Merge pull request #201 from togoid/main

release 2023-12-06

config/dataset.yaml

@@ -497,7 +497,7 @@ nbdc_human_db:
     - ["hum0004","hum0006","hum0007","hum0008","hum0010","hum0001","hum0011","hum0012","hum0018","hum0019"]
     - ["hum0004.v1","hum0006.v5","hum0007.v1","hum0008.v1","hum0010.v1","hum0001.v1","hum0011.v1","hum0012.v1","hum0018.v1","hum0019.v1"]
 ncbigene:
-  label: NCBI gene
+  label: NCBI Gene
   catalog: nbdc00073
   category: Gene
   regex: '^(?<id>\d+)$'

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 1.1
-Datasets last updated: 2023-11-27
+Datasets last updated: 2023-12-04
 
 ## 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 2023-11-27)
+## Statistics (as of 2023-12-04)
 - 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: 2023-11-27
+Datasets last updated: 2023-12-04
 
 ## 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: 2023-11-27
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## 統計 (2023-11-27)
+## 統計 (2023-12-04)
 - 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	1906757
-assembly_insdc-biosample.tsv	1918263
-assembly_insdc-insdc_master.tsv	1852636
-bioproject-biosample.tsv	2303395
-bioproject-geo_series.tsv	196587
-bioproject-pubmed.tsv	257770
-bioproject_umbrella-bioproject.tsv	98690
-biosample-bioproject.tsv	2303395
+assembly_insdc-bioproject.tsv	1924605
+assembly_insdc-biosample.tsv	1936253
+assembly_insdc-insdc_master.tsv	1869243
+bioproject-biosample.tsv	2324769
+bioproject-geo_series.tsv	196884
+bioproject-pubmed.tsv	257946
+bioproject_umbrella-bioproject.tsv	100103
+biosample-bioproject.tsv	2324769
 cellosaurus-ncit_disease.tsv	68557
 cellosaurus-orphanet_phenotype.tsv	38153
 chebi-inchi_key.tsv	141392
@@ -38,10 +38,10 @@ ensembl_gene-ensembl_protein.tsv	12180884
 ensembl_gene-ensembl_transcript.tsv	14437446
 ensembl_gene-hgnc.tsv	44278
 ensembl_gene-ncbigene.tsv	6179217
-ensembl_gene-uniprot.tsv	4503879
+ensembl_gene-uniprot.tsv	4924829
 ensembl_protein-ensembl_transcript.tsv	12180887
 ensembl_transcript-affy_probeset.tsv	218298
-ensembl_transcript-go.tsv	0
+ensembl_transcript-go.tsv	52748677
 ensembl_transcript-hgnc.tsv	219677
 ensembl_transcript-refseq_rna.tsv	10179574
 gea-bioproject.tsv	141
@@ -100,35 +100,35 @@ 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	100568
+mgi_gene-mgi_allele.tsv	100637
 mgi_gene-ncbigene.tsv	55041
-mgi_gene-uniprot.tsv	79654
+mgi_gene-uniprot.tsv	79466
 mgi_genotype-doid.tsv	7723
-mgi_genotype-mgi_allele.tsv	122475
-mgi_genotype-mp.tsv	391915
+mgi_genotype-mgi_allele.tsv	122501
+mgi_genotype-mp.tsv	392060
 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	9166278
-ncbigene-ensembl_protein.tsv	10684938
-ncbigene-ensembl_transcript.tsv	11101841
+ncbigene-ensembl_gene.tsv	9401534
+ncbigene-ensembl_protein.tsv	10957535
+ncbigene-ensembl_transcript.tsv	11411226
 ncbigene-flybase_gene.tsv	25107
 ncbigene-go.tsv	50230587
-ncbigene-hgnc.tsv	43728
+ncbigene-hgnc.tsv	43742
 ncbigene-mgi_gene.tsv	71696
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18383
-ncbigene-refseq_genomic.tsv	211671
-ncbigene-refseq_protein.tsv	60014779
-ncbigene-refseq_rna.tsv	58384699
+ncbigene-omim_gene.tsv	18387
+ncbigene-refseq_genomic.tsv	211687
+ncbigene-refseq_protein.tsv	59978063
+ncbigene-refseq_rna.tsv	58384950
 ncbigene-rgd.tsv	42518
 ncbigene-sgd.tsv	6464
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	49333660
+ncbigene-taxonomy.tsv	49294065
 ncbigene-vgnc.tsv	112107
 ncbigene-wormbase_gene.tsv	19850
 ncbigene-xenbase_gene.tsv	46225
@@ -210,7 +210,7 @@ sra_sample-biosample.tsv	27699956
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	49104
+taxonomy-pubmed.tsv	49106
 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	4541270358
+total	4595278330