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name: LinkML + prefix: linkml - homepage: null name: Lipid Ontology prefix: lipro @@ -1115,6 +1124,9 @@ pattern: - homepage: https://www.thermofisher.com name: Thermo Fisher Scientific prefix: thermofisher +- homepage: https://www.w3.org/TR/owl-time/ + name: Time Ontology in OWL + prefix: time - homepage: http://cell-lines.toku-e.com name: TOKU-E Cell-culture Database prefix: tokue @@ -2107,6 +2119,9 @@ wikidata: - homepage: https://www.ncbi.nlm.nih.gov/gv/mhc/ name: Database of human Major Histocompatibility Complex prefix: dbmhc +- homepage: https://dbpedia.org/ontology + name: DBPedia Ontology + prefix: dbo - homepage: https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe name: NCBI Probe database Public registry of nucleic acid reagents prefix: dbprobe @@ -2837,6 +2852,9 @@ wikidata: - homepage: http://www.genomesonline.org/cgi-bin/GOLD/index.cgi name: GOLD metadata prefix: gold.meta +- homepage: https://books.google.com + name: Google Books + prefix: google.book - homepage: 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"http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=", "dbgap": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=", + "dbo": "https://dbpedia.org/ontology/", "dbprobe": "https://www.ncbi.nlm.nih.gov/probe/?term=", "dbsnp": "https://www.ncbi.nlm.nih.gov/snp/", "dbvar.study": "https://www.ncbi.nlm.nih.gov/dbvar/studies/", @@ -480,6 +481,7 @@ "gold": "https://gold.jgi.doe.gov/resolver?id=", "gold.genome": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=", "gold.meta": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=", + "google.book": "https://books.google.com/books?id=", "google.patent": "https://www.google.com/patents/", "gpcrdb": "https://gpcrdb.org/protein/", "gpmdb": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=", @@ -510,6 +512,7 @@ "hamap": "https://hamap.expasy.org/unirule/", "hancestro": "http://purl.obolibrary.org/obo/HANCESTRO_", "hao": "http://purl.obolibrary.org/obo/HAO_", + "hathitrust": "https://catalog.hathitrust.org/Record/", "hcvdb": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=", "hdr": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=", "hgmd": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=", @@ -625,6 +628,7 @@ "kegg.reaction": "https://www.kegg.jp/entry/", "knapsack": "http://www.knapsackfamily.com/knapsack_core/information.php?word=", "labo": "http://purl.obolibrary.org/obo/LABO_", + "langual": "https://www.langual.org/langual_thesaurus.asp?termid=", "lei": "https://www.gleif.org/lei/", "lepao": "http://purl.obolibrary.org/obo/LEPAO_", "lgai.cede": "https://s3.us-east-2.amazonaws.com/lg.cede/", @@ -638,6 +642,7 @@ "lincs.protein": "https://lincs.hms.harvard.edu/db/proteins/", "lincs.smallmolecule": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/", "linguist": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#", + "linkml": "https://w3id.org/linkml/", "lipidbank": "http://lipidbank.jp/cgi-bin/detail.cgi?id=", "lipidmaps": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=", "lipro": "http://purl.obolibrary.org/obo/LIPRO_", @@ -1110,6 +1115,7 @@ "tgn": "http://vocab.getty.edu/page/tgn/", "thermofisher": "https://www.thermofisher.com/antibody/product/", "tigrfam": "https://www.ncbi.nlm.nih.gov/cdd?term=", + "time": "http://www.w3.org/2006/time#", "tngb": "http://biobanknetwork.telethon.it/Sample/View?sampleId=", "to": "http://purl.obolibrary.org/obo/TO_", "tol": "http://tolweb.org/", diff --git a/exports/contexts/bioregistry.context.ttl b/exports/contexts/bioregistry.context.ttl index 0ea6bf24d..401945155 100644 --- a/exports/contexts/bioregistry.context.ttl +++ b/exports/contexts/bioregistry.context.ttl @@ -270,6 +270,7 @@ [ sh:prefix "dbest" ; sh:namespace "https://www.ncbi.nlm.nih.gov/nucest/" ; sh:pattern "^([A-Z]+)?\d+(\.\d+)?$" ], [ sh:prefix "dbg2introns" ; sh:namespace "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=" ; sh:pattern "^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$" ], [ sh:prefix "dbgap" ; sh:namespace "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=" ; sh:pattern "^phs[0-9]{6}(.v\d+.p\d+)?$" ], + [ sh:prefix "dbo" ; sh:namespace "https://dbpedia.org/ontology/" ], [ sh:prefix "dbprobe" ; sh:namespace "https://www.ncbi.nlm.nih.gov/probe/?term=" ; sh:pattern "^\d+$" ], [ sh:prefix "dbsnp" ; sh:namespace "https://www.ncbi.nlm.nih.gov/snp/" ; sh:pattern "^rs\d+$" ], [ sh:prefix "dbvar.study" ; sh:namespace "https://www.ncbi.nlm.nih.gov/dbvar/studies/" ], @@ -473,7 +474,7 @@ [ sh:prefix "gmd.gcms" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/Spectrums/" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], [ sh:prefix "gmd.profile" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], [ sh:prefix "gmd.ref" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], - [ sh:prefix "gno" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^\d{8}$" ], + [ sh:prefix "gno" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^(\d{8}|(\w+\d+\w+))$" ], [ sh:prefix "gnpis" ; sh:namespace "https://urgi.versailles.inra.fr/gnpis/#result/term=" ; sh:pattern "^[A-Za-z0-9]+$" ], [ sh:prefix "go" ; sh:namespace "http://amigo.geneontology.org/amigo/term/GO:" ; sh:pattern "^\d{7}$" ], [ sh:prefix "go.model" ; sh:namespace "http://noctua.geneontology.org/editor/graph/gomodel:" ], @@ -482,6 +483,7 @@ [ sh:prefix "gold" ; sh:namespace "https://gold.jgi.doe.gov/resolver?id=" ; sh:pattern "^[A-Z][a-z][0-9]+$" ], [ sh:prefix "gold.genome" ; sh:namespace "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=" ; sh:pattern "^(Gi|Gc)\d+$" ], [ sh:prefix "gold.meta" ; sh:namespace "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=" ; sh:pattern "^Gm\d+$" ], + [ sh:prefix "google.book" ; sh:namespace "https://books.google.com/books?id=" ], [ sh:prefix "google.patent" ; sh:namespace "https://www.google.com/patents/" ; sh:pattern "^[A-Z]{2,4}\d+([A-Z])?([0-9])?$" ], [ sh:prefix "gpcrdb" ; sh:namespace "https://gpcrdb.org/protein/" ; sh:pattern "^\w+$" ], [ sh:prefix "gpmdb" ; sh:namespace "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" ; sh:pattern "^GPM\d+$" ], @@ -512,6 +514,7 @@ [ sh:prefix "hamap" ; sh:namespace "https://hamap.expasy.org/unirule/" ; sh:pattern "^MF_\d+$" ], [ sh:prefix "hancestro" ; sh:namespace "http://purl.obolibrary.org/obo/HANCESTRO_" ; sh:pattern "^\d{4}$" ], [ sh:prefix "hao" ; sh:namespace "http://purl.obolibrary.org/obo/HAO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "hathitrust" ; sh:namespace "https://catalog.hathitrust.org/Record/" ; sh:pattern "^\d+$" ], [ sh:prefix "hcvdb" ; sh:namespace "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=" ; sh:pattern "^M\d{5}$" ], [ sh:prefix "hdr" ; sh:namespace "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=" ; sh:pattern "^\d+$" ], [ sh:prefix "hgmd" ; sh:namespace "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=" ; sh:pattern "^[A-Z_0-9]+$" ], @@ -627,6 +630,7 @@ [ sh:prefix "kegg.reaction" ; sh:namespace "https://www.kegg.jp/entry/" ; sh:pattern "^R\d+$" ], [ sh:prefix "knapsack" ; sh:namespace "http://www.knapsackfamily.com/knapsack_core/information.php?word=" ; sh:pattern "^C\d{8}$" ], [ sh:prefix "labo" ; sh:namespace "http://purl.obolibrary.org/obo/LABO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "langual" ; sh:namespace "https://www.langual.org/langual_thesaurus.asp?termid=" ; sh:pattern "^B\d+$" ], [ sh:prefix "lei" ; sh:namespace "https://www.gleif.org/lei/" ; sh:pattern "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$" ], [ sh:prefix "lepao" ; sh:namespace "http://purl.obolibrary.org/obo/LEPAO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "lgai.cede" ; sh:namespace "https://s3.us-east-2.amazonaws.com/lg.cede/" ; sh:pattern "^LGCEDe-S-\d{9}$" ], @@ -640,6 +644,7 @@ [ sh:prefix "lincs.protein" ; sh:namespace "https://lincs.hms.harvard.edu/db/proteins/" ; sh:pattern "^\d+$" ], [ sh:prefix "lincs.smallmolecule" ; sh:namespace "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/" ; sh:pattern "^LSM-\d+$" ], [ sh:prefix "linguist" ; sh:namespace "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#" ; sh:pattern "^[a-zA-Z0-9 +#'*]+$" ], + [ sh:prefix "linkml" ; sh:namespace "https://w3id.org/linkml/" ], [ sh:prefix "lipidbank" ; sh:namespace "http://lipidbank.jp/cgi-bin/detail.cgi?id=" ; sh:pattern "^\w+\d+$" ], [ sh:prefix "lipidmaps" ; sh:namespace "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" ; sh:pattern "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$" ], [ sh:prefix "lipro" ; sh:namespace "http://purl.obolibrary.org/obo/LIPRO_" ], @@ -1112,6 +1117,7 @@ [ sh:prefix "tgn" ; sh:namespace "http://vocab.getty.edu/page/tgn/" ; sh:pattern "^\d+$" ], [ sh:prefix "thermofisher" ; sh:namespace "https://www.thermofisher.com/antibody/product/" ], [ sh:prefix "tigrfam" ; sh:namespace "https://www.ncbi.nlm.nih.gov/cdd?term=" ; sh:pattern "^TIGR\d+$" ], + [ sh:prefix "time" ; sh:namespace "http://www.w3.org/2006/time#" ], [ sh:prefix "tngb" ; sh:namespace "http://biobanknetwork.telethon.it/Sample/View?sampleId=" ; sh:pattern "^\d+$" ], [ sh:prefix "to" ; sh:namespace "http://purl.obolibrary.org/obo/TO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "tol" ; sh:namespace "http://tolweb.org/" ; sh:pattern "^\d+$" ], diff --git a/exports/contexts/obo.context.jsonld b/exports/contexts/obo.context.jsonld index 329d98d6d..c4ca3b97c 100644 --- a/exports/contexts/obo.context.jsonld +++ b/exports/contexts/obo.context.jsonld @@ -492,6 +492,7 @@ "dbest": "https://www.ncbi.nlm.nih.gov/nucest/", "dbg2introns": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=", "dbgap": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=", + "dbo": "https://dbpedia.org/ontology/", "dbprobe": "https://www.ncbi.nlm.nih.gov/probe/?term=", "dbsnp": "https://www.ncbi.nlm.nih.gov/snp/", "dbvar.study": "https://www.ncbi.nlm.nih.gov/dbvar/studies/", @@ -646,6 +647,7 @@ "gold": "https://gold.jgi.doe.gov/resolver?id=", "gold.genome": "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=", "gold.meta": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=", + "google.book": "https://books.google.com/books?id=", "google.patent": "https://www.google.com/patents/", "gpcrdb": "https://gpcrdb.org/protein/", "gpmdb": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=", @@ -672,6 +674,7 @@ "gxa.expt": "https://www.ebi.ac.uk/gxa/experiments/", "gxa.gene": "https://www.ebi.ac.uk/gxa/genes/", "hamap": "https://hamap.expasy.org/unirule/", + "hathitrust": "https://catalog.hathitrust.org/Record/", "hcvdb": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=", "hdr": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=", "hgmd": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=", @@ -771,6 +774,7 @@ "kegg.pathway": "https://www.kegg.jp/entry/", "kegg.reaction": "https://www.kegg.jp/entry/", "knapsack": "http://www.knapsackfamily.com/knapsack_core/information.php?word=", + "langual": "https://www.langual.org/langual_thesaurus.asp?termid=", "lei": "https://www.gleif.org/lei/", "lgai.cede": "https://s3.us-east-2.amazonaws.com/lg.cede/", "licebase": "https://licebase.org/?q=", @@ -783,6 +787,7 @@ "lincs.protein": "https://lincs.hms.harvard.edu/db/proteins/", "lincs.smallmolecule": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/", "linguist": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#", + "linkml": "https://w3id.org/linkml/", "lipidbank": "http://lipidbank.jp/cgi-bin/detail.cgi?id=", "lipidmaps": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=", "loinc": "https://loinc.org/", @@ -1133,6 +1138,7 @@ "tgn": "http://vocab.getty.edu/page/tgn/", "thermofisher": "https://www.thermofisher.com/antibody/product/", "tigrfam": "https://www.ncbi.nlm.nih.gov/cdd?term=", + "time": "http://www.w3.org/2006/time#", "tngb": "http://biobanknetwork.telethon.it/Sample/View?sampleId=", "tol": "http://tolweb.org/", "topdb": "http://topdb.enzim.hu/?m=show&id=", diff --git a/exports/contexts/obo.context.ttl b/exports/contexts/obo.context.ttl index ce8b1a565..901db1da9 100644 --- a/exports/contexts/obo.context.ttl +++ b/exports/contexts/obo.context.ttl @@ -107,7 +107,7 @@ [ sh:prefix "GENEPIO" ; sh:namespace "http://purl.obolibrary.org/obo/GENEPIO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "GENO" ; sh:namespace "http://purl.obolibrary.org/obo/GENO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "GEOGEO" ; sh:namespace "http://purl.obolibrary.org/obo/GEO_" ; sh:pattern "^\d{9}$" ], - [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^\d{8}$" ], + [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^(\d{8}|(\w+\d+\w+))$" ], [ sh:prefix "GO" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "GSSO" ; sh:namespace "http://purl.obolibrary.org/obo/GSSO_" ; sh:pattern "^\d{6}$" ], [ sh:prefix "HABRONATTUS" ; sh:namespace "http://purl.obolibrary.org/obo/HABRONATTUS_" ], @@ -494,6 +494,7 @@ [ sh:prefix "dbest" ; sh:namespace "https://www.ncbi.nlm.nih.gov/nucest/" ; sh:pattern "^([A-Z]+)?\d+(\.\d+)?$" ], [ sh:prefix "dbg2introns" ; sh:namespace "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=" ; sh:pattern "^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$" ], [ sh:prefix "dbgap" ; sh:namespace "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=" ; sh:pattern "^phs[0-9]{6}(.v\d+.p\d+)?$" ], + [ sh:prefix "dbo" ; sh:namespace "https://dbpedia.org/ontology/" ], [ sh:prefix "dbprobe" ; sh:namespace "https://www.ncbi.nlm.nih.gov/probe/?term=" ; sh:pattern "^\d+$" ], [ sh:prefix "dbsnp" ; sh:namespace "https://www.ncbi.nlm.nih.gov/snp/" ; sh:pattern "^rs\d+$" ], [ sh:prefix "dbvar.study" ; sh:namespace "https://www.ncbi.nlm.nih.gov/dbvar/studies/" ], @@ -648,6 +649,7 @@ [ sh:prefix "gold" ; sh:namespace "https://gold.jgi.doe.gov/resolver?id=" ; sh:pattern "^[A-Z][a-z][0-9]+$" ], [ sh:prefix "gold.genome" ; sh:namespace "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=" ; sh:pattern "^(Gi|Gc)\d+$" ], [ sh:prefix "gold.meta" ; sh:namespace "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=" ; sh:pattern "^Gm\d+$" ], + [ sh:prefix "google.book" ; sh:namespace "https://books.google.com/books?id=" ], [ sh:prefix "google.patent" ; sh:namespace "https://www.google.com/patents/" ; sh:pattern "^[A-Z]{2,4}\d+([A-Z])?([0-9])?$" ], [ sh:prefix "gpcrdb" ; sh:namespace "https://gpcrdb.org/protein/" ; sh:pattern "^\w+$" ], [ sh:prefix "gpmdb" ; sh:namespace "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" ; sh:pattern "^GPM\d+$" ], @@ -674,6 +676,7 @@ [ sh:prefix "gxa.expt" ; sh:namespace "https://www.ebi.ac.uk/gxa/experiments/" ; sh:pattern "^[AEP]-\w{4}-\d+$" ], [ sh:prefix "gxa.gene" ; sh:namespace "https://www.ebi.ac.uk/gxa/genes/" ; sh:pattern "^\w+$" ], [ sh:prefix "hamap" ; sh:namespace "https://hamap.expasy.org/unirule/" ; sh:pattern "^MF_\d+$" ], + [ sh:prefix "hathitrust" ; sh:namespace "https://catalog.hathitrust.org/Record/" ; sh:pattern "^\d+$" ], [ sh:prefix "hcvdb" ; sh:namespace "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=" ; sh:pattern "^M\d{5}$" ], [ sh:prefix "hdr" ; sh:namespace "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=" ; sh:pattern "^\d+$" ], [ sh:prefix "hgmd" ; sh:namespace "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=" ; sh:pattern "^[A-Z_0-9]+$" ], @@ -773,6 +776,7 @@ [ sh:prefix "kegg.pathway" ; sh:namespace "https://www.kegg.jp/entry/" ; sh:pattern "^\w{2,4}\d{5}$" ], [ sh:prefix "kegg.reaction" ; sh:namespace "https://www.kegg.jp/entry/" ; sh:pattern "^R\d+$" ], [ sh:prefix "knapsack" ; sh:namespace "http://www.knapsackfamily.com/knapsack_core/information.php?word=" ; sh:pattern "^C\d{8}$" ], + [ sh:prefix "langual" ; sh:namespace "https://www.langual.org/langual_thesaurus.asp?termid=" ; sh:pattern "^B\d+$" ], [ sh:prefix "lei" ; sh:namespace "https://www.gleif.org/lei/" ; sh:pattern "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$" ], [ sh:prefix "lgai.cede" ; sh:namespace "https://s3.us-east-2.amazonaws.com/lg.cede/" ; sh:pattern "^LGCEDe-S-\d{9}$" ], [ sh:prefix "licebase" ; sh:namespace "https://licebase.org/?q=" ; sh:pattern "^[A-Za-z0-9\-\/]+$" ], @@ -785,6 +789,7 @@ [ sh:prefix "lincs.protein" ; sh:namespace "https://lincs.hms.harvard.edu/db/proteins/" ; sh:pattern "^\d+$" ], [ sh:prefix "lincs.smallmolecule" ; sh:namespace "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/" ; sh:pattern "^LSM-\d+$" ], [ sh:prefix "linguist" ; sh:namespace "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#" ; sh:pattern "^[a-zA-Z0-9 +#'*]+$" ], + [ sh:prefix "linkml" ; sh:namespace "https://w3id.org/linkml/" ], [ sh:prefix "lipidbank" ; sh:namespace "http://lipidbank.jp/cgi-bin/detail.cgi?id=" ; sh:pattern "^\w+\d+$" ], [ sh:prefix "lipidmaps" ; sh:namespace "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" ; sh:pattern "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$" ], [ sh:prefix "loinc" ; sh:namespace "https://loinc.org/" ], @@ -1135,6 +1140,7 @@ [ sh:prefix "tgn" ; sh:namespace "http://vocab.getty.edu/page/tgn/" ; sh:pattern "^\d+$" ], [ sh:prefix "thermofisher" ; sh:namespace "https://www.thermofisher.com/antibody/product/" ], [ sh:prefix "tigrfam" ; sh:namespace "https://www.ncbi.nlm.nih.gov/cdd?term=" ; sh:pattern "^TIGR\d+$" ], + [ sh:prefix "time" ; sh:namespace "http://www.w3.org/2006/time#" ], [ sh:prefix "tngb" ; sh:namespace "http://biobanknetwork.telethon.it/Sample/View?sampleId=" ; sh:pattern "^\d+$" ], [ sh:prefix "tol" ; sh:namespace "http://tolweb.org/" ; sh:pattern "^\d+$" ], [ sh:prefix "topdb" ; sh:namespace "http://topdb.enzim.hu/?m=show&id=" ; sh:pattern "^[A-Z0-9]+$" ], diff --git a/exports/contexts/obo_synonyms.context.jsonld b/exports/contexts/obo_synonyms.context.jsonld index ff7155d25..ff5c727c9 100644 --- a/exports/contexts/obo_synonyms.context.jsonld +++ b/exports/contexts/obo_synonyms.context.jsonld @@ -741,6 +741,7 @@ "dbest": "https://www.ncbi.nlm.nih.gov/nucest/", "dbg2introns": "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=", "dbgap": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=", + "dbo": "https://dbpedia.org/ontology/", "dbprobe": "https://www.ncbi.nlm.nih.gov/probe/?term=", "dbsnp": "https://www.ncbi.nlm.nih.gov/snp/", "dbvar.studies": "https://www.ncbi.nlm.nih.gov/dbvar/studies/", @@ -750,6 +751,7 @@ "dc": "http://purl.org/dc/terms/", "dc.terms": "http://purl.org/dc/terms/", "dcat": "http://www.w3.org/ns/dcat#", + "dct": "http://purl.org/dc/terms/", "dcterms": "http://purl.org/dc/terms/", "dctypes": "http://purl.org/dc/dcmitype/", "ddinter.drug": "http://ddinter.scbdd.com/ddinter/drug-detail/", @@ -901,6 +903,7 @@ "gmd.gcms": "http://gmd.mpimp-golm.mpg.de/Spectrums/", "gmd.profile": "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=", "gmd.ref": "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/", + "gnome": "http://purl.obolibrary.org/obo/GNO_", "gnpis": "https://urgi.versailles.inra.fr/gnpis/#result/term=", "go.model": "http://noctua.geneontology.org/editor/graph/gomodel:", "go.resource": "https://bioregistry.io/metaregistry/go/", @@ -914,6 +917,7 @@ "gold.meta": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=", "gomf": "http://purl.obolibrary.org/obo/GO_", "gomfid": "http://purl.obolibrary.org/obo/GO_", + "google.book": "https://books.google.com/books?id=", "google.patent": "https://www.google.com/patents/", "gpcrdb": "https://gpcrdb.org/protein/", "gpmdb": "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=", @@ -941,6 +945,7 @@ "gxa.expt": "https://www.ebi.ac.uk/gxa/experiments/", "gxa.gene": "https://www.ebi.ac.uk/gxa/genes/", "hamap": "https://hamap.expasy.org/unirule/", + "hathitrust": "https://catalog.hathitrust.org/Record/", "hcvdb": "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=", "hdr": "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=", "hgmd": "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=", @@ -1051,6 +1056,7 @@ "kegg_genomes": "http://www.kegg.jp/entry/", "kisao": "http://purl.obolibrary.org/obo/KISAO_", "knapsack": "http://www.knapsackfamily.com/knapsack_core/information.php?word=", + "langual": "https://www.langual.org/langual_thesaurus.asp?termid=", "lei": "https://www.gleif.org/lei/", "lgai.cede": "https://s3.us-east-2.amazonaws.com/lg.cede/", "licebase": "https://licebase.org/?q=", @@ -1064,6 +1070,7 @@ "lincs.protein": "https://lincs.hms.harvard.edu/db/proteins/", "lincs.smallmolecule": "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/", "linguist": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#", + "linkml": "https://w3id.org/linkml/", "lipidbank": "http://lipidbank.jp/cgi-bin/detail.cgi?id=", "lipidmaps": "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=", "loinc": "https://loinc.org/", @@ -1285,6 +1292,7 @@ "pharmgkb.pathways": "http://www.pharmgkb.org/pathway/", "phenolexplorer": "http://phenol-explorer.eu/foods/", "phenx": "https://www.phenxtoolkit.org/protocols/view/", + "phenxtoolkit": "https://www.phenxtoolkit.org/protocols/view/", "phosphosite.protein": "http://www.phosphosite.org/proteinAction.do?id=", "phosphosite.residue": "http://www.phosphosite.org/siteAction.do?id=", "phylomedb": "http://phylomedb.org/?seqid=", @@ -1447,6 +1455,7 @@ "tgn": "http://vocab.getty.edu/page/tgn/", "thermofisher": "https://www.thermofisher.com/antibody/product/", "tigrfam": "https://www.ncbi.nlm.nih.gov/cdd?term=", + "time": "http://www.w3.org/2006/time#", "tngb": "http://biobanknetwork.telethon.it/Sample/View?sampleId=", "tol": "http://tolweb.org/", "tol.webproj": "http://tolweb.org/", diff --git a/exports/contexts/obo_synonyms.context.ttl b/exports/contexts/obo_synonyms.context.ttl index 688224bbd..bb3a33d1d 100644 --- a/exports/contexts/obo_synonyms.context.ttl +++ b/exports/contexts/obo_synonyms.context.ttl @@ -162,7 +162,7 @@ [ sh:prefix "GENO" ; sh:namespace "http://purl.obolibrary.org/obo/GENO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "GEOGEO" ; sh:namespace "http://purl.obolibrary.org/obo/GEO_" ; sh:pattern "^\d{9}$" ], [ sh:prefix "GFAM" ; sh:namespace "https://www.genenames.org/cgi-bin/genefamilies/set/" ; sh:pattern "^\d+$" ], - [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^\d{8}$" ], + [ sh:prefix "GNO" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^(\d{8}|(\w+\d+\w+))$" ], [ sh:prefix "GO" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "GR_GENE" ; sh:namespace "http://www.gramene.org/db/genes/search_gene?acc=" ; sh:pattern "^GR\:\d+$" ], [ sh:prefix "GR_PROTEIN" ; sh:namespace "http://www.gramene.org/db/protein/protein_search?protein_id=" ; sh:pattern "^\d+$" ], @@ -743,6 +743,7 @@ [ sh:prefix "dbest" ; sh:namespace "https://www.ncbi.nlm.nih.gov/nucest/" ; sh:pattern "^([A-Z]+)?\d+(\.\d+)?$" ], [ sh:prefix "dbg2introns" ; sh:namespace "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=" ; sh:pattern "^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$" ], [ sh:prefix "dbgap" ; sh:namespace "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=" ; sh:pattern "^phs[0-9]{6}(.v\d+.p\d+)?$" ], + [ sh:prefix "dbo" ; sh:namespace "https://dbpedia.org/ontology/" ], [ sh:prefix "dbprobe" ; sh:namespace "https://www.ncbi.nlm.nih.gov/probe/?term=" ; sh:pattern "^\d+$" ], [ sh:prefix "dbsnp" ; sh:namespace "https://www.ncbi.nlm.nih.gov/snp/" ; sh:pattern "^rs\d+$" ], [ sh:prefix "dbvar.studies" ; sh:namespace "https://www.ncbi.nlm.nih.gov/dbvar/studies/" ], @@ -752,6 +753,7 @@ [ sh:prefix "dc" ; sh:namespace "http://purl.org/dc/terms/" ], [ sh:prefix "dc.terms" ; sh:namespace "http://purl.org/dc/terms/" ], [ sh:prefix "dcat" ; sh:namespace "http://www.w3.org/ns/dcat#" ], + [ sh:prefix "dct" ; sh:namespace "http://purl.org/dc/terms/" ], [ sh:prefix "dcterms" ; sh:namespace "http://purl.org/dc/terms/" ], [ sh:prefix "dctypes" ; sh:namespace "http://purl.org/dc/dcmitype/" ], [ sh:prefix "ddinter.drug" ; sh:namespace "http://ddinter.scbdd.com/ddinter/drug-detail/" ; sh:pattern "^DDInter\d+$" ], @@ -903,6 +905,7 @@ [ sh:prefix "gmd.gcms" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/Spectrums/" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], [ sh:prefix "gmd.profile" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], [ sh:prefix "gmd.ref" ; sh:namespace "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/" ; sh:pattern "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$" ], + [ sh:prefix "gnome" ; sh:namespace "http://purl.obolibrary.org/obo/GNO_" ; sh:pattern "^(\d{8}|(\w+\d+\w+))$" ], [ sh:prefix "gnpis" ; sh:namespace "https://urgi.versailles.inra.fr/gnpis/#result/term=" ; sh:pattern "^[A-Za-z0-9]+$" ], [ sh:prefix "go.model" ; sh:namespace "http://noctua.geneontology.org/editor/graph/gomodel:" ], [ sh:prefix "go.resource" ; sh:namespace "https://bioregistry.io/metaregistry/go/" ], @@ -916,6 +919,7 @@ [ sh:prefix "gold.meta" ; sh:namespace "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=" ; sh:pattern "^Gm\d+$" ], [ sh:prefix "gomf" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], [ sh:prefix "gomfid" ; sh:namespace "http://purl.obolibrary.org/obo/GO_" ; sh:pattern "^\d{7}$" ], + [ sh:prefix "google.book" ; sh:namespace "https://books.google.com/books?id=" ], [ sh:prefix "google.patent" ; sh:namespace "https://www.google.com/patents/" ; sh:pattern "^[A-Z]{2,4}\d+([A-Z])?([0-9])?$" ], [ sh:prefix "gpcrdb" ; sh:namespace "https://gpcrdb.org/protein/" ; sh:pattern "^\w+$" ], [ sh:prefix "gpmdb" ; sh:namespace "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" ; sh:pattern "^GPM\d+$" ], @@ -943,6 +947,7 @@ [ sh:prefix "gxa.expt" ; sh:namespace "https://www.ebi.ac.uk/gxa/experiments/" ; sh:pattern "^[AEP]-\w{4}-\d+$" ], [ sh:prefix "gxa.gene" ; sh:namespace "https://www.ebi.ac.uk/gxa/genes/" ; sh:pattern "^\w+$" ], [ sh:prefix "hamap" ; sh:namespace "https://hamap.expasy.org/unirule/" ; sh:pattern "^MF_\d+$" ], + [ sh:prefix "hathitrust" ; sh:namespace "https://catalog.hathitrust.org/Record/" ; sh:pattern "^\d+$" ], [ sh:prefix "hcvdb" ; sh:namespace "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=" ; sh:pattern "^M\d{5}$" ], [ sh:prefix "hdr" ; sh:namespace "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=" ; sh:pattern "^\d+$" ], [ sh:prefix "hgmd" ; sh:namespace "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=" ; sh:pattern "^[A-Z_0-9]+$" ], @@ -1053,6 +1058,7 @@ [ sh:prefix "kegg_genomes" ; sh:namespace "http://www.kegg.jp/entry/" ; sh:pattern "^(T0\d+|\w{3,5})$" ], [ sh:prefix "kisao" ; sh:namespace "http://purl.obolibrary.org/obo/KISAO_" ; sh:pattern "^\d+$" ], [ sh:prefix "knapsack" ; sh:namespace "http://www.knapsackfamily.com/knapsack_core/information.php?word=" ; sh:pattern "^C\d{8}$" ], + [ sh:prefix "langual" ; sh:namespace "https://www.langual.org/langual_thesaurus.asp?termid=" ; sh:pattern "^B\d+$" ], [ sh:prefix "lei" ; sh:namespace "https://www.gleif.org/lei/" ; sh:pattern "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$" ], [ sh:prefix "lgai.cede" ; sh:namespace "https://s3.us-east-2.amazonaws.com/lg.cede/" ; sh:pattern "^LGCEDe-S-\d{9}$" ], [ sh:prefix "licebase" ; sh:namespace "https://licebase.org/?q=" ; sh:pattern "^[A-Za-z0-9\-\/]+$" ], @@ -1066,6 +1072,7 @@ [ sh:prefix "lincs.protein" ; sh:namespace "https://lincs.hms.harvard.edu/db/proteins/" ; sh:pattern "^\d+$" ], [ sh:prefix "lincs.smallmolecule" ; sh:namespace "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/" ; sh:pattern "^LSM-\d+$" ], [ sh:prefix "linguist" ; sh:namespace "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#" ; sh:pattern "^[a-zA-Z0-9 +#'*]+$" ], + [ sh:prefix "linkml" ; sh:namespace "https://w3id.org/linkml/" ], [ sh:prefix "lipidbank" ; sh:namespace "http://lipidbank.jp/cgi-bin/detail.cgi?id=" ; sh:pattern "^\w+\d+$" ], [ sh:prefix "lipidmaps" ; sh:namespace "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=" ; sh:pattern "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$" ], [ sh:prefix "loinc" ; sh:namespace "https://loinc.org/" ], @@ -1287,6 +1294,7 @@ [ sh:prefix "pharmgkb.pathways" ; sh:namespace "http://www.pharmgkb.org/pathway/" ; sh:pattern "^PA\d+$" ], [ sh:prefix "phenolexplorer" ; sh:namespace "http://phenol-explorer.eu/foods/" ; sh:pattern "^\d+$" ], [ sh:prefix "phenx" ; sh:namespace "https://www.phenxtoolkit.org/protocols/view/" ; sh:pattern "^\d+$" ], + [ sh:prefix "phenxtoolkit" ; sh:namespace "https://www.phenxtoolkit.org/protocols/view/" ; sh:pattern "^\d+$" ], [ sh:prefix "phosphosite.protein" ; sh:namespace "http://www.phosphosite.org/proteinAction.do?id=" ; sh:pattern "^\d{5}$" ], [ sh:prefix "phosphosite.residue" ; sh:namespace "http://www.phosphosite.org/siteAction.do?id=" ; sh:pattern "^\d+$" ], [ sh:prefix "phylomedb" ; sh:namespace "http://phylomedb.org/?seqid=" ; sh:pattern "^\w+$" ], @@ -1449,6 +1457,7 @@ [ sh:prefix "tgn" ; sh:namespace "http://vocab.getty.edu/page/tgn/" ; sh:pattern "^\d+$" ], [ sh:prefix "thermofisher" ; sh:namespace "https://www.thermofisher.com/antibody/product/" ], [ sh:prefix "tigrfam" ; sh:namespace "https://www.ncbi.nlm.nih.gov/cdd?term=" ; sh:pattern "^TIGR\d+$" ], + [ sh:prefix "time" ; sh:namespace "http://www.w3.org/2006/time#" ], [ sh:prefix "tngb" ; sh:namespace "http://biobanknetwork.telethon.it/Sample/View?sampleId=" ; sh:pattern "^\d+$" ], [ sh:prefix "tol" ; sh:namespace "http://tolweb.org/" ; sh:pattern "^\d+$" ], [ sh:prefix "tol.webproj" ; sh:namespace "http://tolweb.org/" ; sh:pattern "^\d+$" ], diff --git a/exports/rdf/bioregistry.jsonld b/exports/rdf/bioregistry.jsonld index 989839fcd..2b62676b9 100644 --- a/exports/rdf/bioregistry.jsonld +++ b/exports/rdf/bioregistry.jsonld @@ -42,45208 +42,38662 @@ }, "@graph": [ { - "@id": 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This collection refers to growth stage ontology information in Gramene.", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Gramene Growth Stage Ontology" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "@id": "https://www.re3data.org/repository/r3d100010650" + }, { - "@id": "https://bioregistry.io/metaregistry/n2t/gramene.growthstage" + "@id": "https://prefixcommons.org/?q=ncbigene" }, { - "@id": "https://registry.identifiers.org/registry/gramene.growthstage" + "@id": "http://edamontology.org/data_1027" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/GRAMENE.GROWTHSTAGE" + "@id": "https://bioregistry.io/metaregistry/n2t/ncbigene" + }, + { + "@id": "https://bioregistry.io/metaregistry/biocontext/NCBIGene" + }, + { + "@id": "https://registry.identifiers.org/registry/ncbigene" + }, + { + "@id": "https://www.wikidata.org/wiki/Property:P351" + }, + { + "@id": "https://bioregistry.io/metaregistry/ncbi/GeneID" + }, + { + "@id": "https://fairsharing.org/FAIRsharing.5h3maw" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://www.gramene.org/", - "https://bioregistry.io/schema/#0000005": "0007133", - "https://bioregistry.io/schema/#0000006": "http://www.gramene.org/db/ontology/search?id=GRO:$1", - "https://bioregistry.io/schema/#0000008": "^\\d{7}$", + "http://xmlns.com/foaf/0.1/homepage": "https://www.ncbi.nlm.nih.gov/gene", + "https://bioregistry.io/schema/#0000005": "100010", + "https://bioregistry.io/schema/#0000006": "https://www.ncbi.nlm.nih.gov/gene/$1", + "https://bioregistry.io/schema/#0000008": "^\\d+$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioportal.bioontology.org/ontologies/RGD", + "@id": "http://aber-owl.net/ontology/GEO", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" + "@id": "https://bioregistry.io/metaregistry/aberowl" } }, { - "@id": "https://www.uniprot.org/database/DB-GeneDB", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/uniprot" + "@id": "https://orcid.org/0000-0002-2265-5572", + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "Michael Y Galperin" } }, { - "@id": "https://registry.identifiers.org/registry/ped.ensemble", + "@id": "https://registry.identifiers.org/registry/hssp", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/miriam" } }, { - "@id": "https://bioregistry.io/metaregistry/n2t/umbbd.compound", + "@id": "https://bioregistry.io/metaregistry/n2t/inchikey", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/n2t" } }, { - "@id": "https://bioportal.bioontology.org/ontologies/REPRODUCE-ME", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://prefixcommons.org/?q=propreo", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" - } - }, - { - "@id": "http://aber-owl.net/ontology/MIRO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/aberowl" - } - }, - { - "@id": "https://bioregistry.io/registry/mirbase", + "@id": "https://bioregistry.io/registry/obcs", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).", + "http://purl.org/dc/elements/1.1/description": "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. 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This collection references mouse.", + "http://purl.org/dc/elements/1.1/description": "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "FuncBase Mouse" + "@value": "BDGP insertion DB" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://registry.identifiers.org/registry/funcbase.mouse" + "@id": "https://bioregistry.io/metaregistry/biocontext/BDGP.INSERTION" }, { - "@id": "https://bioregistry.io/metaregistry/n2t/funcbase.mouse" + "@id": "https://registry.identifiers.org/registry/bdgp.insertion" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/FUNCBASE.MOUSE" + "@id": "https://bioregistry.io/metaregistry/n2t/bdgp.insertion" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://func.mshri.on.ca/mouse/", - "https://bioregistry.io/schema/#0000005": "1351341", - "https://bioregistry.io/schema/#0000006": "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1", - "https://bioregistry.io/schema/#0000008": "^\\d+$", + "http://xmlns.com/foaf/0.1/homepage": "http://flypush.imgen.bcm.tmc.edu/pscreen/", + "https://bioregistry.io/schema/#0000005": "KG09531", + "https://bioregistry.io/schema/#0000006": "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1", + "https://bioregistry.io/schema/#0000008": "^\\w+$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioregistry.io/registry/signaling-gateway", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.", + "@id": "https://registry.identifiers.org/registry/mycobank", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Signaling Gateway" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "@id": "https://bioregistry.io/metaregistry/miriam" + } + }, + { + "@id": "https://bioregistry.io/registry/cath.superfamily", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification.", + "http://purl.org/dc/terms/isPartOf": [ { - "@id": "https://registry.identifiers.org/registry/signaling-gateway" + "@id": "https://bioregistry.io/registry/cath" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/SIGNALING-GATEWAY" + "@id": "https://bioregistry.io/metaregistry/bioregistry" + } + ], + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "CATH superfamily" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "https://bioregistry.io/metaregistry/biocontext/CATH.SUPERFAMILY" }, { - "@id": "https://prefixcommons.org/?q=signaling-gateway" + "@id": "https://registry.identifiers.org/registry/cath.superfamily" }, { - "@id": "https://bioregistry.io/metaregistry/n2t/signaling-gateway" + "@id": "https://bioregistry.io/metaregistry/n2t/cath.superfamily" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://www.signaling-gateway.org/molecule", - "https://bioregistry.io/schema/#0000005": "A001094", - "https://bioregistry.io/schema/#0000006": "http://www.signaling-gateway.org/molecule/query?afcsid=$1", - "https://bioregistry.io/schema/#0000008": "^A\\d{6}$", + "http://xmlns.com/foaf/0.1/homepage": "http://www.cathdb.info/", + "https://bioregistry.io/schema/#0000005": "1.10.10.200", + "https://bioregistry.io/schema/#0000006": "http://www.cathdb.info/cathnode/$1", + "https://bioregistry.io/schema/#0000008": "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioportal.bioontology.org/ontologies/OGMS", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://www.ebi.ac.uk/ols/ontologies/cdno", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/ols" - } - }, - { - "@id": "https://www.uniprot.org/database/DB-PRIDE", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/uniprot" - } - }, - { - "@id": "https://prefixcommons.org/?q=icd", + "@id": "https://bioregistry.io/metaregistry/n2t/gold.genome", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" + "@id": "https://bioregistry.io/metaregistry/n2t" } }, { - "@id": "https://registry.identifiers.org/registry/umbbd.reaction", + "@id": "https://bioregistry.io/registry/pharmgkb.drug", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. 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This collection references yeast.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Rat Genome Database qTL" + "@value": "FuncBase Yeast" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://bioregistry.io/metaregistry/n2t/rgd.qtl" + "@id": "https://bioregistry.io/metaregistry/n2t/funcbase.yeast" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/RGD.QTL" + "@id": "https://bioregistry.io/metaregistry/biocontext/FUNCBASE.YEAST" }, { - "@id": "https://registry.identifiers.org/registry/rgd.qtl" + "@id": "https://registry.identifiers.org/registry/funcbase.yeast" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://rgd.mcw.edu/", - "https://bioregistry.io/schema/#0000005": "1354581", - "https://bioregistry.io/schema/#0000006": "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1", + "http://xmlns.com/foaf/0.1/homepage": "http://func.mshri.on.ca/yeast", + "https://bioregistry.io/schema/#0000005": "2701", + "https://bioregistry.io/schema/#0000006": "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1", "https://bioregistry.io/schema/#0000008": "^\\d+$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioregistry.io/metaregistry/n2t/dictybase.est", + "@id": "https://fairsharing.org/FAIRsharing.b2979t", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" + "@id": "https://bioregistry.io/metaregistry/fairsharing" } }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/pav", + "@id": "https://www.ebi.ac.uk/ols/ontologies/mfomd", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" + "@id": "https://bioregistry.io/metaregistry/ols" } }, { - "@id": "http://www.ontobee.org/ontology/FOVT", + "@id": "https://bioregistry.io/metaregistry/go/RNAmods", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/ontobee" + "@id": "https://bioregistry.io/metaregistry/go" } }, { - "@id": "https://bioregistry.io/registry/cath.domain", + "@id": "https://registry.identifiers.org/registry/signor", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/miriam" + } + }, + { + "@id": "https://bioregistry.io/registry/noncodev3", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains.", + "http://purl.org/dc/elements/1.1/description": "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "CATH domain" + "@value": "NONCODE v3" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://bioregistry.io/metaregistry/n2t/cath.domain" - }, - { - "@id": "http://edamontology.org/data_1040" + "@id": "https://registry.identifiers.org/registry/noncodev3" }, { - "@id": "https://registry.identifiers.org/registry/cath.domain" + "@id": "https://bioregistry.io/metaregistry/biocontext/NONCODEV3" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/CATH.DOMAIN" + "@id": "https://bioregistry.io/metaregistry/n2t/noncodev3" } ], - "http://xmlns.com/foaf/0.1/homepage": "http://www.cathdb.info/", - "https://bioregistry.io/schema/#0000005": "1cukA01", - "https://bioregistry.io/schema/#0000006": "http://www.cathdb.info/domain/$1", - "https://bioregistry.io/schema/#0000008": "^\\w+$", + "http://xmlns.com/foaf/0.1/homepage": "http://www.noncode.org/", + "https://bioregistry.io/schema/#0000005": "377550", + "https://bioregistry.io/schema/#0000006": "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1", + "https://bioregistry.io/schema/#0000008": "^\\d+$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://bioregistry.io/metaregistry/n2t/cst", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" - } - }, - { - "@id": "http://www.obofoundry.org/ontology/fao", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/obofoundry" - } - }, - { - "@id": "https://fairsharing.org/FAIRsharing.9vtwjs", + "@id": "https://bioregistry.io/metaregistry/go/CASSPC", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/go" } }, { @@ -45253,1018 +38707,1054 @@ } }, { - "@id": "https://prefixcommons.org/?q=swo", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" - } - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/XCO", + "@id": "https://www.re3data.org/repository/r3d100010539", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" + "@id": "https://bioregistry.io/metaregistry/re3data" } }, { - "@id": "https://bioregistry.io/registry/phenx", + "@id": "https://bioregistry.io/registry/eol", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "A Web-based catalog of recommended measurement protocols", + "http://purl.org/dc/elements/1.1/description": "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "PhenX Toolkit" + "@value": "Environment Ontology for Livestock" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "https://fairsharing.org/FAIRsharing.y5jcwa" + "@id": "https://fairsharing.org/FAIRsharing.w7bw2y" }, { - "@id": "https://bioportal.bioontology.org/ontologies/PHENX" + "@id": "https://bioportal.bioontology.org/ontologies/EOL" }, { - "@id": "http://aber-owl.net/ontology/PHENX" + "@id": "http://aber-owl.net/ontology/EOL" + }, + { + "@id": "http://agroportal.lirmm.fr/ontologies/EOL" + }, + { + "@id": "https://www.re3data.org/repository/r3d100011663" + }, + { + "@id": "https://www.ebi.ac.uk/ols/ontologies/eol" } ], - "http://xmlns.com/foaf/0.1/homepage": "https://www.phenxtoolkit.org/", - "https://bioregistry.io/schema/#0000005": "130502", - "https://bioregistry.io/schema/#0000006": "https://www.phenxtoolkit.org/protocols/view/$1", - "https://bioregistry.io/schema/#0000008": "^\\d+$", + "http://xmlns.com/foaf/0.1/homepage": "http://www.atol-ontology.com", + "https://bioregistry.io/schema/#0000005": "0001927", + "https://bioregistry.io/schema/#0000008": "^\\d{7}$", "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://prefixcommons.org/?q=genetree", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" + "@id": "https://bioregistry.io/registry/fbsp", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.", + "http://purl.org/dc/terms/isPartOf": [ + { + "@id": "https://bioregistry.io/registry/flybase" + }, + { + "@id": "https://bioregistry.io/metaregistry/bioregistry" + } + ], + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "Fly taxonomy" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "https://bioportal.bioontology.org/ontologies/FB-SP" + }, + { + "@id": "https://bioregistry.io/metaregistry/biocontext/FBSP" + }, + { + "@id": "http://aber-owl.net/ontology/FB-SP" + }, + { + "@id": "http://www.obofoundry.org/ontology/fbsp" + } + ], + "http://xmlns.com/foaf/0.1/homepage": "http://www.flybase.org/", + "https://bioregistry.io/schema/#0000005": "00000000", + "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/FBSP_$1", + "https://bioregistry.io/schema/#0000008": "^\\d{8}$", + "https://bioregistry.io/schema/#0000012": true, + "https://bioregistry.io/schema/#0000019": { + "@id": "https://orcid.org/0000-0002-1373-1705" } }, { - "@id": "https://bioregistry.io/registry/go.model", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/elements/1.1/description": "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. 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It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions.", + "http://purl.org/dc/elements/1.1/description": "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. 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Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. 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"@id": "https://registry.identifiers.org/registry/cath.superfamily" + "@id": "https://registry.identifiers.org/registry/storedb" }, { - "@id": "https://registry.identifiers.org/registry/combine.specifications" + "@id": "https://registry.identifiers.org/registry/compulyeast" }, { - "@id": "https://registry.identifiers.org/registry/napp" + "@id": "https://registry.identifiers.org/registry/protonet.cluster" }, { - "@id": "https://registry.identifiers.org/registry/tair.locus" + "@id": "https://registry.identifiers.org/registry/oryzabase.stage" }, { - "@id": "https://registry.identifiers.org/registry/funderregistry" + "@id": "https://registry.identifiers.org/registry/dashr.expression" }, { - "@id": "https://registry.identifiers.org/registry/hgnc.symbol" + "@id": "https://registry.identifiers.org/registry/panther.pathway" }, { - "@id": "https://registry.identifiers.org/registry/ctd.chemical" + "@id": "https://registry.identifiers.org/registry/wikipedia.en" }, { - "@id": "https://registry.identifiers.org/registry/hpa" + "@id": "https://registry.identifiers.org/registry/go_ref" }, { - "@id": "https://registry.identifiers.org/registry/narcis" + "@id": "https://registry.identifiers.org/registry/cst.ab" }, { - "@id": "https://registry.identifiers.org/registry/smart" + "@id": "https://registry.identifiers.org/registry/ricenetdb.mirna" }, { - "@id": "https://registry.identifiers.org/registry/ndc" + "@id": "https://registry.identifiers.org/registry/ttd.target" }, { - "@id": "https://registry.identifiers.org/registry/polbase" + "@id": "https://registry.identifiers.org/registry/aop.stressor" }, { - "@id": "https://registry.identifiers.org/registry/cdd" + "@id": "https://registry.identifiers.org/registry/glida.ligand" }, { - "@id": "https://registry.identifiers.org/registry/wormpep" + "@id": "https://registry.identifiers.org/registry/vfdb.gene" }, { - "@id": "https://registry.identifiers.org/registry/dictybase.est" + "@id": "https://registry.identifiers.org/registry/tair.protein" }, { - "@id": "https://registry.identifiers.org/registry/nextdb" + "@id": "https://registry.identifiers.org/registry/panther.node" }, { - "@id": "https://registry.identifiers.org/registry/aspgd.locus" + "@id": "https://registry.identifiers.org/registry/biomodels.db" }, { - "@id": "https://registry.identifiers.org/registry/mgnify.samp" + "@id": "https://registry.identifiers.org/registry/odam" }, { - "@id": "https://registry.identifiers.org/registry/pubchem.substance" + "@id": "https://registry.identifiers.org/registry/occ" }, { - "@id": "https://registry.identifiers.org/registry/cldb" + "@id": "https://registry.identifiers.org/registry/cadsr" }, { - "@id": "https://registry.identifiers.org/registry/arrayexpress" + "@id": "https://registry.identifiers.org/registry/rebase" }, { - "@id": "https://registry.identifiers.org/registry/paleodb" + "@id": "https://registry.identifiers.org/registry/oma.protein" }, { - "@id": "https://registry.identifiers.org/registry/zfin" + "@id": "https://registry.identifiers.org/registry/sasbdb" }, { - "@id": "https://registry.identifiers.org/registry/mmp.db" + "@id": "https://registry.identifiers.org/registry/cldb" }, { - "@id": "https://registry.identifiers.org/registry/vbase2" + "@id": "https://registry.identifiers.org/registry/mgnify.samp" }, { - "@id": "https://registry.identifiers.org/registry/prodom" + "@id": "https://registry.identifiers.org/registry/ga4ghdos" }, { - "@id": "https://registry.identifiers.org/registry/chembl" + "@id": "https://registry.identifiers.org/registry/uniparc" }, { - "@id": "https://registry.identifiers.org/registry/umbbd.rule" + "@id": "https://registry.identifiers.org/registry/agricola" }, { - "@id": "https://registry.identifiers.org/registry/mobidb" + "@id": "https://registry.identifiers.org/registry/bioproject" }, { - "@id": "https://registry.identifiers.org/registry/microscope" + "@id": "https://registry.identifiers.org/registry/mdm" }, { - "@id": "https://registry.identifiers.org/registry/biostudies" + "@id": "https://registry.identifiers.org/registry/ccds" }, { - "@id": "https://registry.identifiers.org/registry/affy.probeset" + "@id": "https://registry.identifiers.org/registry/facebase" }, { - "@id": "https://registry.identifiers.org/registry/pathwaycommons" + "@id": "https://registry.identifiers.org/registry/ncit" }, { - "@id": "https://registry.identifiers.org/registry/envo" + "@id": "https://registry.identifiers.org/registry/topdb" }, { - "@id": "https://registry.identifiers.org/registry/sgn" + "@id": "https://registry.identifiers.org/registry/sbo" }, { - "@id": "https://registry.identifiers.org/registry/pharmgkb.gene" + "@id": "https://registry.identifiers.org/registry/umbbd.pathway" }, { - "@id": "https://registry.identifiers.org/registry/lgic" + "@id": "https://registry.identifiers.org/registry/mmrrc" }, { - "@id": "https://registry.identifiers.org/registry/ma" + "@id": "https://registry.identifiers.org/registry/ensembl.bacteria" }, { - "@id": "https://registry.identifiers.org/registry/goa" + "@id": "https://registry.identifiers.org/registry/gtex" }, { - "@id": "https://registry.identifiers.org/registry/encode" + "@id": "https://registry.identifiers.org/registry/mipmod" }, { - 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"@id": "https://registry.identifiers.org/registry/vectorbase" + "@id": "https://registry.identifiers.org/registry/p3db.protein" }, { - "@id": "https://registry.identifiers.org/registry/supfam" + "@id": "https://registry.identifiers.org/registry/ena.embl" }, { - "@id": "https://registry.identifiers.org/registry/oci" + "@id": "https://registry.identifiers.org/registry/pride" }, { - "@id": "https://registry.identifiers.org/registry/kegg.metagenome" + "@id": "https://registry.identifiers.org/registry/efo" }, { - "@id": "https://registry.identifiers.org/registry/crisprdb" + "@id": "https://registry.identifiers.org/registry/chembl.target" }, { - "@id": "https://registry.identifiers.org/registry/apd" + "@id": "https://registry.identifiers.org/registry/jstor" }, { - "@id": "https://registry.identifiers.org/registry/ilx" + "@id": "https://registry.identifiers.org/registry/pseudomonas" }, { - "@id": "https://registry.identifiers.org/registry/intact.molecule" + "@id": "https://registry.identifiers.org/registry/signaling-gateway" }, { - 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"@id": "https://registry.identifiers.org/registry/oryzabase.reference" + "@id": "https://registry.identifiers.org/registry/matrixdb.association" }, { - "@id": "https://registry.identifiers.org/registry/gdsc" + "@id": "https://registry.identifiers.org/registry/nbrc" }, { - "@id": "https://registry.identifiers.org/registry/psipar" + "@id": "https://registry.identifiers.org/registry/seed.compound" }, { - "@id": "https://registry.identifiers.org/registry/snp2tfbs" + "@id": "https://registry.identifiers.org/registry/wb.rnai" }, { - "@id": "https://registry.identifiers.org/registry/charprot" + "@id": "https://registry.identifiers.org/registry/biosample" }, { - "@id": "https://registry.identifiers.org/registry/ttd.drug" + "@id": "https://registry.identifiers.org/registry/ensembl.metazoa" }, { - "@id": "https://registry.identifiers.org/registry/re3data" + "@id": "https://registry.identifiers.org/registry/dg.5b0d" }, { - "@id": "https://registry.identifiers.org/registry/glytoucan" + "@id": "https://registry.identifiers.org/registry/gcst" }, { - "@id": "https://registry.identifiers.org/registry/jcggdb" + "@id": "https://registry.identifiers.org/registry/atcvet" }, { - "@id": "https://registry.identifiers.org/registry/ena.embl" + "@id": "https://registry.identifiers.org/registry/rgd.qtl" }, { - "@id": "https://registry.identifiers.org/registry/atfdb.family" + "@id": "https://registry.identifiers.org/registry/pharmgkb.gene" }, { - "@id": "https://registry.identifiers.org/registry/storedb" + "@id": "https://registry.identifiers.org/registry/mpid" }, { - "@id": "https://registry.identifiers.org/registry/orphanet" + "@id": "https://registry.identifiers.org/registry/begdb" }, { - "@id": "https://registry.identifiers.org/registry/ctd.gene" + "@id": "https://registry.identifiers.org/registry/paxdb.organism" }, { - "@id": "https://registry.identifiers.org/registry/pgx" + "@id": "https://registry.identifiers.org/registry/worms" }, { - "@id": "https://registry.identifiers.org/registry/t3db" + "@id": "https://registry.identifiers.org/registry/planttfdb" }, { - "@id": "https://registry.identifiers.org/registry/ricegap" + "@id": "https://registry.identifiers.org/registry/neurovault.collection" }, { - "@id": "https://registry.identifiers.org/registry/ecyano.entity" + "@id": "https://registry.identifiers.org/registry/phytozome.locus" }, { - "@id": "https://registry.identifiers.org/registry/jaxmice" + "@id": "https://registry.identifiers.org/registry/mo" }, { - "@id": "https://registry.identifiers.org/registry/edam" + "@id": "https://registry.identifiers.org/registry/hgnc.symbol" }, { - "@id": "https://registry.identifiers.org/registry/autdb" + "@id": "https://registry.identifiers.org/registry/dip" }, { - "@id": "https://registry.identifiers.org/registry/uniparc" + "@id": "https://registry.identifiers.org/registry/chembl.compound" }, { - "@id": "https://registry.identifiers.org/registry/sabiork.compound" + "@id": "https://registry.identifiers.org/registry/taxonomy" }, { - "@id": "https://registry.identifiers.org/registry/cas" + "@id": "https://registry.identifiers.org/registry/viralzone" }, { - 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"http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://www.wikidata.org/wiki/Property:P7963", + "@id": "https://bioregistry.io/registry/cosmic", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes.", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/wikidata" - } + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "COSMIC Gene" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "http://edamontology.org/data_3264" + }, + { + "@id": "https://bioregistry.io/metaregistry/n2t/cosmic" + }, + { + "@id": "https://registry.identifiers.org/registry/cosmic" + }, + { + "@id": "https://bioregistry.io/metaregistry/cellosaurus/Cosmic" + }, + { + "@id": "https://bioregistry.io/metaregistry/biocontext/COSMIC" + }, + { + "@id": "https://fairsharing.org/FAIRsharing.s5zmbp" + } + ], + "http://xmlns.com/foaf/0.1/homepage": "http://cancer.sanger.ac.uk/cosmic/", + "https://bioregistry.io/schema/#0000005": "BRAF", + "https://bioregistry.io/schema/#0000006": "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1", + "https://bioregistry.io/schema/#0000008": "^[A-Z0-9]+$", + "https://bioregistry.io/schema/#0000012": false }, { - "@id": "https://registry.identifiers.org/registry/pubchem.bioassay", + "@id": "https://prefixcommons.org/?q=vt", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" + "@id": "https://bioregistry.io/metaregistry/prefixcommons" } }, { - "@id": "https://bioportal.bioontology.org/ontologies/AGRO", + "@id": "https://fairsharing.org/FAIRsharing.5701h1", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" + "@id": "https://bioregistry.io/metaregistry/fairsharing" } }, { - "@id": "https://bioregistry.io/metaregistry/n2t/broad", + "@id": "https://bioregistry.io/registry/nmdc", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/elements/1.1/description": "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem.", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "National Microbiome Data Collaborative" + }, + "http://www.w3.org/2004/02/skos/core#exactMatch": { + "@id": "https://registry.identifiers.org/registry/nmdc" + }, + "http://xmlns.com/foaf/0.1/homepage": "https://microbiomedata.org/", + "https://bioregistry.io/schema/#0000005": "y3ax-8bq3-60", + "https://bioregistry.io/schema/#0000006": "https://drs.microbiomedata.org/objects/$1", + "https://bioregistry.io/schema/#0000008": "^[\\w\\-.]{3,}$", + "https://bioregistry.io/schema/#0000012": false, + "https://bioregistry.io/schema/#0000019": { + "@id": "https://orcid.org/0000-0002-8424-0604" + }, + "https://bioregistry.io/schema/#0000021": { + "@id": "https://orcid.org/0000-0003-4423-4370" } } ] diff --git a/exports/rdf/bioregistry.nt b/exports/rdf/bioregistry.nt index 4263a054b..0f3a3ae19 100644 --- a/exports/rdf/bioregistry.nt +++ b/exports/rdf/bioregistry.nt @@ -1,32275 +1,32353 @@ - "false"^^ . - . - . - "None"^^ . - . - . - . - . - . - . - . - . - "http://www.pharmgkb.org/"^^ . - "0001011"^^ . - . - "GlyTouCan" . - . - "Yongqun Oliver He" . - "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . - . - . - . - . - "false"^^ . - . - "https://github.com/information-artifact-ontology/IAO/"^^ . - . - . - . - "Orthology Ontology" . - "Core Ontology for Biology and Biomedicine" . - . - "2639"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - . - . - . - . - . - . - . - . - . - . - "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . - . - "Rahuman Sheriff" . - . - . - "Rebecca Jackson" . - . - . - . - . - "408"^^ . - "true"^^ . - . - . - . - "false"^^ . - . - . - . - "https://github.com/evidenceontology/evidenceontology/"^^ . - "^\\d+$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . - . - . - "^\\d+$"^^ . - . - "http://purl.org/cerif/frapo/$1"^^ . - "Selventa legacy complex namespace used with the Biological Expression Language"^^ . - . - . - . - . - . - . - . - . - . - "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . - . - "http://www.antirrhinum.net/"^^ . - "false"^^ . - . - . - . - "C. elegans Small Molecule Identifier Database" . - "PeptideAtlas" . - . - . - . - . - "false"^^ . - "T039"^^ . - "Selventa Chemicals" . - . - . - . - . - "https://glytoucan.org"^^ . - . - "Collection" . - "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . - . - . - "http://www.sparontologies.net/ontologies/c4o"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . - . - "^IID\\d+$"^^ . - . - "^[A-Za-z_0-9]+$"^^ . - "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . - . - . - . - "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . - "1038233"^^ . - "PlasmoDB" . - . - . - . - "ACHN"^^ . - . - "Groundnut ontology" . - . - . - "^DDInter\\d+$"^^ . - "https://purl.obolibrary.org/obo/ohd/home"^^ . - . - "false"^^ . - "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - "http://www.hprd.org/"^^ . - . - . - . - . - "GT10"^^ . - . - . - . - . - . - . - . - . - . + . + . + "false"^^ . + . + . + "IRD Segment Sequence" . + . + . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . . - . - "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . - . - . - . - "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . - "Studies in dbVar."^^ . - . - . - . - . - "Selventa Families" . - "false"^^ . - "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . - "Cu.me.I1"^^ . - . - "3532759"^^ . - "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . - . - "false"^^ . - "Terminology of Anatomy of Human Histology" . - "false"^^ . - "^(Q|P)\\d+$"^^ . - . - . - . - . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/BSPO_$1"^^ . - "https://commonchemistry.cas.org/"^^ . - "^\\d{7}$"^^ . - . - . - "https://www.biorxiv.org/content/10.1101/$1"^^ . - . - . - . - "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . - . - "Michael Witt" . - "119514"^^ . - . - . - . - . - "Anatomical Therapeutic Chemical Vetinary" . - . - . - . - "C. elegans Gross Anatomy Ontology" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "GeoNames" . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Pseudomonas Genome Database" . - . - . - . - . - . - . - "Sickle Cell Disease Ontology" . - . - . - "https://cropontology.org/ontology/CO_345/Brachiaria"^^ . - "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . - "false"^^ . - "Chemistry resources"^^ . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - "National Center for Advancing Translation Sciences BioPlanet" . - . - "false"^^ . - "AC119"^^ . - . - "https://gnome.glyomics.org/"^^ . - "Porifera Ontology" . - . - . - . - . - "Developmental stages of the Zebrafish"^^ . - . - "https://plants.ensembl.org/id/$1"^^ . - . - "000009"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "ProteomicsDB Protein" . - . - . - . - . - . - . - . - . - . - "0174" . - . - . - "Banco de Celulas do Rio de Janeiro" . - . - . - "^\\w+$"^^ . - . - . - "https://sitem.herts.ac.uk/aeru/ppdb/"^^ . - . - . - "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . - . - . - "http://uberon.org"^^ . - . - . - . - . - . - "http://omit.cis.usouthal.edu/"^^ . - "001"^^ . - . - . - . - . - "https://www.metanetx.org/"^^ . - . - "http://purl.obolibrary.org/obo/GNO_$1"^^ . - . - . - "FBtr0084214"^^ . - "https://github.com/bio-ontology-research-group/unit-ontology"^^ . - . - . - . - . - . - . - "0002502"^^ . - . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . - "Tom Gillespie" . - . - "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . - . - . - . - . - . - . - . - "1.10.8.10"^^ . - "false"^^ . - "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - "Electron Microscopy Data Bank" . - . - . - "https://github.com/OpenLHS/CVDO"^^ . - "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . - . - . - "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^ . - . - . - "https://www.vmh.life/#gene/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . - . - . - . - . - . - . - "^[A-Z-_0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "http://sugarbind.expasy.org/$1"^^ . - . - _:N4c27bf9198f24213bf131981fa0717df . - "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . - "https://www.genedb.org/gene/$1"^^ . + . + . + . + . + . + . + "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . + . + "0376"^^ . + . + . + . + . + . + "Open Citation Identifier" . + . + . + "The coding sequence or protein identifiers as maintained in INSDC."^^ . + . + . + . + . + "LDS-1110"^^ . + "https://amzn.com/$1"^^ . + "Biological Collections Ontology" . + . + . + . + . + . + . + "^ST[0-9]{6}$"^^ . + . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . "130502"^^ . - . - . - "John Kunze" . - . - . - "^\\d{7}$"^^ . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . - . - "https://www.proteomicsdb.org/#human"^^ . - "RiceNetDB Gene" . - . - "0019171"^^ . - "http://ctdbase.org/"^^ . - . - . - "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . - . - . - . - "DASHR expression" . - . - . - . - . - "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . - . - "false"^^ . - . - "true"^^ . - . - "eagle-i resource ontology" . - . - . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . - . - . - . - . - "false"^^ . - "Alejandra Gonzalez-Beltran" . - . - . - "Drosophila Phenotype Ontology" . - . - . - . - . - "false"^^ . - . - "Kerafast cell lines" . - "https://pharmacodb.ca/cell_lines/$1"^^ . - . - . - . - "http://data.jrc.ec.europa.eu/"^^ . - . - . - "http://purl.org/spar/datacite/$1"^^ . - . - . - "0000632"^^ . - "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . - . - "000912"^^ . - . - . - . - "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . - . - "https://www.thermofisher.com/antibody/product/$1"^^ . - . - . - . - "http://www.chemspider.com/$1"^^ . - "Rosa2"^^ . - "MetaCyc Reaction" . - "the FAIR Cookbook" . - . - . - . - . - "21393"^^ . - . - . - "0000773"^^ . - . - . - "https://bio.tools/$1"^^ . - "ASPL0000349247"^^ . - . - . - . - . - "EasyChair Topic" . - . - . - . - "PicTar" . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - "Terry Hayamizu" . - . - . - . - . - . - . - . - . - . - . - "90806"^^ . - "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . - . - . - . - "false"^^ . - . - "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . - . - "https://fungidb.org/fungidb/app/record/gene/$1"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/intact/molecule/$1"^^ . - . - "https://www.metanetx.org/"^^ . - . - . - "false"^^ . - "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . - . - "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . - . - "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "http://crdd.osdd.net/servers/virsirnadb"^^ . - . - . - "false"^^ . - . - . - "65"^^ . - . - . - "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "false"^^ . - "Tom Gillespie" . - "Fyler" . - . - . - . - . - . - . - . - "false"^^ . - "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . - "http://www.gabipd.org/"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "01467"^^ . - . - "BioLegend" . - "F-SNP" . - . - "https://www.nemoarchive.org"^^ . - . - . - "http://purl.obolibrary.org/obo/HSAPDV_$1"^^ . - . - . - . - . - "15000"^^ . - "http://purl.obolibrary.org/obo/EPIO_$1"^^ . - . - . - . - . - . - "http://www.w3.org/ns/activitystreams"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . - . - . - . - . - "0000586"^^ . - "Environmental conditions, treatments and exposures ontology" . - . - . - . - . - . - . - . - . - "International Nucleotide Sequence Database Collaboration (INSDC) Run" . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . - . - . - . - . - "Symptom Ontology" . - . - . - . - . - . - . - . - "GnpIS" . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - "Python"^^ . - . - . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - . - "false"^^ . - . - "Plasmodium Life Cycle" . - . - . - . - "Virtual Fly Brain" . - "IM-19210-3"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "^\\d{6}$"^^ . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . - "http://purl.obolibrary.org/obo/TAHE_$1"^^ . - . - "http://eggnog.embl.de/version_3.0/"^^ . - . - . - "Chemical Methods Ontology" . - . - . - "false"^^ . - . - . - "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . - . - . - "http://purl.obolibrary.org/obo/CDNO_$1"^^ . - . - . - . - "http://www.signaling-gateway.org/molecule"^^ . - . - . - "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . - . - . - . - . - . - . - "An ontology of traits covering vertebrates"^^ . - . - . - . - . - . - . - "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . - "Cell line collections"^^ . - . - . - . - "8000221"^^ . - "Ensembl Bacteria" . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - . - "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . - . - . - "^\\d+$"^^ . - . - . - "https://www.datanator.info/gene/$1"^^ . - . - . - . - . - . - . - "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . - . - . - "617102"^^ . - "SABIO-RK Reaction" . - . - . - "false"^^ . - . - . - . - . - "http://microsporidiadb.org/micro/"^^ . - "http://purl.obolibrary.org/obo/PAO_$1"^^ . - "Ontology about the gross anatomy of the C. elegans"^^ . - . - "AgroPortal" . - . - . - "identifier for a scientific journal, in the UniProt database"^^ . - . - . - "false"^^ . - "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . - . - . - "2966"^^ . - . - . - . - . - . - "AY109603"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://ncim.nci.nih.gov/"^^ . - . - . - "https://github.com/obophenotype/bio-attribute-ontology"^^ . - . - . - "false"^^ . - . - "SIDER Drug" . - . - . - "http://sideeffects.embl.de/drugs/$1"^^ . - "https://www.enzolifesciences.com/$1"^^ . - "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . - . - . - . - "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . - . - . - . - "https://openalex.org/$1"^^ . - "^[0-9]+$"^^ . - . - "false"^^ . - . - "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait"^^ . - . - . - . - . - "Developing Mouse Brain Atlas" . - "^\\d+$"^^ . - . - . - . - "false"^^ . - "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"^^ . - "H-InvDb Locus" . - . - "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . - . - "^NBK\\d+$"^^ . - . - . - . - . - . - "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . - . - "090924"^^ . - . - "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. "^^ . - . - "^YMDB\\d+$"^^ . - . - . - . - . - "http://sideeffects.embl.de/"^^ . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . - "Peroxibase" . - "aap-1"^^ . - "false"^^ . - . - "false"^^ . - "Janna Hastings" . - . - . - "International Classification of Diseases, 10th Revision, Clinical Modification" . - "Phy000CLXM_RAT"^^ . - . - . - . - . - . - . - . - . - "https://www.atlassian.com/"^^ . - . - . - . - . - "DragonDB DNA" . - . - . - "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . - . - . - . - . - . - . - . - "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . - . - "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . - "^[A-Z0-9]+$"^^ . - . - "614"^^ . - . - . - _:N25fbccd5a08f4f199ab2f46ac7cbe0ab . - "HPSI0114i-bezi_1"^^ . - . - "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . - "https://fungidb.org/fungidb"^^ . - "Identifier for a species on the noaa fisheries website"^^ . - "false"^^ . - . - . - . - . - "Allen Institute Ontologies" . - . - "2.7.1.1"^^ . - . - . - . - . - . - "1"^^ . - . - "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . - . - . - "https://www.uniprot.org/"^^ . - "https://www.ebi.ac.uk/metagenomics"^^ . - . - . - . - . - . - . - "false"^^ . - . - "http://merops.sanger.ac.uk/index.htm"^^ . - . - . - . - . - . - . - . - "^\\d{4}$"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . -_:N3ebf828b73254ba1aff2e01aadd41f48 "Nathan Baker" . - . - . - . - "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182"^^ . - . - "Mathias Brochhausen" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "9606117"^^ . - . - . - . - . - "http://supfam.org/SUPERFAMILY/"^^ . - . - "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^ . - . - . - . - . - . - . - "http://variationontology.org"^^ . - . - "^[1-9]\\d{5}$"^^ . - . - . - . - . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . - . - "C12345"^^ . - . - "UDB000691"^^ . - . - "International Medical Device Regulators Forum" . - . - "CAPS-DB" . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - "2029"^^ . - "0000547"^^ . - . - . - "http://stormo.wustl.edu/ScerTF/details/$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - "SUPERFAMILY" . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . - "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . - . - . - . - "false"^^ . - . - . - . - "^[0-9]*$"^^ . - . - . - . - . - . - "Rat Genome Database qTL" . - . - . - "https://www.ebi.ac.uk/intenz/"^^ . - "Citation Counting and Context Characterisation Ontology" . - . - . - . - "http://purl.obolibrary.org/obo/SEP_$1"^^ . - . - "Genomic Epidemiology Ontology" . - . - . - "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . - . - . - . - . - "https://www.wormbase.org/db/seq/protein?name=$1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "0000685"^^ . - "https://rfam.xfam.org/"^^ . - . - . - . - . - "284196006"^^ . - . - "Health Data Research Innovation Gateway" . - . - . - . - "General Multilingual Environmental Thesaurus" . - "http://www.gramene.org/db/ontology/search?id=$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . - . - . - . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "http://elm.eu.org/"^^ . - . - "Vertebrate trait ontology" . - . - . - . - "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi"^^ . - . - "HGNC Gene Group" . - . - "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . - "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . - . - . - . - "https://www.metanetx.org/comp_info/$1"^^ . - . - "Clinical measurement ontology" . - "0000295"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . - . - . - "0001017"^^ . - "DBSALT001211"^^ . - . - "1"^^ . - . - . - "https://www.psidev.info/peff"^^ . - . - "http://purl.obolibrary.org/obo/OARCS_$1"^^ . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - . - . - . - . - . - . - "Barley ontology" . - . - . - . - "http://www.kazusa.or.jp/huge/"^^ . - . - "virsi1909"^^ . - . - . - . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - "Cellular Microscopy Phenotype Ontology" . - . - . - . - . - "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . - . - . - . - . - . - "https://metazoa.ensembl.org/id/$1"^^ . - . - . - . - . - . - "http://www.genome.ad.jp/kegg/docs/upd_ligand.html"^^ . - "https://github.com/DrugTargetOntology/DTO"^^ . - "http://purl.obolibrary.org/obo/FLU_$1"^^ . - "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . - . - "278"^^ . - . - . - . - "Antibiotic Resistance Genes Database" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . - . - "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . - . - . - "International Classification of Diseases, 10th Revision" . - "The international standard for identifying health measurements, observations, and documents."^^ . - . - . - . - "0000047"^^ . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "iRefWeb" . - "ECOLI:CYT-D-UBIOX-CPLX"^^ . - . - . - . - . - "^e\\d+$"^^ . - . - "https://www.w3.org/ns/prov"^^ . - . - . - "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . - . - . - . - . - . - . - . - "http://www.chemspider.com/"^^ . - . - "Human Cell Atlas Ontology" . - . - "0002350"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . - . - . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^ . - . - . - "^PR\\d{5}$"^^ . - . - . - "false"^^ . - . - "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . - . - "false"^^ . - . - "An ontology of human and animal behaviours and behavioural phenotypes"^^ . - . - . - "SwissLipid" . - . - "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^ . - . - . - . - . - "^SAM[NED](\\w)?\\d+$"^^ . - . - "1784"^^ . - "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . - . - . - . - . - . - . - . - . - "P3DB Site" . - "false"^^ . - . - . - . - "0000590"^^ . - . - "Chinese Biological Abstracts" . - . - . - . - . - "http://www.cba.ac.cn"^^ . - "HGNC Symbol" . - . - . - . - . - . - . - "International Standard Serial Number" . - . - . - . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - . - . -_:Ne588226fa953447e8b6d3e4cf8af70b6 "InterPro Help" . - . - "false"^^ . - "http://tritrypdb.org/tritrypdb/"^^ . - "EDAM Format" . - . - . - "false"^^ . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . - . - "Carbohydrate Active EnZYmes" . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . - . - _:N2ba76a60509f4cf5aa3ae43fc1644a26 . - . - . - "false"^^ . - . - . - . - "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut"^^ . - . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^ . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - . - . - . - "Melanoma Molecular Map Project Biomaps" . - "95-0166C6"^^ . - "MIR:00000008"^^ . - . - . - . - . - "28789"^^ . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . - . - "^\\d{7}$"^^ . - "MGnify Sample" . - . - . - . - . - . - . - "https://www.gwascentral.org/markers"^^ . - . - . - . - . - . - . - . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "prgr_human"^^ . - . - "0000001"^^ . - "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . - "false"^^ . - . - "Cell line collections"^^ . - . - . - . - . - . - . - . - "false"^^ . - "Semanticscience Integrated Ontology" . - "AADB12"^^ . - . - "^\\d{7}$"^^ . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . - . - . - "Fababean ontology" . - . - "https://caninecommons.cancer.gov/#/"^^ . - "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . - . - "false"^^ . - . - . - . - . - . - "Identifiers.org Ontology" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . - "https://www.w3.org/TR/shacl/"^^ . - "https://www.nextprot.org/"^^ . - "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . - . - "^G[0-9]{5}[A-Z]{2}$"^^ . - . - . - "Drosophila RNAi Screening Center" . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "^[A-Za-z0-9-]+$"^^ . - . - . - . - . - "http://ctdbase.org/"^^ . - "https://www.e-cyanobacterium.org/experiments-repository/"^^ . - . - "UCR00226"^^ . - . - "R00100"^^ . - . - . - "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . - "215"^^ . - . - "0000618"^^ . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - . - . - . - . - . - "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . - . - . - "^\\d+$"^^ . - . - "https://www.ada.org/publications/CDT"^^ . - "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - "^\\d{9}$"^^ . - . - . - "International Classification of Diseases, 9th Revision, Clinical Modification" . - "TriTrypDB" . - . - . - . - "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . - . - . - "http://purl.obolibrary.org/obo/PSO_$1"^^ . - "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . - "https://repeatsdb.org/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/snp/"^^ . - . - . - . - . - "NIF Standard Ontology: Subcellular Entities" . - "false"^^ . - "http://www.wikigenes.org/"^^ . - "false"^^ . - "Rice ontology" . - . - "http://drugcentral.org"^^ . - . - . - . - "false"^^ . - . - "https://www.vectorbase.org/ontology-browser"^^ . - "An ontology for dengue fever."^^ . - . - "https://github.com/SCAI-BIO/EpilepsyOntology"^^ . - . - . - "0000609"^^ . - . - "http://ddinter.scbdd.com"^^ . - . - . - . - . - . - "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . - . - . - "^\\d+$"^^ . - . - "Ontology Lookup Service" . - . - "Dataset"^^ . - "https://go.drugbank.com/salts/$1"^^ . - . - "25011"^^ . - . - . - . - . - . - "Protein Data Bank Ligand" . - "^\\d+$"^^ . - "^\\d+$"^^ . - "^\\w+$"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . - . - "false"^^ . - . - . - . - "https://www.ebi.ac.uk/chebi/"^^ . - "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^ . - . - . - "^[a-z]+(\\..*?)?$"^^ . - . - . - "CIViC Assertion" . - . - . - "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . - "^G(PL|SM|SE|DS)\\d+$"^^ . - . - "http://www.receptors.org/nucleardb/proteins/$1"^^ . - . - . - . - . - . - . - . - "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm"^^ . - . - . - . - . - . - . - . - "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . - "https://n2t.net/$1:"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . - . - . - . - "http://ecoportal.lifewatch.eu" . - "^\\d{5}$"^^ . - . - "http://purl.obolibrary.org/obo/MF_$1"^^ . - . - "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . - . - . - . - . - . - _:N17668a26737c4d38a76d229b061cfa85 . - . - . - . - . - "false"^^ . - . - . - "https://polbase.neb.com/polymerases/$1#sequences"^^ . - "false"^^ . - . - . - "http://www.hprd.org/protein/$1"^^ . - . - . - . - "0000071"^^ . - . - . - . - "Bjoern Peters" . - . - . - . - . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . - . - . - . - "http://www.e-cyanobacterium.org/bcs/entity/"^^ . - . - "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . - . - "Contains entries for various database identifiers" . - . - . - . - . - "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . - . - "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . - . - . - . - "0000021"^^ . - . - . - . - . - "101"^^ . - . - . - . - "https://www.tcdb.org"^^ . - "https://www.worldwildlife.org/biomes"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . - "false"^^ . - . - . - . - . - "The bioRxiv is a preprint server for biology"^^ . - . - . - . - . - . - . - . - . - . - . - "19803"^^ . - . - . - . - . - . - . - . - . - "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . - . - "https://horizondiscovery.com/"^^ . - . - . - . - . - . - . - "http://www.uniprot.org/keywords/"^^ . - . - "JWS Online" . - . - "10015919"^^ . - "00001234"^^ . - "The Echinoderm Anatomy and Development Ontology" . - "^[a-z_A-Z]+$"^^ . - . - "https://www.inaturalist.org/taxa"^^ . - . - . - "https://www.nextprot.org/"^^ . - . - . -_:N66ebab027c6f42a78ee5424816ee2209 "Plant Ontology Administrators" . - "https://www.cropontology.org/rdf/CO_336:$1"^^ . - . - . - . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . - "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . - . - . - "http://www.pocketome.org/files/$1.html"^^ . - . - "MultiCellDS" . - . - . - . - . - . - . - . - . - . - . - "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . - . - . - . - . - "G77500AY"^^ . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . - . - "Blue Brain Project Knowledge Graph" . - . - . - "https://asrp.danforthcenter.org/"^^ . - . - . - "https://metabolome.cgfb.u-bordeaux.fr/"^^ . - . - . - "HomoloGene" . - "Integrated Genomic Resources of human Cell Lines for Identification" . - "Sierra Moxon" . - "Datanator Reaction" . - . - . - . - "false"^^ . - "PhosphoSite Site Group" . - . - . - "false"^^ . - . - "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . - . - . - "Current Dental Terminology" . - . - . - . - "http://research.nhgri.nih.gov/apps/homeodomain/web/"^^ . - . -_:N405d8bfed2434692b307171b8d317ea8 "John Garavelli" . - . - . - . - . - . - . - . - . - "false"^^ . - . - "http://psb.kobic.re.kr/STAP/refinement/"^^ . - . - "https://www.ebi.ac.uk/gxa/"^^ . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MONDO_$1"^^ . - . - . - "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . - "Models developed with the Virtual Cell (VCell) software prorgam."^^ . - . - . - . - . - "The set of prefixes used in the Cellosaurus resource"^^ . - . - . - "Bgee gene" . - . - . - . - "Q-2958"^^ . - . - "PathBank" . - . - . - "https://github.com/ufbmi/dron"^^ . - . - "ZINC1084"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "0000060"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "https://proteinensemble.org/"^^ . - . - "https://datanator.info/"^^ . - . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - . - "Human developmental anatomy, abstract" . - . - . - . - . - . - "0045310"^^ . - . - . - . - . - . - . - "true"^^ . - "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . - "5.1"^^ . - "false"^^ . - . - . - . - "http://cgsc.biology.yale.edu/index.php"^^ . - . - . - . - . - . - . - . - . - "https://www.inaturalist.org/taxa/$1"^^ . - . - "78"^^ . - . - "Chemical Information Ontology" . - "false"^^ . - . - "http://purl.obolibrary.org/obo/BCGO_$1"^^ . - "Sorghum TDv5 - Oct 2019"^^ . - . - "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . - . - . - . - . - . - . - . - . - "70"^^ . - . - . - "false"^^ . - . - . - . - "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . - . - . - "PhylomeDB" . - . - "ToxoDB" . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . - "false"^^ . - . - "^\\d+$"^^ . - "Fission Yeast Phenotype Ontology" . - "^\\d+$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "Collembola Anatomy Ontology" . - . - . - "https://metazoa.ensembl.org/"^^ . - . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/APAONTO"^^ . - "true"^^ . - . - "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . - . - "NIF Standard Ontology: Investigations" . - . - . - . - "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . - "ACC-1"^^ . - . - . - . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/mardb/"^^ . - . - . - _:Ne13938b012994aa0ba4cf64b8ee0d5d4 . - "https://www.gwascentral.org/study/$1"^^ . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "false"^^ . - . - . - . - " http://edamontology.org" . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "https://www.merckmillipore.com/catalogue/item/$1"^^ . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/GECKO_$1"^^ . - . - . - . - "https://data.apps.fao.org/catalog/organization/agrovoc"^^ . - . - . - "https://data.4dnucleome.org/experiment-set-replicates/"^^ . - . - "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . - . - . - . - . - . - . - . - . - . - "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . - . - . - "https://www.uniprot.org/keywords/$1"^^ . - . - . - . - . - . - "http://www.bindingdb.org/compact/$1"^^ . - "https://www.ebi.ac.uk/metabolights/"^^ . - . - . - "KEGG Genome" . - . - . - . - "h_aktPathway"^^ . - "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . - . - . - . - . - . - . - . - "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . - "^\\d+$"^^ . - "false"^^ . - "00000268"^^ . - . - "0100010"^^ . - . - . - . - . - . - . - "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . - . - . - . - . - "http://stitch.embl.de/"^^ . - . - . - . - . - "Chicken Gene Nomenclature Consortium" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . - . - . - "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . - "Cephalopod Ontology" . - . - . - . - . - . - . - . - . - "false"^^ . - "http://www.pharmgkb.org/"^^ . - "http://www.w3.org/2000/01/rdf-schema#$1"^^ . - . - . - . - . - . - "false"^^ . - . - "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . - "Phenoscape Publication" . - "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . - . - . - . - . - "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . - . - "false"^^ . - . - "3G6A5W338E"^^ . - . - . - "https://www.cropontology.org/rdf/CO_327:$1"^^ . - . - . - "Agronomy Vocabulary" . - "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . - . - . - . - . - "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp"^^ . - . - . - . - . - . - "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . - . - . - "^MGYA\\d+$"^^ . - . - . - . - "PyPI" . - . - "4007166"^^ . - . - . - "SCC111"^^ . - . - "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^ . - . - . - . - . - . - . - "^EBI\\-[0-9]+$"^^ . - . - . - . - . - "STOREDB at University of Cambridge" . - "https://www.sigmaaldrich.com"^^ . - . - . - . - . - . - "Yongqunh He" . - . - . - . - . - . - "false"^^ . - . - . - "Michael Y Galperin" . - "^\\d+$"^^ . - . - . - . - . - . - "Physical Medicine and Rehabilitation" . - . - . - . - . - "ACYPI000159"^^ . - "The Drug-Drug Interactions Ontology" . - . - . - . - "^[A-Z0-9]{6,7}$"^^ . - "false"^^ . - . - . - "Protein ANalysis THrough Evolutionary Relationships Classification System" . - "^\\d{7}$"^^ . - . - . - "LG Chemical Entity Detection Dataset (LGCEDe)" . - . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . - "^[0-9]+$"^^ . - "false"^^ . - . - . - . - "Adverse Event Reporting Ontology" . - "http://tuberculist.epfl.ch/"^^ . - . - . - "^S\\w+(\\.)?\\w+(\\.)?$"^^ . - . - "VGNC:3792"^^ . - . - . - . - . - "true"^^ . - "SwissRegulon" . - "false"^^ . - . - "AntiBodies Chemically Defined database" . - . - . - "^\\w+(\\.)?\\d+$"^^ . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - . - "DRSC05221"^^ . - . - . - . - . - . - "AT4G01080"^^ . - . - "https://reporter.nih.gov/"^^ . - "false"^^ . - . - . - . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . - . - . - . - . - "https://www.arraymap.org/pgx:$1"^^ . - . - . - "0002533"^^ . - . - . - "Protein Ensemble Database" . - "http://asap.ahabs.wisc.edu/asap/home.php"^^ . - . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^DP\\d{5}r\\d{3}$"^^ . - . - "^[A-Za-z]+$"^^ . - . - . - "http://github.com/seger/aao"^^ . - . - . - "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . - . - "https://www.vectorbase.org/ontology-browser"^^ . - . - . - . - "0000079"^^ . - . - "NONCODE v4 Transcript" . - . - "http://gpmdb.thegpm.org/"^^ . - . - . - . - "InChI" . - . - "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . - . - . - . - . - . - . - . - "LRG_1"^^ . - . - . - "https://bdsc.indiana.edu/about/mission.html"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://www.mycobank.org/"^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . - . - . - "http://genex.hgu.mrc.ac.uk/"^^ . - "005012"^^ . - . - . - "http://rgd.mcw.edu/"^^ . - . - . - . - . - . - . - . - "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology."^^ . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . - "Systems Biology Ontology" . - . - "https://www.phosphosite.org"^^ . - . - . - . - . - . - "Radiomics Ontology" . - . - . - . -_:N3e9d9e745e624ceda5c54389cfbc918c "Mauno Vihinen" . - "http://www.w3.org/1999/02/22-rdf-syntax-ns"^^ . - "Golm Metabolome Database Profile" . - "http://umbbd.ethz.ch/"^^ . - . - "Research Resource Identification" . - . - "Process Chemistry Ontology" . - "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . - . - . - . - "false"^^ . - "MCDS_C_0000000001"^^ . - . - . - . - . - "frim1"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "^\\w+$"^^ . - . - . - . - . - "Psychology Ontology" . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - "https://github.com/Display-Lab/psdo"^^ . - . - "National Center for Biotechnology Information Registry" . - . - "Cereal Plant Gross Anatomy" . - . - . - . - . - "E-cyanobacterium Experimental Data" . - . - . - . - . - "false"^^ . - . - . - "12345"^^ . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - "true"^^ . - . - "http://napp.u-psud.fr/"^^ . - "P10636"^^ . - . - "1050"^^ . - "false"^^ . - "DataONE" . - . - . - . - . - . - . - . - "Tribolium Genome Database -- Insertion" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . - "A database-specific registry supporting curation in the Gene Ontology"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "Henriette Harmse" . - . - "https://nci-crdc.datacommons.io/"^^ . - "PiroplasmaDB" . - . - . - . - "fluticasone"^^ . - . - . - . - "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "https://www.genome.jp/kegg/drug/"^^ . - . - . - "false"^^ . - "Metabolomics Standards Initiative Ontology" . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "https://github.com/geneontology/go-ontology/tree/master/contrib"^^ . - . - . - "true"^^ . - "9861/3"^^ . - . - . - . - . - . - . - . - "https://www.noguchi.or.jp/"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . - . - "https://kaggle.com"^^ . - . - . - "https://licebase.org/?q=$1"^^ . - . - . - . - . - "^MI\\d{7}$"^^ . - . - . - . - "false"^^ . - "MMP3312982.2"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . - . - . - . - . - "miRBase pre-miRNA" . - "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . - "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . - . - "https://cropontology.org/ontology/CO_330/Potato"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . - . - . - . - "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . - . - . - "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . - . - . - "00073"^^ . - "051"^^ . - . - "true"^^ . - . - "https://www.ncbi.nlm.nih.gov/sra"^^ . - . - . - . - . - . - . - . - "https://www.expasy.org/prosite/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PCL_$1"^^ . - . - . - . - . - . - . - "0745-4570"^^ . - . - . - . - "CO_010" . - "Golm Metabolome Database" . - . - . - . - . - . - "^A\\d+$"^^ . - . - "^S\\d+$"^^ . - . - . - . - . - "https://github.com/rsc-ontologies/rsc-cmo"^^ . - . - "^\\d{7}$"^^ . - "HWUPKR0MPOU8FGXBT394"^^ . - "false"^^ . - "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . - . - "false"^^ . - "http://www.jcm.riken.go.jp/"^^ . - . - . - . - . - "http://www.genome.jp/dbget-bin/www_bfind?enzyme"^^ . - . - . - . - . - "Melissa Haendel" . - . - "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . - "Agilent Probe" . - "T3D0001"^^ . - . - . - . - . - . - "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "Multum MediSource Lexicon" . - . - . - . - . - . - "Documentation of the Phenoscape Curation Workflow"^^ . - . - "http://viaf.org/viaf/$1"^^ . - "5046"^^ . - . - . - . - "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt"^^ . - . - "false"^^ . - "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . - . - . - . - . - . - "true"^^ . - . - "^BE\\d{7}$"^^ . - "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . - . - . - . - . - . - . - "784"^^ . - . - "http://purl.obolibrary.org/obo/OBI_$1"^^ . - . - . - "https://www.storedb.org/"^^ . - . - . - . - . - . - . - . - "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp"^^ . - . - . - "false"^^ . - . - . - "Ximbio" . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - . - "https://web.expasy.org/cellosaurus/CVCL_$1"^^ . - . - . - . - . - . - . - . - _:N62c7e9ef269b441cb4b61f81eba4824c . - . - "false"^^ . - . - . - . - . - . - "https://gpcrdb.org/protein/$1"^^ . - . - "false"^^ . - "Antibiotic Resistance Ontology" . - . - . - "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . - . - . - . - . - . - . - . - . - "true"^^ . - "BloodPAC" . - . - "0.7-123"^^ . - "false"^^ . - "CAA71118.1"^^ . - . - . - "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - . - . - . - . - . - . - "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "IntAct protein interaction database" . - . - "https://disprot.org/"^^ . - . - "http://purl.obolibrary.org/obo/CEPH_$1"^^ . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . - . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . - . - "Feature Annotation Location Description Ontology " . - . - . - "^\\d{5}$"^^ . - . - . - "Plant Growth and Development Stage" . - . - "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . - "Pol Castellano Escuder" . - . - . - . - . - . - . - "http://www.amphibanat.org"^^ . - . - . - . - . - . - "Human Dermatological Disease Ontology" . - "false"^^ . - . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . - . - . - "sbgn.er.level-1.version-1.2"^^ . - . - . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - . - . - . - "https://www.signalingpathways.org/index.jsf"^^ . - . - . - "https://www.flymine.org/come"^^ . - . - . - "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . - . - "^RCB\\d+$"^^ . - . - . - . - . - . - "false"^^ . - "CADAFLAT00006211"^^ . - . - . - . - "PubChem Substance ID (SID)" . - . - "Kidney and Urinary Pathway Ontology" . - . - . - . - "G protein-coupled receptor database" . - "http://compluyeast2dpage.dacya.ucm.es/"^^ . - . - "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . - . - "http://aber-owl.net/ontology/$1" . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . - . - "https://cropontology.org/ontology/CO_340/Cowpea"^^ . - . - . - . - . - . - . - "https://www.orthodb.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://glygen.org/glycan/"^^ . - . - . - . - . - . - "Curation of Neurodegeneration Supporting Ontology" . - . - . - . - . - . - "Jesualdo Tomás Fernández-Breis" . - . - . - . - . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000"^^ . - . - . - . - "John Graybeal" . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_$1" . - . - "false"^^ . - "^HMDB\\d+$"^^ . - . - . - . - "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . - "Cross-linker reagents ontology" . - . - "^c\\d+$"^^ . - . - . - . - "10020.2"^^ . - "K"^^ . - "Data Object Service" . - . - . - . - . - . - "BN000065"^^ . - "Bacterial Diversity Metadatabase" . - "sov:WRfXPg8dantKVubE3HX8pw"^^ . - . - . - "Citation Typing Ontology" . - . - . - . - "https://genome.ucsc.edu/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://civicdb.org/"^^ . - . - "TTDS00056"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . - . - "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en"^^ . - . - . - "https://mmp.sfb.uit.no/databases/marcat/"^^ . - . - . - . - "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . - . - . - . - "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . - . - . - "CPX-263"^^ . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . - . - . - "false"^^ . - . - . - "KIAA0001"^^ . - . - . - "false"^^ . - "http://bioportal.bioontology.org/"^^ . - "false"^^ . - . - "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . - . - . - "The Bioregistry's meta-registry"^^ . - "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^ . - "MNXR101574"^^ . - . - . - . - "YMDB00001"^^ . - . - . - "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . - . - . - "https://www.ebi.ac.uk/biomodels/$1"^^ . - . - "PerkinElmer cell line collection" . - . - "Publons Researcher" . - "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . - . - . - . - "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . - "https://glycopost.glycosmos.org"^^ . - "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . - "false"^^ . - "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . - . - "http://www.antirrhinum.net/"^^ . - "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . - "http://www.semantic-systems-biology.org/apo"^^ . - . - . - . - . - . - . - . - . - "Protein Structural Change Database" . - "^\\d{7}$"^^ . - . - "^\\d{7}$"^^ . - "https://cropontology.org/ontology/CO_323/Barley"^^ . - "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . - . - "https://github.com/sparontologies/fabio"^^ . - . - "BioLegend is a life sciences supply vendor."