Merge pull request #203 from togoid/main

release 2023-12-19

Dockerfile

@@ -6,7 +6,7 @@ RUN apt-get update -y && apt-get install -y \
       libjson-perl=4.04000-1 \
       libany-uri-escape-perl=0.01-3 \
       libwww-perl=6.61-1 \
-      curl=7.81.0-1ubuntu1.14 \
+      curl=7.81.0-1ubuntu1.15 \
       wget=1.21.2-2ubuntu1 \
       gawk=1:5.1.0-1build3 \
       python3=3.10.6-1~22.04 \

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 1.1
-Datasets last updated: 2023-12-11
+Datasets last updated: 2023-12-18
 
 ## 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 currently supports 89 datasets covering various biological categories. 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 2023-12-11)
+## Statistics (as of 2023-12-18)
 - Number of target datasets 
     - 102 (from 72 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. 1.1
-Datasets last updated: 2023-12-11
+Datasets last updated: 2023-12-18
 
 ## 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: 2023-12-11
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## 統計 (2023-12-11)
+## 統計 (2023-12-18)
 - 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。 

log/pair_count.tsv

@@ -1,12 +1,12 @@
 affy_probeset-ncbigene.tsv	19063
-assembly_insdc-bioproject.tsv	1931425
-assembly_insdc-biosample.tsv	1943066
-assembly_insdc-insdc_master.tsv	1875870
-bioproject-biosample.tsv	2359519
-bioproject-geo_series.tsv	197486
-bioproject-pubmed.tsv	258531
-bioproject_umbrella-bioproject.tsv	100433
-biosample-bioproject.tsv	2359519
+assembly_insdc-bioproject.tsv	1945629
+assembly_insdc-biosample.tsv	1957294
+assembly_insdc-insdc_master.tsv	1889897
+bioproject-biosample.tsv	2381354
+bioproject-geo_series.tsv	197910
+bioproject-pubmed.tsv	259137
+bioproject_umbrella-bioproject.tsv	100626
+biosample-bioproject.tsv	2381354
 cellosaurus-ncit_disease.tsv	68557
 cellosaurus-orphanet_phenotype.tsv	38153
 chebi-inchi_key.tsv	141392
@@ -87,8 +87,8 @@ interpro-uniprot.tsv	718778680
 jga_study-jga_dataset.tsv	199
 jga_study-nbdc_human_db.tsv	305
 jga_study-pubmed.tsv	130
-lipidmaps-chebi.tsv	12885
-lipidmaps-inchi_key.tsv	47826
+lipidmaps-chebi.tsv	12890
+lipidmaps-inchi_key.tsv	47841
 lipidmaps-swisslipids.tsv	12345
 mbgd_gene-uniprot.tsv	137319849
 mbgd_organism-taxonomy.tsv	6318
@@ -100,39 +100,39 @@ 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	100681
+mgi_gene-mgi_allele.tsv	100770
 mgi_gene-ncbigene.tsv	55041
 mgi_gene-uniprot.tsv	79466
-mgi_genotype-doid.tsv	7723
-mgi_genotype-mgi_allele.tsv	122501
-mgi_genotype-mp.tsv	392060
+mgi_genotype-doid.tsv	7724
+mgi_genotype-mgi_allele.tsv	122809
+mgi_genotype-mp.tsv	393496
 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	9401535
-ncbigene-ensembl_protein.tsv	10957535
-ncbigene-ensembl_transcript.tsv	11411226
+ncbigene-ensembl_gene.tsv	9485712
+ncbigene-ensembl_protein.tsv	11058301
+ncbigene-ensembl_transcript.tsv	11567584
 ncbigene-flybase_gene.tsv	25107
-ncbigene-go.tsv	59267218
-ncbigene-hgnc.tsv	43742
+ncbigene-go.tsv	68314687
+ncbigene-hgnc.tsv	43739
 ncbigene-mgi_gene.tsv	71696
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18390
-ncbigene-refseq_genomic.tsv	211691
-ncbigene-refseq_protein.tsv	59902828
-ncbigene-refseq_rna.tsv	58545286
-ncbigene-rgd.tsv	42518
+ncbigene-omim_gene.tsv	18398
+ncbigene-refseq_genomic.tsv	211693
+ncbigene-refseq_protein.tsv	60108727
+ncbigene-refseq_rna.tsv	58752275
