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Merge pull request #232 from togoid/main
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release 2024-06-06
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sh-ikeda authored Jun 6, 2024
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4 changes: 2 additions & 2 deletions docs/help.md
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# TogoID ver. 1.1
Datasets last updated: 2024-05-29
Datasets last updated: 2024-06-06

## 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.
Expand All @@ -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 2024-05-29)
## Statistics (as of 2024-06-06)
- Number of target datasets
- 103 (from 72 databases)
- For details on the target DBs and ID examples, please refer to the "DATASETS" tab.
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4 changes: 2 additions & 2 deletions docs/help_ja.md
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# TogoID ver. 1.1
Datasets last updated: 2024-05-29
Datasets last updated: 2024-06-06

## 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。
Expand Down Expand Up @@ -28,7 +28,7 @@ Datasets last updated: 2024-05-29

- [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)

## 統計 (2024-05-29)
## 統計 (2024-06-06)
- 対象データセット数
- 103 (72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。
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3 changes: 3 additions & 0 deletions docs/news.md
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# 2024-06-06
- Weekly update has been completed.

# 2024-05-29
- Weekly update has been completed.

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12 changes: 12 additions & 0 deletions log/error.log
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Expand Up @@ -3,5 +3,17 @@ 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/glytoucan-doid.tsv new file size per old 1596 / 4376 = 0.3647166361974406 < 0.5
# Error: output/tsv/mondo-doid.tsv new file size per old 0 / 155460 = 0.0 < 0.5
# Error: Failed to create output/tsv/mondo-doid.tsv or created file was empty
# Error: output/tsv/mondo-hp_phenotype.tsv new file size per old 0 / 9184 = 0.0 < 0.5
# Error: Failed to create output/tsv/mondo-hp_phenotype.tsv or created file was empty
# Error: output/tsv/mondo-meddra.tsv new file size per old 0 / 25262 = 0.0 < 0.5
# Error: Failed to create output/tsv/mondo-meddra.tsv or created file was empty
# Error: output/tsv/mondo-mesh.tsv new file size per old 0 / 133836 = 0.0 < 0.5
# Error: Failed to create output/tsv/mondo-mesh.tsv or created file was empty
# Error: output/tsv/mondo-omim_phenotype.tsv new file size per old 0 / 145395 = 0.0 < 0.5
# 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/wikipathways-chebi.tsv new file size per old 69817 / 148433 = 0.47036036460894814 < 0.5
# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 57944 / 470542 = 0.12314309880945803 < 0.5
134 changes: 67 additions & 67 deletions log/pair_count.tsv
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
affy_probeset-ncbigene.tsv 19063
assembly_insdc-bioproject.tsv 2257414
assembly_insdc-biosample.tsv 2201866
assembly_insdc-insdc_master.tsv 2126832
assembly_insdc-bioproject.tsv 2269215
assembly_insdc-biosample.tsv 2212826
assembly_insdc-insdc_master.tsv 2137497
bioproject-biosample.tsv 2546485
bioproject-geo_series.tsv 208710
bioproject-pubmed.tsv 270271
bioproject-geo_series.tsv 209067
bioproject-pubmed.tsv 270670
bioproject_umbrella-bioproject.tsv 104586
biosample-bioproject.tsv 18715693
biosample-geo_sample.tsv 9074826
biosample-bioproject.tsv 18755430
biosample-geo_sample.tsv 9081138
cellosaurus-ncit_disease.tsv 71772
cellosaurus-orphanet_phenotype.tsv 39956
chebi-inchi_key.tsv 175447
Expand Down Expand Up @@ -77,18 +77,18 @@ insdc-bioproject.tsv 59409158
insdc-biosample.tsv 193975949
insdc_master-bioproject.tsv 1533582
insdc_master-biosample.tsv 1533178
interpro-go.tsv 30340
interpro-pdb.tsv 1554325
interpro-pfam.tsv 20197
interpro-go.tsv 30300
interpro-pdb.tsv 1591525
interpro-pfam.tsv 20725
interpro-prosite.tsv 1283