^^ . - "long-finned-pilot-whale"^^ . - . - . - "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^ . - . - "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . - . - . - . - . - "false"^^ . - . - "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . - . - "RiceNetDB Protein" . - . - "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . - . - "1"^^ . - . - . - . - "provides for" . - "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "GitHub Pull Request" . - . - . - . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . - "false"^^ . - . - "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . - "^PED\\d{5}e\\d{3}$"^^ . - . - . - . - . - . - . - . - "NONHSAG00001"^^ . - "PseudoGene" . - "https://cropontology.org/ontology/CO_365/Fababean"^^ . - "false"^^ . - . - . - . - "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . - "^\\w+$"^^ . - . - "https://www.uniprot.org/database/$1"^^ . - . - "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^ . - . - "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . - . - . - . - . - "^rs\\d+$"^^ . - "http://omia.angis.org.au/"^^ . - . - . - . - . - . - "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . - . - "Reaxys" . - . - . - . - . - . - . - . - "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . - "10595"^^ . - "5fce9b7300001250"^^ . - "LOC_Os01g49190"^^ . - "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . - . - . - "The Statistical Methods Ontology" . - . - . - "SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints."^^ . - "https://www.cropontology.org/rdf/CO_340:$1"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . - "Oryzabase Strain" . - . - "Colorectal Cancer Atlas" . - . - . - "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . - . - "1000560"^^ . - . - "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto"^^ . - . - . - . - . - . - "http://www.obofoundry.org/ontology/$1" . - . - . - . - "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . - "PhenX Toolkit" . - . - "false"^^ . - . - . - . - . - . - . - . - . - "SPIKE Map" . - . - . - . - . - "https://flowrepository.org/id/$1"^^ . - "25782"^^ . - . - "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . - "^\\d+$"^^ . - . - . - . - . - "https://www.lgresearch.ai"^^ . - . - "http://doqcs.ncbs.res.in/"^^ . - . - . - . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . - . - . - . - . - "UniProt Protein" . - "An identifier for a resource or metaresource." . - . - "Ion Channel Electrophysiology Ontology" . - . - . - . - . - "E-MEXP-1712"^^ . - . - . - . - . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . - . - . - . - . - . - . - . - "ConoServer" . - "Bill Hogan" . - . - . - . - . - . - "00000443"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . - . - . - . - "TAIR Protein" . - . - . - "h2o"^^ . - . - "KEGG Module" . - . - . - "http://purl.obolibrary.org/obo/COB_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^10.\\w{4}/\\w{10}$"^^ . - "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . - . - . - . - "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . - . - . - . - . - "http://search.sisuproject.fi/#/variant/$1"^^ . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . - . - . - . - "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . - . - "https://www.rhea-db.org/"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . - . - . - . - "Software ontology" . - . - . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . - . - . - . - "GlycoEpitope" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . - . - . - . - "MSMEG_3769"^^ . - "http://www.pantherdb.org/"^^ . - . - . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . - . - . - . - . - . - "Suggested Ontology for Pharmacogenomics" . - "false"^^ . - "Medical Dictionary for Regulatory Activities Terminology" . - . - . - . - . - . - . - . - "CAS Chemical Registry" . - . - . - . - . - "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . - . - . - . - . - "0000057"^^ . - "Cooperative Patent Classification" . - . - . - . - "https://www.novusbio.com/products/$1"^^ . - . - "Gene Ontology Causal Assembly Model" . - . - . - "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml"^^ . - . - . - "13"^^ . - "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"^^ . - . - . - . - . - . - . - "Panorama Public" . - . - . - . - . - . - . - . - "Contains information about cells and data sheets related to transfection."^^ . - . - "^\\d{6}$"^^ . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay"^^ . - "447860"^^ . - _:N205262c097fa4e37a6188e1ceacdd13e . - "Pfam Clans" . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - "https://github.com/carrineblank/MicrO"^^ . - . - . - . - . - . - "Dublin Core" . - . - . - . - "false"^^ . - . - . - . - "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . - . - . - . - "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . - . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . - "PGS000018"^^ . - . - . - . - . - . - . - "andreadega/systems-biology-compiler"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "Gs0000008"^^ . - "http://purl.obolibrary.org/obo/CLO_$1"^^ . - . - . - "^r3d\\d{9,9}$"^^ . - . - . - "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . - . - . - . - "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . - "false"^^ . - "^NOR\\d+$"^^ . - "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . - "^\\d{5}$"^^ . - . - "NONHSAT000001"^^ . - . - . - . - "http://bioassayontology.org"^^ . - . - . - "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . - . - "http://autism.mindspec.org/autdb/"^^ . - . - . - "https://www.cropontology.org/rdf/CO_320:$1"^^ . - . - . - . - . - "MIMAT0046872"^^ . - . - . - . - "http://www.antweb.org/specimen.do?name=$1"^^ . - . - "RDF"^^ . - . - "128796-39-4"^^ . - . - . - "Liliana Andres Hernandez" . - . - "false"^^ . - . - "false"^^ . - . - "SASDAX8"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . - . - . - . - "^CHEMBL\\d+$"^^ . - . - . - . - . - "688"^^ . - . - . - . - "clinical LABoratory Ontology" . - "^\\d+$"^^ . - . - "^[A-Z-a-z0-9]+$"^^ . - . - . - "false"^^ . - "http://www.drugbank.ca/targets"^^ . - "Logical Observation Identifiers Names and Codes" . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://rnacentral.org/"^^ . - . - . - . - "^\\w{1,3}$"^^ . - "Cell Lines in PubChem"^^ . - . - . - . - "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . - "false"^^ . - . - "false"^^ . - . - . - "6VDC956"^^ . - . - "^\\S+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "FaBiO, the FRBR-aligned Bibliographic Ontology" . - . - . - . - . - . - "Antibody Registry" . - . - . - . - . - . - . - . - "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"^^ . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.fossilworks.org"^^ . - "Archival Resource Key" . - "http://www.cathdb.info/domain/$1"^^ . - "http://dictybase.org/"^^ . - "An ontology to describe entities related to prescription of drugs"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "https://rfam.xfam.org/family/$1"^^ . - . - . - "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . - . - "0000128"^^ . - . - . - "^\\d+$"^^ . - . - . - "https://schema.org"^^ . - . - . - "0000093"^^ . - . - "ClinVar Submission" . - . - . - . - . - "runBioSimulations" . - . - . - . - . - "ABE-0009634"^^ . - "RGD Disease_Ontology" . - . - . - . - . - "0000062"^^ . - . - . - . - . - "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . - . - "GO Relations" . - . - "https://www.ebi.ac.uk/pride/"^^ . - . - . - . - . - . - . - "false"^^ . - "http://www.nlm.nih.gov/mesh/"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "KEGG Enzyme" . - "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^ . - "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^ . - "0000204"^^ . - "00000000"^^ . - . - . - "https://github.com/pombase/fypo"^^ . - . - "Pfam" . - "false"^^ . - "Vertebrate skeletal anatomy ontology."^^ . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee"^^ . - "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . - "nasa/kepler-exoplanet-search-results"^^ . - "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "75121530"^^ . - . - . - . - "2GC4"^^ . - . - . - . - . - . - . - . - . - "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . - . - "^MIMAT\\d{7}$"^^ . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . - "0221"^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "https://gold.jgi.doe.gov/resolver?id=$1"^^ . - . - . - . - . - . - . - . - . - "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - . - "AmoebaDB" . - . - . - . - . - . - . - . - . - "cho"^^ . - . - . - . - . - . - . - . - "Variation Modelling Collaboration" . - . - "false"^^ . - . - . - "https://cordis.europa.eu/"^^ . - . - "UniProt Post-Translational Modification" . - . - "Ontology of Precision Medicine and Investigation" . - . - . - . - . - "^[\\w\\-.]{3,}$"^^ . - . - . - . - . - . - "SM_UB-81"^^ . - . - . - . - . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . - . - . - . - . - . - "EY223054.1"^^ . - . - . - . - . - . - . - "^[A-Z0-9]+$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PLO_$1"^^ . - "false"^^ . - . - . - . - "Physico-chemical methods and properties" . - "https://monarch-initiative.github.io/mondo"^^ . - . - . - . - . - . - . - "RCV000033555.3"^^ . - . - . - "https://www.uniprot.org/unirule/$1"^^ . - . - "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview"^^ . - . - "https://assets.nemoarchive.org/$1"^^ . - . - . - . - "https://www.cellbiolabs.com/search?keywords=$1"^^ . - . - . - . - "false"^^ . - . - "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . - . - "^\\d{7}$"^^ . - _:N141173d7fe154477b6ac646d37cf2451 . - . - "https://www.w3.org/TR/xml/"^^ . - "false"^^ . - . - . - . - "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . - . - . - "false"^^ . - . - . - "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . - "https://biopragmatics.github.io/providers/sdis/$1"^^ . - . - "0000050"^^ . - . - "ICEberg family" . - . - . - "000000341"^^ . - . - "false"^^ . - "Peter Midford" . - . - . - . - "TIGR protein families" . - . - . - . - . - . - . - "http://autism.mindspec.org/GeneDetail/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://reactome.org/content/detail/$1"^^ . - . - . - . - . - "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "0000187"^^ . - . - . - "false"^^ . - . - "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . - . - . - "0007807"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . - . - "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . - . - . - . - . - . - . - "FAIRsharing.62qk8w" . - "false"^^ . - . - . - "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . - . - . - "Small Molecule Pathway Database" . - . - . - . - "^[A-Z-_0-9]+$"^^ . - . - . - "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . - "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "http://n2t.net/ark:$1"^^ . - . - "^(R)?PXD\\d{6}$"^^ . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - . - "https://github.com/"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . - . - . - "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . - "false"^^ . - . - "https://bacdive.dsmz.de/strain/$1"^^ . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - "https://github.com/data2health/contributor-role-ontology"^^ . - . - "false"^^ . - . - "0002066"^^ . - . - . - "ICEberg element" . - "Ensembl Protists" . - . - "0000086"^^ . - . - . - . - . - . - . - . - . - . - "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . - . - . - "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^ . - . - . - "^\\d+$"^^ . - "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . - . - "DIP-743N"^^ . - "85163"^^ . - "Mike Cherry" . - "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . - . - . - "http://matrixdb.univ-lyon1.fr/"^^ . - . - . - . - . - . - . - "https://www.storedb.org/?STOREDB:DATASET$1"^^ . - "false"^^ . - . - "FuncBase Fly" . - . - . - "https://metacyc.org"^^ . - . - . - . - . - . - "Integrated Microbial Genomes Taxon" . - "^TIGR\\d+$"^^ . - "ModelDB" . - "oct 2016"^^ . - . - . - . - . - . - . - "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . - . - . - "^[0-9]*$"^^ . - . - . - . - "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . - . - . - . - "true"^^ . - "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . - "false"^^ . - . - . - "false"^^ . - . - . - . - "2170610"^^ . - . - . - . - "false"^^ . - . - . - . - "https://code.google.com/archive/p/ontology-for-genetic-interval/"^^ . - . - "hsa00190"^^ . - . - "MolBase" . - "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . - . - . - . - . - . - . - "Citlalli Mejía-Almonte" . - "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . - . - . - "Sweet Potato ontology" . - . - . - . - . - . - . - "^HBG\\d+$"^^ . - . - "https://registry.identifiers.org/registry/$1"^^ . - "false"^^ . - . - . - . - . - . - . - "Deepak Unni" . - . - . - . - "https://github.com/bgsu-rna/rnao"^^ . - . - . - . - "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . - . - . - . - . - "false"^^ . - "https://github.com/INO-ontology/ino"^^ . - "Oryzabase Gene" . - . - . - . - "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . - . - "false"^^ . - "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.radiomics.org/RO"^^ . - "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/MOP_$1"^^ . - . - . - "false"^^ . - "https://qudt.org"^^ . - "false"^^ . - . - . - "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/intact/interaction/$1"^^ . - . - "false"^^ . - . - . - . - . - . - "Genetic and Rare Diseases Information Center" . - "https://web.expasy.org/cellosaurus/"^^ . - "http://www.sasbdb.org/data/$1"^^ . - . - . - . - "^WB[A-Z][a-z]+\\d+$"^^ . - "http://www.nlm.nih.gov/medlineplus/"^^ . - "^\\d{6}$"^^ . - . - "JRBC Cell Bank" . - . - . - . - "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . - . - . - . - . - . - "24801"^^ . - "https://aopwiki.org/"^^ . - . - "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . - . - "Probability Distribution Ontology" . - . - . - "http://www.sparontologies.net/ontologies/cito"^^ . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - . - "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . - . - "^\\d+$"^^ . - "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . - "Frédéric Bastian" . - "https://VirtualFlyBrain.org"^^ . - . - . - . - . - . - "false"^^ . - "Online Mendelian Inheritance in Animals" . - . - "https://horizondiscovery.com/en/search?searchterm=$1"^^ . - "CNP0171505"^^ . - . - . - "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . - . - "0000091"^^ . - . - "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . - . - "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . - "Spectra Hash Code" . - "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . - . - . - "UniRef90_P00750"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "https://fcs-free.org/fcs-database?$1"^^ . - . - . - . - "Anvil" . - . - "Regulation of Transcription Ontology" . - "50885"^^ . - "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . - "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . - . - . - "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . - "1731"^^ . - . - . - . - "false"^^ . - "GM17027"^^ . - . - "http://www.accessdata.fda.gov/scripts/cder/ndc/"^^ . - "Allyson Lister" . - . - "health_care_quality_assessment"^^ . - . - . - . - . - "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . - . - "Social Insect Behavior Ontology" . - "http://cdb.ics.uci.edu/"^^ . - "MIMIC III Database" . - "false"^^ . - "false"^^ . - "^\\d+$"^^ . - "SR0000178"^^ . - . - . - . - . - "http://www.dpvweb.net/"^^ . - . - . - . - "http://www.aphidbase.com/aphidbase"^^ . - "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . - . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - . - . - "FCB005"^^ . - . - . - "false"^^ . - . - "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^ . - "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . - . - . - . - "sharesAuthorInstitutionWith"^^ . - . - . - "http://ecmdb.ca/compounds/$1"^^ . - . - . - . - . - . - "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html"^^ . - . - "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . - "6038"^^ . - "^\\d{8}$"^^ . - "http://www.peptideatlas.org/"^^ . - "^\\d+$"^^ . - "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . - "https://biorxiv.org"^^ . - "ProGlycProt" . - . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "Quantities, Units, Dimensions, and Types Ontology" . - . - . - "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . - . - . - . - . - "https://icahn.mssm.edu/"^^ . - . - . - . - . - "false"^^ . - "http://www.jstor.org/"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "https://www.vmh.life/"^^ . - "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . - . - "http://purl.obolibrary.org/obo/BILA_$1"^^ . - "International repository of Adverse Outcome Pathways."^^ . - "http://sideeffects.embl.de/se/$1"^^ . - . - . - "^B\\d{5}$"^^ . - . - . - . - . - . - . - . - "AD834"^^ . - . - "http://agroportal.lirmm.fr/ontologies/$1" . - . - "http://purl.obolibrary.org/obo/NCRO_$1"^^ . - . - . - "false"^^ . - . - "http://www.obofoundry.org/" . - . - . - "Biotin_biosynthesis"^^ . - "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . - "uBio NameBank" . - . - "3905431"^^ . - . - . - . - . - . - . - "Gene"^^ . - . - . - . - . - . - . - "https://drugs.ncats.io/"^^ . - . - . - "false"^^ . - "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . - "GenPept" . - . - "PSI Extended File Format" . - . - . - "http://purl.obolibrary.org/obo/ICO_$1"^^ . - . - "http://phylomedb.org/"^^ . - "Wikidata Property" . - . - . - "mirEX" . - "https://biopragmatics.github.io/providers/msigdb/$1"^^ . - . - . - . - "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . - . - . - "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . - . - "Signaling Gateway" . - "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - . - . - . - . - "0058"^^ . - . - . - . - "https://www.metabolome-express.org/"^^ . - . - . - . - "BioPortal" . - . - . - . - "false"^^ . - . - "Metabolomics Workbench Study" . - "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . - . - . - "false"^^ . - . - . - . - "277.9"^^ . - "^PGS[0-9]{6}$"^^ . - "https://ratmine.mcw.edu/ontology/disease/"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists"^^ . - . - . - . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marref/"^^ . - . - "http://senselab.med.yale.edu/OdorDB"^^ . - . - . - "^\\d{8}$"^^ . - . - . - "http://bigg.ucsd.edu/universal/reactions"^^ . - . - . - . - . - "Open Data Commons for Spinal Cord Injury" . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MRO_$1"^^ . - . - . - . - "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . - . - . - . - "Human Gene Mutation Database" . - . - . - "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . - . - . - . - . - . - "MCDS_L_0000000001"^^ . - . - . - . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . - "Aceview Worm" . - . - . - . - "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . - "^\\d+$"^^ . - . - . - . - "false"^^ . - . - . - . - "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . - "Linguist" . - . - "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . - "037727"^^ . - . - . - . - . - "^A_\\d+_.+$"^^ . - "Vocabulary of Interlinked Datasets" . - . - . - "https://www.cropontology.org/rdf/CO_358:$1"^^ . - . - . - "https://www.nextmovesoftware.com/namerxn.html"^^ . - "^\\d+$"^^ . - "WBRNAi00086878"^^ . - . - . - "0032571"^^ . - . - . - . - "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . - . - . - . - . - . - . - . - . - . - "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . - "LSM-6306"^^ . - . - . - . - "https://proteinensemble.org/$1"^^ . - . - . - . - "http://www.w3.org/ns/dcat#$1"^^ . - . - . - "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . - "http://purl.obolibrary.org/obo/REX_$1"^^ . - "https://www.abmgood.com/Cell-Biology.html"^^ . - . - "728"^^ . - . - . - . - . - . - . -_:Nd43cb5600ccf4f7a985affd5767ee387 "SEP developers via the PSI and MSI mailing lists" . - "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . - "https://www.omim.org/phenotypicSeriesTitles/all"^^ . - "Digital archive of scholarly articles" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://korkinlab.org/dommino"^^ . - . - "VMH reaction" . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - . - "0000108"^^ . - "false"^^ . - "https://ccg.epfl.ch/snp2tfbs/"^^ . - . - "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_334:$1"^^ . - . - . - . - . - "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . - . - . - . - . - . - . - . - . - . - . - "Mouse Developmental Stages" . - "GCF_000005845.2"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - . - "http://sed-ml.org/"^^ . - . - . - . - . - . - . - . - . - "https://datanator.info/"^^ . - . - . - . - . - . - . - . - "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . - . - . - . - "https://www.metanetx.org/chem_info/$1"^^ . - . - . - . - "Human Plasma Membrane Receptome Families" . - . - "ExAC Gene" . - . - "false"^^ . - . - . - "FR-FCM-ZYGW"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^[A-Za-z0-9\\/]+$"^^ . -_:N876775752ea24733b68c737a615f6f5c "Thorsten Henrich" . - . - "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . - . - "NIF Standard Ontology: Qualities" . - . - . - . - . - . - "0000485"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - "^\\d{7}(_\\d)?$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "0000072"^^ . - . - "BioNumbers" . - "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . - "false"^^ . - . - "^HIX\\d{7}(\\.\\d+)?$"^^ . - . - . - . - . - . - "http://www.drugbank.ca/drugs/$1"^^ . - . - . - . - . - . - "http://pombe.oridb.org/details.php?id=$1"^^ . - . - "https://scicrunch.org/resolver/RRID:$1"^^ . - . - . - . - "MEROPS Family" . - . - . - "GL50803_102438"^^ . - "false"^^ . - . - . - "Datasets inside StoreDB"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^BAMSC\\d+$"^^ . - . - . - . - "false"^^ . - . - "Anatomical Entity Ontology" . - "http://cerevisiae.oridb.org/index.php"^^ . - . - . - . - . - . - . - "Drosophila development" . - "0000127"^^ . - . - "^[A-Za-z0-9]+$"^^ . - . - "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^ . - . - "^\\d+$"^^ . - "PjrpzUIAAAAJ"^^ . - "3403"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "http://exac.broadinstitute.org/transcript/$1"^^ . - "false"^^ . - "Toxic Process Ontology" . - . - . - "^\\d{7}$"^^ . - . - . - "G-Rich Sequences Database" . - . - . - . - . - . - . - . - "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . - . - . - "^Os\\S+g\\d{7}$"^^ . - "Jennifer C. Giron" . - . - . - . - . - . - . - . - . - . - "https://easychair.org/cfp/"^^ . - . - "https://www.discoverx.com/products-applications/cell-lines"^^ . - . - . - . - "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . - . - "Decentralized Identifier" . - . - . - "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO"^^ . - . - "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . - . - . - "true"^^ . - . - "http://www.proteinatlas.org/$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - "NeuroNames" . - . - . - . - . - . - . - "RNA Modification Database" . - "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . - "Mouse Brain Atlas" . - . - . - "^NCT\\d{8}$"^^ . - . - "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . - "http://www.3dmet.dna.affrc.go.jp/"^^ . - "^[A-Z]+[A-Z-0-9]{2,}$"^^ . - "https://fairsharing.org/$1"^^ . - . - . - . - "https://github.com/BiodiversityOntologies/bco"^^ . - . - "false"^^ . - . - . - "^RCV\\d+(\\.\\d+)?$"^^ . - "RSC3"^^ . - . - . - "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . - . - "^[0-9A-Za-z\\-.]+$"^^ . - "Chemical Information Ontology" . - . - "^\\S+$"^^ . - "false"^^ . - "Search Tool for Interactions of Chemicals" . - "TRQ"^^ . - "VMH Gene" . - . - . - "http://edamontology.org/format_$1"^^ . - . - . - . - . - "Vaccine Ontology" . - "true"^^ . - . - . - "cd00400"^^ . - "http://flypush.imgen.bcm.tmc.edu/pscreen/"^^ . - "^\\d{7}$"^^ . - . - . - "https://www.ensembl.org/"^^ . - . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/"^^ . - "Cell line collections"^^ . - . - . - "http://bidd.group/NPASS/"^^ . - . - "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . - . - "false"^^ . - . - . - "http://ligand-depot.rutgers.edu/index.html"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "NeuroMorpho" . - . - "KEGG Reaction Class" . - "MCDS_S_0000000001"^^ . - "https://github.com/SpeciesFileGroup/nomen"^^ . - . - . - . - . - . - . - . - . - "https://www.bindingdb.org"^^ . - . - . -_:N7284ed18d6474b58beb7ba64dfe2a03f "David Blackburn" . - . - . - . - . - . - . - . - . - "J55.713G"^^ . - "http://tolweb.org/tree/"^^ . - . - . - "Comprehensive Resource of Mammalian protein complexes" . - . - . - . - . - . - . - "0400109"^^ . - . - . - "http://purl.obolibrary.org/obo/CMO_$1"^^ . - "^\\d+$"^^ . - . - "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . - "^\\d+$"^^ . - . - "0000062"^^ . - . - . - . - . - "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . - . - . - . - . - . - . - . - "1000003"^^ . - . - "https://bio.tools/"^^ . - "false"^^ . - . - . - . - . - "^[a-z_\\.]+$"^^ . - . - . - . - "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"^^ . - . - . - . - . - "2649230"^^ . - . - . - . - . - . - . - "http://www.massbank.jp"^^ . - . - . - . - . - . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page"^^ . - . - . - . - . - "https://odc-tbi.org"^^ . - "International Fungal Working Group Fungal Barcoding." . - . - . - "^\\d{6}$"^^ . - . - "George Gkoutos" . - . - . - "false"^^ . - . - "http://proteomecentral.proteomexchange.org/"^^ . - . - . - . - . - . - "true"^^ . - . - "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . - . - . - . - . - . - . - "0001807"^^ . - . - . - "Tom Gillespie" . - . - . - "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . - "BioModels Database" . - . - . - . - . - . - . - "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . - . - . - "http://www.kegg.jp/entry/$1"^^ . - "https://github.com/biolink/biolink-model" . - . - . - . - . - "Human Medical Genetics" . - "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . - . - . - "http://senselab.med.yale.edu/NeuronDB/"^^ . - . - "101775319"^^ . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . - . - . - "OriDB Schizosaccharomyces" . - . - . - . - . - . - "http://drugcentral.org/drugcard/$1"^^ . - . - "https://www.storedb.org/"^^ . - . - . - "Jingshan Huang" . - . - . - . - "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . - . - "false"^^ . - . - "Confidence Information Ontology" . - "Asiyah Yu Lin" . - "false"^^ . - . - "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . - . - . - . - . - . - . - . - . - . - "National Bibliography Number" . - . - . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . - . - . - . - . - . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . - . - . - . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/PLANP_$1"^^ . - "^MSV\\d+$"^^ . - . - . - . - . - . - . - . - "030719"^^ . - . - . - "^\\d+$"^^ . - . - "https://www.ccdc.cam.ac.uk/"^^ . - . - . - . - . - . - . - "^[0-9]{10}$"^^ . - . - . - . - "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . - . - . - . - . - . - . - . - . - . - "http://www.pombase.org/"^^ . - . - . - . - "^TS-\\d{4}$"^^ . - . - "BRENDA Ligand Group" . - . - "2gc4E"^^ . - "http://modelseed.org/biochem/reactions/$1"^^ . - "https://bioregistry.io/collection"^^ . - . - "http://solgenomics.net/"^^ . - . - . - . - . - . - . - "Metabolomics Workbench Project" . - . - "http://www.ymdb.ca"^^ . - . - "Conserved Domain Database at NCBI" . - . - . - "^\\d{7}$"^^ . - . - . - . - "https://github.com/insect-morphology/lepao"^^ . - . - "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/gtr/"^^ . - . - . - "Kinetic Simulation Algorithm Ontology" . - . - . - . - . - . - . - . - "https://ligandbook.org/"^^ . - . - "^oai\\:cwi\\.nl\\:\\d+$"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . - . - . - "A manually curated resource for the representation and annotation of metabolic pathways"^^ . - . - . - "https://github.com/rsc-ontologies/rxno"^^ . - . - . - . - . - . - . - . - "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^ . - . - . - "PGOHUM00000289843"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - "Microarray experimental conditions" . - . - "PubMed" . - . - "European Registry of Materials" . - "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . - "OMA Group" . - . - . - . - "https://www.nlm.nih.gov/research/umls/rxnorm/"^^ . - . - . - "Dictyostelium discoideum phenotype ontology" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "European Bank for induced pluripotent Stem Cells" . - . - . - "MTBLS1"^^ . - . - . - . - . - . - . - . - . - . - . - "HGVPM623"^^ . - . - . - "false"^^ . - . - . - "1968"^^ . - . - "^\\w+$"^^ . - "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . - "Pathogen Host Interaction Phenotype Ontology" . - "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . - . - . - . - . - . - "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - . - . - . - . - . - . - "http://senselab.med.yale.edu/OrDB/"^^ . - . - . - . - . - "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . - . - . - . - "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - . - . - "Zebrafish Phenotype Ontology" . - . - "The International Standard Book Number (ISBN) is for identifying printed books."^^ . - . - "false"^^ . - "http://purl.obolibrary.org/obo/DUO_$1"^^ . - "false"^^ . - . - "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - "^P\\d+$"^^ . - . - . - . - . - "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . - "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . - . - . - . - . - . - . - . - . - . - "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^ . - "false"^^ . - . - . - "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^ . - . - . - "Global Proteome Machine Database" . - "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . - "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . - "Database of Arabidopsis Transcription Factors" . - . - . - . - "^NONHSAG\\d{5}$"^^ . - "^\\d{7}$"^^ . - . - . - "^\\d+$"^^ . - . - "^CONSO\\d{5}$"^^ . - . - . - . - . - "^MMP\\d+.\\d+$"^^ . - "MIRT000002"^^ . - "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . - . - "false"^^ . - . - "Arabidopsis Information Portal" . - . - "http://caps.ncbs.res.in/pass2"^^ . - . - . - . - . - "true"^^ . - "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . - . - . - . - . - "AA0001"^^ . - "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^ . - "CORDIS Article" . - . - . - . - "false"^^ . - . - . - . - "http://linkedlifedata.com/resource/umls/id/$1"^^ . - . - "http://www.semantic-systems-biology.org/apo"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "false"^^ . - . - "false"^^ . - "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . - . - "http://github.com/ga4gh/data-object-service-schemas"^^ . - . - . - . - "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . - "FunderRegistry" . - . - . - "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . - . - . - "FlyBase Qualifiers" . - . - . - . - . - . - . - . - "https://www.disprot.org/$1"^^ . - "Beet Ontology ontology" . - . - "^\\d{7}$"^^ . - . - "Open Researcher and Contributor" . - "lectins/172"^^ . - . - . - "http://purl.obolibrary.org/obo/MMUSDV_$1"^^ . - . - . - . - . - . - . - . - "https://www.pgscatalog.org/pgs/$1"^^ . - . - . - "12929"^^ . - "Mental Disease Ontology" . - . - . - . - "SitEx" . - . - . - . - . - "https://sed-ml.org/urns.html#language:$1"^^ . - "http://www.sparontologies.net/ontologies/frapo"^^ . - . - . - "James C. Hu" . -_:Nb05e5db256fe46d79efe2cf9dca6406b "Schober Daniel" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - "GOLD metadata" . - . - . - "https://aftol.umn.edu"^^ . - . - . - . - . - . - . - . - "^[A-Za-z0-9_-]+$"^^ . - . - . - . - "Resources mentioned in \"Sharing biological data: why, when, and how\"" . - . - . - "TS-0001"^^ . - . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - "https://biopragmatics.github.io/providers/sfam/$1"^^ . - . - "false"^^ . - . - . - "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . - . - "http://www.ontobee.org/ontology/$1" . - "BugBase Protocol" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . - . - . - . - . - "http://multicellds.org/MultiCellDB.php"^^ . - _:N7284ed18d6474b58beb7ba64dfe2a03f . - . - . - . - . - . - "https://www.oclc.org/en/about.html"^^ . - . - "9008500"^^ . - . - . - . - "https://www.cropontology.org/rdf/CO_335:$1"^^ . - . - "^TS-\\d+$"^^ . - . - . - "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Jackson Laboratories Strain" . - . - "https://www.ncbi.nlm.nih.gov/protein"^^ . - . - . - . - "http://purl.obolibrary.org/obo/DRON_$1"^^ . - "https://www.animalgenome.org/QTLdb"^^ . - "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . - "http://smart.embl-heidelberg.de/"^^ . - "https://cropontology.org/ontology/CO_338/Chickpea"^^ . - "G. Thomas Hayman" . - . - "Candida Genome Database" . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . - "https://www.geonames.org"^^ . - . - . - . - . - "G24361QY"^^ . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/$1"^^ . - . - "https://www.cropontology.org/rdf/CO_360:$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://www.genome.jp/kegg/ko.html"^^ . - "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - "https://easychair.org/cfp/$1"^^ . - . - . - . - . - . - . - . - "^\\d{4}-\\d{3}[\\dX]$"^^ . - . - . - . - "Medaka fish anatomy and development" . - "I31.952"^^ . - . - "19333"^^ . - . - . - . - "false"^^ . - . - . - "^[1-9][0-9]{14}$"^^ . - "false"^^ . - "^\\d+$"^^ . - . - . - "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . - . - "false"^^ . - . - . - . - . - "BRAF"^^ . - . - "DepMap Cell Lines" . - . - "has provider formatter" . - "http://viralzone.expasy.org/all_by_protein/$1.html"^^ . - . - . - "^[a-zA-Z]+.+$"^^ . - "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . - . - . - "^\\w+$"^^ . - "KEGG Drug" . - . - "false"^^ . - . - . - "false"^^ . - . - . - "https://github.com/obophenotype/ncbitaxon"^^ . - "^\\d{7}$"^^ . - "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . - . - . - . - "http://neuinfo.org/"^^ . - "false"^^ . - . - . - . - . - . - . - . - "0000509"^^ . - . - . - . - . - . - "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules"^^ . - . - . - . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - . - . - . - . - . - . - "http://europepmc.org/articles/$1"^^ . - . - "https://github.com/obophenotype/planarian-phenotype-ontology"^^ . - "http://purl.obolibrary.org/obo/FOVT_$1"^^ . - . - . - . - "YAL001C"^^ . - . - . - . - . - . - . - . - . - . - . - . - "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - "2019-08-03_00000089_1"^^ . - . - . - . - "Flybase Cell Line" . - . - . - . - . - "0000000"^^ . - . - . - . - . - . - . - "Ontology of units of Measure" . - . - . - . - . - . - . - . - . - . - "90062901"^^ . - . - "https://bioinformatics.cineca.it/PMDB/"^^ . - . - . - "true"^^ . - "http://purl.obolibrary.org/obo/VT_$1"^^ . - . - . - "false"^^ . - . - . - "https://flowrepository.org/"^^ . - . - . - . - . - "0000101"^^ . - . - . - . - . - . - . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . - . - . - "https://github.com/obophenotype/upheno"^^ . - . - "NIF Standard Ontology: Cognitive Function" . - . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . - . - . - "https://w3id.org"^^ . - . - . - "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . - "^[1-9]\\d{0,5}$"^^ . - . - "SUM Breast Cancer Cell Line Knowledge Base" . - . - "https://bioregistry.io/metaregistry/biocontext/$1" . - . - "Stacia R Engel" . - "^\\d{7}$"^^ . - "https://smpdb.ca/view/$1"^^ . - . - . - "A10BA02"^^ . - . - . - . - "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^ . - "https://www.brenda-enzymes.de/ligand.php"^^ . - . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . - . - . - . - "false"^^ . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/IMR_$1"^^ . - "https://morpheus.gitlab.io/models/$1"^^ . - . - . - . - "PS00001"^^ . - . - . - "1000001"^^ . - . - "EDDA Study Designs Taxonomy" . - "Web Elements" . - . - "CranioMaxilloFacial ontology" . - . - . - . - . - . - . - . - . - . - . - "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . - . - . - . - . - . - "BDGP insertion DB" . - . - . - "https://hpscreg.eu/"^^ . - . - . - "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . - . - . - . - . - . - "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^ . - "Name-to-Thing" . - . - . - "A registry of life science prefxes"^^ . - "100"^^ . - . - . - . - "false"^^ . - "4019477"^^ . - . - . - "0000001"^^ . - . - . - . - . - . - "Animal Genome Pig QTL" . - . - . - . - "FAIR* Reviews Ontology" . - . - . - . - "E-cyanobacterium entity" . - . - . - "http://taibnet.sinica.edu.tw/home.php"^^ . - "Fernanda Dorea" . - . - . - . - . - . - . - . - "^DDB\\d+$"^^ . - . - "https://gsso.research.cchmc.org/"^^ . - "^\\d{7}$"^^ . - . - "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - "https://www.w3.org/2004/02/skos/"^^ . - . - "^PROB_c\\d+$"^^ . - . - . - . - "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . - . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^ . - . - . - . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - "Tohoku University cell line catalog" . - "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . - "0002959"^^ . - "false"^^ . - . - . - "false"^^ . - "4892"^^ . - "Bgee organ" . - "Gazetteer" . - "^\\d+$"^^ . - . - . - . - . - "https://jcoin.datacommons.io"^^ . - . - . - . - . - . - "Physico-chemical process" . - "false"^^ . - . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/MFO_$1"^^ . - . - . - . - . - . - . - . - . - . - . - "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . - . - . - . - . - . - . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . - . - "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html"^^ . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . - "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . - . - . - "0000390"^^ . - . - . - . - . - "http://www.genome.jp/kegg/reaction/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . - . - "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^ . - . - "Obstetric and Neonatal Ontology" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "DragonDB Allele" . - . - "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . - . - . - . - . - . - . - . - . - . - "https://bacdive.dsmz.de/"^^ . - . - "false"^^ . - . - . - . - . - . - "Donny Winston" . - . - . - "false"^^ . - . - "https://kidsfirstdrc.org"^^ . - . - . - "https://publons.com/researcher/$1"^^ . - . - "0001114"^^ . - . - . - . - . - "false"^^ . - . - . - "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . - "false"^^ . - . - . - "0000319"^^ . - . - . - . - "ASPL0000349247"^^ . - . - . - "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . - "http://viaf.org"^^ . - . - "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . - . - "SCC111"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "00000180"^^ . - . - . - "https://www.glycoepitope.jp/epitopes/"^^ . - "DDB0191090"^^ . - "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . - "Japan Chemical Substance Dictionary" . - . - "Dengue Fever Ontology" . - . - "http://www.hipsci.org"^^ . - "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . - . - "456789"^^ . - . - . - . - "https://proconsortium.org/app/entry/PR:$1"^^ . - . - . - . - . - . - . - . - . - "has example" . - . - "latitude"^^ . - . - . - . - . - "0000106"^^ . - . - "0000111"^^ . - "https://www.ncbi.nlm.nih.gov/PubMed/"^^ . - . - . - "Prefix.cc" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "0002058"^^ . - . - . - . - "^\\d+$"^^ . - "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . - . - "http://pbil.univ-lyon1.fr/databases/hogenom/"^^ . - "http://www.chemspider.com/"^^ . - "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . - . - . - "false"^^ . - . - . - "true"^^ . - . - . - . - . - . - "Human Phenotype Ontology" . - . - . - "false"^^ . - "https://data.4dnucleome.org/biosources/$1"^^ . - "Cluster of orthologous genes" . - . - "A controlled vocabulary to support the study of transcription in the human brain"^^ . - . - "^\\d+$"^^ . - "Internal OBO and PyOBO Relations" . - . - . - . - . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - "^\\w+$"^^ . - . - . - . - . - . - . - "OncoTree" . - "false"^^ . - . - . - . - "Hymenoptera Anatomy Ontology" . - . - . - . - . - "false"^^ . - . - . - . - . - "^[SED]R[APRSXZ]\\d+$"^^ . - . - "http://seed-viewer.theseed.org/seedviewer.cgi"^^ . - . - . - . - . - . - . - "PIR Superfamily Classification System" . - "false"^^ . - . - . - . - . - "288"^^ . - . - "EDI_244000"^^ . - . - . - . - . - . - . - . - "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . - "http://www.mirbase.org/"^^ . - "^\\d+$"^^ . - "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . - . - "Infectious Disease Ontology" . - "P12345"^^ . - . - "1004" . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . - . - . - . - . - "http://cell-lines.toku-e.com"^^ . - . - "http://www.geneontology.org/gocam"^^ . - . - . - . - . - . - . - "https://web.expasy.org/cellosaurus/"^^ . - "Molecular Interactions Controlled Vocabulary" . - . - "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . - . - . - "Cell line databases/resources"^^ . - "http://www.atol-ontology.com"^^ . - . - . - "FB00000917"^^ . - . - . - . - . - . - . - . - "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . - _:N66ebab027c6f42a78ee5424816ee2209 . - . - "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . - . - . - . - "COlleCtion of Open Natural ProdUcTs" . - . - . - . - "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . - . - . - "https://www.wormbase.org/db/seq/protein"^^ . - . - "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . - "false"^^ . - "RDF Schema" . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.kegg.jp/entry/$1"^^ . - "ZDB-GENE-041118-11"^^ . - "^[0-9]+:[0-9]+$"^^ . - . - . - . - . - "false"^^ . - "Discourse Elements Ontology" . - "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . - . - . - . - . - . - . - . - "0000487"^^ . - . - "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"^^ . - "GeneDB" . - . - . - . - . - . - . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . - . - . - "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . - . - . - "https://github.com/obophenotype/sibo"^^ . - "17165"^^ . - . - . - . - "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . - . - . - "miRTarBase" . - . - . - "https://github.com/OAE-ontology/OAE/"^^ . - . - . - . - "https://datacite.org"^^ . - . - . - "PWY3O-214"^^ . - "chebi" . - "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . - "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . - . - "http://jaxmice.jax.org/strain/$1.html"^^ . - "false"^^ . - . - . - . - . - . - "Relation Ontology" . - . - . - "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . - . - "The main contact person for a registry" . - . - . - . - "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^ . - . - . - . - "CALIPHO Group Ontology of Human Anatomy" . - . - . - . - . - . - . - . - "https://github.com/MPIO-Developers/MPIO"^^ . - . - . - . - "ARP-1513"^^ . - . - "http://pathway.yeastgenome.org/"^^ . - . - "https://github.com/obophenotype/c-elegans-development-ontology"^^ . - . - "Carrine Blank" . - . - "^T3D\\d+$"^^ . - . - . - "false"^^ . - "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all"^^ . - . - . - . - "0004"^^ . - . - "^\\d+$"^^ . - . - "false"^^ . - "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . - . - . - "https://www.xenbase.org/"^^ . - . - "ECOCYC" . - . - . - "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . - "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "Morpheus model repository" . - . - . - . - . - . - . - . - . - . - "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . - . - . - . - . - . - . - . - . - . - . - "has download URL" . - . - . - . - "NITE Biological Resource Center" . - "^\\d+$"^^ . - "false"^^ . - . - . - "^Rv\\d{4}(A|B|c)?$"^^ . - . - "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . - . - . - "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . - . - . - . - "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . - . - "NodeShape"^^ . - . - . - . - "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . - . - . - "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . - . - . - . - "https://www.ebi.ac.uk/merops"^^ . - . - . - . - "0101963"^^ . - . - . - . - . - . - "01N50ZZ"^^ . - "09200010"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "Allotrope Merged Ontology Suite"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - "https://www.goreni.org/gr3_nomenclature.php"^^ . - "http://purl.obolibrary.org/obo/ONE_$1"^^ . - . - . - . - "0000210"^^ . - . - . - . - "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . - "ChemIDplus" . - . - . - . - "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . - . - . - "https://www.cropontology.org/rdf/CO_366:$1"^^ . - . - . - "0007114"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Uber Anatomy Ontology" . - . - "false"^^ . - . - "System Science of Biological Dynamics dataset" . - "10153"^^ . - . - "GO Chemicals" . - . - . - . - . - . - . - . - . - "false"^^ . - "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . - . - . - . - "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . - . - "BIOMD0000000048"^^ . - . - . - . - "false"^^ . - "https://www.gtexportal.org/home/gene/$1"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ipd/estdab/"^^ . - . - . - "false"^^ . - "Agronomy Ontology" . - . - . - "false"^^ . - . - "9"^^ . - . - "NBK331"^^ . - . - . - . - . - "0004486"^^ . - . - "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . - "AURKA"^^ . - "true"^^ . - . - "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . - "HEX1"^^ . - . - . - . - "FlyBase Gene" . - "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . - "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^ . - "172"^^ . - . - . - . - . - . - "WormBase database of nematode biology" . - . - . - "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^ . - . - . - . - . - . - . - . - . - "https://www.kew.org/data/grasses-db/www/$1"^^ . - . - . - . - "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . - . - "MINT-10000"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^PASS\\d{5}$"^^ . - "4349895"^^ . - . - . - . - . - . - . - . - . - . - . - "Molecule role (INOH Protein name/family name ontology)" . - "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Life cycle stages for Human"^^ . - . - . - . - "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - "NIF Standard Ontology: Digital Resources" . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - "Locus Reference Genomic" . - . - "0001885"^^ . - . - . - . - . - "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . - "GitHub is an online host of Git source code repositories."^^ . - . - . - . - "MIR:00100005"^^ . - . - "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . - . - . - . - "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . - . - . - . - . - . - . - . - . - . - "CNBG_0001"^^ . - . - . - . - . - "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . - . - . - . - "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . - . - . - . - . - . - . - "http://www.pathwaycommons.org/pc/"^^ . - . - . - "^CCDS\\d+\\.\\d+$"^^ . - . - . - . - . - _:N8c5dcd9b34684b1b96b6c48d1e5d2a99 . - . - . - . - . - . - "MIRIAM Registry collection" . - . - "https://glyconavi.org/hub/?id=$1"^^ . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . - . - . - . - . - "Ascomycete phenotype ontology" . - . - . - "true"^^ . - . - . - . - . - "https://ximbio.com/reagent/$1"^^ . - . - . - . - . - "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . - . - . - . - . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^ . - "^[A-Za-z_0-9]+$"^^ . - . - . - "Q9UKQ2"^^ . - "https://www.wormbase.org/"^^ . - "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"^^ . - "Assists in resolving data across cloud resources."^^ . - "0002005"^^ . - . - "Open Data for Access and Mining" . - . - . - "false"^^ . - . - "^((VGNC|vgnc):)?\\d{1,9}$"^^ . - "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . - . - "A0118748"^^ . - . - "https://github.com/OOSTT/OOSTT"^^ . - . - "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . - . - . - "https://github.com/EBISPOT/DUO"^^ . - "4"^^ . - . - "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . - "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . - "false"^^ . - . - . - . - . - . - "http://www.violinet.org/vaccineontology"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - . - . - "http://doqcs.ncbs.res.in/"^^ . - . - "CLPUB00496"^^ . - "miRBase mature miRNA" . - . - . - . - . - . - . - . - . - "https://doulix.com"^^ . - . - . - "CATH domain" . - . - . - . - "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . - . - . - "Oryzabase Reference" . - . - . - . - "BRENDA tissue / enzyme source" . - "^\\d+$"^^ . - . - . - . - "Fungal Nomenclature and Species Bank" . - "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . - . - . - . - . - "Tom Gillespie" . - . - . - . - . - . - "http://flyrnai.org/"^^ . - . - . - "T30002"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - "Foundational Model of Anatomy" . - "https://www.wormbase.org/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "DEF"^^ . - . - . - . - "Pazar Transcription Factor" . - "FBgn0000015"^^ . - "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . - . - . - . - "true"^^ . - . - . - . - . - . - . - "KEGG Reaction" . - . - "CTD Disease" . - "0003463"^^ . - "false"^^ . - "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . - "false"^^ . - . - . - . - . - "3075966"^^ . - "http://www.protonet.cs.huji.ac.il/"^^ . - . - . - . - . - "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . - "5.A.1.1.1"^^ . - . - . - "http://modelseed.org/biochem/compounds/$1"^^ . - . - . - . - . - "^[\\d.]+$"^^ . - "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . - "false"^^ . - . - . - . - . - "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . - . - . - "Primate Brain Atlas" . - . - . - . - . - "https://doi.org/$1"^^ . - "https://wiki.phenoscape.org/wiki/Curation_workflow"^^ . - "^.+$"^^ . - . - "false"^^ . - "https://portal.gdc.cancer.gov/cases/$1"^^ . - . - . - . - . - "An ontology of prokaryotic phenotypic and metabolic characters"^^ . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - "Luis González-Montaña" . - . - . - . - . - . - . - "http://www.isni.org"^^ . - . - . - . - . - "MIPModDB" . - . - . - . - . - . - "PhosphoPoint Kinase" . - "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . - . - . - . - "00000021"^^ . - "Coronavirus Infectious Disease Ontology" . - "^\\d{7}$"^^ . - . - "true"^^ . - . - "^\\d+$"^^ . - "http://www.cropontology.org/ontology/CO_327/Pearl%20millet"^^ . - . - "BAMSC981"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . - . - . - . - . - . - "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^ . - . - "false"^^ . - . -_:N8c5dcd9b34684b1b96b6c48d1e5d2a99 "Jonathan Bard" . - . - . - . - . - . - . - "0000013"^^ . - . - . - . - . - "^spike\\d{5}$"^^ . - . - "Meng LIU" . - "http://purl.obolibrary.org/obo/TRANS_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Nucleotide Sequence Database" . - . - . - "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - "None"^^ . - . - . - . - . - . - "http://purl.org/dc/terms/$1"^^ . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - "^[AEP]-\\w{4}-\\d+$"^^ . - "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . - . - . - . - "886"^^ . - "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^ . - "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . - "1000"^^ . - . - . - . - . - . - . - "Addgene Plasmid Repository" . - "false"^^ . - "Mechanism, Annotation and Classification in Enzymes" . - "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/LABO_$1"^^ . - "Foods in FooDB"^^ . - "PASS01237"^^ . - . - "MagnitudeValueType"^^ . - "true"^^ . - "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . - "International Genome Sample Resource" . - "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . - . - . - . - "^(Gi|Gc)\\d+$"^^ . - "PR00001"^^ . - . - . - "Molecular Modeling Database" . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . - . - "https://portal.issn.org/resource/ISSN/$1"^^ . - . - . - . - . - . - "https://www.rebuildingakidney.org/id/$1"^^ . - . - . - . - . - . - . - "Ax1"^^ . - "false"^^ . - . - "^PAR:\\d+$"^^ . - . - "https://www.getty.edu/research/tools/vocabularies/tgn/"^^ . - "https://disprot.org/$1"^^ . - "https://cls.shop/"^^ . - . - "http://func.mshri.on.ca/mouse/"^^ . - . - . - "https://www.thermofisher.com"^^ . - "None"^^ . - . - . - "SciCrunch Registry" . - . - . - . - . - . - . - "2842"^^ . - . - . - . - "^\\d+$"^^ . - . - "https://web.www.healthdatagateway.org/dataset/$1"^^ . - "https://github.com/monarch-initiative/GENO-ontology/"^^ . - . - "Nico Matentzoglu" . - "XUO" . - . - . - . - . - . - . - . - "http://vegbank.org/cite/$1"^^ . - "https://github.com/obo-behavior/behavior-ontology/"^^ . - . - . - . - . - . - "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "Vertebrate Gene Nomenclature Committee" . - "LOC_Os02g13300"^^ . - . - "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . - . - "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . - . - "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . - "https://www.uniprot.org/diseases/$1"^^ . - . - . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . - "BacMap Map" . - . - "G8944"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "3966782"^^ . - . - "^\\d{7}$"^^ . - "Assembling the Fungal Tree of Life - Taxonomy" . - . - . - . - . - "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . - . - . - . - "Salk Institute for Biological Studies" . - . - "DrugBank" . - . - "false"^^ . - . - "http://ensembl.org/glossary"^^ . - "http://purl.obolibrary.org/obo/ZECO_$1"^^ . - . - "AntWeb ID" . - . - . - "^\\d{7}$"^^ . - "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . - . - . - . - . - . - . - . - "992"^^ . - . - "Mouse Developmental Anatomy Ontology" . - "https://github.com/aellenhicks/htn_owl"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d{8}$"^^ . - . - "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . - "false"^^ . - . - . - . - . - . - "http://ontoneo.com"^^ . - . - . - . - "^\\w+$"^^ . - "^\\d{7}$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - "Image Data Resource" . - "^\\d+$"^^ . - . - "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . - . - . - "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . - "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . - "https://lhncbc.nlm.nih.gov/semanticnetwork/"^^ . - . - "^GPM\\d+$"^^ . - "2701"^^ . - . - . - . - . - "http://arabidopsis.org/index.jsp"^^ . - . - "biopragmatics/bioregistry/416"^^ . - . - . - "https://reaxys.emolecules.com"^^ . - . - . - . - . - "C6155"^^ . - . - . - "false"^^ . - . - . - "002804"^^ . - . - "^(cl|tum)\\d+$"^^ . - . - "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . - . - . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "Ontology of Microbial Phenotypes" . - . - "AU124"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "0000947"^^ . - "ISCW007415"^^ . - . - "https://github.com/OpenLHS/PDRO"^^ . - "https://github.com/AgriculturalSemantics/agro"^^ . - "false"^^ . - . - "12345"^^ . - . - . - . - . - "RXN-14904"^^ . - . - . - . - . - . - . - "false"^^ . - "http://teddyontology.sourceforge.net/"^^ . - "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . - . - . - "Diseases Database" . - . - "false"^^ . - . - "^TC\\d+$"^^ . - . - . - "Mammalian Feeding Muscle Ontology" . - "JCRB1355"^^ . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "false"^^ . - . - "https://www.cropontology.org/rdf/CO_333:$1"^^ . - . - . - . - . - . - . - . - "http://www.depod.bioss.uni-freiburg.de"^^ . - . - . - . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "Schema for the export of the Bioregistry as RDF"^^ . - "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . - . - . - . - . - "Identifiers.org" . - "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . - "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . - . - "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . - . - . - . - "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . - "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/"^^ . - . - . - . - "false"^^ . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . - . - . - . - . - . - "2008-005144-16"^^ . - . - "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . - . - "https://www.imanislife.com/collections/cell-lines/"^^ . - . - . - . - "^[a-z0-9]+$"^^ . - "http://qudt.org/schema/qudt#$1"^^ . - . - . - "false"^^ . - "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . - . - "http://phenol-explorer.eu/foods/$1"^^ . - . - . - . - . - . - . - . - "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . - . - . - "European Paediatric Cardiac Codes" . - . - "ClinVar Record" . - "OntoBee" . - . - . - . - . - "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . - . - . - . - "182"^^ . - . - "1023371"^^ . - "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . - "http://purl.obolibrary.org/obo/EMAP_$1"^^ . - . - "^(G|P|U|C|S)\\d{5}$"^^ . - . - "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . - . - "ANOVA"^^ . - . - . - . - . - . - . - . - "ViralZone" . - . - . - "https://foodb.ca/foods"^^ . - . - . - "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . - . - "https://w3id.org/biolink/vocab/$1"^^ . - "An ontology to describe entities related to cardiovascular diseases"^^ . - . - . - . - . - . - . - . - "A download link for the given resource" . - . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . - "NeuroVault Image" . - . - . - "^[0-9]+$"^^ . - . - . - . - . - "http://rebase.neb.com/rebase/"^^ . - . - . - . - "MNXC15"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . - . - . - . - "^[a-z0-9\\-_]+$"^^ . - "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . - "The Prescription of Drugs Ontology" . - . - . - "http://www.wikigenes.org/e/gene/e/$1.html"^^ . - . - "Europe PMC Preprints" . - "false"^^ . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - . - "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . - . - . - "A hierarchical classification of congenital heart disease "^^ . - . - . - . - . - . - "Higher-level classifications of COG Pathways"^^ . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . - . - . - "Cell line databases/resources"^^ . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - . - "PANTHER Pathway Component" . - . - . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/"^^ . - . - "MultiCellDS collection" . - . - . - . - . - . - "1242"^^ . - "IPI"^^ . - "https://www.mlcommons.org/mlc-id/$1"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1"^^ . - . - . - . - . - "http://www.w3.org/2001/XMLSchema#$1"^^ . - . - "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . - . - . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . - . - . - "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . - "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . - . - . - . - . - . - . - "NINDS Human Cell and Data Repository" . - . - . - . - "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^ . - . - . - "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . - . - . - . - . - . - . - . - . - "0011124"^^ . - . - "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "E-MTAB-2037"^^ . - "^\\d+$"^^ . - . - . - "http://biohackathon.org/resource/faldo"^^ . - . - . - . - "0000858"^^ . - . - . - . - "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . - . - "KEGG Disease" . - . - . - "^MNEST\\d+$"^^ . - . - "^\\d{7}$"^^ . - "A nomenclatural ontology for biological names" . - "false"^^ . - . - . - . - . - "false"^^ . - "Cellosaurus" . - "H-InvDb Transcript" . - . - . - "0011140"^^ . - . - . - . - "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . - . - . - . - . - . - . - "The Amphioxus Development and Anatomy Ontology" . - . - . - . - "CHEBI" . - "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . - . - . - "0000512"^^ . - . - "0000006"^^ . - . - . - "http://bacmap.wishartlab.com/"^^ . - . - . - _:N1ba6405f9f084822bd133523fd7c1e55 . - . - . - . - "https://github.com/obophenotype/cephalopod-ontology"^^ . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - "BioSystems" . - . - . - "https://github.com/NCI-Thesaurus/thesaurus-obo-edition"^^ . - . - . - . - . - . - "https://www.bio.di.uminho.pt/"^^ . - "ACM1_HUMAN"^^ . - "Neural ElectroMagnetic Ontology" . - . - . - "false"^^ . - . - . - "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . - . - "https://www.google.com/patents/"^^ . - "http://purl.obolibrary.org/obo/TAO_$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . - . - . - . - . - . - . - . - "Ligand Expo" . - . - . - "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - "https://github.com/EcologicalSemantics/ecocore"^^ . - . - . - . - . - "NA06985"^^ . - "https://n2t.net"^^ . - . - . - . - "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . - . - . - . - . - "XML Schema Definition" . - . - "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . - . - "977869"^^ . - "^\\d{8}$"^^ . - . - . - . - . - . - . - . - "Berkeley Drosophila Genome Project EST database" . - "http://www.cellresource.cn"^^ . - . - "EG10173"^^ . - . - . - . - . - "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . - . - . - "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "MatrixDB" . - "^[8-9]\\d{3}(/[0-3])?$"^^ . - "0000005"^^ . - . - . - "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . - "http://beetlebase.org/"^^ . - . - . - . - . - . - "^EG\\d+$"^^ . - . - . - . - . - . - "11"^^ . - "0002999"^^ . - . - "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . - "http://kinase.bioinformatics.tw/"^^ . - . - . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . - . - . - "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - . - . - . - "http://degradome.uniovi.es/"^^ . - . - "0005147"^^ . - . - . - . - . - "neXtProt family" . - "false"^^ . - . - . - "PRJDB3"^^ . - . - . - . - . - "http://aber-owl.net" . - . - . - "https://www.metanetx.org/"^^ . - "false"^^ . - . - "https://open.med.harvard.edu/wiki/display/eaglei/Ontology"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . - . - "http://browser.planteome.org/amigo"^^ . - . - "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . - . - . - . - "http://www.cghtmd.jp/CGHDatabase/index_e.jsp"^^ . - "Intrinsically Disordered Proteins Ontology" . - "0000194"^^ . - . - . - "http://www.allergome.org/"^^ . - . - "SIGNOR Relation" . - . - "GenProp0699"^^ . - "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . - "1100107"^^ . - . - . - . - . - . - "Pablo Porras Millán" . - "https://www.yeastgenome.org/"^^ . - "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . - "http://purl.obolibrary.org/obo/CMF_$1"^^ . - . - . - . - . - . - . - . - . - "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . - . - "^HGVM\\d+$"^^ . - . - . - . - . - . - . - "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . - . - . - . - . - . - . - . - "GPIb_IX_V"^^ . - . - . - . - . - . - . - "Gene Ontology Registry" . - "false"^^ . - . - . - "0000000"^^ . - "false"^^ . - . - . - . - . - . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^GCST\\d{6}\\d*$"^^ . - "urn:nbn:fi:tkk-004781"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "00050"^^ . - . - "Workflow"^^ . - "http://www.ncbi.nlm.nih.gov/CCDS/"^^ . - . - "An ontology covering the taxonomy of teleosts (bony fish)"^^ . - "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . - . - "http://purl.obolibrary.org/obo/ICEO_$1"^^ . - . - . - "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . - . - . - . - . - "https://www.reaxys.com"^^ . - . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . - "^\\w+$"^^ . - . - "false"^^ . - "Jennifer Smith" . - . - . - . - "false"^^ . - . - . - . - . - "http://www.peptideatlas.org/PASS/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . - . - "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . - "273"^^ . - . - . - . - . - . - . - . - . - . - "6b1"^^ . - . - . - . - "Curated Drug-Drug Interactions Database - Interaction" . - . - "false"^^ . - "Nucleotide" . - . - . - . - . - . - "false"^^ . - . - "Genetics Home Reference" . - . - "false"^^ . - "Signaling Pathways Project" . - "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "Bio-Pesticides DataBase" . - . - . - . - . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "https://www.w3.org/TR/owl-features/"^^ . - . - "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . - . - . - . - "Bioregistry Metaregistry" . - . - . - . -_:N3eafaa6720aa47748ed435d032917ea0 "Maria Herrero" . - "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."^^ . - . - . - . - . - . - "false"^^ . - "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html"^^ . - "0000069"^^ . - . - "Coriell Institute for Medical Research" . - . - . - "true"^^ . - . - . - . - "0000029"^^ . - . - "Cell line collections"^^ . - . - . - . - . - . - "https://bioregistry.io/resolve/github/issue/$1"^^ . - . - . - . - . - "false"^^ . - . - . - "https://pypi.org/project/$1"^^ . - . - "https://github.com/VEuPathDB-ontology/MIRO"^^ . - "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . - . - . - "http://www.marinespecies.org/"^^ . - . - . - . - "false"^^ . - "Wikidata" . - "nstd102"^^ . - . - . - . - . - . - . - . - "ChEMBL" . - "http://www.kegg.jp/entry/$1"^^ . - . - . - "The Virus Infectious Disease Ontology" . - "Software"^^ . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - . - . - "The Bioinorganic Motif Database" . - . - . - . - . - . - "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . - . - . - "http://comgen.pl/mirex/?page=home"^^ . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "https://pdc.cancer.gov/pdc/study/$1"^^ . - . - . - . - . - . - "Edison Ong" . - . - . - . - . - . - "NCI Pathway Interaction Database: Pathway" . - . - . - . - . - . - . - "A frontend to Wikidata"^^ . - . - . - . - . - "false"^^ . - "https://eol.org"^^ . - "false"^^ . - . - . - . - . - . - . - "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . - . - . - . - . - . - . - . - . - "Genomics of Drug Sensitivity in Cancer" . - . - "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . - "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . - "01406"^^ . - . - . - "EcoPortal" . - . - . - . - . - . - . - . - "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . - . - . - . - . - . - . - . - . - . - "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . - "true"^^ . - "Study inside StoreDB"^^ . - . - . - . - "false"^^ . - . - . - "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . - . - "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . - . - . - . - . - . - "D053716"^^ . - "World Wildlife Fund Ecoregion" . - "https://github.com/EBISPOT/amphx_ontology"^^ . - . - . - "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . - . - "MicrosporidiaDB" . - . - . - "http://purl.obolibrary.org/obo/ATO_$1"^^ . - . - "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . - . - "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . - "^\\d+$"^^ . - . - "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . - . - . - "^\\d{7}$"^^ . - "https://www.ebi.ac.uk/ega/studies/$1"^^ . - . - . - "^\\d{7}$"^^ . - "http://www.w3.org/ns/prov#$1"^^ . - . - . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/IDODEN"^^ . - . - "Yeast phenotypes" . - "Registry of Research Data Repositories" . - . - . - . - "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . - . - "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . - . - "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . - . - "BQJCRHHNABKAKU"^^ . - . - . - "false"^^ . - . - . - "https://animaldiversity.org/accounts/$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . - . - . - . - . - "BindingDB" . - . - . - "00620027"^^ . - . - . - . - "false"^^ . - . - . - "ChEBI"^^ . - "^\\d{7}$"^^ . - "Chen Yang" . - . - . - . - . - "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . - "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . - . - . - . - . - . - "RAP-DB Locus" . - . - . - . - . - . - "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . - . - . - . - . - . - . - . - . - "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . - . - . - . - . - "Arabidopsis Small RNA Project" . - . - "false"^^ . - "ChEBI Integrated Role Ontology" . - "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . - "http://prodom.prabi.fr/prodom/current/html/home.php"^^ . - . - . - . - . - . - . - "https://www.uniprot.org/docs/tisslist.txt"^^ . - . - . - . - . - "https://github.com/luis-gonzalez-m/Collembola"^^ . - . - . - "Publishing Roles Ontology" . - . - "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "090701"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - "Eschmeyer's Catalog of Fishes" . - . - . - . - "false"^^ . - . - . - "TVAG_386080"^^ . - . - . - "4776"^^ . - . - "https://www.ncbi.nlm.nih.gov/books/$1"^^ . - . - "false"^^ . - . - "0000124"^^ . - "false"^^ . - . - . - . - . - . - . - "Friend of a Friend" . - . - . - . - . - . - . - . - . - "^FB\\w{2}\\d{7}$"^^ . - . - . - "https://fungi.ensembl.org/id/$1"^^ . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - "CORDIS Project" . - "https://www.cropontology.org/rdf/CO_347:$1"^^ . - . - . - "https://scicrunch.org/browse/resourcedashboard"^^ . - . - . - . - . - . - . - "HomologyRelation"^^ . - . - . - . - "false"^^ . - "G00123"^^ . - . - . - . - . - . - . - . - "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "BioSample" . - "Semantic Web Context" . - . - . - . - . - . - . - . - . - . - "Prefix Commons" . - . - . - "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . - . - . - "1-FEH+w3"^^ . - "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^ . - . - . - . - . - . - "Information about the C57BL/6J. Includes genetic background and disease data."^^ . - . - . - . - "0000404"^^ . - . - "hsa-let-7a"^^ . - "http://www.kazusa.or.jp/rouge/"^^ . - . - "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/ZFS_$1"^^ . - . - "false"^^ . - . - "00000022"^^ . - "STOREDB at University of Cambridge" . - . - . - . - . - . - . - . - . - . - . - . - . - "WikiGenes" . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "https://cellbank.nibiohn.go.jp"^^ . - . - . - "http://purl.obolibrary.org/obo/OPMI_$1"^^ . - . - "true"^^ . - "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . - . - "false"^^ . - . - . - . - . - "^\\d{6}$"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - "true"^^ . - "false"^^ . - . - "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . - . - . - . - . - "false"^^ . - . - . - "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . - . - "128011350"^^ . - . - . - . - . - . - . - . - . - . - . - "BitterDB Receptor" . - . - . - "^Os\\S+t\\d{7}-\\d{2}$"^^ . - . - "http://mona.fiehnlab.ucdavis.edu/"^^ . - . - "GALEN" . - . - . - "MHC Restriction Ontology" . - . - . - "Enzyme Commission Code" . - . - . - "https://smpdb.ca/"^^ . - . - . - . - "false"^^ . - "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$"^^ . - "false"^^ . - . - "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . - . - . - "^\\d{7}$"^^ . - . - "http://www.homd.org/index.php"^^ . - "^ACYPI\\d{6}(-RA)?$"^^ . - "^\\w+$"^^ . - . - "microRNA Ontology" . - . - . - . - "http://bigg.ucsd.edu/models"^^ . - "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . - . - . - "Os01t0883800-02"^^ . - . - "^SIGNOR\\-[A-Z]+\\d+$"^^ . - . - "Unified Medical Language System Atomic Unique Identifier" . - "false"^^ . - . - . - . - "0000001"^^ . - . - . - . - . - "https://www.lgcstandards-atcc.org"^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.boldsystems.org/"^^ . - "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . - . -_:N17668a26737c4d38a76d229b061cfa85 "Julie Thompson" . - "^[0-9]+$"^^ . - "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^PA\\w+$"^^ . - . - "false"^^ . - "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . - . - "^\\d{7}$"^^ . - "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . - . - . - "^[a-z][a-z]/[0-9]+$"^^ . - . - . - . - "Stemcell Knowledge and Information Portal" . - . - . - . - "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^ . - "false"^^ . - . - . - . - "83088"^^ . - . - . - . - . - . - "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . - "https://www.wikidata.org/wiki/Property:$1" . - . - . - . - . - . - "Resource Description Framework" . - . - . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "false"^^ . - "165a"^^ . - . - "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . - . - "false"^^ . - . - "Resource" . - . - . - . - . - "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo"^^ . - . - . - . - "7499841"^^ . - . - . - . - . - "1a05"^^ . - "AS000060"^^ . - . - "http://crispr.i2bc.paris-saclay.fr/"^^ . - "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . - . - "^[1-9]\\d*$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "131"^^ . - . - . - "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . - . - . - "^\\d{7}$"^^ . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - "^LRG_\\d+$"^^ . - "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . - "TR0000001"^^ . - "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . - . - "Crop Ontology Curation Tool" . - "PR000001"^^ . - . - . - . - "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . - . - . - . - "false"^^ . - "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . - "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . - . - . - "100810"^^ . - . - . - . - . - . - "VFG2154"^^ . - . - . - . - . - . - . - . - "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . - . - . - . - . - . - "Biological Imaging Methods Ontology" . - "http://cutdb.burnham.org"^^ . - . - . - . - . - . - . - "false"^^ . - . - "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html"^^ . - . - . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . - . - . - "http://www.cathdb.info/"^^ . - . - . - . - . - . - . - . - . - . - "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . - . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . - "false"^^ . - "DragonDB Protein" . - "Benjamin Gyori" . - "false"^^ . - . - . - "http://cellimagelibrary.org/"^^ . - "true"^^ . - . - "false"^^ . - . - . - . - . - . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . - "https://www.doi.org/"^^ . - . - . - "Rat Genome Database strain" . - . - "false"^^ . - . - "AKR-270"^^ . - . - . - . - "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en"^^ . - . - "0000190"^^ . - . - "0001"^^ . - "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . - . - . - "TC010103"^^ . - . - "Biological Spatial Ontology" . - . - . - "10531"^^ . - . - . - . - . - . - "http://www.cathdb.info/cathnode/$1"^^ . - "https://loinc.org/"^^ . - . - . - . - . - "A controlled vocabulary to describe phenotypic traits in plants."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . -_:N8f13ab592d71468f95827752341fe101 "Fahim Imam" . - "Immune Epitope Database" . - . - . - . - . - . - . - . - . - . - . - . - . - "^bsg-[dscp]?\\d{6}$"^^ . - . - . - . - . - . - . - "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^ . - . - . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - "^\\d+$"^^ . - . - "Genomes Online Database" . - . - . - "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . - . - . - . - . - . - "000140" . - . - . - "EDAM Ontology" . - . - . - . - . - . - . - . - . - "http://www.lipidmaps.org"^^ . - . - . - "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . - "http://www.sparontologies.net/ontologies/biro"^^ . - "^\\d+$"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . - . - "false"^^ . - . - . - . - . - "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . - "http://bioportal.bioontology.org/ontologies/OPB"^^ . - . - . - "IA"^^ . - . - . - . - . - . - "5359"^^ . - . - . - . - "false"^^ . - . - . - . - "http://dictybase.org/gene/$1"^^ . - "https://github.com/"^^ . - . - . - "JCGG-STR008690"^^ . - "2"^^ . - . - . - . - . - "^IPR\\d{6}$"^^ . - . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . - "141"^^ . - . - . - . - . - . - "https://cordis.europa.eu/"^^ . - "Wasila Dahdul" . - . - . - . - . - . - . - "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . - . - "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^ . - . - "http://pax-db.org/"^^ . - "^\\d+$"^^ . - "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . - "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - . - . - . - . - . - . - . - . - . - "THE1B"^^ . - . - "Monarch Disease Ontology" . - . - . - "117"^^ . - "https://www.uniprot.org/tissues/$1"^^ . - . - . - "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . - . - . - "false"^^ . - . - . - "MassIVE" . - "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . - "^\\d+$"^^ . - . - "true"^^ . - . - . - . - . - . - . - "http://thebiogrid.org/"^^ . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "http://www.transcriptionfactor.org/"^^ . - "Index Fungorum" . - "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . - . - "Database of human Major Histocompatibility Complex" . - . - "D00123"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar"^^ . - "Lonza" . - "^A\\d{6}$"^^ . - "http://purl.obolibrary.org/obo/CLAO_$1"^^ . - "4000027"^^ . - . - . - . - "22RV1_12_2019"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - "GWAS Catalog" . - "https://www.who.int/classifications/icd/adaptations/oncology/en/"^^ . - "http://www.proteinmodelportal.org/"^^ . - . - "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . - "0010316"^^ . - . - . - "http://purl.obolibrary.org/obo/HSO_$1"^^ . - "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries."^^ . - "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . - "https://pharmacodb.ca/datasets"^^ . - . - . - "https://www.insdc.org/"^^ . - . - . - . - . - . - "https://medlineplus.gov/genetics/condition/$1"^^ . - "CAA71118.1"^^ . - "European Searchable Tumour Line Database" . - "http://purl.obolibrary.org/obo/fbcv"^^ . - . - "^\\d+$"^^ . - . - . - "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . - . - "^\\d{7}$"^^ . - . - . - "http://mycobrowser.epfl.ch/leprosy.html"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"^^ . - . - . - . - "false"^^ . - "http://www.vbase2.org/vbase2.php"^^ . - . - . - . - . - . - . - "false"^^ . - "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . - . - . - . - . - . - "http://purl.uniprot.org/uniprot/$1"^^ . - . - . - . - . - . - . - "12300"^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . - . - . - . - . - . - . - "LMPR0102010012"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "Clair Kronk" . - "^DBSALT\\d{6}$"^^ . - . - "https://data.4dnucleome.org/biosources"^^ . - . - "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "^\\w+(\\.)?(\\d+)?$"^^ . - . - . - . - . - "0000-0002-5355-2576"^^ . - . - "false"^^ . - . - . - . - "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . - "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^ . - "National Experimental Cell Resource Sharing Platform" . - . - . - "bsg-000052"^^ . - "RC00001"^^ . - . - . - . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - . - . - "EBI-366083"^^ . - . - "false"^^ . - . - "1433C_TOBAC_1_252"^^ . - . - "^\\w+$"^^ . - "http://www.yeastgenome.org/"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ADO_$1"^^ . - . - "http://www.pantherdb.org/"^^ . - "ChEBI Data Sources" . - "false"^^ . - . - "false"^^ . - "^P\\w+$"^^ . - "https://www.uniprot.org/journals"^^ . - . - "UCR00513"^^ . - . - "Minimum Anformation About a Phylogenetic Analysis Ontology" . - . - . - . - . - "http://www.affymetrix.com/"^^ . - . - . - . - "^[-A-Za-z0-9\\_]*$"^^ . - . - . - "false"^^ . - . - . - "https://github.com/aszool/oarcs"^^ . - "Vertebrate Homologous Organ Group Ontology" . - "Cell line databases/resources"^^ . - . - . - . - "^DB-\\d{4}$"^^ . - . - . - . - . - . - "40565"^^ . - . - . - "http://cellimagelibrary.org/images/$1"^^ . - . - "Oral Health and Disease Ontology" . - "false"^^ . - . - . - . - . - "^\\w+$"^^ . - . - . - "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://www.hgmd.cf.ac.uk/ac/index.php"^^ . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"^^ . - "false"^^ . - . - . - . - . - "RL3R1_HUMAN"^^ . - "https://human.brain-map.org"^^ . - . - . - "Ensembl Glossary" . - "MetaboLights Compound" . - "http://purl.obolibrary.org/obo/$1"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . - "^\\d+$"^^ . - _:N588fa78509cf44fcb7a6ae69d44fdcad . - . - . - "^\\d{7}$"^^ . - . - . - . - "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . - . - . - . - . - . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "31"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "IUPHAR family" . - . - "false"^^ . - . - . - . - . - . - "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . - . - "false"^^ . - "dictyBase Expressed Sequence Tag" . - . - "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - "GWAS Central Study" . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/$1" . - . - . - . - . - "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . - "CellBank Australia" . - . - . - "http://www.wormbase.org/get?name=$1"^^ . - . - "MIPF0000002"^^ . - . - "^SM\\d{5}$"^^ . - . - "true"^^ . - . - "NIH RePORTER" . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^ . - "https://www.ncbi.nlm.nih.gov/projects/RefSeq/"^^ . - . - "http://tables.pseudogene.org/[?species_name]/$1"^^ . - "false"^^ . - . - . - "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . - "^.*?--%3E.*?$"^^ . - . - . - . - . - . - "^[1-9][0-9]{3,6}$"^^ . - "false"^^ . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . - "Ontology about the development and life stages of the C. elegans"^^ . - "Leszek Vincent" . - . - . - "false"^^ . - . - . - "false"^^ . - . - "Data Catalog" . - . - . - . - . - . - . - "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"^^ . - "http://pombe.oridb.org/index.php"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . - . - . - . - "Cell Line Database" . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - "5601141"^^ . - . - "http://bigg.ucsd.edu/universal/metabolites"^^ . - . - . - . - . - . - . - . - "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . - . - . - "DrugBank Target v4" . - "^\\d+$"^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1"^^ . - . - "The Behaviour Change Intervention Ontology" . - . - . - . - "0376"^^ . - . - . - . - . - . - "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . - "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . - . - "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . - . - . - "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . - . - "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . - "true"^^ . - . - "^(ENSFM|ENSGTV:)\\d+$"^^ . - "false"^^ . - "^PS\\d{5}$"^^ . - . - . - "http://webapps2.ucalgary.ca/~groupii/"^^ . - . - . - "false"^^ . - . - . - . - "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . - "https://www.geonames.org/$1"^^ . - . - . - "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . - "eagle-i" . - . - . - "http://purl.obolibrary.org/obo/OMO_$1"^^ . - . - "Network of Different Plant Genomic Research Projects" . - . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "FuTRES Ontology of Vertebrate Traits" . - . - . - . - . - . - . - . - . - . - . - "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - "false"^^ . - . - . - . - "http://ciliate.org/index.php/feature/details/$1"^^ . - . - . - "https://www.fdilab.org"^^ . - . - . - . - "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . - "100000000000001"^^ . - "Cancer Data Standards Registry and Repository" . - . - "SubstrateDB" . - "https://identifiers.org/$1:$2" . - . - . - . - "https://repo.napdi.org/study/$1"^^ . - "18"^^ . - . - . - "Software Heritage" . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - "^[a-zA-Z0-9_-]{3,}$"^^ . - "0000009"^^ . - "1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/fbbt"^^ . - "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . - . - . - . - "derivatives%2Fthiocyclam%20hydrochloride"^^ . - . - "^\\d+$"^^ . - . - . - "true"^^ . - . - . - "https://cropontology.org/ontology/CO_324/Sorghum"^^ . - "http://www.hmdb.ca/metabolites/$1"^^ . - . - . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "Catalytic Site Atlas" . - "0002233"^^ . - . - "^R\\d+$"^^ . - . - . - . - "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . - . - . - "00007294"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PDRO_$1"^^ . - "Sample processing and separation techniques" . - "Bilateria anatomy" . - . - . - . - . - . - . - . - . - . - "^bt\\d+$"^^ . - "D00001"^^ . - "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . - "GPM32310002988"^^ . - . - "FlyBrain Neuron Database" . - "http://www.pazar.info/"^^ . - . - "^\\d+$"^^ . - . - . - "16S rRNA gene database" . - "MeSH 2013" . - "false"^^ . - "https://www.ebi.ac.uk/ena/"^^ . - . - "Current Procedural Terminology" . - . - . - "http://biohackathon.org/resource/faldo#$1"^^ . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - "false"^^ . - . - . - "Bio-MINDER Tissue Database" . - . - "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . - . - . - . - "http://scipion.i2pc.es/ontology/cryoem"^^ . - "nsv3875336"^^ . - . - . - . - . - "https://www.picb.ac.cn/limore/home"^^ . - . - "Alpha Tom Kodamullil" . - . - . - . - . - . - "false"^^ . - . - . -_:Nb0ec7efeb75b4de9b762aee59d29de3f "Stephen Larson" . - . - "^\\d{8}$"^^ . - . - . - . - "Gramene QTL" . - "AspGD Protein" . - "false"^^ . - "Matt Yoder" . - "https://loinc.org/$1"^^ . - . - . - . - . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . - "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . - . - . - . - . - "false"^^ . - "0000008"^^ . - "https://github.com/DIDEO/DIDEO"^^ . - . - . - "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . - "URS0000759CF4"^^ . - "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . - "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - . - . - . - . - "RepeatsDB Protein" . - . - "^PDC\\d+$"^^ . - "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . - . - . - "0001191"^^ . - . - . - . - . - . - . - . - . - . - . - "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . - "Tom Gillespie" . - "http://cutdb.burnham.org/relation/show/$1"^^ . - "https://www.ebi.ac.uk/arrayexpress/"^^ . - "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ONS_$1"^^ . - . - "Mathematical modeling ontology" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "http://www.protonet.cs.huji.ac.il/"^^ . - "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - "^[A-Za-z]+\\/[0-9]+$"^^ . - "434"^^ . - . - . - . - . - . - . - "1001"^^ . - "1664"^^ . - . - "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . - "SugarBind" . - . - . - "http://purl.bioontology.org/ontology/MEDDRA/$1"^^ . - "https://www.iedb.org/reference/$1"^^ . - . - . - . - . - "https://github.com/obophenotype/human-developmental-anatomy-ontology/"^^ . - . - . - . - . - . - . - . - . - "AGRO" . - . - . - . - "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . - "false"^^ . - . - . - "ScerTF" . - . - "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . - . - . - . - . - . - . - . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv"^^ . - "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - . - . - . - . - "ViralZone" . - "Anne Morgat" . - "https://github.com/insect-morphology/colao"^^ . - . - "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . - . - "http://tfclass.bioinf.med.uni-goettingen.de"^^ . - . - . - . - . - . - . - "Database for Prokaryotic Operons" . - . - "Name Reaction Ontology" . - "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . - . - . - . - . - "CALM1"^^ . - . - . - "false"^^ . - . - . - "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . - . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - "NONCODE v4 Gene" . - "http://www.drugbank.ca"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/RS_$1"^^ . - . - . - . - "TIGR00010"^^ . - "foaf" . - . - . - . - . - . - . - . - . - . - "github" . - "false"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OMP_$1"^^ . - . - . - . - . - "23"^^ . - . - "false"^^ . - "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . - . - . - . - "https://bdsc.indiana.edu/stocks/$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "Tetrahymena Genome Database" . - . - "63250"^^ . - . - . - "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - . - . - "false"^^ . - "^DB\\d{5}$"^^ . - . - . - . - . - . - "Healthcare Common Procedure Coding System" . - . - . - . - "https://www.ebi.ac.uk/miriam/"^^ . - "0005250"^^ . - . - . - "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . - . - . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . - "AMDEFA"^^ . - "http://addgene.org/$1"^^ . - . - . - "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . - . - . - . - . - "Clare Pilgrim" . - . - . - "http://purl.obolibrary.org/obo/RNAO_$1"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"^^ . - . - . - . - . - . - . - . - . - . - "http://www.maizemap.org/"^^ . - "^\\d{8}$"^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . - . - . - . - . - . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . - . - . - . - "Proteoform Atlas" . - "http://www.cs.tau.ac.il/~spike/"^^ . - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - "false"^^ . - "Livestock Breed Ontology" . - . - . - . - . - "http://pax-db.org/"^^ . - . - "FlyBase Controlled Vocabulary" . - . - . - "http://purl.obolibrary.org/obo/VO_$1"^^ . - . - . - . - "1354581"^^ . - . - . - . - "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . - . - . - "https://github.com/obophenotype/c-elegans-phenotype-ontology"^^ . - . - . - . - . - . - . - "Leigh Carmody" . - . - . - . - . - . - . - . - . - . - "5HT3Arano"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "International Histocompatibility Workshop cell lines" . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . - "http://purl.obolibrary.org/obo/WBbt_$1"^^ . - . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . - . - . - . - . - "Xenobiotics Metabolism Database" . - . - . - _:N8c9982accff54cf18941c023927a9382 . - . - "1122888"^^ . - "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . - . - "false"^^ . - . - "^\\d{6,7}$"^^ . - . - . - "^.+$"^^ . - "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . - "true"^^ . - . - . - . - "https://bioregistry.io"^^ . - . - . - . - . - . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - "Cell line collections"^^ . - . - "http://4dx.embl.de/4DXpress"^^ . - . - "false"^^ . - . - "Benjamin M. Gyori" . - . - . - . - . - . - . - . - . - . - . - . - "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . - "BLL"^^ . - . -_:N1fc20d2185a94201a849b6d0bd829d82 "Fahim Imam" . - . - "HIP000030660"^^ . - . - "http://purl.obolibrary.org/obo/EHDA_$1"^^ . - . - . - "0000001"^^ . - . - . - . - . - "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . - . - . - . - . - "false"^^ . - "false"^^ . - "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . - . - "eNanoMapper Ontology" . - . - . - . - . - . - . - . - "OSC1416"^^ . - . - "http://bioportal.bioontology.org/ontologies/MEDDRA"^^ . - . - "BioGRID" . - . - . - . - "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . - . - "http://id.nlm.nih.gov/mesh/"^^ . - . - "false"^^ . - "Mental Functioning Ontology" . - "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . - . - . - "https://cropontology.org/ontology/CO_356/Vitis"^^ . - . - "https://progenetix.org/"^^ . - . - "false"^^ . - . - "http://purl.org/spar/scoro/$1"^^ . - "The set of prefixes used in the Cellosaurus resource" . - "false"^^ . - "false"^^ . - . - "C0017565"^^ . - "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . - . - "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . - "^\\d+$"^^ . - . - . - . - "https://github.com/ufbmi/geographical-entity-ontology/wiki"^^ . - . - . - . - . - . - . - "16941567"^^ . - . - . - "https://bioportal.bioontology.org/ontologies/VSO"^^ . - . - . - "ClinVar Submitter" . - . - . - . - "false"^^ . - "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . - . - "https://www.ncbi.nlm.nih.gov/homologene/"^^ . - . - . - . - . - . - . - "https://www.cancerrxgene.org"^^ . - . - . - "WBGene00000001"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1"^^ . - . - . - . - "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . - . - . - . - "Information Artifact Ontology" . - . - . - "false"^^ . - . - . - . - . - "http://www.sequenceontology.org/"^^ . - . - . - "http://www.snomedbrowser.com/"^^ . - . - . - . - . - . - . - . - . - "http://ecoliwiki.net/colipedia/"^^ . - . - "RiceNetDB Reaction" . - "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^ . - . - "false"^^ . - . - . - _:Nc0ecb24abbb543e7b3a16d1ba11c38a8 . - . - . - . - "101"^^ . - "http://mirtarbase.mbc.nctu.edu.tw/"^^ . - . - . - . - . - . - . - . - . - . - . - "0000030"^^ . - . - "false"^^ . - . - . - . - "Ontology of Zebrafish Experimental Conditions"^^ . - . - "true"^^ . - "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . - . - . - . - . - . - . - . - . - "http://trace.ddbj.nig.ac.jp/bioproject/"^^ . - . - "Computational and Informatics Resources for Glycoscience" . - "https://odc-tbi.org/data/$1"^^ . - . - . - . - "https://github.com/github/linguist"^^ . - . - . - . - . - . - "https://www.cropontology.org/rdf/CO_331:$1"^^ . - . - . - . - . - "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . - . - . - . - . - . - "https://www.cdc.gov/nchs/icd/icd9.htm"^^ . - . - . - . - . - "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1"^^ . - . - . - "false"^^ . - . - . - "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . - . - . - . - . - . - . - . - "^RF\\d{5}$"^^ . - . - . - "false"^^ . - . - . - . - . - . - "0000000"^^ . - . - . - . - "00000105"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Pathway Commons" . - . - . - . - . - . - "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - . - . - . - "LL379-9"^^ . - "false"^^ . - "https://biomodels.net/vocab/idot.rdf#$1"^^ . - . - "^\\d+$"^^ . - "^[A-Za-z0-9]+$"^^ . - "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . - . - . - . - "false"^^ . - "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . - . - . - . - "0000003"^^ . - . - "true"^^ . - . - . - . - . - "BioCatalogue Service" . - . - . - . - "NCBI dbSNP" . - "A web-developer centric archive of prefixes and URI prefixes" . - . - "^AA\\d{4}$"^^ . - . - . - . - "Human Brain Atlas" . - . - . - . - "^\\d+$"^^ . - "OMA HOGs" . - . - . - "International repository of Adverse Outcome Pathways."^^ . - "CharProt" . - . - . - . - . - . - . - . - . - "Robert Hoehndorf" . - . - . - . - . - "false"^^ . - . - "SABIO-RK Compound" . - . - "NCATS Drugs" . - . - . - . - . - . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - "false"^^ . - . - "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . - . - . - . - . - . - . - . - . - . - "December 2019"^^ . - . - "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "ProteomicsDB Peptide" . - . - . - "William Hogan" . - . - . - . - "https://www.uniprot.org/diseases/"^^ . - . - . - . - "Fernanda Farinelli" . - . - . - "300165/p13898_2106T"^^ . - . - "Mouse adult gross anatomy" . - "https://github.com/OGMS/ogms"^^ . - . - . - "^[1-9][0-9]*$"^^ . - . - "false"^^ . - . - . - "W2741809807"^^ . - . - . - . - "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . - . - "false"^^ . - . - "Microbial Conditions Ontology" . - . - "http://purl.obolibrary.org/obo/PDUMDV_$1"^^ . - "Plant Genome Network" . - "3SBPLMKKVEVR"^^ . - . - "http://en.wikipedia.org/wiki/Gene_Wiki"^^ . - "hsa-mir-200a"^^ . - "https://ontochem.com/"^^ . