Merge pull request #277 from togoid/main

release 2024-11-18

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-11-14
+Datasets last updated: 2024-11-18
 
 ## 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 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.
@@ -10,7 +10,7 @@ Datasets last updated: 2024-11-14
 ## Video tutorial
 - [How to use TogoID: an exploratory ID converter to bridge biological datasets](https://youtu.be/gXnvm6Fn4R8)
 
-## Statistics (as of 2024-11-14)
+## Statistics (as of 2024-11-18)
 - Number of target datasets 
     - 105 (from 73 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. 2.0
-Datasets last updated: 2024-11-14
+Datasets last updated: 2024-11-18
 
 ## 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。
@@ -10,7 +10,7 @@ Datasets last updated: 2024-11-14
 ## 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)
 
-## 統計 (2024-11-14)
+## 統計 (2024-11-18)
 - 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。 

docs/news.md

@@ -1,3 +1,6 @@
+# 2024-11-18
+- Weekly update has been completed.
+
 # 2024-11-14
 - Weekly update has been completed.
 

log/error.log

@@ -3,7 +3,7 @@ Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi
 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: HTTP Error 500: Internal Server Error: 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: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/partialmatch?wurcs=WURCS%3D2.0%2F4%2C10%2C9%2F%5Ba2122h-1b_1-5%5D%5Ba2112h-1b_1-5%5D%5BAad21122h-2a_2-6_5%2ANCC%2F3%3DO%5D%5Ba2112h-1b_1-5_2%2ANCC%2F3%3DO%5D%2F1-2-3-3-3-4-2-3-3-3%2Fa4-b1_b3-c2_b4-f1_c8-d2_d8-e2_f3-g1_f6-j2_g3-h2_h8-i2&rootnode=true G14091MR
 # 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
 # Error: output/tsv/glytoucan-doid.tsv new file size per old 1538 / 4376 = 0.35146252285191953 < 0.5
@@ -75,5 +75,4 @@ Error: HTTP Error 500: Internal Server Error: https://api.alpha.glycosmos.org/pa
 # 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 73351 / 148433 = 0.49416908638914525 < 0.5
-# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 59666 / 470542 = 0.12680270836609697 < 0.5
+# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 60240 / 470542 = 0.12802257821830995 < 0.5