interpro-pubmed.tsv 110966
interpro-reactome_pathway.tsv 464216
interpro-smart.tsv 1275
interpro-uniprot.tsv 769495433
interpro-pubmed.tsv 112259
interpro-reactome_pathway.tsv 469324
interpro-smart.tsv 1274
interpro-uniprot.tsv 756717820
jga_study-jga_dataset.tsv 199
jga_study-nbdc_human_db.tsv 305
jga_study-pubmed.tsv 130
lipidmaps-chebi.tsv 12914
lipidmaps-chebi.tsv 12915
lipidmaps-inchi_key.tsv 48021
lipidmaps-swisslipids.tsv 12348
mbgd_gene-uniprot.tsv 137319849
Expand All @@ -101,35 +101,35 @@ medgen-omim_phenotype.tsv 11043
medgen-orphanet_phenotype.tsv 9063
mgi_gene-ensembl_gene.tsv 56432
mgi_gene-hgnc.tsv 24587
mgi_gene-mgi_allele.tsv 108940
mgi_gene-mgi_allele.tsv 109003
mgi_gene-ncbigene.tsv 55039
mgi_gene-uniprot.tsv 79233
mgi_genotype-doid.tsv 7806
mgi_genotype-mgi_allele.tsv 123869
mgi_genotype-mp.tsv 398348
mgi_genotype-doid.tsv 7810
mgi_genotype-mgi_allele.tsv 123933
mgi_genotype-mp.tsv 398536
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 10550874
ncbigene-ensembl_protein.tsv 12333211
ncbigene-ensembl_transcript.tsv 12902456
ncbigene-ensembl_gene.tsv 10810327
ncbigene-ensembl_protein.tsv 12612609
ncbigene-ensembl_transcript.tsv 13223731
ncbigene-flybase_gene.tsv 25078
ncbigene-go.tsv 95956265
ncbigene-go.tsv 96036753
ncbigene-hgnc.tsv 43777
ncbigene-mgi_gene.tsv 71686
ncbigene-mirbase.tsv 17541
ncbigene-omim_gene.tsv 18514
ncbigene-refseq_genomic.tsv 211743
ncbigene-refseq_protein.tsv 64268565
ncbigene-refseq_rna.tsv 62980257
ncbigene-omim_gene.tsv 18520
ncbigene-refseq_genomic.tsv 211742
ncbigene-refseq_protein.tsv 64337032
ncbigene-refseq_rna.tsv 63029318
ncbigene-rgd.tsv 47293
ncbigene-sgd.tsv 6464
ncbigene-tair.tsv 32835
ncbigene-taxonomy.tsv 52874459
ncbigene-taxonomy.tsv 52932438
ncbigene-vgnc.tsv 112122
ncbigene-wormbase_gene.tsv 19848
ncbigene-xenbase_gene.tsv 46792
Expand All @@ -152,13 +152,13 @@ pdb-interpro.tsv 726658
pdb-pdb_ccd.tsv 530587
pdb-pfam.tsv 339565
pdb-uniprot.tsv 341431
prosite-prosite_prorule.tsv 1450
prosite-prosite_prorule.tsv 1452
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 118049971
pubchem_compound-inchi_key.tsv 118052227
pubchem_pathway-ncbigene.tsv 33861
pubchem_pathway-pathbank.tsv 69387
pubchem_pathway-pubchem_compound.tsv 1253395
Expand Down Expand Up @@ -186,32 +186,32 @@ refseq_rna-refseq_protein.tsv 54154462
refseq_rna-taxonomy.tsv 62348147
rhea-chebi.tsv 206037
rhea-ec.tsv 7598
rhea-go.tsv 4414
rhea-go.tsv 4429
rhea-pubmed.tsv 138072
rhea-reactome_reaction.tsv 1480
rhea-uniprot.tsv 41622619
sra_accession-bioproject.tsv 500356
sra_accession-biosample.tsv 29863488
rhea-uniprot.tsv 40452196
sra_accession-bioproject.tsv 500713
sra_accession-biosample.tsv 29894648
sra_accession-sra_analysis.tsv 329141
sra_accession-sra_experiment.tsv 32984291
sra_accession-sra_project.tsv 581607
sra_accession-sra_run.tsv 37637535
sra_accession-sra_sample.tsv 32172339
sra_experiment-bioproject.tsv 28809975
sra_experiment-biosample.tsv 29153854
sra_experiment-sra_project.tsv 29154115
sra_experiment-sra_sample.tsv 29153947
sra_project-bioproject.tsv 503746
sra_run-bioproject.tsv 30657856
sra_run-biosample.tsv 30950442
sra_run-sra_experiment.tsv 31040243
sra_run-sra_project.tsv 31014770
sra_run-sra_sample.tsv 30950540
sra_sample-biosample.tsv 29881118
sra_accession-sra_experiment.tsv 33069706
sra_accession-sra_project.tsv 582908
sra_accession-sra_run.tsv 37725549
sra_accession-sra_sample.tsv 32244776
sra_experiment-bioproject.tsv 28847508
sra_experiment-biosample.tsv 29191261
sra_experiment-sra_project.tsv 29191648
sra_experiment-sra_sample.tsv 29191480
sra_project-bioproject.tsv 504103
sra_run-bioproject.tsv 30695410
sra_run-biosample.tsv 30987870
sra_run-sra_experiment.tsv 31077797
sra_run-sra_project.tsv 31052324
sra_run-sra_sample.tsv 30988094
sra_sample-biosample.tsv 29912817
swisslipids-chebi.tsv 4276
swisslipids-hmdb.tsv 26026
swisslipids-inchi_key.tsv 593209
taxonomy-pubmed.tsv 49795
taxonomy-pubmed.tsv 49849
togovar-clinvar.tsv 401823
togovar-dbsnp.tsv 66877211
togovar-ensembl_gene.tsv 72473309