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . - . - . - . - . - . - . - "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . - . - "https://topfind.clip.msl.ubc.ca"^^ . - . - . - . - . - . - . - "http://www.informatics.jax.org/searches/MP_form.shtml"^^ . - "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^ . - . - "Microbial Protein Interaction Database" . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . - . - . - . - . - . - "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . - "Barry Smith" . - "Cambridge Structural Database" . - . - . - . - "https://bioportal.bioontology.org/" . - "https://github.com/OpenLHS/LABO"^^ . - . - . - "https://gdc.cancer.gov"^^ . - . - . - . - . - . - "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "0000070"^^ . - "https://swissmodel.expasy.org"^^ . - . - "^r\\d+$"^^ . - "37232"^^ . - . - "http://bis.zju.edu.cn/ricenetdb"^^ . - . - . - . - "http://xmlns.com/foaf/0.1/$1"^^ . - . - . - . - . - . - . - "http://www.mesquiteproject.org/ontology/Loggerhead/index.html"^^ . - . - . - "https://www.allotrope.org/"^^ . - . - . - . - "0000139"^^ . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . - . - "ECU03_0820i"^^ . - . - . - . - "^[a-z0-9\\-]+$"^^ . - "^\\d{7}$"^^ . - . - . - "http://purl.obolibrary.org/obo/OAE_$1"^^ . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - "Common Access to Biological Resources and Information Project" . - . - . - . - . - . - . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"^^ . - . - . - "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . - . - . - . - "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . - "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.metabolomicsworkbench.org/"^^ . - "0000006"^^ . - "https://cdno.info/"^^ . - "http://www.ebi.ac.uk/efo/EFO_$1"^^ . - . - . - "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . - "0000728"^^ . - "An issue in any public repository on GitHub."^^ . - . - "https://www.cropontology.org/rdf/CO_337:$1"^^ . - . - . - . - . - . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . - . - . - "^\\d{7}$"^^ . - "https://web.expasy.org/abcd/ABCD_$1"^^ . - . - . - . - "http://www2.idac.tohoku.ac.jp/dep/ccr/"^^ . - "http://purl.obolibrary.org/obo/CTENO_$1"^^ . - . - . - . - . - "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . - . - . - "https://www.kyinno.com/"^^ . - "https://www.ncbi.nlm.nih.gov/gv/mhc/"^^ . - . - . - "https://clinicaltrials.gov/ct2/show/$1"^^ . - "Interaction Network Ontology" . - "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . - . - . - "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . - "^[A-Z\\-]+$"^^ . - . - . - . - "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . - . - "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "false"^^ . - . - "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . - "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . - . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd"^^ . - . - "http://darcsite.genzentrum.lmu.de/darc/index.php"^^ . - . - . - "3305"^^ . - "false"^^ . - "^\\d+$"^^ . - . - "http://www.geneontology.org/formats/oboInOwl#$1"^^ . - . - "http://www.plantontology.org"^^ . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - . - . - . - "https://biological-expression-language.github.io/"^^ . - . - . - . - . - "http://www.gramene.org/"^^ . - . - "^[A-Z0-9]+$"^^ . - "Histopathology Ontology" . - "http://www.t3db.org/toxins/$1"^^ . - . - . - "Google Scholar Researcher" . - . - . - . - "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . - "https://datalab.rwth-aachen.de/MINDER"^^ . - "Dictyostelium discoideum anatomy" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CIO_$1"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . - "https://medical-data-models.org/"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "0000046"^^ . -_:N205262c097fa4e37a6188e1ceacdd13e "David Blackburn" . - . - "^\\d{6}$"^^ . - . - . - "http://aims.fao.org/aos/agrovoc/c_$1"^^ . - . - . - . - . - "Interlab Cell Line Collection" . - "https://www.fisheries.noaa.gov/species/$1"^^ . - . - . - . - . - . - "20090303"^^ . - . - "http://purl.obolibrary.org/obo/ERO_$1"^^ . - "false"^^ . - "NIA Mouse cDNA Project" . - . - "CiteXplore" . - . - . - . - "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . - . - "http://purl.obolibrary.org/obo/aero"^^ . - . - "https://repeatsdb.org/"^^ . - . - "https://www.cropontology.org/rdf/CO_343:$1"^^ . - "A0A009E7X8"^^ . - . - . - . - . - . - "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . - . - "^((HGNC|hgnc):)?\\d{1,5}$"^^ . -_:Ne7c10d4402c34331a10bead187346055 "Fahim Imam" . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/ordo"^^ . - . - . - . - "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . - . - . - . - . - . - . - . - . - . - "Zebrafish developmental stages ontology" . - . - "^HIP\\d{9}(\\.\\d+)?$"^^ . - . - "http://www.dukeontologygroup.org/Projects.html"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . - . - "The Food Ontology" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Nonribosomal Peptides Database" . - "http://purl.obolibrary.org/obo/TTO_$1"^^ . - . - . - "0010034"^^ . - . - . - "false"^^ . - . - "LINCS Cell" . - "Gene Ontology Registry" . - . - . - . - . - "http://purl.org/spar/doco/$1"^^ . - "https://bacteria.ensembl.org/"^^ . - "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)"^^ . - . - "false"^^ . - "icdom:8500_3"^^ . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . - . - . - . - . - . - . - "0000208"^^ . - "http://purl.obolibrary.org/obo/NBO_$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/TXPO_$1"^^ . - "https://www.kerafast.com/"^^ . - . - "https://github.com/infectious-disease-ontology-extensions/ido-covid-19"^^ . - . - "http://www.human-phenotype-ontology.org/"^^ . - "false"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . - . - . - . - "false"^^ . - . - . - "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/CRO_$1"^^ . - "Snapshot" . - "Microbial Conditions Ontology is an ontology..."^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - "https://www.grid.ac/"^^ . - . - . - "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . - . - "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . - "100010"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\w{1,2}\\d+$"^^ . - . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - . - "https://github.com/linikujp/OGSF"^^ . - "00001"^^ . - . - "1h68"^^ . - . - . - "Tick Anatomy Ontology" . - . - . - . - "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . - . - . - "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. "^^ . - . - . - "false"^^ . - . - . - "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . - . - . - . - . - . - . - . - . - "Cell line collections"^^ . - "Guide to Pharmacology Target" . - "https://www.uniprot.org/locations/"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "1017"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . - . - . - "false"^^ . - . - "Network Data Exchange" . - . - . - . - . - . - "090201"^^ . - . - . - . - . - . - . - "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^ . - "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"^^ . - . - . - . - . - . - "Event (INOH pathway ontology)" . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv"^^ . - "^[0-9]{4}$"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "CIAT Common bean trait dictionary - version August 2014"^^ . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . - "https://www.yeastgenome.org/locus/$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - "http://www.w3.org/2004/02/skos/core#$1"^^ . - . - . - "O08709"^^ . - "chebi" . - "NIF Standard Ontology: Molecules" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TADS_$1"^^ . - . - "false"^^ . - "GE86325"^^ . - "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^ . - . - "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . - "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . - . - "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . - . - . - . - . - . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . - . - "true"^^ . - "Mosquito insecticide resistance" . - . - . - . - . - . - . - . - . - . - "Veterans Health Administration (VHA) unique identifier" . - . - "The cBioPortal for Cancer Genomics" . - "false"^^ . - . - . - . - . - . - "https://www.vmh.life/"^^ . - . - . - . - "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/echinoderm-ontology/ecao_ontology"^^ . - "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . - . - . - . - "2224"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "91005"^^ . - "false"^^ . - . - "version 2019 - pvs"^^ . - . - . - "https://bams1.org"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://www.narcis.nl/publication/RecordID/$1"^^ . - "N1899"^^ . - "^\\d+$"^^ . - . - . - "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . - . - . - . - . - . - . - . - "https://www.salk.edu/"^^ . - . - . - . - "true"^^ . - "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . - . - "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . - . - "Cell line collections"^^ . - . - "false"^^ . - . - "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - . - . - . - . - . - "http://www.sparontologies.net/ontologies/bido"^^ . - . - "Data Use Ontology" . - . - "^P\\d{5}$"^^ . - . - . - . - . - "https://jjj.bio.vu.nl/models/$1"^^ . - "false"^^ . - . - "90901"^^ . - . - . - . - . - . - "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://www.cropontology.org/rdf/CO_324:$1"^^ . - . - . - . - "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . - . - "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . - . - . - . - . - . - . - . - . - . - "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . - . - . - "An ontology designed to support the semantic annotation of epidemiology resources"^^ . - . - "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings."^^ . - . - . - "false"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . - . - . - . - "UniPathway Compound" . - . - . - . - . - . - . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/"^^ . - . - . - . - . - . - . - . - . - . - "16793"^^ . - "http://purl.obolibrary.org/obo/RXNO_$1"^^ . - . - . - . - . - . - . - . - . - "http://edamontology.org/topic_$1"^^ . - "0001927"^^ . - . - . - . - "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . - "BioTools" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d{8}$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "ML0224"^^ . - . - "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . - . - . - . - . - . - . - . - "^S-[A-Z]{4}[A-Z\\d\\-]+$"^^ . - "^\\d+$"^^ . - "^[A-Z]{2}\\d+$"^^ . - . - . - . - . - "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . - . - . - "Health Surveillance Ontology" . - . - . - . - . - . - . - "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . - . - "NeuroLex Anatomy" . - . - . - . - "false"^^ . - "0000000"^^ . - "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . - "http://www.phenol-explorer.eu/foods/"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Clement Jonquet" . - . - . - . - "CY077097"^^ . - "AP011135"^^ . - "https://ifaa.unifr.ch/"^^ . - . - . - . - . - "false"^^ . - . - "Zebrafish Information Network Gene" . - . - . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - . - "https://depmap.org/portal"^^ . - . - "Rfam database of RNA families" . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - "http://fishbase.org"^^ . - . - . - . - . - "^[A-Z0-9]+$"^^ . - "Gene Ontology Annotation Database" . - "http://www.phosphosite.org/siteAction.do?id=$1"^^ . - . - . - . - "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . - . - "Pankaj Jaiswal" . - . - . - "false"^^ . - . - "false"^^ . - . - "^[A-Za-z_0-9]+$"^^ . - "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^ . - . - . - "0000031"^^ . - . - . - . - "Encyclopedia of DNA Elements" . - . - . - "false"^^ . - "CTD Chemical" . - "https://www.kaggle.com/$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "true"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/ZP_$1"^^ . - . - . - . - . - . - . - "https://aopwiki.org/aops/$1"^^ . - . - . - . - "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . - "Michel Dumontier" . - . - . - . - . - "http://purl.org/pav/$1"^^ . - . - . - . - . - . - . - . - "KW-1273"^^ . - "PA146123006"^^ . - . - . - "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . - . - . - . - . - "0000054"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^[EL]D[SG]-\\d+$"^^ . - . - . - . - "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . - . - . - . - "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . - . - . - . - . - . - . - "CRISPRdb" . - . - . - "http://www.knapsackfamily.com/KNApSAcK/"^^ . - "false"^^ . - . - . - . - "Sigma Aldrich" . - "false"^^ . - "Bacillus subtilis genome sequencing project" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "osa-miR446"^^ . - "http://compbio.cs.queensu.ca/F-SNP/"^^ . - "http://zinc15.docking.org/substances/$1"^^ . - . - "http://biobanknetwork.telethon.it/"^^ . - . - "false"^^ . - . - "http://geneontology.org/docs/ontology-relations/"^^ . - . - . - . - . - "https://biocyc.org/gene?id=$1"^^ . - "false"^^ . - . - "MaizeGDB Locus" . - . - . - . - "Ontology about C. elegans and other nematode phenotypes"^^ . - "y3ax-8bq3-60"^^ . - "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . - . - . - . - . - "grid.225360.0"^^ . - . - "http://www.ymdb.ca/compounds/$1"^^ . - "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . - "CompTox Chemistry Dashboard" . - . - "http://www.candidagenome.org/"^^ . - . - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . - . - . - "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . - . - . - . - "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . - "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . - . - . - "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^ . - . - . - "0000400"^^ . - . - . - . - . - "https://www.ideal-db.org"^^ . - "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . - . - . - . - "^\\d+$"^^ . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - "https://www.pirbright.ac.uk/node/$1"^^ . - . - . - . - . - . - . - "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . - . - . - . - . - "Tom Gillespie" . - . - . - . - . - . - . - . - "TreeFam" . - . - . - "GitHub Issue" . - . - "false"^^ . - "http://www.plantontology.org"^^ . - . - . - . - . - "10.1621/vwN2g2HaX3"^^ . - "Yvonne Bradford" . - . - . - . - . - . - . - . - "http://epd.vital-it.ch/"^^ . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - "https://w3c-ccg.github.io/did-spec/"^^ . - _:N24d1369259724e22befc4951f66bc5b4 . - "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . - "^RC\\d+$"^^ . - . - . - "https://cropontology.org/ontology/CO_325/Banana"^^ . - . - . - . - . - "https://panoramaweb.org"^^ . - . - . - . - . - . - "iECABU_c1320"^^ . - . - . - "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . - "00020134"^^ . - . - . - . - "RNA ontology" . - "^SL-\\d+$"^^ . - . - . - . - . - . - "https://www.wikidata.org"^^ . - . - "http://exac.broadinstitute.org/"^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - . - "https://prefixcommons.org/?q=$1" . - "https://github.com/evoinfo/cdao"^^ . - . - . - . - . - . - _:Nb1c75d7f39034870890b7a86604e9033 . - "The reviewer of a prefix" . - "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "0000140"^^ . - . - "true"^^ . - "eggNOG" . - "MMP743597.11"^^ . - . - "Plant Environment Ontology" . - . - . - . - . - "^\\d+$"^^ . - "false"^^ . - "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . - . - . - . - . - . - . - . - "http://ardb.cbcb.umd.edu/"^^ . - . - "false"^^ . - . - "http://www.pharmgkb.org/pathway/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx"^^ . - . - . - . - "true"^^ . - "PhosphoSite Protein" . - . - . - . - . - "http://www.pombase.org/spombe/result/$1"^^ . - . - . - "BEI Resources" . - . - . - . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/"^^ . - . - . - . - . - . - "Dr. Alpha Tom Kodamullil" . - "https://pharmacodb.ca/cell_lines"^^ . - . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . - . - . - "false"^^ . - . - . - "http://xmlns.com/foaf/spec/"^^ . - . - "https://bioportal.bioontology.org/ontologies/NPO"^^ . - "817732"^^ . - "OBO Foundry" . - "http://www.expasy.org/viralzone/"^^ . - "^KW-\\d{4}$"^^ . - . - . - . - . - . - . - . - . - "https://www.gsea-msigdb.org"^^ . - . - . - "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . - . - . - . - "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . - . - . - "Neuronal cell types"^^ . - . - "^[A-Za-z_0-9]+$"^^ . - . - "C0020004/4992"^^ . - . - . - "^\\d+$"^^ . - . - . - "46977"^^ . - . - . - . - . - . - . - "Habronattus courtship" . - . - . - . - . - . - . - . - "1351341"^^ . - . - "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Gene Regulation Ontology" . - . - . - . - . - "Decentralized Biomedical Ontology" . - . - "P00747__P07355"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "https://github.com/$1"^^ . - . - "Draft version"^^ . - "51"^^ . - . - . - . - "Community development of interoperable ontologies for the biological sciences"^^ . - . - . - "https://archive.softwareheritage.org/browse/swh:$1"^^ . - . - . - . - "^[A-Za-z-0-9_]+$"^^ . - . - "0000003"^^ . - . - . - . - . - . - . - . - . - . - . - . - "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . - "NIH HIV Reagent Program" . - . - . - . - "^\\d{4,}((_[asx])?_at)$"^^ . - . - . - "A database of fly neurons and pathways with an associated 3D viewer."^^ . - . - . - . - . - "bt0001"^^ . - . - . - . - . - . - . - . - . - "002678"^^ . - . - "http://www.pocketome.org/sfSearch.cgi?act=browseall"^^ . - . - . - "smp-m3w9hbe"^^ . - . - . - "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page"^^ . - . - "^\\d{7}$"^^ . - "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - "true"^^ . - . - . - . - "26753"^^ . - . - "http://www.gramene.org/plant_ontology/"^^ . - "https://e-cyanobacterium.org/bcs/rule/$1"^^ . - . - . - . - . - . - "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . - . - . - . - . - "false"^^ . - . - "Matúš Kalaš" . - . - . - . - "KEGG Genes" . - "false"^^ . - . - "https://web.expasy.org/variant_pages/VAR_$1.html"^^ . - . - . - "http://www.homd.org/index.php"^^ . - . - . - . - "4DN"^^ . - "26"^^ . - "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . - . - "PK-DB" . - "false"^^ . - "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - . - . - . - . - . - "https://github.com/qfo/OrthologyOntology"^^ . - . - . - . - . - . - "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . - . - . - . - . - "Protein modification" . - "false"^^ . - . - . - . - . - . - "http://planteome.org/"^^ . - . - "Ontology for Biomedical Investigations" . - . - . - . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . - "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . - . - "http://umbbd.ethz.ch/"^^ . - . - . - . - . - . - . - . - "Costal and Marine Ecological Classification Standard" . - . - "D0001"^^ . - "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . - . - . - . - . - . - "https://bioregistry.io/collection/$1"^^ . - "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"^^ . - "https://www.deciphergenomics.org/"^^ . - . - . - "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - "0000095"^^ . - "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . - . - . - "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . -_:N588fa78509cf44fcb7a6ae69d44fdcad "Plant Ontology Administrators" . - . - "false"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/dbEST/index.html"^^ . - . - "false"^^ . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - . - "Pier Luigi Buttigieg" . - . - . - "false"^^ . - . - "https://www.genenames.org"^^ . - . - . - "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . - "https://github.com/ohmi-ontology/ohmi"^^ . - . - "Ontologized MIABIS" . - "Mike Tyers" . - "Entrez Gene" . - . - . - "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . - . - . - . - . - . - . - . - . - "AphidBase Transcript" . - "https://www.ncbi.nlm.nih.gov/protein"^^ . - "WiCell Research Institute Cell Collection" . - . - . - . - . - . - "^\\d{6}$"^^ . - . - . - "https://cls.shop/$1"^^ . - . - "Hypertension Ontology" . - . - "Cell line collections"^^ . - . - . - . - . - "https://www.ebi.ac.uk/chembl/entity/$1"^^ . - . - "false"^^ . - . - "http://www.cellsignal.com/products/$1.html"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "OriDB Saccharomyces" . - "https://github.com/obophenotype/planaria-ontology"^^ . - "EB0170"^^ . - "International Classification of Diseases for Oncology" . - . - "^[0-9]+$"^^ . - . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . - . - "http://proconsortium.org"^^ . - . - . - . - . - . - . - . - . - . - . - "Mutant Mouse Resource and Research Centers" . - "https://www.gwascentral.org/studies"^^ . - . - . - . - "Degradome Database" . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . - . - "https://europepmc.org"^^ . - . - . - "https://www.ndexbio.org/viewer/networks/$1"^^ . - . - "OpenCitations Corpus" . - "GitLab" . - . - . - . - . - . - "http://purl.org/spar/bido/$1"^^ . - . - "ND50028"^^ . - . - "July 2018"^^ . - "The COVID-19 Infectious Disease Ontology" . - . - . - . - "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . - . - . - "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology"^^ . - "^[A-Z_a-z]+$"^^ . - "^\\d{7}$"^^ . - . - "Ontology of Vaccine Adverse Events" . - . - . - . - . - . - "Plant Experimental Conditions Ontology" . - . - . - "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . - . - "MarCat" . - "NMR Restraints Grid" . - "Q-2958"^^ . - . - . - . - "Carissa Park" . - "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . - "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . - "Proteomics data and process provenance" . - . - "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . - "^MMAR\\_\\d+$"^^ . - . - "https://fairsharing.org/" . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://browser.planteome.org/amigo"^^ . - . - . - "false"^^ . - "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . - "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . - "PaxDb Protein" . - . - "https://www.dsmz.de"^^ . - . - . - . - . - . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . - . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - . - . - . - . - "75"^^ . - . - . - . - "https://pharmacodb.ca/tissues/$1"^^ . - . - . - . - . - . - "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . - . - "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . - . - "^\\d{6}$"^^ . - . - . - . - . - "PIRSF000100"^^ . - . - . - "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . - . - . - . - . - . - . - . - "9606"^^ . - . - "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . - "0000072"^^ . - "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . - . - "https://www.cropontology.org/rdf/CO_325:$1"^^ . - "Protein Interaction Network Analysis" . - . - . - . - . - . - . - . - "CCDS13573.1"^^ . - . - . - . - . - "0471491039"^^ . - "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . - . - . - . - "Ontology for genetic interval" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - "Gi07796"^^ . - "https://labsyspharm.github.io/lspci/$1"^^ . - "Minimal Information About Anatomy ontology" . - "^MTBLS\\d+$"^^ . - "false"^^ . - . - . - . - "https://sumlineknowledgebase.com/?page_id=$1"^^ . - "r0001"^^ . - . - . - . - . - . - . - . - . - . - "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . - . - "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x"^^ . - . - . - . - "https://www.ebi.ac.uk/pdbe/emdb"^^ . - . - . - "http://braininfo.rprc.washington.edu/"^^ . - . - "false"^^ . - . - "false"^^ . - . - "http://flybase.org/"^^ . - . - . - . - . - . - . - "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology"^^ . - . - . - . - . - "0000121"^^ . - . - . - . - "GrassBase" . - . - "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^ . - . - . - "false"^^ . - "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license."^^ . - . - . - . - . - . - . - "1-18"^^ . - "true"^^ . - . - . - . - . - . - . - . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - "authoredBy"^^ . - . - . - "has responsible" . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/biosamples/"^^ . -_:N3b4e286bf1584db39cc4e530d6f77656 "Thorsten Heinrich" . - . - "This collection contains various brain atlases from the Allen Institute." . - "SNP to Transcription Factor Binding Sites" . - "Alan Wood's Pesticides" . - "P23298"^^ . - "^rs[0-9]+$"^^ . - "http://bis.zju.edu.cn/ricenetdb"^^ . - "^\\d{7}$"^^ . - . - "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^ . - . - . - "PubChem CID" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "MarRef" . - . - . - . - . - "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^ . - "TF101014"^^ . - . - . - . - "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . - . - . - "HOMD Taxonomy" . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - . - "4238"^^ . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . - . - . - "https://www.ebi.ac.uk/GOA/"^^ . - . - . - . - "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . - . - . - . - "false"^^ . - . - . - . - "^[0-9a-z]{24,24}$"^^ . - . - "FaceBase Data Repository" . - "A0001"^^ . - "^(\\w+)?\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "17254"^^ . - . - . - . - "true"^^ . - "PA131"^^ . - . - . - . - "http://www.ebi.ac.uk/interpro/index.html"^^ . - . - "PROV Namespace" . - . - . - "false"^^ . - . - . - . - . - "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "Terminologia Embryologica" . - . - "false"^^ . - . - . - "Val Wood" . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - "https://www.uniprot.org/database/"^^ . - . - "https://civicdb.org/links/evidence/$1"^^ . - . - . - . - "Rodent Unidentified Gene-Encoded Large Proteins" . - "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . - . - . - "http://getentry.ddbj.nig.ac.jp"^^ . - "http://lgsun.grc.nia.nih.gov/cDNA/"^^ . - . - . - "http://rgd.mcw.edu/rgdweb/search/strains.html"^^ . - . - "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . - . - . - "Protein Ensemble Database ensemble" . - . - . - . - . - . - "Terminology of Anatomy of Human Embryology" . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "false"^^ . - . - "Manually curated collections of resources stored in the bioregistry"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "AutDB" . - . - . - "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . - . - . - . - . - . - "HMS LINCS Compound" . - . - "false"^^ . - . - . - . - . - . - . - "Mouse pathology ontology" . - "DTXSID2021028"^^ . - . - . - . - . - "PKDB00198"^^ . - . - . - "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . - . - . - . - . - "https://github.com/MIT-LCP/mimic-omop"^^ . - "https://www.yeastgenome.org/observable/APO:$1"^^ . - . - "Eukaryotic Linear Motif Resource" . - "^\\w+$"^^ . - . - "false"^^ . - . - "https://zenodo.org/record/$1"^^ . - . - "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . - . - . - "false"^^ . - "false"^^ . - "false"^^ . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . - . - . - "https://odc-sci.org/data/$1"^^ . - . - "false"^^ . - . - . - . - . - . - "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^ . - . - . - . - "RxNorm" . - "true"^^ . - . - . - "http://dictybase.org"^^ . - . - . - "Database of Genomic Structural Variation - Study" . - . - "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . - . - . - . - "biopragmatics/bioregistry"^^ . - . - "Human Proteome Map Peptide" . - . - . - "https://www.novusbio.com"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "01001"^^ . - . - . - . - . - "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . - . - . - . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . - . - . - . - . - "Bactibase" . - . - . - "^GenProp\\d+$"^^ . - "AP00378"^^ . - "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . - . - . - . - . - . - . - . - . - . - "http://purl.org/spar/pro/$1"^^ . - "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - . - . - . - "^[A-Z0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "European Genome-phenome Archive Study" . - . - . - "https://www.hdruk.ac.uk"^^ . - . - . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . - . - "Uberon Property" . - . - . - "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - . - . - "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^ . - "Aspergillus Genome Database" . - "Statistical Torsional Angles Potentials" . - . - . - . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - . - . - . - . - . - . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi"^^ . - . - . - "false"^^ . - . - . - . - "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . - "false"^^ . - . - . - . - "^AS\\d{6}$"^^ . - . - "MetaNetX chemical" . - . - . - . - . - . - . - . - . - "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906"^^ . - "false"^^ . - . - "https://pharmacodb.ca/tissues"^^ . - . - "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . - "^EB\\d+$"^^ . - "e999"^^ . - "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . - "https://github.com/obophenotype/fungal-anatomy-ontology/"^^ . - . - . - . - . - "https://omim.org/"^^ . - "0007133"^^ . - "ZINC is not Commercial" . - . - "4DN" . - . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - . - . - . - . - . - "60316"^^ . - . - "Datanator Metabolite" . - "false"^^ . - . - . - . - . - "false"^^ . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index"^^ . - . - . - . - . - "^[A-Z]C\\d{1,3}$"^^ . - . - . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF"^^ . - . - . - "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . - . - . - . - . - . - . - . - . - "Assembly" . - . - . - . - "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . - "Ontology of Adverse Events" . - . - . - "false"^^ . - . - . - . - . - "http://dictybase.org/gene/$1"^^ . - . - . - . - . - . - "45539"^^ . - . - . - . - "Lipid Ontology" . - . - "Fission Yeast Experimental Conditions Ontology" . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . - . - _:Ne588226fa953447e8b6d3e4cf8af70b6 . - . - . - . - "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . - . - . - . - "false"^^ . - . - . - . - "https://repeatsdb.org/protein/$1"^^ . - . - . - . - . - "0000001"^^ . - "http://purl.org/spar/cito/$1"^^ . - . - . - . - "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . - . - "243002_at"^^ . - . - . - . - "false"^^ . - "MNEST029358"^^ . - "http://purl.obolibrary.org/obo/ZEA_$1"^^ . - "MycoBrowser smegmatis" . - "http://www.bioinfo.org/NONCODEv4/"^^ . - "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . - "4D Nucleome Data Portal Experiment Replicate" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Ontology of Biological Attributes" . - . - . - . - "67035"^^ . - "^\\d{7}$"^^ . - "https://github.com/insect-morphology/aism"^^ . - "https://clinicaltrials.gov/"^^ . - "Applied Biological Materials cell line products" . - . - . - . - "0000044"^^ . - . - "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . - "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . - . - . - . - "false"^^ . - . - "Human Induced Pluripotent Stem Cells Initiative" . - "false"^^ . - "false"^^ . - "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "Intrinsically Disordered proteins with Extensive Annotations and Literature" . - . - . - . - "M77F7JM"^^ . - . - . - . - . - . - . - . - . - "ENST00000407236"^^ . - "Henning Hermjakob" . - . - . - . - . - . - "Protein Affinity Reagents" . - . - . - . - . - . - "NOR00681"^^ . - . - . - "false"^^ . - . - . - . - "true"^^ . - . - . - . - . - "^[a-z][a-zA-Z]+$"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm"^^ . - "^\\d{7}$"^^ . - "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . - . - "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - "Ramona Walls" . - . - . - . - . - . - . - "https://psidev.info/sepcv"^^ . - . - . - . - . - "chebi" . - . - "CONSO00010"^^ . - . - "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . - . - . - "Cell line databases/resources"^^ . - "LDS-1110"^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . - . - "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . - . - "BeAn 70563"^^ . - . - . - "false"^^ . - . - "00100037"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.encodeproject.org/$1"^^ . - . - . - "https://go.drugbank.com/categories"^^ . - . - "false"^^ . - . - . - . - . -_:N62c7e9ef269b441cb4b61f81eba4824c "Pantelis Topalis" . - "http://www.w3.org/2002/07/owl#$1"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Pierre-Alain Binz" . - "false"^^ . - "false"^^ . - . - "http://www.drugbank.ca"^^ . - "http://www.gpcrdb.org/"^^ . - "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . - . - "false"^^ . - "Georgeta Bordea" . - . - . - . - . - "https://biosimulations.org/projects/$1"^^ . - "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . - _:Nb05e5db256fe46d79efe2cf9dca6406b . - . - . - . - "Ath_AT1G01030.1"^^ . - . - "^\\d+$"^^ . - . - "https://arxiv.org/abs/$1"^^ . - . - . - . - . - "false"^^ . - . - "PTN000000026"^^ . - . - . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . - "Tom Gillespie" . - . - "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . - . - . - "Ontology for MicroRNA Target" . - "false"^^ . - "false"^^ . - . - "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . - . - "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^ . - . - . - . - . - . - "https://dailymed.nlm.nih.gov/dailymed/"^^ . - "false"^^ . - . - . - . - "MINID Test" . - . - . - . - . - . - "https://www.uniprot.org/docs/ptmlist"^^ . - . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^ . - . - . - . - . - "PTM-0450"^^ . - "^[A-Z]{2}[A-Z0-9][0-9]{5}$"^^ . - "false"^^ . - . - "sourceDateStart"^^ . - "Melanie Courtot" . - . - . - . - . - "^K[0-9]+$"^^ . - . - . - "1000"^^ . - . - . - . - . - "http://aclame.ulb.ac.be/"^^ . - "https://hawaii.eagle-i.net"^^ . - . - . - "SBGN Bricks data and ontology" . - "https://www.brainspan.org/"^^ . - . - . - . - "Funding, Research Administration and Projects Ontology" . - . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . - "^(E|D|S)RR[0-9]{6,}$"^^ . - "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"^^ . - . - . - "https://prefixcommons.org" . - . - "http://www.vbase2.org/vgene.php?id=$1"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/ECTO_$1"^^ . - . - _:N3ebf828b73254ba1aff2e01aadd41f48 . - . - . - . - . - "COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1"^^ . - . - . - "false"^^ . - . - "https://github.com/"^^ . - . - . - "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . - "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . - . - . - "Cell line databases/resources"^^ . - . - "0000519"^^ . - . - . - . - "CAL0003079"^^ . - "https://ecmdb.ca"^^ . - . - . - "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . - "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . - . - . - . - . - . - "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . - "MetaNetX compartment" . - "http://www.sparontologies.net/ontologies/pwo"^^ . - . - "http://www.imdrf.org/"^^ . - "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . - "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . - . - "true"^^ . - . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . - . - . - . - . - . - . - . - "1915"^^ . - . - . - . - "false"^^ . - "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . - . - . - . - . - . - "https://scdontology.h3abionet.org/"^^ . - . - "Petra Fey" . - "false"^^ . - . - . - "https://www.genome.jp/kegg/pathway.html"^^ . - . - "COG Categories" . - "An ontology of phenotypes covering microbes"^^ . - . - "http://purl.obolibrary.org/obo/FIX_$1"^^ . - . - "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . - . - . - . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - "KEGG Glycan" . - "doi"^^ . - . - . - . - . - . - "Livestock Product Trait Ontology" . - "https://www.deciphergenomics.org/syndrome/$1"^^ . - "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . - . - . - "https://dip.doe-mbi.ucla.edu/"^^ . - . - "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . - "589462"^^ . - "^\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . - . - . - . - . - . - "https://www.cropontology.org/rdf/CO_346:$1"^^ . - . - "false"^^ . - . - . - . - "Genitourinary Development Molecular Anatomy Project" . - . - . - "^[0-9]+$"^^ . - . - "377550"^^ . - . - . - . - "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . - . - "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . - . - . - "http://purl.obolibrary.org/obo/COLAO_$1"^^ . - . - . - . - . - . - . - "Benchmark Energy & Geometry Database" . - "https://www.vectorbase.org/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FOBI_$1"^^ . - "1948"^^ . - "FBgn0011293"^^ . - "Hazardous Substances Data Bank" . - "ai10e-kctd13b"^^ . - . - "false"^^ . - . - . - "NCBI Gene Expression Omnibus" . - "DI-04240"^^ . - . - "http://www.mgc.ac.cn/VFs/"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://ccr.coriell.org/"^^ . - "Continuous Automated Model Evaluation" . - "FAIRSharing" . - . - "^\\d+$"^^ . - . - "Molbase" . - . - "^\\d{7}$"^^ . - . - "http://www.w3.org/ns/oa"^^ . - . - . - . - . - . - . - . - . -_:Nbd5897134eac42569c7558a528fd2f83 "chEBI" . - . - "Enzo Life Sciences is an antibody vendor."^^ . - . - . - . - . - . - . - "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . - "https://github.com/IEDB/MRO"^^ . - "false"^^ . - . - . - . - . - "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . - "true"^^ . - "9002859"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "false"^^ . - "TOKU-E Cell-culture Database" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - "^\\w+$"^^ . - . - . - . - "false"^^ . - "https://data.bloodpac.org/."^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - "false"^^ . - . - . - "0000022"^^ . - . - "https://www.kegg.jp/entry/$1"^^ . - . - . - "false"^^ . - . - "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . - . - . - . - . - "https://co.mbine.org/standards/"^^ . - "Reference"^^ . - . - . - "FooDB Food" . - . - "CoVoc Coronavirus Vocabulary" . - . - . - . - . - . - "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . - . - . - . - . - "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - . - "https://bioportal.bioontology.org/ontologies/SWEET"^^ . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . - "^ML\\w+$"^^ . - . - "90801"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "8497"^^ . - . - "50018"^^ . - "MRA-253"^^ . - . - . - . - . - . - . - "P01116"^^ . - "1044544"^^ . - "Alexander Diehl" . - . - . - . - . - . - "https://vega.archive.ensembl.org/index.html"^^ . - "Sorghum ontology" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - "551115"^^ . - . - . - . - "A formal ontology of phenotypes observed in fission yeast."^^ . - . - . - "Environment Ontology" . - "http://www.proteomexchange.org/"^^ . - "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . - . - . - . - . - "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^ . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home"^^ . - . - . - . - "https://www.ebi.ac.uk/chembldb"^^ . - . - "false"^^ . - . - "http://vegbank.org/"^^ . - "0002989"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "https://portal.bluebrain.epfl.ch"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "0000189"^^ . - "Reaxys eMolecules" . - . - . - "http://aps.unmc.edu/AP/"^^ . - . - . - "190000021540"^^ . - . - . - . - "http://www.kupkb.org/"^^ . - . - . - . - . - "^[A-Z][a-z][0-9]+$"^^ . - . - . - . - . - . - . - . - "https://icd.codes/icd10cm/$1"^^ . - "Population and Community Ontology" . - . - . - . - . - . - . - "false"^^ . - . - . - "https://github.com/PlantPhenoOntology/PPO"^^ . - . - "ABC"^^ . - . - "https://github.com/obophenotype/ctenophore-ontology"^^ . - . - "^\\w{14}$"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Ontology for Nutritional Epidemiology" . - . - . - . - . - "International repository of Adverse Outcome Pathways."^^ . - . - . - . - "false"^^ . - "http://www.cropontology.org/ontology/CO_347/Castor%20bean"^^ . - "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . - . - "ACH-000001"^^ . - . - . - . - . - "Cancer Staging Terms" . - . - . - "false"^^ . - . - . - . - . - "http://www.sparontologies.net/ontologies/doco"^^ . - . - . - "false"^^ . - "false"^^ . - . - "GXA Gene" . - "Q2207226"^^ . - "https://github.com/cido-ontology/cido"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - "BacMap Biography" . - "154022"^^ . - . - "SMP0000219"^^ . - . - "NCBI Taxonomy" . - . - . - . - "https://cell.brc.riken.jp/en/rcb"^^ . - . - . - . - . - . - "^cpd\\d+$"^^ . - . - "http://www.sparontologies.net/ontologies/fr"^^ . - "^T3\\d+$"^^ . - . - . - . - . - "Sequencing Initiative Suomi" . - . - "^\\d+$"^^ . - "AKR"^^ . - . - . - "false"^^ . - . - . - . - . - "true"^^ . - "false"^^ . - . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . - . - "false"^^ . - . - "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . - . - "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . - "MultiCellDS Digital Cell Line" . - . - "ClinicalTrials.gov" . - "PA448710"^^ . - . - . - "Literature references in Gramene"^^ . - . - . - "https://ximbio.com"^^ . - . - . - "http://antibodyregistry.org/"^^ . - . - "csv"^^ . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/OGI_$1"^^ . - . - . - . - . - "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . - . - "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"^^ . - "HOMD Sequence Metainformation" . - "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . - . - "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^ . - . - "International Classification of Diseases, 9th Revision" . - . - "0000048"^^ . - "^DI-\\d{5}$"^^ . - "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . - . - . - . - . - . - "false"^^ . - "Analyses of microbiome data within MGnify"^^ . - . - . - . - . - "Chris Grove" . - . - . - "https://tree.opentreeoflife.org"^^ . - . - "G00054MO"^^ . - . - . - . - . - "1000001"^^ . - . - . - . - . - . - . - . - "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . - "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - "http://amoebadb.org/amoeba/"^^ . - . - . - "Information for ligand groups (chemical classes)."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://pfam.xfam.org"^^ . - "0459895"^^ . - . - "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . - . - . - "https://www.ebi.ac.uk/metagenomics/"^^ . - "https://licebase.org"^^ . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - "^MMP\\d+.\\d+$"^^ . - . - "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Nathan Edwards" . - . - "false"^^ . - . - "T01B6.1"^^ . - . - . - . - "https://www.ebi.ac.uk/gxa/genes/$1"^^ . - . - . - "Viral Bioinformatics Resource Center" . - . - "https://www.who.int/teams/health-product-and-policy-standards/inn"^^ . - . - . - . - . - . - "true"^^ . - "MMAR_2462"^^ . - . - . - . - . - . - . - "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . - . - "0000001"^^ . - . - . - . - . - . - "https://herv.img.cas.cz/"^^ . - . - . - . - . - . - . - . - . - . - . - "https://pathbank.org/view/$1"^^ . - "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^ . - . - "false"^^ . - . - "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . - . - . - "https://run.biosimulations.org/simulations/$1"^^ . - "Chemical Component Dictionary" . - "https://cropontology.org/ontology/CO_350/Oat"^^ . - . - . - . - . - . - . - "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . - . - "http://www.e-cyanobacterium.org/bcs/rule/"^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "^ENSG\\d{11}$"^^ . - "https://bioportal.bioontology.org/ontologies/ECG"^^ . - . - . - . - . - . - . - "The responsible person for a resource" . - . - . - "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . - . - "^[a-z0-9]{32,32}$"^^ . - . - "Kyoto Encyclopedia of Genes and Genomes" . - "false"^^ . - . - "http://www.cbioportal.org"^^ . - "true"^^ . - . - "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1"^^ . - . - "false"^^ . - . - . - . - "DB-0174"^^ . - . - . - "http://pax-db.org/#!species/$1"^^ . - . - . - "Tb927.8.620"^^ . - . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - . - . - "Alliance of Genome Resources Knowledge Base" . - . - . - . - . - . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv"^^ . - . - . - "1000160"^^ . - . - . - . - . - . - . - . - . - . - "http://arabidopsis.org/index.jsp"^^ . - . - . - "^\\d+$"^^ . - . - . - "https://www.encodeproject.org"^^ . - "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . - . - "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . - "Drug Target Ontology" . - "C. elegans phenotype" . - "https://www.alzforum.org/mutations"^^ . - "^\\d{7}$"^^ . - "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . - . - "^PA\\d+$"^^ . - . - . - . - . - . - "http://europepmc.org/"^^ . - . - . - "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . - . - . - "https://catalog.bcrc.firdi.org.tw"^^ . - . - . - . - "false"^^ . - "NX_O00165"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Allotrope Merged Ontology Suite" . - "STOREDB at University of Cambridge" . - . - . -_:Nbb8dc8af4b014a46b6acbb066b38604b "Burke Squires" . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . - "http://www.cazy.org/$1.html"^^ . - "^DBCAT\\d+$"^^ . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - . - . - . - . - . - . - "https://dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - . - . - . - . - . - "http://www.chemspider.com/"^^ . - "^[A-Za-z0-9+_.%-:]+$"^^ . - "^ENST\\d{11}$"^^ . - . - . - . - . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . - . - "https://sed-ml.org/urns.html#format:$1"^^ . - . - . - . - "PELNAW"^^ . - . - . - . - . - . - _:Nbb8dc8af4b014a46b6acbb066b38604b . - "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^ . - "Bacterial Tyrosine Kinase Database" . - . - "^MSMEG\\w+$"^^ . - . - . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . - "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - "1000"^^ . - . - . - . - . - . - "Tom Gillespie" . - "Maize gross anatomy" . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "0000423"^^ . - . - . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . - "false"^^ . - _:N9f8bc228d3d4416796eff1e6e0747849 . - . - . - . - . - "^PED\\d{5}$"^^ . - "IntAct Molecule" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Illumina Probe Identifier" . - "http://wheat.pw.usda.gov"^^ . - . - . - . - . - . - . - "https://web.expasy.org/variant_pages"^^ . - "Adnan Malik" . - . - . - . - . - . - . - . - "GCST000035"^^ . - "https://omabrowser.org/cgi-bin/gateway.pl"^^ . - "UM-BBD Compound" . - . - . - . - . - . - "ProteomeXchange" . - "^\\d+$"^^ . - . - . - . - . - . - "CutDB" . - . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . - . - "false"^^ . - . - . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . - . - . - . - "E5.11.2.0.0.0.4"^^ . - "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . - "0001009"^^ . - . - . - . - . - . - . - . - "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . - "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/projects/gap"^^ . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - "Bioregistry Schema" . - _:N7c963f68a1fe42beadc6cc49111f5668 . - . - . - . - . - . - "http://omia.angis.org.au/$1/"^^ . - . - . - "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure"^^ . - . - . - "miR-1"^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . - "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . - . - . - . - . - . - "19-T4"^^ . - . - . - "^CL\\d+$"^^ . - . - "https://www.re3data.org" . - . - "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . - . - . - . - . - . - "AOPWiki (Stressor)" . - "Legacy disease classes that later became MONDO"^^ . - . - . - . - . - . - . - . - . - "Dictybase Gene" . - "^\\d+$"^^ . - . - . - "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . - . - . - . - . - . - . - "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^ . - . - . - . - . - . - "Cellosaurus Publication" . - . - . - . - . - "ClinGen Allele Registry" . - "Dendritic cell" . - . - . - . - . - . - . - . - "100000"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "785"^^ . - . - . - "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - "4685"^^ . - . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - "PXD000440"^^ . - . - . - . - . - . - . - "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . - . - "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . - "https://ssbd.riken.jp"^^ . - . - "false"^^ . - . - . - . - "false"^^ . - "^PD\\d+$"^^ . - "http://dictybase.org/"^^ . - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . - . - . - . - "^[1-9][0-9]*$"^^ . - . - "http://purl.obolibrary.org/obo/OGMS_$1"^^ . - . - "https://www.kew.org/data/grasses-syn/index.htm"^^ . - "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . - "false"^^ . - . - . - "2679240"^^ . - . - "false"^^ . - . - "70"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . - . - . - "false"^^ . - . - . - "https://github.com/HUPO-PSI/psi-mi-CV"^^ . - . - "http://purl.org/spar/pwo/$1"^^ . - . - . - "http://www.molbase.com/"^^ . - . - . - . - "false"^^ . - . - "false"^^ . - . - "Yeast Intron Database v3" . - . - . - "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . - . - . - "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . - "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . - "https://github.com/jannahastings/mental-functioning-ontology"^^ . - "false"^^ . - . - . - . - . - "^UCR\\d{5}$"^^ . - "^\\d{7}$"^^ . - "PolBase" . - . - "KNApSAcK" . - . - . - . - . - "Amazon Standard Identification Number" . - . - . - . - . - "false"^^ . - "0001079"^^ . - . - . - . - . - . - . - "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies"^^ . - . - . - "Electrocardiogram Ontology" . - . - "true"^^ . - . - . - . - . - "false"^^ . - "PhosphoPoint Phosphoprotein" . - . - "F0001"^^ . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . - "Food-Biomarker Ontology" . - "http://oryzatagline.cirad.fr/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - "57"^^ . - "false"^^ . - "Rebuilding a Kidney" . - . - . - . - . - . - . - "50-00-0"^^ . - . - . - . - . - "http://www.ebi.ac.uk/cmpo"^^ . - . - "Paul Fabry" . - . - . - "^\\d{7}$"^^ . - . - . - . - "Bibliographic Reference Ontology" . - . - "Simplified molecular-input line-entry system" . - . - . - "DiscoverX cell line products" . - "http://neuinfo.org/"^^ . - . - . - . - . - "^[0-9]{8}$"^^ . - . - . - . -_:N7165961ce33340f9b8be6ad633b83081 "INOH curators" . - "http://www.bioguo.org/AnimalTFDB/family_index.php"^^ . - "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . - . - "https://scholia.toolforge.org/"^^ . - . - . - . - . - . - . - . - "Human Proteome Map Protein" . - . - . - "Phenotype And Trait Ontology" . - . - . - . - . - "^\\d{7}$"^^ . - . - "http://soybase.org/"^^ . - . - . - . - . - "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . - . - . - "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . - . - "74"^^ . - "Scopus Researcher" . - . - . - "false"^^ . - "http://nbn-resolving.org/resolve_urn.htm"^^ . - . - "Evidence ontology" . - . - . - . - . - . - . - . - . - "has resolver formatter" . - "false"^^ . - . - . - . - . - "http://www.pantherdb.org/"^^ . - "false"^^ . - "false"^^ . - "^[A-Za-z 0-9]+$"^^ . - . - "Wikidata Property" . - . - . - . - . - "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://func.mshri.on.ca/human/"^^ . - . - "A modeling paradigm-specific registry of prefixes and their URL expansions" . - . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . - . - . - "Human Ancestry Ontology" . - . - "^\\d{7}$"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Variation Ontology" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/VHOG_$1"^^ . - . - "Subcellular Anatomy Ontology" . - . - . - . - . - . - . - "Regulation of Transcription"^^ . - . - . - . - . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . - . - . - . - "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . - . - . - "^MF_\\d+$"^^ . - . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - . - . - "http://www.guidetopharmacology.org/targets.jsp"^^ . - . - . - "Gramene Taxonomy" . - "100000001"^^ . - . - . - . - . - . - . - . - . - . - "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . - . - . - . - . - . - "https://omabrowser.org/cgi-bin/gateway.pl"^^ . - . - . - "true"^^ . - . - "hsa-mir-200a"^^ . - . - "Hector Escriva" . - . - "http://purl.obolibrary.org/obo/AGRO_$1"^^ . - "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . - . - . - "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . - . - . - . - "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . - . - . - . - . - . - "Saccharomyces Genome Database" . - . - . - . - "KYinno cell lines" . - . - . - "^CHEMBL\\d+$"^^ . - "false"^^ . - . - "http://multicellds.org/MultiCellDB.php"^^ . - . - . - . - . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - "true"^^ . - . - . - . - . - . - . - . - . - . - . - "AAA35559"^^ . - . - "FuncBase Yeast" . - "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . - . - . - . - . - "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . - "false"^^ . - "http://amigo.geneontology.org/amigo/term/GO:$1"^^ . - . - . - . - . - . - . - . - "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . - . - "3304"^^ . - . - "false"^^ . - . - "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . - . - "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . - "false"^^ . - . - "^\\d{7}$"^^ . - "Allergome" . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . - . - . - "^\\d+$"^^ . - . - "http://umbbd.ethz.ch/"^^ . - . - . - "0000000"^^ . - "CGH Data Base" . - . - . - . - . - . - "MF_01400"^^ . - "Medical Data Models" . - . - . - . - . - "false"^^ . - . - "17186"^^ . - . - . - "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . - . - . - . - "false"^^ . - . - . - . - "http://piroplasmadb.org/"^^ . - . - . - . - . - . - "true"^^ . - "https://bioregistry.io/$1:$2" . - "http://purl.org/dc/terms/$1"^^ . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . - . - "https://gitlab.com/"^^ . - "Darren Natale" . - "0000435"^^ . - "E-cyanobacterium model" . - "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . - . - . - "https://www.kegg.jp/entry/$1"^^ . - . - . - . - . - "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . - "Mouse gross anatomy and development, timed" . - . - . - "http://www.lrg-sequence.org/"^^ . - . - "Yam ontology" . - . - . - . - "false"^^ . - "http://cellimagelibrary.org/"^^ . - . - . - . - . - . - "Cellular Phenotypes" . - "An ontology of core ecological entities" . - "Bitbucket" . - "^\\d+$"^^ . - . - . - . - . - . - "0000032"^^ . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . - "^\\d{3}$"^^ . - . - . - . - "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "^\\d{8}$"^^ . - . - . - . - . - . - . - . - . - "0000000"^^ . - . - "^\\d+$"^^ . - . - . - . - "Germplasm Resources Information Network" . - . - "false"^^ . - "https://www.cropontology.org/rdf/CO_345:$1"^^ . - "ValidatorDB" . - "SRX000007"^^ . - . - . - "1000000"^^ . - "PROB_c0000005"^^ . - . - . - . - . - . - . - . - . - "VEuPathDB ontology" . - "00023232"^^ . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - "https://github.com/obi-bcgo/bcgo"^^ . - . - "JCOIN" . - . - . - . - . - . - . - . - . - . - . - "0000550"^^ . - . - . - . - "FlyBase internal citation identifiers"^^ . - . - . - . - . - . - . - "SIDER Side Effect" . - . - "DrugBank Salts" . - . - "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . - . - "^\\w+$"^^ . - . - . - . - "https://covid19.sfb.uit.no"^^ . - . - "Ali Syed" . - "^\\d+$"^^ . - . - . - . - "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . - . - . - . - . - . - "https://www.w3.org/ns/dcat"^^ . - "http://purl.obolibrary.org/obo/AEO_$1"^^ . - . - . - . - "Minimal Anatomical Terminology" . - "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . - . - "^\\d+$"^^ . - "true"^^ . - . - . - "http://planteome.org/"^^ . - . - . - "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . - . - . - . - "http://emouseatlas.org"^^ . - "^[A-Z0-9]{4}$"^^ . - . - . - . - "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . - "https://progenetix.org/services/ids/$1"^^ . - . - . - . - . - . - "false"^^ . - . - "^BSU\\d{5}$"^^ . - . - "CCDC Number" . - . - . - . - . - . - . - "false"^^ . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://comptox.epa.gov/dashboard"^^ . - . - . - . - . - . - . - . - . - "https://www.internationalgenome.org/"^^ . - . - . - . - . - . - . - . - . - "LOC_Os01g49190.1"^^ . - . - . - . - . - . - . - . - . - "BindingDB is the first public database of protein-small molecule affinity data."^^ . - . - "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . - "Amos Bairoch" . - . - "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . - . - . - . - . - . - . - . - . - . - . - "Integrative and Conjugative Element Ontology" . - . - . - . - "3355"^^ . - . - . - . - . - . - . - "http://www.antirrhinum.net/"^^ . - . - . - . - . - . - . - "C. elegans development ontology" . - . - . - . - . - . - "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . - "http://neuinfo.org/"^^ . - "false"^^ . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "http://www.narcis.nl"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PECO_$1"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . - . - . - "Ada Hamosh" . - "Mosquito gross anatomy ontology" . - . - "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . - . - . - "https://stemcells.nindsgenetics.org"^^ . - "http://datf.cbi.pku.edu.cn/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Os01g0883800"^^ . - "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . - . - "268"^^ . - "http://purl.obolibrary.org/obo/SCDO_$1"^^ . - . - "Molecular Process Ontology" . - . - . - . - . - . - . - "hsa-let-7a-2-3p"^^ . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^ . - . - . - "^AT\\d+$"^^ . - "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . - . - "https://www.re3data.org/repository/$1" . - . - . - . - . - . - . - . - . - . - "ECMDB00005"^^ . - . - . - "Comparative Data Analysis Ontology" . - . - . - . - "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . - "Gene Ontology" . - "Ceri Van Slyke" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . - "false"^^ . - "https://foodon.org/"^^ . - . - . - . - . - . - . - . - . - "0000004"^^ . - . - "false"^^ . - . - "false"^^ . - "MSV000082131"^^ . - "false"^^ . - . - . - "https://www.vmh.life/#metabolite/$1"^^ . - . - . - . - . - . - . - "AddexBio cell line products" . - . - . - . - . - . - . - . - . - "http://sourceforge.net/p/mamo-ontology/wiki/Home/"^^ . - . - . - . - . - "true"^^ . - . - "A comprehensive compendium of human long non-coding RNAs"^^ . - . - . - "false"^^ . - . - . - . - "CHEBI" . - "http://bigg.ucsd.edu/models/$1"^^ . - . - . - "Geographical Entity Ontology" . - . - . - "International Classification of Diseases, 10th Revision, Procedure Coding System" . - . - "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . - . - . - "https://europepmc.org/article/CBA/$1"^^ . - _:N5c8bdad6547e49cfb162052b88d629dd . - . - "http://en.wikipedia.org/wiki/$1"^^ . - . - . - . - . - . - "C00000001"^^ . - . - "https://www.ebi.ac.uk/chembldb/"^^ . - . - . - "^COG\\d+$"^^ . - . - . - . - . - "MLCommons Association" . - . - . - "http://edamontology.org"^^ . - . - "false"^^ . - . - . - "Ontology of standardized units"^^ . - "HBB"^^ . - "https://github.com/arpcard/aro"^^ . - . - . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . - "^[0-9]+$"^^ . - . - "BioContext contains modular JSON-LD contexts for bioinformatics data." . - . - . - . - "false"^^ . - . - . - . - . - . - "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . - "SED-ML model format" . - "^\\d{7}$"^^ . - . - . - . - "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . - . - . - . - . - "morpheus.lab/morpheus"^^ . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . - . - . - . - "Suzi Aleksander" . - . - . - . - . - . - . - "Identifier for a species in iNaturalist"^^ . - "https://gitlab.com/fortunalab/ontoavida"^^ . - "0000144"^^ . - . - "Gene Wiki" . - . - . - "^\\w+$"^^ . - . - "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines)."^^ . - . - . - . - . - . - "Small Angle Scattering Biological Data Bank" . - . - . - . - "0000288"^^ . - . - "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "true"^^ . - "http://rhesus.amu.edu.pl/mirnest/copy/"^^ . - . - . - . - "^[0-9a-zA-Z]{8}$"^^ . - . - . - . - "http://www.ensembl.org/"^^ . - . - . - . - . - "http://www.cazy.org/"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/Genbank/"^^ . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1"^^ . - "^\\d+$"^^ . - "http://bigg.ucsd.edu/compartments/$1"^^ . - "151022"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/ZFA_$1"^^ . - . - "UniProt Diseases" . - . - . - "http://swift.cmbi.kun.nl/swift/hssp/"^^ . - . - . - . - . - "Chris Mungall" . - . - "Hepatitis C Virus Database" . - . - "http://www.evoio.org/wiki/MIAPA"^^ . - "false"^^ . - . - "http://www.hmdb.ca/"^^ . - . - . - . - . - . - . - "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . - . - . - . - "Thermo Fisher Scientific" . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - "TTHERM_00648910"^^ . - . - "false"^^ . - . - . - "http://antibodyregistry.org/AB_$1"^^ . - . - . - . - . - . - "https://github.com/EBISPOT/ancestro"^^ . - . - . - "Homologous Vertebrate Genes Database" . - "http://unite.ut.ee/"^^ . - . - . - "https://cropontology.org/ontology/CO_358/Cotton"^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/pathways"^^ . - . - . - . - "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . - "^[A-Z]+$"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - "http://www.pharmgkb.org/"^^ . - . - . - . - . - . - . - "BRENDA, The Comprehensive Enzyme Information System" . - "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . - . - "https://europepmc.org/article/ppr/$1"^^ . - . - . - . - . - "^DDB_G\\d+$"^^ . - . - . - . - . - "David Osumi-Sutherland" . - "^\\d+$"^^ . - "false"^^ . - . - . - "https://vectorbase.org/vectorbase/app/record/gene/$1"^^ . - . - "42840"^^ . - "https://github.com/DiseaseOntology/PathogenTransmissionOntology"^^ . - "chebi"^^ . - . - . - . - . - . - "http://data.europa.eu/89h/$1"^^ . - "false"^^ . - "http://en.wikipedia.org/wiki/Main_Page"^^ . - . - . - . - . - . - "http://scicrunch.org/resolver/SCR_$1"^^ . - "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . - . - . - "http://geneontology.org/" . - . - . - "Paul Schofield" . - . - . - . - . - . - . - . - . - . - . - "http://ecolexicon.ugr.es/en/index.htm"^^ . - "28"^^ . - . - . - . - . - "^LTS\\d{7}$"^^ . - "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . - . - . - . - . - "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . - "Anne Thessen" . - . - . - "1"^^ . - . - . - . - . - . - . - . - . - "https://protists.ensembl.org/id/$1"^^ . - . - "http://purl.obolibrary.org/obo/OPL_$1"^^ . - "http://euhcvdb.ibcp.fr"^^ . - . - . - "false"^^ . - . - . - "https://www.ebi.ac.uk/interpro/genomeproperties/"^^ . - . - . - . - . - . - . - "http://www.bioinfo.org/NONCODEv4/"^^ . - "http://130.88.97.239/dbbrowser/sprint/"^^ . - . - . - . - . - . - . - . - . - "0005452"^^ . - . - . - . - "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . - . - "B00162"^^ . - . - "false"^^ . - . - . - . - . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^ . - "https://prefix.cc/$1" . - . - . - . - . - . - . - "BiGG Model" . - "eVOC (Expressed Sequence Annotation for Humans)" . - "^D\\d+$"^^ . - . - "UniProt journal ID" . - . - . - . - . - . - . - "57-27-2"^^ . - . - "false"^^ . - . - . - . - . - "REBASE restriction enzyme database" . - . - . - . - "https://sitem.herts.ac.uk/aeru/vsdb"^^ . - . - "http://compbio.soe.ucsc.edu/yeast_introns.html"^^ . - "c"^^ . - "^\\d+$"^^ . - . - . - "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^ . - . - "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . - . - . - . - . - . - . - "false"^^ . - "OTTHUMG00000169812"^^ . - . - . - . - . - . - . - . - . - "BiGG Metabolite" . - . - "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . - . - . - "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . - . - . - . - . - "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . - . - "0000091"^^ . - . - . - . - . - "13GS"^^ . - "http://www.gramene.org/"^^ . - . - "http://vocab.getty.edu/page/tgn/$1"^^ . - "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . - . - "^PR\\d{5}$"^^ . - . - "Scholarly Contributions and Roles Ontology" . - "false"^^ . - . - . - "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . - . - . - . - . - . - . - "Ontology for Nutritional Studies" . - . - . - "https://cropontology.org/ontology/CO_343/Yam"^^ . - . - . - "The upper level ontology upon which OBO Foundry ontologies are built."^^ . - . - . - "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . - . - . - . - . - "http://thebiogrid.org/$1"^^ . - . - . - "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^ . - . - . - "https://www.arraymap.org"^^ . - . - "false"^^ . - . - . - "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "SubtiWiki" . - "351"^^ . - "false"^^ . - "false"^^ . - . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . - . - . - "GR:0080039"^^ . - "0001290"^^ . - "https://www.cropontology.org/rdf/CO_357:$1"^^ . - . - "0000008"^^ . - . - . - . - "0001655"^^ . - . - . - . - . - . - . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^ . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . - "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . - "https://github.com/ApolloDev/apollo-sv"^^ . - . - "https://reg.clinicalgenome.org"^^ . - "Q9P0K8"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . - . - . - "http://www.aspgd.org/"^^ . - "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . - . - . - "http://repository.topdownproteomics.org/proteoforms/$1"^^ . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - "Cell line collections"^^ . - "Xenopus Phenotype Ontology" . - "http://www.coloncanceratlas.org"^^ . - "0000066"^^ . - . - "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . - . - "0000252"^^ . - "https://envipath.org/package/$1"^^ . - . - "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - "Tom Gillespie" . - . - . - . - . - . - "A vocabulary and ontology repository for agronomy and related domains." . - "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . - . - "Bill Duncan" . - . - . - "Plant Transcription Factor Database" . - "http://pgscatalog.org"^^ . - "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . - "Database of small human noncoding RNAs" . - . - . - "https://github.com/obophenotype/biological-spatial-ontology"^^ . - . - . - . - "GXA Expt" . - . - . - . - . - . - . - "International repository of Adverse Outcome Pathways."^^ . - "^GR\\:\\d+$"^^ . - . - . - . - "Registry" . - . - . - . - . - . - . - . - . - . - . - "Cell Line Ontology" . - "false"^^ . - . - . - "false"^^ . - "http://sabiork.h-its.org/newSearch?q=$1"^^ . - . - . - "false"^^ . - . - . - . - . - "https://www.phenxtoolkit.org/"^^ . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - . - "DICOM Controlled Terminology" . - . - . - "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . - . - "http://www.evocontology.org/"^^ . - . - . - . - . - . - . - . - "Human Unidentified Gene-Encoded" . - . - . - "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . - "^ERM[0-9]{8}$"^^ . - "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . - "Christian-Alexander Dudek" . - . - . - "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . - . - "^(D|PP|R|T|H|X|AI)?\\d+$"^^ . - "Cell line collections"^^ . - . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . - . - . - . - . - . - "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . - "https://sorgerlab.github.io/famplex/"^^ . - "https://cmecscatalog.org/cmecs"^^ . - "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - "https://viralzone.expasy.org/$1"^^ . - . - . - _:N3b4e286bf1584db39cc4e530d6f77656 . - "false"^^ . - "Odor Molecules DataBase" . - . - . - "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1"^^ . - . - . - "https://odc-sci.org"^^ . - . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - . - . - . - "National Drug Data File" . - . - . - "^virsi\\d+$"^^ . - . - "http://hawaii.eagle-i.net/i/$1"^^ . - . - . - . - . - "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . - . - "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . - . - . - "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . - . - . - "ESi007-A"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - "A01M1/026"^^ . - . - . - . - . - "https://cropontology.org/ontology/CO_336/Soybean"^^ . - . - "https://amzn.com/$1"^^ . - . - "A pull request in any public repository on GitHub."^^ . - . - "Lindsay Cowell" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . - . - "^\\d+$"^^ . - "https://pdc.cancer.gov/pdc"^^ . - . - "^\\d{7}$"^^ . - . - "Mungbean ontology" . - "https://bgee.org/?page=gene&gene_id=$1"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - "Database of Complete Genome Homologous Genes Families" . - . - . - . - . - "false"^^ . - . - . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . - . - . - . - "true"^^ . - "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . - "Compluyeast-2D-DB" . - . - "DBG2 Introns" . - . - . - "false"^^ . - . - . - "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^ . - . - . - . - "131392"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MAO_$1"^^ . - . - . - . - . - "rxn00001"^^ . - . - . - . - . - . - . - . - . - . - . - "1199"^^ . - . - "307"^^ . - "http://purl.obolibrary.org/obo/AAO_$1"^^ . - . - . - "http://mint.bio.uniroma2.it/mint/"^^ . - . - . - "http://www.pseudomonas.com/"^^ . - "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - "^A\\d{4}$"^^ . - . - "^C\\d+$"^^ . - . - "false"^^ . - "https://w3id.org/reproduceme/research"^^ . - . - . - "^\\w+$"^^ . - . - . - . - . - "Observational Medical Outcomes Partnership" . - . - . - . - . - "http://www.mgc.ac.cn/VFs/"^^ . - . - "Unified Medical Language System Concept Unique Identifier" . - . - "https://www.blueprintnhpatlas.org/"^^ . - . - . - . - . - . - . - "LigandBox" . - . - . - . - . - "PomBase" . - . - . - "^ENSG\\d{11}$"^^ . - "nextProt" . - . - . - . - "false"^^ . - . - . - . - . - "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . - "^CHEMBL\\d+$"^^ . - . - . - "false"^^ . - . - "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . - . - . - . - "Vital Sign Ontology" . - "false"^^ . - "http://foodb.ca/compounds/$1"^^ . - "^[0-9\\.]+$"^^ . - . - "UniProt Resource" . - "^\\d+$"^^ . - "https://civicdb.org/"^^ . - . - . - . - . - "http://jcggdb.jp/index_en.html"^^ . - . - "Consensus CDS" . - "^UPC\\d{5}$"^^ . - "^PMC\\d+$"^^ . - . - "Unique Ingredient Identifier" . - . - . - "http://www.obofoundry.org/"^^ . - . - "https://www.facebase.org"^^ . - "NIF Standard Ontology: Brain Regions" . - "https://fairsharing.org/"^^ . - . - "The LifeWatch ERIC repository of semantic resources for the ecological domain." . - . - "has responsible" . - . - "K00973"^^ . - . - . - . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Global Research Identifier Database" . - . - "Conferences in EasyChair"^^ . - . - "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . - . - . - . - . - . - . - "false"^^ . - "S000002493"^^ . - . - . - . - "Beta Cell Genomics Ontology" . - . - . - . - . - . - . - . - "0000001"^^ . - "http://www.iclc.it"^^ . - "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . - . - . - . - . - "Spectral Database for Organic Compounds" . - "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . - "9-1-1 Complex"^^ . - "false"^^ . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_356:$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://biomodels.net/vocab/idot.rdf"^^ . - "Schema.org" . - . - . - "false"^^ . - "false"^^ . - . - . - "^([a-z]{3,5}_)?M\\d{5}$"^^ . - "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^MIRT\\d{6}$"^^ . - . - "https://www.metanetx.org/equa_info/$1"^^ . - . - . - . - . - "17:41223048"^^ . - . - "false"^^ . - . - . - . - . - . - . - "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm"^^ . - . - . - . - . - "1058367"^^ . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . - . - "false"^^ . - . - . - . - . - . - "Platynereis stage ontology" . - . - . - "false"^^ . - . - . - . - "Stephen Fisher" . - "false"^^ . - . - . - . - "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . - . - . - "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . - "Jie Zheng" . - . - . - . - "D001151"^^ . - . - . - . - "UniProt Isoform" . - "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"^^ . - "P3DB Protein" . - . - "Woody Plant Ontology ontology" . - "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^ . - . - . - . - . - . - . - . - . - . - . - "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "miRNEST" . - . - "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - "Transcription Factor Database" . - . - . - "http://www.uniprot.org"^^ . - . - . - . - "5fde96bdc5f1aa9ff0cce18a"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . - . - . - . - "https://github.com/rsc-ontologies/rxno"^^ . - . - "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . - . - . - . - . - "false"^^ . - . - . - "Cell Biolabs cell line products" . - "HGNC gene family" . - . - . - . - "EGAS00000000001"^^ . - . - . - "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://www.humancellatlas.org"^^ . - . - "https://reporter.nih.gov/project-details/$1"^^ . - . - . - "Sol Genomics Network" . - . - . - . - . - . - "00000001"^^ . - "https://easychair.org/cfp/"^^ . - . - . - "0000029"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . - . - . - . - . - . - . - "Antimicrobial Peptide Database" . - . - . - "false"^^ . - . - "2023"^^ . - . - . - . - "dsmz_mutz-id:ACC 291"^^ . - . - . - . - "https://rnacentral.org/rna/$1"^^ . - . - . - . - "http://www.gramene.org/"^^ . - "https://www.ncbi.nlm.nih.gov/geo/"^^ . - . - . - . - . - "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . - . - . - . - . - . - . - . - "https://gudmap.org/id/$1"^^ . - . - . - "http://vbrc.org/"^^ . - "https://www.biocarta.com/"^^ . - "DAP000773"^^ . - "http://www.sparontologies.net/ontologies/datacite"^^ . - . - . - . - "ChEMBL target" . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . - "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "Raymond Lee" . - "false"^^ . - . - . - "Planarian Phenotype Ontology" . - . - "^\\d+$"^^ . - "http://www.indexfungorum.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . - . - "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . - . - . - "^\\d+$"^^ . - . - . - "Richard Cyganiak" . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . - . - "^\\w+\\_\\w+$"^^ . - "^SCV\\d+(\\.\\d+)?$"^^ . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . - . - . - . - . - "LINCS Small Molecule" . - "Cell Version Control Repository" . - "mKIAA4200"^^ . - "false"^^ . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - "https://www.ebi.ac.uk/ena/browse/genome-assembly-database"^^ . - "^[0-9]+-[0-9]+$"^^ . - "Cell Cycle Ontology" . - "^\\d+$"^^ . - . - . - . - "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . - . - . - . - "^ILMN_\\d+$"^^ . - . - "Matthew Brush" . - . - "Human Developmental Stages" . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - . - . - "http://lisanwanglab.org/DASHR/entry/$1"^^ . - . - "C2584994"^^ . - . - . - . - . - . - . - . - "Medaka Developmental Stages" . - "false"^^ . - . - "Veterans Administration National Drug File" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://ascl.net/$1"^^ . - . - . - "HUGO Gene Nomenclature Committee" . - "Annotated Regulatory Binding Sites" . - "NIF Standard Ontology: Cell Types" . - "false"^^ . - . - . - "CHEMBL4303805"^^ . - "false"^^ . - . - . - . - "Dublin Core Types" . - . - . - . - . - "Units of measurement ontology" . - . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - "Experimental condition ontology" . - . - . - "Progenetix" . - . - . - . - . - "http://purl.obolibrary.org/obo/VARIO_$1"^^ . - "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - . - "false"^^ . - . - "ForwardStrandPosition"^^ . - "^\\w+$"^^ . - . - . - . - "familyName"^^ . - . - "https://ega-archive.org/"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . - . - "BBA0001"^^ . - "^\\d+$"^^ . - "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"^^ . - . - . - . - . - . - . - . - . - . - "068078"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - "System Science of Biological Dynamics project" . - . - "http://rgd.mcw.edu/"^^ . - "Antibiotic resistance genes and mutations"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MO_$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/LPT_$1"^^ . - "^\\d+$"^^ . - . - . - "XB-GENE-922462"^^ . - . - . - . - "0000184"^^ . - . - . - . - "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^ . - . - . - . - . - "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . - "https://www.uniprot.org/database/" . - . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/FBdv_$1"^^ . - . - "oai:cwi.nl:4725"^^ . - . - . - "^\\d{8}$"^^ . - . - . - . - . - . - "http://www.unimod.org/"^^ . - . - . - . - . - . - "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . - . - . - . - . - . - "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . - . - . - . - . - . - . - . - . - "BCRTi001-A"^^ . - . - . - . - . - . - . - . - . - . - "https://ifaa.unifr.ch/"^^ . - . - "Ontology of Organizational Structures of Trauma centers and Trauma systems" . - . - . - . - . - . - . - . - "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . - . - "http://ecogene.org/"^^ . - . - "https://github.com/CTDbase/exposure-ontology"^^ . - . - "Taxonomic rank vocabulary" . - . - . - . - "https://openalex.org/"^^ . - . - . - . - . - "QJ51RV02"^^ . - . - . - "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . - . - . - . - "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html"^^ . - "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . - "0000984"^^ . - . - . - "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . - "Ontology of Genetic Susceptibility Factor" . - . - . - "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . - "ADM1"^^ . - . - "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . - "http://www.yeastrc.org/pdr/"^^ . - . - "https://e-cyanobacterium.org/models/model/$1"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . - "Broad Fungal Genome Initiative" . - . - . - . - . - . - "http://www.genenames.org"^^ . - . - . - . - . - . - . - . - . - "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . - . - . - . - . - . - . - . - . - "true"^^ . - . - "1257009"^^ . - . - . - . - . - . - "485991"^^ . - "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . - "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . - . - "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . - "^\\d+$"^^ . - . - "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://kim.bio.upenn.edu/software/ornaseq.shtml"^^ . - . - . - "Mass spectrometry ontology" . - . - "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . - . - "false"^^ . - . - "SEQF1003"^^ . - "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . - . - "Measurement method ontology" . - . - . - "2h6o"^^ . - . - "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . - "https://envipath.org/"^^ . - "false"^^ . - "rateRule"^^ . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - . - "ab-1-ha"^^ . - . - . - . - . - . - "Life cycle stages for Platynereis dumerilii"^^ . - . - . - . - "^NPC\\d+$"^^ . - . - . - . - "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . - . - . - . - "NIF Standard Ontology: OEN Terms in Neurolex" . - "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . - . - . - "https://www.gbif.org/species"^^ . - . - . - . - . - "https://www.enzolifesciences.com"^^ . - . - . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee"^^ . - . - . - "https://mouse.brain-map.org"^^ . - . - . - "https://vertebrate.genenames.org"^^ . - . - . - . - "https://bykdb.ibcp.fr/BYKdb/"^^ . - . - . - . - . - "Redistributor of bilogics and biomedical supplies"^^ . - "https://www.ncbi.nlm.nih.gov/dbvar"^^ . - . - . - . - "1"^^ . - . - . - "BioSimulators" . - . - . - . - "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . - . - . - "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . - . - "^EBI\\-[0-9]+$"^^ . - . - "http://purl.obolibrary.org/obo/BCO_$1"^^ . - "National Academic Research and Collaborations Information System" . - . - . - . - . - "Mammalian Phenotype Ontology" . - "false"^^ . - "http://dictybase.org/"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - "Oryzabase Stage" . - . - . - . - . - . - . - . - . - "OBO Metadata Ontology" . - . - . - "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . - . - . - "false"^^ . - . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . - "https://github.com/phenoscape/teleost-taxonomy-ontology"^^ . - . - "TTD Target" . - . - . - . - "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . - "Agricultural Online Access" . - "http://hymao.org"^^ . - . - . - "http://edamontology.org"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "false"^^ . - "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . - . - . - "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . - . - "false"^^ . - "InterLex" . - . - . - . - "false"^^ . - . - . - . - . - "Xeni Kechagioglou" . - . - . - . - "http://www.semantic-systems-biology.org/apo"^^ . - . - . - . - . - . - "https://cropontology.org/ontology/CO_326/Coconut"^^ . - . - . - "Sebastian Koehler" . - . - "http://www.ebi.ac.uk/sbo/"^^ . - . - "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . - . - . - . - . - . - . - . - "Gerhard Mayer" . - "false"^^ . - . - "GDS1234"^^ . - . - . - . - . - . - "https://foodb.ca/"^^ . - . - . - . - "Gene Ontology Database references" . - . - "^\\d{7}$"^^ . - "http://www.cropontology.org/ontology/CO_335/Common%20Bean"^^ . - "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . - "false"^^ . - "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . - . - . - . - . - "https://www.kerafast.com/Search?SearchTerm="$1""^^ . - . - . - "true"^^ . - "Web Ontology Language" . - . - . - . - . - . - "https://pharmacome.github.io/conso/"^^ . - . - "https://github.com/OPMI/opmi"^^ . - . - . - . - . - . - . - . - "false"^^ . - "https://w3id.org/hso"^^ . - . - "Korean Cell Line Bank" . - . - . - "137"^^ . - "https://plants.ensembl.org/"^^ . - . - . - "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . - . - . - . - "http://purl.obolibrary.org/obo/fbdv"^^ . - "https://w3id.org/oc/corpus/$1"^^ . - . - . - . - . - . - . - "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . - "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . - . - . - "Fungal gross anatomy" . - . - . - . - . - "https://biopragmatics.github.io/providers/schem/$1"^^ . - "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . - "National Library of Medicine Catalog" . - "false"^^ . - . - "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . - . - . - "Japan Collection of Microorganisms" . - . - "https://www.ncbi.nlm.nih.gov/nucest"^^ . - . - . - "d4e2515"^^ . - . - . - "false"^^ . - "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . - . - . - . - . - "Wikipedia" . - . - . - . - "Molecular Interaction Database" . - . - "EST database maintained at the NCBI." . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/OPL-ontology/OPL"^^ . - . - . - . - . - "CHEBI" . - . - . - . - . - "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . - "051"^^ . - "Insertion sequence elements database" . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Luis A. Gonzalez-Montana" . - . - . - "P00024"^^ . - . - . - . - . - . - . - . - . - "Ontology from the APA"^^ . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - "Danielle Welter" . - "^\\d+$"^^ . - . - . - . - "false"^^ . - . - "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . - "1"^^ . - "false"^^ . - . - "MatrixDB Association" . - "TTD Drug" . - . - "http://www.nlm.nih.gov/mesh/"^^ . - "false"^^ . - . - . - . - "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"^^ . - . - "OSR0818"^^ . - . - . - "https://developingmouse.brain-map.org/"^^ . - "false"^^ . - . - . - "false"^^ . - . - "Integrated Canine Data Commons" . - . - . - . - . - . - . - . - . - . - . - . - "^PAp[0-9]{8}$"^^ . - . - . - . - "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . - . - . - "false"^^ . - "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . - "false"^^ . - . - "2004-2820"^^ . - "http://genatlas.medecine.univ-paris5.fr/"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . - . - "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . - . - . - "https://cropontology.org/ontology/CO_322/Maize"^^ . - "https://www.kegg.jp/entry/$1"^^ . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . - . - . - . - "http://www.sparontologies.net/ontologies/deo"^^ . - . - . - . - . - . - . - . - . - . - . - . - "0000081"^^ . - . - . - . - . - . - . - . - . - . - "http://msi-ontology.sourceforge.net/"^^ . - "Integrated Microbial Genomes Gene" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . - . - . - . - . - "https://smid-db.org/smid/$1"^^ . - . - "https://github.com/obophenotype/chiro"^^ . - . - . - "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . - . - . - "DisProt" . - . - . - "http://www.receptors.org/nucleardb/"^^ . - . - "WP732"^^ . - . - . - . - . - "https://www.wikidata.org/"^^ . - . - . - "CorrDB" . - . - . - . - . - . - "https://bitbucket.org/hegroup/ogg"^^ . - . - "Life cycle stages for Medaka"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/TGMA_$1"^^ . - . - . - . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes."^^ . - "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . - . - . - . - "TF0001053"^^ . - "MolMeDB" . - . - . - . - "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^ . - . - . - "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . - . - . - "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . - . - . - . - . - . - . - "0000255"^^ . - "false"^^ . - "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . - . - "0000002"^^ . - . - . - . - . - "Daniel C. Berrios" . - "1250"^^ . - . - "http://purl.obolibrary.org/obo/EPO_$1"^^ . - . - "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^ . - "uc001rvw.5"^^ . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - "Gramene Reference" . - "NCBI Bookshelf" . - . - "Common Anatomy Reference Ontology" . - . - . - . - "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . - . - . - . - "false"^^ . - "false"^^ . - "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . - "Bloomington Drosophila Stock Center" . - "^FR\\-FCM\\-\\w{4}$"^^ . - . - "false"^^ . - "false"^^ . - . - . - . - "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . - . - "https://cropontology.org/ontology/CO_341/Pigeonpea"^^ . - . - . - "10004892"^^ . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - "^EDI_\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "FuncBase Mouse" . - . - . - "false"^^ . - "https://www.vmh.life/"^^ . - . - . - "240-17-488-3-4-12"^^ . - "AberOWL" . - . - . - . - "0000046"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . - . - . - . - "LiceBase" . - "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . - . - . - . - . - . - "^(\\w){3}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "An ontology built for representating the organizational components of trauma centers and trauma systems."^^ . - . - . - "false"^^ . - "jrc-eurl-ecvam-chemagora"^^ . - "NIF Gross Anatomy" . - . - . - . - "C063233"^^ . - . - "false"^^ . - . - . - "https://github.com/pato-ontology/pato/"^^ . - "Sugar Kelp trait ontology" . - . - . - . - . - . - "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - "R-BTA-418592"^^ . - . - . - . - . - "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . - "https://www.gleif.org/lei/$1"^^ . - "Laurel Cooper" . - . - . - . - "^PTM-\\d{4}$"^^ . - . - . - . - . - "^BG\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/VTO_$1"^^ . - . - "^\\d+$"^^ . - "http://senselab.med.yale.edu/ModelDB/"^^ . - "http://scop.mrc-lmb.cam.ac.uk/scop/"^^ . - . - . - . - . - . - "0000066"^^ . - . - . - . - . - "Chickpea ontology" . - . - "AT1G73965"^^ . - . - . - . - . - . - . - . - . - . - "GeneCards" . - . - . - "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . - . - . - . - "miRBase Families" . - "PaxDb Organism" . - . - . - . - . - . - . - "Database of Genomic Structural Variation - Variant" . - . - "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . - . - "0000001"^^ . - . - "http://purl.obolibrary.org/obo/VSAO_$1"^^ . - "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . - "false"^^ . - "http://zfin.org"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - "https://hpscreg.eu/cell-line/$1"^^ . - . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . - . - "label"^^ . - "false"^^ . - . - "http://www.geosamples.org/"^^ . - "^FDB\\d+$"^^ . - . - . - . - "The SEED;" . - "Cotton ontology from CottonGen database - June 2019"^^ . - . - "Sirarat Sarntivijai" . - "https://pharmacodb.ca/datasets/$1"^^ . - . - . - "http://arabidopsis.info/"^^ . - . - . - "http://vocab.deri.ie/void"^^ . - . - . - . - . - . - "DUO is an ontology which represent data use conditions."^^ . - . - "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . - "^\\d{4}$"^^ . - "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . - . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - . - . - "MassBank" . - . - . - "^ACH-\\d+$"^^ . - . - "http://substrate.burnham.org/"^^ . - . - . - . - "false"^^ . - "Bambara groundnut ontology" . - . - . - "http://opencitations.net"^^ . - . - . - . - . - . - "KEGG Metagenome" . - "false"^^ . - . - . - "2842"^^ . - . - . - "http://purl.uniprot.org/annotation/$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\w+$"^^ . - . - "false"^^ . - "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . - . - "https://www.nlm.nih.gov/research/umls"^^ . - . - . - . - . - . - . - "http://string.embl.de/"^^ . - "Saccharomyces genome database pathways" . - . - . - . - . - "^C\\d{4}$"^^ . - . - "0001"^^ . - "SNOMED CT (International Edition)" . - . - . - "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . - "ebf69ca24298b28b2361e7d43eb52d6c"^^ . - "H00076"^^ . - "https://dandiarchive.org/dandiset/$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - "GlycoNAVI" . - "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . - . - "UniProt Variants" . - . - . - . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . - . - "10194"^^ . - "false"^^ . - . - . - . - . - . - "https://publons.com/researcher"^^ . - . - . - "https://www.ebi.ac.uk"^^ . - . - . - . - . - "http://isbndb.com/"^^ . - . - "http://dictybase.org/"^^ . - "Digital Object Identifier" . - "0000001"^^ . - . - . - "false"^^ . - . - "false"^^ . - "0000598"^^ . - "Identifiers.org namespace" . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . - . - "Pigeonpea ontology" . - . - . - . - . - . - . - . - . - "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . - . - . - . - . - . - . - "http://www.genome.jp/kegg/catalog/org_list.html"^^ . - . - "false"^^ . - . - . - "^CNP\\d{7}$"^^ . - "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . - . - . - . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF"^^ . - "NOAA Fisheries Species Directory" . - . - "Molecular database for the identification of fungi" . - . - . - . - . - . - . - _:Ne7c10d4402c34331a10bead187346055 . - . - "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . - . - . - "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . - . - "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . - "false"^^ . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - "ITO_01625"^^ . - . - "0000015"^^ . - . - "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . - . - "false"^^ . - . - "^TF\\w+$"^^ . - . - "https://www.ebi.ac.uk/chebi/"^^ . - "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - "false"^^ . - "BioPortal Prefixes" . - "SNR17A"^^ . - "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . - . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - "https://urgi.versailles.inra.fr/gnpis/"^^ . - . - . - . - "false"^^ . - . - . - "false"^^ . - "http://paleodb.org/"^^ . - . - . - . - . - "http://jcggdb.jp/idb/jcggdb/$1"^^ . - "Cell Ontology" . - . - . - . - . - . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . - . - . - . - . - . - "^OSC\\d{4}$"^^ . - . - "false"^^ . - . - . - . - . - "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . - . - . - "ProtoNet ProteinCard" . - "https://genelab-data.ndc.nasa.gov/genelab/"^^ . - . - "https://www.vmh.life/#reaction/$1"^^ . - . - "^\\d+$"^^ . - . - "A database for Triticeae and Avena gene symbols."^^ . - . - . - . - "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "0000504"^^ . - "Assists in resolving data across cloud resources."^^ . - . - . - "1.1.1.1"^^ . - . - . - . - . - . - . - . - . - . - "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1"^^ . - . - "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . - "Biomedical Informatics Research Network Lexicon" . - . - . - "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . - . - . - "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . - "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . - . - . - . - . - . - "true"^^ . - . - . - "Spider Ontology" . - . - "false"^^ . - . - . - "http://edamontology.org/data_$1"^^ . - "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . - . - "http://www.upol.cz/en/"^^ . - "RAP-DB Transcript" . - . - . - . - "6472"^^ . - . - . - . - . - "18030"^^ . - . - . - "https://doulix.com"^^ . - "NanoParticle Ontology" . - . - . - . - "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "http://www.pathbase.net"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "NIF Standard Ontology: External" . - "BRIP1"^^ . - . - . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . - "false"^^ . - . - . - . - "An ontology of Drosophila melanogaster developmental stages."^^ . - "^\\d+$"^^ . - . - . - . - . - "^[a-zA-Z0-9\\-:#\\.]+$"^^ . - . - . - "http://purl.org/spar/biro/$1"^^ . - . - "^\\d{7}$"^^ . - . - "https://www.rhea-db.org/rhea/$1"^^ . - "Wormpep" . - . - . - . - "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . - . - "http://ciliate.org/index.php/"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "https://labsyspharm.github.io/lspci/"^^ . - . - "https://smid-db.org/"^^ . - . - "VIRsiRNA" . - . - . - . - . - . - . - "Plant Phenology Ontology" . - . - . - "^LGCEDe-S-\\d{9}$"^^ . - "false"^^ . - "Semantic Types Ontology" . - "http://www.humanproteomemap.org/index.php"^^ . - . - "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . - "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . - . - "^\\d{7}$"^^ . - . - "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . - . - "http://purl.obolibrary.org/obo/XPO_$1"^^ . - . - "PTHR12345"^^ . - . - . - . - . - "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . - "http://purl.obolibrary.org/obo/MPIO_$1"^^ . - . - "https://www.uniprot.org/unirule/"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/EXO_$1"^^ . - . - . - . - . - . - . - . - . - . - "https://github.com/ICO-ontology/ICO"^^ . - "ArrayExpress Platform" . - . - . - "https://www.xenbase.org/entry/$1"^^ . - . - . - "Willy Wong" . - . - . - . - . - "http://www.phosphosite.org/homeAction.do"^^ . - . - . - . - "false"^^ . - . - . - . - "http://bugs.sgul.ac.uk/E-BUGS"^^ . - . - . - "BioContext" . - "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology"^^ . - . - . - . - "SNHG3"^^ . - . - . - . - "LIPID MAPS" . - . - . - . