Merge pull request #270 from togoid/main

release 2024-10-21

Rakefile

@@ -633,7 +633,7 @@ namespace :prepare do
     $stderr.puts "## Prepare input files for HGNC"
     download_lock(INPUT_HGNC_DIR) do
       updated = false
-      input_file = "#{INPUT_HGNC_DIR}/hgnc_complete_set.tsv"
+      input_file = "#{INPUT_HGNC_DIR}/hgnc_complete_set.txt"
       input_url  = "https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt"
       if update_input_file?(input_file, input_url)
         download_file(INPUT_HGNC_DIR, input_url)

config/hgnc-ccds/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$25{gsub("\"","",$25); split($25,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$25{gsub("\"","",$25); split($25,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-ec/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$47{gsub("\"","",$47); split($47,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$47{gsub("\"","",$47); split($47,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-ensembl_gene/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$20{gsub("\"","",$20); split($20,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$20{gsub("\"","",$20); split($20,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-hgnc_symbol/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$2{print substr($1,6) "\t" $2}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$2{print substr($1,6) "\t" $2}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-insdc/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$23{gsub("\"","",$23); split($23,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$23{gsub("\"","",$23); split($23,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-lrg/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$30{gsub("\"","",$30); split($30,a,"|"); for(k in a){if(a[k]~/^LRG_[0-9]+$/) print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$30{gsub("\"","",$30); split($30,a,"|"); for(k in a){if(a[k]~/^LRG_[0-9]+$/) print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-mgi_gene/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$28{gsub("\"","",$28); split($28,a,"|"); for(k in a)print substr($1,6) "\t" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$28{gsub("\"","",$28); split($28,a,"|"); for(k in a)print substr($1,6) "\t" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-mirbase/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$33{gsub("\"","",$33); split($33,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$33{gsub("\"","",$33); split($33,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-ncbigene/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$19{gsub("\"","",$19); split($19,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$19{gsub("\"","",$19); split($19,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-omim_gene/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$32{gsub("\"","",$32); split($32,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$32{gsub("\"","",$32); split($32,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-pubmed/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$27{gsub("\"","",$27); split($27,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$27{gsub("\"","",$27); split($27,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-refseq_genomic/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$24{gsub("\"","",$24); split($24,a,"|"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$24{gsub("\"","",$24); split($24,a,"|"); for(k in a){if(a[k]~/^NG_/)print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-refseq_rna/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$24{gsub("\"","",$24); split($24,a,"|"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$24{gsub("\"","",$24); split($24,a,"|"); for(k in a){if(a[k]~/^[NX][MR]_/)print substr($1,6) "\t" a[k]}}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-rgd/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$29{gsub("\"","",$29); split($29,a,"|"); for(k in a)print substr($1,6) "\t" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$29{gsub("\"","",$29); split($29,a,"|"); for(k in a)print substr($1,6) "\t" substr(a[k],5)}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

config/hgnc-uniprot/config.yaml

@@ -4,4 +4,4 @@ link:
   file: sample.tsv
 update:
   frequency: Bimonthly
-  method: awk -F "\t" 'FNR>=2&&$26{gsub("\"","",$26); split($26,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.tsv
+  method: awk -F "\t" 'FNR>=2&&$26{gsub("\"","",$26); split($26,a,"|"); for(k in a)print substr($1,6) "\t" a[k]}' $TOGOID_ROOT/input/hgnc/hgnc_complete_set.txt

docs/help.md

@@ -1,5 +1,5 @@
 # TogoID ver. 2.0
-Datasets last updated: 2024-10-15
+Datasets last updated: 2024-10-21
 
 ## 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.
@@ -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 2024-10-15)
+## Statistics (as of 2024-10-21)
 - 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: 2024-10-15
+Datasets last updated: 2024-10-21
 
 ## 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: 2024-10-15
 
 - [API Documentation (Swagger)](https://togoid.dbcls.jp/apidoc/)
 
-## 統計 (2024-10-15)
+## 統計 (2024-10-21)
 - 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

@@ -5,6 +5,9 @@
 - TogoID now supports handling multiple semantic relations between the same dataset pair (e.g., try converting between GlyTouCan and UniProt).  
 A detailed document is currently being prepared.
 
