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Merge pull request #206 from togoid/main
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release 2023-01-10
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@sh-ikeda
sh-ikeda authored Jan 10, 2024
2 parents 6161d13 + 1ca86d9 commit e07778f
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4 changes: 2 additions & 2 deletions docs/help.md
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# TogoID ver. 1.1
Datasets last updated: 2024-01-04
Datasets last updated: 2024-01-09

## 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 2024-01-04)
## Statistics (as of 2024-01-09)
- Number of target datasets
- 102 (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: 2024-01-04
Datasets last updated: 2024-01-09

## 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: 2024-01-04

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

## 統計 (2024-01-04)
## 統計 (2024-01-09)
- 対象データセット数
- 102 (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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84 changes: 42 additions & 42 deletions log/pair_count.tsv
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affy_probeset-ncbigene.tsv 19063
assembly_insdc-bioproject.tsv 1989580
assembly_insdc-biosample.tsv 1984072
assembly_insdc-insdc_master.tsv 1916377
bioproject-biosample.tsv 2410970
bioproject-geo_series.tsv 198656
bioproject-pubmed.tsv 259987
bioproject_umbrella-bioproject.tsv 101117
biosample-bioproject.tsv 2410970
assembly_insdc-bioproject.tsv 2003442
assembly_insdc-biosample.tsv 1997918
assembly_insdc-insdc_master.tsv 1929712
bioproject-biosample.tsv 2441819
bioproject-geo_series.tsv 199634
bioproject-pubmed.tsv 260578
bioproject_umbrella-bioproject.tsv 101333
biosample-bioproject.tsv 2441819
cellosaurus-ncit_disease.tsv 68557
cellosaurus-orphanet_phenotype.tsv 38153
chebi-inchi_key.tsv 141392
Expand Down Expand Up @@ -100,38 +100,38 @@ medgen-omim_phenotype.tsv 11043
medgen-orphanet_phenotype.tsv 9063
mgi_gene-ensembl_gene.tsv 56590
mgi_gene-hgnc.tsv 24607
mgi_gene-mgi_allele.tsv 100920
mgi_gene-mgi_allele.tsv 100994
mgi_gene-ncbigene.tsv 55041
mgi_gene-uniprot.tsv 79465
mgi_genotype-doid.tsv 7726
mgi_genotype-mgi_allele.tsv 122848
mgi_genotype-mp.tsv 393685
mgi_genotype-doid.tsv 7727
mgi_genotype-mgi_allele.tsv 122855
mgi_genotype-mp.tsv 393800
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 9483561
ncbigene-ensembl_protein.tsv 11050619
ncbigene-ensembl_transcript.tsv 11556119
ncbigene-ensembl_gene.tsv 9501433
ncbigene-ensembl_protein.tsv 11074957
ncbigene-ensembl_transcript.tsv 11581579
ncbigene-flybase_gene.tsv 25078
ncbigene-go.tsv 85487668
ncbigene-go.tsv 89652984
ncbigene-hgnc.tsv 43773
ncbigene-mgi_gene.tsv 71696
ncbigene-mirbase.tsv 17541
ncbigene-omim_gene.tsv 18410
ncbigene-refseq_genomic.tsv 211699
ncbigene-refseq_protein.tsv 60665296
ncbigene-refseq_rna.tsv 59361685
ncbigene-omim_gene.tsv 18412
ncbigene-refseq_genomic.tsv 211701
ncbigene-refseq_protein.tsv 60744557
ncbigene-refseq_rna.tsv 59440601
ncbigene-rgd.tsv 42516
ncbigene-sgd.tsv 6464
ncbigene-tair.tsv 32835
ncbigene-taxonomy.tsv 49723430
ncbigene-taxonomy.tsv 49773087
ncbigene-vgnc.tsv 112107
ncbigene-wormbase_gene.tsv 19850
ncbigene-xenbase_gene.tsv 46225
ncbigene-xenbase_gene.tsv 46228
ncbigene-zfin_gene.tsv 27134
ncit_disease-ncit_tissue.tsv 26233
oma_protein-ensembl_gene.tsv 2460780
Expand All @@ -157,7 +157,7 @@ pubchem_compound-chebi.tsv 141021
pubchem_compound-chembl_compound.tsv 2327813
pubchem_compound-drugbank.tsv 10789
pubchem_compound-glytoucan.tsv 31767
pubchem_compound-inchi_key.tsv 116110427
pubchem_compound-inchi_key.tsv 116112134
pubchem_pathway-ncbigene.tsv 32308
pubchem_pathway-pathbank.tsv 69387
pubchem_pathway-pubchem_compound.tsv 1252527
Expand Down Expand Up @@ -189,28 +189,28 @@ rhea-go.tsv 4387
rhea-pubmed.tsv 135188
rhea-reactome_reaction.tsv 1438
rhea-uniprot.tsv 36026464
sra_accession-bioproject.tsv 470711
sra_accession-biosample.tsv 28283897
sra_accession-bioproject.tsv 470936
sra_accession-biosample.tsv 28310278
sra_accession-sra_analysis.tsv 329045
sra_accession-sra_experiment.tsv 31120557