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/XL_$1"^^ . - "false"^^ . - "OMIM Phenotypic Series" . - . - . - "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^ . - . - . - . - "http://www.sasbdb.org/"^^ . - . - . - . - . - . - . - "0000049"^^ . - "https://www.cellbiolabs.com"^^ . - "^\\d+$"^^ . - "false"^^ . - . - "false"^^ . - . - . - "^\\d{8}$"^^ . - . - . - . - "0004828"^^ . - "Electron Microscopy Public Image Archive" . - "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . - . - . - . - . - . - . - "A Web-based catalog of recommended measurement protocols"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - "Lutz Fischer" . - . - . - . - . - . - . - . - . - "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . - "http://www-is.biotoul.fr/i"^^ . - . - . - . - "https://aopwiki.org/stressors/$1"^^ . - . - . - . - . - "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^ . - . - . - . - . - "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . - . - . - . - . - . - . - . - "http://pax-db.org/#!protein/$1"^^ . - "TA14985"^^ . - . - . - . - . - . - . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . - . - . - "https://www.cbioportal.org/study/summary?id=$1"^^ . - . - . - . - . - "2005080"^^ . - . - "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . - "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . - . - . - . - "International Standard Name Identifier" . - . - . - . - . - . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . - "Database of Quantitative Cellular Signaling: Pathway" . - . - "^PIRSF\\d{6}$"^^ . - . - . - . - . - "2000191"^^ . - . - "INSDC CDS" . - . - "rs11603840"^^ . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . - . - . - "Abdomen"^^ . - . - "DG00301"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Coli Genetic Stock Center" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "pubmed"^^ . - "false"^^ . - . - . - . - . - . - . - "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . - "https://signor.uniroma2.it"^^ . - . - . - "0001021"^^ . - . - . - . - "http://oncotree.mskcc.org"^^ . - . - "https://omim.org/entry/$1"^^ . - "http://www.genecards.org/"^^ . - "https://www.lji.org/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "false"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . - . - "Fossilworks Journal" . - . - . - _:Nd55a18af996344cea976fd45b4111aef . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "InTextReferencePointer"^^ . - . - "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."^^ . - "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . - "^(MNXR\\d+|EMPTY)$"^^ . - . - "Homeodomain Research" . - . - . - "true"^^ . - . - "true"^^ . - "https://w3id.org/faircookbook/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://nanocommons.github.io/identifiers/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://rapdb.dna.affrc.go.jp/"^^ . - . - . - . - . - . - . - . - . - . - "https://bioregistry.io/registry/$1"^^ . - "^\\d+$"^^ . -_:Ndf46391bdd1b4e34b8b76d723ba55299 "Satya S. Sahoo" . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "http://www.cellsignal.com/catalog/index.html"^^ . - "FungiDB" . - . - . - "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . - . - "^\\d{7}$"^^ . - "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/"^^ . - "0005067"^^ . - . - "Animal natural history and life history" . - "laml_tcga_pub"^^ . - . - "false"^^ . - . - . - "false"^^ . - "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^ . - . - . - "^TTDS\\d+$"^^ . - . - . - . - . - . - "DrugBank Drug Category" . - "ZFA description."^^ . - . - . - "https://registry.identifiers.org/registry"^^ . - . - . - . - . - "https://www.gwascentral.org/marker/$1"^^ . - "false"^^ . - . - . - . - . - "https://www.geonames.org/export/codes.html"^^ . - . - . - "false"^^ . - "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . - "Francesco Vitali" . - . - . - . - . - . - . - . - . - "https://hpo.jax.org/app/browse/term/HP:$1"^^ . - . - . - . - . - "General Standard for Food Additives Online Database" . - . - . - . - . - . - "0009089"^^ . - "LTS0004651"^^ . - . - . - . - "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . - . - . - . - . - . - . - "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^ . - . - "https://www.ebi.ac.uk"^^ . - . - "http://purl.org/spar/deo/$1"^^ . - "ReviewVersion"^^ . - . - . - . - . - . - . - "2gc4"^^ . - . - . - . - . - . - . - . - "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . - . - "Blue Brain Project Topological sampling Knowledge Graph" . - . - . - "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . - "identifierPattern"^^ . - "http://www.pdb.org/"^^ . - . - "biopragmatics/bioregistry/424"^^ . - . - . - . - . - . - . - . - . - . - . - "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . - . - "^GN_[A-Za-z0-9_:]+$"^^ . - "004435"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "Federica Quaglia" . - . - "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . - . - "Tom Gillespie" . - . - . - "false"^^ . - . - . - "906801"^^ . - "UniRef" . - "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . - . - . - . - . - . - . - . - . - "arXiv" . - . - . - . - . - "0000019"^^ . - . - "false"^^ . - . - . - . - "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . - "https://www.ebi.ac.uk/gxa/"^^ . - "Represent chemical entities having particular CHEBI roles"^^ . - "https://www.ebi.ac.uk/uniparc/"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "000000021"^^ . - . - . - . - . - "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . - "false"^^ . - "https://www.auckland.ac.nz/en.html"^^ . - "^\\w+$"^^ . - . - . - "false"^^ . - "NCBI Probe database Public registry of nucleic acid reagents" . - . - . - . - . - "PSEEN0001"^^ . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - "https://cellrepo.ico2s.org/repositories/$1"^^ . - "http://purl.obolibrary.org/obo/IEV_$1"^^ . - . - . - . - . - . - . - . - . - . - "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . - . - . - . - "^(C|D)\\d{6,9}$"^^ . - "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"^^ . - . - . - . - . - "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . - . - . - . - . - . - "https://github.com/OMIABIS/omiabis-dev"^^ . - "Zebrafish anatomy and development ontology" . - "A type for entries in the Bioregistry's metaregistry." . - . - . - . - . - . - . - "false"^^ . - . - . - "Search Tool for Retrieval of Interacting Genes/Proteins" . - "0000001"^^ . - "false"^^ . - "false"^^ . - "8639.1"^^ . - . - . - . - . - . - "true"^^ . - "VB.Ob.3736.GRSM125"^^ . - "Dublin Core Metadata Vocabulary" . - . - "Aclame" . - . -_:N5c8bdad6547e49cfb162052b88d629dd "Jonathan Bard" . - . - . - "MGYA00002270"^^ . - . - "https://www.proteomicsdb.org/#peptideSearch"^^ . - . - "Database of Genotypes and Phenotypes" . - "Michelle Giglio" . - . - . - . - . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/DINTO_$1"^^ . - . - . - "http://www.animaldiversity.org"^^ . - "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . - "^(STUDY|FILE|DATASET)\\d+$"^^ . - . - . - . - . - "false"^^ . - . - "http://www.antweb.org/"^^ . - . - "false"^^ . - . - . - "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"^^ . - . - . - . - . - . - . - . - . - . - "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . - "Soybean ontology" . - "PD10000"^^ . - "http://purl.obolibrary.org/obo/XAO_$1"^^ . - . - . - . - . - . - . - . - "http://www.alanwood.net/pesticides/$1.html"^^ . - . - . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - . - . - . - . - . - "false"^^ . - "GPST000024"^^ . - . - . - "false"^^ . - . - "Natural Product Activity and Species Source Database" . - "https://gen3.theanvil.io"^^ . - . - "000410"^^ . - "Toxin and Toxin Target Database" . - "false"^^ . - . - . - . - . - . - . - . - . - "DailyMed" . - "dictyBase" . - . - . - "false"^^ . - . - . - . - . - "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . - . - . - . - . - . - "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . - "hasOpenAccessRating"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - _:N3eafaa6720aa47748ed435d032917ea0 . - "NeuroVault Collection" . - . - . - . - . - "78073"^^ . - . - . - . - . - . - . - . - . - "https://flybase.org/reports/$1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . - . - "false"^^ . - . - . - "Tree of Life Web Project ID" . - . - . - "https://github.com/micheldumontier/semanticscience"^^ . - "true"^^ . - . - . - "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^ . - "^PRJ[DEN][A-Z]\\d+$"^^ . - . - "EcoCyc" . - . - . - "https://www.cancerrxgene.org/translation/Drug/$1"^^ . - . - "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . - "Life cycle stages for Mus Musculus"^^ . - "^C\\d+$"^^ . - . - . - "http://www.noncode.org/"^^ . - . - . - "Cell line collections"^^ . - "Orientations of Proteins in Membranes Database" . - . - "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . - . - . - . - "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . - . - . - "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . - . - "Person" . - . - . - . - . - . - . - . - "0000574"^^ . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - "https://www.vectorbase.org/ontology-browser"^^ . - . - . - . - . - . - "Protein Model Portal" . - . - . - . - "A001094"^^ . - "1"^^ . - . - . - . - . - . - . - "5621"^^ . - . - . - . - . - . - . - "false"^^ . - "http://www.geneontology.org/cgi-bin/references.cgi"^^ . - "false"^^ . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - "https://portal.bluebrain.epfl.ch"^^ . - . - . - . - . - . - "InterPro" . - "NLXCELL conatins cell types with a focus on neuron types."^^ . - . - "Gramene Gene" . - . - "false"^^ . - . - . - "false"^^ . - . - "http://www.gramene.org/"^^ . - . - "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . - . - "0000038"^^ . - . - . - . - "^[0-9]{12}$"^^ . - . - . - . - . - "Food Interactions with Drugs Evidence Ontology" . - . - . - . - . - . - . - . - "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . - . - . - . - . - "Grant"^^ . - . - "^IHW\\d+$"^^ . - . - . - . - "9001411"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "https://pbil.univ-lyon1.fr/databases/hovergen.php"^^ . - . - "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . - . - "https://hamap.expasy.org/unirule/$1"^^ . - "Cell line collections"^^ . - "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. "^^ . - . - . - "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . - . - "https://eol.org/pages/$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - "^rs\\d+$"^^ . - "Virtual International Authority File" . - . - . - . - . - . - . - "http://classyfire.wishartlab.com/"^^ . - . - . - "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . - "PF11779"^^ . - . - . - "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . - . - . - . - . - . - . - . - "http://www.sparontologies.net/ontologies/frbr"^^ . - . - "false"^^ . - "MI0026471"^^ . - . - . - "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . - "RoleInTime"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "4544"^^ . - "^\\d{7}$"^^ . - . - . - "33607"^^ . - . - . - . - . - "re3data" . - . - . - . - . - . - . - . - . - . - . - . - "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . - . - "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . - . - "http://geneontology.org/docs/guide-go-evidence-codes/"^^ . - . - "YOR172W_571.0"^^ . - . - . - . - "000000012281955X"^^ . - . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . - . - . - . - "rs17852708"^^ . - . - . - "http://www.pharmgkb.org/"^^ . - . - . - "C34"^^ . - . - . - "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1"^^ . - . - . - . - . - "AURKA"^^ . - "DICOM Controlled Terminology"^^ . - . - . - . - "https://protists.ensembl.org"^^ . - . - "http://purl.obolibrary.org/obo/SWO_$1"^^ . - . - . - . - . - . - "Troy Pells" . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . - "http://purl.obolibrary.org/obo/CIDO_$1"^^ . - . - . - . - . - . - "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . - . - "https://cordis.europa.eu/article/id/$1"^^ . - . - . - . - "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . - . - "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . - . - . - . - . - . - . - "1829126"^^ . - . - . - . - . - . - . - "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . - . - "https://medlineplus.gov/genetics/condition"^^ . - . - . - . - "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . - . - . - . - . - . - . - . - "https://health.uconn.edu/"^^ . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - "http://www.alanwood.net/pesticides"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "DDB0016567"^^ . - "cpd15380"^^ . - . - . - . - . - "^CE\\d{5}$"^^ . - "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . - . - "https://www.cropontology.org/rdf/CO_341:$1"^^ . - . - . - "enviPath" . - . - "75"^^ . - . - . - . - "0000712_1"^^ . - "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . - . - . - . - . - "PharmGKB Disease" . - "Adrien Rougny" . - . - . - "1"^^ . - . - "5282"^^ . - "https://www.ebi.ac.uk/pdbe/emdb/"^^ . - . - . - . - "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . - . - . - "^CH_\\d+$"^^ . - . - "Genetic Testing Registry" . - . - . - . - . - . - . - . - . - . - . - "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . - . - . - . - . - . - . - "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . - "http://www.xenbase.org/anatomy/xao.do?method=display"^^ . - "SED-ML data format" . - . - . - . - "http://www.pharmgkb.org/drug/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "Oryzabase Mutant" . - . - . - . - . - . - . - "Human Metabolome Database" . - . - . - . - . - . - . - "http://bioportal.bioontology.org/ontologies/LBO"^^ . - . - . - . - . - . - "https://bacteria.ensembl.org/id/$1"^^ . - . - "Rat Strain Ontology" . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . - . - . - . - . - . - "Prefix Commons" . - . - "NIST Chemistry WebBook" . - "false"^^ . - "0000011"^^ . - . - . - "http://purl.obolibrary.org/obo/AERO_$1"^^ . - "HBG004341"^^ . - "Cellosaurus Registry" . - . - . - "00000001"^^ . - . - . - . - . - "Social Behavior in insects"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "Kids First" . - . - . - . - . - . - . - . - . - . - "^NONHSAT\\d{6}$"^^ . - "2200934"^^ . - "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . - "ENSFM00500000270089"^^ . - . - "https://www.ebi.ac.uk/intact/"^^ . - . - . - . - . - "false"^^ . - . - "Insect Resistance Ontology" . - . - "Terminology for Description of Dynamics" . - "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . - . - "GCA_000155495.1"^^ . - . - "GWAS Central Phenotype" . - . - . - . - . - . - "ENSG00000139618"^^ . - . - . - . - . - . - "https://proteinensemble.org/"^^ . - . - . - . - . - . - . - . - "EDAM Data" . - . - . - "false"^^ . - "Bob Thacker" . - . - . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"^^ . - . - "0000634"^^ . - . - "false"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . - . - "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . - . - . - . - "Human Protein Reference Database" . - . - . - "false"^^ . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "109082"^^ . - . - "0000780"^^ . - . - . - . - . - . - "http://www.wormbase.org/get?name=$1"^^ . - . - . - "https://bioregistry.io" . - . - . - . - . - "63189"^^ . - . - . - "SM00015"^^ . - . - . - . -_:Nd55a18af996344cea976fd45b4111aef "Christos (Kitsos) Louis" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ECAO_$1"^^ . - . - . - "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . - . - "false"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . - . - . - . - . - "DECIPHER CNV Syndromes" . - "KEGG Orthology" . - . - . - . - . - . - . - "Encyclopedia of Life" . - . - "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . - . - . - . - . - . - "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . - "Medical Action Ontology" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^ . - . - . - . - . - . - "Disease Drivers Ontology" . - . - "http://www.fludb.org/"^^ . - "Brassica ontology" . - "^\\d{7}$"^^ . - . - . - . - "https://www.hivreagentprogram.org/Home.aspx"^^ . - . - . - "Sugar Kelp trait ontology"^^ . - "Plant Ontology" . - . - . - . - . - . - . - . - . - . - . - "VFDB Genus" . - . - "LGCEDe-S-000002244"^^ . - "https://www.genenames.org/"^^ . - . - . - . - "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . - . - . - . - . - . - . - . - . - "^ST[0-9]{6}$"^^ . - . - . - . - "56305849200"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "https://sorgerlab.github.io/famplex/$1"^^ . - "https://github.com/PRIDE-Utilities/pride-ontology"^^ . - . - . - . - . - . - "http://www.massbank.jp/RecordDisplay?id=$1"^^ . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1"^^ . - "http://www.disease-ontology.org"^^ . - . - . - . - . - . - . - . - "FDB002100"^^ . - . - . - "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . - . - . - . - . - . - . - . - "000000159"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "The coding sequence or protein identifiers as maintained in INSDC."^^ . - "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . - . - . - . - . - . - . - . - . - . - "NIF Standard Ontology" . - . - . - . - . - . - . - . - . - "Ontology for the Anatomy of the Insect SkeletoMuscular system" . - . - "HGVST1828"^^ . - "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . - . - . - . - . - . - "https://www.eionet.europa.eu/gemet/en/themes/"^^ . - . - "67"^^ . - . - . - "false"^^ . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - "false"^^ . - . - "^CPX-[0-9]+$"^^ . - . - "false"^^ . - . - . - "^\\d{7,8}$"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - "false"^^ . - . - "http://sabiork.h-its.org/"^^ . - "https://civicdb.org/links/assertions/$1"^^ . - "https://www.uniprot.org/locations/$1"^^ . - . - "^[A-Z_]{3}[0-9]{4,}$"^^ . - "https://biopragmatics.github.io/providers/scomp/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/INO_$1"^^ . - . - . - "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . - "AB0"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Sanger Cell Model Passports" . - "^\\d{5}$"^^ . - . - . - . - . - . - . - . - . - . - . - "CPD-10330"^^ . - . - "https://cryptodb.org/cryptodb/"^^ . - . - "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://fdasis.nlm.nih.gov/srs/"^^ . - "1.10.10.200"^^ . - . - "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . - "Daniel Himmelstein" . - "http://neuromorpho.org/index.jsp"^^ . - . - . - . - . - . - . - "^\\w+(\\-|\\.|\\w)*$"^^ . - . - "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . - . - . - . - . - . - . - . - . - . - . - "http://jjj.biochem.sun.ac.za/models/"^^ . - . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . - . - "ERR436051"^^ . - . - "Trish Whetzel" . - . - . - . - . - "3hB06"^^ . - "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . - "https://www.ebi.ac.uk/chembldb/"^^ . - "false"^^ . - . - . - . - "Veterinary Substances DataBase" . - . - . - "https://github.com/proco-ontology/PROCO"^^ . - . - . - "MGnify Project" . - . - "WormBase RNAi" . - . - . - . - . - . - . - "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^ . - . - "^M\\d{5}$"^^ . - . - . - . - . - . - . - . - . - . - "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . - "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"^^ . - "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . - "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "^\\w+$"^^ . - . - . - . - . - . - . - "UniProt Keywords" . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - "http://www.guidetopharmacology.org/"^^ . - . - . - . - . - . - "false"^^ . - . - "Biosapiens Protein Feature Ontology" . - . - . - . - . - . - "false"^^ . - "http://www.isni.org/isni/$1"^^ . - . - . - . - . - "Long Term Ecological Research Controlled Vocabulary" . - . - . - . - "^\\w+$"^^ . - "^[A-Za-z]+$"^^ . - "3546"^^ . - "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . - "https://cropontology.org/ontology/CO_337/Groundnut"^^ . - "false"^^ . - . - . - . - . - . - . - . - "https://www.brenda-enzymes.de/ligand.php"^^ . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . - "http://edamontology.org"^^ . - . - . - "false"^^ . - . - . - . - "https://cropontology.org/ontology/CO_348/Brassica"^^ . - . - . - . - . - "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . - "true"^^ . - . - "0000411"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "false"^^ . - "An ontology for the description of Drosophila melanogaster phenotypes."^^ . - . - . - . - "Zenodo" . - . - . - . - . - . - "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . - . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MCO_$1"^^ . - . - "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . - . - . - . - . - . - . - "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . - "58788"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FBSP_$1"^^ . - "eVOC mouse development stage" . - "https://www.cropontology.org/rdf/CO_350:$1"^^ . - . - . - . - . - "4447"^^ . - . - . - . - "false"^^ . - . - . - "Biological Magnetic Resonance Data Bank" . - . - "00005254"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . - "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . - . - . - . - . - "false"^^ . - . - . - "SWISS-MODEL Repository" . - . - "https://www.atcc.org/products/$1"^^ . - . - "http://n2t.net/"^^ . - "Canadian Drug Product Database" . - "Oat ontology" . - "http://purl.obolibrary.org/obo/OHPI_$1"^^ . - "145"^^ . - . - . - . - "false"^^ . - . - . - . - . - "1200"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "0000254"^^ . - "PDB Structure" . - . - "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - . - "Selventa Diseases" . - "0000000"^^ . - . - "http://opm.phar.umich.edu/"^^ . - . - . - . - . - "https://www.flymine.org/come/entry?gn=$1"^^ . - "https://www.kegg.jp/entry/$1"^^ . - "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . - . - . - "https://www.ebi.ac.uk/ega/studies"^^ . - . - . - . - . - . - . - . - . - . - "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . - . - . - . - . - "Rat Genome Database" . - . - . - . - . - "false"^^ . - "true"^^ . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . - "BiGG Reaction" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/biostudies/"^^ . - "false"^^ . - . - . - "https://github.com/BgeeDB/confidence-information-ontology"^^ . - "title"^^ . - . - . - . - . - "false"^^ . - . - . - . - "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . - "false"^^ . - . - "Barcode of Life database" . - . - . - . - . - "DP00003"^^ . - "https://repeatsdb.org/structure/$1"^^ . - "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . - "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . - . - . - . - . - . - . - . - "595"^^ . - . - . - "false"^^ . - "0000389"^^ . - . - . - "X58356"^^ . - . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "MCDS_S_0000000001"^^ . - "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . - . - "^\\d+$"^^ . - . - "http://www.conoserver.org/"^^ . - . - . - . - . - . - . - "aaeA"^^ . - . - . - "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . - "http://edamontology.org"^^ . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - . - . - . - . - "Sigma Aldrich is a life sciences supply vendor."^^ . - . - . - "Karen Eilbeck" . - . - . - . - "Selventa legacy disease namespace used with the Biological Expression Language"^^ . - . - . - . - "baseDimensionEnumeration"^^ . - "^\\d+$"^^ . - . - . - "^(ZINC)?\\d+$"^^ . - . - "Vocabulary used in the RDF representation of SBML models."^^ . - . - . - . - "Golm Metabolome Database GC-MS spectra" . - . - . - . - . - "Lucas Leclere" . - "An ontology to represent genomics cohort attributes."^^ . - . - . - . - . - . - "ADA"^^ . - "false"^^ . - . - "https://prefixcommons.org"^^ . - "PDC000351"^^ . - "false"^^ . - . - . - "^([hm]\\_)?\\w+Pathway$"^^ . - . - "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . - . - . - . - . - . - . - . - . - . - . - "34"^^ . - . - . - . - . - . - . - "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . - . - . - . - . - "http://www.psidev.info/MOD"^^ . - "436605"^^ . - "http://swissregulon.unibas.ch/query/$1"^^ . - "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . - . - _:N405d8bfed2434692b307171b8d317ea8 . - "T0599"^^ . - . - . - . - . - . - . - . - . - . - "^(cd)?\\d{5}$"^^ . - . - "http://purl.obolibrary.org/obo/FAO_$1"^^ . - . - . - . - . - . - "false"^^ . - "JAX Mice" . - . - "https://github.com/obophenotype/caro/"^^ . - . - . - . - . - . - "^Q[A-Z0-9]+$"^^ . - "https://www.ncbi.nlm.nih.gov/assembly/$1"^^ . - . - "ProtClustDB" . - . - "^[A-Za-z0-9-]+$"^^ . - "ArrayExpress" . - . - . - . - "false"^^ . - . - . - . - . - . - "Regulation of Gene Expression"^^ . - . - . - . - "KEGG Pathways Database" . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "https://github.com/PHI-base/phipo"^^ . - "false"^^ . - . - . - . - . - "has pattern" . - . - . - . - . - "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - "35742"^^ . - "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . - "Online Computer Library Center WorldCat" . - . - . - . - . - "https://orcid.org"^^ . - "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . - . - . - . - . - . - . - . - . - "GeneTree" . - "SIGNOR-C41"^^ . - "KC-0979"^^ . - . - . - . - "Anatomical Therapeutic Chemical Classification System" . - "Catalog of purchasable reagents and building blocks"^^ . - "hasDbXref"^^ . - "Catalogue of Life in Taiwan" . - . - . - . - . - . - "false"^^ . - . - . - . - "493771"^^ . - "90801"^^ . - . - . - . - . - "http://kinase.bioinformatics.tw/"^^ . - . - "^EGAS\\d{11}$"^^ . - . - . - . - . - . - . - "https://signor.uniroma2.it/"^^ . - . - . - . - . - . - . - . - . - "https://github.com/BgeeDB/homology-ontology"^^ . - . - . - . - "false"^^ . - . - . - "http://www.kegg.jp/"^^ . - "false"^^ . - "European Nucleotide Archive" . - "Complex Portal" . - . - . - "https://metacyc.org"^^ . - "http://pid.nci.nih.gov/"^^ . - "File inside StoreDB"^^ . - . - . - "http://purl.obolibrary.org/obo/CARO_$1"^^ . - . - "false"^^ . - . - "https://www.cropontology.org/rdf/CO_365:$1"^^ . - . - "IID00001"^^ . - "https://www.imexconsortium.org/"^^ . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . - "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . - . - . - "Alayne Cuzick" . - . - "false"^^ . - . - . - "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . - . - "false"^^ . - "false"^^ . - . - "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . - . - "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . - . - . - "https://web.expasy.org/cellosaurus/" . - . - "Loggerhead nesting" . - . - . - . - . -_:Neb3cb9b18833405fb91839f2f128d866 "Matt Berriman" . - "TrichDB" . - . - . - . - . - "false"^^ . - "https://www.alliancegenome.org/accession/$1"^^ . - "http://purl.obolibrary.org/obo/OLATDV_$1"^^ . - . - "https://pk-db.com/data/$1"^^ . - . - . - "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . - . - "https://github.com/infectious-disease-ontology-extensions/ido-virus"^^ . - . - "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . - "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "^PTN\\d{9}$"^^ . - "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . - . - . - . - "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . - "1.1.1.1"^^ . - "^(T0\\d+|\\w{3,5})$"^^ . - . - "http://www.snomedbrowser.com/Codes/Details/$1"^^ . - "Mark Engelstad" . - . - . - . - . - . - . - . - . - . - "Genetic Code" . - "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . - . - . - . - . - "false"^^ . - "Cell line databases/resources"^^ . - . - "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . - . - "http://purl.obolibrary.org/obo/MAT_$1"^^ . - "Polymorphism and mutation databases"^^ . - . - . - "https://github.com/phenoscape/vertebrate-taxonomy-ontology"^^ . - "Informed Consent Ontology" . - . - . - "NAD%20biosynthesis"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^\\d{1,5}$"^^ . - "^\\d+$"^^ . - . - . - . - "https://herv.img.cas.cz/s/$1"^^ . - . - . - "Vertebrate Genome Annotation Database" . - "false"^^ . - . - . - "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . - "http://eawag-bbd.ethz.ch/$1/$1_map.html"^^ . - "S1"^^ . - . - . - "0000013"^^ . - . - . - . - "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . - "NCI Thesaurus" . - . - . - "Exposure ontology" . - "http://stitch.embl.de/interactions/$1"^^ . - . - . - "https://nanocommons.github.io/identifiers/registry#$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "https://www.addexbio.com/productshow?id=4"^^ . - . - . - . - . - "https://bioregistry.io/resolve/github/pull/$1"^^ . - "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . - . - "false"^^ . - . - "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "Vitis ontology" . - . - . - . - . - "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . - . - . - "CE28239"^^ . - "https://www.gtexportal.org"^^ . - . - "https://www.re3data.org/repository/$1"^^ . - "Sequence Read Archive" . - "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . - "0001157"^^ . - "11303"^^ . - . - . - . - "http://rdfs.org/ns/void#$1"^^ . - . - . - . - . - . - "Ontology"^^ . - . - . - "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . - . - . - "Enzo Life Sciences" . - . - "false"^^ . - "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . - "0000639"^^ . - . - . - . - . - "87"^^ . - . - . - . - . - . - . - "false"^^ . - "APID Interactomes" . - . - . - . - . - . - . - . - . - . - . - "Search PRINTS-S" . - . - . - . - "http://environmentontology.github.io/gaz/"^^ . - "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . - "^[0-9]+$"^^ . - "NeuronDB" . - . - "false"^^ . - . - . - . - . - . - "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . - "https://www.uniprot.org"^^ . - . - "http://bacmap.wishartlab.com/organisms/$1"^^ . - "https://github.com/jannahastings/emotion-ontology"^^ . - . - . - . - "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . - . - . - . - . - . - "Castor bean ontology" . - . - "https://www.nescent.org/phenoscape/Main_Page"^^ . - . - "Cell line collections"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PORO_$1"^^ . - . - . - "EJH014"^^ . - . - "http://www.jstor.org/stable/$1"^^ . - . - . - . - "^\\d+(\\w+)?$"^^ . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.org/vocab/frbr/core#$1"^^ . - . - "http://lincsportal.ccs.miami.edu/cells/"^^ . - . - . - "74"^^ . - . - "https://www.ensembl.org/id/$1"^^ . - . - . - "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . - "0000026"^^ . - "https://n2t.net/$1:$2" . - "false"^^ . - . - "http://wodaklab.org/iRefWeb/"^^ . - "Bioinformatics operations, data types, formats, identifiers and topics" . - . - . - "false"^^ . - . - . - . - . - . - "^M\\d{4}$"^^ . - "false"^^ . - . - . - . - . - . - "https://github.com/prefixcommons/biocontext" . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TO_$1"^^ . - "ENCSR163RYW"^^ . - . - . - . - . - . - "https://webbook.nist.gov/chemistry/"^^ . - "false"^^ . - "miriam"^^ . - "PRINTS compendium of protein fingerprints" . - "^\\d+$"^^ . - "http://exac.broadinstitute.org/"^^ . - "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . - "Cell line collections"^^ . - . - "Protein Alignment organised as Structural Superfamily" . - . - . - . - "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^ . - . - "25512"^^ . - . - . - "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . - . - . - . - . - . - "Topology Data Bank of Transmembrane Proteins" . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://www.wikipathways.org/"^^ . - . - . - "Activity"^^ . - . - . - . - "http://www.ecogene.org/gene/$1"^^ . - . - _:Na8665fde304c426a92ab0fed3bd06d09 . - . - "IPR016380"^^ . - . - "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . - "false"^^ . - . - . - . - "^(data|topic|operation|format)\\_\\d{4}$"^^ . - . - "RIKEN Bioresource Center Cell Bank" . - . - . - . - "DP00086r013"^^ . - . - "^[0-9]+$"^^ . - "Sofia Robb" . - . - . - . - "http://genolist.pasteur.fr/SubtiList/"^^ . - "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . - . - . - "Teleost Anatomy Ontology" . - "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . - . - . - . - "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . - . - . - "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/RBO_$1"^^ . - . - "true"^^ . - . - . - . - . - "false"^^ . - "https://glygen.org/glycan/$1"^^ . - . - "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . - . - . - . - . - . - . - . - . - . - . - "00042"^^ . - . - . - . - . - . - "https://www.ndexbio.org"^^ . - "https://www.cellbankaustralia.com/$1.html"^^ . - "http://purl.obolibrary.org/obo/CDAO_$1"^^ . - "https://github.com/OBOFoundry/COB"^^ . - . - . - . - . - . - . - . - "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . - "^\\d{7}$"^^ . - . - . - "Imanis Life Sciences cell line products" . - "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . - . - "http://hpc-bioinformatics.cineca.it/fusion/main"^^ . - . - . - . - . - . - . - . - . - . - . - . - "44259"^^ . - . - . - . - "http://www.sanger.ac.uk/Users/mb4/PLO/"^^ . - "Rice Genome Annotation Project" . - . - "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . - . - "^\\d{7}$"^^ . - "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . - "https://www.ncbi.nlm.nih.gov/genome"^^ . - . - . - . - "https://microbiomedata.org/"^^ . - "false"^^ . - "true"^^ . - . - . - "56586"^^ . - . - . - . - . - . - . - "A type for entries in the Bioregistry's collections" . - . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . - . - . - . - . - . - . - . - . - "https://medical-data-models.org/forms/$1"^^ . - . - . - . - . - . - "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . - "http://e-cyanobacterium.org/models/"^^ . - "Minimum PDDI Information Ontology" . - . - . - . - . - . - "Terminologia Histologica" . - . - . - . - "false"^^ . - . - "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . - . - "http://microbialphenotypes.org"^^ . - . - . - . - "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . - . - . - . - . - . - "https://github.com/IHCC-cohorts/GECKO"^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - "http://plasmodb.org/plasmo/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://www.semantic-systems-biology.org/apo"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/metabolights/$1"^^ . - . - . - "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . - "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . - "http://www.p3db.org/"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . - "Merck Millipore (EMD Millipore)" . - "http://www.oid-info.com/introduction.htm"^^ . - . - . - . - . - . - "false"^^ . - "Jonathan Karr" . - . - "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - "https://www.perkinelmer.com/"^^ . - . - . - "^\\d{10}$"^^ . - . - . - . - . - "https://w3id.org/oc/corpus"^^ . - . - . - "https://idr.openmicroscopy.org"^^ . - "6017782"^^ . - . - . - . - . - . - "^LSM-\\d+$"^^ . - . - . - . - "F4521"^^ . - . - . - . - "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "^MMP\\d+.\\d+$"^^ . - "http://www.ontobee.org/" . - "false"^^ . - . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . - "^PM\\d{7}$"^^ . - . - . - . - . - . - . - . - "102l"^^ . - . - . - . - "Extensible Markup Language" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "Nicole Vasilevsky" . - "http://bgee.unil.ch/bgee/bgee"^^ . - . - "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^ . - . - "GrainGenes" . - "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . - . - . - "16333295"^^ . - . - "^K\\d+$"^^ . - . - . - "0000171"^^ . - . - . - . - "MarFun" . - . - . - . - "false"^^ . - . - . - "http://agroportal.lirmm.fr" . - . - "5688061"^^ . - . - . - "Drosophila Genomics Resource Center" . - "false"^^ . - "Zebrafish Experimental Conditions Ontology" . - . - . - "Hilmar Lapp" . - . - "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . - "true"^^ . - "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1"^^ . - "GeneFarm" . - . - . - "http://www.sparontologies.net/ontologies/fivestars"^^ . - "M0001"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/CTO_$1"^^ . - . - . - . - . - . - "1455"^^ . - . - "Rv1908c"^^ . - "http://exac.broadinstitute.org/gene/$1"^^ . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^ . - . - "Amphibian taxonomy" . - . - . - . - . - "^\\d+$"^^ . - "https://oborel.github.io/"^^ . - . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/"^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - "http://www.w3.org/2001/XMLSchema"^^ . - "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . - "false"^^ . - . - . - . - "BP100000"^^ . - . - . - . - . - . - "^MMP\\d+.\\d+$"^^ . - . - "IHW09326"^^ . - "http://purl.obolibrary.org/obo/MFMO_$1"^^ . - . - . - "lang"^^ . - . - . - "^\\d{7}$"^^ . - "Cancer cell LInes GEne fusions portAl" . - . - . - "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . - "false"^^ . - . - . - . - . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - "101"^^ . - . - . - . - . - . - . - . - "^[CD]\\d+$"^^ . - . - "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^ . - "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . - "Classification of Transcription Factors in Mammalia" . - . - . - . - . - "https://hamap.expasy.org/"^^ . - . - . - . - . - "Robert Druzinsky" . - . - . - "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . - . - "MMP02954345.1"^^ . - "NCBI Protein" . - . - "MobiDB" . - "^PS\\d+$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "0000066"^^ . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . - . - . - . - . - "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . - "Universal Natural Products Database" . - "^[0-9]+\\.[0-9]+$"^^ . - . - "http://phylomedb.org/?seqid=$1"^^ . - "https://ligandbook.org/package/$1"^^ . - "^OSR\\d{4}$"^^ . - . - "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . - "Chemical Entities of Biological Interest" . - . - . - . - . - "^\\d{7}$"^^ . - "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . - . - . - . - "^WP\\d{1,5}(\\_r\\d+)?$"^^ . - "Epilepsy and Seizure Ontology" . - . - . - . - . - . - . - . - "^\\d{6}$"^^ . - . - . - . - . - . - . - . - "KEGG Environ" . - . - . - . - . - . - . - "Ontology for Avida digital evolution platform" . - . - "https://github.com/tis-lab/reagent-ontology"^^ . - . - . - "BIOZIL" . - . - . - "https://biolink.github.io/biolink-model/"^^ . - . - "Open Data Commons for Traumatic Brain Injury" . - . - . - "0010039"^^ . - . - "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . - . - "https://omabrowser.org"^^ . - "splash10-0zq2000000-77302b0326a418630a84"^^ . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast."^^ . - "LipidBank" . - "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . - . - . - "false"^^ . - . - . - . - "https://www.disprot.org/ontology"^^ . - . - . - . - . - "Document Components Ontology" . - . - . - . - . - "https://www.phenxtoolkit.org/protocols/view/$1"^^ . - . - . - . - . - "https://thebiogrid.org/"^^ . - . - . - "false"^^ . - . - . - . - "An application ontology for use with miRNA databases."^^ . - "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . - "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "234"^^ . - . - . - "The pattern for identifiers in the given resource" . - "http://arabidopsis.org/index.jsp"^^ . - . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . - "false"^^ . - . - . - "^[0-9]+$"^^ . - . - . - "http://bis.zju.edu.cn/ricenetdb/"^^ . - . - . - . - . - "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . - . - . - . - "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . - . - . - . - . - "4DNSR73BT2A2"^^ . - "https://gold.jgi.doe.gov/"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "0000460"^^ . - "Alex Bateman" . - . - . - . - . - . - . - . - . - . - . - . - "UniProt Archive" . - . - . - . - "Li7"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . - . - "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . - . - "1484"^^ . - . - "Alzforum Mutations" . - . - . - "0002927"^^ . - "A0014"^^ . - . - . - . - . - "https://drs.microbiomedata.org/objects/$1"^^ . - "false"^^ . - . - "false"^^ . - . - "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . - . - "b97957"^^ . - "^\\w.+$"^^ . - . - "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . - . - "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . - . - . - . - "http://www.cathdb.info/"^^ . - "https://aopwiki.org/events/$1"^^ . - "1000100"^^ . - . - "C0001"^^ . - . - . - . - "046"^^ . - . - . - "https://web.expasy.org/cellosaurus/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - . - . - . - . - "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . - "http://lisanwanglab.org/DASHR/"^^ . - . - . - . - . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . - "Bibliometric Data Ontology" . - "false"^^ . - . - . - . - . - . - . - "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . - . - . - . - . - . - . - "http://www.cellsignal.com/reference/pathway/$1.html"^^ . - . - . - . - . - "https://www.ohdsi.org/data-standardization/the-common-data-model/"^^ . - "0003"^^ . - . - . - . - . - . - "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . - . - . - . - "UniGene" . - . - "Ontology of RNA Sequencing" . - "false"^^ . - . - . - . - "LK99"^^ . - . - . - "1"^^ . - . - "SAMEA2397676"^^ . - . - . - . - . - . - "false"^^ . - "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"^^ . - . - . - "^\\d+$"^^ . - . - "true"^^ . - "https://www.ebi.ac.uk/metagenomics"^^ . - "AB_262044"^^ . - "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . - . - "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . - . - . - . - . - "true"^^ . - "^\\d{7}$"^^ . - . - . - . - "2673500"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - "ala"^^ . - . - "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^ . - . - "1a24"^^ . - . - . - . - . - "has reviewer" . - . - "Neuro Behavior Ontology" . - . - . - "http://fossilworks.org"^^ . - . - "Database portal containing replicate experiments of different assays and samples"^^ . - . - "Online Mendelian Inheritance in Man" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - _:N8f13ab592d71468f95827752341fe101 . - . - . - "^[\\w\\d\\.-]*$"^^ . - . - "Ontology for Biobanking" . - . - . - "EMLSAT00000003403"^^ . - "^\\d{8}$"^^ . - . - . - "GOLD genome" . - "^\\d{7}$"^^ . - "https://lincs.hms.harvard.edu/db/sm/"^^ . - "http://jaxmice.jax.org/"^^ . - . - . - . - "^\\d{4}$"^^ . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . - . - . - "Simple Knowledge Organization System" . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - . - "0000690"^^ . - . - "false"^^ . - . - . - . - . - "https://github.com/geneontology/go-ontology"^^ . - . - "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . - . - . - "EBI-2307691"^^ . - . - . - . - . - . - "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . - . - . - . - . - . - . - . - . - . - . - . - "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . - "false"^^ . - . - . - "DDInter20"^^ . - . - "Scientific Evidence and Provenance Information Ontology" . - . - . - "false"^^ . - "https://doulix.com/constructs/$1"^^ . - "false"^^ . - . - . - "phs000768.v2.p1"^^ . - . - . - . - . - . - "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . - . - "CHEMBL465070"^^ . - . - . - "Cube db" . - "https://pictar.mdc-berlin.de/"^^ . - . - . - . - . - . - . - . - "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . - . - "75"^^ . - "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . - . - "^\\d+$"^^ . - . - . - "LOTUS Initiative for Open Natural Products Research" . - . - "false"^^ . - "0000001"^^ . - . - "false"^^ . - . - "0000003"^^ . - . - "false"^^ . - "https://vcell.org/biomodel-$1"^^ . - . - . - . - . - . - "Human developmental anatomy, abstract version" . - . - . - . - "^\\d{7}$"^^ . - "The Ontology of Genes and Genomes" . - . - "http://purl.obolibrary.org/obo/GAZ_$1"^^ . - . - . - "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . - . - . - . - . - "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . - "https://ssbd.riken.jp/database/project/$1"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "Animal Genome Sheep QTL" . - . - "OMA Protein" . - . - . - "BCRC Strain Collection Catalog" . - . - "false"^^ . - . - "http://www.flybase.org/"^^ . - . - . - "S-EPMC6266652"^^ . - . - "https://omabrowser.org/oma/hog/HOG:$1"^^ . - . - "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . - "Metabolome Express" . - . - . - "COG Pathways" . - "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . - . - . - . - "chromium"^^ . - . - . - "COVID-19 Surveillance Ontology" . - . - . - "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . - . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/"^^ . - "http://www.metabolomicsworkbench.org/"^^ . - . - "http://www.humanproteomemap.org/index.php"^^ . - . - . - . - . - . - "false"^^ . - "DataCite Ontology" . - "000000024"^^ . - "http://purl.obolibrary.org/obo/HTN_$1"^^ . - . - . - . - . - . - . - . - . - "AOPWiki (Key Event)" . - . - . - . - . - . - . - . - "1466"^^ . - . - "https://github.com/phenoscape/taxrank"^^ . - "Banana ontology" . - . - . - . - . - "10142"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - . - "Semantic Web for Earth and Environment Technology Ontology" . - . - "Pubmed Central" . - "http://www.nbrc.nite.go.jp/e/index.html"^^ . - "https://www.ebi.ac.uk/ena/data/view/$1"^^ . - . - . - . - . - . - . - . - . - . - "PANTHER Node" . - . - "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . - . - . - . - "Orphanet" . - . - . - . - "false"^^ . - . - . - . - . - "true"^^ . - "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . - . - "Cell line collections"^^ . - . - . - . - . - . - "Human Dephosphorylation Database" . - "100"^^ . - . - "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^ . - . - . - . - "Database of Sequence Tagged Sites" . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . - . - . - . - . - . - . - . - "^\\d{8}$"^^ . - . - . - "false"^^ . - . - . - . - . - "http://csbl.bmb.uga.edu/DOOR/operon.php"^^ . - "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "EchoBASE post-genomic database for Escherichia coli" . - . - . - . - "cgd7_230"^^ . - . - "false"^^ . - . - . - . - . - . - . - "3000045"^^ . - "https://fcs-free.org"^^ . - "10.1101/2022.07.08.499378"^^ . - . - . - "P0DP23"^^ . - . - . - . - . - . - . - "https://www.biomodels.net/kisao/KISAO#KISAO_$1"^^ . - "^DRSC\\d+$"^^ . - "false"^^ . - . - . - "1"^^ . - . - "https://www.biocatalogue.org/services/$1"^^ . - . - "DB14938"^^ . - . - . - . - "true"^^ . - . - . - . - . - . - . - "12dgr161"^^ . - "Potato ontology" . - . - "090803"^^ . - . - "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . - . - "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . - . - "^[A-Z]+[0-9]+$"^^ . - "false"^^ . - . - . - "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . - "98034"^^ . - "http://www.pharmgkb.org/disease/$1"^^ . - . - . - "^C\\d{8}$"^^ . - "false"^^ . - . - "P4355"^^ . - . - . - . - "NucleaRDB" . - "https://orcid.org/$1"^^ . - . - . - . - . - "Sustainable Development Goals Interface Ontology" . - . - "false"^^ . - . - . - . - "3618"^^ . - . - . - . - . - . - . - "3771992"^^ . - . - . - "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^ . - . - "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . - . - . - . - . - . - . - . - . - . - "ProtoNet Cluster" . - "Q0VCA6"^^ . - . - . - . - "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . - . - . - "true"^^ . - . - "Biological Expression Language" . - . - . - "OrthoDB" . - . - "false"^^ . - . - . - . - . -_:N058aa60ca0674ad4a89d43450ed0cc9e "Pierre Sprumont" . - "Guide to Pharmacology Ligand" . - . - . - . - "^\\d{7}$"^^ . - _:N1fc20d2185a94201a849b6d0bd829d82 . - "Animal Genome QTL" . - . - . - . - "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . - . - "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . - . - "false"^^ . - . - _:Nd43cb5600ccf4f7a985affd5767ee387 . - . - . - . - "false"^^ . - . - . - . - "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . - "http://www.informatics.jax.org/"^^ . - "Jennifer C. Girón" . - . - "^PR[0-9]{6}$"^^ . - . - . - "https://www.webelements.com/"^^ . - "Genome assembly database" . - . - . - . - . - . - "EDAM Operation" . - "http://www.kegg.jp/entry/$1"^^ . - "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . - "The Python Package Index (PyPI) is a repository for Python packages."^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe"^^ . - "NCT00222573"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/MPATH_$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . - . - "http://www.imgt.org/ligmdb/view?id=$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://lncipedia.org"^^ . - . - . - . - . - "PF3D7_1328700"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "0000199"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Astrophysics Source Code Library" . - . - . - . - . - . - . - . - "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . - . - . - . - . - "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . - . - . - . - "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/"^^ . - "http://ifomis.org/bfo/"^^ . - "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . - . - "NCBI Genome" . - "https://www.storedb.org/?$1"^^ . - "634515043"^^ . - . - . - . - . - . - "Novus Biologicals" . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - "S7000002168151102"^^ . - . - . - . - . - . - . - "false"^^ . - . - "Japan Consortium for Glycobiology and Glycotechnology Database" . - . - . - . - . - . - . - . - "46"^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PCO_$1"^^ . - . - . - "^\\w+$"^^ . - . - . - "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - "http://masspec.scripps.edu/"^^ . - "Cowpea ontology" . - "https://www.cameo3d.org/sp/targets/target/$1"^^ . - "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . - "https://prosite.expasy.org/$1"^^ . - . - _:N63e482e1c00245d2abd0b0b2fbb19710 . - . - . - "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . - . - . - . - . - . - "Erik Segerdell" . - . - . - "0000010"^^ . - "https://www.crossref.org/"^^ . - . - . - . - "http://www.mirbase.org/"^^ . - "http://bactibase.hammamilab.org/$1"^^ . - . - . - . - "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . - . - . - . - . - "false"^^ . - . - . - . - "https://github.com/obophenotype/xenopus-phenotype-ontology"^^ . - . - "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^ . - "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . - . - "Non-Coding RNA Ontology" . - . - "^JCGG-STR\\d{6}$"^^ . - "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . - "https://gitlab.com/$1"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - "^\\d{7}$"^^ . - "https://pubchem.ncbi.nlm.nih.gov/classification/"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - "CIViC Evidence" . - . - . - "https://bioportal.bioontology.org/ontologies/EDDA"^^ . - . - . - . - . - "SPCC13B11.01"^^ . - "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . - . - . - . - . - . - . - "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . - . - . - . - . - "http://lsdis.cs.uga.edu/projects/glycomics/propreo/"^^ . - . - . - . - . - "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1"^^ . - . - "BG11523"^^ . - "false"^^ . - . - . - "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . - . - "^DG\\d+$"^^ . - . - "Metabolic Encyclopedia of metabolic and other pathways" . - . - . - . - "http://img.jgi.doe.gov/"^^ . - . - . - "Coconut ontology" . - "false"^^ . - "true"^^ . - . - . - . - "https://www.imanislife.com/?s=$1"^^ . - . - . - . - . - . - . - . - "C. elegans ORFeome cloning project" . - . - "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR"^^ . - . - . - "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . - . - . - "Akt_PKB"^^ . - "KEGG Compound" . - . - . - "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . - . - "false"^^ . - . - "http://edamontology.org"^^ . - . - . - . - . - "PA447218"^^ . -_:N8b3bddd7a3864dada8d8c456168158d8 "Adrien Coulet" . - . - . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "^\\d+$"^^ . - . - . - "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . - . - . - "0000001"^^ . - "false"^^ . - . - . - . - . - "0290"^^ . - . - . - "https://www.wormbase.org/get?name=$1"^^ . - . - . - . - . - "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . - "false"^^ . - . - . - "^[a-z0-9-]+$"^^ . - . - "version Dec 2019"^^ . - "http://www.russelllab.org/miRNAs/"^^ . - "http://greengenes.lbl.gov/"^^ . - "ArrayGroup"^^ . - "false"^^ . - "NPC139585"^^ . - . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . - . - "^\\d+$"^^ . - . - "https://www.humanbehaviourchange.org/"^^ . - . - . - "IMGT/HLA human major histocompatibility complex sequence database" . - . - . - "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^ . - . - . - "false"^^ . - . - "rsk00410"^^ . - "Jim Balhoff" . - "3"^^ . - . - . - "0001350"^^ . - "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^ . - "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology"^^ . - "https://knowledge.lonza.com/cell?id=$1"^^ . - . - . - . - "Lycalopex_vetulus"^^ . - . - "^\\w+_COVID19_[-\\w]+$"^^ . - "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . - . - . - . - . - . - "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . - . - "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . - . - . - . - . - "PROSITE" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "https://www.cropontology.org/rdf/CO_330:$1"^^ . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "00000099"^^ . - "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . - "http://bugs.sgul.ac.uk/E-BUGS"^^ . - . - . - . - "Regulation of Gene Expression Ontology" . - "2022.07.08.499378"^^ . - "http://purl.org/dc/dcmitype/$1"^^ . - "false"^^ . - . - "http://prism.case.edu/prism/index.php/EpilepsyOntology"^^ . - . - . - "https://github.com/Radiobiology-Informatics-Consortium/RBO"^^ . - . - "^EMD-\\d{4}$"^^ . - . - . - . - . - "0000041"^^ . - . - "^\\w+$"^^ . - . - . - "European Collection of Authenticated Cell Culture" . - . - . - . - . - . - "true"^^ . - . - . - . - . - "1915"^^ . - . - . - . - . - "false"^^ . - "RNAcentral" . - . - . - "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . - . - . - "http://www.bmrb.wisc.edu/"^^ . - "LINCS Data" . - . - . - . - . - . - "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . - . - . - . - . - . - "false"^^ . - "Brian Aevermann" . - . - . - "Database of Aligned Ribosomal Complexes" . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "http://environmentontology.org/"^^ . - . - . - "HsapDO:0000004"^^ . - . - . - . - . - . - . - . - . - . - . - "Miguel A. Fortuna" . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "http://www.diseasesdatabase.com/"^^ . - . - . - . - . - "https://www.uniprot.org/database/DB-$1" . - "COSMIC Gene" . - "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . - . - . - . - . - "Cell line databases/resources"^^ . - "https://www.jax.org/strain/$1"^^ . - . - "Oryza Tag Line" . - . - . - . - . - . - "^\\d+$"^^ . - "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . - "humIGHV025"^^ . - . - "true"^^ . - . - . - . - "NASC code" . - . - "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . - . - . - . - . - . - . - . - . - . - . - "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . - . - . - "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . - . - "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . - . - "false"^^ . - . - "http://code.google.com/p/mirna-ontology/"^^ . - "^\\w+$"^^ . - "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . - . - . - . - "https://gitub.u-bordeaux.fr/erias/fideo"^^ . - "FishBase" . - "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . - "false"^^ . - "14"^^ . - . - "^\\d+$"^^ . - "^MIR:000\\d{5}$"^^ . - "^WBRNAi\\d{8}$"^^ . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . - "https://thebiogrid.org/interaction/$1"^^ . - "https://code.google.com/p/craniomaxillofacial-ontology/"^^ . - . - . - . - . - . - . - . - . - . - . - "0000080"^^ . - "Cell Image Library" . - . - . - . - . - . - . - . - "https://github.com/obophenotype/porifera-ontology"^^ . - "00000014"^^ . - . - "AT1G01010"^^ . - . - . - . - . - . - "vcell"^^ . - "Disease Class" . - "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/PPO_$1"^^ . - "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1"^^ . - . - . - . - "GLDS-141"^^ . - . - . - . - . - . - . - . - "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . - "Glyma0021s00410"^^ . - "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . - . - . - . - . - "https://bioregistry.io/metaregistry/"^^ . - "Contributor Role Ontology" . - . - . - . - . - . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://mobidb.org/$1"^^ . - . - . - "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . - . - . - "http://gmd.mpimp-golm.mpg.de/"^^ . - . - . - "https://www.icd10data.com/ICD10CM"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . - . - "^\\d{7}$"^^ . - . - . - "https://www.cropontology.org" . - . - . - . - . - "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"^^ . - . - "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . - "c0001"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . - "http://www.gramene.org/"^^ . - . - "http://zfin.org/$1"^^ . - "^PA\\d+$"^^ . - "The RNA Modification Database" . - "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . - . - . - "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . - "false"^^ . - . - "https://github.com/SED-ML/KiSAO"^^ . - . - . - . - . - . - . - . - . - . - "http://umbbd.ethz.ch/"^^ . - . - . - . - . - . - "http://www.treefam.org/"^^ . - . - . - . - . - . - . - . - . - "^\\d{4,}$"^^ . - . - . - "http://www.fao.org/gsfaonline"^^ . - . - . - . - "http://treebase.org/"^^ . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - . - "Database of biopesticides maintained by the University of Hertfordshire "^^ . - . - . - . - . - "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . - . - "Wheat ontology" . - . - . - . - "Yeast Intron Database v4.3" . - "EcoLexicon" . - . - . - "53504"^^ . - . - . - "false"^^ . - . - . - . - . - . - "http://www.w3.org/XML/1998/namespace#$1"^^ . - . - . - . - "https://covid19.sfb.uit.no/api/records/$1"^^ . - . - "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . - "https://www.alliancegenome.org"^^ . - . - . - . - . - "http://exac.broadinstitute.org/variant/$1"^^ . - . - "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . - . - . - . - "http://biocyc.org/getid?id=$1"^^ . - . - . - "https://www.ebi.ac.uk/intact/"^^ . - "https://worldwide.espacenet.com/classification"^^ . - . - "Tick Cell Biobank" . - "^\\d+$"^^ . - "0000052"^^ . - . - "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes."^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . - "^\\w+$"^^ . - . - . - . - . - "A-GEOD-50"^^ . - . - . - . - "false"^^ . - . - "MM00040"^^ . - . - . - "^\\d{7}$"^^ . - "http://www.sisuproject.fi/"^^ . - . - "false"^^ . - "0000001"^^ . - . - _:N7165961ce33340f9b8be6ad633b83081 . - . - . - "http://bcrj.org.br/celula/bcrj"^^ . - . - "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . - . - . - . - "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^ . - . - . - . - . - "Cell Signaling Technology Antibody" . - . - "false"^^ . - . - "Rhea, the Annotated Reactions Database" . - . - . - "48439"^^ . - . - . - "Kaggle" . - "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . - . - . - . - . - . - . - "0000546"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - "http://tolweb.org/$1"^^ . - . - . - . - . - . - "https://github.com/jannahastings/mental-functioning-ontology"^^ . - "https://www.ccdc.cam.ac.uk/"^^ . - . - "E. coli Metabolite Database" . - "1"^^ . - "http://www.yeastgenome.org/"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . - "https://bioregistry.io/schema/#$1"^^ . - . - . - . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - . - . - . - . - "Plant Stress Ontology" . - . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . - . - . - . - "638309541"^^ . - . - . - . - . - . - . - . -_:N4c27bf9198f24213bf131981fa0717df "Vivian Lee" . - . - . - "http://si.washington.edu/projects/fma"^^ . - "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . - . - . - . - . - . - . - . - . - . - . - "http://www.fungalbarcoding.org/"^^ . - . - "EasyChair Call for Paper" . - . - . - . - . - . - . - "http://www.violinet.org/ovae/"^^ . - . - "Andrew G. McArthur" . - "Golm Metabolome Database Reference Substance" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^ . - . - . - . - . - . - . - . - "KEGG Drug Group" . - . - . - "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . - . - . - "International Nonproprietary Names" . - "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . - . - . - . - "false"^^ . - "NLXORG covers organisms."^^ . - . - "^F\\d{4}$"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "^Y[A-Z]{2}\\d+[CW]$"^^ . - . - . - . - "https://github.com/rdruzinsky/feedontology"^^ . - "false"^^ . - "SABIO-RK EC Record" . - . - . - . - . - "Egon Willighagen" . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . - . - . - . - . - . - "0000041"^^ . - "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . - . - "Provisional Cell Ontology" . - . - . - . - . - . - . - "Martin Ramirez" . - . - . - . - "false"^^ . - . - . - . - . - "https://registry.identifiers.org/registry?query=\"MIR:$1\""^^ . - . - "100101"^^ . - "^[A-Z0-9]{6,7}$"^^ . - . - . - . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - "http://www.antirrhinum.net/"^^ . - . - "O80725"^^ . - . - "https://www.cbioportal.org/study/summary?id=ccle_broad_2019"^^ . - . - . - "false"^^ . - . - . - . - "https://aopwiki.org/"^^ . - . - . - "^EP\\d{4}$"^^ . - "false"^^ . - "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . - "http://www.ebi.ac.uk/chebi"^^ . - . - . - . - "false"^^ . - . - "NP_012345"^^ . - "^FCB\\d{3}$"^^ . - . - . - "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^ . - . - . - "Identifier for an entity in open tree of life"^^ . - . - . - . - . - . - . - . - . - "GWAS Central Marker" . - . - . - "sbml.level-3.version-2"^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - "^[A-Za-z0-9+_.%-:]+$"^^ . - . - . - . - "https://www.genome.jp/kegg/ligand.html"^^ . - . - . - "^[A-Za-z-0-9]+$"^^ . - . - . - . - . - "1981638"^^ . - . - "PharmacoDB Tissues" . - . - . - . - . - "Radiation Biology Ontology" . - . - . - . - "http://purl.obolibrary.org/obo/OBA_$1"^^ . - "^\\d+$"^^ . - . - "DBCAT000600"^^ . - "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^ . - "Elizabeth Arnaud" . - . - . - . - "https://www.cropontology.org/rdf/CO_339:$1"^^ . - . - "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OHMI_$1"^^ . - . - . - . - . - "Brachiaria ontology" . - . - . - . - "false"^^ . - . - . - . - "GR_tax:013681"^^ . - "NIF Standard Ontology: Chemical" . - . - "CASRAI Contributor Roles Taxonomy" . - . - "SBML RDF Vocabulary" . - . - "https://casrai.org/credit/"^^ . - "^\\d{6}$"^^ . - . - "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . - . - . - . - . - "https://skip.stemcellinformatics.org/en/"^^ . - . - . - . - . - . - . - . - "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/ontoice/ICEO"^^ . - . - . - . - . - "1251"^^ . - . - . - . - "false"^^ . - "Activity Streams" . - . - . - "BE0000048"^^ . - . - "^\\d+$"^^ . - . - . - "false"^^ . - "^\\d+$"^^ . - "1"^^ . -_:N25fbccd5a08f4f199ab2f46ac7cbe0ab "Daniel Sonenshine" . - . - "^C\\d+$"^^ . - "false"^^ . - . - "MimoDB" . - . - . - . - . - . - "^TTHERM\\_\\d+$"^^ . - "^\\w+$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "^\\d{7}$"^^ . - . - "968"^^ . - . - . - . - "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^ . - "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "Damion Dooley" . - . - . - . - "https://www.webelements.com/$1"^^ . - "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/STATO_$1"^^ . - . - . - . - "https://doulix.com/biomodules/$1"^^ . - "false"^^ . - "^\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/MIRO_$1"^^ . - . - "1046"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . - . - . - . - . - "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . - "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . - . - "https://fairsharing.org/$1" . - "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . - . - . - "false"^^ . - . - "http://func.mshri.on.ca/fly"^^ . - . - . - . - . - "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . - "NIF Standard Ontology: Neurolex" . - . - . - . - "BioData Catalyst" . - . - . - "https://www.wicell.org"^^ . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . - . - . - . - . - "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . - . - . - . - . - . - . - "MEROPS Entry" . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - "Structural Classification of Protein" . - . - "http://www.receptome.org"^^ . - . - . - . - . - . - . - . - . - "ENVO" . - "ClassyFire" . - "https://mips.helmholtz-muenchen.de/genre/proj/corum/"^^ . - . - "https://www.biolegend.com"^^ . - . - "1"^^ . - "https://morpheus.gitlab.io/"^^ . - . - . - . - . - . - . - "Experimental Factor Ontology" . - "Jade Hotchkiss" . - . - "http://purl.obolibrary.org/obo/RO_$1"^^ . - "doi" . - "http://aber-owl.net/ontology/$1/#/Browse/" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Basic Formal Ontology" . - "A person" . - . - . - . - "https://www.worldwildlife.org/ecoregions/$1"^^ . - "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1"^^ . - . - . - . - . - "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed."^^ . - . - "^\\d{7}$"^^ . - "PhosphoSite Residue" . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "0000001"^^ . - "false"^^ . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - "C138986"^^ . - . - . - "Cardiovascular Disease Ontology" . - "Bgee stage" . - "false"^^ . - "http://www.sparontologies.net/ontologies/pro"^^ . - "^[0-9a-zA-Z]+$"^^ . - "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^ . - "2.16.840"^^ . - "0000024"^^ . - . - . - . - "PubChem Element" . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . - . - "22-46615880-T-C"^^ . - "MedlinePlus Health Topics" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "Distributed Archives for Neurophysiology Data Integration" . - . - . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - . - "Application ontology for entities related to insecticide resistance in mosquitos"^^ . - "false"^^ . - . - . - . - "false"^^ . - "Pesticide Properties DataBase" . - . - . - . - . - . - . - . - "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . - . - . - . - . - . - . - . - . - "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . - "false"^^ . - . - . - "Ontology of rat strains"^^ . - . - . - . - "A Systematic Annotation Package for Community Analysis of Genomes" . - . - "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^ . - . - "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . - . - . - "0110974"^^ . - . - . - . - . - "^[0-9]+$"^^ . - . - "false"^^ . - "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . - "https://flybase.org/reports/FBrf$1"^^ . - "app-d678n-tottori"^^ . - . - "http://www.ubio.org"^^ . - "https://pir.georgetown.edu/"^^ . - "NASA GeneLab" . - "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . - . - . - . - "https://gen3.biodatacatalyst.nhlbi.nih.gov"^^ . - "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . - . - "false"^^ . - . - "https://ssbd.riken.jp/database/dataset/$1"^^ . - "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . - "M58335"^^ . - . - "Meghan Balk" . - . - . - . - "Mouse Genome Informatics" . - . - "^[AMCST][0-9x][0-9]$"^^ . - . - . - . - . - "false"^^ . - "http://www.phytozome.net/"^^ . - "CH_001923"^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . - . - "ALA"^^ . - . - . - . - . - "BioStudies database" . - "false"^^ . - . - . - . - . - . - "https://github.com/semanticchemistry/semanticchemistry" . - . - . - . - . - . - . - . - . - "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . - . - . - . - . - . - "https://www.wikidata.org" . - . -_:Na8665fde304c426a92ab0fed3bd06d09 "WikiData Support" . - . - . - . - . - "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . - . - "^\\d+$"^^ . - . - . - . - "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . - . - . - . - . - "PM0012345"^^ . - . - . - . - "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . - "0000109"^^ . - . - . - . - "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . - . - "RiceNetDB Compound" . - . - "false"^^ . - "veNOG12876"^^ . - . - . - "^\\d+$"^^ . - . - . - "Circular double stranded DNA sequences composed" . - "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . - . - . - . - . - . - "^rxn\\d+$"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships"^^ . - . - . - . - . - "Genatlas" . - . - . - . - . - . - . - "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - "BibliographicRecord"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "Cell line collections"^^ . - . - . - "false"^^ . - . - . - . - . - "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . - . - _:N8b3bddd7a3864dada8d8c456168158d8 . - . - . - . - . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/SPD_$1"^^ . - . - "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters"^^ . - "UniPathway Reaction" . - "http://purl.obolibrary.org/obo/MICRO_$1"^^ . - . - "^\\d+$"^^ . - "http://zinc15.docking.org/"^^ . - . - "false"^^ . - . - . - . - . - . - . - "SFB_COVID19_MW286762"^^ . - "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . - . - . - . - . - . - . - . - . - . - "http://www.genome.jp/kegg/reaction/"^^ . - "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . - . - "http://genepio.org/"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/flu/"^^ . - . - "PB000166"^^ . - . - . - . - "true"^^ . - . - "http://www.pharmgkb.org/gene/$1"^^ . - "International Molecular Exchange" . - "https://github.com/flora-phenotype-ontology/flopoontology"^^ . - . - . - . - . - . - . - . - . - "EMD-1001"^^ . - . - . - "Cancer Cell Line Encyclopedia Cells" . - . - "false"^^ . - "http://www.jcvi.org/mpidb/about.php"^^ . - . - . - . - . - "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html"^^ . - "http://www.inoh.org"^^ . - . - . - . - "OpenAlex" . - . - . - . - . - . - . - "false"^^ . - "EcoliWiki from EcoliHub" . - . - "^\\d+$"^^ . - "4214"^^ . - "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . - "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . - . - "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . - "false"^^ . - . - . - . - . - . - . - . - "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . - "false"^^ . - . - . - . - . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . - . - . - "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . - . - . - "https://uniresolver.io/#did:$1"^^ . - . - . - . - . - . - . - . - . - "MU9_3181"^^ . - . - . - . - . - . - "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . - "0001417"^^ . - . - . - . - . - . - . - . - . - "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . - "2.1.1"^^ . - . - . - . - . - "https://www.ebi.ac.uk/miriam/main/$1"^^ . - "^\\d+$"^^ . - . - . - "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . - . - "false"^^ . - "false"^^ . - . - . - "https://neurovault.org/collections/$1"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "IRD Segment Sequence" . - . - . - "^M\\d+$"^^ . - . - "PharmGKB Drug" . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "Glycan Naming and Subsumption Ontology" . - . - "false"^^ . - . - . - . - "bioregistry"^^ . - "000204"^^ . - "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . + . + . + "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . + . + "Crop Ontology Curation Tool" . + . + "^(Gi|Gc)\\d+$"^^ . + . + . + . + "https://europepmc.org"^^ . + . + . + "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . + . + . + . + . + . + . + "^FR\\-FCM\\-\\w{4}$"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^ . + . + . + "^[0-9]+$"^^ . + "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . + "0002533"^^ . + "http://rgd.mcw.edu/rgdweb/search/strains.html"^^ . + "174"^^ . + . + . + . + . + . + . + "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . + . + . + . + . + . + . + . + "http://oncotree.mskcc.org"^^ . + . + "Q-2958"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "0000069"^^ . + . + . + . + . + . + "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . + . + . + . + . + . + . + "^\\d{8}$"^^ . + . + . + . + . + . + . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway collection references pathway information, primarily for signaling pathways, each with subfamilies and protein sequences mapped to individual pathway components."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://neuromorpho.org/index.jsp"^^ . + . + . + . + . + . + . + "NLXORG covers organisms."^^ . + . + . + . + . + "MMP743597.11"^^ . + . + "http://purl.obolibrary.org/obo/TRANS_$1"^^ . + . + "^HIT\\d{9}(\\.\\d+)?$"^^ . + "M00002"^^ . + . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + "TIGR00010"^^ . + "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^ . + . + . + . + . + . + "https://odc-sci.org/data/$1"^^ . + "^[\\w\\d\\.-]*$"^^ . + . + . + . + . + "BioGRID" . + "CUT"^^ . + . + . + . + . + . + . + "https://catalog.hathitrust.org/Record/$1"^^ . + . + "^\\d{7}$"^^ . + "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . + . + . + "EDAM is a comprehensive ontology of well-established, familiar concepts that are prevalent within computational biology, bioinformatics, and bioimage informatics. EDAM includes types of data and data identifiers, data formats, operations, and topics related to data analysis in life sciences. EDAM provides a set of concepts with preferred terms and synonyms, related terms, definitions, and other information - organised into a simple and intuitive hierarchy for convenient use." . + "true"^^ . + . + . + "http://www.phosphosite.org/siteAction.do?id=$1"^^ . + . + "Human Brain Atlas" . + "AphidBase Transcript" . + "FlyBase Controlled Vocabulary" . + . + . + "http://sourceforge.net/p/mamo-ontology/wiki/Home/"^^ . + . + "http://purl.obolibrary.org/obo/CLO_$1"^^ . + . + . + . + "false"^^ . + "Terminology for Description of Dynamics" . + . + . + "AD834"^^ . + "PlasmoDB" . + . + "Pfam Clans" . + . + . + . + . + "GT10"^^ . + . + . + "European Bank for induced pluripotent Stem Cells" . + "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . + . + . + . + . + . + . + . + . + . + "James C. Hu" . + . + . + . + . + "12300"^^ . "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . - "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . - . - . - "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000"^^ . - "^[AEP]-\\w{4}-\\d+$"^^ . - . - . - . + . + . + "false"^^ . + . + . + "^LGCEDe-S-\\d{9}$"^^ . + . + . + . + . + . + . + . + "eggNOG" . + "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . + "https://www.ebi.ac.uk/interpro/genomeproperties/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/HSAPDV_$1"^^ . + . + "http://www.hmdb.ca/"^^ . + . + . + "ESi007-A"^^ . + "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . + . + . + . + . + . + . + "Allergome" . + . + . + . + . + . + . + "http://browser.planteome.org/amigo"^^ . + . + "ENSGT00550000074763"^^ . + . + . + "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . + "Workflow"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . + . + . + "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . + . + . + . + "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . + . + "493771"^^ . + . + "Minimal Anatomical Terminology" . + . + . + . + . + . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Protein' view."^^ . + "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . + "^\\d+$"^^ . + . + "General Multilingual Environmental Thesaurus" . + "https://github.com/obophenotype/c-elegans-development-ontology"^^ . + . + "141"^^ . + "4.2.78"^^ . + . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "DECIPHER CNV Syndromes" . + . + . + . + . + . + "Human developmental anatomy, timed version" . + . + "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . + . + . + "Cell Line Ontology [derivative]" . + . + . + . + "The Statistical Methods Ontology" . + . + "false"^^ . + "false"^^ . + . + . + "Lycalopex_vetulus"^^ . + "https://cordis.europa.eu/"^^ . + "Flybase Cell Line" . + . + . + . + . + . + "A Systematic Annotation Package for Community Analysis of Genomes" . + "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . + . + . + . + "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . + . + . + . + "https://bioregistry.io/metaregistry/"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.pharmgkb.org/drug/$1"^^ . + "http://cutdb.burnham.org/relation/show/$1"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "0000000"^^ . + "false"^^ . + . + . + . + . + . + "National Center for Biotechnology Information Registry" . + . + "An identifier for a resource or metaresource." . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . + "CO_010" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "PDC000351"^^ . + . + "false"^^ . + "false"^^ . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . + . + "UPI000000000A"^^ . + . + . + . + . + . + "An ontology to standardize research output of nutritional epidemiologic studies."^^ . + . + . + "61467"^^ . + "http://senselab.med.yale.edu/ModelDB/"^^ . + . + . + "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . + "^[0-9]+$"^^ . + "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . + "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . + . + . + "GeneCards" . + "http://degradome.uniovi.es/"^^ . + . + "http://www.disease-ontology.org"^^ . + . + . + . + . + . + "http://obi-ontology.org"^^ . + . + "16793"^^ . + "http://sabiork.h-its.org/"^^ . + . + . + . + . + . + . + . + "https://www.phenxtoolkit.org/protocols/view/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . + . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/VO_$1"^^ . + . + "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . + . + "https://www.hathitrust.org"^^ . + . + "https://comptox.epa.gov/dashboard/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . + "https://www.ncbi.nlm.nih.gov/proteinclusters?db=proteinclusters"^^ . + . + . + . + . + . + . + . + "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . + . + . + . + . + . . - . - "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . - "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . - . - . - . - . - "http://func.mshri.on.ca/yeast"^^ . - . - . - "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . - . - . - "0000001"^^ . - . - . - . - "false"^^ . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "http://patft.uspto.gov/netahtml/PTO/index.html"^^ . - . - "false"^^ . - "Fetal Calf Serum-Free Database" . - "false"^^ . - . - "false"^^ . - . - . - . - "AgentIdentifierScheme"^^ . - "https://www.aapc.com/codes/cpt-codes/$1"^^ . - . - . - . - "https://schema.org/$1"^^ . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . - "true"^^ . - . - "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . - . - . - "false"^^ . - . - . - . - . - . - . + "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . + . + "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . + . + . + . + . + "Cardiovascular Disease Ontology" . + . + . + "http://dictybase.org/"^^ . + . + "http://www.semantic-systems-biology.org/apo"^^ . + "http://www-is.biotoul.fr/i"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd"^^ . + . + . + . + . + . + "An Archival Resource Key (ARK) is a Uniform Resource Locator (URL) that is a multi-purpose persistent identifier for information objects of any type."^^ . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "EHDAA:2185"^^ . + "638309541"^^ . + . + . + . + . + "MTBLS1"^^ . + . + . + . + . + "NCBI Bookshelf" . + . + "http://purl.obolibrary.org/obo/PORO_$1"^^ . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "KEGG Orthology" . + . + . + "http://www.drugbank.ca"^^ . + . + "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . + . + "http://datf.cbi.pku.edu.cn/"^^ . + . + . + . + . + . + . + . + . + . + "foaf" . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "https://pfam.xfam.org"^^ . + . + . + "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . + "Information Artifact Ontology" . + . + . + . + "Alejandra Gonzalez-Beltran" . + . + . + "^((VGNC|vgnc):)?\\d{1,9}$"^^ . + . + . + "https://cellrepo.ico2s.org/"^^ . + "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + "Provisional Cell Ontology" . + "Scholia Registry" . + . + . + "Mouse pathology ontology" . + . + . + "https://biosimulators.org/"^^ . + . + . + "RiceNetDB Gene" . + "false"^^ . + . + "^[A-Z0-9]{4}$"^^ . + "EMLSAT00000003403"^^ . + . + . + . + "VEuPathDB ontology" . + . + . + "Vertebrate Skeletal Anatomy Ontology" . + "0002350"^^ . + . + . + . + . + . + "PF3D7_1328700"^^ . + "2004-2820"^^ . + "https://pharmacome.github.io/conso/"^^ . + . + . + . + . + "GWAS Central Phenotype" . + . + . + . + . + . + "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + "01467"^^ . + "International Geo Sample Number" . + . + . + . + . + . + "Semantic Web Context" . + "^B\\d+$"^^ . + . + . + . + "0002959"^^ . + "TTHERM_00648910"^^ . + . + "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . + "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . + "^\\d{6}$"^^ . + "false"^^ . + . + . + "3305"^^ . + . + "false"^^ . + "http://en.wikipedia.org/wiki/Main_Page"^^ . + . + . + . + "CALIPHO Group Ontology of Human Anatomy" . + "false"^^ . + "^\\d{4}-\\d{3}[\\dX]$"^^ . + . + "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . + . + "http://lincs.hms.harvard.edu/db/proteins/"^^ . + "^\\d+$"^^ . + . + "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "SNR17A"^^ . + . + "000000024"^^ . + . + "1000000"^^ . + "https://go.drugbank.com/categories"^^ . + "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . + . + . + . + "9001411"^^ . + "1000003"^^ . + . + "https://www.wwpdb.org/"^^ . + . + . + . + . + "Cell line databases/resources"^^ . + "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + "0011124"^^ . + "https://medical-data-models.org/forms/$1"^^ . + . + "0000001"^^ . + . + . + . + . + "Francesco Vitali" . + . + . + . + . + . + . + . + . + . + . + . + . + "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . + "WBGene00000001"^^ . + . + . + . + . + . + . + . + . + "BioGRID Interactions" . + . + . + . + "https://github.com/obophenotype/human-developmental-anatomy-ontology"^^ . + "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/index.html"^^ . + . + . + "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . + "http://www.ecogene.org/gene/$1"^^ . + . + "^\\d+$"^^ . + "0000295"^^ . + . + . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + . + . + . + "Bio-Pesticides DataBase" . + "https://glycopost.glycosmos.org"^^ . + . + "http://toxodb.org/toxo/"^^ . + . + "jrc-eurl-ecvam-chemagora"^^ . + "CASRAI Contributor Roles Taxonomy" . + . + . + "0009089"^^ . + . + . + . + "https://www.w3.org/2003/01/geo/wgs84_pos"^^ . + . + . + . + . + "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . + . + "https://scholar.google.com/"^^ . + . + "http://www.cathdb.info"^^ . + "^\\d+$"^^ . + . + . + "EGAD00000000001"^^ . + "Medaka fish anatomy and development" . + . + "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . + . + . + . + . + "PhosphoPoint Kinase" . + . + "https://www.storedb.org/"^^ . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + . + "Cell Lines in PubChem"^^ . + . + . + "http://arabidopsis.org/index.jsp"^^ . + . + "0000030"^^ . + . + . + . + "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . + . + . + . + . + . + . + . + "https://github.com/futres/fovt"^^ . + "Repeated CRISPR (\"clustered regularly interspaced short palindromic repeats\") elements found in archaebacteria and eubacteria are believed to defend against viral infection, potentially targeting invading DNA for degradation. CRISPRdb is a database that stores information on CRISPRs that are automatically extracted from newly released genome sequence data."^^ . + "https://depmap.org/portal"^^ . + . + . + "Pathogen Host Interaction Phenotype Ontology" . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references strain reports, which include a description of strain origin, disease, phenotype, genetics and immunology."^^ . + . + "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + . + "false"^^ . + "Fossilworks Taxon" . + . + . + "EchoBASE post-genomic database for Escherichia coli" . + . + "LTS0004651"^^ . + "^\\d{7}$"^^ . + . + "https://www-snorna.biotoul.fr/"^^ . + . + . + . + . + "A0001"^^ . + . + . + "ClinVar Variation" . + "^TIGR\\d+$"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + . + . + "SUPERFAMILY" . + . + . + "Ontology of Zebrafish Experimental Conditions"^^ . + "false"^^ . + "1000160"^^ . + . + . + . + . + "http://www.alanwood.net/pesticides"^^ . + . + "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . + . + . + "Sigma Aldrich" . + . + "http://www.obofoundry.org/"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "PMC3084216"^^ . + . + "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . + "UniSTS is a comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences."^^ . + "491187"^^ . + "https://scholia.toolforge.org/"^^ . + . + . + . + . + "^GR\\_tax\\:\\d+$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . + "NeuronDB" . + "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . + "PomBase is a model organism database established to provide access to molecular data and biological information for the fission yeast Schizosaccharomyces pombe. It encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets."^^ . + . + "00000099"^^ . + "0110974"^^ . + . + "^\\d+$"^^ . + . + "https://cell.brc.riken.jp/en/rcb"^^ . + "Yam ontology" . + . + . + . + . + . + . + "0000109"^^ . + . + . + . + "false"^^ . + . + . + . + . + "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . + . + . + . + "InTextReferencePointer"^^ . + . + . + . + . + "^\\d{8}$"^^ . + "https://identifiers.org/$1:$2" . + . + "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . + . + . + . + . + . + "GWAS Central Marker" . + "10001-101"^^ . + . + . + . + "BCRC Strain Collection Catalog" . + . + . + . + . + . + . + "false"^^ . + "^[0-9]{1,7}$"^^ . + "Assembling the Fungal Tree of Life - Taxonomy" . + "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n"^^ . + . + . + . + . + . + . + "6038"^^ . + "^\\w+$"^^ . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + "Selventa legacy complex namespace used with the Biological Expression Language"^^ . + "022586"^^ . + "^[\\d.]+$"^^ . + . + "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . + . + . + . + . + . + "^[A-Za-z0-9_-]+$"^^ . + "CutDB" . + . + . + . + . + "CNP0171505"^^ . + . + "DBCAT000600"^^ . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi"^^ . + . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + "https://www.biolegend.com"^^ . + "casent0106247"^^ . + "https://www.yeastgenome.org/locus/$1"^^ . + . + . + . + . + "false"^^ . + "https://www.mmrrc.org"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "https://dip.doe-mbi.ucla.edu/"^^ . + . + "^(SMP|PW)\\d+$"^^ . + . + "^[A-Za-z0-9-]+$"^^ . + . + . + . + . + "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . +_:Neeb545bd1981481a87d11abe1a29209a "Satya S. Sahoo" . + . + . + . + . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . + . + . + . + "Rice Genome Annotation Project" . + "https://www.yeastgenome.org/"^^ . + "WikiPathways is a resource providing an open and public collection of pathway maps created and curated by the community in a Wiki like style.\r\nAll content is under the Creative Commons Attribution 3.0 Unported license."^^ . + . + . + "https://cancer.sanger.ac.uk/cell_lines/"^^ . + . + . + . + . + "A language for validating RDF graphs against a set of conditions"^^ . + . + . + . + . + . + "http://viralzone.expasy.org/all_by_protein/$1.html"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "A structured controlled vocabulary for the anatomy of fungi."^^ . + . + . + "^\\d{7}$"^^ . + . + "The Radiomics Ontology aims to cover the radiomics feature domain with a strong focus on first order, shape, textural radiomics features. In addition, in the original version. it includes classes about segmentation algorithms and imaging filters. Due to a recent collaboration with the IBSI (International Biomarkers Standardization Initiative), the ontology has been expanded (v 1.6) and it includes all the entities presented in the IBSI document. Therefore, a broad coverage of not only radiomics features, but also every entity (e.g. software properties, filter properties, features extraction parameters) involved into radiomics computation has been added. In the latest version (v2.0), the ontology URIs have been updated to reflect the codes avaialble in the IBSI latest manual. [bioportal]"^^ . + . + . + . + . + "http://stormo.wustl.edu/ScerTF/"^^ . + . + "false"^^ . + . + "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . + . + "0000006"^^ . + "Tick Anatomy Ontology" . + . + "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . + "^EG\\d+$"^^ . + . + . + "BN000065"^^ . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + . + . + . + . + . + . + "0000003"^^ . + . + "^([a-z]{3,5}_)?M\\d{5}$"^^ . + . + . + . + . + . + "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . + . + . + . + . + . + . + . + . + . + "http://www.proteomexchange.org/"^^ . + "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . + "https://cellbank.snu.ac.kr/english"^^ . + "https://fungi.ensembl.org/id/$1"^^ . + . + . + . + . + . + . + . + "baseDimensionEnumeration"^^ . + . + "Current Dental Terminology" . + . + . + "false"^^ . + . + . + . + . + . + "http://www.uniprot.org/keywords/"^^ . + . + . + . + . + "http://www.phenol-explorer.eu/foods/"^^ . + "0000550"^^ . + . + . + . + . + . + . + "http://www.cathdb.info/"^^ . + . + . + . + . + . + . + . + . + . + "https://www.fredhutch.org/en/research/institutes-networks-ircs/international-histocompatibility-working-group.html"^^ . + "https://www.ebi.ac.uk/ena/"^^ . + "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . + . + . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + . + . + "https://gsso.research.cchmc.org/"^^ . + "^(cd)?\\d{5}$"^^ . + "false"^^ . + "0000091"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "The Vital Sign Ontology (VSO) is an extension of the Ontology for General Medical Science (OGMS). VSO covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements. "^^ . + "^[0-9][A-Za-z0-9]{3}$"^^ . + "https://www.kew.org/data/grasses-syn/index.htm"^^ . + "false"^^ . + . + "http://www.cazy.org/"^^ . + "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + . + . + "false"^^ . + "^\\w+$"^^ . + . + . + . + "60316"^^ . + "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . + "Zebrafish Experimental Conditions Ontology" . + . + . + . + . + . + "https://pbil.univ-lyon1.fr/databases/hovergen.php"^^ . + . + "Tetrahymena Genome Database" . + . + "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . + . + . + "Wikidata" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "Cell Cycle Ontology" . + . + "false"^^ . + . + . + . + "https://www.grid.ac/"^^ . + . + . + "false"^^ . + . + "3304"^^ . + "long-finned-pilot-whale"^^ . + . + . + "http://www.boldsystems.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "^\\w+(\\.)?(\\d+)?$"^^ . + "GeoNames Feature Code" . + "MGnify Project" . + . + . + "https://openalex.org/$1"^^ . + . + "false"^^ . + . + . + "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . + . + . + . + . + "http://mona.fiehnlab.ucdavis.edu/"^^ . + "http://purl.obolibrary.org/obo/OMP_$1"^^ . + . + . + "feature"^^ . + . + "https://github.com/obophenotype/zebrafish-phenotype-ontology"^^ . + . + . + . + . + "http://purl.org/spar/doco/$1"^^ . + "ai10e-kctd13b"^^ . + . + . + "PhosphoSite Residue" . + "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . + . + "false"^^ . + . + . + . + . + . + . + "Chemical Information Ontology" . + . + "false"^^ . + . + "^\\d{5}$"^^ . + "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . + . + . + . + . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "AB0"^^ . + "Cassava ontology" . + . + "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . + . + "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references microarray experiments."^^ . + . + . + . + . + . + "http://string.embl.de/interactions/$1"^^ . + "PharmGKB Pathways" . + "https://www.ncbi.nlm.nih.gov/genome"^^ . + . + . + . + . + . + . + "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . + "^ENST\\d{11}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "IUPHAR family" . + "https://www.iedb.org/reference/$1"^^ . + "2h6o"^^ . + . + . + . + . + . + . + . + . + "1199"^^ . + . + . + . + . + "https://www.uniprot.org/"^^ . + "ChEMBL target" . + . + . + "http://purl.org/spar/c4o/$1"^^ . + . + "http://purl.obolibrary.org/obo/FYPO_$1"^^ . + . + . + . + . + . + . + "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . + . + . + "http://www.radiomics.org/RO"^^ . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + "Frederic Bastian" . + . + . + . + . + . + . + . + "^PKDB[0-9]{5}$"^^ . + "NASC code" . + "^[0-9]+$"^^ . + . + "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^ . + . + . + . + "The Bioregistry's meta-registry"^^ . + . + . + "Interlab Cell Line Collection" . + . + "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . + . + . + . + . + "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references protein abundance information by species."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + . + "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . + . + . + "^NPC\\d+$"^^ . + . + . + "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . + . + . + . + . + . + . + . + . + "The Identifiers.org registry contains registered namespace and provider prefixes with associated access URIs for a large number of high quality data collections. These prefixes are used in web resolution of compact identifiers of the form “PREFIX:ACCESSION” or \"PROVIDER/PREFIX:ACCESSION” commonly used to specify bioinformatics and other data resources."^^ . + . "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . - . - . - . - . - "http://ctdbase.org/"^^ . - . - "AN0097748"^^ . - . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . - . - . - "https://www.fisheries.noaa.gov/species-directory"^^ . - . - "International Classifications of Diseases" . - . - . - . - "http://www.inoh.org"^^ . - . - . - . - . - . - . - . - "https://www.biozol.de/en/product/$1"^^ . - "https://cropontology.org/ontology/CO_339/Lentil"^^ . - . - "https://github.com/monarch-initiative/SEPIO-ontology"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Human developmental anatomy, timed version" . - . - "TAIR Gene" . - . - . - . - . - . - "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^ . - "^\\d{7}$"^^ . - "RF00230"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/complexportal"^^ . - . - . - "http://viralzone.expasy.org/"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^[A-Z0-9]{5}\\d+$"^^ . - . - . - . - "https://www.ebi.ac.uk/miriam/"^^ . - . + . + . + "^\\d+$"^^ . + . + . + . + "ClinVar Record" . + . + "https://www.uniprot.org/docs/tisslist.txt"^^ . + "http://lisanwanglab.org/DASHR/"^^ . + . + "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . + . + . + . + . + "The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles."^^ . + . + . + . + . + . + . + . + "https://sed-ml.org/urns.html#language:$1"^^ . + . + . + . + . + . + "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . + "false"^^ . + "Activity"^^ . + . + . + . + "^MF_\\d+$"^^ . + "^\\d+$"^^ . + . + "Bactibase" . + . + . + . + "^[a-z0-9-]+$"^^ . + . + . + . + . + "^ACH-\\d+$"^^ . + . + "https://registry.identifiers.org/registry"^^ . + "^GenProp\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "Expression"^^ . + . + . + . + . + . + . + . + . + "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . + "http://www.phytozome.net/"^^ . + "Enzo Life Sciences is an antibody vendor."^^ . + . + . + . + . + . + . + "cho"^^ . + . + "Ligandbook is a public repository for force field parameters with a special emphasis on small molecules and known ligands of proteins. It acts as a warehouse for parameter files that are supplied by the community."^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + . + . + "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . + "International Nucleotide Sequence Database Collaboration (INSDC) Run" . + . + "0001114"^^ . + . + . + . + "false"^^ . + . + "^TA\\d+$"^^ . + "Yeast Intron Database v4.3" . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "Protein Model Portal" . + "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . + . + "false"^^ . + . + . + "https://www.ebi.ac.uk/ols/ontologies/envo/terms?obo_id=ENVO:$1"^^ . + . + "https://www.vmh.life/#metabolite/$1"^^ . + . + "http://www.sequenceontology.org/miso/current_release/term/SO:$1"^^ . + . + "^(cl|tum)\\d+$"^^ . + . + . + . + . + "0000435"^^ . + . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . + "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . + . + . + . + . + . + "false"^^ . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + . + "^\\d{7,8}$"^^ . + . + "Dublin Core Types" . + . + . + "National Drug Code" . + . + "57-27-2"^^ . + . + "^\\d{6}$"^^ . + . + "Ascomycete phenotype ontology" . + . + . + "Curation of Neurodegeneration Supporting Ontology" . + . + . + "^\\d+$"^^ . + . + . + . + "Life cycle stages for Platynereis dumerilii"^^ . + . + . + . + . + . + . + . + "ENSG00000169174"^^ . + . + . + . + "https://foodb.ca/"^^ . + . + . + . + . + "Jade Hotchkiss" . + "Antibiotic resistance genes and mutations"^^ . + . + "http://purl.org/spar/biro/$1"^^ . + . + . + . + . + . + . + . + . + "BioCarta Pathway" . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/HOM_$1"^^ . + . + . + "false"^^ . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "Merck Millipore (EMD Millipore)" . + . + . + . + "^(R)?PXD\\d{6}$"^^ . + "false"^^ . + . + . + . + . + "app-d678n-tottori"^^ . + . + . + "^\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/VARIO_$1"^^ . + . + "http://www.guidetopharmacology.org/targets.jsp"^^ . + . + "Genome assembly database" . + . + . + . + "FuncBase Yeast" . + "true"^^ . + "false"^^ . + . + "Michael Witt" . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OARCS_$1"^^ . + . + . + "http://purl.obolibrary.org/obo/MRO_$1"^^ . + "http://data.europa.eu/89h/$1"^^ . + . + . + "http://bioportal.bioontology.org/ontologies/MEDDRA"^^ . + . + . + . + "https://github.com/EBISPOT/clyh_ontology"^^ . + "^\\d{7}$"^^ . + "false"^^ . + "56"^^ . + . + "false"^^ . + . + . + . + "Physical Medicine and Rehabilitation" . + "Wasila Dahdul" . + . + . + . + "https://bioportal.bioontology.org/ontologies/BIRNLEX"^^ . + "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . + . + . + "CONSO00010"^^ . + "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^ . + "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + . + . + . + . + . + . + "UCSC Genome Browser" . + "https://kidsfirstdrc.org"^^ . + . + . + . + . + . + "Broad Fungal Genome Initiative" . + . + . + "false"^^ . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + . + . + . + . + . + "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . + . + . + . + . + "Progenetix" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "NCBI Registry" . + . + . + "^\\w+$"^^ . + "https://www.orthodb.org"^^ . + . + . + "OrthoDB" . + "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . + . + "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . + "The Ontology of Genes and Genomes" . + . + "^FCB\\d{3}$"^^ . + . + "1257009"^^ . + . + . + . + . + . + . + . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . + "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . + . + . + . + . + . + "3075966"^^ . + "9606117"^^ . + "Tohoku University cell line catalog" . + . + . + . + . + . + . + . + . + "Cellosaurus" . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . + . + . + "Sorghum ontology" . + . + . + . + . + . + "AC119"^^ . + "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . + . + . + . + . + "http://www.molbase.com/"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/intact/"^^ . + "https://disprot.org/$1"^^ . + . + . + . + "NCBI Probe database Public registry of nucleic acid reagents" . + "^DRSC\\d+$"^^ . + . + . + . + . + . + . + "Chris Grove" . + . + "UniPathway Compound" . + . + . + . + . + . + "doi"^^ . + . + . + . + . + . + . + . + . + . + . + "0000000"^^ . + "false"^^ . + . + "false"^^ . + "false"^^ . + . + . + . + . + "Computer Retrieval of Information on Science Projects Thesaurus" . + "^KIAA\\d{4}$"^^ . + "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + "HPA000698"^^ . + . + "false"^^ . + "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . + . + . + . + "0400109"^^ . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1"^^ . + . + "^(\\w+)?\\d+$"^^ . + "PROV Namespace" . + "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . + . + . + "https://omabrowser.org"^^ . + "Pesticide Properties DataBase" . + . + . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "An issue in any public repository on GitHub."^^ . + . + "Cell line collections"^^ . + . + . + . + . + . + . + . + . + . + . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp"^^ . + "^\\d+$"^^ . + . + "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . + . + "AMDEFA"^^ . + . + . + "17:41223048"^^ . + "Discourse Elements Ontology" . + . + . + . + . + "^\\d{6}$"^^ . + "false"^^ . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This collection refers to growth stage ontology information in Gramene."^^ . + . + . + . + . + . + . + "ARP-1513"^^ . + "https://github.com/cido-ontology/cido"^^ . + . + . + "https://www.gwascentral.org/phenotypes"^^ . + . + "CryptoDB" . + . + . + . + . + "https://datanator.info/reaction/$1"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "Miguel A. Fortuna" . + "Mental Functioning Ontology" . + "DP00086r013"^^ . + "^\\d+$"^^ . + . + "BIOZIL" . + "^m\\w+$"^^ . + "HPSI0114i-bezi_1"^^ . + . + . + . + . + . + "^SIGNOR-\\d+$"^^ . + "^\\d+$"^^ . + "ppr103739"^^ . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + "Environment Ontology for Livestock" . + . + . + "Terry Hayamizu" . + . + . + "http://www.ebi.ac.uk/cmpo"^^ . + . + . + . + . + . + . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + . + . + . + "PM0012345"^^ . + "false"^^ . + . + . + . + . + . + "http://teddyontology.sourceforge.net/"^^ . + . + "Grant"^^ . + "https://github.com/echinoderm-ontology/ecao_ontology"^^ . + . + . + . + . + . + "http://www.cropontology.org/ontology/CO_360/Sugar%20Kelp%20trait"^^ . + "has responsible" . + "9008500"^^ . + . + . + . + . + . + . + "Jesualdo Tomás Fernández-Breis" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . + . + "Amazon Standard Identification Number" . + . + . + "https://github.com/ufbmi/geographical-entity-ontology/wiki"^^ . + "http://uri.neuinfo.org/nif/nifstd/$1"^^ . + . + "hsa-mir-200a"^^ . + "false"^^ . + . + "false"^^ . + "http://www.sparontologies.net/ontologies/frbr"^^ . + "http://www.uniprot.org"^^ . + . + "http://www.proglycprot.org/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "2673500"^^ . + . + "false"^^ . + . + "Minimum PDDI Information Ontology" . + . + "https://gudmap.org/id/$1"^^ . + . + . + "false"^^ . + . + "3D Metabolites" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . + . + "false"^^ . + . + "http://si.washington.edu/projects/fma"^^ . + . + . + . + "false"^^ . + "UniPathway Reaction" . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + . + . + . + "http://bioinfo.lifl.fr/norine/"^^ . + . + "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . + "The Behaviour Change Intervention Ontology" . + . + . + . + . + . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . + "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . + . + . + "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . + "Database of Macromolecular Interactions" . + . + . + . + . + . + "false"^^ . + . + . + "International Genome Sample Resource" . + "ForwardStrandPosition"^^ . + . + . + . + . + . + . + . + . + . + . + "ISCW007415"^^ . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "284196006"^^ . + . + . + . + . + "https://www.storedb.org/?$1"^^ . + . + . + . + . + . + "File inside StoreDB"^^ . + . + "HGVST1828"^^ . + . + . + . + . + . + . + "Potato ontology" . + "ECU03_0820i"^^ . + "false"^^ . + . + . + "Metabolomics Standards Initiative Ontology" . + . + "http://research.nhgri.nih.gov/apps/homeodomain/web/"^^ . + "numpy"^^ . + "FB00000917"^^ . + . + "Thermo Fisher Scientific" . + . + . + "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . + . + . + "PB000166"^^ . + . + "BDGP insertion DB" . + . + "Rat Genome Database" . + . + . + . + "0000984"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://scop.mrc-lmb.cam.ac.uk/scop/"^^ . + . + . + . + "http://www.vbase2.org/vbase2.php"^^ . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + "Molecular Process Ontology" . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "^[A-Z_0-9]+$"^^ . + . + "An ontology that provides a structured vocabulary for rhetorical elements within documents (e.g., Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix). It is imported by DoCO."^^ . + "hasDbXref"^^ . + "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . + "Hilmar Lapp" . + . + . + . + . + "https://datalab.rwth-aachen.de/MINDER"^^ . + . + . + . + "LINCS Protein" . + "^[0-9\\-_]+$"^^ . + "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . + . + "http://www.signaling-gateway.org/molecule"^^ . + "false"^^ . + "http://www.kegg.jp/entry/$1"^^ . + "1801.012"^^ . + "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . + . + "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . + . + . + . + "Variation Modelling Collaboration" . + . + . + "0000000"^^ . + . + . + . + "Collection"^^ . + "https://bgee.org/?page=gene&gene_id=$1"^^ . + "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . + . + . + "http://purl.org/dc/terms/$1"^^ . + "PXD000500"^^ . + "https://github.com/ICO-ontology/ICO"^^ . + . + . + "false"^^ . + "https://bioportal.bioontology.org/ontologies/SWEET"^^ . + . + . + . + . + "C. elegans development ontology" . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + . + "http://unite.ut.ee/"^^ . + "Amphibian taxonomy" . + . + . + "The Foundational Model of Anatomy Ontology (FMA) is a biomedical informatics ontology. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."^^ . + . + . + "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . + . + . + "MeSH 2013" . + . + "European Paediatric Cardiac Codes" . + "^SIGNOR\\-[A-Z]+\\d+$"^^ . + . + "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . + . + . + . + . + "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . + . + "0001011"^^ . + . + . + "TarBase" . + "6200"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "GR_tax:013681"^^ . + . + . + . + "C6155"^^ . + . + . + . + . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . + . + . + "14362"^^ . + . + "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "00000001"^^ . + . + . + "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . + . + . + . + . + . + . + . + . + . + "https://cropontology.org/ontology/CO_322/Maize"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + "https://omim.org/entry/$1"^^ . + . + . + "http://planttfdb.cbi.pku.edu.cn"^^ . + "AT1402"^^ . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Identifiers.org Terms" . + . + "false"^^ . + . + . + . + . + . + . + . + . + "The RNA Modification Database" . + . + . + "http://www.cellresource.cn"^^ . + . + . + . + . + . + "https://hawaii.eagle-i.net"^^ . + . + . + . + "https://fungidb.org/fungidb"^^ . + "true"^^ . + . + . + . + . + . + "BAMS (Brain Architectural Management System) describes vertebrate neuroinformatics data at four levels of organization: expressed molecules, neuron types and classes, brain regions, and networks of brain regions."^^ . + . + . + "http://www.antweb.org/"^^ . + . + . + . + "NeuroMorpho" . + . + . + . + . + "^\\d+$"^^ . + "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . + . + . + . + . + . + . + . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . + . + "7123"^^ . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + "RC00001"^^ . + . + . + "https://www.icd10data.com/ICD10CM"^^ . + "https://www.atcc.org/products/$1"^^ . + . + . + . + . + "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . + . + "http://cell-lines.toku-e.com"^^ . + . + "^\\d+$"^^ . + "false"^^ . + . + . + . + . + . + . + . + "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . + . + . + "^\\d{7}$"^^ . + . + "c"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "International repository of Adverse Outcome Pathways."^^ . + . + "http://www.isni.org/isni/$1"^^ . + . + . + . + . + . + "http://pax-db.org/#!species/$1"^^ . + "Google Patents" . + . + . + . + . + . + . + "https://coconut.naturalproducts.net"^^ . + "100010"^^ . + . + . + . + . + . + . + . + "false"^^ . +_:Na4993da9f93f43338e0547ea8674d1c5 "Julie Thompson" . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/MOP_$1"^^ . + "false"^^ . + . + . + "http://www.kazusa.or.jp/rouge/"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/HTN_$1"^^ . + . + . + . + "https://omim.org/phenotypicSeries/$1"^^ . + "International Molecular Exchange" . + . + . + "true"^^ . + . + . + "OriDB Saccharomyces" . + . + . + "http://purl.obolibrary.org/obo/OBCS_$1"^^ . + . + . + "Schema.org" . + . + . + . + "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . + . + . + . + "http://purl.obolibrary.org/obo/EXO_$1"^^ . + . + . + "Jingshan Huang" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + "rxn00001"^^ . + "https://github.com/obi-bcgo/bcgo"^^ . + "Gene Ontology Registry" . + . + "Rhea, the Annotated Reactions Database" . + . + . + "Tick Cell Biobank" . + . + . + . + . + "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . + "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . + "http://string.embl.de/"^^ . + . + . + . + . + "http://labda.inf.uc3m.es/doku.php?id=es:labda_dinto"^^ . + . . - "bsu:BSU01340"^^ . - . - . - . - . - . - . - "false"^^ . - . - "http://substrate.burnham.org/protein/annotation/$1/html"^^ . - . - . - . - . - "http://ecocyc.org/"^^ . - . - . - . - . - "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . - . - . - "false"^^ . - . - "0001410"^^ . - "^\\d{7}$"^^ . - . - . - "http://purl.obolibrary.org/obo/CVDO_$1"^^ . - . - "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . - "false"^^ . - "false"^^ . - "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "http://www.treefam.org/family/$1"^^ . - "NameRXN" . - . - . - . - . - . - "http://nematode.lab.nig.ac.jp/"^^ . - . - . - "SABIO Reaction Kinetics" . - . - . - . - . - "false"^^ . - . - . - . + . + . + . + . + . + . + "Database of small human noncoding RNAs" . + . + . + "^\\d{7}$"^^ . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + "Q-2958"^^ . + . + . + . + "^\\d+$"^^ . + . + "^ML\\w+$"^^ . + . + . + . + . + "FlyBase Gene" . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/EDDA"^^ . + "None"^^ . + . + . + . + . + "Identifier for an entity in open tree of life"^^ . + . + . + "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . + . + . + "https://github.com/NCI-Thesaurus/thesaurus-obo-edition"^^ . + . + "The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community."^^ . + "^CHEMBL\\d+$"^^ . + . + . + . + . + . + . + "The bioRxiv is a preprint server for biology"^^ . + "https://cordis.europa.eu/article/id/$1"^^ . + . + . + . + "95-0166C6"^^ . + "^\\w+\\_\\d+(\\.\\d+)?$"^^ . + . + . + "true"^^ . + . + . + . + . . - "2200950"^^ . - . - "A vendor of antibodies and other biologics"^^ . - "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - . - . - "https://toxpilot.nibiohn.go.jp/"^^ . - . - . - "https://www.clinicaltrialsregister.eu/"^^ . - . - . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . - "false"^^ . - . + "16941567"^^ . + . + "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . + "Matt Yoder" . + "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . + . + . + . + . + . + . + "http://drugcentral.org/drugcard/$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml"^^ . + . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . + "https://www.worldwildlife.org/ecoregions/$1"^^ . + "Informed Consent Ontology" . + . + . + "Obstetric and Neonatal Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . + . + "Exposure ontology" . + . + "http://fossilworks.org"^^ . + . + "^PR\\d{5}$"^^ . + "^\\d+$"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/CTO_$1"^^ . + . + . + . + . + . + . + . + "Astrophysics Source Code Library" . + . + "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . + . + . + . + . + . + "false"^^ . + "09200010"^^ . + . + . + "^\\d{8}$"^^ . + . + . + . + . + . + . + "0000001"^^ . + "1017"^^ . + "http://www.kegg.jp/entry/$1"^^ . + . + . + . + . + . + "^([A-Z]+-)?\\d+$"^^ . + "2842"^^ . + . + . + . + . + . + . + . + "Pier Luigi Buttigieg" . + . + "2005080"^^ . + . + . + "false"^^ . + . + "Measurement method ontology" . + . + . + . + "None"^^ . + "T039"^^ . + . + "http://peroxibase.toulouse.inra.fr/"^^ . "^\\w+$"^^ . - . - . - . - . - "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . - . - . - "false"^^ . - . - . - "http://bigg.ucsd.edu/compartments/"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . + . + . + . + . + "THE1B"^^ . + . + . + . + . + . + . + . + . + "LINCS Cell" . + . + . + "Created by researchers and data managers professionals, the FAIR Cookbook is an online resource for the Life Sciences with recipes that help you to make and keep data Findable, Accessible, Interoperable, and Reusable (FAIR).\n\n"^^ . + "^\\d+$"^^ . + "GM17027"^^ . + . + . + . + "http://www.wormbase.org/get?name=$1"^^ . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^ . + . + "C12345"^^ . + "^A[A-Z]+\\d+$"^^ . + . + "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . + . + "InterLex" . + . + . + . + "Digital archive of scholarly articles" . + . + "Catalytic Site Atlas" . + . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to reaction information."^^ . + "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . + . + . + . + . + . + . + "A web-developer centric archive of prefixes and URI prefixes" . + . + . + . + "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . + "NONHSAG00001"^^ . + . + . + . + . + . + . + . + "http://phylomedb.org/?seqid=$1"^^ . + . + "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . + "true"^^ . + . + . + . + . + "Akt_PKB"^^ . + . + "https://rfam.xfam.org/"^^ . + . + . + "MF_01400"^^ . + "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . + "GPST000024"^^ . + . + . + "enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products."^^ . + "iECABU_c1320"^^ . + "http://purl.obolibrary.org/obo/PAO_$1"^^ . + . + . + "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . + . + . + . + "LiceBase" . + . + . + "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . + . + . + "http://www.gabipd.org/"^^ . + . + . + . + . + "0000001"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "https://github.com/flora-phenotype-ontology/flopoontology"^^ . + . + . + "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . + . + "^C\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "BSU29180"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + . + "http://github.com/ga4gh/data-object-service-schemas"^^ . + . + "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "ToxoDB" . + . + . + . + . + . + . + . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . + . + "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + . + . + . + "false"^^ . + . + "BRIP1"^^ . + . + . + . + . + . + . + . + "AB_262044"^^ . + "37232"^^ . + "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . + . + "1044544"^^ . + . + . + . + . + "Brassica ontology" . + . + . + "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . + . + . + . + . + . + . + "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . + . + . + . + . + . + "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_Summary"^^ . + . + . + . + "T0599"^^ . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "Matthew Brush" . + . + . + "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . + . + "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . + . + . + . + . + "http://bgee.unil.ch/bgee/bgee"^^ . + "NucleaRDB" . + . + . + . + "false"^^ . + . + . + . + . + "Curated Drug-Drug Interactions Database - Interaction" . + . + "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . + "https://www.nextprot.org/term/FA-$1"^^ . + . + . + . + "https://bdsc.indiana.edu/about/mission.html"^^ . + . + . + . + . + "Charles Ettensohn" . + "0007133"^^ . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm"^^ . + . + . + . + . + "Common Access to Biological Resources and Information Project" . + . + "false"^^ . + . + "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . + . + . + "00050"^^ . + "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "DDInter20"^^ . + . + . + . + . + . + . + "^\\d{7}(_\\d)?$"^^ . + . + "https://prefix.cc/$1" . + . + "^\\d+$"^^ . + . + . + . + "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . + . + . + . + . + . + . + "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . + . + . + . + "RNA Modification Database" . + "74"^^ . + . + . + "Os01g0883800"^^ . + . + . + "Uberon Property" . + . + . + . + . + . + . + . + "http://antibodyregistry.org/"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=unists"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "BAC045"^^ . + . + . + "^\\d+$"^^ . + . + "Mungbean ontology" . + . + . + . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + . + . + . + . + "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . + . + . + "false"^^ . + . + "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . + . + . + "https://covid19.sfb.uit.no/api/records/$1"^^ . + "^\\d+$"^^ . + "false"^^ . + . + "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . + "http://www.ymdb.ca/compounds/$1"^^ . + . + . + . + "^[CD]\\d+$"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . + "https://www.genome.jp/kegg/ligand.html"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/FBcv_$1"^^ . + "^\\d+$"^^ . + . + "false"^^ . + "International Standard Name Identifier" . + "^\\d+$"^^ . + . + . + . + "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . + . + . + . + . + . + "Sequencing Initiative Suomi" . + . + . + . + . + . + . + "^[8-9]\\d{3}(/[0-3])?$"^^ . + . + . + . + "0001021"^^ . + . + . + . + . + "5601141"^^ . + . + "3355"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . + . + "https://www.dataone.org"^^ . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "Phenol-Explorer" . + "https://www.enzolifesciences.com/$1"^^ . + . + "https://aopwiki.org/relationships/$1"^^ . + . + "https://www.biorxiv.org/content/10.1101/$1"^^ . + . + "https://code.google.com/p/craniomaxillofacial-ontology/"^^ . + . + . + "^\\d{7}$"^^ . + . + "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . + . + . + . + . + . + "https://www.vectorbase.org/ontology-browser"^^ . + "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . + "false"^^ . + "https://www.google.com/patents/"^^ . + . + "https://www.ncbi.nlm.nih.gov/gene"^^ . + . + "Close to 5K Categorizations for drugs, similar to ATCC."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000088"^^ . + . + . + "false"^^ . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "01406"^^ . + "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . + "The SugarBind Database captures knowledge of glycan binding of human pathogen lectins and adhesins, where each glycan-protein binding pair is associated with at least one published reference. It provides information on the pathogen agent, the lectin/adhesin involved, and the human glycan ligand. This collection provides information on ligands."^^ . + "DICOM Controlled Terminology" . + "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . + "https://www.alliancegenome.org/accession/$1"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/IAO_$1"^^ . + "https://github.com/pato-ontology/pato/"^^ . + . + . + "^[0-9]+$"^^ . + . + . + "https://eol.org"^^ . + . + . + . + . + . + . + "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . + . + . + "false"^^ . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + _:Nbbb5805961a642eeaa98e85edf81b16d . + . + . + . + "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . + . + "^\\d+$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/ido/terms?obo_id=IDO:$1"^^ . + . + . + . + "Citation Typing Ontology" . + . + . + . + . + "http://repository.topdownproteomics.org/proteoforms"^^ . + . + . + . + . + "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references chicken QTLs."^^ . + "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . + . + . + . + "Bgee stage" . + . + . "https://www.uniprot.org/uniref/$1"^^ . - . - . - . - "appears in" . - . - . - . - "0000005"^^ . - "true"^^ . - "false"^^ . - "SSF57615"^^ . - . - . - . - . - . - . - . - "^DP\\d{5}$"^^ . - . - . - . - . - . - . - . - "Span" . - "^\\d+$"^^ . - . - . -_:N2ba76a60509f4cf5aa3ae43fc1644a26 "eVOC mailing list" . - . - . - "http://4dx.embl.de/platy"^^ . - . - . - . - . - "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . - . - . - "Open Citation Identifier" . - . - . - "March 2017 version "^^ . - . - "https://biopragmatics.github.io/debio"^^ . - "Multiple alignment" . - "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . - . - . - . - . - . - "http://www-deletion.stanford.edu/YDPM/"^^ . - . - "false"^^ . - . - . - . - . - . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - "false"^^ . - "^SEQF\\d+$"^^ . - . - . - "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . - "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . - "^[WAICV]\\d{2,}$"^^ . - . - "Cell Lines Service" . - . - . - "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . - . - . - . - . - . - "IntellectualContribution"^^ . - . - "snoRNABase" . - "SCV000151292"^^ . - . - "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . - . - . - "YRC PDR" . - . - "0000001"^^ . - . - . - "^A\\d+$"^^ . - . - . - "https://www.itis.gov/"^^ . - . - . - . - . - . - . - "^ENSGT\\d+$"^^ . - "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . - . - . - . - "false"^^ . - "false"^^ . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . - "false"^^ . - . - "81944ba1-81d0-436e-8552-33d77a27834b"^^ . - . - . - "Charles Tapley Hoyt" . - "https://flybrain-ndb.virtualflybrain.org"^^ . - . - . - . - "BioAssay Ontology" . - . + "^\\d+$"^^ . + "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . + "https://urgi.versailles.inra.fr/gnpis/"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "Yuki Yamagata" . + . + . + . + . + "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . + . + . + "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . + . + "http://www.genome.jp/kegg/genes.html"^^ . + . + . + . + . + . + "http://www.t3db.org/toxins/$1"^^ . + "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . + "Ax1"^^ . + "MolBase" . + . + . + "SysBioCancer2022"^^ . + . + . + . + "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . + . + . + . + . + . + . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . + . + "https://bio.tools/"^^ . + . + . + . + . + . + . + "Environment Ontology" . + . + . + "5fde96bdc5f1aa9ff0cce18a"^^ . + . + . + . + . + "0101963"^^ . + "^[a-z0-9\\_]+$"^^ . + . + . + . + . + "https://github.com/github/linguist"^^ . + . + . + "0000564"^^ . + . + . + "RCB0002"^^ . + . + "COc1ccc2c(c1)OC[C@H]1[C@@H]2C2=C(OC1(C)C)C1=C(C(=O)C2=O)[C@H]2c3ccc(OC)cc3OC[C@H]2C(C)(C)O1"^^ . + . + "GCA_000155495.1"^^ . + "false"^^ . + "http://www.informatics.jax.org/"^^ . . - "https://link.springer.com/bookseries/562"^^ . - . - . - "NONCODE v3" . - . - "^SIGNOR-\\d+$"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/chembl"^^ . - . - . - . - . - . - . - . - . - "63"^^ . - . - . - . - . - . - . - . - . - . + . + . + "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . + . + . + . + . + . + "https://horizondiscovery.com/en/search?searchterm=$1"^^ . + . + . + . + . + . + . + . + . + . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "^c\\d+$"^^ . + . + "https://w3c-ccg.github.io/did-spec/"^^ . + . + "biopragmatics/bioregistry/424"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "http://ciliate.org/index.php/"^^ . + "false"^^ . + "false"^^ . + "RAP-DB Transcript" . + "MultiCellDS Digital snapshot" . + . + . + . + "KEGG Genes" . + . + "NCBI Taxonomy" . + "NIF Standard Ontology: Organisms" . + . + . + . + . + "An ontology to describe entities related to cardiovascular diseases"^^ . + . + . + . + "19803"^^ . + . + "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . + . + "Daniel Himmelstein" . + "HIX0004394"^^ . + . + . + "PjrpzUIAAAAJ"^^ . + . + "DG00301"^^ . + . + "http://www.hipsci.org"^^ . + "https://kaggle.com"^^ . + . + . "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/UBERON_$1"^^ . - . - . - . - . - "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - "00020007"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - "OSR00185W"^^ . - . - . - . - . - . - . - . - . - . - . - . - "MNXM1723"^^ . - "false"^^ . - . - "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . - . - "http://bcrj.org.br/celula/$1"^^ . - . - . - . - . - . - . - . - "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . - "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . - . - "A language for validating RDF graphs against a set of conditions"^^ . - . - . - . - . - . - . - . - . - "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . - . - "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . - "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . - . - . - . - "^\\d{7}$"^^ . - "COSMIC Cell Lines" . - "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . - . - . - . - . + "SNHG3"^^ . + . + . + . + "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . + . + . + "^\\d+$"^^ . + . + . + . + "https://vcell.org/biomodel-$1"^^ . + "December 2019"^^ . + "https://www.uniprot.org/journals"^^ . + "hsa00190"^^ . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + . + . + . + "http://bioinfo.iitk.ac.in/MIPModDB"^^ . + "false"^^ . + . + . + . + "Costal and Marine Ecological Classification Standard" . + "^\\d{7}$"^^ . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references yeast."^^ . + . + "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species."^^ . + . + . + "BioCyc collection of metabolic pathway databases" . + "http://www.inoh.org"^^ . + . + "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + "false"^^ . + . + . + . + "OpenCitations Corpus" . + . + . + . + . + . + . + . + . + "Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output."^^ . + . + . + "https://knowledge.lonza.com/cell?id=$1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "https://hpo.jax.org/app/browse/term/HP:$1"^^ . + . + . + . + "^LRG_\\d+$"^^ . + "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . + . + . + "false"^^ . + . + . + . + . + "0000013"^^ . + . + "Applied Biological Materials cell line products" . + . + "J55.713G"^^ . + . + . + . + . + . + "Ontology Lookup Service" . + . + . + . + "http://www.semantic-systems-biology.org/apo"^^ . + . + "0000005"^^ . + . + "Protein Model Database" . + "1004" . + . + . + "LMPR0102010012"^^ . + . + . + . + . + . + "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . + . + . + . + "HOSAPI0399"^^ . + . + . + "ChemDB" . + "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . + . + . + "Cross-linker reagents ontology" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "https://bioregistry.io/schema"^^ . + . + . + . + "true"^^ . + . + . + "identifier for a scientific journal, in the UniProt database"^^ . + . + "^\\d+$"^^ . + . + . + "http://purl.org/dc/dcmitype/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . + . + "false"^^ . + "^\\d+$"^^ . + "http://www.evoio.org/wiki/MIAPA"^^ . + . + . + . + "Chicken Gene Nomenclature Consortium" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . + . + . + . + . + . + "^DAP\\d+$"^^ . + "http://purl.obolibrary.org/obo/CLAO_$1"^^ . + . + "GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55,000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55,000 probes represent well annotated, full length, and partial human gene sequences from major public databases. GE Healthcare/Amersham Biosciences CodeLink? Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release)."^^ . + . + "https://www.ebi.ac.uk/pdbe/emdb/"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "Golm Metabolome Database Reference Substance" . + . + . + "^[A-Za-z 0-9]+$"^^ . + . + "Integrated Microbial Genomes Gene" . + . + . + . + "http://purl.obolibrary.org/obo/CMO_$1"^^ . + . + "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . + . + . + "Yongqunh He" . + . + "0001350"^^ . + "75"^^ . + . + . + . + . + . + . + . + . + . + . + "Vocabulary used in the RDF representation of SBML models."^^ . + "Lutz Fischer" . + . + . + . + "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . + . + . + . + . + . + "Agricultural Online Access" . + "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . + . + . + "http://purl.obolibrary.org/obo/EV_$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "VGNC:3792"^^ . + "JRBC Cell Bank" . + . + . + . + "00000001"^^ . + . + "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . + . + . + "5HT3Arano"^^ . + . + "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . + . + . + . + . + . + "^BE\\d{7}$"^^ . + . + . + "NA06985"^^ . + . + . + . + . + . + . + "false"^^ . + "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . + . + . + . + "false"^^ . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + "CL0192"^^ . + "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . + . + . + "NCI Pathway Interaction Database: Pathway" . + "TGME49_053730"^^ . + "GLIDA Ligand" . + "0174" . + . + "false"^^ . + . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . + . + . + . + "The Topology Data Bank of Transmembrane Proteins (TOPDB) is a collection of transmembrane protein datasets containing experimentally derived topology information. It contains information gathered from the literature and from public databases availableon transmembrane proteins. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases."^^ . + "https://worldwide.espacenet.com/classification"^^ . + "Human Unidentified Gene-Encoded" . + "http://www.w3.org/2000/01/rdf-schema#$1"^^ . + . + . + . + "2170610"^^ . + "MHC Restriction Ontology" . + . + . + . + . + . + . + . + "Ontology of Biological and Clinical Statistics" . + "PRIDE Controlled Vocabulary" . + "Bioregistry Schema" . + "^\\d{7}$"^^ . + . + "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . + "P53350"^^ . + "false"^^ . + "false"^^ . + . + . + "FAIRsharing Subject Ontology" . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^M\\d{5}$"^^ . + . + . + "TTDS00056"^^ . + . + . + "canal"^^ . + . + . + "https://www.ebi.ac.uk/pride/"^^ . + . + . + . + . + . + "true"^^ . + . + "^.+$"^^ . + . + . + "https://github.com/HajoRijgersberg/OM"^^ . + . + . + . + . + "https://sumlineknowledgebase.com/?page_id=$1"^^ . + . + . + . + . + . + . + "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . + . + . + . + . + "false"^^ . + "KC-0979"^^ . + "http://www.gramene.org/"^^ . + "http://purl.obolibrary.org/obo/OBA_$1"^^ . + . + "https://github.com/obophenotype/c-elegans-gross-anatomy-ontology"^^ . + "http://cerevisiae.oridb.org/index.php"^^ . + . + . + . + . + "^TTDS\\d+$"^^ . + "75"^^ . + . + "http://aber-owl.net/ontology/$1/#/Browse/" . + "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . + . + . + "1731"^^ . + . + "0745-4570"^^ . + . + . + "http://purl.obolibrary.org/obo/EMAP_$1"^^ . + "Drosophila RNAi Screening Center" . + . + "ProtoNet Cluster" . + . + "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + "https://www.proteomicsdb.org/#human"^^ . + . + . + . +_:N7b59c458f6594259b5c01f83c7244ec1 "Jonathan Bard" . + . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + "^MIRT\\d{6}$"^^ . + . + . + . + . + . + "International Classification of Diseases for Oncology" . + . + "NAD%20biosynthesis"^^ . + . + . + . + "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . + . + . + . + . + "P00024"^^ . + "Cellosaurus Registry" . + . + _:N01ec5917f175401382cf32118f4788a1 . + . + "Vertebrate Gene Nomenclature Committee" . + "Meghan Balk" . + . + "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . + . + . + . + . + . + "http://www.kegg.jp/kegg/module.html"^^ . + . +_:N2ce010b595fb47858314c144c196f4be "InterPro Help" . + . + "true"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . + "https://github.com/phenoscape/teleost-taxonomy-ontology"^^ . + . + . + "fluticasone"^^ . + . + . + "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "AICARTRANSIMPCYCLO-CPLX"^^ . - . - . - . - . - "7123"^^ . - . - . - "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . - . - . - . - . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/medgen/"^^ . - "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . - . - . - . - . - . - "MicrobeamManipulation"^^ . - "C023"^^ . - "false"^^ . - "Natural Product-Drug Interaction Research Data Repository" . - "^\\d{7}$"^^ . - "http://www.york.ac.uk/"^^ . - . - . - . - "^[A-Z]\\d+(\\.[-\\d+])?$"^^ . - . - . - . - . - . - "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . - "HGVM15354"^^ . - "^\\d+$"^^ . + . + "CellBank Australia collects novel cell lines, developed by Australian researchers, submits these cell lines to rigorous testing to confirm their integrity, and then distributes the cell lines to researchers throughout the world."^^ . + . + . + . + . + . + "Brian Aevermann" . + "^G[0-9]{5}[A-Z]{2}$"^^ . + . + "LK99"^^ . + . + . + . + "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . + . + . + "Animal Genome QTL" . + "http://research.amnh.org/atol/files/"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "https://www.wormbase.org/get?name=$1"^^ . + . + . + . + . + . + . + "Europe PMC Preprints" . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + . + . + . + _:N2ce010b595fb47858314c144c196f4be . + "^\\d{7}$"^^ . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/XL_$1"^^ . +_:N25c06a6dd2664015838bd96124c9e999 "eVOC mailing list" . + . + . + . + . + . + . + . + . + . + "H3.03.00.0.00007"^^ . + "Adverse Event Reporting Ontology" . + . + "^CHEMBL\\d+$"^^ . + "Cell line collections"^^ . + "^\\d+$"^^ . + "http://swift.cmbi.kun.nl/swift/hssp/"^^ . + . + . + "https://www.omim.org/phenotypicSeriesTitles/all"^^ . + "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . + "AT1G01030.1"^^ . + . + . + . + . + . + . + . + "Antibody Registry" . + "https://odc-tbi.org"^^ . + . + . + . + "^\\d{7}$"^^ . + "GL50803_102438"^^ . + "National Bibliography Number" . + "false"^^ . + . + . + . + . + . + . + "000000341"^^ . + . + . + "HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers."^^ . + . + . + . + "COG Categories" . + "046"^^ . + . + . + "virsi1909"^^ . + . + "European Food Information Resource Network" . + "http://purl.obolibrary.org/obo/ONS_$1"^^ . + "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Leszek Vincent" . + "5.A.1.1.1"^^ . + . + "UCR00226"^^ . + "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . + . + . + "^DBSALT\\d{6}$"^^ . + "GeoNames" . + . + . + . + . + . + "https://catalog.bcrc.firdi.org.tw"^^ . + "^D\\d+$"^^ . + . + "http://www.genenames.org"^^ . + . + . + "false"^^ . + "https://sed-ml.org/urns.html#format:$1"^^ . + "true"^^ . + . + . + "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . + "Taxonomic rank vocabulary" . + . + . + . + "http://scipion.i2pc.es/ontology/cryoem"^^ . + . + "http://xmlns.com/foaf/spec/"^^ . + . + . + "Cell line databases/resources"^^ . + . + . + "^Os\\S+t\\d{7}-\\d{2}$"^^ . + . + . + "^H\\d+$"^^ . + . + "http://pathway.yeastgenome.org/"^^ . + "vcell"^^ . + "SCC111"^^ . + . + "http://lincsportal.ccs.miami.edu/SmallMolecules/"^^ . + . + "https://www.ebi.ac.uk/interpro/entry/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . + "https://www.cropontology.org/rdf/CO_337:$1"^^ . + . + "The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the nightshade family, which includes species such as tomato, potato, pepper, petunia and eggplant."^^ . + . + . + . + . + "CAA71118.1"^^ . + "false"^^ . + "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . + . + "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . + . + "Radiomics Ontology" . + . + "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . + . + . + . + . + . + . + . + . + . + . + "0005452"^^ . + . + . + . + "false"^^ . + . + . + . + . + "https://cameo3d.org"^^ . + . + "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . + . + "https://www.disprot.org/$1"^^ . + "https://www.thermofisher.com/antibody/product/$1"^^ . + "false"^^ . + . + . + . + "0000003"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "0000194"^^ . + . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + "^\\d{7}$"^^ . + "^(data|topic|operation|format)\\_\\d{4}$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "A manually curated resource for the representation and annotation of metabolic pathways"^^ . + . + . + . + . + "0000144"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . + "Snapshot" . + . + . + . + "http://www.sparontologies.net/ontologies/scoro"^^ . + "^\\d+$"^^ . + . + . + . + "^\\d{7}$"^^ . + "LINCS Data" . + "https://www.worldcat.org/oclc/$1"^^ . + . + . + . + . + . + "Rv1908c"^^ . + . + "false"^^ . + . + . + . + . + "0440"^^ . + . + "NBK331"^^ . + . + . + . + . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . + . + . + . + "false"^^ . + "^TF\\w+$"^^ . + "false"^^ . + . + . + "Nucleic Acids Phylogenetic Profiling" . + . + . + "false"^^ . + . + "https://www.bio.di.uminho.pt/"^^ . + . + "ArrayGroup"^^ . + . + "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . + "http://purl.obolibrary.org/obo/TAHH_$1"^^ . + "2966"^^ . + "NodeShape"^^ . + "false"^^ . + . + . + . + . + "Addgene Plasmid Repository" . + . . - "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"^^ . - . - . - "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^ . - "Computer Retrieval of Information on Science Projects Thesaurus" . - . - . - . - . - "Gemina Symptom Ontology" . - . - "A type for entries in the Bioregistry's registry." . - . - . - "Five Stars of Online Research Articles Ontology" . - "^XB\\-\\w+\\-\\d+$"^^ . - . - . - . - "true"^^ . - "EP0311"^^ . - . - . - . - . - "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . - "Ontology of Arthropod Circulatory Systems" . - "prefLabel"^^ . - . - . - . - . - . - . - . - "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^ . - "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . - . - . - "http://planttfdb.cbi.pku.edu.cn"^^ . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . - "^T[A-Z]\\d{7}$"^^ . - . - "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1"^^ . - . - . - . - . - . - . - . - . - "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "603903"^^ . - "AHR"^^ . - . - . - "ICARDA - TDv5 - Sept 2018"^^ . - . - . - . - . - . - . - . - "2404"^^ . - . - "Bioregistry" . - "false"^^ . - "https://datanator.info/reaction/$1"^^ . - . - "1cukA01"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - "http://www.maizegdb.org/"^^ . - "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . - "false"^^ . - . - . - . - . - . - "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . - . - . - "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . - "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . - . - "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . - "true"^^ . - . - "https://knowledge.lonza.com"^^ . - "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . - . - . - . - . - . - "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - "Cell line databases/resources"^^ . - "00000098"^^ . - "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - . - "Wes Schafer" . - . - . - "http://purl.obolibrary.org/obo/ARO_$1"^^ . - . - . - . - . - "false"^^ . - . - "Tissue List" . - "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . - . - "https://biosimulators.org/"^^ . - . - . - "^[1-9]\\d{0,6}$"^^ . - . - . - "https://bioregistry.io/schema"^^ . - . - . - . - . - "^[A-Z]{6}(\\d{2})?$"^^ . - . - "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . - "https://www.glycoepitope.jp/epitopes/$1"^^ . - "An ontology to standardize research output of nutritional epidemiologic studies."^^ . - . - "false"^^ . - . - . - "https://pav-ontology.github.io/pav/"^^ . - "https://flybase.org/reports/FBtc$1"^^ . - . - . - . - . - . - . - "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . + . + "COG0001"^^ . + . + . + . + "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . + . + . + . + "false"^^ . + . + . + . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This provides protein information for a given gene model and provides links to other sources such as UniProtKB and GenPept"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . + . + . + "1000290"^^ . + "MGnify Sample" . + . + . + "https://smid-db.org/"^^ . + "TopFIND is a database of protein termini, terminus modifications and their proteolytic processing in the species: Homo sapiens, Mus musculus, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli."^^ . + . + . + . + . + . + . + . + "CIViC Assertion" . + "172"^^ . + . + "ala"^^ . + . + . + . + . +_:N5bee6a16e0df451ea1b8859d30049123 "Jonathan Bard" . + . + "^\\d{7}$"^^ . + . + "false"^^ . + "0000005"^^ . + . + . + . + . + "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . + "false"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/"^^ . + . + "System Science of Biological Dynamics dataset" . + "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . + . + . + "Yongqun Oliver He" . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + . + . + . + . + . + . + "http://pax-db.org/"^^ . + "Degradome Database" . + . + . + . + . + "^\\d+$"^^ . + . + "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . + "http://www.protonet.cs.huji.ac.il/"^^ . + . + . + . + . + . + "true"^^ . + . + "http://edamontology.org/data_$1" . + "S-EPMC6266652"^^ . + . + "Olfactory Receptor Database" . + . + . + . + . + "https://cropontology.org/ontology/CO_326/Coconut"^^ . + . + . + . + . + . + . + . "Identifier for a journal article in the fossilworks website"^^ . - . - "Cell line collections"^^ . - . - . - . - . - "false"^^ . - "^M[0-9]{4,}$"^^ . + . + . + "APID Interactomes" . + "https://github.com/aellenhicks/htn_owl"^^ . + "NX_O00165"^^ . + "false"^^ . + . + . + . + _:Nb4b44e0828c943bfbebdd12972a19af7 . + "^\\d{7}$"^^ . + . + "0000609"^^ . + . + . + . + "BARC-013845-01256"^^ . + . + . + "https://www.geonames.org"^^ . + . + . + . + . + . + "http://intron.ucsc.edu/yeast4.3/"^^ . + "https://bioportal.bioontology.org/" . + . + . + . + . + "HOGENOM is a database of homologous genes from fully sequenced organisms (bacteria, archeae and eukarya). This collection references phylogenetic trees which can be retrieved using either UniProt accession numbers, or HOGENOM tree family identifier."^^ . + . + . + . + . + "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . + "^\\w+$"^^ . + . + "Cu.me.I1"^^ . + . + "Database of Complete Genome Homologous Genes Families" . + . + . + . + "65"^^ . + . + . + . + . + . + "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . + . + . + . + . + . + . + . + . + "https://www.imanislife.com/collections/cell-lines/"^^ . + . + "2.1.1"^^ . + "http://compluyeast2dpage.dacya.ucm.es/"^^ . + . + . + . + "15000"^^ . . - . - . - "Description of Plant Viruses" . - . - . - "false"^^ . - . - "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . - "The National Center for Advancing Translational Sciences](http://www.ncats.nih.gov/) (NCATS) has developed Inxight Drugs as a comprehensive portal for drug development information. NCATS Inxight Drugs contains information on ingredients in medicinal products, including:\n\n- US Approved Drugs\n- Marketed Drugs\n- Investigational Drugs\n- Other Substances"^^ . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . - . - . - . - "4.2.78"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + _:N0597ed38091d45928f0fa91cf0458b61 . + . + . + . + "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . + . + . + "false"^^ . + "1122888"^^ . + . + . + . + . + . + . + . + . + "Oryzabase Gene" . + . + . + . + "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . + . + . + . + "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . + . + . + . + "https://www.gleif.org/"^^ . + "Alayne Cuzick" . + "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . + . + "https://pathbank.org"^^ . + . + . + . + . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . + "The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. This collection pertains to specifications of the standard formats developed by the Computational Modeling in Biology Network."^^ . + . + . + "https://datacite.org"^^ . + . + . + . + . + "KG09531"^^ . + "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + . + . + . + . + "BioContext" . + "PharmacoDB Cells" . + "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms."^^ . + . + . + . + . + . + . + . + . + "http://sabiork.h-its.org/"^^ . + . + . + . + . + . + . + "http://viaf.org"^^ . + . + "false"^^ . + "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . + . + . + "Global LEI Index" . + . + . + "Database of human Major Histocompatibility Complex" . + . + . + "^\\w+$"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/"^^ . + . + "A10BA02"^^ . + . + . + . + . + . + . + . + . + . + "0011140"^^ . + . + . + . + "false"^^ . + "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . + "NIF Standard Ontology: OEN Terms in Neurolex" . + "^\\d{8}$"^^ . + . + "DIP-743N"^^ . + . + . + "FooDB is resource on food and its constituent compounds. It includes data on the compound’s nomenclature, its description, information on its structure, chemical class, its physico-chemical data, its food source(s), its color, its aroma, its taste, its physiological effect, presumptive health effects (from published studies), and concentrations in various foods. This collection references compounds."^^ . + "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . + . + . + . + _:N8020408e4b514ad0b734401375de1070 . + . + "Cell Lines Service" . + . + . + "false"^^ . + . + "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . + . + . + . + . + . + . + . + . + . + "LOTUS Initiative for Open Natural Products Research" . + "http://omia.angis.org.au/"^^ . + . + "European Searchable Tumour Line Database" . + . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/projects/RefSeq/"^^ . + . + . + . + "^[A-Z]+$"^^ . + . + . + "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . + . + . + "false"^^ . + . + . + . + "http://purl.org/spar/datacite/$1"^^ . + . + "http://purl.bioontology.org/ontology/STY/$1"^^ . + . + . + . + "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . + . + . + . + . + . + . + . + . + "Citation Counting and Context Characterisation Ontology" . + . + "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^\\d{4}$"^^ . + . + . + "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . + "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . + . + . + . + "http://trichdb.org/trichdb/"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "Ligand-Gated Ion Channel database" . + . + "true"^^ . + . + "Genitourinary Development Molecular Anatomy Project" . + . + . + . + . + . + . + . + "Ensembl Bacteria" . + . + . + "https://github.com/AnimalGenome/livestock-product-trait-ontology"^^ . + . + "Ontology of rat strains"^^ . + "http://purl.obolibrary.org/obo/STATO_$1"^^ . + . + . + . + . + . + . + . + "^\\w+$"^^ . + "^UPI[A-F0-9]{10}$"^^ . + . + . + . + . + . + . + . + "Social Behavior in insects"^^ . + . + . + . + . + . + . + . + "http://www.chemspider.com/"^^ . + . + "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . + "Bio-MINDER Tissue Database" . + . + . + . + . + . + "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . + "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . + "IM-19210-3"^^ . + . + "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . + . + . + "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . + . + . + "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . + . + . + "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . + "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx"^^ . + "^DB\\d{5}$"^^ . + . + . + "false"^^ . + "^\\d+$"^^ . + "https://uniresolver.io/#did:$1"^^ . + "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . + . + . + . + . + . + "http://www.isni.org"^^ . + . + . + . + "^[SCTAGMNU]\\d+$"^^ . + . + . + . + "false"^^ . + . + "1174"^^ . + "false"^^ . + . + "PhylomeDB" . + "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . + . + . + . + . + "688"^^ . + . + "NCI Metathesaurus (NCIm) is a wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. It integrates terms and definitions from different terminologies, including NCI Thesaurus, however the representation is not identical."^^ . + . + "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . + . + . + . + "Jennifer Smith" . + "SABIO Reaction Kinetics" . + . + . + . + "Tom Gillespie" . + . + "Database of Aligned Ribosomal Complexes" . + . + "true"^^ . + . + . + . + "https://github.com/monarch-initiative/SEPIO-ontology"^^ . + . + . + . + "https://lincs.hms.harvard.edu/db/sm/"^^ . + . + . + . + . + "false"^^ . + . + . + "Quantities, Units, Dimensions, and Types Ontology" . + . + "Mathematical modeling ontology" . + "BRENDA Ligand Group" . + . + . + . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + "Basic Formal Ontology" . + . + . + "http://purl.obolibrary.org/obo/MICRO_$1"^^ . + . + . + . + . + "https://prefixcommons.org"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "https://metazoa.ensembl.org/"^^ . + "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . + "0000288"^^ . + . + "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . + . + . + . + . + "100000000000001"^^ . + . + . + "false"^^ . + "Human Cell Atlas Ontology" . + . + . + "false"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . + . + "false"^^ . + "14"^^ . + . + . + . + . + . + . + . + . + . + . + "Ontology about the gross anatomy of the C. elegans"^^ . + "https://www.ohdsi.org/data-standardization/the-common-data-model/"^^ . + . + "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . + . + . + . + "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . + . + "GrassBase" . + . + . + . + . + "https://github.com/insect-morphology/colao"^^ . + "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . + "21393"^^ . + "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . + . + . + . + . + "STUDY1040"^^ . + "ValidatorDB" . + "1050"^^ . + . + . + "true"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . + . + . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . + . + . + . + "COVID-19 Surveillance Ontology" . + "BioLegend" . + "David Osumi-Sutherland" . + . + "A vendor of antibodies and other biologics"^^ . + "http://ecmdb.ca/compounds/$1"^^ . + . + . + . + . + . + . + . + . + "1h68"^^ . + . + . + . + . + . + "true"^^ . + . + "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . + . + . + . + . + . + . + . + . + "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . + . + . + "0001290"^^ . + . + "LNCipedia" . + . + . + . + . + . + "Zebrafish anatomy and development ontology" . + . + . + "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . + "true"^^ . + . + . + . + . + "W2741809807"^^ . + . + . + . + . + . + "true"^^ . + "https://www.gsea-msigdb.org"^^ . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + . + . + . + . + . + . + "Integrated Canine Data Commons" . + . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . + "Ontology for Biomedical Investigations" . + . + . + "Illumina Probe Identifier" . + "true"^^ . + "Saccharomyces genome database pathways" . + . + "2008-005144-16"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "U49845"^^ . + . + . + . + . + . + "Multum MediSource Lexicon" . + . + . + . + "false"^^ . + . + . + "^SL-\\d+$"^^ . + "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . + . + . + "false"^^ . + . + "1000001"^^ . + "false"^^ . + . + "provides for" . + . + . + "false"^^ . + . + . + . + "H-InvDb Transcript" . + . + . + "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . + . + . + "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . + . + . + "000140" . + . + . + . + . + . + "000410"^^ . + . + . + "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . + "^\\d{7}$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "MaizeGDB Locus" . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + "https://winter.group.shef.ac.uk/molbase/"^^ . + "https://proteinensemble.org/"^^ . + . + . + . + . + . + "ClassyFire" . + . + . + "NIH HIV Reagent Program" . + . + . + . + . + . + "https://nci-crdc.datacommons.io/"^^ . + "false"^^ . + "false"^^ . + . + "https://www.cropontology.org/rdf/CO_346:$1"^^ . + . + . + . + "Drivers of human diseases including environmental, maternal and social exposures."^^ . + "bioregistry"^^ . + . + "false"^^ . + "https://github.com/MPIO-Developers/MPIO"^^ . + . + . + "RDF"^^ . + . + . + "0000690"^^ . + "iRefWeb" . + "^\\d{8}$"^^ . + . + "false"^^ . + . + "https://github.com/ohmi-ontology/ohmi"^^ . + . + . + . + . + . + "DATF contains known and predicted Arabidopsis transcription factors (1827 genes in 56 families) with the unique information of 1177 cloned sequences and many other features including 3D structure templates, EST expression information, transcription factor binding sites and nuclear location signals."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.animalgenome.org"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . + "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . + . + . + . + . + "^EBI\\-[0-9]+$"^^ . + "https://github.com/micheldumontier/semanticscience"^^ . + "LSM-6306"^^ . + . + . + . + . + . + "^\\w+$"^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "http://www.bioinfo.org/NONCODEv4/"^^ . + "288"^^ . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/$1"^^ . + . + "MarRef" . + . + . + . + . + . + "BioLegend is a life sciences supply vendor."^^ . + "Zach Landis-Lewis" . + . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "NCI Data Commons Framework Services" . + "An ontology for the description of Drosophila melanogaster phenotypes."^^ . + . + . + . + "https://github.com/rsc-ontologies/rxno"^^ . + . + "The web-based FAIRSharing catalogues aim to centralize bioscience data policies, reporting standards and links to other related portals. This collection references bioinformatics data exchange standards, which includes 'Reporting Guidelines', Format Specifications and Terminologies."^^ . + . + . + . + . + "http://www.informatics.jax.org/expression.shtml"^^ . + . + "^[A-Z-_0-9]+$"^^ . + . + . + "Sue Bello" . + "http://www.genoscope.cns.fr/agc/microscope"^^ . + "false"^^ . + "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + . + . + . + "NeuroNames" . + . + "ChEBI"^^ . + "false"^^ . + "https://www.cbioportal.org/study/summary?id=ccle_broad_2019"^^ . + . + . + . + . + "0007114"^^ . + . + "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . + . + . + . + . + . + "has resolver formatter" . + . + . + . + . + "ERM00000044"^^ . + . + . + . + . + . + . + . + . + . + "http://doqcs.ncbs.res.in/"^^ . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "Genomic Data Commons Data Portal" . + . + . + "^\\d{7}$"^^ . + . + . + "SEED Compound" . + . + . + . + . + . + . + . + . + "OntoBee" . + "false"^^ . + . + . + "GiardiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + "Uber Anatomy Ontology" . + . + . + . + . + "false"^^ . + . + . + . + . + . + "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . + . + "false"^^ . + . + "DAP000773"^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . + "https://health.uconn.edu/"^^ . + . + . + "https://www.wikidata.org/"^^ . + . + . + "https://cells.ebisc.org/$1"^^ . + . + . + . + . + . + . + "false"^^ . + "4000027"^^ . + . + "^[A-Za-z0-9]+$"^^ . + "Allyson Lister" . + . + . + "https://sorgerlab.github.io/famplex/$1"^^ . + . + . + "Hymenoptera Anatomy Ontology" . + . + "A pull request in any public repository on GitHub."^^ . + . + "NIF Standard Ontology: External" . + "https://orcid.org"^^ . + . + "Cellosaurus Publication" . + "http://www.ncbi.nlm.nih.gov/CCDS/"^^ . + . + "BugBase Expt" . + "http://www.sparontologies.net/ontologies/frapo"^^ . + . + "http://cutdb.burnham.org"^^ . + . + "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . + "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . + . + . + . + . +_:N5fed7daf26c145b8b2a06ae29999a945 "Adrien Coulet" . + . + . + . . - "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . - "^\\d{8}$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/HOM_$1"^^ . - . - . - . - . - . - . - . - . - "Variants in dbVar."^^ . - . - . - "^L\\d+$"^^ . - . - . - . - . - . - "http://www.proglycprot.org/"^^ . - . - "https://bitbucket.org/$1"^^ . - . - . - . - . - "Terms from the source appear in the target resource" . - "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . - . + "true"^^ . + . + . + . + . + "https://bgee.org/"^^ . + . + . + . + "Bioinformatics operations, data types, formats, identifiers and topics" . + . + "Neuronal cell types"^^ . + "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . + . + . + . + . + . + . + "Pazar Transcription Factor" . + . + . + . + "Agilent Probe" . + . + "^\\d+$"^^ . + . + . + . + "Cell line collections"^^ . + . + "1100107"^^ . + . + . + . + . + "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + "http://neuinfo.org/"^^ . + . + . + "http://purl.obolibrary.org/obo/ZEA_$1"^^ . + . + "^Rv\\d{4}(A|B|c)?$"^^ . + . + "false"^^ . + . + . + . + "http://www.w3.org/2001/XMLSchema"^^ . + "false"^^ . + . + . + . + . + . + "NPC139585"^^ . + "MIPModDB" . + "EDAM Operation" . + . + "https://loinc.org/"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "Antibiotic Resistance Ontology" . + . + "Information for ligand groups (chemical classes)."^^ . + . + "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . + . + . + "false"^^ . + . + . + . + "300108/p3934_A-172"^^ . + . + . + "^BG\\d+$"^^ . + "4D Nucleome Data Portal Biosource" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . + . + "^\\d{5}$"^^ . + . + . + . + "false"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "https://www.rhea-db.org/rhea/$1"^^ . + "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . + "^\\d{7}$"^^ . + . + "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . + . + "https://www.fisheries.noaa.gov/species-directory"^^ . + . + "Decentralized Biomedical Ontology" . + . + . + . + . + "^\\d+$"^^ . + "BacMap Map" . + . + . + . + "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . + "http://sabiork.h-its.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . + . + . + . + "^[A-Z]+[0-9]+$"^^ . + . + . + "https://web.archive.org/web/20091223034048/http://crisp.cit.nih.gov/Thesaurus/index.htm"^^ . + "https://www.nescent.org/phenoscape/Main_Page"^^ . + . + . + . + "https://github.com/OGMS/ogms"^^ . + . + . + "https://www.who.int/teams/health-product-and-policy-standards/inn"^^ . + . + . + . + . + . + . + "Orphanet" . + "^\\d+$"^^ . + "CRISPRdb" . + . + . + . + "^[A-Z0-9]{6,7}$"^^ . + "^[A-Z0-9]{6,7}$"^^ . + "The Hazardous Substances Data Bank (HSDB) is a toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas."^^ . + . + . + . + . + . + "^[a-z]+(\\..*?)?$"^^ . + "https://www.vectorbase.org/ontology-browser"^^ . + "^\\d{7}$"^^ . + "BeetleBase is a comprehensive sequence database and community resource for Tribolium genetics, genomics and developmental biology. It incorporates information about genes, mutants, genetic markers, expressed sequence tags and publications."^^ . + . + "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . + . + . + "http://neurovault.org"^^ . + . + . + "Nico Matentzoglu" . + . + . + "false"^^ . + . + "false"^^ . + . + . + "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . + "http://jglobal.jst.go.jp/en/"^^ . + . + . + . + "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . + . + . + . + . + . + "Genetic Testing Registry" . + "^\\d{7}$"^^ . + . + "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . + . + . + . + "Leigh Carmody" . + . + . + . + "https://www.ebi.ac.uk/metabolights/$1"^^ . + . + . + . + . + . + . + "EDI_244000"^^ . + . + "false"^^ . + . + . + "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . + "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.drugbank.ca/targets"^^ . + . + . + . + "5"^^ . + . + . + "^D\\d+$"^^ . + . + "Robert Druzinsky" . + "https://bioregistry.io/metaregistry/scholia/$1"^^ . + . + . + . + . + . + . + "NIF Standard Ontology: Molecules" . + . + "^[a-z_\\.]+$"^^ . + "^\\d+$"^^ . + . + . + . + "https://www.biocatalogue.org/"^^ . + . + "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . + "^NONHSAT\\d{6}$"^^ . + "false"^^ . + . + . + "false"^^ . + . + "M77F7JM"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^NBK\\d+$"^^ . + "TrichDB" . + . + "true"^^ . + . + . + . + . + "https://github.com/ybradford/zebrafish-experimental-conditions-ontology"^^ . + . + . + "false"^^ . + . + . + "^NX_\\w+$"^^ . + . + "OSR00185W"^^ . + . + . + "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . + "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . + "http://www.chemspider.com/inchikey=$1"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/projects/gap"^^ . + . + "https://www.ebi.ac.uk/ega/studies"^^ . + . + "false"^^ . + "https://repeatsdb.org/"^^ . + . + "false"^^ . + . + . + . + "http://www.pocketome.org/files/$1.html"^^ . + "TR0000001"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/OlatDv"^^ . + . + . + . + . + . + . + . + . + . + "Extensible Markup Language" . + . + "https://github.com/ontoice/ICEO"^^ . + . + . + "Research Resource Identification" . + . + . + "false"^^ . + . + . + . + "http://smart.embl-heidelberg.de/"^^ . + . + . + . + "has responsible" . + "https://gitub.u-bordeaux.fr/erias/fideo"^^ . + . + . + . + "false"^^ . + "^\\d{7}$"^^ . + "http://modelseed.org/biochem/compounds/$1"^^ . + . + "EB0170"^^ . + . + . + . + . + . + . + "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . + "https://www.ebi.ac.uk/ols/ontologies/cl/terms?obo_id=CL:$1"^^ . + "http://www.russelllab.org/miRNAs/"^^ . + . + . + . + "https://www.facebase.org"^^ . + . + "^[A-Z-_0-9]+$"^^ . + . + . + "http://bugs.sgul.ac.uk/E-BUGS"^^ . + "https://cropontology.org/ontology/CO_345/Brachiaria"^^ . + "false"^^ . + "MeSH 2012" . + . + . + "NCI Metathesaurus" . + "https://www.ebi.ac.uk/ontology-lookup/?termId=$1"^^ . + "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . + . + "https://www.vectorbase.org/"^^ . + . + "false"^^ . + . + . + "Dongsheng Cao" . + . + "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . + "408"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_343:$1"^^ . + "https://mlcommons.org/en/"^^ . + . + . + . + . + . + . + . + "PANTHER Pathway" . + . + "false"^^ . + . + "^A\\d{6}$"^^ . + "false"^^ . + "http://bugs.sgul.ac.uk/E-BUGS"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "051"^^ . + . + "RA01.0"^^ . + "Alliance of Genome Resources Knowledge Base" . + . + "^\\d\\w+$"^^ . + "Current Procedural Terminology" . + . + "https://www.wormbase.org/"^^ . + . + . + . + "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . + . + . + . + "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . + "56586"^^ . + . + . + "https://www.fisheries.noaa.gov/species/$1"^^ . + . + "Lonza" . + . + . + . + . + "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . + . + "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . + . + "https://github.com/information-artifact-ontology/IAO/"^^ . + "^[\\w\\-.]{3,}$"^^ . + "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . + "3532759"^^ . + "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . + . + . + "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . . - . - . - . - "http://merops.sanger.ac.uk/index.htm"^^ . - "https://bioportal.bioontology.org/"^^ . - . - "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"^^ . - . - "http://www.arachnoserver.org/"^^ . - . - . - . - . - "^FOOD\\d+$"^^ . - . - "Shapes Constraint Language" . - . - . - "ExAC Variant" . - "http://worfdb.dfci.harvard.edu/"^^ . - "^\\d{7}$"^^ . - "TopFind" . - . - "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . - "Biological Collections Ontology" . - "GO Evidence Code" . - "^ECMDB\\d+$"^^ . - "0000001"^^ . - . - "https://bioregistry.io/metaregistry/go/$1"^^ . - . - . - . - "http://www.psidev.info/groups/controlled-vocabularies"^^ . - "Glycine max Genome Database" . - . - . - "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . - "10001-101"^^ . - "John Beverly" . - . - "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . - . - "false"^^ . - . - "^P(X|R)D\\d{6}$"^^ . - . - . - . - . - . - "Database of Quantitative Cellular Signaling: Model" . - . - . - "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . - "false"^^ . - . - "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . - "VFDB Gene" . - "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . - . - "SEED Compound" . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "https://bioregistry.io/metaregistry/scholia/$1"^^ . - . - . - "FuncBase Human" . - . - . - "http://www.ebi.ac.uk/efo"^^ . - . - . - . - . - "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . - . - . - "http://www.drugbank.ca/biodb/bio_entities/$1"^^ . - "http://mycobrowser.epfl.ch/smegmalist.html"^^ . - . - . - "false"^^ . - . - "Liver Cancer Model Repository" . - . - _:N3e9d9e745e624ceda5c54389cfbc918c . - . - "Performance Summary Display Ontology" . - "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . - . - "BugBase Expt" . - . - . - . - . - "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . - "ls-c35719-120"^^ . - . - . - . - . + . + . + "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . +_:Ne3ce3dae718c46279289e72cb5a0dceb "Thorsten Henrich" . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/PECO_$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "http://www.mycobank.org/"^^ . + . + . + . + "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "https://www.cropontology.org/rdf/CO_336:$1"^^ . + . + . + . + "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . + . + "https://web.expasy.org/cellosaurus/" . + "false"^^ . + . + . + . + . + . + . + . + . + . + "The Carbohydrate-Active Enzyme (CAZy) database is a resource specialized in enzymes that build and breakdown complex carbohydrates and glycoconjugates. These enzymes are classified into families based on structural features."^^ . + "SUM Breast Cancer Cell Line Knowledge Base" . + . + . + . + . + . + "Affymetrix Probeset" . + "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . + . + "Global Biodiversity Information Facility" . + . + . + . + . + "1000"^^ . + . + "https://www.ebi.ac.uk"^^ . + "mKIAA4200"^^ . + . + . + . + "false"^^ . + "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . + . + . + . + . + "http://opm.phar.umich.edu/"^^ . + . + "https://github.com/obcs/obcs"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . + . + . + . + . + "B00162"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + "false"^^ . + . + . + "0045310"^^ . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + "http://www.antirrhinum.net/"^^ . + . + . + . + . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp"^^ . + . + "http://www.mgc.ac.cn/VFs/"^^ . + . + "https://mmp.sfb.uit.no/databases/marcat/"^^ . + . + . + . + . + . + "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . + . + "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . + . + . + "728"^^ . + . + . + "^LTS\\d{7}$"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/nlmcatalog"^^ . + . + . "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . - . - "https://github.com/calipho-sib/controlled-vocabulary"^^ . - "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . - . - "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . - . - "false"^^ . - . - . - . - . - . - "UPI000000000A"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/semanticchemistry/semanticchemistry"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . - . - "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records."^^ . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . - . + . + "TB2:S1000"^^ . + "^\\d+$"^^ . + . + . + . + . + "KEGG Glycan" . + "false"^^ . + . + . + . + . + "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + "Anatomical Therapeutic Chemical Vetinary" . + . + "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . + . + "0.7-123"^^ . + . + . + "Amos Bairoch" . + . + . + . + "0000088"^^ . + . + "https://nanocommons.github.io/identifiers/registry#$1"^^ . + . + . + . + "^PR\\d{5}$"^^ . + "https://www.allotrope.org/"^^ . + . + "false"^^ . + . + . + . + "TS-0285"^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/probonto/terms?short_form=$1"^^ . + . + . + "Rat Genome Database strain" . + . + "https://www.reaxys.com"^^ . + "The PIR SuperFamily concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships."^^ . + . + . + . + . + . + . + "http://doqcs.ncbs.res.in/"^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "002678"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + "NeXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data. \n(Developed by the SIB Swiss Institute of Bioinformatics)"^^ . + . + . + . + . + . + . + "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . + "https://web.expasy.org/abcd/ABCD_$1"^^ . + "The COVID-19 Infectious Disease Ontology (IDO-COVID-19) is an extension of the Infectious Disease Ontology (IDO) and the Virus Infectious Disease Ontology (VIDO). IDO-COVID-19 follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used to represent infection by the SARS-CoV-2 virus strain, and the associated COVID-19 disease."^^ . + . + . + . + . + . + "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . + . + . + "A database-specific registry supporting curation in the Gene Ontology"^^ . + "http://nbn-resolving.org/resolve_urn.htm"^^ . + . + "K00001"^^ . + . + "Sugar Kelp trait ontology" . + . + "Health Surveillance Ontology" . + . + "http://genex.hgu.mrc.ac.uk/"^^ . + "http://ecogene.org/"^^ . + "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "002804"^^ . + . + . + "false"^^ . + . + . + . + "200282"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^PMC\\d+$"^^ . + . + . + . + "false"^^ . + "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . + "SM00015"^^ . + . + "Documentation of the Phenoscape Curation Workflow"^^ . + . + . + "http://www.bioinf.manchester.ac.uk/dbbrowser/sprint/"^^ . + . + . + . + . + . + . + . + "http://www.ontobee.org/ontology/$1" . + "00020134"^^ . + . + "false"^^ . + "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . + . + . + . + . + "false"^^ . + . + . + . + "24801"^^ . + "false"^^ . + . + "miRBase mature miRNA" . + . + . + . + . + . + . + "^\\w\\d+$"^^ . . - . - "false"^^ . - "false"^^ . - . - . - "http://birdgenenames.org/cgnc/"^^ . - . . - "^\\d{8}$"^^ . - "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . - . - . - . - "N0000001662"^^ . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . - "CA981206459"^^ . - . - "1868"^^ . - . - "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . - . - . - "https://www.mmrrc.org"^^ . - "https://www.uniprot.org/journals/$1"^^ . - . - "Cassava ontology" . - . - "https://github.com/allysonlister/swo"^^ . - . - . - . - "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . - . - "ArrayMap" . - . - "PharmacoDB Cells" . - . - . - "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . - . - . - "https://models.physiomeproject.org/exposure/$1"^^ . - . - "Ligand-Gated Ion Channel database" . - . - . - "https://www.ebi.ac.uk/gwas/studies/$1"^^ . - . - . - "The Genomes OnLine Database (GOLD) catalogues genome and metagenome sequencing projects from around the world, along with their associated metadata. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing Project and Analysis Project."^^ . - "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . - . - "https://github.com/obophenotype/zebrafish-phenotype-ontology"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . - . - "^[0-9]+$"^^ . - . - . - . - . - "Transporter Classification Database" . - . - . - . - . - . - . - . - "ThermoFisher is a life sciences supply vendor."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . - . - . - "false"^^ . - . - "https://dandiarchive.org/"^^ . - "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^ . - "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . - . - . - . - . - . - "Cellosaurus identifeirs for publications, like Pubmed"^^ . - . - . - . - . - "AOPWiki (Key Event Relationship)" . - "https://scicrunch.org/resolver"^^ . - "false"^^ . - . - . - "1000290"^^ . - . - . - . - "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^ . - . - . - "false"^^ . - . - "0000012b-5661-2f63-2f73-b43980000000"^^ . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . - . - . - . - "FlowRepository" . - "PharmacoDB Datasets" . - . - . - . - "^\\d+$"^^ . - . + . + "Plant Genome Network" . + . + . + . + "https://www.humancellatlas.org"^^ . + . + "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . + . + . + . + . + . + . + . + . + "An ontology that permits the number of in-text citations of a cited source to be recorded, together with their textual citation contexts, along with the number of citations a cited entity has received globally on a particular date."^^ . + "A structured controlled vocabulary for the anatomy of Graminae. Please note that this ontology has now been superseded by the Plant Ontology."^^ . + . + . + . + . + "SFB_COVID19_MW286762"^^ . + "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . + . + "https://ligandbook.org/package/$1"^^ . + . + . + . + "36"^^ . + . + . + . + . + "FooDB Food" . + . + . + . + "^[\\w\\-:,]{3,64}$"^^ . + . + "0000001"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . + . + . + . + "Hathi Trust Digital Library" . + . + . + . + . + . + . + . + . + . + "Gene Wiki" . + . + . + . + . + . + . + . + . + . + "Petra Fey" . + "Plant Environment Ontology" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/IMR_$1"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "International Classification of Diseases, 10th Revision, Clinical Modification" . + . + "false"^^ . + "https://www.clinicaltrialsregister.eu/"^^ . + . + . + . + "true"^^ . + "https://www.ebi.ac.uk/ena/data/view/$1"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "OMA Group" . + "^[0-9]+$"^^ . + . + . + "^\\d{7}$"^^ . + "https://www.storedb.org/"^^ . + . + "Pseudomonas Genome Database" . + . + "^D\\d{4}$"^^ . + . + . + . + . + "https://www.picb.ac.cn/limore/home"^^ . + . + . + . + . + "false"^^ . + "Salk Institute for Biological Studies" . + "^[A-Z]{6}(\\d{2})?$"^^ . + . + . + "0000062"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . + "George Gkoutos" . + . + . + . + . + . + . + . + . + . + "http://pombe.oridb.org/index.php"^^ . + "false"^^ . + . + . + . + "^MNEST\\d+$"^^ . + "false"^^ . + . + . + . + . + . + "^[A-Za-z0-9+_.%-:]+$"^^ . + . + . + . + "https://www.goreni.org/gr3_nomenclature.php"^^ . + "false"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + "3"^^ . + "false"^^ . + . + . + . + . + . + . + . + "2.7.1.1"^^ . + . + . + "https://www.ebi.ac.uk/miriam/"^^ . + "NIF Standard Ontology: Brain Regions" . + . + . + "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . + . + . + "NCBI PubChem database of bioassay records" . + . + "http://substrate.burnham.org/"^^ . + . + . + . + . + "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . + "http://biocyc.org/getid?id=$1"^^ . + . + "JCRB1355"^^ . + . + "CategorialBibliometricData"^^ . + . + "http://swissregulon.unibas.ch/query/$1"^^ . + . + . + "Reaxys" . + "http://napp.u-psud.fr/"^^ . + . + "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . + . + . + "COSMIC Gene" . + . + "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . + . + "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^ . + . + . + . + . + . + . + . + . + "biosimulations" . + . + . + . + . + . + . + . + . + . + "https://github.com/SDG-InterfaceOntology/sdgio"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.fdilab.org"^^ . + . + "Eukaryotic Promoter Database" . + . + . + "Ontology of Adverse Events" . + . + . + "C0020004/4992"^^ . + . + . + . + . + . + . + . + "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . + . + . + . + . + "Tree of Life Web Project ID" . + . + . + "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . + . + "0000010"^^ . + . + "Cell Signaling Technology Antibody" . + . + . + . + . + "y3ax-8bq3-60"^^ . + . + . + . + "OMA Protein" . + . + "https://e-cyanobacterium.org/models/model/$1"^^ . + . + . + . + . + . + "An ontology designed to support the semantic annotation of epidemiology resources"^^ . + . + . + . + . + . + "Rebuilding a Kidney" . + "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . + . + . + . + "Conferences in EasyChair"^^ . + . + . + . + . + . + . + "0000-0002-5355-2576"^^ . + . + . + . + . + "Rice Trait Dictionary in template v 5.0 - IRRI - March 2016 - Based on SES, RD, UPOV variables and on variables used by CIAT, FLAR and the GRISP Phenotyping Network variables"^^ . + "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . + . + . + "true"^^ . + "true"^^ . + "Cell line databases/resources"^^ . + . + . + . + . + "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . + . + . + . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/"^^ . + . + . + . + . + . + "0000205"^^ . + . + . + . + "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . + . + . + . + "Bibliographic Reference Ontology" . + . + "The Leibniz Institute DSMZ is the most diverse biological resource center in the world and one of the largest collections of microorganisms and cell cultures worldwide (bacteria, archaea, protists, yeasts, fungi, bacteriophages, plant viruses, genomic bacterial DNA as well as human and animal cell lines)."^^ . + "^ACYPI\\d{6}(-RA)?$"^^ . + "https://www.cropontology.org/rdf/CO_359:$1"^^ . + "false"^^ . + "https://proteinensemble.org/"^^ . + . + "Human developmental anatomy, abstract" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "^P\\d+$"^^ . + . + . + "Polymorphism and mutation databases"^^ . + . + . + _:N376e1439b73f4439a8ae10ac8236a8a7 . + "E5.11.2.0.0.0.4"^^ . + . + . + . + "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . + . + . + "http://addgene.org/$1"^^ . + . + . + "https://nmrshiftdb.nmr.uni-koeln.de"^^ . + . + . + . + . + . + . + . + "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "Alexander Diehl" . + . + . + "http://purl.obolibrary.org/obo/OBIB_$1"^^ . + . + . + . + "http://www.xenbase.org/anatomy/xao.do?method=display"^^ . + . + . . - . - . - . - . - "false"^^ . - "false"^^ . - "Sue Bello" . -_:N8f018e94918f4ace800449033ce895e0 "Christipher Baker" . - "Biolink Model" . - "false"^^ . - "HD+118-001"^^ . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - . - . - . - . - . - "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools.: Antibodies, Model Organisms, and Databases / Software tools.\r\nThe initiative works with participating journals to intercept manuscripts in the publication process that use these resources, and allows publication authors to incorporate RRIDs within the methods sections. It also provides resolver services that access curated data from 10 data sources: the antibody registry (a curated catalog of antibodies), the SciCrunch registry (a curated catalog of software tools and databases), and model organism nomenclature authority databases (MGI, FlyBase, WormBase, RGD), as well as various stock centers. These RRIDs are aggregated and can be searched through SciCrunch."^^ . - . - . - . - . - "Coleoptera Anatomy Ontology" . - "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . - "MycoBrowser marinum" . - "false"^^ . - . - . - . - "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . - . - . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . - . - . - . - . - "https://fair-research.org"^^ . - . - "https://flybase.org"^^ . - "http://github.com/ga4gh/data-object-service-schemas"^^ . - . - . - . - . - . - . - . - . - "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . - . - . - "http://www.whocc.no/atcvet/atcvet_index/"^^ . - . - . - . - "4900"^^ . - . - "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies."^^ . - . - . - . - . - . - . - "1"^^ . - . - . - "Influenza Ontology" . - . - "^PF\\d{5}$"^^ . - . - "false"^^ . - . - . - . + . + "Bioregistry Metaregistry" . + . + . + . + . + . + "false"^^ . + . + . + . + "000912"^^ . + . + . + . + . + "This is a code repository for the SIB - Swiss Institute of Bioinformatics CALIPHO group neXtProt project, which is a comprehensive human-centric discovery platform, that offers a integration of and navigation through protein-related data. CALIPHO is an interdisciplinary team which aims to use a variety of methodologies to help uncover the function of uncharacterized human proteins."^^ . + . + . + . + "false"^^ . + "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . + "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^ . + "EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. Here, you can browse, upload and download the raw images used to build a 3D structure"^^ . + "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^ . + "false"^^ . + "MINID Test" . + "http://www.lipidmaps.org"^^ . + . + . + "http://patft.uspto.gov/netahtml/PTO/index.html"^^ . + . + . + . + . + . + . + "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . + . + "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^ . + . + . + . + "http://dictybase.org/"^^ . + . + . + "http://flypush.imgen.bcm.tmc.edu/pscreen/"^^ . + . + . + . + . + . + . + . + . + "The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded."^^ . + "false"^^ . + "An ontology of core ecological entities" . + "https://github.com/MSI-Metabolomics-Standards-Initiative/MSIO"^^ . + . + "ISfinder is a database of bacterial insertion sequences (IS). It assigns IS nomenclature and acts as a repository for ISs. Each IS is annotated with information such as the open reading frame DNA sequence, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography, where available."^^ . + "AP00378"^^ . + "^\\d{7}$"^^ . + . + "http://jaxmice.jax.org/"^^ . + . + . + . + . + "false"^^ . + "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . + . + . + "false"^^ . + . + "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . + . + . + . + "false"^^ . + . + . + . . - "https://www.gbif.org/species/$1"^^ . - . - "KG09531"^^ . - . - . - "false"^^ . - . - "FxnI151FMs"^^ . - . - . - . - . - . - "10087"^^ . - . - . - "CryptoDB" . - . - "Close to 5K Categorizations for drugs, similar to ATCC."^^ . - "false"^^ . - "^D\\d{4}$"^^ . - "^[a-zA-Z0-9 +#'*]+$"^^ . - . - . - . - . - . - "0000198"^^ . - . - . - . - . - . - . - "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . - " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . - "https://biosimulators.org/simulators/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "CQG5"^^ . - . - . - . - . - . - . - . - "Identifiers.org Terms" . - . - . - . - . - . - . - "^T\\d{3}$"^^ . - "https://stemcells.nindsgenetics.org?line=$1"^^ . - "http://purl.obolibrary.org/obo/TAHH_$1"^^ . - "false"^^ . - . - "http://yetfasco.ccbr.utoronto.ca/"^^ . - . - . - . - "Gm00047"^^ . - . - . - . - . - . - . - "http://toxodb.org/toxo/"^^ . - . - "/12345/fk1234"^^ . - "false"^^ . - "http://img.jgi.doe.gov/"^^ . - . - "Gene Expression Ontology"^^ . - . - . - "https://www.biocatalogue.org/"^^ . - . - . - . - . - "171"^^ . - . - . - . - . - "American Type Culture Collection" . - . - . - . - "Simple Modular Architecture Research Tool" . - . - . - "https://github.com/geneontology/unipathway"^^ . - "Drivers of human diseases including environmental, maternal and social exposures."^^ . - "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . - "NIF Standard Ontology: Organisms" . - "false"^^ . - . - "UPC04349"^^ . - "https://lotus.naturalproducts.net"^^ . - . - . - . - . - "https://www.cropontology.org/rdf/CO_322:$1"^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . - "3"^^ . - "Cell line databases/resources"^^ . - . - . - "CUT"^^ . - "false"^^ . - . - "false"^^ . - . - . - . - . - "^[A-Za-z0-9-]+$"^^ . - . - . - . - "Molecular Signatures Database" . - "https://cropontology.org/ontology/CO_334/Cassava"^^ . - "^UPI[A-F0-9]{10}$"^^ . - "false"^^ . - . - . - "https://github.com/ClinicalTrialOntology/CTO/"^^ . - . - "https://bioregistry.io/metaregistry/ncbi/$1"^^ . - "SRS086444"^^ . - . - "^\\d+$"^^ . -_:N8c9982accff54cf18941c023927a9382 "GenBank Support" . - "http://www.proteinatlas.org/"^^ . - "CHEBI" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Telethon Network of Genetic Biobanks" . - "https://depmap.org/portal/cell_line/$1"^^ . - . - . - "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . - . - . - . - . - . - "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . - . - . - . - . - "has canonical" . - . - . - . - "Identifiers.org Ontology"^^ . - "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . - . - . - . - . - . - "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . - . - "World Register of Marine Species" . - "http://topdb.enzim.hu/?m=show&id=$1"^^ . - . - . - "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . + . + . + "https://odc-sci.org"^^ . + . + "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . + . + "Os01t0883800-02"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "HUGO Gene Nomenclature Committee" . + . + "98"^^ . + . + . + . + "false"^^ . + . + . + . + "World Wildlife Fund Ecoregion" . + . + "PSEEN0001"^^ . + . + "CIAT Common bean trait dictionary - version August 2014"^^ . + "BioProject" . + "^[A-Za-z0-9+_.%-:]+$"^^ . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + "http://www.genome.jp/kegg/catalog/org_list3.html"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MPIO_$1"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MCO_$1"^^ . + . + . + . + "appears in" . + "Human Gene Mutation Database" . + . + . + "0058"^^ . + . + . + "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . + . + "PR00001"^^ . + "false"^^ . + "https://www.uniprot.org/keywords/$1"^^ . + . + . + . + "http://purl.obolibrary.org/obo/NBO_$1"^^ . + . + "https://www.cropontology.org/rdf/CO_357:$1"^^ . + "https://github.com/$1"^^ . + "Wes Schafer" . + "http://www.snomedbrowser.com/"^^ . + . + . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/periodic-table"^^ . + . + "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . + . + . + . +_:Nab1e039fd9a3451dbad75da2e0d784fa "Fahim Imam" . + . + . + . + . + . + "Langua aLimentaria Thesaurus" . + . + . + . + . + . + . + . + . + . + . + "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . + "MycoBrowser smegmatis" . + "0004828"^^ . + . + "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . + . + "https://ssbd.riken.jp"^^ . + . + "A comprehensive compendium of human long non-coding RNAs"^^ . + . + . + "Microbial Conditions Ontology is an ontology..."^^ . + . + . + . + "GN_G03681DA"^^ . + "http://purl.obolibrary.org/obo/MAO_$1"^^ . + . + . + "https://ontochem.com/"^^ . + . + . + . + "An ontology of human and animal behaviours and behavioural phenotypes"^^ . + "^\\d{8}$"^^ . + . + . + "Xeni Kechagioglou" . + . + . + . + . + . + "BEI Resources" . + . + . + . + "false"^^ . + "1-FEH+w3"^^ . + . + "GlycoPOST" . + "true"^^ . + . + "false"^^ . + . + . + . + "Selventa Chemicals" . + . + "false"^^ . + . + . + . + . + . + "https://www.uniprot.org/database/"^^ . + . + . + . + . + "https://www.biozol.de/en"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + "http://www.informatics.jax.org/accession/MGI:$1"^^ . + . + . + "http://neuinfo.org/"^^ . + . + . + . + . + . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:0000000"^^ . + . + "https://github.com/obophenotype/ncbitaxon"^^ . + . + . + "Genetic and Rare Diseases Information Center" . + . + . + . + "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . + . + . + "Rahuman Sheriff" . + "Molecular database for the identification of fungi" . + "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . + . + "true"^^ . + . + "Drug Central" . + . + . + . + "false"^^ . + . + . + "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . + . + . + . + . + . + "91005"^^ . + "https://www.genedb.org/gene/$1"^^ . + "https://signor.uniroma2.it"^^ . + . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/ECG"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "Cell Version Control Repository" . + . + . + "100"^^ . + . + "https://www.ebi.ac.uk/metagenomics"^^ . + . + . + "false"^^ . + "false"^^ . + . + "CLV_MEL_PAP_1"^^ . + "Sequence Read Archive" . + . + . + . + . + "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . + "Regulation of Gene Expression"^^ . + "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"^^ . + . + . + "959"^^ . + . + . + "European Genome-phenome Archive Dataset" . + . + . + . + "https://rnacentral.org/"^^ . + "http://purl.obolibrary.org/obo/OAE_$1"^^ . + . + . + . + "TreeFam" . + . + . + . + "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . + . + . + . + . + "false"^^ . + . . - . - "^\\d{7}$"^^ . - . - . - "https://www.scopus.com"^^ . - . - . - "Database of Interacting Proteins" . - . - . - . - . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Z0-9]+$"^^ . + "http://purl.obolibrary.org/obo/OGI_$1"^^ . + . + "true"^^ . + "https://flybase.org"^^ . + . + "00042"^^ . + . + . + "MimoDB is a database collecting peptides that have been selected from random peptide libraries based on their ability to bind small compounds, nucleic acids, proteins, cells, tissues and organs. It also stores other information such as the corresponding target, template, library, and structures. As of March 2016, this database was renamed Biopanning Data Bank."^^ . + . + . + "High-quality Automated and Manual Annotation of microbial Proteomes" . + . + . + "http://korkinlab.org/dommino"^^ . + . + "true"^^ . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The kinetic record data set provides information regarding the kinetic law, measurement conditions, parameter details and other reference information."^^ . + "false"^^ . + "Orthology Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . + . + "Prefix.cc" . + "0000041"^^ . + "^[0-9]*$"^^ . + "https://horizondiscovery.com/"^^ . + "https://glytoucan.org/"^^ . + . + "false"^^ . + "http://www.sasbdb.org/data/$1"^^ . + . + . + "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . + . + . + . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . + "Nematode Expression Pattern DataBase" . + . + . + . + . + . + "Platynereis stage ontology" . + . + "https://cropontology.org/ontology/CO_343/Yam"^^ . + . + "https://www.genome.jp/kegg/pathway.html"^^ . + "https://www.psidev.info/peff"^^ . + "0000184"^^ . + "http://bioportal.bioontology.org/ontologies/BAO/bao:BAO_$1"^^ . + "false"^^ . + "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . + . + . + "https://github.com/evoinfo/cdao"^^ . + . + . + . + "http://purl.obolibrary.org/obo/flu/"^^ . + "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . + . + . + . + . + "https://www.nlm.nih.gov/research/umls/rxnorm/"^^ . + . + "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . + . + "false"^^ . + . + "^[EL]D[SG]-\\d+$"^^ . + . + "Database of homology-derived secondary structure of proteins" . + . + . + "Q9UKQ2"^^ . + . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + "^PRJ[DEN][A-Z]\\d+$"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^ . + "false"^^ . + . + . + . + . + . + . + "http://www.kazusa.or.jp/huge/"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "https://portal.bluebrain.epfl.ch"^^ . + . + "^C\\d+$"^^ . + "ENSG00000139618"^^ . + . + "0000252"^^ . + . + . + "4019477"^^ . + . + . + . + . + . + "A formal represention for drug-drug interactions knowledge."^^ . + . + "HBG284870"^^ . + . + "TF0001053"^^ . + "https://github.com/obophenotype/xenopus-phenotype-ontology"^^ . + "true"^^ . + . + . + "Chemical Component Dictionary" . + "https://bio.tools/$1"^^ . + . + . + "false"^^ . + . + . + "RF00230"^^ . + . + . + "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ZFA_$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^HMDB\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . + . + . + . + "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . + "false"^^ . + . + . + . + . + "Sunflower ontology" . + "https://stemcells.nindsgenetics.org"^^ . + "Adnan Malik" . + . + . + "^\\w+$"^^ . + "false"^^ . + . + . + . + "http://www.violinet.org/ovae/"^^ . + . + . + . + . + . + "false"^^ . + "http://exac.broadinstitute.org/"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . + . + . + "0000199"^^ . + . + . + . + . + . + "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . + "Plant Trait Ontology" . + . + . + "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . + . + "^\\d+$"^^ . + "BioModels Database" . + "http://edamontology.org/format_$1"^^ . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/IEV_$1"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^[a-zA-Z0-9\\-:#\\.]+$"^^ . + "1466"^^ . + . + . + . + . + . + . + "https://code.google.com/p/epidemiology-ontology/"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_333:$1"^^ . + "http://purl.obolibrary.org/obo/ATO_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "Database of Quantitative Cellular Signaling: Pathway" . + . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . + "Human developmental anatomy, abstract version" . + "false"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + "OGG is a biological ontology in the area of genes and genomes. OGG uses the Basic Formal Ontology (BFO) as its upper level ontology. This OGG document contains the genes and genomes of a list of selected organisms, including human, two viruses (HIV and influenza virus), and bacteria (B. melitensis strain 16M, E. coli strain K-12 substrain MG1655, M. tuberculosis strain H37Rv, and P. aeruginosa strain PAO1). More OGG information for other organisms (e.g., mouse, zebrafish, fruit fly, yeast, etc.) may be found in other OGG subsets. "^^ . + . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references models."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "0000712_1"^^ . + "The Spectral Database for Organic Compounds (SDBS) is an integrated spectral database system for organic compounds. It provides access to 6 different types of spectra for each compound, including Mass spectrum (EI-MS), a Fourier transform infrared spectrum (FT-IR), and NMR spectra."^^ . + . + . + . + . + "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1"^^ . + "https://aopwiki.org/events/$1"^^ . + . + "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . + . + "268"^^ . + . + "^\\d+\\-\\d+\\-\\d+$"^^ . + . + . + _:Nf53f81f057be4231ab960d9b04974303 . + . + . + . + . + . + . + . . - "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . - . - "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . - . - "false"^^ . - "^[A-Z]+[0-9]+$"^^ . - . - . - "https://www.python.org/psf/"^^ . - "0440"^^ . - . - "https://n2t.net/$1:" . - . - . - "https://ssbd.riken.jp"^^ . - . - . - "https://www.datanator.info/metabolite/$1"^^ . - . - . - . - . - . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . - . - . - "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology"^^ . - "https://download.nextprot.org/pub/current_release/controlled_vocabularies/"^^ . - . - "https://www.aepc.org/european-paediatric-cardiac-coding"^^ . - "A*01:01:01:01"^^ . - . - . - . - . - "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . - "^\\d+$"^^ . - "http://rna.rega.kuleuven.be/rnamods/"^^ . - . - . - . - . - . - "http://www.cathdb.info"^^ . - "biosimulations" . - . - . - "^FB\\d{8}$"^^ . - . - . - . - . - . - "Tom Gillespie" . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . - "https://github.com/EnvironmentOntology/environmental-exposure-ontology"^^ . - . - . - . - . - . - . - . - "10343835"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PLANA_$1"^^ . - . - . - . - . - . - "200282"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - "NCI Data Commons Framework Services" . - . - . - . - . - "491187"^^ . - . + . + . + . + . + . + "CAS Chemical Registry" . + . + . + "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . + . + . + . + . + . + . + . + "https://data.4dnucleome.org/biosources"^^ . + . + "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . + . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/fbcv"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . + . + . + . + . + . + . + . + "Multiple alignment" . + "Cellular Microscopy Phenotype Ontology" . + . + . + . + "^\\d{7}$"^^ . + "http://www.bioinfo.org/NONCODEv4/"^^ . + . + . + . + "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . + . + "^AS\\d{6}$"^^ . + . + "^\\d{7}$"^^ . + "ALX-210-175"^^ . + "27106865"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[a-z_A-Z0-9]+$"^^ . + . + . + . + . + . + "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . + . + "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . + . + . + . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . + . + "10087"^^ . + . + . . - "false"^^ . - "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . - . - . - . - "ExAC Transcript" . - . - . - "^\\d{4}$"^^ . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . - "https://europepmc.org/article/CTX/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/fbcv"^^ . - . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . - . - . - "http://www.whocc.no/atc_ddd_index/"^^ . - "http://rgd.mcw.edu/"^^ . - "^\\d{7}$"^^ . + "false"^^ . + . + "false"^^ . + . + . + "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . + . + "https://scdontology.h3abionet.org/"^^ . + . + . + . + "false"^^ . + . + . + . + "784"^^ . + . + . + . + "https://fcs-free.org/fcs-database?$1"^^ . + . + . + "AU124"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.insdc.org/"^^ . + . + . + "Medical Data Models" . + "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "PANTHER Pathway Component" . + . + . + . + . + "8639.1"^^ . + . + . + . + . + . + . + "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . + . + . + "https://glycopost.glycosmos.org/entry/$1"^^ . + "http://www.violinet.org/vaccineontology"^^ . + . + "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . + . + "ClinGen Allele Registry" . + . + . + "^A_\\d+_.+$"^^ . + "false"^^ . + . + . + . + "false"^^ . + . + . + "GDS1234"^^ . + . + "http://nematode.lab.nig.ac.jp/"^^ . + "HomologyRelation"^^ . + . + "false"^^ . + . + "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . + . + . + . + "https://flybase.org/reports/$1"^^ . + . + . + . + . + . + . + . + "frim1"^^ . + . + . + "1915"^^ . + . + "http://flyrnai.org/"^^ . + . + "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "Cryo Electron Microscopy ontology" . + . + "TreeFam is a database of phylogenetic trees of gene families found in animals. Automatically generated trees are curated, to create a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments."^^ . + . + "System Science of Biological Dynamics project" . + . + . + "false"^^ . + "http://www.iclc.it"^^ . + . + . + "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=$1"^^ . + "http://bigg.ucsd.edu/universal/reactions"^^ . + . + "MSMEG_3769"^^ . + . + "http://exac.broadinstitute.org/variant/$1"^^ . + . + . + "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . + . + . + . + . + . + "https://www.elsevier.com/books/nadas-pediatric-cardiology/9781416023906"^^ . + "0000947"^^ . + . + . + . + . + "Ligand Expo" . + "false"^^ . + . + "http://www.ncbi.nlm.nih.gov/unigene"^^ . + . + . + . + . + . + . + . + . + "http://rna-mdb.cas.albany.edu/RNAmods/rnaover.htm"^^ . + . + "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . + "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . + . + . + "https://w3id.org"^^ . + . + "0032571"^^ . + . + . + . + "PaxDb Organism" . + "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . + . + "http://www.alanwood.net/pesticides/$1.html"^^ . + "0003"^^ . + "589462"^^ . + . + . + . + . + "dictyBase Expressed Sequence Tag" . + . + "https://www.cropontology.org/rdf/CO_335:$1"^^ . + "International Classifications of Diseases" . + "http://ardb.cbcb.umd.edu/"^^ . + . + . + . + . + . + "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . + "false"^^ . + . + . + "10153"^^ . + . + . + . + "true"^^ . + _:N1c1286af71f04954ae8d36f0142abbb3 . + . + . + . + . + . + "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . + "Legacy disease classes that later became MONDO"^^ . + "false"^^ . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . + "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . + . + "false"^^ . + . + "PELNAW"^^ . + "false"^^ . + . + . + "CiteXplore" . + "SubstrateDB" . + "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . + . + . + "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . + . + . + "PRO_0000016681"^^ . + . + . + . + . + "The Obstetric and Neonatal Ontology is a structured controlled vocabulary to provide a representation of the data from electronic health records (EHRs) involved in the care of the pregnant woman, and of her baby."^^ . + "false"^^ . + "265"^^ . + . + . + . + . + . + "IID00001"^^ . + "C34"^^ . + . + . + . + "http://mint.bio.uniroma2.it/mint/"^^ . + . + . + "sov:WRfXPg8dantKVubE3HX8pw"^^ . + "false"^^ . + . + . + . + "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . + . + . + . + "ABL1"^^ . + . + "http://bactibase.hammamilab.org/$1"^^ . + "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . + "^\\d{7}$"^^ . + . + "17165"^^ . + . + . + . + . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index"^^ . + . + . + . + . + "Kinetic Simulation Algorithm Ontology" . + "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . + . + . + . + . + . + . + "Gemina Symptom Ontology" . + . + . . - . - . - . - . - . - "true"^^ . - "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . - . - "FAIRsharing" . - "24867"^^ . - "https://www.cropontology.org/rdf/CO_338:$1"^^ . - "http://probonto.org"^^ . - . - "^.*/.*$"^^ . - . - . - "https://www.disprot.org"^^ . - . - . - . - . - "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . - "https://pathbank.org"^^ . - . - . - "Adriano Rutz" . - . - . - . - . - . - . - "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . - . - "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "40000617"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - "https://glytoucan.org/"^^ . - . - "https://bionumbers.hms.harvard.edu"^^ . - . - . - "WGS-95-1333"^^ . - . - . - . - . - . - . - . + "false"^^ . + . + . + "E-MTAB-2037"^^ . + . + . + "false"^^ . + . + . + "http://www.cropontology.org/ontology/CO_366/Bambara%20groundnut"^^ . + . + . + "true"^^ . + "307"^^ . + . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . + . + "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . + . + . + . + . + . + . + . + . + . + . + . + "1"^^ . + "Tb927.8.620"^^ . + . + "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . + . + . + . + . + . + . + "false"^^ . + "^\\d+$"^^ . + "https://www.dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + . + . + . + . + . + . + . + "00000000"^^ . + . + . + . + . + . + "Developmental stages of the Zebrafish"^^ . + . + . + . + "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . + "https://github.com/PopulationAndCommunityOntology/pco"^^ . + . + . + . + "true"^^ . + "http://www.indexfungorum.org"^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/snp/"^^ . + . + . + . + . + "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . + . + . + . + "2029"^^ . + . + . + . + . + . + "MEROPS Entry" . + . + . + "Data Use Ontology" . + . + "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . + "http://hawaii.eagle-i.net/i/$1"^^ . + "MU9_3181"^^ . + "https://www.ebi.ac.uk/ols/ontologies/fma/terms?obo_id=FMA:$1"^^ . + . + . + . + . + . + "An ontology of physico-chemical methods and properties."^^ . + . + . + "Peroxibase" . + . + "Elizabeth Arnaud" . + "false"^^ . + . + . + "83088"^^ . + "false"^^ . + "https://github.com/data2health/contributor-role-ontology"^^ . + . + "Oryzabase Stage" . + . + "Redistributor of bilogics and biomedical supplies"^^ . + . + . + "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . + . + . + "http://purl.obolibrary.org/obo/COB_$1"^^ . + . + . + . + . + . + "https://progenetix.org/services/ids/$1"^^ . + . + "Heather Piwowar" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "UniProt Cross-ref database" . + . + . + . + "Glyma0021s00410"^^ . + . + . + . + . + "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . + . + "https://www.alliancegenome.org"^^ . + "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "PharmacoDB Tissues" . + . + "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . + . + . + . + "false"^^ . + "http://eawag-bbd.ethz.ch/$1/$1_map.html"^^ . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "DNA barcoding is the use of short standardised segments of the genome for identification of species in all the Kingdoms of Life. The goal of the Fungal Barcoding site is to promote the DNA barcoding of fungi and other fungus-like organisms."^^ . + "760050"^^ . + . + . + "0000038"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://doulix.com/constructs/$1"^^ . + "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . + "https://www.cropontology.org/rdf/CO_334:$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "00001234"^^ . + "Gramene Gene" . + . + . + "spike00001"^^ . + . + "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . + . + . + . + . + . + . + . + "^\\w+$"^^ . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/pride/archive/assays/$1"^^ . + . + "https://github.com/EBISPOT/ancestro"^^ . + "false"^^ . + . + . + . + . + . + . + "BioData Catalyst" . + . + . + . + "^[A-Z_a-z]+$"^^ . + . + "https://caninecommons.cancer.gov/#/"^^ . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . + . + . + "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . + . + . +_:Nbbb5805961a642eeaa98e85edf81b16d "Maria Herrero" . + . + "3771877"^^ . + . + . + "Compositional Dietary Nutrition Ontology" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . + "Analyses of microbiome data within MGnify"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.org/spar/deo/$1"^^ . + . + . + . + . + "^[A-Z0-9]+$"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . + . + . + . + . + . + "https://zenodo.org"^^ . + . + . + "^\\d+$"^^ . + . + "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . + . + . + . + . + "Enzyme Commission Code" . + "false"^^ . + . + . + . + "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . + . + . + . + . + "http://ciliate.org/index.php/feature/details/$1"^^ . + "^\\d+$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "Histopathology Ontology" . + . + . + "0000773"^^ . + . + . + "false"^^ . + . "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification."^^ . - . - "http://purl.obolibrary.org/obo/OVAE_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . - "Quality"^^ . - "https://icahn.mssm.edu/"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "Cryo Electron Microscopy ontology" . - . + . + "P4355"^^ . + "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . + "https://github.com/prefixcommons/biocontext" . + . + . + . + "^T[A-Z]\\d{7}$"^^ . + "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . + . + . + "https://www.w3.org/TR/xml/"^^ . + "0000210"^^ . + . + . + . + "http://www.noncode.org/"^^ . + . + "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. SubstrateDB contains molecular information on documented protease substrates."^^ . + . + "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . + . + "Amphibian gross anatomy" . + . + . + "^\\d+$"^^ . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + "Metabolomics Workbench Study" . + "^\\d+$"^^ . + "true"^^ . + . + . + "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . + . + . + . + . + . + . + . + "https://www.salk.edu/"^^ . + . + "^F\\d{4}$"^^ . + . + . + "COSMIC Cell Lines" . + . + . + . + . + . + "^DTXSID\\d+$"^^ . + "ProteomicsDB Protein" . + . + "https://github.com/sparontologies/fabio"^^ . + "0000547"^^ . + "^\\d{4,}$"^^ . + "false"^^ . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . + "EBI-2307691"^^ . + . + "https://github.com/OpenLHS/CVDO"^^ . + . + "Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis."^^ . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . + "lang"^^ . + . + "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . + . + "http://ligand-depot.rutgers.edu/index.html"^^ . + . + "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . + . + . + "uBio NameBank" . + . + . + . + . + "http://ecoliwiki.net/colipedia/"^^ . + "false"^^ . + . + "http://www.genomesonline.org/cgi-bin/GOLD/index.cgi"^^ . + "https://www.lji.org/"^^ . + . + "SubtiWiki" . + . + . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + . + "^\\d+$"^^ . + . + . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + "^C\\d{8}$"^^ . + . + . + "1"^^ . + . + "Troy Pells" . + . + . + "false"^^ . + . + "http://purl.bioontology.org/ontology/MEDDRA/$1"^^ . + "42840"^^ . + "false"^^ . + "AURKA"^^ . + . + "http://www.accessdata.fda.gov/scripts/cder/ndc/"^^ . + "http://www.tcdb.org/search/result.php?tc=$1"^^ . + "European Collection of Authenticated Cell Culture" . + . + . + . + . + . + . + . + "http://www.fao.org/gsfaonline"^^ . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . + "http://proteomecentral.proteomexchange.org/"^^ . + "CCLE_867"^^ . + . + . + . + . + "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . + . + . + . + "Terms from the source appear in the target resource" . + . + . + . + . + "^[A-Z0-9*:]+$"^^ . + . + . + . + . + . + . + . + "^WBRNAi\\d{8}$"^^ . + . + . + . + "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . + . + . + "0000728"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "G-Rich Sequences Database" . + "D0001"^^ . + . + "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . + . + "https://code.google.com/archive/p/ontology-for-genetic-interval/"^^ . + . + . + "Selventa legacy disease namespace used with the Biological Expression Language"^^ . + . + . + . + . + . + . + "http://wheat.pw.usda.gov"^^ . + . + "http://bacmap.wishartlab.com/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.ebi.ac.uk/interpro/index.html"^^ . + . + . + "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . + . + . + . + . + . + . . - . - "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . - "BioCarta Pathway" . - "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . - "http://pkuxxj.pku.edu.cn/UNPD/"^^ . - . - . - "https://cropontology.org/ontology/CO_320/Rice"^^ . - . - . - . - . - . - . - . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . - . - . - . - . - "https://www.cropontology.org/rdf/CO_348:$1"^^ . - . - . - . - "4685"^^ . - _:N058aa60ca0674ad4a89d43450ed0cc9e . + . + . + . + . + "https://icd.who.int/browse10"^^ . + "^\\d{7}$"^^ . + . + "https://www.brenda-enzymes.de/ligand.php"^^ . + . + . + . + "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . + . + "Animal Genome Chicken QTL" . + . + . + . + . + . + . + . + "http://www.gramene.org/"^^ . + "AgentIdentifierScheme"^^ . + "^M\\d+$"^^ . + . + "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . + . + "false"^^ . + . + . + . + . + "IntellectualContribution"^^ . + . + . + "https://neurovault.org/collections/$1"^^ . + "false"^^ . + "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . + "https://github.com/qfo/OrthologyOntology"^^ . + "^EBI\\-[0-9]+$"^^ . + . + "Woody Plant Ontology ontology" . + "^\\d+$"^^ . + . + . + "http://ddinter.scbdd.com"^^ . + . + "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . + . + . + "^[1-9][0-9]*$"^^ . + . + . + . + . + "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . + "The MDM (Medical Data Models) Portal is a meta-data registry for creating, analysing, sharing and reusing medical forms. Electronic forms are central in numerous processes involving data, including the collection of data through electronic health records (EHRs), Electronic Data Capture (EDC), and as case report forms (CRFs) for clinical trials. The MDM Portal provides medical forms in numerous export formats, facilitating the sharing and reuse of medical data models and exchange between information systems."^^ . + . + . + . + . + . + . + . + "Bioregistry Collections" . + "false"^^ . + . + "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . + "Ontology of RNA Sequencing" . + . + "http://bioinformatics.hsanmartino.it/hypercldb/indexes.html"^^ . + . + "https://www.genenames.org"^^ . + "ICARDA - TDv5 - Sept 2018"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "http://solgenomics.net/"^^ . + . + . + . + . + "785"^^ . + . + "ArrayMap" . + . + . + "MGYA00002270"^^ . + . + "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . + "false"^^ . + . + "0000198"^^ . + "The International Standard Book Number (ISBN) is for identifying printed books."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "SED-ML data format" . + . + . + "K00973"^^ . + . + . + "https://github.com/monarch-initiative/GENO-ontology/"^^ . + . + . + "A controlled vocabulary to support the study of transcription in the primate brain"^^ . + . + . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + "Database portal containing replicate experiments of different assays and samples"^^ . + "http://hymao.org"^^ . + "Integrated Taxonomic Information System" . + . + . + . + . + . + . + . + "Yeast Intron Database v3" . + . + . + . + "https://www.cropontology.org/rdf/CO_338:$1"^^ . + . + "LIPID MAPS" . + . + . + "https://doulix.com"^^ . + "https://doulix.com"^^ . + . + "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . + . + . + . + "false"^^ . + "^(STUDY|FILE|DATASET)\\d+$"^^ . + "https://www.ebi.ac.uk/arrayexpress/files/A-GEHB-1/A-GEHB-1.adf.txt"^^ . + . + . + . + . + . + "false"^^ . + "https://download.nextprot.org/pub/current_release/controlled_vocabularies/"^^ . + . + "0000046"^^ . + "false"^^ . + . + . + "1"^^ . + "BugBase Protocol" . + . + . + "http://www.hgmd.cf.ac.uk/ac/index.php"^^ . + . + . + . + "4DN"^^ . + _:Nad924b2bf8224737a794ca80599d6e2d . + "false"^^ . + . + . +_:N4a0800839ffe4d7aa96d4a23053dfc1d "Mauno Vihinen" . + . + . + . + . + "8000221"^^ . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/"^^ . + . + "false"^^ . + . + . + . + "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . + . + . + . + . + "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . + "Vertebrate trait ontology" . + . + "Stacia R Engel" . + "false"^^ . + . + "ChEBI Integrated Role Ontology" . + "http://sabiork.h-its.org/newSearch?q=$1"^^ . + . + . + . + . + . + . + . + "Dublin Core Metadata Vocabulary" . + . + . + . + . + . + "^\\w+:[\\w\\d\\.-]*$"^^ . + . + . + . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . + . + "63"^^ . + . + "http://www.orpha.net/consor/"^^ . + . + . + "0000509"^^ . + "http://www.expasy.org/viralzone/"^^ . + . + . + . + "false"^^ . + "false"^^ . + "^\\d{7}$"^^ . + "UniProt journal ID" . + . + "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "HOMD Taxonomy" . + . + . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + . + "http://ecoportal.lifewatch.eu/ontologies/$1" . + . + . + "https://www.grid.ac/institutes/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "Database of the dielectric properties of biological tissues."^^ . + . + . + . + . + "Zoë May Pendlington" . + "0000187"^^ . + "AmoebaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . + . + . + . + "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations."^^ . + . + "E-cyanobacterium entity" . + "0000546"^^ . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/CMF_$1"^^ . + . + . + . + . + . + . + . + . + . + "Linguist" . + "WGS84 Geo Positioning" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "ALIENSPECIES" . + . + . + . + . + . + . + "http://wiki.phenoscape.org/wiki/Teleost_Anatomy_Ontology"^^ . + . + "hsa-mir-200a"^^ . + . + . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . + . + . + "BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy."^^ . + . + "The Oral Health and Disease Ontology was created, initially, to represent the content of dental practice health records."^^ . + "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . + . + "https://repeatsdb.org/protein/$1"^^ . + "http://www.receptors.org/nucleardb/"^^ . + . + . + . + . + . + "https://n2t.net"^^ . + "http://tables.pseudogene.org/[?species_name]/$1"^^ . + . + . + . + . + . + . + "http://www.amphibanat.org"^^ . + "true"^^ . + . + "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . + . + "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . + . + . + "https://protists.ensembl.org"^^ . + . + . + . + . + "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . + "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . + . + . + . + . + "L000001"^^ . + "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + "Ceri Van Slyke" . + "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . + . + "^\\d{8}$"^^ . + . + "http://biohackathon.org/resource/faldo#$1"^^ . + "http://www.kegg.jp/entry/$1"^^ . + . + "Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. This collections also references outgroup organisms."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "http://www.fossilworks.org"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + . + "http://prism.case.edu/prism/index.php/EpilepsyOntology"^^ . + . + . + . + "Germplasm Resources Information Network" . + . + "Plant Experimental Conditions Ontology" . + . + . + . + . + . + "InterPro" . + . + . + "^[A-Z_]{3}[0-9]{4,}$"^^ . + "Allotrope Merged Ontology Suite" . + . + . + "false"^^ . + . + . + "NASA GeneLab" . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "Scientific Evidence and Provenance Information Ontology" . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . + "Application ontology for entities related to insecticide resistance in mosquitos"^^ . + . + "3000045"^^ . + "https://www.ebi.ac.uk/gxa/"^^ . + . + "false"^^ . + "false"^^ . + "Human Phenotype Ontology" . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . + . + . + . + . + . + "Nicole Vasilevsky" . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + . + . + . + . + . + . + "Database of Quantitative Cellular Signaling: Model" . + . + . + "false"^^ . + . "http://bioportal.bioontology.org/ontologies/$1"^^ . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - . - "false"^^ . - . - . - . - . - "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^ . - . + . + . + . + . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + "The Human Phenotype Ontology (HPO) aims to provide a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM."^^ . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + "http://www.metabolomicsworkbench.org/"^^ . + . + . + . + . + . + "http://archive.gramene.org/db/ontology/search?query=EO:$1"^^ . + . + . + "9861/3"^^ . + . + . + . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "0000574"^^ . + . + . + "https://cordis.europa.eu/project/id/$1"^^ . + . + . + . + "^\\w+$"^^ . + . + "true"^^ . + . + "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . + . + . + . + "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . + . + . + "0000010"^^ . + . + . + "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . + . + "false"^^ . + "Agronomy Vocabulary" . + . + "http://purl.obolibrary.org/obo/XAO_$1"^^ . + . + . + . + . + . + . + . + "MMP3312982.2"^^ . + . + . + . + "3"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + "^MSMEG\\w+$"^^ . + "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . + "https://github.com/MIT-LCP/mimic-omop"^^ . + . + . + . + . + . + . + . + "https://www.uniprot.org/tissues/$1"^^ . + . + "^[A-Za-z0-9]+$"^^ . + "1664"^^ . + . + . + "1a05"^^ . + . + . + . + . + . + . + . + . + . + "FBtr0084214"^^ . + . + . + "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . + "YRC PDR" . + . + "https://www.wikidata.org"^^ . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "https://flybase.org/reports/FBrf$1"^^ . + "false"^^ . + . + . + . + "http://vocab.getty.edu/page/tgn/$1"^^ . + "https://glygen.org/glycan/"^^ . + . + "https://prefix.cc/" . + "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . + "false"^^ . + . + . + . + "Sorghum TDv5 - Oct 2019"^^ . + . + . + . + . + "^IM-\\d+(-?)(\\d+?)$"^^ . + . + . + . + "SL-0002"^^ . + . + . + "http://geneontology.org/"^^ . + "https://skip.stemcellinformatics.org/en/"^^ . + . + . + . + . + . + . + "Gramene QTL" . + . + . + . + . + . + "https://www.nlm.nih.gov/research/umls"^^ . + "Process Chemistry Ontology" . + "false"^^ . + . + "Phytozome is a project to facilitate comparative genomic studies amongst green plants. Famlies of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. This collection references locus information."^^ . + . + "false"^^ . + . + "Gene Ontology Registry" . + . + . + . + . + . + . + "PhosphoSite Site Group" . + "https://bacteria.ensembl.org/id/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . + . + . + . + "false"^^ . + . + . + "2200950"^^ . + . + . + "BT20_BREAST"^^ . + "0000008"^^ . + . + . + "https://data.4dnucleome.org/biosources/$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + "3G6A5W338E"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.wormbase.org/db/seq/protein"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "PANTHER Node" . + . + . + "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . + . + . + . + . + . + "https://www.reactome.org/"^^ . + "false"^^ . + "http://umbbd.ethz.ch/servlets/pageservlet?ptype=allrules"^^ . +_:Na0aa5749d1e349baa4882573a6e90561 "Matt Berriman" . + . + . + . + . + "LOC_Os01g49190.1"^^ . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + . + . + "ModelDB" . + "false"^^ . + "http://purl.obolibrary.org/obo/OPL_$1"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "https://www.araport.org/"^^ . + "false"^^ . + . + "DailyMed" . + . + . + "Vitis ontology" . + . + . + . + . + . + . + . + "http://genome.crg.es/datasets/abs2005/"^^ . + . + . + "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there."^^ . + . + . + . + . + . + "^[a-z]+(\\..*?)?$"^^ . + . + . + . + . + . + . + . + . + . + "https://bioinformatics.cineca.it/PMDB/"^^ . + . + . + "https://github.com/bio-ontology-research-group/unit-ontology"^^ . + . + "000000012281955X"^^ . + "https://www.wwpdb.org/pdb?id=$1"^^ . + . + . + . + . + . + . + . + "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . + . + . + . + . + "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . + . + "http://www.yeastgenome.org/"^^ . + . + . + . + "International repository of Adverse Outcome Pathways."^^ . + . + . + . + . + "https://www.merckmillipore.com/"^^ . + . + "https://github.com/tis-lab/reagent-ontology"^^ . + . + . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + . + "false"^^ . + . + "^(C|D)\\d{6,9}$"^^ . + . + "false"^^ . + . + . + "NMR Restraints Grid" . + . + "https://books.google.com"^^ . + "https://pathbank.org/view/$1"^^ . + "MetaCyc Reaction" . + . + . + . + . + "false"^^ . + . + "0000047"^^ . + "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology"^^ . + . + "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "https://smpdb.ca/view/$1"^^ . + . + . + . + . + "false"^^ . + "false"^^ . + "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . + "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . + . + . + . + . + . + . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . + . + . + . + . + . + . + . + . + "^r\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/fbcv"^^ . + . + . + . + . + "https://commonchemistry.cas.org/"^^ . + "false"^^ . + . + "CALM1"^^ . + . + "^PA\\d+$"^^ . + . + . + . + "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . + "http://purl.obolibrary.org/obo/AAO_$1"^^ . + "3966782"^^ . + . + . + . + . + "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . + "SMP0000219"^^ . + . + "https://medlineplus.gov/genetics/condition/$1"^^ . + "Chemical Information Ontology" . + . + . + . + "National Library of Medicine Catalog" . + . + "Mouse Brain Atlas" . + "Biological Spatial Ontology" . + . + "false"^^ . + . + . + . + "false"^^ . + "https://www.biomodels.net/kisao/KISAO#KISAO_$1"^^ . + . + . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb"^^ . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . + . + . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . + "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . + . + "Psychology Ontology" . + "31623"^^ . + . + . + . + "1000"^^ . + . + . + . + "http://purl.obolibrary.org/obo/AERO_$1"^^ . + . + "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . + . + "http://www.coloncanceratlas.org"^^ . + "false"^^ . + . + "false"^^ . + "Lipid Ontology" . + . + "^\\d+$"^^ . + . + "https://www.genome.jp/kegg/drug/"^^ . + "https://cropontology.org/ontology/CO_324/Sorghum"^^ . + . + "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . + . + . + "https://sumlineknowledgebase.com/"^^ . + . + "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . + "6b1"^^ . + "false"^^ . + . + . + "^RCV\\d+(\\.\\d+)?$"^^ . + "false"^^ . + "0000054"^^ . + . +_:N907212973ffd49a0a6ebca87b43aea0e "Animal Diversity Web technical staff" . + . + . + . + . + . + "The Mammalian Feeding Muscle Ontology is an antomy ontology for the muscles of the head and neck that participate in feeding, swallowing, and other oral-pharyngeal behaviors."^^ . + . + . + "The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family. It contains sets of curated homeodomain sequences from fully sequenced genomes, including experimentally derived homeodomain structures, homeodomain protein-protein interactions, homeodomain DNA-binding sites and homeodomain proteins implicated in human genetic disorders."^^ . + . + "Flora Phenotype Ontology" . + "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . + "^[A-Z0-9]+$"^^ . + . + . + . + "https://www.deciphergenomics.org/"^^ . + "^\\d{7}$"^^ . + "Pubmed Central" . + . + . + . + . + "^\\d{7}$"^^ . + "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . + "http://n2t.net/"^^ . + "false"^^ . + . + . + . + . + . + . + "^\\S+$"^^ . + . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . + "false"^^ . + . + . + . + . + . + . + "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . + "Drosophila gross anatomy" . + . + . + "false"^^ . + . + "GitHub Pull Request" . + . + . + . + . + . + . + "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . + . + "GrainGenes" . + . + . + "0000000"^^ . + . + "http://www.sparontologies.net/ontologies/datacite"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/PubMed/"^^ . + . + "https://gdc.cancer.gov"^^ . + . + . + . + "https://reaxys.emolecules.com"^^ . + . + . + "false"^^ . + . + . + . + "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + "C. elegans ORFeome cloning project" . + . + . + . + . + . + . + . + . + "https://www.wikidata.org/wiki/Property:$1" . + . + . + "Influenza Ontology" . + "Malaria Ontology" . + . + . + "http://purl.obolibrary.org/obo/HAO_$1"^^ . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://rgd.mcw.edu/rgdweb/ontology/annot.html?acc_id=PW:$1"^^ . + . + "Hector Escriva" . + . + "0000685"^^ . + . + . + . + . + . + . + . + "Protein Data Bank Ligand" . + "http://www.genome.jp/kegg/catalog/org_list.html"^^ . + . + "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . + . + . + . + . + . + . + . + . + "http://www.peptideatlas.org/PASS/$1"^^ . + "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . + "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . + . + . + . + . + "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . + "26957"^^ . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual models."^^ . + . + . + . + . + . + "http://www.loria.fr/~coulet/sopharm2.0_description.php"^^ . + . + . + . + "O80725"^^ . + . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to enzyme information."^^ . + . + . + . + . + "GO Evidence Code" . + "https://www.internationalgenome.org/data-portal/sample/$1"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . + . + "http://www.pombase.org/"^^ . + . + . + . + "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . + . + . + "The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download."^^ . + . + . + . + . + . + "ACYPI000159"^^ . + . + . + . + "CCDS13573.1"^^ . + . + . + "Cellosaurus Registry" . + "false"^^ . + "Cooperative Patent Classification" . + . + . + . + "https://co.mbine.org/specifications/$1"^^ . + . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . + . + . + "http://www.genome.jp/kegg/ko.html"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "UniProt Post-Translational Modification" . + "Yeast Metabolome Database" . + "^\\d{7}$"^^ . + . + . + . "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - . - . - . - . - . - . - . - . - . - "ENSGT00550000074763"^^ . - . - . - . - . - "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . - "http://bioinfo.iitk.ac.in/MIPModDB"^^ . - . - . - "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . - "false"^^ . - . - . - . - . - . + . + . + "false"^^ . + . + . + . + "Ensembl Protists" . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "Frédéric Bastian" . + . + . + . + . + . + . + . + . + "FlowRepository is a database of flow cytometry experiments where you can query and download data collected and annotated according to the MIFlowCyt standard. It is primarily used as a data deposition place for experimental findings published in peer-reviewed journals in the flow cytometry field."^^ . + . + "http://purl.obolibrary.org/obo/EPIO_$1"^^ . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . + "^\\d+$"^^ . + . + . + . + "https://registry.identifiers.org/registry/$1" . + . + . + "^HBG\\d+$"^^ . + . + . + "^RF\\d{5}$"^^ . + "OncoTree" . + . + "The Human Protein Atlas (HPA) is a publicly available database with high-resolution images showing the spatial distribution of proteins in different normal and cancer human cell lines. Primary access to this collection is through Ensembl Gene identifiers."^^ . + . + . + . +_:N78c3148fdc9e429f9a7d8c471866311e "Stephen Larson" . + "0000255"^^ . + "Signaling Gateway" . + . + . + . + "version Dec 2019"^^ . + . + . + . + . + . + . + . + . + "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . + . + . + "Name-to-Thing" . + "false"^^ . + "false"^^ . + "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . + . + . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . + . + "GlycoNAVI" . + . + "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . + "The Tree of Life Web Project (ToL) is a collaborative effort of biologists and nature enthusiasts from around the world. On more than 10,000 World Wide Web pages, the project provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history (phylogeny). \r\n\r\nEach page contains information about a particular group, with pages linked one to another hierarchically, in the form of the evolutionary tree of life. Starting with the root of all Life on Earth and moving out along diverging branches to individual species, the structure of the ToL project thus illustrates the genetic connections between all living things."^^ . + . + . + "https://icahn.mssm.edu/"^^ . + "^\\d{7}$"^^ . + "Maize gross anatomy" . + "http://purl.obolibrary.org/obo/CDAO_$1"^^ . + "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . + . + . + . + . + "A type for entries in the Bioregistry's registry." . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT"^^ . + . + . + . + . + . + "false"^^ . + . + "485991"^^ . + "Cell line collections"^^ . + . + . + . + . + "DI-04240"^^ . "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . - . - "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . - . - . - . - . - . - . - . - . - "0000003"^^ . - . - . - . - . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - "^M\\d+$"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . + . + . + . + . + "ExAC Transcript" . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Record Report, based on RCV accession."^^ . + . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + . + "false"^^ . + . + . + . + . + "http://zfin.org/$1"^^ . + "Social Insect Behavior Ontology" . + . + "AutDB is a curated database for autism research. It is built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The four modules of AutDB include information on Human Genes, Animal models, Protein Interactions (PIN) and Copy Number Variants (CNV) respectively. It provides an annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder."^^ . + . + "Animal Genome Cattle QTL" . + "http://edamontology.org/data_$1"^^ . + . + "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.allergome.org/"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "https://ssbd.riken.jp"^^ . + . + "ReviewVersion"^^ . + . + "http://rebase.neb.com/rebase/enz/$1.html"^^ . + . + . + . + . + "http://www.oid-info.com/introduction.htm"^^ . + . + "KEGG Enzyme" . + . + "true"^^ . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . + "https://plants.ensembl.org/"^^ . + . + . + . + . + . + "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . + . + "030719"^^ . + . + . + . + . + . + . + "^[a-zA-Z0-9_\\.]+$"^^ . + . + . + "false"^^ . + . + . + "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . + "http://www.aspgd.org/"^^ . + . + . + . + . + "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . + . + . + . + . + "EBI-366083"^^ . + . + "An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow)."^^ . + . + . + . + "Population and Community Ontology" . + . + . + "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . + . + . + . + . + . + "false"^^ . + . + "Teleost Anatomy Ontology" . + . + . + "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . + . + . + . + "Guide to Pharmacology Target" . + . + . + . + . + . + . + . + "GeneTree" . + . + . + . + . + "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . + . + "Pablo Porras Millán" . + . + . + . + . + . + "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . + . + "A0118748"^^ . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . + . + . + . + . + . + . + . + "Linear double stranded DNA sequences" . + . + "false"^^ . + . + . + . + . + "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "0002066"^^ . + . + "http://purl.obolibrary.org/obo/CTENO_$1"^^ . + . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + . + "Oral Health and Disease Ontology" . + "false"^^ . + . + "false"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . + "https://webbook.nist.gov/chemistry/"^^ . + "CE28239"^^ . + "true"^^ . + "Genotype Ontology" . + "false"^^ . + "https://www.alzforum.org/mutations"^^ . + . + "2"^^ . + . + . + . + "https://github.com/bgsu-rna/rnao"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "http://www.proteinmodelportal.org/"^^ . + "0000015"^^ . + . + "2000191"^^ . + "^(\\w+)?\\d+$"^^ . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . + . + . + "phs000768.v2.p1"^^ . + . + . + "https://easychair.org/cfp/"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "81944ba1-81d0-436e-8552-33d77a27834b"^^ . + . + "prefLabel"^^ . + . + . + . + . + . + . + . + . + . + "The Astrophysics Source Code Library (ASCL) is a free online registry for software that have been used in research that has appeared in, or been submitted to, peer-reviewed publications. The ASCL is indexed by the SAO/NASA Astrophysics Data System (ADS) and Web of Science's Data Citation Index (WoS DCI), and is citable by using the unique ascl ID assigned to each code. The ascl ID can be used to link to the code entry by prefacing the number with ascl.net (i.e., ascl.net/1201.001)."^^ . + . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "Interaction Network Ontology" . + . + . + . + . + "familyName"^^ . + . + . + . + . + . + . + "WiCell Research Institute Cell Collection" . + . + . + . + "47419"^^ . + . + . + . + . + . + . + . + . + "Dublin Core" . + . + _:N5fed7daf26c145b8b2a06ae29999a945 . + . + "http://www.orpha.net/ORDO/Orphanet_$1"^^ . + "Pharmacogenetics and Pharmacogenomics Knowledge Base" . + . + "https://github.com/obophenotype/caro/"^^ . + . + "https://archive.softwareheritage.org/browse/swh:$1"^^ . + "http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . + . + . + . + . + . + . + "YOR172W_571.0"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ECTO_$1"^^ . + . + "0000639"^^ . + "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . + . + "Biological Imaging Methods Ontology" . + . + . + . + . + . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + . + . + . + "Carissa Park" . + . + . + "Ontology Concept Identifiers" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . + "Glycine max Genome Database" . + . + . + . + _:N02c318a846114c1b8cea4e7ba1bc42d4 . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://licebase.org/?q=$1"^^ . + . + "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^ . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . + . + . + "https://ssbd.riken.jp/database/dataset/$1"^^ . + "http://www.pocketome.org/sfSearch.cgi?act=browseall"^^ . + "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . + . + . + . + "http://bacmap.wishartlab.com/"^^ . + "Electron Microscopy Public Image Archive" . + . + . + . + "https://github.com/SpeciesFileGroup/nomen"^^ . + "HMDB00001"^^ . + . + . + . + . + "https://www.proteomicsdb.org/#peptideSearch"^^ . + . + "Ion Channel Electrophysiology Ontology" . + "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . + "H-InvDb Protein" . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + . + "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . + . + "Nucleotide Sequence Database" . + . + . + . + . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + . + . + . + "BE0000048"^^ . + "906801"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + "http://variationontology.org"^^ . + "false"^^ . + "neXtProt family" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . + "http://probonto.org"^^ . + . + . + . + . + . + "0000002"^^ . + . + . + . + "Human Protein Atlas tissue profile information" . + "^LSM-\\d+$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/MAXO_$1"^^ . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl"^^ . + . + "http://purl.obolibrary.org/obo/INO_$1"^^ . + "^[-A-Za-z0-9\\_]*$"^^ . + . + . + . + . + "AGRO" . + . + . + . + . + . + "https://github.com/jannahastings/mental-functioning-ontology"^^ . + "https://schema.org"^^ . + . + . + "https://www.kerafast.com/Search?SearchTerm="$1""^^ . + . + "^\\d+$"^^ . + "https://github.com/ufbmi/OMRSE/wiki/OMRSE-Overview"^^ . + . + . + . + "AOPWiki (Key Event Relationship)" . + "Global biodiversity database on finfishes. It offers a wide range of information on all species currently known in the world: taxonomy, biology, trophic ecology, life history, and uses, as well as historical data reaching back to 250 years."^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ena/browse/genome-assembly-database"^^ . + . + . + . + "false"^^ . + . + "https://cropontology.org/ontology/CO_346/Mungbean"^^ . + . + . + "^\\d+$"^^ . + "DrugBank Salts" . + . + . + . + "1784"^^ . + . + . + "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . + . + . + "137"^^ . + . + "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . + "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . + . + . + "http://purl.org/pav/$1"^^ . + . + . + . + . + . + . + . + "Microbial Protein Interaction Database" . + . + . + "General Standard for Food Additives Online Database" . + . + "Cereal Plant Gross Anatomy" . + "http://purl.obolibrary.org/obo/WBbt_$1"^^ . + "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . + . + . + "S7000002168151102"^^ . + . + "1915"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "^\\d{4}$"^^ . + "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . + . + . + "false"^^ . + . + "Chemical Entities of Biological Interest" . + . + . + "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . + . + "International Classification of Diseases, 10th Revision, Procedure Coding System" . + . + "https://www.uniprot.org/diseases/"^^ . + . + . + . + . + "The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. > This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO. "^^ . + . + "https://doi.org/$1"^^ . + "http://wheat.pw.usda.gov"^^ . + . + . + . + "Gramene Growth Stage Ontology" . + "false"^^ . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . + . + . + . + . + . + . + . + . + "^oai\\:cwi\\.nl\\:\\d+$"^^ . + . + . + . + "TriTrypDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://eggnog.embl.de/version_3.0/"^^ . + "https://cropontology.org/ontology/CO_339/Lentil"^^ . + "G00054MO"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "^UPC\\d{5}$"^^ . + . + "false"^^ . + . + . + "https://www.w3.org/TR/owl-time/"^^ . + . + "Sequence types and features ontology" . + "Ontology about the development and life stages of the C. elegans"^^ . + "HGVPM623"^^ . + . + . + . + . + . + "ABE-0009634"^^ . + "Bjoern Peters" . + "https://icd.who.int/"^^ . + "http://purl.obolibrary.org/obo/FOVT_$1"^^ . + . + . + "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . + . + "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . + . + . + . + . + . + "T30002"^^ . + . + "0000171"^^ . + . + . + . + "false"^^ . + . + "BRENDA Ligand" . + "false"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "^PED\\d{5}$"^^ . + . + . + . + . + . + "Signaling Network Open Resource" . + "Tom Gillespie" . + . + "MolMeDB" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . + . + . + . + . + . + . + . + "MIRIAM Registry collection" . + . + "ArachnoServer" . + . + "false"^^ . + "https://www.ebi.ac.uk/ols/ontologies/cheminf/terms?iri=http%3A%2F%2Fsemanticscience.org%2Fresource%2FCHEMINF_$1" . + . + . + . + . + . + . + . + "^\\w+\\d+$"^^ . + . + . + "^T\\d{3}$"^^ . + . + . + . + . + . + "false"^^ . + . + "AT4G01080"^^ . + "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . + "Dictyostelium discoideum phenotype ontology" . + . + "http://purl.obolibrary.org/obo/XPO_$1"^^ . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + . + . + "PGS000018"^^ . + "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . + "https://www.cellbankaustralia.com/$1.html"^^ . + . + "https://www.ncbi.nlm.nih.gov/books/$1"^^ . + "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . + . + . + "Assists in resolving data across cloud resources."^^ . + . + "The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Each disease entry contains a list of known genetic factors (disease genes), environmental factors, diagnostic markers, and therapeutic drugs. Diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system."^^ . + "GitHub Issue" . + "00000021"^^ . + . + "^DB-\\d{4}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + _:N1e27e616ec1647758de207a85c698acd . + "false"^^ . + . + "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . + . + . + . + . + . + "Allen Institute Ontologies" . + . + "E-MEXP-1712"^^ . + "^FB\\w{2}\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . + "GPIb_IX_V"^^ . + "^\\d{8}$"^^ . + . + . + . + "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . + "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + . + . + . . - . - . - "Polygenic Score Catalog" . - . - . - "http://www.chemspider.com/inchikey=$1"^^ . - "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . - . - . - "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . - . - . - "https://github.com/pombase/fypo"^^ . - . - . - . - . - "CC-BY-1.0"^^ . - . - . - . - . - . - "https://coconut.naturalproducts.net"^^ . - "http://www.p3db.org/"^^ . - . - . - . - . - . - . - "https://aopwiki.org/"^^ . + "An ontology written in OWL 2 DL to enable characterization of the five attributes of an online journal article - peer review, open access, enriched content, available datasets and machine-readable metadata."^^ . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://drs.microbiomedata.org/objects/$1"^^ . + . + . + . + "1cukA01"^^ . + . + . + . + . + . + . + . + . + . + . + "10.1101/2022.07.08.499378"^^ . + . + . + . + . + "^[0-9\\.]+$"^^ . + "Database of Genomic Structural Variation - Study" . + . + . + "TopFind" . + . + . + "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . + "https://cropontology.org/ontology/CO_348/Brassica"^^ . + . + . + . + . + . + "https://bionumbers.hms.harvard.edu"^^ . + "DisProt" . + . + . + . + . + "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . + . + . + "ClinicalTrials.gov" . + . + . + . + . + "^\\d{7}$"^^ . + "https://medical-data-models.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + . + "Toxic Process Ontology" . + . + "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . + "http://zinc15.docking.org/substances/$1"^^ . + "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "MetaNetX chemical" . + "PubChem Classification" . + . + . + "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . + . + "Biolink Model Registry" . + . + "https://www.ccdc.cam.ac.uk/"^^ . + . + . + "101"^^ . + . + "Bill Duncan" . + . + . + "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . + . + . + . + . + . + . + "c0001"^^ . + . + "http://biohackathon.org/resource/faldo"^^ . + . + "^\\w+$"^^ . + "Pocketome" . + . + "^\\d{4,}((_[asx])?_at)$"^^ . + "B2067"^^ . + . + . + . + "http://rna.rega.kuleuven.be/rnamods/"^^ . + . + . + "^[1-9]\\d{0,6}$"^^ . + "label"^^ . + . + . + . + "^\\w+$"^^ . + . + . + "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . + . + . + . + . + "http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=$1"^^ . + . + "FunderRegistry" . + "http://www.ebi.ac.uk/chebi"^^ . + . + . + . + . + "0000400"^^ . + . + "CORDIS Article" . + . + . + . + . + "http://www.cathdb.info/cathnode/$1"^^ . + . + . + "false"^^ . + . + . + "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . + . + "Veterans Health Administration (VHA) unique identifier" . + . + . + . + . + . + "http://www.genome.jp/kegg/disease/"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "https://www.ebi.ac.uk/biostudies/"^^ . + "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . + "http://www.genome.jp/kegg/reaction/"^^ . + . + . + "^M[0-9]{4,}$"^^ . + . + "https://dandiarchive.org/"^^ . + "0010034"^^ . + "false"^^ . + "^GR\\:\\d+$"^^ . + "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . + "CIP - potato ontology - december 2018"^^ . + . + "runBioSimulations" . + "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . + . + . + . + . + "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . + "http://edamontology.org/topic_$1"^^ . + "true"^^ . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria tuberculosis information."^^ . + . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . + . + . + . + "https://www.gbif.org/species/$1"^^ . + . + . + . + . + . + . + "DragonDB Allele" . + . + . + . + . + "https://www.gtexportal.org"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "^\\d+$"^^ . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . + . + "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . + "ECOCYC"^^ . + "Structural Classification of Protein" . + . + "Common Bean ontology" . + . + . + . + "false"^^ . + . + . + . + . + . + "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . + "https://www.kegg.jp/entry/$1"^^ . + . + . + . + . + "https://pk-db.com/data/$1"^^ . + . + . + . + "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . + "http://purl.obolibrary.org/obo/MO_$1"^^ . + . + . + . + . + "US4145692"^^ . + "https://github.com/DIDEO/DIDEO"^^ . + . + . + "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . + . + . + "^\\d+$"^^ . + "Database of Sequence Tagged Sites" . + . + . + "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . + . + . + . + "M1"^^ . + . + "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . + . + . + "0001707"^^ . + . + "false"^^ . + . + . + "Phy000CLXM_RAT"^^ . + "Complex Portal" . + . + . + . + . + "Marie-Angélique Laporte" . + . + "^[0-9]+:[0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + "A database for Triticeae and Avena gene symbols."^^ . + "Bloomington Drosophila Stock Center" . + . + . + . + . + "Consensus CDS" . + "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . + . + . + . + . + . + . + "Mouse adult gross anatomy" . + "false"^^ . + "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . + . + . + "648028003"^^ . + "^OSR\\d{4}$"^^ . + "false"^^ . + . + "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . + . + . + . + "false"^^ . + . + . + . + . + "^[WAICV]\\d{2,}$"^^ . + "https://www.cdc.gov/nchs/icd/icd9.htm"^^ . + . + . + "https://www.ensembl.org/id/$1"^^ . + "MCDS_C_0000000001"^^ . + . + . + . + "https://www.ebi.ac.uk/biosamples/"^^ . + . + . + "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . + . + "false"^^ . + . + "^TS-\\d{4}$"^^ . + . + "http://search.sisuproject.fi/#/variant/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv"^^ . + . + . + . + "^\\d{7}$"^^ . + "1351341"^^ . + "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . + "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . . - . - . - "http://www.gudmap.org/"^^ . - . - "http://neurovault.org"^^ . - "false"^^ . - "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . - . - "false"^^ . - . - "https://cropontology.org/ontology/CO_359/Sunflower"^^ . - . + . + . + . + "CTD Gene" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.abmgood.com/catalogsearch/result/?cat=&q=$1"^^ . + "false"^^ . + . + "Gramene Taxonomy" . + "Ontology of Host Pathogen Interactions" . + "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . + "CAPS-DB" . + . + "http://www.sbgnbricks.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "A registry of commonly used prefixes in the life sciences and linked data" . + . + "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "^\\d{6}$"^^ . + . + . + "http://stitch.embl.de/interactions/$1"^^ . + . + "^\\d+$"^^ . + "A representation of the variety of methods used to make clinical and phenotype measurements. "^^ . + . + . + . + . + "^\\d+$"^^ . + "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . + "https://gitlab.com/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . + . + "Archival Resource Key" . + "Radiation Biology Ontology" . + "https://github.com/AgriculturalSemantics/agro"^^ . + . + "false"^^ . + "false"^^ . + . + "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . + "The Python Package Index (PyPI) is a repository for Python packages."^^ . + . + . + "FuTRES Ontology of Vertebrate Traits" . + "Lentil ontology" . + . + . + "https://www.ebi.ac.uk/citexplore/"^^ . + "CA981206459"^^ . + . + . + "Hazardous Substances Data Bank" . + . + . + "Cell line databases/resources"^^ . + . + . + . + . + . + . + . + "true"^^ . + . + "SPIKE (Signaling Pathways Integrated Knowledge Engine) is a repository that can store, organise and allow retrieval of pathway information in a way that will be useful for the research community. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways. Pathways are regularly updated, and additional pathways are gradually added. The complete database and the individual maps are freely exportable in several formats. This collection references pathway maps."^^ . + . + . + "https://www.webelements.com/"^^ . + "Intrinsically Disordered Proteins Ontology" . + "^\\d+$"^^ . + . + "375364"^^ . + . + . + . + . + "^PIRSF\\d{6}$"^^ . + . + "^\\d+$"^^ . + . + . + "https://www.vmh.life/"^^ . + . + . + . + . + . + "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . + . + . + . + . + . + "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . + "https://github.com/obophenotype/planarian-phenotype-ontology"^^ . + . + . + "false"^^ . + . + . + . + . + "Jennifer C. Girón" . + . + "chebi" . + "NIF Standard Ontology: Neurolex" . + . + . + "Colorectal Cancer Atlas" . + "^\\d{7}$"^^ . + "MimoDB" . + . + . + . + "https://w3id.org/faircookbook/$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + "0001017"^^ . + . + . + . + "https://www.jax.org/strain"^^ . + . + "BIOMD0000000048"^^ . + "The allele registry provides and maintains identifiers for genetic variants"^^ . + . + "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . + "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . + . + "^\\d+$"^^ . + . . - . - . - . - . - "HPA000698"^^ . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "developed by ICARDA - Dec 2018"^^ . - "Ontology for Parasite LifeCycle" . - "https://ocid.ontochem.com/prefname?ocid=$1"^^ . - . - . - . - "^CAL\\d{7}$"^^ . - "http://sideeffects.embl.de/"^^ . - "https://rapdb.dna.affrc.go.jp/"^^ . - . - . - . - "http://www.ncbi.nlm.nih.gov/unigene"^^ . - "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . - "https://flybase.org"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "VegBank" . - "Cell line collections"^^ . + . + . + . + . + . + . + . + . + "hsa-let-7a"^^ . + . + . + "CAE46076"^^ . + . + "A gazetteer constructed on ontological principles"^^ . + . + . + "Ontology of Precision Medicine and Investigation" . + . + "false"^^ . + . + . + . + . + . + . + . + . + "An anatomical and developmental ontology for cephalopods"^^ . + "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . + . + . + . + "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . + . + "https://www.flymine.org/come/entry?gn=$1"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "Cancer cell LInes GEne fusions portAl" . + . + . + . + "Sofia Robb" . + . + "https://www.kew.org/data/grasses-db/www/$1"^^ . + . + "0001807"^^ . + . + "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . + . + . + "3618"^^ . + . + . + "false"^^ . + . + . + . + "The GWAS Catalog provides a consistent, searchable, visualisable and freely available database of published SNP-trait associations, which can be easily integrated with other resources, and is accessed by scientists, clinicians and other users worldwide."^^ . + . + "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . + . + . + . + "AgroPortal" . + "^M\\d+$"^^ . + "VIRsiRNA" . + . + . + . + . + "UNITE is a fungal rDNA internal transcribed spacer (ITS) sequence database. It focuses on high-quality ITS sequences generated from fruiting bodies collected and identified by experts and deposited in public herbaria. Entries may be supplemented with metadata on describing locality, habitat, soil, climate, and interacting taxa."^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . + . + . + "LCL-2085"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "http://www.depod.bioss.uni-freiburg.de"^^ . + . + . + . + "0000001"^^ . + . + "false"^^ . + . + . + . + "051"^^ . + . + . + . + . + "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . + . + "5688061"^^ . + "http://multicellds.org/MultiCellDB.php"^^ . + "AOPWiki (Key Event)" . + . + . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . + . + . + "http://merops.sanger.ac.uk/index.htm"^^ . + . + "PaxDb is a resource dedicated to integrating information on absolute protein abundance levels across different organisms. Publicly available experimental data are mapped onto a common namespace and, in the case of tandem mass spectrometry data, re-processed using a standardized spectral counting pipeline. Data sets are scored and ranked to assess consistency against externally provided protein-network information. PaxDb provides whole-organism data as well as tissue-resolved data, for numerous proteins. This collection references individual protein abundance levels."^^ . + . + "^\\w+$"^^ . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "ICEberg family" . + "sourceDateStart"^^ . + . + "^\\w+$"^^ . + . + . + . + "BioStudies database" . + . + . + . + "Immune Epitope Database" . + . + . + . + . + . + . + "^CONSO\\d{5}$"^^ . + . + "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . + . + . + . + . + "Medical Action Ontology" . + "The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO)."^^ . + "12345"^^ . + . + "https://www.glycoepitope.jp/epitopes/$1"^^ . + "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . + "WormBase database of nematode biology" . + . + "https://www.uniprot.org/locations/"^^ . + "https://www.wikidata.org/wiki/Property:$1"^^ . + . + . + . + . + "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . + . + . + . + . + . . - "21723"^^ . - "https://dgrc.bio.indiana.edu/cells/Catalog"^^ . - "Bioregistry" . - "http://www.cathdb.info/cathnode/$1"^^ . - . - "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . - "The allele registry provides and maintains identifiers for genetic variants"^^ . - . - . - "https://cellrepo.ico2s.org/"^^ . - . - "false"^^ . - . - "false"^^ . - "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . - "Genomic Data Commons Data Portal" . - . - . - "BARC-013845-01256"^^ . - . - . - "^\\w+:[\\w\\d\\.-]*$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "https://github.com/obophenotype/mouse-anatomy-ontology"^^ . - . - . - . - . - . - "Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. It analyzes comparable taxonomical samples for all paralogues under consideration, storing functional specialisation at the level of residues. The data are presented as a table of per-residue scores, and mapped onto related structures where available."^^ . - . - "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . - . - . - "RepeatsDB Structure" . - . - . - "BSU29180"^^ . - . - . - "Proteomic Data Commons" . - "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html"^^ . - . - . - "UniProt Chain" . - . - . - . - . - . - . - . - . - "0000253"^^ . - . - . - . - . - "false"^^ . - . - . - "http://mged.sourceforge.net/ontologies/MGEDontology.php"^^ . - "Protein Model Database" . - . - "CL070"^^ . - . - . - . - . - . - . - "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1"^^ . - . - "265"^^ . - . - "Development Data Object Service" . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - . - "14362"^^ . - . - . - "Animal Genome Chicken QTL" . - "false"^^ . - . - . - "0000000"^^ . - . - . + . + "https://cellmodelpassports.sanger.ac.uk/"^^ . + . + "http://130.88.97.239/dbbrowser/sprint/"^^ . + . + "MassBank" . + . + . + "AspGD Protein" . + . + . + . + . + "http://neurovault.org"^^ . + . + . + . + . + . +_:N53c97813ee374354bc16b388728eb62a "Plant Ontology Administrators" . + . + . + . + . + . + . + "0187632"^^ . + . + . + . + . + . + . + . + "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . + . + . + . + . + "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . + . . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "1868"^^ . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS cell model system can have the following cell categories: cell lines, primary cells, induced pluripotent stem cells, differentiated cells, and embryonic stem cells. The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease."^^ . - . - . - "00103"^^ . - "^\\d+\\-\\d+\\-\\d+$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . - . - "https://github.com/obcs/obcs"^^ . - . - . - "PharmGKB Pathways" . - "SysBioCancer2022"^^ . - "^\\d{7}$"^^ . - . - "http://www.cellsignal.com/pathways/index.html"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . - "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . - "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^ . - "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . - . - . - "false"^^ . - . - "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . - "ppr103739"^^ . - . - "Wikipedia is a multilingual, web-based, free-content encyclopedia project based on an openly editable model. It is written collaboratively by largely anonymous Internet volunteers who write without pay."^^ . - . - . - "M0001"^^ . - . - . - . - . - "Google Patents" . - . - . - . - "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . - . - . - . - "^PA\\d+$"^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . - "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "Human Endogenous Retrovirus Database" . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . - . - "false"^^ . - . - "false"^^ . - "PMC3084216"^^ . - . - . - . - . - "MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . - . - . - . - . - "http://cerevisiae.oridb.org/details.php?id=$1"^^ . - "http://www.loria.fr/~coulet/sopharm2.0_description.php"^^ . - . - . - "Ecological terms"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.imgt.org/"^^ . - . - "https://nmrshiftdb.nmr.uni-koeln.de"^^ . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . - . + . + . + . + . + . + . + . + . + . + "IHW09326"^^ . + "Simplified molecular-input line-entry system" . + . + . + . + "false"^^ . + . + "SPCC13B11.01"^^ . + . + . + . + "^[A-Za-z0-9\\-\\_]+$"^^ . + . + "Scopus Researcher" . + . + . + . + "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . + . + . + "S1"^^ . + . + "false"^^ . + . + "Mouse Developmental Stages" . + . + . + "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + "https://www.ncbi.nlm.nih.gov/homologene/"^^ . + . + . + . + . + "^SAM[NED](\\w)?\\d+$"^^ . + . + "VMH reaction" . + . + . + . + . + "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . + . + . + . + . + . + . + "https://github.com/cyang0128/Nutritional-epidemiologic-ontologies"^^ . + . + "https://www.disprot.org/idpo/IDPO:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://glyconavi.org/hub/?id=$1"^^ . + . + . + . + "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . + "BioSystems" . + . + . + . + . + . + . + . "http://stato-ontology.org/"^^ . - "false"^^ . - . - . - "PTPN1"^^ . - . - . - "false"^^ . - . - "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . - "SNR17A"^^ . - . - . - "https://prefix.cc/" . - . - . - . - "https://www.drugbank.ca/categories/$1"^^ . - . - . - . - "https://cellmodelpassports.sanger.ac.uk/"^^ . - . - _:Nbd5897134eac42569c7558a528fd2f83 . - . - . + . + . + "false"^^ . + . + . + "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . + . + . + . + . + . + . + . + . + . + . + . "NMR Shift Database" . - . - . - . - . - . - . - . - "http://www.sequenceontology.org/miso/current_release/term/SO:$1"^^ . - "Gramene protein" . - "false"^^ . - . - . - . - . - . - "http://www.tcdb.org/search/result.php?tc=$1"^^ . - . - . - . - "https://www.genedb.org/"^^ . - . - . - . - "false"^^ . - "https://icahn.mssm.edu/"^^ . - "^\\d{7}$"^^ . - "http://ddinter.scbdd.com"^^ . - . - "http://www.brenda-enzymes.org"^^ . - . - . - "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . - . - . - . - . - . - . - . - . - "H-InvDb Protein" . - "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . - . - "1018"^^ . - . - . - . - . - . - . - . - . - "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . - . - . - "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . - "https://cameo3d.org"^^ . - . - "648028003"^^ . - . - "false"^^ . - "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . - . - "false"^^ . - "ClinVar Variation" . - . - . - . - "^[SCTAGMNU]\\d+$"^^ . - . - "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . - "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . - . - . - . - . - "Zoë May Pendlington" . - . - "false"^^ . - . - "rs121909098"^^ . - "3771877"^^ . - . - . - "false"^^ . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "MRA-253"^^ . + "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://publons.com/researcher/$1"^^ . + . + . + . + "false"^^ . + . + . + "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . + "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . + . + "Comparative Data Analysis Ontology" . + . + . + "false"^^ . + "0000004"^^ . + . + . + . + . + "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . + . + . + . + . + "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . + . + . + "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . + "false"^^ . + . + . + . + . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 3. This was replaced in 2013 by version 4."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "false"^^ . + "https://biopragmatics.github.io/providers/scomp/$1"^^ . + "12345"^^ . + . + . + "http://www.genome.jp/dbget-bin/www_bfind?enzyme"^^ . + . + . + "Ontology for Biobanking" . + "75"^^ . + "0000009"^^ . + . + . + "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . + "^\\d{7}$"^^ . + . + "March 2017 version "^^ . + . + . + . + . + "https://github.com/OOSTT/OOSTT"^^ . + . + . + . + . + "false"^^ . + "The YEast Intron Database (version 3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. An updated version of the database is available through [MIR:00000521]."^^ . + . + . + . + . + . + . + "http://thebiogrid.org/$1"^^ . + "243002_at"^^ . + . + . + "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . + . + . + . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . + . + . + . + "^\\d+$"^^ . + "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . + . + "00100037"^^ . + . + . + . + . + "HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries."^^ . + . + . + . + "World Register of Marine Species" . + . + "XML Schema Definition" . + . + "^\\d+$"^^ . + . + . + "CHEMBL465070"^^ . + "Span" . + . + . + . + . + . + . + "ebf69ca24298b28b2361e7d43eb52d6c"^^ . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . + . + . + "Protein Interaction Network Analysis (PINA) platform is an integrated platform for protein interaction network construction, filtering, analysis, visualization and management. It integrates protein-protein interaction data from six public curated databases and builds a complete, non-redundant protein interaction dataset for six model organisms."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^[A-Z0-9]+$"^^ . + "false"^^ . + . + . + "2842"^^ . + . + "^\\d+$"^^ . + "AOPWiki" . + . + . + . + . + "^T3\\d+$"^^ . + "false"^^ . + . + "pgxbs-kftva5zv"^^ . + . + . + . + . + . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + "https://glytoucan.org"^^ . + "http://bgee.unil.ch/bgee/bgee"^^ . + . + "00000014"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . + . + "false"^^ . + . + . + . + "FOOD00020"^^ . + "http://purl.obolibrary.org/obo/CVDO_$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . + . + . + . + . + . + "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . + . + "false"^^ . + . + . + . + . + "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . + . + "KEGG Module" . + . + . + . + "Lindsay Cowell" . + "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . + "0000048"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/SWO_$1"^^ . + . + . + . + "BioContext contains modular JSON-LD contexts for bioinformatics data." . + "true"^^ . + . + . + "https://labsyspharm.github.io/lspci/"^^ . + "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . + "false"^^ . + . + "FlyBase Qualifiers" . + . + "Mouse Developmental Anatomy Ontology" . + . + "GenPept" . + "false"^^ . + "GO Relations" . + "biopragmatics/bioregistry"^^ . + . + "Mass spectrometry ontology" . + . + . + "^\\d+$"^^ . + "Internal OBO and PyOBO Relations" . + "^\\d+$"^^ . + . + . + . + . + "MNXC15"^^ . + "Pankaj Jaiswal" . + "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/"^^ . + . + "Citlalli Mejía-Almonte" . + . + . + . + . + . + . + "Identifiers.org Registry" . + . + . + . + "9606"^^ . + . + "https://github.com/Display-Lab/psdo"^^ . + . + . + . + . + . + "Fungal gross anatomy" . + "Brachiaria ontology" . + "3"^^ . + . + . + . + . + "Henriette Harmse" . + "BioSample" . + . + "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "Image Data Resource" . + "40565"^^ . + "ZINC1084"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + . + . + . + "D001151"^^ . + . + . + . + . + . + . + . + "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . + "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . + . + . + . + . + "http://www.sequenceontology.org/"^^ . + "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . + . + "Software ontology" . + . + . + . + . + "false"^^ . + . + "https://github.com/Planteome/plant-stress-ontology"^^ . + "^S\\w+(\\.)?\\w+(\\.)?$"^^ . + . + "http://seed-viewer.theseed.org/seedviewer.cgi"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "MIPModDb is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins, identified from complete genome sequence. It provides key information of MIPs based on their sequence and structures."^^ . + . + "false"^^ . + "1.10.10.200"^^ . + . + . + "Terminologia Embryologica" . + . +_:N5c7b97145e734231bba094ae4ad12b0a "Fahim Imam" . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + "Regulation of Gene Expression Ontology" . + . + . + . + . + "https://europepmc.org/article/CTX/$1"^^ . + . + "https://www.xenbase.org/"^^ . + "http://purl.obolibrary.org/obo/COLAO_$1"^^ . + "2022.07.08.499378"^^ . + . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + "90062901"^^ . + . + . + . + "https://cropontology.org/ontology/CO_323/Barley"^^ . + "1981638"^^ . + . + "^\\d{7}$"^^ . + . + "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . + . + "https://cls.shop/$1"^^ . + . + "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + "https://protists.ensembl.org/id/$1"^^ . + "https://github.com/pombase/fypo"^^ . + . + . + . + "The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community."^^ . + "LigandBook" . + . + . + "Ontology of Medically Related Social Entities" . + . + . + "https://www.cropontology.org/rdf/CO_320:$1"^^ . + "^[A-Z-a-z0-9]+$"^^ . + . + "http://www.pharmgkb.org/"^^ . + . + . + . + . + . + . + . + . + . + "Terminology of Anatomy of Human Histology" . + . + . + . + . + "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . + . + . + . + . + . + "BiGG Metabolite" . + . "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . - "https://winter.group.shef.ac.uk/molbase/"^^ . - . - "https://github.com/pcastellanoescuder/FoodBiomarkerOntology"^^ . - "false"^^ . - . - "6200"^^ . - . - . - . - . - "PAp00000009"^^ . - "^\\d{5}$"^^ . + . + . + . + "NIF Standard Ontology: Digital Resources" . + . + . + . + "PerkinElmer cell line collection" . + . + . + "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . + . + "http://purl.obolibrary.org/obo/OHPI_$1"^^ . + . + . + . + . + "https://bioregistry.io" . + "false"^^ . + . + . + "true"^^ . + "https://github.com/SED-ML/KiSAO"^^ . + . + . + . + . + . + "^\\d{8}$"^^ . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + . + "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . + "5282"^^ . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "Compluyeast-2D-DB" . + . + . + "008893080"^^ . + . + . + "https://www.cropontology.org" . + "The International Harmonization of Nomenclature and Diagnostic criteria" . + "false"^^ . + . + . + . + . + . + . + "https://github.com/obophenotype/human-developmental-anatomy-ontology/"^^ . + "BacMap Biography" . + "http://www.t3db.org/"^^ . + . + . + . + . + . + . + . + "0000040"^^ . + . + "https://www.cancerrxgene.org"^^ . + . + "The need of a common ontology for describing orthology information in biological research communities has led to the creation of the Orthology Ontology (ORTH). ORTH ontology is designed to describe sequence homology data available in multiple orthology databases on the Web (e.g.: OMA, OrthoDB, HieranoiDB, and etc.). By sequence homology data, we mostly mean gene region, gene and protein centric orthology, paralogy, and xenology information. Depending on the database, the homology information is structured in different ways. ORTH ontology accommodates these disparate data structures namely Hierarchical Orthologous Group (HOG), cluster of homologous sequences and homologous-pairwise relations between sequences. In addition to the specific ORTH terms, this specification includes terms of the imported ontologies (e.g. Semanticscience Integrated Ontology, SIO) which are pertinents to represent the information from various orthology databases in a homogeneous way."^^ . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/metagenomics/"^^ . + . + . + "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^ . + "Open Data Commons for Traumatic Brain Injury" . + . + "derivatives%2Fthiocyclam%20hydrochloride"^^ . + . + . + . + . + . + "true"^^ . + . + . + "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . + "16333295"^^ . + . + . + . + "http://modelseed.org/biochem/reactions/"^^ . + . + "Cell Image Library" . + . + "false"^^ . + . + "http://soybase.org/"^^ . + "4DNESWX1J3QU"^^ . + "Ontology for Nutritional Epidemiology" . + "^\\d{7}$"^^ . + . + . + "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . + . + "0000001"^^ . + "2649230"^^ . + . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. For GC-MS profiling analyses, polar metabolite extracts are chemically converted, i.e. derivatised into less polar and volatile compounds, so called analytes. This collection references analytes."^^ . + "http://www.metabolomicsworkbench.org/"^^ . + . + "Agronomy Ontology" . + . + . + . + "http://www.gpcrdb.org/"^^ . + . + . + . + . + "GlycomeDB" . + "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . + . + . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . + . + . + "Studies in dbVar."^^ . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . + . + . + . + "^HGVM\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "SPIKE Map" . + "Q13485"^^ . + . + . + "0000080"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "https://www.vmh.life/"^^ . + "^\\d{7}$"^^ . + . + "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . + . + . + . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + "Systems Biology Ontology" . + "http://www.cba.ac.cn"^^ . + . + . + "27267"^^ . + "LOC_Os02g13300"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://progenetix.org/"^^ . + "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . + "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "Insertion sequence elements database" . + . + "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . + . + . + "http://www.imdrf.org/"^^ . + . + . + . + . + . + . + . + "DBG2 Introns" . + "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . + . + . + . + "ChemSpider" . + "false"^^ . + . + . + . + "45539"^^ . + "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . + . + . + . + . + "^\\w{4}$"^^ . + . + "^Os\\S+g\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ERP004492"^^ . + "http://www.ensembl.org/"^^ . + "chebi" . + . + . + . + . + . + "https://gold.jgi.doe.gov/"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "HGVM15354"^^ . + . + "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . + . + . + . + . + "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . + . + "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . + "Hypertension Ontology" . + . + "^(ZINC)?\\d+$"^^ . + . + . + . + "https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO"^^ . + "false"^^ . + "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . + "000000021"^^ . + . + . + . + "National Academic Research and Collaborations Information System" . + . + "^\\d{7}$"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + "^\\d+$"^^ . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . + . + . + "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . + "http://sideeffects.embl.de/drugs/$1"^^ . + . + . + . + . + . + . + "Health Data Research Innovation Gateway" . + . + . + "false"^^ . + . + . + . + "Software"^^ . + . + . + . + "OBCS stands for the Ontology of Biological and Clinical Statistics. OBCS is an ontology in the domain of biological and clinical statistics. It is aligned with the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI). OBCS imports all possible biostatistics terms in OBI and includes many additional biostatistics terms, some of which were proposed and discussed in the OBI face-to-face workshop in Ann Arbor in 2012. "^^ . + . + "bioregistry"^^ . + . + . + . + "false"^^ . + . + . + "4390079"^^ . + "https://purl.obolibrary.org/obo/ohd/home"^^ . + . + . + . + "false"^^ . + . + . + . + . + "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . + . + "false"^^ . + "https://www.animalgenome.org/QTLdb"^^ . + "false"^^ . + . + "Cambridge Structural Database" . + . + . + "http://www.pantherdb.org/"^^ . + . + . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . + . + . + . + . + . + . + . + . + . + . + . + "WikiPathways" . + . + . + . + "https://github.com/EBISPOT/DUO"^^ . + . + . . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - "https://github.com/Planteome/plant-stress-ontology"^^ . + "^\\d{7}$"^^ . + . + . + . + "chebi" . + "false"^^ . + . + "Cotton ontology" . + "false"^^ . + "https://www.wicell.org"^^ . + . + . + . + "false"^^ . + . + . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl"^^ . + "false"^^ . + . + "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . + "false"^^ . + "^[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$"^^ . + . + . + "^\\d{7}$"^^ . + . + "^G(PL|SM|SE|DS)\\d+$"^^ . + . + "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "70"^^ . + . + . + . + . + "http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=$1"^^ . + . + . + . + . + . + . + . + . + . + "GlycomeDB is the result of a systematic data integration effort, and provides an overview of all carbohydrate structures available in public databases, as well as cross-links."^^ . + . + . + . + . + . + . + "https://schema.org/$1"^^ . + . + "^ENSG\\d{11}$"^^ . + "^\\d{7}$"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "Cell line collections"^^ . + . + . + . + "http://www.uniprot.org/"^^ . + "http://purl.obolibrary.org/obo/BILA_$1"^^ . + . + "Clinical Trials Ontology" . + . + "https://www.ebi.ac.uk/arrayexpress/files/A-MEXP-2320/A-MEXP-2320.adf.txt"^^ . + "false"^^ . + . + "http://pbil.univ-lyon1.fr/databases/hogenom/"^^ . + "false"^^ . + "dictyBase" . + . + . + . + . + "1250"^^ . + . + "^\\d+$"^^ . + . + "http://www.w3.org/ns/oa"^^ . + . + "Mouse Genome Informatics" . + . + . + . + . + "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . + . + "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . + . + . + . + . + "A-GEOD-50"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^[CN]*\\d{4,7}$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PPO_$1"^^ . + "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . + . + "false"^^ . + . + . + "http://pax-db.org/#!protein/$1"^^ . + "false"^^ . + . + . + "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . + . + . + . + . + . + "Plant Ontology" . + "http://data.jrc.ec.europa.eu/"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + "https://www.xenbase.org/entry/$1"^^ . + . + . + . + . + . + . + . + . + "http://www.swisslipids.org/#/"^^ . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . + . + "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . + . + . + . + . + "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . + . + . + . + . + . + "An application ontology for use with miRNA databases."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "miriam"^^ . + "https://www.ebi.ac.uk/chembldb/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "00573"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . + "false"^^ . + . + . + "The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions."^^ . + . + . + "0000630"^^ . + "http://bidd.nus.edu.sg/group/ttd/ttd.asp"^^ . + . + . + . + . + . + . + . + . + "TIGR protein families" . + . + "http://stitch.embl.de/"^^ . + . + "false"^^ . + . + "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . + "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . + . + . + . + . + . + "http://planteome.org/"^^ . + . + "0000404"^^ . + . + "^CNP\\d{7}$"^^ . + "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . + . + . + "^\\d+$"^^ . + "http://mycobrowser.epfl.ch/smegmalist.html"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + "AutDB" . + . + . + . + "S000002493"^^ . + . + . + . + . + "qafeQTWIWmcC"^^ . + "http://epd.vital-it.ch/"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/"^^ . + . + . + . + "John Kunze" . + "Medical Subject Headings" . + . + "Life cycle stages for Medaka"^^ . + "http://bis.zju.edu.cn/ricenetdb/"^^ . + . + . + "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . + . + . + . + . + . + . + "https://github.com/OAE-ontology/OAE/"^^ . + . + . + "false"^^ . + . + . + "Ontology of Physics for Biology" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "Infectious Disease Ontology" . + . + "Proteomics data and process provenance" . + "Ontology for Avida digital evolution platform" . + . + "The ATCvet system for the classification of veterinary medicines is based on the same overall principles as the ATC system for substances used in human medicine. In ATCvet systems, preparations are divided into groups, according to their therapeutic use. First, they are divided into 15 anatomical groups (1st level), classified as QA-QV in the ATCvet system, on the basis of their main therapeutic use."^^ . + "0000121"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "https://biopragmatics.github.io/providers/msigdb/$1"^^ . + . + . + "Tom Gillespie" . + . + . + . + "http://www.hipsci.org/lines/#/lines/$1"^^ . + . + . + . + "PDB Structure" . + . + "23"^^ . + . + "KEGG Pathways Database" . + . + . + . + . + . + . + . + . + "1354581"^^ . + . + "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . + "10004892"^^ . + . + "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . + "Ontologized MIABIS" . + "^\\w+$"^^ . + . + . + "UR000124451"^^ . + "^[0-9]*$"^^ . + . + "EJH014"^^ . + " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . + "67035"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "0000001"^^ . + . + . + . + . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . + . + . + . + . + . + . + . + . + . +_:N28878dcda46d47efbf4dee8308457a62 "Fahim Imam" . + . + . + . + "HWUPKR0MPOU8FGXBT394"^^ . + . + . + . + "Healthcare Common Procedure Coding System" . + . + . + . + . + . + . + . + . + "Maize ontology" . + "Cell line collections"^^ . + . + . + . + . + . + . + "https://github.com/geneontology/unipathway"^^ . + . + . + . + "1251"^^ . + . + . + "N1899"^^ . + . + . + "CL070"^^ . + . + "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . + . + "Aclame" . + . + . + . + "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . + . + . + . + "068078"^^ . + . + "Online Computer Library Center WorldCat" . + . + . + "An ontology covering the taxonomy of teleosts (bony fish)"^^ . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/VTO_$1"^^ . + "Identifiers.org is an established resolving system that enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain."^^ . + . + . + . + . . - "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . - . - . - "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . + "^[a-zA-Z0-9_-]{3,}$"^^ . + . + . + . + . + "false"^^ . + "Minimal Information About Anatomy ontology" . + . + . + "false"^^ . + . + "Intelligence Task Ontology" . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + "aaeA"^^ . + . + "Kids First" . + . + . + . + . + "false"^^ . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + "A frontend to Wikidata"^^ . + "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . + "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^PDC\\d+$"^^ . + . + . + . + . + . + "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . + . + . + . + . + . +_:N1e27e616ec1647758de207a85c698acd "Marc Ciriello" . + . + . + . + . + . + . + "Porifera Ontology" . + . + "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . + . + . + . + . + "AT1G73965"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "https://www.cropontology.org/rdf/CO_340:$1"^^ . + . + . + . + "Draft version"^^ . + . + "http://purl.obolibrary.org/obo/GAZ_$1"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . + "Medical Dictionary for Regulatory Activities Terminology" . + . + "http://purl.obolibrary.org/obo/MMO_$1"^^ . + . + . + . + . + . + "040000"^^ . + . + . + "Coronavirus Infectious Disease Ontology" . + "Friend of a Friend" . + "true"^^ . + . + . + . + "0000634"^^ . + . + . + "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . + . + "https://github.com/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . + "http://purl.obolibrary.org/obo/TAO_$1"^^ . + . + . + . + . + "Database of Interacting Proteins" . + . + "http://classyfire.wishartlab.com/"^^ . + . + . + . + . + . + "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . + "Planarian Phenotype Ontology" . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . + . + . + . + . + . + . + . + "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . + "https://github.com/phenoscape/vertebrate-taxonomy-ontology"^^ . + . + . + "^\\d{7}$"^^ . + "false"^^ . + "https://www.alzforum.org/mutations/$1"^^ . + . + "Protein ANalysis THrough Evolutionary Relationships Classification System" . + . + "^rs\\d+$"^^ . + . + . + "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . + . + "false"^^ . + "false"^^ . + . + . + "true"^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + . + . + . + . + "Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents. The information includes chemical compounds, chemical reactions, chemical properties, related bibliographic data, substance data with synthesis planning information, as well as experimental procedures from selected journals and patents. It is licensed by Elsevier."^^ . + . + . + "http://www.snomedbrowser.com/Codes/Details/$1"^^ . + "75121530"^^ . + "http://purl.obolibrary.org/obo/PCL_$1"^^ . + . + . + "false"^^ . + . + "^\\d+$"^^ . + "false"^^ . + . + . + . + "This ontology lists all variables used for woody plant observations. Terms are collected from various sources (past and ongoing projects at national and international levels). Curators: Celia Michotey (INRAE) & Ines Chaves (IBET) - Version 2 submitted on Jun 2020 by INRAE."^^ . + . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + "^CH_\\d+$"^^ . + . + . + "^DG\\d+$"^^ . + "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . + . + "http://cbg.garvan.unsw.edu.au/pina/"^^ . + "http://purl.obolibrary.org/obo/OPMI_$1"^^ . + . + "false"^^ . + "0000071"^^ . + . + "false"^^ . + . + . + . + "https://github.com/calipho-sib/controlled-vocabulary"^^ . + . + . + . + . + . + "DARC (Database of Aligned Ribosomal Complexes) stores available cryo-EM (electron microscopy) data and atomic coordinates of ribosomal particles from the PDB, which are aligned within a common coordinate system. The aligned coordinate system simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors."^^ . + . + . + . + "0000026"^^ . + "C138986"^^ . + . + . + . + . + . + "ILMN_129894"^^ . + . + . + "https://pharmacodb.ca/datasets"^^ . + "http://www.cathdb.info/cathnode/$1"^^ . + . + . + "ChEMBL" . + "true"^^ . + . + "https://github.com/monarch-initiative/MAxO"^^ . + . + "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . + . + . + . + . + "false"^^ . + . + "https://openalex.org/"^^ . + "https://www.gwascentral.org/studies"^^ . + . + . + . + _:N922882227fd14068a34892c3f5c41820 . + . + . + . + . + . + . + . + "^C\\d+$"^^ . + "^[a-z][a-z]/[0-9]+$"^^ . + . + "^\\d{5,}$"^^ . + "431472"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "https://bioregistry.io/resolve/github/pull/$1"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . + "false"^^ . + "https://github.com/luis-gonzalez-m/Collembola"^^ . + "^\\d{7}$"^^ . + "HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein."^^ . + "false"^^ . + "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . + . + . + "The METLIN (Metabolite and Tandem Mass Spectrometry) Database is a repository of metabolite information as well as tandem mass spectrometry data, providing public access to its comprehensive MS and MS/MS metabolite data. An annotated list of known metabolites and their mass, chemical formula, and structure are available, with each metabolite linked to external resources for further reference and inquiry."^^ . + . + . + "Sirarat Sarntivijai" . + . + "Simple Modular Architecture Research Tool" . + "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1"^^ . + "^casent\\d+(\\-D\\d+)?$"^^ . + "COMBINE specifications" . + . + "FuncBase Mouse" . + "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . + . + "SIDER Drug" . + . + . + . + . + . + . + . + . + . + . + "https://github.com/obophenotype/cephalopod-ontology"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "prgr_human"^^ . + . + _:N907212973ffd49a0a6ebca87b43aea0e . + . + "https://github.com/microbial-conditions-ontology/microbial-conditions-ontology"^^ . + "CTD Disease" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "https://ccg.epfl.ch/snp2tfbs/"^^ . + . + "^DP\\d{5}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "https://microbiomedata.org/"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . + . + . + . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . + "false"^^ . + "https://bioportal.bioontology.org/ontologies/IDODEN"^^ . + "^\\d+$"^^ . + "false"^^ . + . + . + . + "NLXCELL conatins cell types with a focus on neuron types."^^ . + . + . + "false"^^ . + . + "FooDB Compound" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.org/spar/pro/$1"^^ . + "microRNA Ontology" . + . + . + . + . + . + . + . + . + . + "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets."^^ . + . + "http://www.sparontologies.net/ontologies/fivestars"^^ . + . + "^XB\\-\\w+\\-\\d+$"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . + . + "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . + "Cowpea ontology" . + . + . + . + . + "0000001"^^ . + . + . + "Publishing Workflow Ontology" . + . + . + . + "http://www.bindingdb.org/compact/$1"^^ . + . + "European Nucleotide Archive" . + . + . + . + "https://github.com/obophenotype/mouse-anatomy-ontology"^^ . + . + "EcoCyc" . + "http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=$1"^^ . + . + . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . + . + . + . + "1"^^ . + . + "0000052"^^ . + _:N7b59c458f6594259b5c01f83c7244ec1 . + . + . + . + . + . + . + "Kaggle" . + . + "http://www.massbank.jp/RecordDisplay?id=$1"^^ . + . + . + . + "http://www.massbank.jp"^^ . + . + . + . + . + . + "^\\d{10}$"^^ . + . + . + . + "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . + . + . + "101"^^ . + . + . + . + . + . + . + . + "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . + "0000460"^^ . + . + . + . + "false"^^ . + . + . + "Sample processing and separation techniques" . + . + . + "^C\\d+$"^^ . + . + . + "Alzheimer's Disease Ontology" . + . + . + "Bioregistry" . + . + . + . + . + "https://www.ebi.ac.uk/imgt/hla/allele.html"^^ . + "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . + . + . + . + "17186"^^ . + . + . + . + "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . + . + . + . + "https://www.re3data.org/repository/$1"^^ . + "http://www.cs.tau.ac.il/~spike/"^^ . + . + . + . + . + "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . + "hsa-let-7a-2-3p"^^ . + . + . + . + "131"^^ . + "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . + "C. elegans Small Molecule Identifier Database" . + "Rebecca Jackson" . + . + . + . + . + "Tom Gillespie" . + . + "false"^^ . + "false"^^ . + . + . +_:N62e97b7f4c3648b4a1ab89e34dcbe1a0 "Pantelis Topalis" . + "^FB\\d{8}$"^^ . + . + . + . + . + . + "98034"^^ . + . + . + . + . + "http://www.arachnoserver.org/"^^ . + . + . + . + . + . + . + . + . + "https://rapdb.dna.affrc.go.jp/"^^ . + "http://www.pathwaycommons.org/pc/"^^ . + . + . + "0000079"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . + "Pathway ontology" . + . + . + . + . + . + "^\\d{7}$"^^ . + "The upper level ontology upon which OBO Foundry ontologies are built."^^ . + . + . + . + . + . + "JAX Mice" . + "^\\d+$"^^ . + . + . + "http://geneontology.org/" . + . + . + . + . + "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . + . + . + "0000111"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "https://spdx.org/licenses/$1"^^ . + . + . + . + . + "https://biomodels.net/vocab/idot.rdf#$1"^^ . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2012."^^ . + . + . + . + . + . + "false"^^ . + "^TS-\\d+$"^^ . + . + . + . + . + . + "PharmacoDB Datasets" . + . + . + . + "ExAC Gene" . + "RiceNetDB Reaction" . + . + . + "Identifiers.org Ontology"^^ . + "Bitbucket" . + . + . + . + "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "http://lincs.hms.harvard.edu/db/proteins/"^^ . - . - "811"^^ . - . - "http://pantree.org/"^^ . - . - . - "http://geneontology.org/"^^ . - . - . - "^DAP\\d+$"^^ . - "EGAD00000000001"^^ . - . - . - "GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://github.com/PopulationAndCommunityOntology/pco"^^ . - . - . - . - . - . - . - "http://stormo.wustl.edu/ScerTF/"^^ . - "https://www.araport.org/"^^ . - "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . - . - . - "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . - . - . - . - . - . - . - . - . - . - . - "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . + . + . + "Human Disease Ontology" . + . + . + "Tom Gillespie" . + . + "https://github.com/AnimalGenome/vertebrate-trait-ontology"^^ . + "http://www.sparontologies.net/ontologies/biro"^^ . + "^\\d{7}$"^^ . + "0002999"^^ . + . + . + "Chemistry resources"^^ . + "false"^^ . + . + . + . + . + "A vocabulary and ontology repository for agronomy and related domains." . + . + . + "icdom:8500_3"^^ . + "The goal of the CAMEO (Continuous Automated Model EvaluatiOn) community project is to continuously evaluate the accuracy and reliability of protein structure prediction servers, offering scores on tertiary and quaternary structure prediction, model quality estimation, accessible surface area prediction, ligand binding site residue prediction and contact prediction services in a fully automated manner. These predictions are regularly compared against reference structures from PDB."^^ . + . + . + "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . + . + . + . + . + "^MIR:001\\d{5}$"^^ . + . + . + . + "Matúš Kalaš" . + . + "false"^^ . + . + "false"^^ . + . + . + "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . + . + . + . + . + "EDAM Ontology" . + . + "E-cyanobacterium model" . + . + "https://github.com/rdruzinsky/feedontology"^^ . + . + "Janna Hastings" . + . + . + . + . + . + . + . + . + . + . + "http://www.humanproteomemap.org/index.php"^^ . + . + . + . + . + . + "NCT00222573"^^ . + _:N727c7ef1cd614439b275141a746eb837 . + . + . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . + . + . + . + . + . + . + "90801"^^ . + . + "http://www.pantherdb.org/"^^ . + . + "10142"^^ . + "http://purl.obolibrary.org/obo/CEPH_$1"^^ . + "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . + "https://www.dsmz.de"^^ . + . + . + . + . + "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . + . + . + . + "^[a-z]+(\\-[a-z]+)*$"^^ . + . + . + . + "0000001"^^ . + . + . + "P23298"^^ . + "Google Scholar Researcher" . + "Chen Yang" . + . + . + . + "Ontology of Arthropod Circulatory Systems" . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "nsv3875336"^^ . + . + . + . + . + . + "https://www.jax.org/strain/$1"^^ . + "An ontology that allows the description of numerical and categorical bibliometric data (e.g., journal impact factor, author h-index, categories describing research careers) in RDF."^^ . + . + . + "http://purl.obolibrary.org/obo/CRO_$1"^^ . + . + . + "https://fungidb.org/fungidb/app/record/gene/$1"^^ . + . + "https://github.com/enpadasi/Ontology-for-Nutritional-Studies"^^ . + . + . + . + . + . + "Transporter Classification Database" . + . + . + . + . + "GeneFarm" . + . + . + . + "false"^^ . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . + . "Ctenophore Ontology" . - "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . - . - "PeptideAtlas Dataset" . - "https://drugs.ncats.io/drug/$1"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . - "Name-to-Thing" . - . - . - . + "true"^^ . + "Universal Spectrum Identifier" . + "^DI-\\d{5}$"^^ . + "0000079"^^ . + . + . + "Contains information about cells and data sheets related to transfection."^^ . + . + . + . + . + "false"^^ . + "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . + . + "false"^^ . + . + . + . + . + . + "https://www.cropontology.org/rdf/CO_323:$1"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://mips.helmholtz-muenchen.de/genre/proj/corum/"^^ . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + . + "Disease Drivers Ontology" . + . + "http://purl.obolibrary.org/obo/PLANA_$1"^^ . + . + . + . + . + . + . + "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . + _:N5c7b97145e734231bba094ae4ad12b0a . + "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . + . + . + . + . + . + . + "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . + . + "false"^^ . + "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . + "http://purl.obolibrary.org/obo/MIRO_$1"^^ . + . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.gleif.org/lei/$1"^^ . + . + . + "miR-1"^^ . + . + . + . + . + "http://vocab.deri.ie/void"^^ . + "John Beverly" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + . + "AY109603"^^ . + . + . + . + . + . + "http://www.sparontologies.net/ontologies/pwo"^^ . + . + "ENSFM00500000270089"^^ . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/"^^ . + . + . + . + . + "This collection contains various brain atlases from the Allen Institute." . + . + . + . + . + . + . + . + . + . + . + . + "https://n2t.net" . + "http://bioportal.bioontology.org/ontologies/LBO"^^ . + "1"^^ . + "MCDS_L_0000000001"^^ . + . + "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . + . + . + "Virtual International Authority File" . + . + . + . + . + . + . + . + . + . + . + "https://www.phosphosite.org"^^ . + . + . + . + . + . + "true"^^ . + . + . + . + "Eschmeyer's Catalog of Fishes" . + "Kerafast cell lines" . + "^\\d+$"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . + "4349895"^^ . + "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . + "false"^^ . + "C063233"^^ . + "https://icahn.mssm.edu/"^^ . + . + "ISA1083-2"^^ . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . + "RNA ontology" . . - . - . - "http://www.genome.jp/kegg/genes.html"^^ . - "false"^^ . - . - "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . - . - "^\\d+$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/HAO_$1"^^ . - . - . - "MarDB" . - . - . - "^\\w+\\d+$"^^ . - . - . - "false"^^ . - . - . - "OID Repository" . - . - "^\\d+$"^^ . - . - . - "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . - "^\\d+$"^^ . - . - "A representation of the variety of methods used to make clinical and phenotype measurements. "^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . - . - . - . - "Metabolites in the Xenobiotics Metabolism Database."^^ . - "http://www.cropontology.org/ontology/CO_333/Beet%20Ontology"^^ . - "Description of Plant Viruses (DPV) provides information about viruses, viroids and satellites of plants, fungi and protozoa. It provides taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences. The database also holds detailed information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene."^^ . - "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . - "false"^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "100"^^ . - . - . - "Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites."^^ . - . - "http://mobidb.bio.unipd.it"^^ . - . - . - . - . - "Genotype-Tissue Expression" . - "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . - "AT1402"^^ . - . - . - . - "ChemSpider" . - "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . - . - "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . + "http://bgee.unil.ch/bgee/bgee"^^ . + . + "false"^^ . + . + . + "Systems Science of Biological Dynamics database (SSBD:database) is an added-value database for biological dynamics. It provides a rich set of open resources for analyzing quantitative data and microscopy images of biological objects, such as single-molecule, cell, tissue, individual, etc., and software tools for analysis. Quantitative biological data and microscopy images are collected from a variety of species, sources, and methods. These include data obtained from both experiments and computational simulations."^^ . + . + . + . + . + . + . + "KNApSAcK" . + . + "http://www.phosphosite.org/homeAction.do"^^ . + . + . + . + . + . + "Search the world's most comprehensive index of full-text books."^^ . + . + "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . + . + . + . + "https://pharmacodb.ca/tissues/$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + "Oryzabase Reference" . + . + . + . + "CCDC Number" . + . + . + . + . + . + . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to anatomical structures."^^ . + . + . + . + . + . + . + "^\\d+(\\w+)?$"^^ . + . + "http://jcggdb.jp/index_en.html"^^ . + "false"^^ . + . + . + . + . + . + "^RCB\\d+$"^^ . + "http://purl.obolibrary.org/obo/FBSP_$1"^^ . + . + "FBgn0000015"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "d4e2515"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "16S rRNA gene database" . + . + . + . + "https://www.cropontology.org/rdf/CO_321:$1"^^ . + . + "NIF Standard Ontology: Chemical" . + . + . + "false"^^ . + . + "MedGen is a portal for information about conditions and phenotypes related to Medical Genetics. Terms from multiple sources are aggregated into concepts, each of which is assigned a unique identifier and a preferred name and symbol. The core content of the record may include names, identifiers used by other databases, mode of inheritance, clinical features, and map location of the loci affecting the disorder."^^ . + . + "^(E|D|S)RR[0-9]{6,}$"^^ . + . + . + . + "Kyoto Encyclopedia of Genes and Genomes" . + "Vertebrate skeletal anatomy ontology."^^ . + . + . + . + . + . + . + "false"^^ . + . + "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . + . + . + . + "The Pathway Interaction Database is a highly-structured, curated collection of information about known human biomolecular interactions and key cellular processes assembled into signaling pathways. This datatype provides access to pathway information."^^ . + "0000519"^^ . + . + . + "Open Tree of Life" . + "Wheat ontology" . + "HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees."^^ . + . + "Cell line databases/resources"^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/VHOG_$1"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . + . + . + . + "http://www.sanger.ac.uk/Users/mb4/PLO/"^^ . + . + "http://purl.obolibrary.org/obo/OHMI_$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "Michel Dumontier" . + . + "https://github.com/pombase/fypo"^^ . + "https://www.ebi.ac.uk/chembldb/"^^ . + . + "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . + . + "https://www.wormbase.org/"^^ . + . + "rs121909098"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "FOAF is a project devoted to linking people and information using the Web. Regardless of whether information is in people's heads, in physical or digital documents, or in the form of factual data, it can be linked. FOAF integrates three kinds of network: social networks of human collaboration, friendship and association; representational networks that describe a simplified view of a cartoon universe in factual terms, and information networks that use Web-based linking to share independently published descriptions of this inter-connected world."^^ . + "http://purl.obolibrary.org/obo/TAHE_$1"^^ . + "The OM ontology provides classes, instances, and properties that represent the different concepts used for defining and using measures and units. It includes, for instance, common units such as the SI units meter and kilogram, but also units from other systems of units such as the mile or nautical mile. For many application areas it includes more specific units and quantities, such as the unit of the Hubble constant: km/s/Mpc, or the quantity vaselife. OM defines the complete set of concepts in the domain as distinguished in the textual standards. As a result the ontology can answer a wider range of competency questions than the existing approaches do. The following application areas are supported by OM: Geometry; Mechanics; Thermodynamics; Electromagnetism; Fluid mechanics; Chemical physics; Photometry; Radiometry and Radiobiology; Nuclear physics; Astronomy and Astrophysics; Cosmology; Earth science; Meteorology; Material science; Microbiology; Economics; Information technology; Typography; Shipping; Food engineering; Post-harvest; technology; Dynamics of texture and taste; Packaging"^^ . + "https://biosimulators.org/simulators/$1"^^ . + . + "false"^^ . + . + "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . + . + "true"^^ . + "United States Patent and Trademark Office" . + . + . + . + . + . + . + . + . + . + . + "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . + . + "The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi."^^ . + "https://lhncbc.nlm.nih.gov/semanticnetwork/"^^ . + . + "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . + . + . + . + "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . + . + . + "PF11_0344"^^ . + . + . + . + . + "A_24_P98555"^^ . + . + . + . + . + "http://code.google.com/p/mirna-ontology/"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . + "Selventa Families" . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . + . + . + . + . + . + "ALA"^^ . + "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . + . + . + "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . + . + . + "SBML RDF Vocabulary" . + . + . + . + . + . + "^S\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "19333"^^ . + . + . + . + _:Nfff0b0e50fe140a784b0c43f793a22cc . + . + "The Cooperative Patent Classification (CPC) is a patent classification system, developed jointly by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO). It is based on the previous European classification system (ECLA), which itself was a version of the International Patent Classification (IPC) system. The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013."^^ . + . + . + "Hierarchical orthologous groups predicted by OMA (Orthologous MAtrix) database. Hierarchical orthologous groups are sets of genes that have started diverging from a single common ancestor gene at a certain taxonomic level of reference. "^^ . + . + . + "PaxDb Protein" . + . + "Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions."^^ . + "GLIDA GPCR" . + . + . + . + "634515043"^^ . + . + "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . + "^\\w+$"^^ . + . + . + . + . + . + . + . + "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . + . + . + "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . + . + . + . + . + . + "RiceNetDB miRNA" . + . + . + . + . + "PED00037"^^ . + . + "true"^^ . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + "Quality"^^ . + . + . + . + . + "AURKA"^^ . + "Variants in dbVar."^^ . + "false"^^ . + "false"^^ . + "Chris Stoeckert" . + . + . + . + . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . + . + . + . + . + "false"^^ . + . + "0000031"^^ . + . + . + "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . + . + . + "UniProt Chain" . + . + "WP732"^^ . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + "277.9"^^ . + . + . + . + "false"^^ . + . + . + "http://www.uniprot.org/uniprot/$1"^^ . + . + . + . + "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . + "PKDB00198"^^ . + . + . + "Chemical Methods Ontology" . + . + . + . + . + . + . + . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "119514"^^ . + "^\\d{6}$"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . + . + . + . + _:N5bee6a16e0df451ea1b8859d30049123 . + "http://rebase.neb.com/rebase/"^^ . + . + . + . + "Wikipedia" . + . + . + "http://bigg.ucsd.edu/compartments/$1"^^ . + . + . + . + "Benchmark Energy & Geometry Database" . + . + . + "false"^^ . + . + . + . + . + "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . + "DataCollection"^^ . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . + "An ontology to capture confidence information about annotations."^^ . + . + "false"^^ . + "^[0-9a-z]{24,24}$"^^ . + "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . + . + . + . + . . - . - . - . - . - . - . - . - . - . - . - . - "431472"^^ . - . - . - . - . - "A Locus Reference Genomic (LRG) is a manually curated record that contains stable genomic, transcript and protein reference sequences for reporting clinically relevant sequence variants. All LRGs are generated and maintained by the NCBI and EMBL-EBI."^^ . - . - . - "Drug Central" . - "false"^^ . - . - "^\\d{5,}$"^^ . - . - "ChemDB" . - "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . - . - "https://www.ebi.ac.uk/ols" . + . + . + "The COVID-19 Infectious Disease Ontology" . + . + . + . + . + . + . + "https://cropontology.org/ontology/CO_358/Cotton"^^ . + "Cell line collections"^^ . + . + . + . + . + . + . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "https://dashr1.lisanwanglab.org/show-expression-table.php?start=0"^^ . + "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . + . + . + "false"^^ . + "re3data" . + . + . + . + . + . + . + "00000001"^^ . + "https://metacyc.org"^^ . + "OBO Metadata Ontology" . + "NITE Biological Resource Center" . + . + . + . + . + . + "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "iNaturalist Taxonomy" . + "Cancer Cell Line Encyclopedia Cells" . + "^\\d+$"^^ . + "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . + . + . + "^SCV\\d+(\\.\\d+)?$"^^ . + "http://lgsun.grc.nia.nih.gov/cDNA/"^^ . + . + . + . + . + . + . + "0001009"^^ . + "Michelle Giglio" . + "0001410"^^ . + . + . + . + "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . + . + . + . + "https://oborel.github.io/"^^ . + "^[a-z][a-zA-Z]+$"^^ . + . + . + . + . + . + "http://www.pharmgkb.org/disease/$1"^^ . + . + "https://www.metanetx.org/"^^ . + "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . + . + . + . + "0002902"^^ . + . + . + . + . + "The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with tools to facilitate research on the GenitoUrinary (GU) tract."^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + . + . + "http://mged.sourceforge.net/ontologies/MGEDontology.php"^^ . + . + . + . + "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . + . + . + "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://repeatsdb.org/structure/$1"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + "http://www.sisuproject.fi/"^^ . + . + "false"^^ . + "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . + . + . + . + "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . + . + . + "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . + . + "http://www.ontobee.org/" . + "https://github.com/information-artifact-ontology/ontology-metadata"^^ . + "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . + . + . + "sbml.level-3.version-2"^^ . + "false"^^ . + . + "^[0-9]*$"^^ . + . + . + "http://purl.obolibrary.org/obo/TADS_$1"^^ . + . + . + . + . + "^ERM[0-9]{8}$"^^ . + "false"^^ . + . + . + . + . + . + . + . + "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "https://aopwiki.org/"^^ . + . + . + . + . + "^MMAR\\_\\d+$"^^ . + "https://www.genome.jp/kegg/glycan/"^^ . + . + . + . + . + "https://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PAR"^^ . + "0000080"^^ . + "Tom Gillespie" . + . + . + "1"^^ . + "false"^^ . + "https://www.phenxtoolkit.org/"^^ . + "Community development of interoperable ontologies for the biological sciences"^^ . + "^\\w+$"^^ . + "NONHSAT000001"^^ . + . + . + . + . + . + "https://www.storedb.org/"^^ . + . + "http://omnisearch.soc.southalabama.edu/w/index.php/Ontology"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "https://hpscreg.eu/cell-line/$1"^^ . + "false"^^ . + . + "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . + . + . + . + . + . + "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . + . + . + "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . + "http://www.transcriptionfactor.org/"^^ . + . + . + . + . + . + "https://www.datanator.info/metabolite/$1"^^ . + "https://dandiarchive.org/dandiset/$1"^^ . + . + . + . + . + . + "FungiDB is a genomic resource for fungal genomes. It contains contains genome sequence and annotation from several fungal classes, including the Ascomycota classes, Eurotiomycetes, Sordariomycetes, Saccharomycetes and the Basidiomycota orders, Pucciniomycetes and Tremellomycetes, and the basal 'Zygomycete' lineage Mucormycotina."^^ . + . + . + . + . . - . - . - . - "^KIAA\\d{4}$"^^ . - "http://www-bionet.sscc.ru/sitex/"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/BIRNLEX"^^ . - . - . - . - . - "false"^^ . - . - . - "Lynn Schriml" . - . - . - "http://bactibase.hammamilab.org"^^ . - . - . - . - . - . - . - . - "^[A-Z0-9*:]+$"^^ . - . - . - . - "PAR:0116"^^ . - . - . - . - . - . - . - "CLV_MEL_PAP_1"^^ . - . - . - . - . - "P53350"^^ . - "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains genomic sequence information."^^ . - . - . - . - "^[a-z]+(\\-[a-z]+)*$"^^ . - . - . - . - . - . - . - "Q5BJF6-3"^^ . - . - . - . - . - . - . - . - "http://www.mirbase.org/"^^ . - . - . - . + . + "The Yeast Transcription Factor Specificity Compendium (YeTFasCO) is a database of transcription factor specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats."^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . + . + . + . + "https://repo.napdi.org/"^^ . + . + . + . + "false"^^ . + . + . + "OpenAlex" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Each OCI (Open Citation Identifier) has a simple structure: oci:number-number, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entitiy - see https://opencitations.wordpress.com/2018/02/19/citations-as-first-class-data-entities-introduction/ for additional information.\r\n\r\nOCIs for citations stored within the OpenCitations Corpus are constructed by combining the OpenCitations Corpus local identifiers for the citing and cited bibliographic resources, separating them with a dash. For example, oci:2544384-7295288 is a valid OCI for the citation between two papers stored within the OpenCitations Corpus.\r\n\r\nOCIs can also be created for bibliographic resources described in an external bibliographic database, if they are similarly identified there by identifiers having a unique numerical part. For example, the OCI for the citation that exists between Wikidata resources Q27931310 and Q22252312 is oci:01027931310–01022252312.\r\n\r\nOCIs can also be created for bibliographic resources described in external bibliographic database such as Crossref or DataCite where they are identified by alphanumeric Digital Object Identifiers (DOIs), rather than purely numerical strings."^^ . + "^\\d+$"^^ . + "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?expt_id=$1&action=view"^^ . + . + . + . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. This is the reference gene model for a given locus."^^ . + . + . + . + "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . + "false"^^ . + . + . + "false"^^ . + "https://www.ada.org/publications/CDT"^^ . + . + "0000066"^^ . + . + "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "37"^^ . + . + . + . + . + "Colin Batchelor" . + . + . + . + . + "http://www.viprbrc.org/brc/home.do?decorator=vipr"^^ . + . + . + . + . + "^[1-9][0-9]{3,6}$"^^ . + . + "Antimicrobial Peptide Database" . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "Vital Sign Ontology" . + "LOC_Os01g49190"^^ . + "https://metacyc.org"^^ . + "http://ccdb.ucsd.edu/CCDBWebSite/sao.html"^^ . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/omit/terms?short_form=OMIT_$1"^^ . + . + "^\\d{7}$"^^ . + "BCRTi001-A"^^ . + . + . + . + . + . + "The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns."^^ . + . + . + . + . + . + . + "h2o"^^ . + . + . + "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . + . + . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + . + . + . + "1.1.1.1"^^ . + "false"^^ . + "false"^^ . + . + . + "00000268"^^ . + . + "https://bioportal.bioontology.org/ontologies/APAONTO"^^ . + . + . + "DataONE" . + . + "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . + . + . + . + . + . + . + . + "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . + . + "https://www.cropontology.org/rdf/CO_345:$1"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . + . + . + "MMAR_2462"^^ . + . + . + "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . + . + "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + "^[1-9][0-9]{14}$"^^ . + . + "https://www.storedb.org/?STOREDB:DATASET$1"^^ . + . + . + . + . + "SIDER Side Effect" . + . + "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . + . + . + "https://github.com/OMIABIS/omiabis-dev"^^ . + . + "MatrixDB Association" . + . + . + . + "Aspergillus Genome Database" . + . + . + . + . + . + . + . + "https://www.uniprot.org/database/$1"^^ . + . + . + "Oryza Tag Line" . + . + "csv"^^ . + . + "^.*/.*$"^^ . + . + . + . + . + . + "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . + . + . + "^[0-9]+$"^^ . + . + . + "http://dictybase.org"^^ . + . + . + . + "http://www.hprd.org/"^^ . + . + "^SMP\\d+$"^^ . + "http://www.maizegdb.org/"^^ . + "TreeBASE" . + . + . + . + "false"^^ . + . + "Pearl millet ontology" . + "https://www.ncbi.nlm.nih.gov/"^^ . + . + . + "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . + . + . + "sharesAuthorInstitutionWith"^^ . + . + . + "67"^^ . + . + "https://github.com/semanticchemistry/semanticchemistry" . + . + . + "http://www.cropontology.org/ontology/CO_357/Woody%20Plant%20Ontology"^^ . + "^[a-zA-Z0-9_\\.]+$"^^ . + . + "false"^^ . + "^[1-9]\\d{5}$"^^ . + . + "SWISS-MODEL Repository" . + . + "http://www.pharmgkb.org/"^^ . + . + . + "101"^^ . + "https://n2t.net/$1:" . + . + . + . + . + . + . + "http://autism.mindspec.org/autdb/"^^ . + . . - . - "^\\w\\d+$"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "^[A-Z_0-9]+$"^^ . - "http://purl.obolibrary.org/obo/FYPO_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.grid.ac/institutes/$1"^^ . - . - . - "^[0-9\\-_]+$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "http://rebase.neb.com/rebase/enz/$1.html"^^ . - . - . - . - . - "CAE46076"^^ . - "98"^^ . - . - . -_:N9f8bc228d3d4416796eff1e6e0747849 "Pantelis Topalis" . - . - "Software Package Data Exchange License" . - "BT20_BREAST"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - _:Nb0ec7efeb75b4de9b762aee59d29de3f . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "High-quality Automated and Manual Annotation of microbial Proteomes" . - . - . - . - . - . - "Clinical Trials Ontology" . - . - "MIRIAM Registry resource" . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . - . - . - "achcar11"^^ . - . - . - . - . - . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . - . - . - "European Genome-phenome Archive Dataset" . - . - . - . - . - . - . - . - "47419"^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/clinvar/"^^ . - "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . - . - . - "27267"^^ . - "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . - "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . - "false"^^ . - . - . - "Virus Pathogen Resource" . - "A structured controlled vocabulary for the anatomy of fungi."^^ . - . - . - "^m\\w+$"^^ . - . - "https://pharmacome.github.io/conso/$1"^^ . - . - . - . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . - "https://zenodo.org"^^ . - . - . - . - . - . - "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . - "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . - . - "Pocketome" . - . - "^PRO_[0-9]{10}$"^^ . - "AT1G01030.1"^^ . - "002368"^^ . - . - . - "0000138"^^ . - "http://purl.obolibrary.org/obo/MAXO_$1"^^ . - . - . - . - . - . - . - . - "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . - "^\\d{5}$"^^ . - "https://fair-research.org"^^ . - "Sequence types and features ontology" . - . - . - "https://www.ebi.ac.uk/interpro/entry/$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . - "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - "0000111"^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://cropontology.org/ontology/CO_321/Wheat"^^ . - . - "false"^^ . - . - . - "The Mammalian Phenotype Ontology (MP) classifies and organises phenotypic information related to the mouse and other mammalian species. This ontology has been applied to mouse phenotype descriptions in various databases allowing comparisons of data from diverse mammalian sources. It can facilitate in the identification of appropriate experimental disease models, and aid in the discovery of candidate disease genes and molecular signaling pathways."^^ . - . - . - "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . - . - . - . - "false"^^ . - "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . - . - . + . + . + . + . + . + "http://www.nlm.nih.gov/mesh/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . + . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "http://repository.topdownproteomics.org/proteoforms/$1"^^ . + "Cell line databases/resources"^^ . + . + . + "July 2018"^^ . + . + . + . + . + . + . + . + "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . + . + . + . + "http://www.pharmgkb.org/pathway/$1"^^ . + "http://sed-ml.org/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/SPD_$1"^^ . + . + . + . + . + . + . + . + "Ontology for MicroRNA Target" . + "https://www.uniprot.org/locations/$1"^^ . + . + . + . + . + . + . + "HBB"^^ . + . + "https://www.ebi.ac.uk/metabolights/"^^ . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=pcassay"^^ . + . + "http://purl.obolibrary.org/obo/REX_$1"^^ . + "50018"^^ . + "http://www.genome.jp/kegg/reaction/"^^ . "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "5277619"^^ . - . - . - . - "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . - "false"^^ . - "https://www.wwpdb.org/"^^ . - "Cellosaurus Registry" . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "MeSH 2012" . - . - "https://www.merckmillipore.com/"^^ . - . - . - . - "European Food Information Resource Network" . - "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "https://web.expasy.org/abcd/"^^ . - . - "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . - . - . - . - "1755"^^ . - . - . - . - . - . - . - . - "^[CN]*\\d{4,7}$"^^ . - . - . - . - . - "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "NLXFUNC covers terms for cognitive function."^^ . - . - "Dimension"^^ . - . - . - . - . - . - "https://n2t.net" . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues."^^ . - . - . - "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . - . - . - . - . - "PXD000500"^^ . - . - "false"^^ . - "^\\d+$"^^ . - "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . - "1398574"^^ . - "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . - . - "0001000"^^ . - . - . - "GlycoPOST is a mass spectrometry data repository for glycomics and glycoproteomics. Users can release their \"raw/processed\" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information Required for a Glycomics Experiment (MIRAGE) guidelines."^^ . - . - "^\\d+$"^^ . - "Fly taxonomy" . - . - "false"^^ . - . - . - . - "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . - . - . - . - . - "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . - . - . - . - . - . - "BAC045"^^ . - "https://commonchemistry.cas.org/detail?ref=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.bioontology.org/ontology/OPB?conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . - . - . - . - . + . + . + . + . + "https://polbase.neb.com/polymerases/$1#sequences"^^ . + "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . + . + . + . + . + . + "The set of prefixes used in the Cellosaurus resource"^^ . + . + . + . + "https://flybase.org"^^ . + "190000021540"^^ . + . + "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . + . + "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . + . + . + . + . + . + . + "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . + . + . + . + "http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html"^^ . + . + . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + . + "Name-to-Thing" . + . + . + "https://www.merckmillipore.com/catalogue/item/$1"^^ . + . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://w3id.org/oc/oci/$1"^^ . + . + . + . + . + "0290"^^ . + . + . + . + . + "Feature Annotation Location Description Ontology " . + . + . + . + "FxnI151FMs"^^ . + "Vaccine Ontology" . + . + . + . + "https://www.e-cyanobacterium.org/experiments-repository/"^^ . + . + . + . + . + "humIGHV025"^^ . + "false"^^ . + . + "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp"^^ . + . + "https://civicdb.org/"^^ . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/"^^ . + . + . + _:N78c3148fdc9e429f9a7d8c471866311e . + "Information for ligands in the BRENDA database."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.w3.org/ns/activitystreams#$1"^^ . + . + "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . + . + . + . + "false"^^ . + . + "VegBank is the vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification. VegBank consists of three linked databases that contain (1) vegetation plot records, (2) vegetation types recognized in the U.S. National Vegetation Classification and other vegetation types submitted by users, and (3) all plant taxa recognized by ITIS/USDA as well as all other plant taxa recorded in plot records. Vegetation records, community types and plant taxa may be submitted to VegBank and may be subsequently searched, viewed, annotated, revised, interpreted, downloaded, and cited. "^^ . + "SIDM01262"^^ . + "http://www.sparontologies.net/ontologies/doco"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . + "r3d100010772" . + . + . + . + . + "^\\d+$"^^ . + "Ontology from the APA"^^ . + . + . + . + . + "https://go.drugbank.com/salts/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "0000339"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^(imp|gen)\\d{5}$"^^ . + "0000066"^^ . + . + "Cell line collections"^^ . + . + . + . + . + "Banana ontology" . + "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . + . + . + "^(MNXM\\d+|BIOMASS|WATER)$"^^ . + . + . + . + . + . + "https://rarediseases.info.nih.gov/diseases"^^ . + . + . + "http://ecocyc.org/"^^ . + "PRINTS compendium of protein fingerprints" . + . + . + "^[a-z_A-Z]+$"^^ . + . + . + . + "miRNA Target Prediction at EMBL" . + . + . + . + . + "false"^^ . + "^\\w+$"^^ . + . + . + "https://pictar.mdc-berlin.de/"^^ . + . + "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . + . + . + . + "false"^^ . + "Biolink Model" . + . + "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . + . + . + "^\\d{3}$"^^ . + . + . + . + . + "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . + . + . + "http://purl.obolibrary.org/obo/DINTO_$1"^^ . + "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . + . + . + . + . + "Human Dephosphorylation Database" . + . + "BloodPAC" . + . + . + "Open Data Commons for Spinal Cord Injury" . + "false"^^ . + . + "http://www.gramene.org/db/ontology/search?id=$1"^^ . + . + . + . + "http://bacmap.wishartlab.com/organisms/$1"^^ . + . + . + . + "false"^^ . + "An ontology of prokaryotic phenotypic and metabolic characters"^^ . + "PubChem CID" . + . + "^\\d+$"^^ . + "https://cropontology.org/ontology/CO_341/Pigeonpea"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + "SPRINT (Search PRINTS-S) provides an interface to the PRINTS-S database. PRINTS-S is the relational cousin of the PRINTS data bank of protein family fingerprints."^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/uo/terms?obo_id=UO:$1"^^ . + "UniProt Protein" . + "8497"^^ . + . + . + "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . + . + . + . + . + "SwissLipids is a curated resource that provides information about known lipids, including lipid structure, metabolism, interactions, and subcellular and tissue localization. Information is curated from peer-reviewed literature and referenced using established ontologies, and provided with full provenance and evidence codes for curated assertions."^^ . + . + . + . + . + "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "KW-1273"^^ . + "http://www.sparontologies.net/ontologies/c4o"^^ . + "https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp"^^ . + "NIF Gross Anatomy" . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . + "https://biopragmatics.github.io/providers/schem/$1"^^ . + . + . + . + . + . + "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references drugs in SIDER."^^ . + . + . + "51"^^ . + "false"^^ . + "false"^^ . + . + . + . + "false"^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + . + . + "https://bioregistry.io/resolve/github/issue/$1"^^ . + . + . + . . - . - . - . - "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . - . - "false"^^ . - "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . - "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . - "Chris Stoeckert" . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - . - . - "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . - . - "false"^^ . - . - . - "GN_G03681DA"^^ . - "ERM00000044"^^ . - . - . - . - . - . - "P00266"^^ . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . - . - . - . - . - "https://biopragmatics.github.io/debio/$1"^^ . - "Cell line databases/resources"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . - "true"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . + . + . + . + . + "snoRNABase" . + . + . + . + "Shur-Jen Wang" . + _:N4a0800839ffe4d7aa96d4a23053dfc1d . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . + . + . + . + . + . + "International Classification of Diseases, 10th Revision" . + . + . + . + . + . + "http://bactibase.hammamilab.org"^^ . + . + . + . + "International Classification of Diseases, 11th Revision" . + . + . + "MIR:00100005"^^ . + "^\\S+$"^^ . + . + . + . + . + . + "eNanoMapper Ontology" . + "http://www.informatics.jax.org/searches/MP_form.shtml"^^ . + "GXA Gene" . + . + . + . + . + . + "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . + "http://www.pombase.org/spombe/result/$1"^^ . + "Ada Hamosh" . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://aps.unmc.edu/AP/"^^ . + . + . + . + . + . + . + "Database for Prokaryotic Operons" . + . + . + . + "^\\d+$"^^ . + . + "Japan Collection of Microorganisms" . + . + . + . + . + . + . + . + . + . + "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"^^ . + "^\\d+$"^^ . + . + "^\\w+$"^^ . + . + "https://ligandbook.org/"^^ . + "^CAL\\d{7}$"^^ . + . + "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . + . + . + . + . + "ML0224"^^ . + . + . + "https://identifiers.org" . + . + . + . + "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . + "false"^^ . + . +_:N376e1439b73f4439a8ae10ac8236a8a7 "Schober Daniel" . + . + . + "http://darcsite.genzentrum.lmu.de/darc/index.php"^^ . + "Ramona Walls" . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.lgresearch.ai"^^ . + . + . + . + . + . + . + "Alex Bateman" . + . + . + . + . + "https://www.beiresources.org"^^ . + . + "22-46615880-T-C"^^ . + . + "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . + "http://purl.obolibrary.org/obo/OLATDV_$1"^^ . + . + . + "1"^^ . + "Resource Description Framework" . + . + . + "Coleoptera Anatomy Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + "^[A-Za-z]+\\/[0-9]+$"^^ . + . + . + . + . + "http://www.lrg-sequence.org/"^^ . + . + . + . + . + "https://licebase.org"^^ . + "Catalog of purchasable reagents and building blocks"^^ . + . + . + . + . + "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_D.html"^^ . + "http://www.ebi.ac.uk/efo/EFO_$1"^^ . + . + . + . + . + . + . + "http://www.cathdb.info/domain/$1"^^ . + . + . + . + . + "http://www.affymetrix.com/"^^ . + "false"^^ . + "IntAct protein interaction database" . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"^^ . + "EP0311"^^ . + "Bilateria anatomy" . + . + "http://www.w3.org/2001/XMLSchema#$1"^^ . + . + . + . + . + . + "3403"^^ . + "DiscoverX cell line products" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + . + . + . + . + . + . + . + "20090303"^^ . + "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . + . + . + "http://purl.obolibrary.org/obo/MFO_$1"^^ . + . + . + . + . + . + . + . + . + "Animal Trait Ontology for Livestock" . + . + . + "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . + . + . + . + . + . + . + . + . + "VegBank" . + . + "Dictyostelium discoideum anatomy" . + "TAIR Protein" . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + "Federica Quaglia" . + . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology"^^ . + . + "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . + "31"^^ . + . + "Cell line collections"^^ . + . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + . + . + . + . + . + . + . + "AddexBio cell line products" . + . + . + "http://www.dpvweb.net/"^^ . + "G00123"^^ . + "DRSC05221"^^ . + "0019171"^^ . + . + . + "CHEBI"^^ . + . + . + . + . + "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . + . + . + . + "The National Drug File (NDF) is produced by the U.S. Department of Veterans Affairs, Veterans Health Administration (VHA). NDF is a centrally maintained electronic drug list used by the VHA hospitals and clinics. Facilities use the NDF to check drug interactions, to manage orders, and to send outpatient prescriptions to regional automated mail-out pharmacies. NDF includes information on clinical drugs, drug classes, ingredients and National Drug Code (NDC) Directory codes. "^^ . + "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . + . + "PAp00000009"^^ . + "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . + "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . + . + "true"^^ . + . + . + . + . + . + . + "false"^^ . + "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . + . + "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . + . + "Selventa Diseases" . + "https://www.ebi.ac.uk/ols/ontologies/foodon/terms?obo_id=FOODON:$1"^^ . + . + . + . + . + . + . + "HUMAN16963"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^C?\\d+$"^^ . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . + . + "Metabolite and Tandem Mass Spectrometry Database" . + "http://purl.obolibrary.org/obo/GENO_$1"^^ . + "00000180"^^ . + . + . + . + . + . + . + . + . + "Dr. Alpha Tom Kodamullil" . + . + . + . + "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . + . + "br/1"^^ . + . + . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . + . + . + "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . + . + . + . + . + . + "https://www.ndexbio.org"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "0000000"^^ . + . + "International repository of Adverse Outcome Pathways."^^ . + . + . + "http://immunet.cn/bdb/"^^ . + . + . + . + . + "Provenance, Authoring, and Versioning Vocabulary" . + . + . + . + . + "The core Ontology of Clinical Trials (CTO) will serve as a structured resource integrating basic terms and concepts in the context of clinical trials. Thereby covering clinicaltrails.gov. CoreCTO will serve as a basic ontology to generate extended versions for specific applications such as annotation of variables in study documents from clinical trials."^^ . + "MycoBrowser marinum" . + "http://purl.obolibrary.org/obo/FBbi_$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . + . + "false"^^ . + . + . + . + . + "https://tree.opentreeoflife.org"^^ . + . + . + . + . + . + . + . . - . - "^\\d{7}$"^^ . - . - . - "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . - "104674"^^ . - . - . - . - . - "0000564"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . + . + . + . + . . - . - "A database for Triticeae and Avena references."^^ . - . - "SPAR Ontologies" . - . - "https://www.brenda-enzymes.org/"^^ . - . - . - . - "The Drug Ontology" . - . - . - . - . - . - "^\\d{7}$"^^ . - "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . - . - "https://www.jax.org/strain"^^ . - "https://github.com/futres/fovt"^^ . - . - "http://cicblade.dep.usal.es:8080/APID/"^^ . - . - . - . - . - "Human Disease Ontology" . - . - . - . - . - . - . - . - . - "TFClass is a classification of eukaryotic transcription factors based on the characteristics of their DNA-binding domains. It comprises four general levels (superclass, class, family, subfamily) and two levels of instantiation (genus and molecular species). Two of them (subfamily and factor species) are optional. More detailed explanations about the classification scheme and its criteria are given here.."^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns."^^ . - . - "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . - . - . - . - . - . - . - . - . - . - "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . - . - . - . - "false"^^ . - "0001707"^^ . - . - . + . + . + . + . + . + "false"^^ . + . + . + . + "HEX1"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Schema for the export of the Bioregistry as RDF"^^ . + "KYinno cell lines" . + . + "0000586"^^ . + . + . + . + . + "https://caninecommons.cancer.gov/#/study/$1"^^ . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "000009"^^ . + . + . + . + . + . + . + "Microbial Conditions Ontology" . + "^\\d+$"^^ . + . + . + "0000081"^^ . + . + "Rosa2"^^ . + "Models developed with the Virtual Cell (VCell) software prorgam."^^ . + . + . + . + . + . + . + "Chlamydia"^^ . + . + . + . + . + "BRENDA, The Comprehensive Enzyme Information System" . + . + . + . + . + . + . + . + . + . + "CranioMaxilloFacial ontology" . + . + "false"^^ . + "RDF Schema" . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . + . + "https://www.ebi.ac.uk/chembl/entity/$1"^^ . + . + . + . + . + . + "AOPWiki (Stressor)" . + . + . + . + . + . + "2019-08-03_00000089_1"^^ . + . + . + "Jonathan Karr" . + . + . + . + . + "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . + . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "mirEX is a comprehensive platform for comparative analysis of primary microRNA expression data, storing RT–qPCR-based gene expression profile over seven development stages of Arabidopsis. It also provides RNA structural models, publicly available deep sequencing results and experimental procedure details. This collection provides profile information for a single microRNA over all development stages."^^ . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Lepidoptera Anatomy Ontology" . + . + "false"^^ . + . + "0001885"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "REPRODUCE-ME Ontology" . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/docs/ptmlist"^^ . + . + . + . + . + . + . + "Mouse gross anatomy and development, timed" . + . + . + . + "http://viaf.org/viaf/$1"^^ . + . + "Banco de Celulas do Rio de Janeiro" . + . + "0000125"^^ . + "A001094"^^ . + . + "Preprints are articles which have not been peer-reviewed from various preprint servers and open research platforms such as bioRxiv, ChemRxiv, PeerJ Preprints and F1000."^^ . + "MIRT000002"^^ . + . + "Software Package Data Exchange License" . + "https://covid19.sfb.uit.no"^^ . + . + "false"^^ . + . + "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . + . + "PR00001"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . . - . - . - . - "^\\d{7}$"^^ . - . - "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . - . - "Q13485"^^ . - "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . - "https://archive.softwareheritage.org"^^ . - . - . - . - . - . - . - . - . - . - . - "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . - . - "false"^^ . - . - "https://www.va.gov/health"^^ . - . - "^GE\\d+$"^^ . - . - . - . - . - "http://research.amnh.org/atol/files/"^^ . + "ExAC Variant" . + . + . + . + . + . + . + . + . + . + "https://nanocommons.github.io/identifiers/"^^ . + "http://h-invitational.jp/hinv/ahg-db/index.jsp"^^ . + "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . + . + . + . + "Publons Researcher" . + "http://www.3dmet.dna.affrc.go.jp/"^^ . + "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . + "Molecular Interactions Controlled Vocabulary" . + . + "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . + "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to protein-level information, providing a list of phosphorylation sites for each protein in the database."^^ . + . + . + . + . + . + "https://bacdive.dsmz.de/strain/$1"^^ . + . + "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . + "Fossilworks Journal" . + . + . + . + "Database of Genotypes and Phenotypes" . + . + "Chinese Biological Abstracts" . + "true"^^ . + . + . + . + "Circular double stranded DNA sequences composed" . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "http://www.mesquiteproject.org/ontology/Loggerhead/index.html"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/eco/terms?obo_id=ECO:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + "DDB_G0267522"^^ . + . + "SEQF1003"^^ . + "false"^^ . + "CGH Data Base" . + . + . + "^[A-Z0-9]+$"^^ . + . + . + "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . + . + . + . + . + . + . + . + "2gc4"^^ . + . + "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . + . + "false"^^ . + . + "https://www.nextmovesoftware.com/namerxn.html"^^ . + . + . + "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . + . + . + "splash10-0zq2000000-77302b0326a418630a84"^^ . + . + "^\\d+$"^^ . + . + . + "ECMDB00005"^^ . + . + . + . + . + "http://bigg.ucsd.edu/compartments/"^^ . + . + "https://www.imexconsortium.org/"^^ . + . + "http://purl.obolibrary.org/obo/RO_$1"^^ . + . + . + . + "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . + . + "https://www.cropontology.org/rdf/CO_325:$1"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . + "FAIRSharing" . + . + . + "Suzi Aleksander" . + . + . + "Relation Ontology" . + . + "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . + . + . + . + . + . + . + . + . + "https://www.genedb.org/"^^ . + . + . + "http://www.gramene.org"^^ . + "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . + . + . + . + "Pol Castellano Escuder" . + . + . + . + . + . + "0000215"^^ . + "true"^^ . + . + . + "BindingDB" . + "https://smpdb.ca/"^^ . + "5359"^^ . + "https://obophenotype.github.io/cell-ontology/"^^ . + "Protein Ensemble Database" . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + "0000060"^^ . + "https://www.gbif.org/species"^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/GNO_$1"^^ . + . + . + "https://www.ebi.ac.uk/intenz/"^^ . + . + "C. elegans phenotype" . + . + "Melissa Haendel" . + . + . + "false"^^ . + "http://sugarbind.expasy.org/$1"^^ . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . + "http://www.w3.org/2004/02/skos/core#$1"^^ . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . "false"^^ . - "Integrated Taxonomic Information System" . - . - . - . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - "^\\d{7}$"^^ . - . - . - "https://molmedb.upol.cz/mol/$1"^^ . - . - . - . - . - "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . - "50943"^^ . - . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . - . - "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . - . - "MGnify Analysis" . - "Yeast Metabolome Database" . - . - "https://www.ebi.ac.uk/ols/ontologies/pato/terms?obo_id=PATO:$1"^^ . - . - . - . - . - . - "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . - . - . - . - "Ontology of Physics for Biology" . - . - . - . - . - "M00002"^^ . - . - "https://www.beiresources.org"^^ . - . - "false"^^ . - "2244"^^ . - "^[A-Za-z0-9]+$"^^ . - "The Arabidopsis Information Resource" . - "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . - . - . - . + "http://www.wikipathways.org/"^^ . + "false"^^ . + . + . + . + "http://paleodb.org/"^^ . + . + . + . + . + "http://www.protonet.cs.huji.ac.il/"^^ . + "^SEQF\\d+$"^^ . + . + "Cell line databases/resources"^^ . + . + . + . + "false"^^ . + "ProteomicsDB Peptide" . + "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . + "ASRP1423"^^ . + . + . + . + . + "J0705A10"^^ . + "^[0-9]+$"^^ . + "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . + . + "^([hm]\\_)?\\w+Pathway$"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . + . + . + "https://pypi.org/project/$1"^^ . + "true"^^ . + . + "Literature references in Gramene"^^ . + "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references individual protein records."^^ . + "^[0-9a-zA-Z]{8}$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/doid/terms?obo_id=DOID:$1"^^ . + "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . + . + "Physico-chemical methods and properties" . + . + . + . + . + . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . + . + "The International Histocompatibility Working Group provides a comprehensive inventory of HLA reference genes to support worldwide research in immunogenetics. We also offer selected cell lines and DNA from our substantial DNA Bank of more than 1,000 cell lines from selected families, as well as individuals with diverse ethnicity and immunologic characteristics."^^ . + "http://beetlebase.org/"^^ . + "https://github.com/VEuPathDB-ontology/VEuPathDB-ontology"^^ . + . + . + . + "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . + . + . + "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . + . + "http://purl.obolibrary.org/obo/OGMS_$1"^^ . + . + "false"^^ . + . + "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . + . + . + . + "Tom Gillespie" . + . + "https://n2t.net/$1:"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/TGMA_$1"^^ . + . + . + . + . + . + "http://senselab.med.yale.edu/OrDB/"^^ . + . + . + . + "Chris Mungall" . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://www.cropontology.org/rdf/CO_348:$1"^^ . . - "nb100-56351"^^ . - . - "false"^^ . - . - "http://ccdb.ucsd.edu/CCDBWebSite/sao.html"^^ . - . - . - . - . - "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "https://www.nextprot.org/term/FA-$1"^^ . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . - . - . - . - "^\\d+$"^^ . - . - "A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state."^^ . - . - . - . - . - "https://giardiadb.org/giardiadb/"^^ . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS"^^ . - . - . - . - . - "Identifiers.org Registry" . - . - . - "Call for paper topics in EasyChair"^^ . - "https://bioregistry.io/registry/$1" . - "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . - "false"^^ . - "Genomics Cohorts Knowledge Ontology" . - "P29894"^^ . - . - "false"^^ . - "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . - . - "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"^^ . - "BitterDB Compound" . - . - . - . - . - . - . - . - "HIT000195363"^^ . - . - . - "The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples."^^ . - . - . - . - . - . - . - . - "UR000124451"^^ . - . - "https://foodb.ca/foods/$1"^^ . - . - . - . - . - "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . - . - . - . - . - "^\\d{8}$"^^ . - . - . + . + . + . + . + "Orphanet Rare Disease Ontology" . + "http://purl.obolibrary.org/obo/CLYH_$1"^^ . + . + . + . + "1200"^^ . + . + . + "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . + . + "Amanda Hicks" . + "^\\d+$"^^ . + "false"^^ . + . + . + . + . + . + . + "Database of Genomic Structural Variation - Variant" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research)."^^ . + . + "https://github.com/ClinicalTrialOntology/CTO/"^^ . + . + "http://swissregulon.unibas.ch"^^ . + . + . + "Small Molecule Pathway Database" . + . + "1"^^ . + . + "https://www.storedb.org/"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "false"^^ . + "278"^^ . + . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + "https://scicrunch.org/resolver"^^ . + . + . + . + . + "40000617"^^ . + . + . + . + . + . + . + . + "true"^^ . + "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . + . + "false"^^ . + "https://dbpedia.org/ontology"^^ . + "http://amoebadb.org/amoeba/"^^ . + . + "The Plant TF database (PlantTFDB) systematically identifies transcription factors for plant species. It includes annotation for identified TFs, including information on expression, regulation, interaction, conserved elements, phenotype information. It also provides curated descriptions and cross-references to other life science databases, as well as identifying evolutionary relationship among identified factors."^^ . + "false"^^ . + . + . + . + "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . + "UniProt Isoform" . + . + . + . + "TVAG_386080"^^ . + "false"^^ . + . + . + "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . + "Developing Human Brain Atlas" . + "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . + "https://gpcrdb.org/protein/$1"^^ . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + "0000072"^^ . + "Bacterial Tyrosine Kinase Database" . + "ACM1_HUMAN"^^ . + . + "John Graybeal" . + . + . + "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . + . + . + . + "http://www.w3.org/2006/time#$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/aero"^^ . + . + . + . + . + "http://www.pdb.org/"^^ . + . + . + . + . + "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + "Medaka Developmental Stages" . + . + . + . + "false"^^ . + "Drosophila Phenotype Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "http://tolweb.org/$1"^^ . + . + . + . + . + "https://portal.gdc.cancer.gov/cases/$1"^^ . + . + . + "false"^^ . + . + "0000618"^^ . + . + . + . + . + . + "http://zfin.org"^^ . + "Eukaryotic Linear Motif Resource" . + "true"^^ . + . + "http://fishbase.org"^^ . + "false"^^ . + "Spectra Hash Code" . + . + . + "https://w3id.org/biolink/vocab/$1"^^ . + . + "XB-GENE-922462"^^ . + . + . + . + . + "http://www.wikipathways.org/instance/$1"^^ . + "^S-[A-Z]{4}[A-Z\\d\\-]+$"^^ . + . + . + . + . + . + . + . + . + . + "UniProt Variants" . + "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . + . + . + . + "https://www.hdruk.ac.uk"^^ . + . + . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + "^FDB\\d+$"^^ . + "http://purl.obolibrary.org/obo/BCGO_$1"^^ . + . + . + "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . + . + . + "^C\\d+$"^^ . + . + . + "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . + "1829126"^^ . + . + . + . + . + . + "has example" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . +_:Nf53f81f057be4231ab960d9b04974303 "Jonathan Bard" . + "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . + "https://www.drugbank.ca/categories/$1"^^ . + "Cell line collections"^^ . + . + . + "https://github.com/obophenotype/bio-attribute-ontology"^^ . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + . + . + "MMP3888430"^^ . + . + . + . + "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . + . + "Higher-level classifications of COG Pathways"^^ . + . + . + . + "http://www.wikigenes.org/e/gene/e/$1.html"^^ . + . + . + "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . + "UniGene" . + . + "https://www.ncbi.nlm.nih.gov/protein"^^ . + "The Ontology for Avida (OntoAvida) project aims to develop an integrated vocabulary for the description of the most widely used computational approach for performing experimental evolution using digital organisms (i.e., self-replicating computer programs that evolve within a user-defined computational environment).\n\nThe lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight.\n\nOntoAvida was initially developed by https://fortunalab.org, the computational biology lab at the Doñana Biological Station (a research institute of the Spanish National Research Council based at Seville, Spain). Contributors to OntoAvida are expected to include members of the Digital Evolution Laboratory (https://devolab.org/) at Michigan State University (USA).\n\nMore information can be found at https://obofoundry.org/ontology/ontoavida.html"^^ . + . + . + "Mosquito insecticide resistance" . + "false"^^ . + . + . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloging of books, documents, etc. This collection references MeSH terms published in 2013."^^ . + . + "false"^^ . + . + . + "The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research."^^ . + . + . + "A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum"^^ . + . + . + . + . + . + "00000443"^^ . + . + . + "Peter Midford" . + . + . + . + . + . + "https://www.ensembl.org/"^^ . + . + . + "ab-1-ha"^^ . + "Virus Pathogen Resource" . + . + "PseudoGene" . + "Glycan Naming and Subsumption Ontology" . + "^\\d{7}$"^^ . + . + "http://ensembl.org/glossary"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "^bt\\d+$"^^ . + "ClinVar Submitter" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000208"^^ . + . + "An identifier for an atom; the smallest unit of naming in a source, viz, a specific string with specific code values and identifiers from a specific source. As such, they can be thought of as representing a single meaning with a source Atoms are the units of terminology that come from sources and form the building blocks of the concepts in the Metathesaurus."^^ . + . + . + . + . + . + . + . + . + . + "0000029"^^ . + . + "00005254"^^ . + "Proteomic Data Commons" . + . + "DAPK1"^^ . + . + . + "http://birdgenenames.org/cgnc/"^^ . + . + "Abdomen"^^ . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . + . + . + . + . + . + "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . + "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . + "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . + . + . + "Christian-Alexander Dudek" . + . + . + . + . + "https://drugs.ncats.io/"^^ . + . + . + "https://jjj.bio.vu.nl/models/$1"^^ . + . + . + . + . + . + . + . + . + . + . + "^PGS[0-9]{6}$"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "0005250"^^ . + . + . + . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . + . + . + "The Amphioxus Development and Anatomy Ontology" . + "Nucleotide" . + . + . + . + . + . + . + . + . + . + . + . + "http://lincsportal.ccs.miami.edu/cells/"^^ . + . + . + . + "false"^^ . + . + . + . + . + "Disease Class" . + . + . + . + . + . + . + . + . + "Mammalian Phenotype Ontology" . + . + "EasyChair Call for Paper" . + . + "0000780"^^ . + . + . + . + . + . + . + . + . + . + . + "90801"^^ . + . + "false"^^ . + . "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . - . - . - . - "TB2:S1000"^^ . - . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . - "http://sed-ml.org/"^^ . - . - "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . - . - "true"^^ . - . - . - "cl3603"^^ . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - "CHEMBL3467"^^ . - . - . - . - "false"^^ . - "https://arxiv.org/"^^ . - . - . - "http://swissregulon.unibas.ch"^^ . - . - . - . - "https://www.ebi.ac.uk/imgt/hla/allele.html"^^ . - "https://comptox.epa.gov/dashboard/$1"^^ . - . - . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . - "UniProt Subcellular Locations" . - . - . - "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"^^ . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . - "https://w3id.org/oc/oci/$1"^^ . - "pgxbs-kftva5zv"^^ . - . - . - "Lepidoptera Anatomy Ontology" . - . - "^(doi\\:)?\\d{2}\\.\\d{4}.*$"^^ . - . - . - "http://www.informatics.jax.org/expression.shtml"^^ . - . - . - . - . - . - . - "Phenol-Explorer" . - . - . - "TS-0285"^^ . - . - . - . - . - . - . - . - . - . - "^\\d\\w+$"^^ . - . - . - . - . - . - . - . - "Drosophila gross anatomy" . - . - . - . - "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/AISM_$1"^^ . - "http://edamontology.org/data_$1" . - . - . - . - "National Microbiome Data Collaborative" . - . - . - "false"^^ . - . - "http://www.sparontologies.net/ontologies/scoro"^^ . - "^\\d{3}$"^^ . - "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . - "The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources."^^ . - . - "false"^^ . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . - . - "false"^^ . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - . + . + . + "Protein Interaction Network Analysis" . + . + . + . + "0000189"^^ . + . + "^[a-z0-9\\-]+$"^^ . + . + . + . + . + . + . + . + . + . + . + "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . + . + . + . + "AntWeb ID" . + . + . + "PomBase" . + . + . + "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . + "OSR0818"^^ . + . + . + "The Orphanet Rare Disease ontology (ORDO) is a structured vocabulary for rare diseases, capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases.\r\nIt integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) and classifications (ICD10)."^^ . + . + . + . + . + "434"^^ . + "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . + . + . + "false"^^ . + . + . + . + "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . . - "STUDY1040"^^ . - . - . - "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . - . - . - . - . - . - . - . - . - . - "https://www.cdc.gov/nchs/icd/icd9cm.htm"^^ . - . - . - . - . - "false"^^ . - "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . - . - . - . - . - . - . - . - . - "https://www.w3.org/2003/01/geo/wgs84_pos"^^ . - . - . - "GeoNames Feature Code" . - . - . - . - . - . - . - "https://www.swisslipids.org/#/entity/SLM:$1"^^ . - "https://github.com/FAIRsharing/subject-ontology"^^ . - "http://modelseed.org/"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/books"^^ . - . - "http://www.aspgd.org/"^^ . - "http://string.embl.de/interactions/$1"^^ . - . - "BioCarta is a supplier and distributor of characterized reagents and assays for biopharmaceutical and academic research. It catalogs community produced online maps depicting molecular relationships from areas of active research, generating classical pathways as well as suggestions for new pathways. This collections references pathway maps."^^ . - "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . - "false"^^ . - . - . - . - "http://ascl.net/"^^ . - . - "http://geneontology.org/"^^ . - . - "82"^^ . - _:Ndf46391bdd1b4e34b8b76d723ba55299 . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . - "https://www.ebi.ac.uk/sbo/main/SBO:$1"^^ . - . - "https://github.com/EBISPOT/covoc"^^ . - "false"^^ . - "Reference Sequence Collection" . - . - "Cell Line Ontology [derivative]" . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - "Maize ontology" . - . - "Unified Phenotype Ontology" . - "https://github.com/EBISPOT/clyh_ontology"^^ . - "numpy"^^ . - . - . - "4D Nucleome Data Portal Biosource" . - . - "An anatomical and developmental ontology for cephalopods"^^ . - . - "Heather Piwowar" . - . - . - . - . - . - "Higher order grouping of Pfam families"^^ . - "Laboratory of Systems Pharmacology Compound" . - . - . - . - . - "false"^^ . - . - "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^ . - . - . - . - . - "https://www.internationalgenome.org/data-portal/sample/$1"^^ . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - "9781584885658"^^ . - . - . - . - . - . - . - . - . - "Cell line collections"^^ . - "00000001"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . - "https://www.alzforum.org/mutations/$1"^^ . - "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . - . - . - . - . - "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^ . - . - "http://purl.obolibrary.org/obo/CLYH_$1"^^ . - "GlycomeDB" . - "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . - "U49845"^^ . - "1801.012"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "SIDM01262"^^ . - "^\\d{9,9}$"^^ . - . - . - "MEROPS Clan" . - . - . - . - . + . + "false"^^ . + "Registry" . + . + "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . + . + . + . + . + . + . + . + "Feature Type Thesaurus" . + "false"^^ . + "http://purl.obolibrary.org/obo/ICEO_$1"^^ . + "https://www.metanetx.org/"^^ . + . + . + "22RV1_12_2019"^^ . + . + "http://ctdbase.org/"^^ . + . + . + . + . + . + "MINT-10000"^^ . + "http://www.drugbank.ca/drugs/$1"^^ . + _:Nbfb93ee5742149ae8c093731302fd738 . + . + . + "false"^^ . + . + . + "LG Chemical Entity Detection Dataset (LGCEDe)" . + . + . + . + "1"^^ . + . + "Gene"^^ . + . + . + . + . + . + . + "D00123"^^ . + . + . + . + . + . + "CompTox Chemistry Dashboard" . + . + . + "NIF Dysfunction" . + . + . + "ZDB-GENE-041118-11"^^ . + . + . + . + . + . + . + . + . + . + . + . + "MagnitudeValueType"^^ . + . + . + . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . + . + "http://www.dukeontologygroup.org/Projects.html"^^ . + . + . + . + . + . + "http://www.chemspider.com/"^^ . + "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . + "FDB002100"^^ . + "https://github.com/pcastellanoescuder/FoodBiomarkerOntology"^^ . + "European Registry of Materials" . + . + "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . + . + . + . + "false"^^ . + . + "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . + "0000254"^^ . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + "NameRXN" . + . + . + . + . + . + . + "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://spdx.org/licenses"^^ . + "http://www.semantic-systems-biology.org/apo"^^ . + . + . + . + "achcar11"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . + "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . + . + "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . + . + . + "^\\d{6}$"^^ . + "http://www.phosphosite.org/homeAction.do"^^ . + . + "128796-39-4"^^ . + . + . + . + . + "005012"^^ . + . + "http://www.sparontologies.net/ontologies/bido"^^ . + . + "Enzo Life Sciences" . + "smp-m3w9hbe"^^ . + "NIF Cell" . + "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "CHEMBL3307800"^^ . + "The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'."^^ . + "^OSC\\d{4}$"^^ . + . + . + "^AA\\d{4}$"^^ . + "Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases, which you can browse or search. It is a collection of publicly available pathways from multiple organisms that provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language."^^ . + "false"^^ . + . + . + "Luis González-Montaña" . + "https://cropontology.org/ontology/CO_356/Vitis"^^ . + "Mosquito gross anatomy ontology" . + . + "false"^^ . + . + . + . + . + "^\\w{1,2}\\d+$"^^ . + . + . + "^\\d{7}$"^^ . + . + "data_1664"^^ . + "MNXR101574"^^ . + "false"^^ . + . + "BRENDA tissue / enzyme source" . + . + "^\\w+$"^^ . + "http://ontoneo.com"^^ . + . + . + . + "000017"^^ . + . + "Cellular Phenotypes" . + . + . + . + "true"^^ . + . + . + "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/AEO_$1"^^ . + . + . + . + . + . + . + . + "A type for entries in the Bioregistry's collections" . + "International Fungal Working Group Fungal Barcoding." . + . + . + . + . + . + "https://cellbank.nibiohn.go.jp"^^ . . - . - . - . - . - "760050"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - "http://peroxibase.toulouse.inra.fr/"^^ . - . - "Yeast Deletion and the Mitochondrial Proteomics Project" . - "false"^^ . - . - . - . - . - . - . - . - "ALX-210-175"^^ . - . - "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . - . - "false"^^ . - "chebi" . + . + . + . + . + . + . + "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . + "Prefix Commons" . + "BiGG Reaction" . + . + . + . + . + "^\\d{7}$"^^ . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . + . + "false"^^ . + "false"^^ . + "https://labsyspharm.github.io/lspci/$1"^^ . + "false"^^ . + "https://www.vmh.life/#reaction/$1"^^ . + . + "1242"^^ . + . + . + . + . + "Data Object Service" . + . + . + . + . + "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . + "OBO Foundry" . + "is deprecated" . + "https://www.vectorbase.org/ontology-browser"^^ . + . + . + . + "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . + . + . + . + . + . + "ERR436051"^^ . + . + . + . + . + "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . + . + . + "false"^^ . + . + . + "http://planteome.org/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . + . + . + . + . + "0000070"^^ . + . + . + . + "PharmGKB Drug" . + "https://rapdb.dna.affrc.go.jp/"^^ . + . + . + "https://flybase.org/cgi-bin/cvreport.pl?id=FBbt:$1"^^ . + "the European Hepatitis C Virus Database (euHCVdb, http://euhcvdb.ibcp.fr), a collection of computer-annotated sequences based on reference genomes.mainly dedicated to HCV protein sequences, 3D structures and functional analyses."^^ . + . + . + "CHEMBL3467"^^ . + . + . + "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . + "9"^^ . + . + . + "http://mobidb.bio.unipd.it"^^ . + "NP_012345"^^ . + . + "Transport Systems Tracker" . + . + . + . + . + . + "http://ddinter.scbdd.com"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "100"^^ . + "HGNC gene family" . + "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . + "ACHN"^^ . + . + . + . + "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . + . + . + "http://getentry.ddbj.nig.ac.jp"^^ . + . + . + . + . + . + "false"^^ . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF"^^ . + . + . + . + . + . + . + . + . + "Vertebrate Homologous Organ Group Ontology" . + . + . + . + . + "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . + . + . + . + "http://www.oid-info.com/cgi-bin/display?oid=$1&submit=Display&action=display"^^ . + . + . + . + _:Nea857937d23a411e9c73d0450e3d7caa . + . + "SKIP001214"^^ . + . + . + . + . + "CHEBI" . + . + "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . + "http://masspec.scripps.edu/"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/Genbank/"^^ . + "http://www.diseasesdatabase.com/"^^ . + . + . + . + . + . + "LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds."^^ . + . + "4892"^^ . + . + . + "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "FR-FCM-ZYGW"^^ . + . + . + . + . + . + . + "http://www.peptideatlas.org/"^^ . + "ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number."^^ . + . + . + . + "^IHW\\d+$"^^ . + . + "EY223054.1"^^ . + "https://sitem.herts.ac.uk/aeru/ppdb/"^^ . + . + . + . + . + . + . + . + . + . + "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . + . + "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . + . + "https://human.brain-map.org"^^ . + . + . + . + . + . + . + "https://github.com/aszool/oarcs"^^ . + "false"^^ . + "false"^^ . + "http://scicrunch.org/resolver/SCR_$1"^^ . + . + . + "^PF\\d{5}$"^^ . + . + . + "^[1-9]\\d{0,5}$"^^ . + "PIRSF000100"^^ . + . + . + "DASHR expression" . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/ms/terms?obo_id=MS:$1"^^ . + "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view"^^ . + . + "ChemIDplus" . + . + . + "https://wiki.phenoscape.org/wiki/Curation_workflow"^^ . + "http://purl.obolibrary.org/obo/LPT_$1"^^ . + . + . + "DateTimeDescription"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://www.cellsignal.com/reference/pathway/$1.html"^^ . + . + . + . + . + . + _:N25c06a6dd2664015838bd96124c9e999 . + . + . + "http://supfam.org/SUPERFAMILY/"^^ . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "http://pombe.oridb.org/details.php?id=$1"^^ . + . + . + . + . + _:N74b5c109e3c245de9ba35c9a1b1d6b27 . + . + . + . + . + "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + _:Ncf9a92a673f44ee6b9624d114fb8704c . + "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . + . + . + "false"^^ . + "Meng LIU" . + . + . + . + "false"^^ . + "^DDB\\d+$"^^ . + . + . + "4214"^^ . + . + . + . . - . - . - "H3.03.00.0.00007"^^ . - . - "https://aopwiki.org/relationships/$1"^^ . - "Animal Trait Ontology for Livestock" . - "bioRxiv" . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/genbank/"^^ . - "false"^^ . - . - . - . - . - "https://mlcommons.org/en/"^^ . - "http://biomodels.net/rdf/vocabulary.rdf"^^ . - . - "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . - "false"^^ . - . - . - . - . - . - . - . - "0278"^^ . - "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . - . - . - . - "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . - . - . - "https://sitem.herts.ac.uk/aeru/bpdb/index.htm"^^ . - . - "false"^^ . - "Transport Systems Tracker" . + . + . + . + . + . + . + . + . + "http://purl.org/spar/cito/$1"^^ . + "false"^^ . + . + . + "ProteomeXchange" . + . + . + "http://purl.obolibrary.org/obo/DRON_$1"^^ . + . + . + "0000095"^^ . + . + . + . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + "^BAMSC\\d+$"^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . + "The Immune Epitope Database (IEDB) is a freely available resource funded by NIAID. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. The IEDB also hosts tools to assist in the prediction and analysis of epitopes."^^ . + . + "EGAS00000000001"^^ . + . + . + "Willy Wong" . + . + "https://prefixcommons.org" . + . + . + . + . + "International Classification of Diseases, 9th Revision" . + "Publishing Roles Ontology" . + . + . + "Odor Molecules DataBase" . + . + . + . + . + . + . + . + "RCV000033555.3"^^ . + "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://web.expasy.org/cellosaurus/"^^ . + "https://github.com/obophenotype/upheno"^^ . + . + . + . + "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . + . + "false"^^ . + . + "https://lotus.naturalproducts.net"^^ . + . + "https://www.cropontology.org/rdf/CO_327:$1"^^ . + "biopragmatics/bioregistry/416"^^ . + "TriTrypDB" . + . + "false"^^ . + . + "^\\d+$"^^ . + "^\\w+$"^^ . + "http://purl.obolibrary.org/obo/MONDO_$1"^^ . + . + "true"^^ . + . + . + . + . + "Cell line databases/resources"^^ . + "1"^^ . + . + . + . + "NanoParticle Ontology" . + . + . + . + . + "https://portal.issn.org/resource/ISSN/$1"^^ . + . + . + "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^ . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + . + "^\\d+$"^^ . + "Yeast phenotypes" . + . + "Erik Segerdell" . + . + "Catalogue of Life in Taiwan" . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/staticHTML/home"^^ . + . + "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . + "false"^^ . + . + . + . + "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . + . + "^\\w+$"^^ . + . + . + "true"^^ . + "http://purl.obolibrary.org/obo/SIBO_$1"^^ . + "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + . + "https://web.expasy.org/cellosaurus/"^^ . + . + . + "GALEN" . + "http://www.sparontologies.net/ontologies/pro"^^ . + . + . + . + . + . + "3905431"^^ . + . + "GCST000035"^^ . + . + . + "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . + . + . + . + . + . + . + . + . + . "false"^^ . - "^\\d{7}$"^^ . - "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . - . - . - . - . - . - "https://github.com/OHPI/ohpi"^^ . - . - . - "http://repository.topdownproteomics.org/proteoforms"^^ . - "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . - . - . - "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . - . - . - . - . - . - "false"^^ . - "WGS84 Geo Positioning" . - . - "022586"^^ . - . - "0019030"^^ . - "false"^^ . - . - . - "A controlled vocabulary to support the study of transcription in the primate brain"^^ . - . - . - . - . - . - "^([A-Z]+-)?\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - "true"^^ . - . - . - "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html"^^ . - . - "DisProt region" . - . - . - . - . + . + . + . + . + "false"^^ . + "http://worfdb.dfci.harvard.edu/"^^ . + . + . + . + "false"^^ . + . + "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://substrate.burnham.org/protein/annotation/$1/html"^^ . + . + . + "^[A-Za-z0-9\\-\\/]+$"^^ . + . + "Pathway Commons" . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ZFS_$1"^^ . + "false"^^ . + "http://www.genome.ad.jp/kegg/docs/upd_ligand.html"^^ . + . + . + . + "PMC International (PMCI) is a free full-text archive of biomedical and life sciences journal literature. PMCI is a collaborative effort between the U.S. National Institutes of Health and the National Library of Medicine, the publishers whose journal content makes up the PMC archive, and organizations in other countries that share NIH's and NLM's interest in archiving life sciences literature."^^ . + . + . + . + . + . + . + . + . + . + . + . + "CIViC Evidence" . + . + "^\\d{7}$"^^ . + . + . + . + "false"^^ . + . + . + . + "https://bdsc.indiana.edu/stocks/$1"^^ . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_366:$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "DrugBank" . + . + "E-cyanobacterium rule" . + . + . + . + "The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions."^^ . + . + "https://github.com/ufbmi/dron"^^ . + "https://www.pirbright.ac.uk/tick-cell-lines-views-page"^^ . + . + . + "false"^^ . + "http://exac.broadinstitute.org/"^^ . + "https://www.blueprintnhpatlas.org/"^^ . + . + . + "Gramene protein" . + . + . + "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . + "Platynereis Developmental Stages" . + . + . + "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . + . + . + "CTD Chemical" . + . + . + "false"^^ . + "I31.952"^^ . + _:N717b4f9bbb2a42b593c7c8d89eb79f55 . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/PLANP_$1"^^ . + "^\\d+$"^^ . + "false"^^ . + "^DDB_G\\d+$"^^ . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A collection groups one or more individual uniquely identified cell lines, snapshots, or collections. Primary uses are times series (collections of snapshots), patient cohorts (collections of cell lines), and studies (collections of time series collections)."^^ . + . + "latitude"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "The Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid bilayer, together with their structural classification, topology and intracellular localization."^^ . + . + . + . + "false"^^ . + . + . + . + "https://github.com/DiseaseOntology/PathogenTransmissionOntology"^^ . + . + "false"^^ . + . + . + "Open Data for Access and Mining" . + "false"^^ . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + "Henning Hermjakob" . + . + . + . + . + . + . + "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references 'biography' information."^^ . + "http://antibodyregistry.org/AB_$1"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + "http://umbbd.ethz.ch/"^^ . + . + . + "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\\d+)|(NZ\\_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . + . + . + . + "PyPI" . + "Semanticscience Integrated Ontology" . + . + "false"^^ . + . + . + "^\\d+$"^^ . + "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . + "http://purl.obolibrary.org/obo/PSDO_$1"^^ . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . + . + "URS0000759CF4"^^ . + . + . + "Plasmodium Life Cycle" . + . + . + "https://www.cropontology.org/ontology/$1" . + . + . + . + . + "false"^^ . + "OBO in OWL" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "false"^^ . + . + "https://www.hivreagentprogram.org/Home.aspx"^^ . + . + . + . + . + "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . + . + . + . + "0000044"^^ . + . + . + "false"^^ . + "CY077097"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + "http://pgscatalog.org"^^ . + . + "http://purl.obolibrary.org/obo/HSO_$1"^^ . + "0000001"^^ . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/PCO_$1"^^ . + . + . + . + "Cell line databases/resources"^^ . + "000204"^^ . + . + . + . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + "01N50ZZ"^^ . + . + . + . + . + "0004486"^^ . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolotes."^^ . + . + . + . + . + . + . + . + . + . + "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . + . + . + . + "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + . + "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . + . + . + . + . + . + . + "https://cropontology.org/ontology/CO_336/Soybean"^^ . + . + "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . + . + "https://ximbio.com"^^ . + . + "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . + . + "^K\\d+$"^^ . + . + "Ontology of Host-Microbiome Interactions" . + . + . + . + . + . + "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins."^^ . + "false"^^ . + "false"^^ . + . + . + "A0014"^^ . + . + . + . + . + . + "H00076"^^ . + . + . + . + . + "e0333"^^ . + . + . + . + . + "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . + . + . + . + "http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page"^^ . + "^\\d+$"^^ . + "0001000"^^ . + . + . + "^\\d{6}$"^^ . + . + "http://bis.zju.edu.cn/ricenetdb/"^^ . + . + . + . + . + "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . + "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . + . + "^\\d+$"^^ . + "GWAS Catalog" . + . + . + . + . + "false"^^ . + . + "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . + "^\\d+$"^^ . + . + . + . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . + . + . + . + . + "false"^^ . + . + "0000400"^^ . + . + . + . + . + . + . + "false"^^ . + . + "https://thebiogrid.org/"^^ . + "https://www.encodeproject.org/$1"^^ . + . + . + . + . + . + "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . + . + . + . + "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . + . + "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . + . + "Adriano Rutz" . + . + . + . + "Bill Hogan" . + . + "ITO_01625"^^ . + "true"^^ . + "https://data.apps.fao.org/catalog/organization/agrovoc"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFMO_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "Orientations of Proteins in Membranes Database" . + . + . + "Animal Genome Pig QTL" . + . + . + "0000108"^^ . + . + . + . + . + . + . + . + "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . + . + . + "Resource" . + . + . + . + "http://www.obofoundry.org/ontology/$1" . + "0000598"^^ . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . + . + "http://www.wormbase.org/get?name=$1"^^ . + . + . + "^(T0\\d+|\\w{3,5})$"^^ . + . + . + . + "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . + "Ontology of Vaccine Adverse Events" . + . + . + . + . + . + . + "false"^^ . + "http://bigg.ucsd.edu/models"^^ . + "Ali Syed" . + . + "false"^^ . + . + . + . + "The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology."^^ . + "Mike Cherry" . + . + . + "0000487"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . + . + . + . + "The SEED;" . + "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . + . + . + . + "PhosphoSite Protein" . + . + "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . + . + . + . + . + . + "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "Pfam" . + . + "^PTN\\d{9}$"^^ . + . + "http://edamontology.org"^^ . + "https://gold.jgi.doe.gov/resolver?id=$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "imp10873"^^ . + . + . + "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . + . + . + . + . + . + . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . + . + . + "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . + "PubChem Substance ID (SID)" . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + . + "CorrDB" . + . + . + . + "false"^^ . + "http://www.proteinatlas.org/"^^ . + "Ensembl Gene" . + "http://sideeffects.embl.de/"^^ . + . + "RIKEN Bioresource Center Cell Bank" . + . + . + . + . + . + . + . + . + "BioPortal" . + . + . + . + . + . + . + . + . + . + . + . + . + "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . + "^\\w+$"^^ . + . + . + . + "The NeuroLex project is a dynamic lexicon of terms used in neuroscience. It is supported by the Neuroscience Information Framework project and incorporates information from the NIF standardised ontology (NIFSTD), and its predecessor, the Biomedical Informatics Research Network Lexicon (BIRNLex)."^^ . + . + . + . + . + . + . . - "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . - . - "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . - "MobiDB is a database of protein disorder and mobility annotations."^^ . - . - . - "saddan"^^ . - . - "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . - . - "Reactome" . - "true"^^ . - . - . - "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/LIGM is a comprehensive database of fully annotated sequences of Immunoglobulins and T cell receptors from human and other vertebrates."^^ . - . - . + . + . + "TrichDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + "http://modelseed.org/biochem/reactions/$1"^^ . + "A0A009E7X8"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "An ontology of Drosophila melanogaster anatomy."^^ . + . + . + . + . + . + "https://www.cellbiolabs.com"^^ . + . + . + . + . + . + . + "GrainGenes" . + . + "ScerTF" . + . + . + . + . + "false"^^ . + "Biosapiens Protein Feature Ontology" . + . + . + . + . + . + . + "^PA\\d+$"^^ . + . + "MicrobeamManipulation"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "http://www.cropontology.org/ontology/CO_335/Common%20Bean"^^ . + . + "2555646"^^ . + . + . + . + . + "Gmelins Handbuch der anorganischen Chemie" . + . + "https://dublincore.org/specifications/dublin-core/dcmi-terms/"^^ . + "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . + "false"^^ . + . + . + "CC-BY-1.0"^^ . + . + . + . + "http://www.e-cyanobacterium.org/bcs/entity/"^^ . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + "Li7"^^ . + "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . + . + . + "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . + . + . + "^[0-9]+$"^^ . + "https://github.com/Novartis/hpath"^^ . + . + . + "^\\d{3}$"^^ . + "2.16.840"^^ . + . + . + . + . + . + "false"^^ . + . + . + "Human Plasma Membrane Receptome Families" . + . + . + . + . + . + "KEGG Disease" . + . + . + . + "BAMSC981"^^ . + . + . + . + . + "^\\d{5}$"^^ . + "^FOOD\\d+$"^^ . + . + . + . + "Anatomical Entity Ontology" . + . + . + . + . + . + "0000139"^^ . + . + . + "ST000900"^^ . + "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . + . + . + . + . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + "Rat Strain Ontology" . + . + . + . + "^\\d{7}$"^^ . + "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . + "European Genome-phenome Archive Study" . + . + . + . + . + "http://www.sparontologies.net/ontologies/deo"^^ . . - "Flora Phenotype Ontology" . - . - . - . - "Emotion Ontology" . - "nmrCV is a controlled vocabulary to deliver standardized descriptors for the open mark-up language for NMR raw and spectrum data, sanctioned by the metabolomics standards initiative msi."^^ . - . - . - . - . - . - . - . - . - "https://www.rebuildingakidney.org/"^^ . - . - . - . - . - . - "5"^^ . - . - . - "https://www.wwpdb.org/pdb?id=$1"^^ . - . - "false"^^ . - . - "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other."^^ . - . - . - . - . - . - . - "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . - "^SMP\\d+$"^^ . - . - "^\\d{7}$"^^ . - "^GLDS-\\d+$"^^ . - . - . - . - "3"^^ . - . - . - "https://github.com/AnimalGenome/vertebrate-trait-ontology"^^ . - . - . - . - "false"^^ . - . - "The SPDX License List is a list of commonly found licenses and exceptions used in free and open source and other collaborative software or documentation. The purpose of the SPDX License List is to enable easy and efficient identification of such licenses and exceptions in an SPDX document, in source files or elsewhere. The SPDX License List includes a standardized short identifier, full name, vetted license text including matching guidelines markup as appropriate, and a canonical permanent URL for each license and exception."