log/pair_count.tsv

@@ -3,11 +3,11 @@ assembly_insdc-bioproject.tsv	2283159
 assembly_insdc-biosample.tsv	2225812
 assembly_insdc-insdc_master.tsv	2150193
 bioproject-biosample.tsv	2546485
-bioproject-geo_series.tsv	219632
-bioproject-pubmed.tsv	281330
+bioproject-geo_series.tsv	220020
+bioproject-pubmed.tsv	281552
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	20225455
-biosample-geo_sample.tsv	9517180
+biosample-bioproject.tsv	20274353
+biosample-geo_sample.tsv	9528638
 cellosaurus-ncit_disease.tsv	75821
 cellosaurus-orphanet_phenotype.tsv	41448
 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	2937837
-clinvar-hgnc.tsv	3055902
-clinvar-medgen.tsv	4188105
-clinvar-mondo.tsv	1991707
-clinvar-ncbigene.tsv	3056222
-clinvar-omim_phenotype.tsv	1637694
-clinvar-orphanet_phenotype.tsv	1862922
+clinvar-dbsnp.tsv	2937845
+clinvar-hgnc.tsv	3060210
+clinvar-medgen.tsv	4193666
+clinvar-mondo.tsv	1992996
+clinvar-ncbigene.tsv	3060530
+clinvar-omim_phenotype.tsv	1638969
+clinvar-orphanet_phenotype.tsv	1865227
 clinvar-uniprot.tsv	20799
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
@@ -119,39 +119,39 @@ medgen-omim_phenotype.tsv	11043
 medgen-orphanet_phenotype.tsv	9063
 mgi_gene-ensembl_gene.tsv	56426
 mgi_gene-hgnc.tsv	24584
-mgi_gene-mgi_allele.tsv	111129
+mgi_gene-mgi_allele.tsv	111987
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79070
 mgi_genotype-doid.tsv	7839
-mgi_genotype-mgi_allele.tsv	124777
-mgi_genotype-mp.tsv	401337
+mgi_genotype-mgi_allele.tsv	124809
+mgi_genotype-mp.tsv	401409
 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	11671126
-ncbigene-ensembl_protein.tsv	13442166
-ncbigene-ensembl_transcript.tsv	14133624
+ncbigene-ensembl_gene.tsv	11671120
+ncbigene-ensembl_protein.tsv	13442158
+ncbigene-ensembl_transcript.tsv	14133616
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	102174808
-ncbigene-hgnc.tsv	43833
+ncbigene-go.tsv	102174797
+ncbigene-hgnc.tsv	43838
 ncbigene-mgi_gene.tsv	71682
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18544
-ncbigene-refseq_genomic.tsv	211764
-ncbigene-refseq_protein.tsv	69154949
-ncbigene-refseq_rna.tsv	67173056
+ncbigene-omim_gene.tsv	18546
+ncbigene-refseq_genomic.tsv	211768
+ncbigene-refseq_protein.tsv	69217894
+ncbigene-refseq_rna.tsv	67173120
 ncbigene-rgd.tsv	47289
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	57240175
+ncbigene-taxonomy.tsv	57305467
 ncbigene-vgnc.tsv	112162
 ncbigene-wormbase_gene.tsv	28785
 ncbigene-xenbase_gene.tsv	46841
-ncbigene-zfin_gene.tsv	27171
+ncbigene-zfin_gene.tsv	27177
 ncit_disease-ncit_tissue.tsv	27199
 oma_protein-ensembl_gene.tsv	2533621
 oma_protein-ensembl_transcript.tsv	2925554
@@ -170,14 +170,14 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9629383
+pmc-pubmed.tsv	9638140
 prosite-prosite_prorule.tsv	1455
 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	119084186
+pubchem_compound-inchi_key.tsv	119096080
 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	679876
-refseq_protein-uniprot.tsv	154618104
-refseq_rna-dbsnp.tsv	267059416
-refseq_rna-hgnc.tsv	227230
-refseq_rna-ncbigene.tsv	65546825
-refseq_rna-omim_gene.tsv	190869
-refseq_rna-pubmed.tsv	6191600
-refseq_rna-refseq_protein.tsv	56922967
-refseq_rna-taxonomy.tsv	65576846
+refseq_protein-uniprot.tsv	154617878
+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
 rhea-chebi.tsv	216654
 rhea-ec.tsv	7719
 rhea-go.tsv	4435
 rhea-pubmed.tsv	142680
 rhea-reactome_reaction.tsv	1511
 rhea-uniprot.tsv	41448659
-sra_accession-bioproject.tsv	537052
-sra_accession-biosample.tsv	32023315
+sra_accession-bioproject.tsv	537477
+sra_accession-biosample.tsv	32055914
 sra_accession-sra_analysis.tsv	329284
-sra_accession-sra_experiment.tsv	35985315
-sra_accession-sra_project.tsv	623349
-sra_accession-sra_run.tsv	40790046
-sra_accession-sra_sample.tsv	34699841
-sra_experiment-bioproject.tsv	31502359
-sra_experiment-biosample.tsv	31834873
-sra_experiment-sra_project.tsv	31846880
-sra_experiment-sra_sample.tsv	31846603
-sra_project-bioproject.tsv	537071
-sra_run-bioproject.tsv	33386528
-sra_run-biosample.tsv	33719878
-sra_run-sra_experiment.tsv	33751992
-sra_run-sra_project.tsv	33743823
-sra_run-sra_sample.tsv	33731672
-sra_sample-biosample.tsv	32037734
+sra_accession-sra_experiment.tsv	36095148
+sra_accession-sra_project.tsv	624977
+sra_accession-sra_run.tsv	40902883
+sra_accession-sra_sample.tsv	34804828
+sra_experiment-bioproject.tsv	31554967
+sra_experiment-biosample.tsv	31873477
+sra_experiment-sra_project.tsv	31899488
+sra_experiment-sra_sample.tsv	31899211
+sra_project-bioproject.tsv	537496
+sra_run-bioproject.tsv	33441595
+sra_run-biosample.tsv	33758531
+sra_run-sra_experiment.tsv	33817349
+sra_run-sra_project.tsv	33798890
+sra_run-sra_sample.tsv	33786315
+sra_sample-biosample.tsv	32070333
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50581
+taxonomy-pubmed.tsv	50609
 togovar-clinvar.tsv	745335
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -264,10 +264,10 @@ uniprot_reference_proteome-taxonomy.tsv	698680
 uniprot-refseq_protein.tsv	45329880
 uniprot-taxonomy.tsv	248838887
 uniprot-uniprot_mnemonic.tsv	248838887
-wikipathways-chebi.tsv	11471
-wikipathways-doid.tsv	1148
-wikipathways-hmdb.tsv	4125
-wikipathways-lipidmaps.tsv	1398
-wikipathways-ncbigene.tsv	30268
+wikipathways-chebi.tsv	5929
+wikipathways-doid.tsv	1153
+wikipathways-hmdb.tsv	4131
+wikipathways-lipidmaps.tsv	1429
+wikipathways-ncbigene.tsv	30267
 wikipathways-uniprot.tsv	33518
-total	5192207706
+total	5197418100

log/pair_count_history.tsv

@@ -64,3 +64,4 @@ Date	affy_probeset-ncbigene	assembly_insdc-bioproject	assembly_insdc-biosample	a
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