv	35060
+hgnc-ncbigene.tsv	43759
+hgnc-omim_gene.tsv	17378
+hgnc-pubmed.tsv	35087
 hgnc-refseq_genomic.tsv	13532
-hgnc-refseq_rna.tsv	28712
+hgnc-refseq_rna.tsv	28715
 hgnc-rgd.tsv	18945
 hgnc-uniprot.tsv	20374
 hmdb-chebi.tsv	13701
@@ -118,8 +118,8 @@ medgen-ncbigene.tsv	7334
 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	112535
+mgi_gene-hgnc.tsv	24586
+mgi_gene-mgi_allele.tsv	112625
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79092
 mgi_genotype-doid.tsv	7844
@@ -136,21 +136,21 @@ ncbigene-ensembl_gene.tsv	11736534
 ncbigene-ensembl_protein.tsv	13456249
 ncbigene-ensembl_transcript.tsv	14040414
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	103069537
-ncbigene-hgnc.tsv	43859
+ncbigene-go.tsv	103312464
+ncbigene-hgnc.tsv	43873
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18583
-ncbigene-refseq_genomic.tsv	211774
-ncbigene-refseq_protein.tsv	70198561
-ncbigene-refseq_rna.tsv	68005494
+ncbigene-omim_gene.tsv	18585
+ncbigene-refseq_genomic.tsv	211778
+ncbigene-refseq_protein.tsv	70419674
+ncbigene-refseq_rna.tsv	68241100
 ncbigene-rgd.tsv	77241
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	58148816
+ncbigene-taxonomy.tsv	58278792
 ncbigene-vgnc.tsv	112163
 ncbigene-wormbase_gene.tsv	28785
-ncbigene-xenbase_gene.tsv	46840
+ncbigene-xenbase_gene.tsv	48697
 ncbigene-zfin_gene.tsv	27181
 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	9752727
+pmc-pubmed.tsv	9787916
 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	119314791
+pubchem_compound-inchi_key.tsv	119318586
 pubchem_pathway-ncbigene.tsv	33861
 pubchem_pathway-pathbank.tsv	69387
 pubchem_pathway-pubchem_compound.tsv	1253395
@@ -195,42 +195,42 @@ 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	175222283
-refseq_rna-dbsnp.tsv	267033326
-refseq_rna-hgnc.tsv	227308
-refseq_rna-ncbigene.tsv	66957414
-refseq_rna-omim_gene.tsv	190999
-refseq_rna-pubmed.tsv	6311722
-refseq_rna-refseq_protein.tsv	58133044
-refseq_rna-taxonomy.tsv	66987567
+refseq_protein-uniprot.tsv	175208741
+refseq_rna-dbsnp.tsv	335727598
+refseq_rna-hgnc.tsv	227326
+refseq_rna-ncbigene.tsv	67967549
+refseq_rna-omim_gene.tsv	191159
+refseq_rna-pubmed.tsv	6314365
+refseq_rna-refseq_protein.tsv	58946325
+refseq_rna-taxonomy.tsv	67997702
 rhea-chebi.tsv	216654
 rhea-ec.tsv	7719
 rhea-go.tsv	4448
 rhea-pubmed.tsv	142680
 rhea-reactome_reaction.tsv	1511
 rhea-uniprot.tsv	42384671
-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
+sra_accession-bioproject.tsv	549598
+sra_accession-biosample.tsv	32720085
+sra_accession-sra_analysis.tsv	329307
+sra_accession-sra_experiment.tsv	36823437
+sra_accession-sra_project.tsv	637932
+sra_accession-sra_run.tsv	41652904
+sra_accession-sra_sample.tsv	35540965
+sra_experiment-bioproject.tsv	32221936
+sra_experiment-biosample.tsv	32541010
+sra_experiment-sra_project.tsv	32566458
+sra_experiment-sra_sample.tsv	32566197
+sra_project-bioproject.tsv	556479
+sra_run-bioproject.tsv	34139637
+sra_run-biosample.tsv	34451813
+sra_run-sra_experiment.tsv	34505955
+sra_run-sra_project.tsv	34496933
+sra_run-sra_sample.tsv	34477271
+sra_sample-biosample.tsv	32748222
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50753
+taxonomy-pubmed.tsv	50750
 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	5344103538
+total	5418000127