+# 2024-10-21
+- Weekly update has been completed.
+
 # 2024-10-15
 - Weekly update has been completed.
 

log/error.log

@@ -1,11 +1,9 @@
 Error: download_file(input/glytoucan, https://glycosmos.org/download/glycosmos_ggdbs_pubmed.csv): Command failed with status (8): [wget --quiet --recursive --no-parent --no-...]
-Error: check_remote_file_time(input/hgnc/hgnc_complete_set.tsv, https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.tsv): no time information in ""
-Error: Remote file is empty
 Error: check_remote_file_time(input/homologene/homologene.data, https://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current/homologene.data): no time information in ""
 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 502: Bad Gateway: 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 502: Bad Gateway: 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
@@ -73,5 +71,5 @@ Error: HTTP Error 502: Bad Gateway: https://api.alpha.glycosmos.org/partialmatch
 # 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 72255 / 148433 = 0.48678528359596585 < 0.5
-# Error: output/tsv/wikipathways-uniprot.tsv new file size per old 59610 / 470542 = 0.12668369667319815 < 0.5
+# 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

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	217809
-bioproject-pubmed.tsv	279413
+bioproject-geo_series.tsv	218318
+bioproject-pubmed.tsv	280110
 bioproject_umbrella-bioproject.tsv	104586
-biosample-bioproject.tsv	19988521
-biosample-geo_sample.tsv	9447146
+biosample-bioproject.tsv	20027457
+biosample-geo_sample.tsv	9463924
 cellosaurus-ncit_disease.tsv	75821
 cellosaurus-orphanet_phenotype.tsv	41448
 chebi-glytoucan.tsv	10615
@@ -34,27 +34,27 @@ 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	2937791
-clinvar-hgnc.tsv	3044255
-clinvar-medgen.tsv	4171173
-clinvar-mondo.tsv	1988452
-clinvar-ncbigene.tsv	3044575
-clinvar-omim_phenotype.tsv	1635664
-clinvar-orphanet_phenotype.tsv	1860371
+clinvar-dbsnp.tsv	2937807
+clinvar-hgnc.tsv	3048112
+clinvar-medgen.tsv	4176542
+clinvar-mondo.tsv	1989799
+clinvar-ncbigene.tsv	3048432
+clinvar-omim_phenotype.tsv	1636833
+clinvar-orphanet_phenotype.tsv	1861412
 clinvar-uniprot.tsv	20798
 cog-insdc.tsv	115826
 cog-refseq_protein.tsv	3340026
 doid-mesh.tsv	4019
 doid-ncit_disease.tsv	4849
 doid-omim_phenotype.tsv	5671
-ensembl_gene-affy_probeset.tsv	54855
+ensembl_gene-affy_probeset.tsv	55423
 ensembl_gene-ensembl_protein.tsv	12969337
 ensembl_gene-ensembl_transcript.tsv	15910019
 ensembl_gene-hgnc.tsv	47792
 ensembl_gene-ncbigene.tsv	14749031
 ensembl_gene-uniprot.tsv	5546630
 ensembl_protein-ensembl_transcript.tsv	12969340
-ensembl_transcript-affy_probeset.tsv	224377
+ensembl_transcript-affy_probeset.tsv	241195
 ensembl_transcript-go.tsv	55211171
 ensembl_transcript-hgnc.tsv	241612
 ensembl_transcript-refseq_rna.tsv	40165483
@@ -68,19 +68,19 @@ glytoucan-uniprot-TIO_000126.tsv	402
 glytoucan-uniprot-TIO_000128.tsv	310
 glytoucan-uniprot.tsv	82906
 hgnc-ccds.tsv	35510
-hgnc-ec.tsv	2049
-hgnc-ensembl_gene.tsv	41234
-hgnc-hgnc_symbol.tsv	43873
-hgnc-insdc.tsv	21166
+hgnc-ec.tsv	2083
+hgnc-ensembl_gene.tsv	41244
+hgnc-hgnc_symbol.tsv	43882
+hgnc-insdc.tsv	21162
 hgnc-lrg.tsv	1325
-hgnc-mgi_gene.tsv	24071
+hgnc-mgi_gene.tsv	24072
 hgnc-mirbase.tsv	1912
-hgnc-ncbigene.tsv	43815
-hgnc-omim_gene.tsv	17277
-hgnc-pubmed.tsv	34911
-hgnc-refseq_genomic.tsv	13531
-hgnc-refseq_rna.tsv	28774
-hgnc-rgd.tsv	18940
+hgnc-ncbigene.tsv	43813
+hgnc-omim_gene.tsv	17320
+hgnc-pubmed.tsv	34994
+hgnc-refseq_genomic.tsv	13532
+hgnc-refseq_rna.tsv	28776
+hgnc-rgd.tsv	18945
 hgnc-uniprot.tsv	20379
 hmdb-chebi.tsv	13701
 hmdb-inchi_key.tsv	217899
@@ -119,7 +119,7 @@ medgen-omim_phenotype.tsv	11043