sra_accession-sra_project.tsv 550005
sra_accession-sra_run.tsv 35615159
sra_accession-sra_sample.tsv 30437562
sra_experiment-bioproject.tsv 27297751
sra_experiment-biosample.tsv 27636085
sra_experiment-sra_project.tsv 27640654
sra_experiment-sra_sample.tsv 27640473
sra_project-bioproject.tsv 474078
sra_run-bioproject.tsv 29102112
sra_run-biosample.tsv 29426498
sra_run-sra_experiment.tsv 29476791
sra_run-sra_project.tsv 29457753
sra_run-sra_sample.tsv 29431038
sra_sample-biosample.tsv 28306235
sra_accession-sra_experiment.tsv 31194792
sra_accession-sra_project.tsv 551578
sra_accession-sra_run.tsv 35694120
sra_accession-sra_sample.tsv 30501536
sra_experiment-bioproject.tsv 27328875
sra_experiment-biosample.tsv 27660234
sra_experiment-sra_project.tsv 27671778
sra_experiment-sra_sample.tsv 27671597
sra_project-bioproject.tsv 474303
sra_run-bioproject.tsv 29135880
sra_run-biosample.tsv 29451030
sra_run-sra_experiment.tsv 29515727
sra_run-sra_project.tsv 29491521
sra_run-sra_sample.tsv 29463585
sra_sample-biosample.tsv 28332616
swisslipids-chebi.tsv 4276
swisslipids-hmdb.tsv 26026
swisslipids-inchi_key.tsv 593209
taxonomy-pubmed.tsv 49166
taxonomy-pubmed.tsv 49176
togovar-clinvar.tsv 720705
togovar-dbsnp.tsv 66877211
togovar-ensembl_gene.tsv 72473309
Expand Down Expand Up @@ -249,4 +249,4 @@ wikipathways-hmdb.tsv 4013
wikipathways-lipidmaps.tsv 1361
wikipathways-ncbigene.tsv 29837
wikipathways-uniprot.tsv 33518
total 4640572273
total 4645672567
3 changes: 2 additions & 1 deletion log/pair_count_history.tsv
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Expand Up @@ -18,4 +18,5 @@ Date affy_probeset-ncbigene assembly_insdc-bioproject assembly_insdc-biosample a
2023-12-11 19063 1931425 1943066 1875870 2359519 197486 258531 100433 2359519 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12885 47826 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100681 55041 79466 7723 122501 392060 10712 574 1486 8352 9693 10380 2390 9401535 10957535 11411226 25107 59267218 43742 71696 17541 18390 211691 59902828 58545286 42518 6464 32835 49172030 112107 19850 46225 27132 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116069142 32308 69387 1252527 2814 620221 1196 267131 12983 42184 327 400679 919326 202526 3335 15106 182 710946 179950006 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 465022 27780237 270279 30842754 545391 35331467 30086390 26890778 27211369 27233679 27233493 465038 28691217 28992466 29065822 29046856 29015366 27789171 4276 26026 593209 49088 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4605985207 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11468 951 4014 1361 29837 33519
2023-12-16 19063 1945629 1957294 1889897 2381354 197910 259137 100626 2381354 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12890 47841 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100770 55041 79466 7724 122809 393496 10712 574 1486 8352 9693 10380 2390 9485712 11058301 11567584 25107 68314687 43739 71696 17541 18398 211693 60108727 58752275 42517 6464 32835 49342670 112107 19850 46225 27131 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116072087 32308 69387 1252527 2814 620221 1196 264859 12983 40546 332 400679 861452 198020 3335 14362 185 665149 179950008 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 465654 27808778 270359 30935643 547096 35427306 30173279 26934437 27243277 27277338 27277152 465670 28736336 29024695 29111866 29091975 29059787 27817712 4276 26026 593209 49092 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4616648409 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11468 951 4014 1361 29837 33519
2023-12-23 19063 1978955 1974704 1907175 2400240 198341 259732 100932 2400240 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12896 47881 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100839 55041 79466 7726 122846 393676 10712 574 1486 8352 9693 10380 2390 9483591 11050619 11556151 25107 77082572 43773 71696 17541 18404 211695 60300956 58967151 42516 6464 32835 49469530 112107 19850 46225 27132 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116110122 32308 69387 1252527 2814 620221 1196 264859 12983 40546 332 400679 861452 198020 3335 14362 185 665149 179950008 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 466119 27856390 270359 31020050 548219 35512895 30252693 26974495 27280212 27317396 27317210 466135 28778904 29061897 29156098 29134543 29100629 27865324 4276 26026 593209 49132 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4626785801 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11471 951 4013 1361 29837 33518