Expand All @@ -225,29 +225,29 @@ uberon-ncit_tissue.tsv 2578
uniprot-chembl_target.tsv 10144
uniprot-dbsnp.tsv 65716
uniprot-ec.tsv 39722925
uniprot-ensembl_gene.tsv 9485822
uniprot-ensembl_protein.tsv 9698736
uniprot-ensembl_transcript.tsv 9698736
uniprot-go.tsv 476606489
uniprot-hgnc.tsv 81675
uniprot-insdc.tsv 266643040
uniprot-ensembl_gene.tsv 9494738
uniprot-ensembl_protein.tsv 9709163
uniprot-ensembl_transcript.tsv 9709163
uniprot-go.tsv 606663709
uniprot-hgnc.tsv 81713
uniprot-insdc.tsv 260791472
uniprot-intact.tsv 230595
uniprot-ncbigene.tsv 13529658
uniprot-oma_group.tsv 7771800
uniprot-ncbigene.tsv 12810580
uniprot-oma_group.tsv 7668829
uniprot-omim_gene.tsv 16188
uniprot-omim_phenotype.tsv 7077
uniprot-orphanet_phenotype.tsv 8177
uniprot-pdb.tsv 370031
uniprot-reactome_pathway.tsv 260444
uniprot_reference_proteome-assembly_insdc.tsv 475892
uniprot_reference_proteome-assembly_refseq.tsv 194
uniprot_reference_proteome-taxonomy.tsv 544084
uniprot-refseq_protein.tsv 47937966
uniprot-uniprot_mnemonic.tsv 248805733
uniprot-orphanet_phenotype.tsv 8178
uniprot-pdb.tsv 377848
uniprot-reactome_pathway.tsv 282077
uniprot_reference_proteome-assembly_insdc.tsv 571530
uniprot_reference_proteome-assembly_refseq.tsv 193
uniprot_reference_proteome-taxonomy.tsv 639722
uniprot-refseq_protein.tsv 45084699
uniprot-uniprot_mnemonic.tsv 245482527
wikipathways-chebi.tsv 11471
wikipathways-doid.tsv 1060
wikipathways-hmdb.tsv 4116
wikipathways-lipidmaps.tsv 1418
wikipathways-ncbigene.tsv 30222
wikipathways-uniprot.tsv 33518
total 4791824296
total 4897225406
1 change: 1 addition & 0 deletions log/pair_count_history.tsv
Original file line number Diff line number Diff line change
Expand Up @@ -40,3 +40,4 @@ Date affy_probeset-ncbigene assembly_insdc-bioproject assembly_insdc-biosample a
2024-05-11 19063 2248166 2192685 2118114 2546485 207850 269450 104586 18584288 9037022 71772 39956 175447 34347 3101919 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 8272 1711989 115826 3340026 4019 4849 5671 55589 12969337 15910019 47792 14749031 5546630 12969340 229689 55211171 241612 40165483 141 5046 290 1270 50841 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8726 220065 134006 111723 59409158 193975949 1533582 1533178 30340 1554325 20197 1283 110966 464216 1275 769495433 199 305 130 12913 48009 12348 137319849 6318 16674 16849 21567 7229 11043 9063 56432 24586 108175 55039 79233 7802 123478 396585 10712 574 1486 8352 9693 10380 2390 10537078 12317233 12885501 25078 94765962 43777 71686 17541 18503 211774 63831454 62516302 47294 6464 32835 52489491 112122 19850 46792 27142 27199 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1450 4965 174843 2372556 10789 69203 118026500 33861 69387 1253395 2877 623594 1267 267095 13144 40621 336 393545 864463 200045 3318 14374 188 667632 158595251 267499623 227319 60856144 189109 5911087 52967344 60886133 206037 7598 4414 138072 1480 41622619 496059 29646742 329129 32817932 578755 37463398 32018289 28544873 28887862 28889013 28888845 496078 30382495 30674167 30764882 30739409 30675166 29661022 4276 26026 593209 49795 401823 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10144 65716 39722925 9485822 9698736 9698736 476606489 81675 266643040 230595 13529658 7771800 16188 7077 8177 370031 260444 47937966 248805733 475892 194 544084 11471 1059 4091 1418 30164 33518 4781569453
2024-05-18 19063 2252861 2197359 2122585 2546485 208280 269775 104586 18623884 9054512 71772 39956 175447 34347 3101919 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 8272 1711989 115826 3340026 4019 4849 5671 54855 12969337 15910019 47792 14749031 5546630 12969340 224377 55211171 241612 40165483 141 5046 290 1270 50841 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8726 220065 134006 111723 59409158 193975949 1533582 1533178 30340 1554325 20197 1283 110966 464216 1275 769495433 199 305 130 12913 48009 12348 137319849 6318 16674 16849 21567 7229 11043 9063 56432 24587 108898 55039 79233 7803 123520 396692 10712 574 1486 8352 9693 10380 2390 10537076 12317227 12885496 25078 95258680 43777 71686 17541 