+ncbigene-rgd.tsv	42517
 ncbigene-sgd.tsv	6464
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	49172030
+ncbigene-taxonomy.tsv	49342670
 ncbigene-vgnc.tsv	112107
 ncbigene-wormbase_gene.tsv	19850
 ncbigene-xenbase_gene.tsv	46225
-ncbigene-zfin_gene.tsv	27132
+ncbigene-zfin_gene.tsv	27131
 ncit_disease-ncit_tissue.tsv	26233
 oma_protein-ensembl_gene.tsv	2460780
 oma_protein-ensembl_transcript.tsv	2804840
@@ -157,25 +157,25 @@ 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	116069142
+pubchem_compound-inchi_key.tsv	116072087
 pubchem_pathway-ncbigene.tsv	32308
 pubchem_pathway-pathbank.tsv	69387
 pubchem_pathway-pubchem_compound.tsv	1252527
 pubchem_pathway-reactome_pathway.tsv	2814
 pubchem_pathway-uniprot.tsv	620221
 pubchem_pathway-wikipathways.tsv	1196
-reactome_pathway-chebi.tsv	267131
+reactome_pathway-chebi.tsv	264859
 reactome_pathway-go.tsv	12983
-reactome_pathway-iuphar_ligand.tsv	42184
-reactome_pathway-mirbase.tsv	327
+reactome_pathway-iuphar_ligand.tsv	40546
+reactome_pathway-mirbase.tsv	332
 reactome_pathway-reactome_reaction.tsv	400679
-reactome_pathway-uniprot.tsv	919326
-reactome_reaction-chebi.tsv	202526
+reactome_pathway-uniprot.tsv	861452
+reactome_reaction-chebi.tsv	198020
 reactome_reaction-go.tsv	3335
-reactome_reaction-iuphar_ligand.tsv	15106
-reactome_reaction-mirbase.tsv	182
-reactome_reaction-uniprot.tsv	710946
-refseq_protein-uniprot.tsv	179950006
+reactome_reaction-iuphar_ligand.tsv	14362
+reactome_reaction-mirbase.tsv	185
+reactome_reaction-uniprot.tsv	665149
+refseq_protein-uniprot.tsv	179950008
 refseq_rna-dbsnp.tsv	267549861
 refseq_rna-hgnc.tsv	227165
 refseq_rna-ncbigene.tsv	57852462
@@ -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	465022
-sra_accession-biosample.tsv	27780237
-sra_accession-sra_analysis.tsv	270279
-sra_accession-sra_experiment.tsv	30842754
-sra_accession-sra_project.tsv	545391
-sra_accession-sra_run.tsv	35331467
-sra_accession-sra_sample.tsv	30086390
-sra_experiment-bioproject.tsv	26890778
-sra_experiment-biosample.tsv	27211369
-sra_experiment-sra_project.tsv	27233679
-sra_experiment-sra_sample.tsv	27233493
-sra_project-bioproject.tsv	465038
-sra_run-bioproject.tsv	28691217
-sra_run-biosample.tsv	28992466
-sra_run-sra_experiment.tsv	29065822
-sra_run-sra_project.tsv	29046856
-sra_run-sra_sample.tsv	29015366
-sra_sample-biosample.tsv	27789171
+sra_accession-bioproject.tsv	465654
+sra_accession-biosample.tsv	27808778
+sra_accession-sra_analysis.tsv	270359
+sra_accession-sra_experiment.tsv	30935643
+sra_accession-sra_project.tsv	547096
+sra_accession-sra_run.tsv	35427306
+sra_accession-sra_sample.tsv	30173279
+sra_experiment-bioproject.tsv	26934437
+sra_experiment-biosample.tsv	27243277
+sra_experiment-sra_project.tsv	27277338
+sra_experiment-sra_sample.tsv	27277152
+sra_project-bioproject.tsv	465670
+sra_run-bioproject.tsv	28736336
+sra_run-biosample.tsv	29024695
+sra_run-sra_experiment.tsv	29111866
+sra_run-sra_project.tsv	29091975
+sra_run-sra_sample.tsv	29059787
+sra_sample-biosample.tsv	27817712
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	49088
+taxonomy-pubmed.tsv	49092
 togovar-clinvar.tsv	720705
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -249,4 +249,4 @@ wikipathways-hmdb.tsv	4014
 wikipathways-lipidmaps.tsv	1361
 wikipathways-ncbigene.tsv	29837
 wikipathways-uniprot.tsv	33519
-total	4605985207
+total	4616648409