2023-12-30 19063 1989580 1984072 1916377 2410970 198656 259987 101117 2410970 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12896 47886 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100920 55041 79465 7726 122848 393685 10712 574 1486 8352 9693 10380 2390 9483561 11050619 11556119 25078 85487668 43773 71696 17541 18410 211699 60665296 59361685 42516 6464 32835 49723430 112107 19850 46225 27134 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116110427 32308 69387 1252527 2814 620221 1196 264859 12983 40546 332 400679 861452 198020 3335 14362 185 665149 179950008 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 470711 28283897 329045 31120557 550005 35615159 30437562 27297751 27636085 27640654 27640473 474078 29102112 29426498 29476791 29457753 29431038 28306235 4276 26026 593209 49166 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4640572273 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11471 951 4013 1361 29837 33518
2023-12-30 19063 1989580 1984072 1916377 2410970 198656 259987 101117 2410970 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12896 47886 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100920 55041 79465 7726 122848 393685 10712 574 1486 8352 9693 10380 2390 9483561 11050619 11556119 25078 85487668 43773 71696 17541 18410 211699 60665296 59361685 42516 6464 32835 49723430 112107 19850 46225 27134 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116110427 32308 69387 1252527 2814 620221 1196 264859 12983 40546 332 400679 861452 198020 3335 14362 185 665149 179950008 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 470711 28283897 329045 31120557 550005 35615159 30437562 27297751 27636085 27640654 27640473 474078 29102112 29426498 29476791 29457753 29431038 28306235 4276 26026 593209 49166 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4640572273 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11471 951 4013 1361 29837 33518
2024-01-06 19063 2003442 1997918 1929712 2441819 199634 260578 101333 2441819 68557 38153 141392 34314 3091832 8206 11766 1915138 47707 13954 1878362 433124 1439514 2126 12004 11110 33678 3448 8014 8178 1711989 115826 3340026 4019 4849 5671 54210 12180884 14437446 44278 6179217 4924829 12180887 218298 52748677 219677 10179574 141 5046 290 1270 49240 35219 1995 40970 43667 21167 1325 23383 1912 43615 16942 33774 28381 18954 20365 13701 217899 522 104230 275237 8660 220065 129729 111606 59409158 193975949 1533582 1533178 30407 1402682 20191 1283 109057 435537 1275 718778680 199 305 130 12896 47886 12345 137319849 6318 16674 16849 21567 7229 11043 9063 56590 24607 100994 55041 79465 7727 122855 393800 10712 574 1486 8352 9693 10380 2390 9501433 11074957 11581579 25078 89652984 43773 71696 17541 18412 211701 60744557 59440601 42516 6464 32835 49773087 112107 19850 46228 27134 26233 2460780 2804840 4800754 18299774 4319 4337 4316 4298 1192 1798 7832 8040 1685211 726658 530587 339565 341431 1461 4812 141021 2327813 10789 31767 116112134 32308 69387 1252527 2814 620221 1196 264859 12983 40546 332 400679 861452 198020 3335 14362 185 665149 179950008 267549861 227165 57852462 188790 5817042 50390902 57882313 201816 7528 4387 135188 1438 36026464 470936 28310278 329045 31194792 551578 35694120 30501536 27328875 27660234 27671778 27671597 474303 29135880 29451030 29515727 29491521 29463585 28332616 4276 26026 593209 49176 720705 66877211 72473309 287277970 60732887 935843 60001809 692119 173346179 4645672567 2586 10146 65606 39736080 9437437 9647434 9647434 466768100 81875 284374766 230955 13734202 12027805 16106 7021 8188 355933 259506 49539508 251702059 437326 151 505473 11471 951 4013 1361 29837 33518
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