 medgen-orphanet_phenotype.tsv	9063
 mgi_gene-ensembl_gene.tsv	56426
 mgi_gene-hgnc.tsv	24587
-mgi_gene-mgi_allele.tsv	110437
+mgi_gene-mgi_allele.tsv	110465
 mgi_gene-ncbigene.tsv	90618
 mgi_gene-uniprot.tsv	79034
 mgi_genotype-doid.tsv	7837
@@ -136,18 +136,18 @@ ncbigene-ensembl_gene.tsv	11654277
 ncbigene-ensembl_protein.tsv	13449374
 ncbigene-ensembl_transcript.tsv	14177749
 ncbigene-flybase_gene.tsv	25078
-ncbigene-go.tsv	101041913
-ncbigene-hgnc.tsv	43827
-ncbigene-mgi_gene.tsv	71684
+ncbigene-go.tsv	101431326
+ncbigene-hgnc.tsv	43828
+ncbigene-mgi_gene.tsv	71683
 ncbigene-mirbase.tsv	17541
-ncbigene-omim_gene.tsv	18527
-ncbigene-refseq_genomic.tsv	211762
-ncbigene-refseq_protein.tsv	68217911
-ncbigene-refseq_rna.tsv	66619410
+ncbigene-omim_gene.tsv	18530
+ncbigene-refseq_genomic.tsv	211763
+ncbigene-refseq_protein.tsv	68719760
+ncbigene-refseq_rna.tsv	66732541
 ncbigene-rgd.tsv	47288
 ncbigene-sgd.tsv	6471
 ncbigene-tair.tsv	32835
-ncbigene-taxonomy.tsv	56353463
+ncbigene-taxonomy.tsv	56873692
 ncbigene-vgnc.tsv	112162
 ncbigene-wormbase_gene.tsv	28779
 ncbigene-xenbase_gene.tsv	46842
@@ -170,14 +170,14 @@ pdb-interpro.tsv	726658
 pdb-pdb_ccd.tsv	530587
 pdb-pfam.tsv	339565
 pdb-uniprot.tsv	341431
-pmc-pubmed.tsv	9561234
+pmc-pubmed.tsv	9575886
 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	118680448
+pubchem_compound-inchi_key.tsv	118727283
 pubchem_pathway-ncbigene.tsv	33861
 pubchem_pathway-pathbank.tsv	69387
 pubchem_pathway-pubchem_compound.tsv	1253395
@@ -195,7 +195,7 @@ 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	154618594
+refseq_protein-uniprot.tsv	154618423
 refseq_rna-dbsnp.tsv	267059416
 refseq_rna-hgnc.tsv	227230
 refseq_rna-ncbigene.tsv	65546825
@@ -209,28 +209,28 @@ rhea-go.tsv	4435
 rhea-pubmed.tsv	142680
 rhea-reactome_reaction.tsv	1511
 rhea-uniprot.tsv	41448659
-sra_accession-bioproject.tsv	529462
-sra_accession-biosample.tsv	31680248
+sra_accession-bioproject.tsv	529783
+sra_accession-biosample.tsv	31699855
 sra_accession-sra_analysis.tsv	329243
-sra_accession-sra_experiment.tsv	35570093
-sra_accession-sra_project.tsv	616586
-sra_accession-sra_run.tsv	40350221
-sra_accession-sra_sample.tsv	34372201
-sra_experiment-bioproject.tsv	31035975
-sra_experiment-biosample.tsv	31352287
-sra_experiment-sra_project.tsv	31380496
-sra_experiment-sra_sample.tsv	31380303
-sra_project-bioproject.tsv	532904
-sra_run-bioproject.tsv	32903026
-sra_run-biosample.tsv	33216964
-sra_run-sra_experiment.tsv	33268661
-sra_run-sra_project.tsv	33260321
-sra_run-sra_sample.tsv	33246345
-sra_sample-biosample.tsv	31701362
+sra_accession-sra_experiment.tsv	35659853
+sra_accession-sra_project.tsv	617870
+sra_accession-sra_run.tsv	40455586
+sra_accession-sra_sample.tsv	34436063
+sra_experiment-bioproject.tsv	31083409
+sra_experiment-biosample.tsv	31394401
+sra_experiment-sra_project.tsv	31427930
+sra_experiment-sra_sample.tsv	31427737
+sra_project-bioproject.tsv	533225
+sra_run-bioproject.tsv	32951299
+sra_run-biosample.tsv	33259254
+sra_run-sra_experiment.tsv	33317034
+sra_run-sra_project.tsv	33308594
+sra_run-sra_sample.tsv	33294197
+sra_sample-biosample.tsv	31720969
 swisslipids-chebi.tsv	4276
 swisslipids-hmdb.tsv	26026
 swisslipids-inchi_key.tsv	593209
-taxonomy-pubmed.tsv	50493
+taxonomy-pubmed.tsv	50481
 togovar-clinvar.tsv	745335
 togovar-dbsnp.tsv	66877211
 togovar-ensembl_gene.tsv	72473309
@@ -266,8 +266,8 @@ uniprot-taxonomy.tsv	248838887
 uniprot-uniprot_mnemonic.tsv	248838887
 wikipathways-chebi.tsv	11471
 wikipathways-doid.tsv	1148
-wikipathways-hmdb.tsv	4119
+wikipathways-hmdb.tsv	4125
 wikipathways-lipidmaps.tsv	1398
-wikipathways-ncbigene.tsv	30258
+wikipathways-ncbigene.tsv	30268
 wikipathways-uniprot.tsv	33518
-total	5181681751
+total	5184078473