18509 211772 64134006 62863887 47294 6464 32835 52761191 112122 19850 46792 27142 27199 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1450 4965 174843 2372556 10789 69203 118042692 33861 69387 1253395 2877 623594 1267 267095 13144 40621 336 393545 864463 200045 3318 14374 188 667632 158597481 267451107 227363 62318158 189290 5974072 54154462 62348147 206037 7598 4414 138072 1480 41622619 496420 29678859 329141 32892257 580141 37542076 32084513 28579615 28922471 28923755 28923587 496439 30418679 30710218 30801066 30775593 30711350 29693139 4276 26026 593209 49793 401823 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10144 65716 39722925 9485822 9698736 9698736 476606489 81675 266643040 230595 13529658 7771800 16188 7077 8177 370031 260444 47937966 248805733 475892 194 544084 11471 1060 4116 1418 30222 33518 4787800055
2024-05-26 19063 2257414 2201866 2126832 2546485 208710 270271 104586 18715693 9074826 71772 39956 175447 34347 3101919 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 8272 1711989 115826 3340026 4019 4849 5671 54855 12969337 15910019 47792 14749031 5546630 12969340 224377 55211171 241612 40165483 141 5046 290 1270 50841 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8726 220065 134006 111723 59409158 193975949 1533582 1533178 30340 1554325 20197 1283 110966 464216 1275 769495433 199 305 130 12914 48021 12348 137319849 6318 16674 16849 21567 7229 11043 9063 56432 24587 108940 55039 79233 7806 123869 398348 10712 574 1486 8352 9693 10380 2390 10550874 12333211 12902456 25078 95956265 43777 71686 17541 18514 211743 64268565 62980257 47293 6464 32835 52874459 112122 19848 46792 27142 27199 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1450 4965 174843 2372556 10789 69203 118049971 33861 69387 1253395 2877 623594 1267 267095 13144 40621 336 393545 864463 200045 3318 14374 188 667632 158597481 267451107 227363 62318158 189290 5974072 54154462 62348147 206037 7598 4414 138072 1480 41622619 500356 29863488 329141 32984291 581607 37637535 32172339 28809975 29153854 29154115 29153947 503746 30657856 30950442 31040243 31014770 30950540 29881118 4276 26026 593209 49795 401823 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10144 65716 39722925 9485822 9698736 9698736 476606489 81675 266643040 230595 13529658 7771800 16188 7077 8177 370031 260444 47937966 248805733 475892 194 544084 11471 1060 4116 1418 30222 33518 4791824296
2024-06-04 19063 2269215 2212826 2137497 2546485 209067 270670 104586 18755430 9081138 71772 39956 175447 34347 3101919 8211 11771 1915184 47707 14012 1878399 433145 1449263 2126 11847 10947 34588 3549 8047 8272 1711989 115826 3340026 4019 4849 5671 54855 12969337 15910019 47792 14749031 5546630 12969340 224377 55211171 241612 40165483 141 5046 290 1270 50841 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8726 220065 134006 111723 59409158 193975949 1533582 1533178 30300 1591525 20725 1283 112259 469324 1274 756717820 199 305 130 12915 48021 12348 137319849 6318 16674 16849 21567 7229 11043 9063 56432 24587 109003 55039 79233 7810 123933 398536 10712 574 1486 8352 9693 10380 2390 10810327 12612609 13223731 25078 96036753 43777 71686 17541 18520 211742 64337032 63029318 47293 6464 32835 52932438 112122 19848 46792 27142 27199 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1452 4965 174843 2372556 10789 69203 118052227 33861 69387 1253395 2877 623594 1267 267095 13144 40621 336 393545 864463 200045 3318 14374 188 667632 158597481 267451107 227363 62318158 189290 5974072 54154462 62348147 206037 7598 4429 138072 1480 40452196 500713 29894648 329141 33069706 582908 37725549 32244776 28847508 29191261 29191648 29191480 504103 30695410 30987870 31077797 31052324 30988094 29912817 4276 26026 593209 49849 401823 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 2578 10144 65716 39722925 9494738 9709163 9709163 606663709 81713 260791472 230595 12810580 7668829 16188 7077 8178 377848 282077 45084699 245482527 571530 193 639722 11471 1060 4116 1418 30222 33518 4897225406
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