^^ . - . - "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . - "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . - . - . - . - . - "4390079"^^ . - "https://github.com/obophenotype/developmental-stage-ontologies/wiki/PdumDv"^^ . - . - "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . - "http://igsn.org/$1"^^ . - . - "^\\d+$"^^ . - . - "data_1664"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - . - "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . - . - "0007404"^^ . - . - "false"^^ . - "^\\d{6}$"^^ . - . - . - "false"^^ . - "NIF Cell" . - . - "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Schizosaccharomyces pombe."^^ . - "FAIRsharing Subject Ontology" . - "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . - . - "880798137"^^ . - . + "http://www.geneontology.org/gocam"^^ . + "Genetic Code" . + . + . + "6VDC956"^^ . + . + "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . + "An ontology to represent genomics cohort attributes."^^ . + . + "AmoebaDB" . + "Symptom Ontology" . + . + . + . + "decimal"^^ . + . + "The Virus Infectious Disease Ontology" . + . + "false"^^ . + "https://github.com/EBISPOT/covoc"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "VFG2154"^^ . + . + "https://aftol.umn.edu"^^ . + . + "0000390"^^ . + . + . + . + "false"^^ . + . + . + . + "Ontology of units of Measure" . + "http://viralzone.expasy.org/"^^ . + "false"^^ . + "2404"^^ . + "http://purl.obolibrary.org/obo/MPATH_$1"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with bacterial genomes."^^ . + . + . + "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . + . + . + "Pigeonpea ontology" . + "rateRule"^^ . + . + . + . + . + . + . + "https://portal.issn.org"^^ . + . + . + . + "http://rgd.mcw.edu/"^^ . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . + "Paul Schofield" . + . + "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . + "Toxin and Toxin Target Database" . + . + "false"^^ . + . + . + . + . + "http://matrixdb.univ-lyon1.fr/"^^ . + . + . + "http://www.narcis.nl/publication/RecordID/$1"^^ . + "10343835"^^ . + . + . + "Ecological terms"^^ . + "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . + . + . + . + "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . + . + "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "Database of Escherichia coli Sequence and Function" . + . + . + "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . + . + . + "Pathogen Transmission Ontology" . + . + . + . + . + . + . + . + . + . + . + "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references G-protein coupled receptors."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://civicdb.org/links/assertions/$1"^^ . + "https://github.com/OpenLHS/PDRO"^^ . + . + "EcoLexicon" . + . + "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . + "^\\d+$"^^ . + . + . + . + . + "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + "https://www.uniprot.org/database/" . + . + "false"^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "RAP-DB Locus" . + "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . + . + . + . + "Search Tool for Retrieval of Interacting Genes/Proteins" . + . + "http://omia.angis.org.au/$1/"^^ . + . + . + . + . + . + . + . + . + . + . + "PubMed" . + "false"^^ . + "http://purl.obolibrary.org/obo/RBO_$1"^^ . + "^\\w+(\\.\\d+)$"^^ . + . + . + . + . + . + "28789"^^ . + . + "false"^^ . + "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . + . + . + . + . + . + . + . + "Gene Ontology" . + . + . + . + "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . + "http://purl.obolibrary.org/obo/RXNO_$1"^^ . + . + "http://purl.obolibrary.org/obo/EHDA_$1"^^ . + . + . + . + . + "Livestock Breed Ontology" . + . + . + . + . + . + . + "http://sed-ml.org/"^^ . + . + . + . + . + "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . + "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . + "P3DB Site" . + "^ENSGT\\d+$"^^ . + . + . + . + "^(\\w){3}$"^^ . + . + "http://www.humanproteomemap.org/index.php"^^ . + "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . + "T01B6.1"^^ . + . + . + . + . + . + . + . + . + . + "24867"^^ . "C0026339"^^ . - . - "0000983"^^ . - "casent0106247"^^ . - . - "COMBINE specifications" . - . - "false"^^ . - . - . - . - . - "http://virtualflybrain.org/reports/$1"^^ . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . - . - "false"^^ . - "true"^^ . - . - . - . - "https://vocab.lternet.edu/vocab/vocab/index.php"^^ . - "0000025"^^ . - . - "27106865"^^ . - . + . + "Person" . + . + . + . + "Gene Regulation Ontology" . + . + . + . + . + . + . + . + "90000018"^^ . + . + "627"^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "http://arabidopsis.org/index.jsp"^^ . + . + . + . + . + . + . + . + . + . + "ENCSR163RYW"^^ . + "false"^^ . + . + . + . + . + "Groundnut ontology" . + . + "SCV000151292"^^ . + "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . + . + . + . + "MIMIC III Database" . + . + "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . + . + . + . + "https://thebiogrid.org/interaction/$1"^^ . + "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references experiments and assays."^^ . + . + "^\\d{7}$"^^ . + . + . + "Foods in FooDB"^^ . + "false"^^ . + . + "0000013"^^ . + . + . + "^[0-9]+$"^^ . + "^\\d{8}$"^^ . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . + "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Plant Anatomy Ontology" . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . + "http://purl.obolibrary.org/obo/OMO_$1"^^ . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . +_:N0597ed38091d45928f0fa91cf0458b61 "David Blackburn" . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "Cotton ontology from CottonGen database - June 2019"^^ . + . + . + . + "false"^^ . + . + . + . + "https://tripod.nih.gov/bioplanet/"^^ . + . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/ONE_$1"^^ . + "https://proteinensemble.org/$1"^^ . + . + . + . + . + "http://www.sparontologies.net/ontologies/fr"^^ . + "https://www.kerafast.com/"^^ . + . + "^\\w+$"^^ . + . + "false"^^ . + . + "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . + "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . + . + "false"^^ . + . + "http://www.enanomapper.net/"^^ . + "https://easychair.org/cfp/"^^ . + . + . + "http://isbndb.com/"^^ . + "^\\d+$"^^ . + . + . + "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . + . + "Kidney and Urinary Pathway Ontology" . + "^\\d{7}$"^^ . + . + . + . + . + . + "0000127"^^ . + . + . + . + . + . + . + "0000072"^^ . + . + "CABRI (Common Access to Biotechnological Resources and Information) is an online service where users can search a number of European Biological Resource Centre catalogues. It lists the availability of a particular organism or genetic resource and defines the set of technical specifications and procedures which should be used to handle it."^^ . + "http://www.maizemap.org/"^^ . + "http://genepio.org/"^^ . + . + . + . + "https://drugs.ncats.io/drug/$1"^^ . + "https://omim.org/"^^ . + . + . + "http://vegbank.org/"^^ . + . + . + "false"^^ . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + . + "PubMed is a service of the U.S. National Library of Medicine that includes citations from MEDLINE and other life science journals for biomedical articles back to the 1950s."^^ . + "^\\d{7}$"^^ . + "International Classification of Diseases, 9th Revision, Clinical Modification" . + . + . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . + . + "^\\d+$"^^ . + . + "SNOMED CT (International Edition)" . + . + . + . + "Golm Metabolome Database" . + . + . + . + . + . + . + "E-cyanobacterium experiments is a repository of wet-lab experiments related to cyanobacteria. The emphasis is placed on annotation via mapping to local database of biological knowledge and mathematical models along with the complete experimental setup supporting the reproducibility of the experiments."^^ . + . + "https://www.novusbio.com"^^ . + . + . + . + . + . + . + . + "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . + . + "https://www.langual.org"^^ . + . + . + . + . + "http://130.88.97.239/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false®expr=off&prints_accn=$1"^^ . + . + "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . + . + . + "Reference"^^ . + . + "T3D0001"^^ . + . + "Datanator Metabolite" . + . + "has pattern" . + . + . + . + "MM00040"^^ . + "UniProt Diseases" . + . + . + . + . + "^GCST\\d{6}\\d*$"^^ . + "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . + . + . + . + . + . + . + . + . + "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . + "https://github.com/BiodiversityOntologies/bco"^^ . + . + . + "false"^^ . + "Barcode of Life database" . + . + . + . + . + . + . + "false"^^ . + "Animal TFDB Family" . + . + . + "https://github.com/PlantPhenoOntology/PPO"^^ . + . + "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . + . + . + "false"^^ . + . + . + "https://flybrain-ndb.virtualflybrain.org"^^ . + . + "ATL98012"^^ . + . + . + . + "The Integrated Canine Data Commons is one of several repositories within the NCI Cancer Research Data Commons (CRDC), a cloud-based data science infrastructure that provides secure access to a large, comprehensive, and expanding collection of cancer research data. The ICDC was established to further research on human cancers by enabling comparative analysis with canine cancer."^^ . + "BBA0001"^^ . + "^[a-z0-9]{32,32}$"^^ . + . + "Fernanda Dorea" . + . + "http://www.w3.org/XML/1998/namespace#$1"^^ . + "false"^^ . + . + . + "http://github.com/seger/aao"^^ . + . + . + "Ruili Huang" . + . + . + . + . + . + . + "886"^^ . + . + . + . + "https://monarch-initiative.github.io/mondo"^^ . + . + "http://www.jcvi.org/mpidb/about.php"^^ . + . + . + "Decentralized Identifier" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "KEGG Environ" . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/GSSO_$1"^^ . + . + . + . + . + . + . + . + . + "A controlled vocabulary to describe phenotypic traits in plants."^^ . + "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . + "PRIDE Project" . + "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . + "http://rgd.mcw.edu/"^^ . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + . + . + "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . + . + . + . + "Alpha Tom Kodamullil" . + "SR0000178"^^ . + . + "^[A-Za-z]+$"^^ . + "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^ . + . + "false"^^ . + "A01M1/026"^^ . + . + "^\\d+$"^^ . + . + . + "Xenopus Phenotype Ontology" . + "false"^^ . + . + "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . + . + . + "http://e-cyanobacterium.org/models/"^^ . + "https://bioregistry.io/metaregistry/$1"^^ . + . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . + . + . + "nstd102"^^ . + "Ontology of Biological Attributes" . + . + . + . + . + . + "^[A-Za-z0-9-]+$"^^ . + . + "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . + . + "false"^^ . + "GenProp0699"^^ . + "PXD000440"^^ . + . + . + "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . + . + "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . + . + . + "http://www.imgt.org/"^^ . + . + . + . + "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . + . + . + . + . + . +_:N218fe6712b8d48939ba7aa2d08418b48 "Pierre Sprumont" . + . + . + "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . + . + . + "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . + . + . + . + . + . + "551115"^^ . + "FuncBase Human" . + "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . + "Protein Alignment organised as Structural Superfamily" . + . + . + . +_:Naab6944c589a4e388b5102c114aedfe1 "Burke Squires" . + . + . + "http://4dx.embl.de/platy"^^ . + . + . + . + . + . + "Suggested Ontology for Pharmacogenomics" . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + "Mammalian Feeding Muscle Ontology" . + . + . + "https://gitlab.com/fortunalab/ontoavida"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html"^^ . + . + . + "https://www.deciphergenomics.org/syndrome/$1"^^ . + "The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature."^^ . + . + . + "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . + . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt"^^ . + . + "UCR00513"^^ . + . + "^\\d{5}$"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . + . + . + . + . + "3771992"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "https://bgee.org/bgee/bgee?page=documentation#sectionHomologyRelationships"^^ . + "^\\d+$"^^ . + "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . + . + . + "http://www.obofoundry.org/" . + . + "^\\d{7}$"^^ . + . + . + "http://purl.obolibrary.org/obo/PDRO_$1"^^ . + "false"^^ . + . + . + "https://depmap.org/portal/cell_line/$1"^^ . + . + . + . + . + . + . + . + . + . + "https://www.gwascentral.org/study/$1"^^ . + . + . + . + . + "https://www.genome.jp/kegg/reaction/"^^ . + "Units of measurement ontology" . + "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + . + . + . . - . - "^[A-Z0-9]+$"^^ . - . - "false"^^ . - . - "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . - . - . - "^\\d{7}$"^^ . - "HOSAPI0399"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/ols/ontologies/sio/terms?short_form=$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "http://agricola.nal.usda.gov/"^^ . - "http://www.kegg.jp/kegg/module.html"^^ . - . - "Olfactory Receptor Database" . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "Feature Type Thesaurus" . - "Marie-Angélique Laporte" . - "Vertebrate Skeletal Anatomy Ontology" . - . - . - . - . - . - . - . - "ABL1"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "^UDB\\d{6}$"^^ . - "^\\d+\\-\\d+\\-\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "GlycoPOST" . - . - . - . - . - "DataCollection"^^ . - . - . - . - . - . - "https://glycopost.glycosmos.org/entry/$1"^^ . - . - . - "false"^^ . - "http://biocyc.org"^^ . - "Database of Macromolecular Interactions" . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "0000010"^^ . - . - "false"^^ . - . - "false"^^ . - . - "CHEBI" . - "Database of the dielectric properties of biological tissues."^^ . + . + "false"^^ . + . + . + "https://www.ebi.ac.uk/complexportal"^^ . + "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . + . + . + . + "https://civicdb.org/links/evidence/$1"^^ . + . + . + "http://edamontology.org"^^ . + . + . + . + . + . + . + . + "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . + "^\\d{7}$"^^ . + . + . + . + "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . + . + . + . + . + "4685"^^ . + "https://www.brainspan.org/"^^ . + "3546"^^ . + . + . + "MultiCellDS" . + . + . + . + . + . + "https://github.com/IEDB/MRO"^^ . + . + . + . + "depends on" . + . + . + . + "false"^^ . + "https://prosite.expasy.org/$1"^^ . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references mouse."^^ . + . + . + "MEROPS Family" . + "http://euhcvdb.ibcp.fr"^^ . + "The Cell: An Image Library™ is a freely accessible, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes."^^ . + . + . + . + "COlleCtion of Open Natural ProdUcTs" . + . + "http://crispr.i2bc.paris-saclay.fr/"^^ . + "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . + . + . . - . - . - . - . - . - . - . - . + . + "http://www.sasbdb.org/"^^ . + "^A\\d{4}$"^^ . + . + . + "Beta Cell Genomics Ontology" . + . + "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . + . + . + "CATH Protein Structural Domain Superfamily" . + . + . + . + "SABIO-RK Compound" . + . + . + . + . + "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . + . + . + . + "Japan Chemical Substance Dictionary" . + . + "^\\d{5}$"^^ . + . + . + . + . + "https://neurovault.org/images/$1"^^ . + . + . + "Comprehensive Resource of Mammalian protein complexes" . + . + . + "^\\w{1,3}$"^^ . + . + . + . + . + . + "PA448710"^^ . + . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "e0333"^^ . - "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . - . + . + "0001"^^ . + . + . + . + . + . + "CATH superfamily" . + "SASDAX8"^^ . + "http://www.proteinatlas.org/$1"^^ . + . + . + "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . + "The Ligand-Gated Ion Channel database provides nucleic and proteic sequences of the subunits of ligand-gated ion channels. These transmembrane proteins can exist under different conformations, at least one of which forms a pore through the membrane connecting two neighbouring compartments. The database can be used to generate multiple sequence alignments from selected subunits, and gives the atomic coordinates of subunits, or portion of subunits, where available."^^ . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + . + . + . + . + "https://www.novusbio.com/products/$1"^^ . + "^\\d{7}$"^^ . + . + . + . + "FAIR* Reviews Ontology" . + . + . + . + . + . + "http://func.mshri.on.ca/human/"^^ . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . + . + . + . + "Bioregistry" . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references transcript information."^^ . + "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . + "MEROPS Clan" . + . + . + . + . + "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . + . + . + . + . + . + "false"^^ . + . + "http://mycobrowser.epfl.ch/marinolist.html"^^ . + "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . + "0000006"^^ . + . + . + . + . + . + "http://www.vbase2.org/vgene.php?id=$1"^^ . + . + "false"^^ . + "false"^^ . + . + "Cell Line Ontology" . + "0000001"^^ . + "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . + . + . + . + "http://www.marinespecies.org/"^^ . + . + . + . + . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . + . + . + "^\\d+$"^^ . + . + . + "PRJDB3"^^ . + . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . + . + "Datanator Gene" . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + . + . + . + . + "0000086"^^ . + . + "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . + . + . + "Genomes Online Database" . + "false"^^ . + . + "1000560"^^ . + . + . + . + . + "https://bykdb.ibcp.fr/BYKdb/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q=$1"^^ . + "ZINC is not Commercial" . + . + "Pierre-Alain Binz" . + . + . + . + . + . + . + . + . + "https://archive.softwareheritage.org"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . + . + . + "0005926"^^ . + "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . + . + . + . + . + "0000003"^^ . + . + . + . + . + . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/VSO"^^ . + "^\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . + "21723"^^ . + "https://www.rhea-db.org/"^^ . + "https://data.4dnucleome.org/experiment-set-replicates/"^^ . + . + . + . + "A person" . + . + "International Nonproprietary Names" . + . + "https://github.com/obophenotype/sibo"^^ . + "https://pdc.cancer.gov/pdc/study/$1"^^ . + . + . + . + "Asiyah Yu Lin" . . - . - "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . - "Protein covalent bond" . - . - . - "https://sumlineknowledgebase.com/"^^ . - . - . - . - . - "DAPK1"^^ . - "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . - . - . - . - . - . - . - "BRENDA Ligand" . - "The GOA (Gene Ontology Annotation) project provides high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI). This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups."^^ . - "349124"^^ . - "true"^^ . - . - . - . - . - . - "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . - . - . - "Bgee family" . - . - . - . - "false"^^ . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "http://trichdb.org/trichdb/"^^ . - "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . - . - . - . - "http://www.hipsci.org/lines/#/lines/$1"^^ . - . - "NIFEXT covers IRIs that were \"external\" identifiers that were brought into the ontology at some point in time. This was done before most of the current standard ontology and identifier management practices had been developed."^^ . - . - . - . - . - . - "221058"^^ . - . - "http://bis.zju.edu.cn/ricenetdb"^^ . - . - . - . - "http://www.uniprot.org/uniprot/$1"^^ . - . - "^[a-z_A-Z0-9]+$"^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - "https://spdx.org/licenses"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d{3}$"^^ . - "https://proteinensemble.org/$1"^^ . - . - . - . - "FamPlex" . - "HBG284870"^^ . - . - "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . - . - . - . - . - "https://xmetdb.org"^^ . - "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . + "LigandBox" . + . + . + "^\\d{7}$"^^ . + . + . + "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . + . + "https://www.cancerrxgene.org/translation/Drug/$1"^^ . + "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . + . + "false"^^ . + "Blue Brain Project Knowledge Graph" . + . + . + . + "Prefix Commons" . + . + . + . + "http://autism.mindspec.org/GeneDetail/$1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + "Human Metabolome Database" . + . + "5fce9b7300001250"^^ . + . + . + . + "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . + . + . + "https://www.itis.gov/"^^ . + . + . + . + . + "false"^^ . + . + . + . + "0000485"^^ . + . + "0221"^^ . + . + "https://www.yeastgenome.org/observable/APO:$1"^^ . + . + . + . + . + . + . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . + "MNXM1723"^^ . + "http://tolweb.org/tree/"^^ . + "Collection" . + . + . + . + "false"^^ . + . + . + . + "Higher order grouping of Pfam families"^^ . . - . - . - "Browser for the periodic table of the elements"^^ . - . - . - . - "000017"^^ . - . - . - . - . - "^[1-9]\\d{0,5}$"^^ . - "^\\d+$"^^ . - . - "SKIP001214"^^ . - . - . - . - "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . - . - "ChEMBL" . - . - "^[0-9]*$"^^ . - "^[AEP]-\\w{4}-\\d+$"^^ . - . - "false"^^ . - "https://www.storedb.org/"^^ . - "^DTXSID\\d+$"^^ . - . - "FlyBase Reference Report" . - . - . - . - . - "http://www.wikidata.org/entity/$1"^^ . - . - "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . - . - . - "^\\d{7}$"^^ . - . - "None"^^ . - "^[\\w\\-:,]{3,64}$"^^ . - . - . + . + "http://www.cellsignal.com/catalog/index.html"^^ . + . + . + . + "^CCDS\\d+\\.\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "Topology Data Bank of Transmembrane Proteins" . + "^EGAD\\d{11}$"^^ . + . + . + . + "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . + . + . + "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . + . + . + . + . + . + "25782"^^ . + "true"^^ . + . + . + . + . + . + . + "https://easychair.org/cfp/$1"^^ . + . + . + . + "RoleInTime"^^ . + . + . + . + . + . + . + "Metabolites in the Xenobiotics Metabolism Database."^^ . + . + . + . + . + . + . + . + . + "http://sugarbind.expasy.org/"^^ . + . + "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . + . + "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . + . + . + . + "https://pharmacodb.ca/cell_lines/$1"^^ . + "https://www.noguchi.or.jp/"^^ . + . + . + . + "http://crdd.osdd.net/servers/virsirnadb"^^ . + . + . + . + . + "^[A-Za-z0-9]+$"^^ . + "http://purl.obolibrary.org/obo/OBI_$1"^^ . + "1"^^ . + . + "MOL000160"^^ . + . + . + "^(G|P|U|C|S)\\d{5}$"^^ . + "Yeast Deletion and the Mitochondrial Proteomics Project" . + . + . + "false"^^ . + "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/index.cgi"^^ . + . "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references families of receptors or subunits."^^ . - . - . - . - "^H\\d+$"^^ . - "Gene Regulation Ontology" . - "LCSCCPN"^^ . + . + . + "56305849200"^^ . + . + . + . + _:Ne3ce3dae718c46279289e72cb5a0dceb . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Locus' view."^^ . + "The Health Data Research Innovation Gateway (the 'Gateway') provides a common entry point to discover and enquire about access to UK health datasets for research and innovation. It provides detailed information about the datasets, which are held by members of the UK Health Data Research Alliance, such as a description, size of the population, and the legal basis for access."^^ . + . + . + . + . + "Genatlas" . + . + "The SCOP (Structural Classification of Protein) database is a comprehensive ordering of all proteins of known structure according to their evolutionary, functional and structural relationships. The basic classification unit is the protein domain. Domains are hierarchically classified into species, proteins, families, superfamilies, folds, and classes."^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://foodb.ca/foods/$1"^^ . + . + . + . + "BioAssay Ontology" . + . + . + . + . + "https://github.com/SCAI-BIO/EpilepsyOntology"^^ . + . + "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "0000106"^^ . + "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . + . + . + _:N87132ab790ed47c0856798958c4f76c4 . + "Tom Gillespie" . + . + . + "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . + . + . + "true"^^ . + "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . + "The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design."^^ . + . + "^\\d{7}$"^^ . + "http://kinase.bioinformatics.tw/"^^ . + . + . + "https://fairsharing.org/" . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/MF_$1"^^ . + . + "miRBase pre-miRNA" . + . + . + . + . + . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . + . + . + . + . + . + . + "https://e-cyanobacterium.org/bcs/rule/$1"^^ . + "http://asap.ahabs.wisc.edu/asap/home.php"^^ . + "false"^^ . + . + "^\\d+$"^^ . + "Ensembl Glossary" . + . + . + . + "http://www.w3.org/1999/02/22-rdf-syntax-ns"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "Integrative and Conjugative Element Ontology" . + "https://vocab.lternet.edu/vocab/vocab/index.php"^^ . + . + . + . + . + . + "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . + "DragonDB Protein" . + "r0001"^^ . + . + "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . + "MetaboLights Compound" . + "^\\d+$"^^ . + . + . + "TC010103"^^ . + . + . + . + . + . + "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . + . + . + "true"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . + "Biological Expression Language" . + . + . + . + . + . + "false"^^ . + . + "laml_tcga_pub"^^ . + . + "KEGG Genome" . + . + "http://www.plantontology.org"^^ . + "false"^^ . + . + "http://purl.obolibrary.org/obo/FOBI_$1"^^ . + . + . + "QJ51RV02"^^ . + . + "false"^^ . + . + . + "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . + . + . + . + . + . + "0000024"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "MeSH (Medical Subject Headings) is the National Library of Medicine's controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. This thesaurus is used by NLM for indexing articles from biomedical journals, cataloguing of books, documents, etc."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "http://www.jstor.org/stable/$1"^^ . + "Physico-chemical process" . + "https://www.ncbi.nlm.nih.gov/dbvar"^^ . + "Bgee gene" . + . + . + . + "A modeling paradigm-specific registry of prefixes and their URL expansions" . + . + . + . + . + "Distributed Archives for Neurophysiology Data Integration" . + . + . + "https://www.lgcstandards-atcc.org"^^ . + . + . + . + . + "true"^^ . + "false"^^ . + "DB-0174"^^ . + . + . + . + . + "Rfam database of RNA families" . + . + . + . + . + . + . + . + . + "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . + . + . + . + "SBGN Bricks data and ontology" . + . + . + . + . + . + "MicrosporidiaDB" . + . + . + . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/MmusDv"^^ . + . + . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references genes."^^ . + . + "http://geneontology.org/docs/ontology-relations/"^^ . + . + "Human Proteome Map Protein" . + . + "false"^^ . + "^\\d{7}$"^^ . + . + . + "The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies."^^ . + . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . + _:Na0aa5749d1e349baa4882573a6e90561 . + . + "https://www.ebi.ac.uk/ols/ontologies/mod/terms?obo_id=MOD:$1"^^ . + . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/geo/"^^ . + "https://mmp.sfb.uit.no/databases/marfun"^^ . + . + "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + . + . + . + . + . + . + . + . + . + . + "Barry Smith" . + . + . + . + . + . + "http://uberon.org"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "MCDS_S_0000000001"^^ . + "4900"^^ . + . "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . - . - . - "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . - "https://www.storedb.org/"^^ . - "http://edamontology.org/operation_$1"^^ . - . - . - . - "https://cordis.europa.eu/project/id/$1"^^ . - . - . - . - "375364"^^ . - "RCB0002"^^ . - . - "EHDAA:2185"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . - . - "2555646"^^ . - " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . - . - "Linear double stranded DNA sequences" . - "false"^^ . - . - . - . - "^\\w+$"^^ . - . - "Pathogen Transmission Ontology" . - . - "CIP - potato ontology - december 2018"^^ . - "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . - "EAWAG Biocatalysis/Biodegradation Database" . - . - . - . - . - "false"^^ . - . - . + . + . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene."^^ . + "^\\d{7}$"^^ . + "https://www.nextprot.org/db/entry/$1"^^ . + . + . + _:N28878dcda46d47efbf4dee8308457a62 . + "http://exac.broadinstitute.org/"^^ . + . + . + . + . + . + . + "urn:nbn:fi:tkk-004781"^^ . + . + . + "http://www.cropontology.org/ontology/CO_331/Sweet%20Potato"^^ . + . + . + . + . + "http://www.gramene.org/plant_ontology/"^^ . + "An ontology for dengue fever."^^ . + "false"^^ . + . + . + "The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis."^^ . + "http://biocyc.org"^^ . + . + . + . + "https://github.com/infectious-disease-ontology-extensions/ido-virus"^^ . + . + . + "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . + . + . + . + . + "Molbase" . + . + . + "100000"^^ . + "^IID\\d+$"^^ . + . + . + . + . + "http://img.jgi.doe.gov/"^^ . + . + . + . + "The PRotein Ontology (PRO) has been designed to describe the relationships of proteins and protein evolutionary classes, to delineate the multiple protein forms of a gene locus (ontology for protein forms), and to interconnect existing ontologies."^^ . + . + . + "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . + . + . + "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . + . + . + "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . + "^\\d+$"^^ . + "^YMDB\\d+$"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . + . + "70"^^ . + . + . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. \r\nPharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies."^^ . + . + "0000111"^^ . + "http://prodom.prabi.fr/prodom/current/html/home.php"^^ . + "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . + . + "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . + . + . + . + . + . + . + . + . + "AHR"^^ . + "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "^\\d{7}$"^^ . + . + . + "https://www.cropontology.org/rdf/CO_356:$1"^^ . + "ProGlycProt (Prokaryotic Glycoprotein) is a repository of bacterial and archaeal glycoproteins with at least one experimentally validated glycosite (glycosylated residue). Each entry in the database is fully cross-referenced and enriched with available published information about source organism, coding gene, protein, glycosites, glycosylation type, attached glycan, associated oligosaccharyl/glycosyl transferases (OSTs/GTs), supporting references, and applicable additional information."^^ . + . + . + . + . + . + "The American Type Culture Collection (ATCC) is a private, nonprofit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the life sciences."^^ . + "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . + . + "false"^^ . + . + "false"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . + "https://www.ebi.ac.uk/sbo/main/SBO:$1"^^ . + . + "http://csbl.bmb.uga.edu/DOOR/operon.php"^^ . + . + . + . + . + "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . + . + . + . + . + . + . + . + "Fungal Nomenclature and Species Bank" . + "false"^^ . + . + . + . + . + . + "0000003"^^ . + "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to expression across species."^^ . + . + "http://lipidbank.jp/index.html"^^ . + . + . + . + "https://loinc.org/$1"^^ . + . + . + . + . + "http://id.nlm.nih.gov/mesh/"^^ . + . + . + . + . + . + . + . + . + "http://yetfasco.ccbr.utoronto.ca/"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "^[0-9]{8}$"^^ . + . + . + . + . + . + "0002989"^^ . + . + "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . + "11303"^^ . + "http://www.treefam.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000057"^^ . + . + . + "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . + "Q9P0K8"^^ . + . + . + . + "Loggerhead nesting" . + "http://geneontology.org/docs/guide-go-evidence-codes/"^^ . + . + "false"^^ . + "SciCrunch Registry" . + . + . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + "clinical LABoratory Ontology" . + "https://www.cropontology.org/rdf/CO_322:$1"^^ . + . + "false"^^ . + "^(Q|P)\\d+$"^^ . + . + "William Hogan" . + . + . + . + . + "^\\d+$"^^ . + "The Tetrahymena Genome Database (TGD) Wiki is a database of information about the Tetrahymena thermophila genome sequence. It provides information curated from the literature about each published gene, including a standardized gene name, a link to the genomic locus, gene product annotations utilizing the Gene Ontology, and links to published literature."^^ . + "false"^^ . + . + "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . + "RiceNetDB Protein" . + "^UCR\\d{5}$"^^ . + "https://www.ideal-db.org"^^ . + "^[A-Za-z0-9-]+$"^^ . + "http://zinc15.docking.org/"^^ . + . + . + . + . + . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . + . + "Barley ontology" . + . + . + . + . + . + . + . + "H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. It provides curated annotations of human genes and transcripts including gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. This datatype provides access to the 'Transcript' view."^^ . + . + . + . + . + . + "Mental Disease Ontology" . + . + . + "0000128"^^ . + "Protein Ensemble Database ensemble" . + "has reviewer" . + . + "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . + . + . + . + . + "MIRIAM Registry is an online resource created to catalogue collections (Gene Ontology, Taxonomy or PubMed are some examples) and the corresponding resources (physical locations) providing access to those data collections. The Registry provides unique and perennial URIs for each entity of those data collections."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://w3id.org/oc/corpus/$1"^^ . + . + . + "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . + "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . + "https://envipath.org/package/$1"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/gv/mhc/"^^ . + "https://omabrowser.org/oma/hog/HOG:$1"^^ . + . + . + . + . + . + . + . + . + "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . + . + . + "151022"^^ . + . + . + "Saccharomyces Genome Database" . + . + "182"^^ . + "http://www.pseudomonas.com/"^^ . + . + . + . + . + . + . + . + . + "https://dgrc.bio.indiana.edu/cells/Catalog"^^ . + . + . + . + . + . + . + . + . + . + "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^ . + . + . + . + . + . + . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . + . + "^PA\\d+$"^^ . + "Allergome is a repository of data related to all IgE-binding compounds. Its purpose is to collect a list of allergenic sources and molecules by using the widest selection criteria and sources."^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "165a"^^ . + "^\\d+$"^^ . + "NCBI Protein" . + . + "http://purl.obolibrary.org/obo/LABO_$1"^^ . + "The international standard for identifying health measurements, observations, and documents."^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + "Laurel Cooper" . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "BioSimulators" . + "Anatomical Therapeutic Chemical Classification System" . + . + "https://www.inaturalist.org/taxa"^^ . + "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . + "0000008"^^ . + . + "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . + . + . + . + . + . + . + "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . + . + . + . + . + . + . + . + . + . + "^MMP\\d+.\\d+$"^^ . + "^\\d{7}$"^^ . + "bsg-000052"^^ . + "http://purl.obolibrary.org/obo/CDNO_$1"^^ . + . + . + . + . + "1868"^^ . + "https://dailymed.nlm.nih.gov/dailymed/"^^ . + . + . + . + "https://biosimulations.org/projects/$1"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_330:$1"^^ . + . + . + "http://tritrypdb.org/tritrypdb/"^^ . + "https://www.ebi.ac.uk/chebi/"^^ . . - "^\\d+$"^^ . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - "^A[A-Z]+\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - "Alzheimer's Disease Ontology" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "26957"^^ . - . - . - . - "^\\d{7}$"^^ . + "false"^^ . + . + . + "false"^^ . + . + "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . + . + "^WP\\d{1,5}(\\_r\\d+)?$"^^ . + . + . + "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . + . + . + . + . + . + "D053716"^^ . + . + . + "https://www.aapc.com/codes/cpt-codes/$1"^^ . + . + . + . + "false"^^ . + . + . + . + "The Echinoderm Anatomy and Development Ontology" . + . + "true"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://pav-ontology.github.io/pav/"^^ . + . + . + "1"^^ . + "false"^^ . + "^\\d+$"^^ . + "Dengue Fever Ontology" . + "ViralZone" . + . + . + . + . + "ev:E00032"^^ . + . + . + . + . + . + . + "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . + "Xenobiotics Metabolism Database" . + . + . + . + "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . + . + . + "http://purl.obolibrary.org/obo/SCDO_$1"^^ . + . + . + . + . + . + "Zenodo" . + "0010316"^^ . +_:N03116f7581dc43f4a75361f1d337a077 "Vivian Lee" . + . + "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . + "https://www.cdc.gov/nchs/icd/icd9cm.htm"^^ . + . + "Proteoform Atlas" . + . + . + "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . + . + "https://github.com/EnvironmentOntology/environmental-exposure-ontology"^^ . + . + . + . + . + "Global Research Identifier Database" . + . + . + . + . + . + . + . + . + "http://greengenes.lbl.gov/"^^ . + . + "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . + . + "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . + "false"^^ . + . + "^\\d+$"^^ . + "11"^^ . + . + . + . + . + "C2584994"^^ . + "Time Ontology in OWL" . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + . + . + . + . + . + . + "https://metacyc.org/compound?orgid=META&id=$1"^^ . + . + "The Veterans Health Administration is America’s largest integrated health care system, providing care at 1,293 health care facilities, including 171 medical centers and 1,112 outpatient sites of care of varying complexity (VHA outpatient clinics), serving 9 million enrolled Veterans each year."^^ . + "The set of prefixes used in the Cellosaurus resource" . + . + . + . + . + . + . + . + . + . + . + . +_:N8020408e4b514ad0b734401375de1070 "GenBank Support" . + . + . + . + "MI0026471"^^ . . - . - . - "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . - . - . - "146421"^^ . - . - . - . - "Gmelins Handbuch der anorganischen Chemie" . - "Animal Genome Cattle QTL" . - "An experimental run, served thrugh the ENA"^^ . - . - . - . - . - . - . - "4DNESWX1J3QU"^^ . - "https://www.worldcat.org/oclc/$1"^^ . - "http://purl.obolibrary.org/obo/GEO_$1"^^ . - "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . - . - . - . - "The Gender, Sex, and Sexual Orientation (GSSO) ontology is an interdisciplinary ontology connecting terms from biology, medicine, psychology, sociology, and gender studies, aiming to bridge gaps between linguistic variations inside and outside of the health care environment. A large focus of the ontology is its consideration of LGBTQIA+ terminology."^^ . - . - . - "^[A-Z0-9]+$"^^ . - "^[a-z_A-Z0-9]+$"^^ . - . - "OBO in OWL" . - . - . - . - "false"^^ . - . - "https://registry.identifiers.org/registry/$1" . - . - "J0705A10"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - "Datanator Gene" . - . - . - "Plant Trait Ontology" . - . - "CHEMBL3307800"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . - "3D Metabolites" . - "http://sugarbind.expasy.org/"^^ . - . - "false"^^ . - "GlycoNAVI is a website for carbohydrate research. It consists of the \"GlycoNAVI Database\" that provides information such as existence ratios and names of glycans, 3D structures of glycans and complex glycoconjugates, and the \"GlycoNAVI tools\" such as editing of 2D structures of glycans, glycan structure viewers, and conversion tools."^^ . - "^\\d{7}$"^^ . - . - . - . - . - "^NX_\\w+$"^^ . - . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - "The Food Interactions with Drugs Evidence Ontology (FIDEO) represents Food-Drug Interactions and underlying interaction mechanisms described in scientific publications, drug and adverse effects databases, and drug interactions compendia. The ontology builds on previous efforts from the FoodOn, DRON, ChEBI, and DIDEO ontologies as well as the Thériaque database. This ontology is maintained at https://gitub.u-bordeaux.fr/erias/fideo, and requests for changes or additions should be filed at the issue tracker there."^^ . - . - "HIX0004394"^^ . - . - "false"^^ . - . - "https://github.com/biobanking/biobanking"^^ . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . - "false"^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - _:Ne7bd6c7896fb4c08888ad9e245938067 . - . - . - . - . - . - . - . - . - "http://bioinformatics.ramapo.edu/GRSDB2/"^^ . - . - . - "AOPWiki" . - "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . - . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . - . - "Amphibian gross anatomy" . - . - "https://obophenotype.github.io/cell-ontology/"^^ . - "https://www.disprot.org/idpo/IDPO:$1"^^ . - . - . - "4145692"^^ . - . - . - . - . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . - . - . - . - . - . - . - . - . - "https://cropontology.org/ontology/CO_346/Mungbean"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . - . - . - . - . - "Shur-Jen Wang" . - . - . - . - . + . + . + "Ontology for genetic interval" . + . + "false"^^ . + "http://agroportal.lirmm.fr/ontologies/$1" . + "false"^^ . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "https://dbpedia.org/ontology/$1"^^ . + . + . + "false"^^ . + "http://geneontology.org/"^^ . + . + . + . + "http://en.wikipedia.org/wiki/Gene_Wiki"^^ . + . + "false"^^ . + . + . + "Animal natural history and life history" . + . + . + . + "false"^^ . + . + . + . + "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . + "The main contact person for a registry" . + . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . + . + "G8944"^^ . + "false"^^ . + . + . + . + "KEGG Modules are manually defined functional units used in the annotation and biological interpretation of sequenced genomes. Each module corresponds to a set of 'KEGG Orthology' (MIR:00000116) entries. KEGG Modules can represent pathway, structural, functional or signature modules."^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . + . + "true"^^ . + "0807.4956v1"^^ . + . + . + . + . + "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . + . + . + "http://www.whocc.no/atcvet/atcvet_index/"^^ . + . + . + "Nonribosomal Peptides Database" . + "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . + . + . + . + . + . + . + "Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland."^^ . + . + "false"^^ . + "Web Ontology Language" . + . + "Gene Expression Ontology" . + . + "^\\w+$"^^ . + "false"^^ . + . + . + . + . + . + . +_:N717b4f9bbb2a42b593c7c8d89eb79f55 "INOH curators" . + "http://aims.fao.org/aos/agrovoc/c_$1"^^ . + . + . + . + . + . + . + . + . + "Benjamin M. Gyori" . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . + . + . + . + . + "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . + . + . + . + "https://cropontology.org/ontology/CO_330/Potato"^^ . + "false"^^ . + "rsk00410"^^ . + . + . + "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . + "false"^^ . + . + . + . + "Entrez Gene" . + "CellBank Australia" . + "Paul Fabry" . + . + . + . + . + . + . + . + "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . + . + . + . + . + . + "false"^^ . + . + . + "DDB0191090"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://aopwiki.org/"^^ . + . + "https://clinicaltrials.gov/ct2/show/$1"^^ . + "false"^^ . + . + . + "false"^^ . + . + "https://github.com/OHPI/ohpi"^^ . + . + . + "The Vocabulary of Interlinked Datasets (VoID) is an RDF Schema vocabulary for expressing metadata about RDF datasets. It is intended as a bridge between the publishers and users of RDF data, with applications ranging from data discovery to cataloging and archiving of datasets. This document provides a formal definition of the new RDF classes and properties introduced for VoID. It is a companion to the main specification document for VoID, Describing Linked Datasets with the VoID Vocabulary."^^ . + "http://bcrj.org.br/celula/bcrj"^^ . + . + . + "http://biobanknetwork.telethon.it/"^^ . + . + . + . + "http://epd.vital-it.ch/cgi-bin/query_result.pl?out_format=NICE&Entry_0=$1"^^ . + . + . + "The reviewer of a prefix" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://pdc.cancer.gov/pdc"^^ . + . + "Egon Willighagen" . + . + . + . + . + "Coli Genetic Stock Center" . + . + . + . + . + . + "Veterinary Substances DataBase" . + . + "^[A-Z\\-]+$"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "http://dictybase.org/gene/$1"^^ . + . + "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . + . + . + . + "KEGG Drug Group" . + . + . + "^\\d{7}$"^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/"^^ . + . + "https://www.cropontology.org/rdf/CO_350:$1"^^ . + . + "BP100000"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/$1"^^ . + "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . + . + . + . + . + . + . + . + "^MSV\\d+$"^^ . + . + . + . + . + "1948"^^ . + . + "http://purl.obolibrary.org/obo/$1_$2" . + . + . + . + "The Arabidopsis Information Resource" . + . + . + . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . + . + "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . + . + . + "ADM1"^^ . + . + "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . + "false"^^ . + . + . + "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . + . + . + . + . + . + . + . + . + . + "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . + . + "false"^^ . + . + . + . + . + . + . + "https://plants.ensembl.org/id/$1"^^ . + . + "https://linkml.io/linkml-model/docs/SchemaDefinition/"^^ . + . + "https://fungi.ensembl.org/"^^ . + "^\\d{7}$"^^ . + . + "Locus Reference Genomic" . + . + . + . + . + . + . + . + "^[0-9]{12}$"^^ . + . + . + . + . + . + . + . + "ProtClustDB" . + . + . + . + . + . + . + . + . + . + . + . + "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . + . + . + . + . + . + . + "http://www.ubio.org"^^ . + . + . + "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . + "^\\d{7}$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://icd.codes/icd10cm/$1"^^ . + . + . + . + . + . + . + . + "https://www.cbioportal.org/study/summary?id=$1"^^ . + . + . + "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . + . + . + . + . + . + . + . + . + . + . + "Food Interactions with Drugs Evidence Ontology" . + . + . + . + . + . + "Genotype-Tissue Expression" . + . + . + . + "https://www.w3.org/ns/prov"^^ . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + "688"^^ . + . + . . - . - . - . - . - . - . - "National Drug Code" . - "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . - "http://purl.obolibrary.org/obo/SIBO_$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "Ontology of Medically Related Social Entities" . - . - . - "An ontology to capture confidence information about annotations."^^ . - . - . - "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . - . - "Plant Anatomy Ontology" . - "Bioregistry Collections" . - "http://urgi.versailles.inra.fr/Genefarm/"^^ . - . - "Sunflower ontology" . - "Cell line collections"^^ . - . - . - "http://bioinfo.lifl.fr/norine/"^^ . - . - . - . - "depends on" . - . + "The DRSC (Drosophila RNAi Screening Cente) tracks both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. It maintains a list of Drosophila gene names, identifiers, symbols and synonyms and provides information for cell-based or in vivo RNAi reagents, other types of reagents, screen results, etc. corresponding for a given gene."^^ . + "2GC4"^^ . + "false"^^ . + . + . + . + . + "Statistical Torsional Angles Potentials" . + . + . + . + . + . + . + . + . + "0000025"^^ . + . + . + "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . + . + "^\\d+\\-\\d+\\-\\d+$"^^ . + "https://reporter.nih.gov/"^^ . + . + . + "EchoBASE is a database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products."^^ . + . + . + . + . + . + "Coconut ontology" . + "26753"^^ . + . + . + "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . + . + "C00000001"^^ . + "http://www.bmrb.wisc.edu/"^^ . + . + . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://purl.org/spar/pwo/$1"^^ . + "Aceview Worm" . + "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . + "^\\d+$"^^ . + . + "https://bacteria.ensembl.org/"^^ . + . + "http://biomodels.net/vocab/idot.rdf"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "NCBI Gene Expression Omnibus" . + . + . + . + "http://www.york.ac.uk/"^^ . + "false"^^ . + . + . + "Document Components Ontology" . + . + . + "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . + "OriDB Schizosaccharomyces" . + . + "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . + . + . + . + "GlyTouCan" . + "false"^^ . + . + . + "http://cellimagelibrary.org/"^^ . + . + . + "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . + . + "Human Medical Genetics" . + . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . + . + . + . + . + "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . + . + "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . + . + "Geographical Entity Ontology" . + . + "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . + . + . + "FamPlex" . + . + . + . + . + . + . + "https://www.internationalgenome.org/"^^ . + . + . . - . - . - . - . - . - . - . - . - . - "International Standard Book Number" . - . - "https://rarediseases.info.nih.gov/diseases"^^ . - . - . - . - . - "A registry of commonly used prefixes in the life sciences and linked data" . - "http://mycobrowser.epfl.ch/marinolist.html"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://apps.who.int/classifications/icd10/browse/2010/en#/$1"^^ . - "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . - "^\\d+$"^^ . - "http://neurovault.org"^^ . - . - . - . - "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . - . - . - . - . - . - "Lentil ontology" . - . - "0000000"^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . - . - . - . - "Ontology of Biological and Clinical Statistics" . - . - "TreeBASE" . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "0000125"^^ . - . - . - . - . - . - . + "false"^^ . + . + . + . + . + "GnpIS" . + "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . + . + . + . + "Study inside StoreDB"^^ . + . + . + . + "COG Pathways" . + . + "SED-ML model format" . + . + . + "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . + . + . + . + . + "Life cycle stages for Human"^^ . + "Natural Product-Drug Interaction Research Data Repository" . + . + "www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . + "^EP\\d{4}$"^^ . + . + . + . + . + . + . + . + "YMDB00001"^^ . + "Horizon Discovery cell line collection" . + . + . + . + "Metabolome Express" . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "SIGNOR-C41"^^ . + . + "http://purl.obolibrary.org/obo/VT_$1"^^ . + "false"^^ . + . + . + "https://bitbucket.org/$1"^^ . + . + . + . + . + . + . + . + "0001191"^^ . + . + "P12345"^^ . + . + "Sweet Potato ontology" . + "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . + . + "http://purl.obolibrary.org/obo/CARO_$1"^^ . + "false"^^ . + . + . + . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + "BG11523"^^ . + . + "^spike\\d{5}$"^^ . + "^[0-9A-Za-z\\-.]+$"^^ . + "health_care_quality_assessment"^^ . + . + . + . + "true"^^ . + . + . + . + "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . + "Search PRINTS-S" . + . + "P3DB Protein" . + . + . + "6472"^^ . + . + . + "http://agricola.nal.usda.gov/"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "https://viralzone.expasy.org/$1"^^ . + . + . + . + . + . + . + . + "A CIViC assertion classifies the clinical significance of a variant-disease relationship under recognized guidelines. The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic or predisposing clinical information for a variant in a specific cancer context. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, and diagnostic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic or Predisposing Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular variant and cancer type, then a corresponding assertion be created in CIViC."^^ . + . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/FLU_$1"^^ . + . + . + "http://purl.obolibrary.org/obo/ADO_$1"^^ . + . + . + . + . + "The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms."^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . + "Terminologia Histologica" . + . + . + "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . + "http://caps.ncbs.res.in/pass2"^^ . + . + "https://web.www.healthdatagateway.org/dataset/$1"^^ . + . + . + "http://www.guidetopharmacology.org/"^^ . + . + . + . + . + . + "00056"^^ . + "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . + . + . + . + . + . + . + "Encyclopedia of Life" . + "0000124"^^ . + . + . + . + . + "Ath_AT1G01030.1"^^ . + . + . + . + . + . + . + "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . + "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . + "https://www.ebi.ac.uk/ega/studies/$1"^^ . + "false"^^ . + "false"^^ . + . + "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . + "false"^^ . + "https://vega.archive.ensembl.org/index.html"^^ . + . + . + . + . + . + . + . + "GLDS-141"^^ . + . + . + "0000001"^^ . + "Arabidopsis Information Portal" . + "http://ctdbase.org/"^^ . + . + "http://taibnet.sinica.edu.tw/home.php"^^ . + . + "AADB12"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "https://github.com/jannahastings/emotion-ontology"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . +_:N02c318a846114c1b8cea4e7ba1bc42d4 "Christos (Kitsos) Louis" . + . + . + "false"^^ . + "^MI\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "^[A-Z]+[0-9]+$"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.addexbio.com/productdetail?pid=$1"^^ . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/ZP_$1"^^ . + . + . + "https://aopwiki.org/"^^ . + "002368"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "0000858"^^ . + . + . + . + . + . + "1038233"^^ . + "^\\d{7}$"^^ . + . + "https://web.expasy.org/variant_pages/VAR_$1.html"^^ . + . + . + "false"^^ . + . + "KEGG Metagenome" . + . + . + "https://casrai.org/credit/"^^ . + "false"^^ . + . + "https://assets.nemoarchive.org/$1"^^ . + . + . + . + "1868"^^ . + "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references RNAi experiments, detailing target and phenotypes."^^ . + . + "false"^^ . + . + "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . + . + "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . + . + "https://web.expasy.org/cellosaurus/CVCL_$1"^^ . + "false"^^ . + . + . + . + "https://www.brenda-enzymes.org/"^^ . + . + . + . + . + "https://wiki.nci.nih.gov/display/caDSR/caDSR+Wiki"^^ . +_:Nfff0b0e50fe140a784b0c43f793a22cc "Christipher Baker" . + "false"^^ . + . + . + . + . + "50-00-0"^^ . + "Electrocardiogram Ontology" . + . + . + . + . + . + . + . + . + . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. These are hierarchically classified and assigned to a Family on the basis of statistically significant similarities in amino acid sequence. Families thought to be homologous are grouped together in a Clan. This collection references peptidase families."^^ . + "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . + . + "^PS\\d+$"^^ . + . + "BioTools" . + "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . + . + . + . + . + . + . + . + . + . + . + "http://snap.humgen.au.dk/views/geneview.cgi?gene=$1"^^ . + "A controlled vocabulary to support the study of transcription in the human brain"^^ . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloguing changes in gene expression and other cellular processes that occur when cells are exposed to perturbing agents. The data is organized and available as datasets, each including experimental data, metadata and a description of the dataset and assay. The dataset group comprises datasets for the same experiment but with different data level results (data processed to a different level)."^^ . + . + . + . + "false"^^ . + "cgd7_230"^^ . + . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + "nextProt" . + "Plant Phenology Ontology" . + . + "GPM32310002988"^^ . + . + . + . + "Experimental Factor Ontology" . + . + . + "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . + . + . + "false"^^ . + . + . + "TubercuList knowledge base" . + . + . + . + . + "Network of Different Plant Genomic Research Projects" . + "r3d100010772"^^ . + . + . + . + . + . + "EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of its genome, and of transcriptional regulation, transporters, and metabolic pathways."^^ . + . + . + . + . + "http://treebase.org/"^^ . + . + "The cBioPortal for Cancer Genomics" . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . + . + . + . + "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . + "HBG004341"^^ . + . + . + . + . + . + . + . + . + . + . + "19-T4"^^ . + "A hierarchical classification of congenital heart disease "^^ . + . + . + "^[a-z_A-Z0-9]+$"^^ . + . + . + "miRNEST" . + . + . + . + "Cell line collections"^^ . + . + . + "The NMR Restraints Grid contains the original NMR data as collected for over 2500 protein and nucleic acid structures with corresponding PDB entries. In addition to the original restraints, most of the distance, dihedral angle and RDC restraint data (>85%) were parsed, and those in over 500 entries were converted and filtered. The converted and filtered data sets constitute the DOCR and FRED databases respectively."^^ . + . + . + . + . + "^\\d{7}$"^^ . + "PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana."^^ . + "2023"^^ . + . + . + "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . + . + . + . + "^HGVPM\\d+$"^^ . + . + . + "false"^^ . + . + . + "mirEX" . + . + . + . + . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + "JCOIN" . + . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-chemical-names.txt"^^ . + . + . + . + . + . + . + "^\\d{8}$"^^ . + . + . + "ABC"^^ . + . + . + "Core Ontology for Biology and Biomedicine" . + . + . + "false"^^ . + . + "false"^^ . + . + "http://edamontology.org"^^ . + "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . + . + "PROB_c0000005"^^ . + "https://vectorbase.org/vectorbase/app/record/gene/$1"^^ . + . + "^PM\\d{7}$"^^ . + . + . + . + "http://purl.org/spar/scoro/$1"^^ . + . + . + . + . + . + "The objective of this project is to provide high quality annotation for the rice genome Oryza sativa spp japonica cv Nipponbare. All genes are annotated with functional annotation including expression data, gene ontologies, and tagged lines."^^ . + "4DN" . + "false"^^ . + . + . + . + . + "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . + . + "https://www.encodeproject.org"^^ . + . + "Minimal Viable Identifier" . + . + . + . + "(Re)Building a Kidney is an NIDDK-funded consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function."^^ . + . + . + . + "https://www.tcdb.org"^^ . + . + . + . + "Common Anatomy Reference Ontology" . + . + . + . + . + . + . + . + "http://senselab.med.yale.edu/NeuronDB/"^^ . + . + "Paragraph"^^ . + . + . + . + "false"^^ . + . + . + . + "An application ontology built for beta cell genomics studies."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "true"^^ . + "false"^^ . + . + "Datasets inside StoreDB"^^ . + "AICARTRANSIMPCYCLO-CPLX"^^ . + . + . + . + . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/$1" . + . + . + . + "false"^^ . + . + . + "00000105"^^ . + . + . + "false"^^ . + "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . + "1433C_TOBAC_1_252"^^ . + . + . + "0004"^^ . + "https://www.glycoepitope.jp/epitopes/"^^ . + . + "ArrayExpress" . + . + "doi" . + . + "https://ssbd.riken.jp/database/project/$1"^^ . + . + . + "false"^^ . + . + "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . + . + . + "https://qudt.org"^^ . + "false"^^ . + "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . + "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . + . + "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . + "false"^^ . + . + "false"^^ . + "http://msi-ontology.sourceforge.net/"^^ . + . + "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . + . + "00007294"^^ . + . + "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . + . + "JWS Online is a repository of curated biochemical pathway models, and additionally provides the ability to run simulations of these models in a web browser."^^ . + . + "^[0-9]{10}$"^^ . + . + . + "miRBase Families" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://scicrunch.org/resolver/RRID:$1"^^ . + . + . + "https://www.uniprot.org/unirule/"^^ . + . + "Developing Mouse Brain Atlas" . + . + . + "^MMP\\d+.\\d+$"^^ . + . + . + . + "https://www.vmh.life/#gene/$1"^^ . + "false"^^ . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . + "http://www.sparontologies.net/ontologies/cito"^^ . + . + . + . + . + "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . + "true"^^ . + . + . + . + . + . + . + "http://www.hprd.org/protein/$1"^^ . + "Ontology for Nutritional Studies" . + "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . + . + "false"^^ . + . + "Stephen Fisher" . + . + . + "false"^^ . + . + . + "https://www.amazon.co.uk/gp/help/customer/display.html/277-3416785-8259466?ie=UTF8&nodeId=898182"^^ . + . + "^\\d{9}$"^^ . + . + . + . + . + "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . + "Identifier for a species on the noaa fisheries website"^^ . + . + "false"^^ . + "https://www.oclc.org/en/about.html"^^ . + "https://pubchem.ncbi.nlm.nih.gov/"^^ . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt"^^ . + "http://purl.obolibrary.org/obo/CHMO_$1"^^ . + . +_:Nff3094148bfc4aa9b3c4139865a0b3ef "Pantelis Topalis" . + . + . + . + "false"^^ . + "true"^^ . + . + "A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene expression, genetic association, and network analysis provide unprecedented means to decode the genetic basis of complex phenotypes, it is important to recognize the possible effects genetic progress in one trait can have on other traits. This database is designed to collect all published livestock genetic/phenotypic trait correlation data, aimed at facilitating genetic network analysis or systems biology studies."^^ . + "The Blood Profiling Atlas in Cancer (BloodPAC) supports the management, analysis and sharing of liquid biopsy data for the oncology research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for cancer treatment and prevention. The data commons supports cross-project analyses by harmonizing data from different projects through the collaborative development of a data dictionary, providing an API for data queries and download, and providing a cloud-based analysis workspace with rich tools and resources."^^ . + "https://europepmc.org/article/ppr/$1"^^ . + . + . + . + . + "UniProt Subcellular Locations" . + . + "^\\d{7}$"^^ . + . + . + "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . + . + "false"^^ . + . + . + "FAIRsharing.62qk8w" . + "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OVAE_$1"^^ . + "false"^^ . + "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . + "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . + . + . + "^PS\\d{5}$"^^ . + . + . + "false"^^ . + . + . + "https://link.springer.com/bookseries/562"^^ . + . + . + . + "has download URL" . + "false"^^ . + . + "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . + . + . + "^\\d{4}$"^^ . + . + "^[a-zA-Z]+.+$"^^ . + . + . + . + . + . + . + . + . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to compound information."^^ . + "Add"^^ . + . + "https://github.com/geneontology/go-ontology/tree/master/contrib"^^ . + . + . + . + . + "Andrew G. McArthur" . + . + . + . + . + . + . + "false"^^ . + . + "https://herv.img.cas.cz/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "STOREDB at University of Cambridge" . + . + "http://purl.org/cerif/frapo/$1"^^ . + . + . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . + "eagle-i" . + . + "International repository of Adverse Outcome Pathways."^^ . + . . - "0005926"^^ . - . - "http://elm.eu.org/elms/elmPages/$1.html"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://rfam.xfam.org/family/$1"^^ . + . + . + . + . + . + . + . + . + "SO is a collaborative ontology project for the definition of sequence features used in biological sequence annotation. It is part of the Open Biomedical Ontologies library."^^ . + . + . + . + . + "BioProject provides an organizational framework to access metadata about research projects and the data from the projects that are deposited into different databases. It provides information about a project’s scope, material, objectives, funding source and general relevance categories."^^ . + . + "TAIR Gene" . + . + "https://asrp.danforthcenter.org/"^^ . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . + "https://bioregistry.io/metaregistry/ncbi/$1"^^ . + "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . + "true"^^ . + . + "false"^^ . + "https://www.gwascentral.org/phenotype/$1"^^ . + . + . + "false"^^ . + . + "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . + . + . + . + . + . + . + . + . + "0007404"^^ . + . + . + "SugarBind" . + "^HIP\\d{9}(\\.\\d+)?$"^^ . + . + "false"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + "CORDIS Project" . + "false"^^ . + "UniRef90_P00750"^^ . + . + . + "false"^^ . + . + . + . + "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "false"^^ . + "GOLD metadata" . + . + . + . + "InChIKey" . + "Semantic Types Ontology" . + _:N03116f7581dc43f4a75361f1d337a077 . . - . - "feature"^^ . - "PubChem Classification" . - . - . - "00573"^^ . - . - "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . - . - . - "http://genome.crg.es/datasets/abs2005/"^^ . - . - . - . - . - . - . - "P683" . - . - . - "T06648"^^ . - . - . - . - "false"^^ . + "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CIO_$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + "C. elegans Gross Anatomy Ontology" . + . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . + . + "false"^^ . + . + . + . . - "GiardiaDB" . - . - . - "false"^^ . - . - . - . - . - . - . - "0187632"^^ . - . - . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - "http://purl.obolibrary.org/obo/OGG_$1"^^ . - . - . - . - "37"^^ . - "United States Patent and Trademark Office" . - "http://db-mml.sjtu.edu.cn/ICEberg/"^^ . - "http://sabiork.h-its.org/"^^ . - "^\\d+$"^^ . - "^\\d+$"^^ . - "Orphanet Rare Disease Ontology" . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - "http://lipidbank.jp/index.html"^^ . - "Cotton ontology" . - . - . - "CATH superfamily" . - . - . - "https://www.animalgenome.org/QTLdb"^^ . - "imp10873"^^ . - "false"^^ . - . - . - . - . - "0000040"^^ . - . - . - "false"^^ . - "Ontology of Host-Microbiome Interactions" . - . - . - "false"^^ . - . - "SMP0000219"^^ . - . - "false"^^ . - . - . - "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . - . - . - . - . - . - "identifier for a fungus taxon in Index Fungorum"^^ . - "https://github.com/SciCrunch/NIF-Ontology"^^ . - . - . - . - "^[a-zA-Z0-9-_]+$"^^ . - . - . - "http://cbg.garvan.unsw.edu.au/pina/"^^ . - "r3d100010772" . - . - . - . - . - . - . - "false"^^ . - "0000449"^^ . - . - . - . - "040000"^^ . - . - . - . - "TGME49_053730"^^ . - . - . - "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . - . - . - "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . - "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . - . - . - "0001998"^^ . - . - . - "Homologous Organ Groups" . - . - . - "false"^^ . - . - . - . - "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "false"^^ . - "PR00001"^^ . - "EDAM Topic" . - . - . - . - . - . - . - "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . - . - "false"^^ . - . - "CCLE_867"^^ . - . - . - . + "https://cellrepo.ico2s.org/repositories/$1"^^ . + . + . + . + . + . + "DICOM Controlled Terminology"^^ . + "^EGAS\\d{11}$"^^ . + "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . + . + "https://github.com/obo-behavior/behavior-ontology/"^^ . + . + . + . + . + . + . + "Alzforum Mutations" . + . + . + "https://cropontology.org/ontology/CO_320/Rice"^^ . + . + . + . + "M94112"^^ . + . + "http://foodb.ca/compounds/$1"^^ . + "pubmed"^^ . + . + "eVOC mouse development stage" . + . + . + . + . + . + . + . + . + . + "https://reg.clinicalgenome.org"^^ . + . + . + "NIF Standard Ontology: Investigations" . + "https://gen3.biodatacatalyst.nhlbi.nih.gov"^^ . + . + . + . + "https://www.thermofisher.com"^^ . + . + "FlyBrain Neuron Database" . + . + . + "false"^^ . + . + . + "http://cancer.sanger.ac.uk/cosmic/"^^ . + "00001"^^ . + . + . + "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . "VMH metabolite" . - . - . - "http://www.gramene.org"^^ . - "false"^^ . - "https://www.cropontology.org/ontology/$1" . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references chemical or metabolic components."^^ . - "https://www.nlm.nih.gov/research/umls"^^ . - "0000078"^^ . - . - "Minimal Viable Identifier" . - . - . - . - "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . - . - . - . - . - "627"^^ . - . - . - . - . - . - "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . - . - . - . - . - "http://www.disease-ontology.org"^^ . - . - "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . - . - . - "TA_H3"^^ . - . - . - . - "https://www.reactome.org/"^^ . - "^[0-9]{15}[0-9X]{1}$"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://jglobal.jst.go.jp/en/"^^ . - . - "false"^^ . - . - . - "959"^^ . - "http://purl.obolibrary.org/obo/CHMO_$1"^^ . - . - . - "http://purl.obolibrary.org/obo/SYMP_$1"^^ . - . - . - "A GO annotation is a statement about the function of a particular gene. Each annotation includes an evidence code to indicate how the annotation to a particular term is supported."^^ . - "http://purl.obolibrary.org/obo/PSDO_$1"^^ . - . - . - "http://purl.obolibrary.org/obo/EV_$1"^^ . - . - "Global Biodiversity Information Facility" . - . - "^\\d{7}$"^^ . - "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . - "false"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.w3.org/ns/activitystreams"^^ . +_:Nad924b2bf8224737a794ca80599d6e2d "Matthew Brush" . + . + . + . + . + . + "https://www.worldwildlife.org/biomes"^^ . + "http://www.w3.org/ns/prov#$1"^^ . + . + . + . + "M0001"^^ . + "http://bidd.group/NPASS/"^^ . + . + "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . + "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . + . + "false"^^ . + . + . + . + "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . + "0000000"^^ . + . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . + . + . + . + "X58356"^^ . + . + . + . + . + . + "Drug Target Ontology" . + . + . + . + "FlowRepository" . + . + . + . + . +_:N922882227fd14068a34892c3f5c41820 "Onard Mejino" . + . + . + "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . + "http://purl.obolibrary.org/obo/TTO_$1"^^ . + "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . + . + . + "Store DB" . + . + "false"^^ . + . + "https://github.com/arpcard/aro"^^ . + . + "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . + . + . + "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . + "true"^^ . + . + . + "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-named-complexes.txt"^^ . + "Clytia hemisphaerica Development and Anatomy Ontology" . + "NIF Standard Ontology: Cell Types" . + . + . + . + . + . + . + . + . + . + . + "^B\\d{5}$"^^ . + . + . + . + "false"^^ . + . + . + . + "http://www.cazy.org/$1.html"^^ . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "Conserved Domain Database at NCBI" . + "FungiDB" . + "0000066"^^ . + . + . + . + . + "0000091"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + "LCSCCPN"^^ . + "uc001rvw.5"^^ . + . + . + . + "https://arxiv.org/abs/$1"^^ . + . + "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . + . + . + . + . + "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . + . + . + . + "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + "^IS\\w+(\\-\\d)?$"^^ . + . + . + "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . + "PharmGKB Disease" . + "Development Data Object Service" . + . + "^e\\d+$"^^ . + . + "Dictybase Gene" . + "MLCommons Association" . + "false"^^ . + . + . + . + . + "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . + . + "http://www.p3db.org/"^^ . + . + "false"^^ . + . + "Cell line collections"^^ . + . + . + . + . + . + "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + "UPC04349"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . + . + . + . + . + . + "https://cropontology.org/ontology/CO_359/Sunflower"^^ . + . + . + "https://www.ccdc.cam.ac.uk/"^^ . + . + . + . + . + . + . + . + . + . + . + "Wikidata Property" . + . + . + . + . + "CATH domain" . + "false"^^ . + "false"^^ . + . + "0100010"^^ . + "http://www.cellbankaustralia.com/cellbank-australia-exclusive-lines/"^^ . + "4685"^^ . + "33607"^^ . + "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . + . + "false"^^ . . - . - . - . - "Homology Ontology" . - . - "false"^^ . - . - "r3d100010772"^^ . - . - . - "https://cancer.sanger.ac.uk/cell_lines/"^^ . - "http://topdb.enzim.hu/"^^ . - "Developing Human Brain Atlas" . - . - "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDFRT"^^ . - . - . - . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + "^NONHSAG\\d{5}$"^^ . + "Berkeley Drosophila Genome Project EST database" . + "^\\d{7}$"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/"^^ . + . + . + "VFDB Gene" . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . + "http://www.pantherdb.org/"^^ . + . + . + . + . + . + . + "https://www.nlm.nih.gov/research/umls"^^ . + . + . + . + . + "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "chebi" . + . + . + . + . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/FAO_$1"^^ . + "Morpheus model repository" . + . + . + . + "BQJCRHHNABKAKU"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/Main_Page"^^ . + . + . + . + "https://www.animalgenome.org/QTLdb"^^ . + "Unified Medical Language System Concept Unique Identifier" . + . + . + . + . + . + "^CL\\d+$"^^ . + . + . + . + . + "Global Proteome Machine Database" . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "The International Standard Serial Number (ISSN) is a unique eight-digit number used to identify a print or electronic periodical publication, rather than individual articles or books."^^ . + . + "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . + "https://www.who.int/classifications/icd/adaptations/oncology/en/"^^ . + . + "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . + "Cell line collections"^^ . + . + . + . + . + "BRAF"^^ . + "https://pir.georgetown.edu/"^^ . + . + . + . + "false"^^ . + . + . + . + "KEGG Drug" . + . + . + . + . + . + "UniRef" . + . + "^EMD-\\d{4}$"^^ . + "false"^^ . + "http://lsdis.cs.uga.edu/projects/glycomics/propreo/"^^ . + "0002502"^^ . + . + "^\\d+$"^^ . + . + . + "215"^^ . + "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . + . + . + . + . + . + . + "National Drug File - Reference Terminology" . + . + . + "https://cropontology.org/ontology/CO_350/Oat"^^ . + "58788"^^ . + . + . + . + . + . + "https://gnome.glyomics.org/"^^ . + "https://github.com/ApolloDev/apollo-sv"^^ . + . + . + . + . + . + . + . + "Registry of Research Data Repositories" . + . + . + . + . + . + . + . + . + "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "nb100-56351"^^ . + . + . + . + . + "221058"^^ . + . + . + "Georgeta Bordea" . + "NIA Mouse cDNA Project" . + . + "18"^^ . + . + . + "false"^^ . + . + "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . + "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . + "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . + . + . + . + "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . + . + . + . + "VMH Gene" . + . + . + . + . + . + . + "^[a-z0-9\\-_]+$"^^ . + . + . + . "https://www.ebi.ac.uk/ols/ontologies/$1" . - "^HGVST\\d+$"^^ . - "http://purl.org/spar/c4o/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . - . - "false"^^ . - . - . - . - "false"^^ . - "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "53504"^^ . - . - . - "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . - . - . - . - . - . - "false"^^ . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . - "Frederic Bastian" . - . - . - "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . - . - "https://chem.nlm.nih.gov/chemidplus/chemidheavy.jsp"^^ . - . - "4005"^^ . - . - "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . - "0000215"^^ . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . - . - . - "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . - . - . - "3000887619"^^ . - "^(ev\\:)?E\\d+$"^^ . - "Add"^^ . - . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/"^^ . - "https://fungi.ensembl.org/"^^ . - . - . - . - . - "false"^^ . - . - . - "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . - . - . - "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . - . - . - . - "false"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "NMR-instrument specific component of metabolomics investigations" . - . - . - . - "^\\d{4}$"^^ . - . - "0002-1975-61"^^ . - "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . - . - . - "Golm Metabolome Database Analyte" . - . - . - . - . - . - . - . - . - "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . - . - "https://www.nextprot.org/db/entry/$1"^^ . - . - . - "ISA1083-2"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . + "2200934"^^ . + . + "10020.2"^^ . + . + . + . + . + "^[AMCST][0-9x][0-9]$"^^ . + . + . + . + . + . + . + . + . + . + "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS."^^ . + . + . + "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . + "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "Jie Zheng" . + . + . + "PSI Extended File Format" . + . + . + "http://piroplasmadb.org/"^^ . + . + "Ontology of Organizational Structures of Trauma centers and Trauma systems" . + "https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe"^^ . + . + "https://ifaa.unifr.ch/"^^ . + "0000078"^^ . + . + "false"^^ . + . + "http://www.drugbank.ca"^^ . + . + . . - "US4145692"^^ . - . - . - . - "http://exac.broadinstitute.org/"^^ . - "LinJ.20.0070"^^ . - . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . - . - . - "TarBase" . - "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."^^ . + "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . + "BibliographicRecord"^^ . + . + . + "KEGG Reaction" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OGG_$1"^^ . + . + "^\\d{8}$"^^ . + "http://www.p3db.org/"^^ . + . + . + "NIST Chemistry WebBook" . + . + . + . + . + . + . + . + . + . + . + . + . + "Wormpep" . + . + "Damion Dooley" . + . + . + . + "https://registry.identifiers.org/registry/$1"^^ . + . + . + . + "PhosphoPoint Phosphoprotein" . + . + . + . + . + . + . + "http://www.hmdb.ca/metabolites/$1"^^ . + "0000504"^^ . + "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . + "https://fcs-free.org"^^ . + "http://merops.sanger.ac.uk/index.htm"^^ . + . + . + "http://www.pharmgkb.org/gene/$1"^^ . + . + "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . + . + "miRTarBase" . + . + "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . + "Emotion Ontology" . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://www.cabri.org/"^^ . + . + . + . + . + "F4521"^^ . + "ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries."^^ . + . + "http://ascl.net/"^^ . + "https://proconsortium.org/app/entry/PR:$1"^^ . + "false"^^ . + . + . + "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^ . + . + . + . + . + . + . + . + . + . + . + "Oryzabase Strain" . + . + . + . + "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . + . + . + "http://www-igbmc.u-strasbg.fr/BioInfo/MAO/mao.html"^^ . + "0000032"^^ . + "https://foodb.ca/foods"^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_331:$1"^^ . + . + "Zebrafish developmental stages ontology" . + . + . + . + . + "https://github.com/insect-morphology/aism"^^ . + . + . + "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . + . + "https://www.auckland.ac.nz/en.html"^^ . + . + "http://ecoportal.lifewatch.eu" . + . + . + . + . + "STOREDB at University of Cambridge" . + . + . + . + "Database of biopesticides maintained by the University of Hertfordshire "^^ . + . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + "Manually curated collections of resources stored in the bioregistry"^^ . + . + . + "TS-0001"^^ . + . + "^[0-9]+$"^^ . + "^\\d+$"^^ . + . + . + "^\\d+$"^^ . + . + "false"^^ . + "Biotin_biosynthesis"^^ . + . + "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . + . + . + "https://github.com/rsc-ontologies/rxno"^^ . + "ICEberg element" . + . + . + "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology."^^ . + . + . + . + . + . + "090201"^^ . + . + "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . + . + "Carbohydrate Active EnZYmes" . + "https://www.ncbi.nlm.nih.gov/research/cog/pathways"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "false"^^ . + . + . + "Q2207226"^^ . + "false"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/"^^ . + . + . + . + . + . + . + "Fission Yeast Experimental Conditions Ontology" . + "^A\\d+$"^^ . + . + "BioCatalogue Service" . + "http://igsn.org/$1"^^ . + . + "RepeatsDB Structure" . + . + . + "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . + . + . + . + . + "true"^^ . + . + . + "false"^^ . + "PF11779"^^ . + "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . + "false"^^ . + "KEGG LIGAND" . + . + "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . + "false"^^ . + . + . + . + . + . + "http://www.flybase.org/"^^ . + . + "http://genatlas.medecine.univ-paris5.fr/"^^ . + . + . + . + . + "ASPL0000349247"^^ . + "Cell Ontology" . + . + "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . + . + . + . + . + "1455"^^ . + . + . + . + . + . + . + "https://github.com/jannahastings/mental-functioning-ontology"^^ . + . + . + "false"^^ . + . + "2639"^^ . + . + "Tom Gillespie" . + . + . + "https://www.ebi.ac.uk/ols/ontologies/mi/terms?obo_id=MI:$1"^^ . + . + "^\\w.+$"^^ . + "35742"^^ . + "false"^^ . + "CHEMBL4303805"^^ . + "0001998"^^ . + . + "http://www.cghtmd.jp/CGHDatabase/index_e.jsp"^^ . + . + . + . + "Assists in resolving data across cloud resources."^^ . + . + "true"^^ . + . + . + "Homology Ontology" . + "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . + . + "^\\d+$"^^ . + "https://github.com/BgeeDB/confidence-information-ontology"^^ . + . + "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . + "MarDB" . + . + . + "^\\d+$"^^ . + "http://mycobrowser.epfl.ch/leprosy.html"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "^\\d{4}$"^^ . + . + . + "false"^^ . + "Evidence codes can be used to specify the type of supporting evidence for a piece of knowledge. This allows inference of a 'level of support' between an entity and an annotation made to an entity."^^ . + "FaceBase Data Repository" . + . + "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . + . + . + . + . + . + . + "https://github.com/INO-ontology/ino"^^ . + "OID Repository" . + "false"^^ . + . + "^GN_[A-Za-z0-9_:]+$"^^ . + . + . + . + "false"^^ . + "A database for Triticeae and Avena references."^^ . + "ICD-10-PCS is being developed as the successor to Volume 3 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM). For more information about ICD-9-CM, see the ICD-9-CM source synopsis.\n\nICD-10-PCS will be the official system of assigning codes to procedures associated with hospital utilization in the United States. ICD-10-PCS codes will support data collection, payment and electronic health records."^^ . + . + "^PAp[0-9]{8}$"^^ . + . + . + . + "DragonDB Locus" . + "^\\d{7}$"^^ . + "Livestock Product Trait Ontology" . + . + "rs11603840"^^ . + . + "N0000001662"^^ . + "http://www.pharmgkb.org/"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/dbEST/index.html"^^ . + . + . + "004435"^^ . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . + "false"^^ . + "false"^^ . + . + . + . + "https://www.nemoarchive.org"^^ . + "Fababean ontology" . + . + . + "^\\d+$"^^ . + . + . + "AAA35559"^^ . + . + . + . + "http://elm.eu.org/elms/elmPages/$1.html"^^ . + "http://purl.obolibrary.org/obo/GECKO_$1"^^ . + "ZFA description."^^ . + . + . + . + . + . + "RxNorm" . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + . + "Monarch Disease Ontology" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "true"^^ . + "https://github.com/"^^ . + "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . + . + . + . + "https://datanator.info/"^^ . + . + . + . + . + . + . + . + . + . + "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . + . + . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . + "false"^^ . + "G protein-coupled receptor database" . + "false"^^ . + . + . + . + "^\\w+$"^^ . + . + . + . + . + . + "Dendritic cell" . + . + . + . + . + "^\\d+$"^^ . + . + "811"^^ . + . + "^\\d{7}$"^^ . + . + "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references protein information."^^ . + . + . + "Melanie Courtot" . + . + . + . + . + . + "Fetal Calf Serum-Free Database" . + "Allotrope Merged Ontology Suite"^^ . + . + . + "AS000060"^^ . + "http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure"^^ . + . + . + "false"^^ . + . + "false"^^ . + "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . + . + . + . + "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . + . + . + "https://www.ebi.ac.uk/metagenomics"^^ . + . + . + "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + "ENST00000407236"^^ . + . + . + . + . + . + . + . + . + "http://purl.uniprot.org/annotation/$1"^^ . + . + . + . + . + . + "0000029"^^ . + "false"^^ . + . + "Subcellular Anatomy Ontology" . + . + "617102"^^ . + . + "https://biorxiv.org"^^ . + "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . + "http://comgen.pl/mirex/?page=home"^^ . + . + . + . + . + "CLPUB00496"^^ . + . + . + . + . + . + "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . + . + "false"^^ . + . + . + "false"^^ . + "http://www.e-cyanobacterium.org/bcs/rule/"^^ . + "12dgr161"^^ . + . + . + "Habronattus courtship" . + . + . + . + . + "https://vertebrate.genenames.org"^^ . + "OMA HOGs" . + . + . + . + . + . + "Information about the C57BL/6J. Includes genetic background and disease data."^^ . + . + . + . + "Edison Ong" . + . + . + "Plant Transcription Factor Database" . + . + . + . + . + . + "^[0-9]+$"^^ . + . + "Insect Resistance Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.cameo3d.org/sp/targets/target/$1"^^ . + . + "false"^^ . + . + "https://www.enzolifesciences.com"^^ . + . + . + . + "154022"^^ . + . + . + . + . + . + . + . + "The GeneCards human gene database stores gene related transcriptomic, genetic, proteomic, functional and disease information. It uses standard nomenclature and approved gene symbols. GeneCards presents a complete summary for each human gene."^^ . + . + "http://www.cropontology.org/ontology/CO_347/Castor%20bean"^^ . + . + "The data sources used in xrefs in the ChEBI ontology. More information in the \"Data Sources\" section of [this document](https://docs.google.com/document/d/13_FqP_8qkDdw5RFv5qMYo7xRyfY4xUiuVtLn845A6Io/edit#heading=h.dkfn7xf53tpx)." . + . + . + . + "D00001"^^ . + . + "http://www.gudmap.org/"^^ . + "http://cgsc.biology.yale.edu/index.php"^^ . + "https://aopwiki.org/aops/$1"^^ . + . + . + . + . + "Ontology of standardized units"^^ . + "https://glygen.org/glycan/$1"^^ . + . + . + . + . + "https://github.com/EcologicalSemantics/ecocore"^^ . + . + . + . + "^TC\\d+$"^^ . + . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + . + "Primate Brain Atlas" . + "https://github.com/proco-ontology/PROCO"^^ . + "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . + . + "TA_H3"^^ . + . + "https://fair-research.org"^^ . + . + . + . + "http://en.wikipedia.org/wiki/$1"^^ . + . + . + "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . + . + . + . + "Stemcell Knowledge and Information Portal" . + . + . + "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . + . + . + . + . + . + . + . + . + . + . + "1001"^^ . + . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . + . + . + . + "^UDB\\d{6}$"^^ . + "false"^^ . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/"^^ . + "http://www.chemspider.com/$1"^^ . + "http://www.cellsignal.com/pathways/index.html"^^ . + "1"^^ . + "http://www.mirbase.org/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + . + . + "Korean Cell Line Bank" . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accurately representing the DNA binding specificity of the annotated transcription factor."^^ . + . + . + "Identifiers.org" . + . + "false"^^ . + "https://clinicaltrials.gov/"^^ . + . + "0000204"^^ . + . + . + "Neural ElectroMagnetic Ontology" . + . + . + . + . + "https://mobidb.org/$1"^^ . + . + . + . + "4238"^^ . + . + "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-$1.md"^^ . + . + . + "http://www.fungalbarcoding.org/"^^ . + . + . + . + . + "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/"^^ . + "Browser for the periodic table of the elements"^^ . + "https://www.atlassian.com/"^^ . + "https://cropontology.org/ontology/CO_321/Wheat"^^ . + . + . + . + . + "Martin Ramirez" . + "300165/p13898_2106T"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . + . + . + . + . + "http://bioportal.bioontology.org/"^^ . + . + . + "https://www.ebi.ac.uk/biomodels/$1"^^ . + . + "false"^^ . + "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . + "1"^^ . + . + . + "Soybean ontology" . + "P00747__P07355"^^ . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . + . + . + . + . + "ls-c35719-120"^^ . + "ECOCYC" . + . + "^\\d{8}$"^^ . + "NeuroLex Anatomy" . + "false"^^ . + . + . + . + . + "https://comptox.epa.gov/dashboard"^^ . + . + "KEGG RCLASS contains classification of reactions based on the chemical structure transformation patterns of substrate-product pairs (reactant pairs), which are represented by the so-called RDM patterns."^^ . + . + . + . + . + . + "http://www.genenames.org"^^ . + "https://eol.org/pages/$1"^^ . + "Integrated Microbial Genomes Taxon" . + . + . + . + . + . + "DTXSID2021028"^^ . + . + . + . + . + "http://sideeffects.embl.de/se/$1"^^ . + "false"^^ . + "OMIM Phenotypic Series" . + . + . + "^\\d{7}$"^^ . + . + . + "The Terminologia Embryologica (TE) is a standardized list of words used in the description of human embryologic and fetal structures. It was produced by the Federative International Committee on Anatomical Terminology on behalf of the International Federation of Associations of Anatomists and posted on the Internet since 2010. [wikipedia]"^^ . + "MassIVE" . + . + . + "Oat ontology" . + . + . + . + "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . + "^IPR\\d{6}$"^^ . + . + "http://purl.obolibrary.org/obo/NCRO_$1"^^ . + . + "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . + . + . + . + . + . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "Clair Kronk" . + "NCBI Genome" . + "131392"^^ . + . + . + "MultiCellDS Digital Cell Line" . + . + . + . + . + "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . + "^\\d{7}$"^^ . + . + . + "Name Reaction Ontology" . + . + . + . + "^\\d{8}$"^^ . + . + "Neuro Behavior Ontology" . + . + "^\\d+$"^^ . + . + "^R\\d+$"^^ . + . + . + . + "https://www.w3.org/TR/shacl/"^^ . + . + . + . + . + "false"^^ . + . + . + "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . + . + . + "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. This collection is a subset of UniProtKB, and provides a means to reference isoform information."^^ . + "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "^[AEP]-\\w{4}-\\d+$"^^ . + "JWS Online" . + . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + "SRX000007"^^ . + "http://compbio.soe.ucsc.edu/yeast_introns.html"^^ . + . + . + "FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them available to the wider research community via this website. Practices emphasize a comprehensive and multidisciplinary approach to understanding the developmental processes that create the face. The data offered spotlights high-throughput genetic, molecular, biological, imaging and computational techniques. One of the missions of this consortium is to facilitate cooperation and collaboration between projects."^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . + "false"^^ . + "4DNSR73BT2A2"^^ . + . + "https://www.genenames.org/"^^ . + . + . + . + . + . + . + "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . + . + . + "http://www.aspgd.org/"^^ . + . + "http://www.mmmp.org/MMMP/public/biomap/listBiomap.mmmp"^^ . + "Bacterial Diversity Metadatabase" . + "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . + "Biological Magnetic Resonance Data Bank" . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . + . + . + . + "CharProt" . + . + "Spider Ontology" . + . + . + "^\\d{7}$"^^ . + "85163"^^ . + "American Type Culture Collection" . + "false"^^ . + "Reference Sequence Collection" . + "0107180"^^ . + "DisProt region" . + "http://www.plantontology.org/amigo/go.cgi?view=details&query=PO:$1"^^ . + . + "https://www.imanislife.com/?s=$1"^^ . + "https://github.com/DrugTargetOntology/DTO"^^ . + . + . + . + "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . + . + . + "https://toxpilot.nibiohn.go.jp/"^^ . + "false"^^ . + . + . + . + . + . + . + "http://fdasis.nlm.nih.gov/srs/"^^ . + . + . + . + . + "Sustainable Development Goals Interface Ontology" . + . + "false"^^ . + . + . + . + "CHEBI" . + "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to gene information."^^ . + . + "https://www.pirbright.ac.uk/node/$1"^^ . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . + . + . + "1.10.8.10"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "5046"^^ . + . + . + "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . + . + . + . + "https://www.perkinelmer.com/"^^ . + . + . + . + . + . + . + "Cell line collections"^^ . + . + . + . + "false"^^ . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/"^^ . + "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . + "The VBRC provides bioinformatics resources to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. The Center consists of a relational database and web application that support the data storage, annotation, analysis, and information exchange goals of this work. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis."^^ . + . + . + . + . + "Performance Summary Display Ontology" . + . + . + . + . + . + . + . + "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . + . + "eagle-i resource ontology" . + . + . + "BeAn 70563"^^ . + "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . + . + . + . + "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances."^^ . + . + "http://addgene.org/"^^ . + . + "false"^^ . + . + . + "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . + . + . + "Molecular Modeling Database" . + . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem bioassay archives active compounds and bioassay results."^^ . + . + . + . + . + "KEGG Reaction Class" . + . + "NeuroLex Dysfunction" . + "^\\d+$"^^ . + . + . + "Gender, Sex, and Sexual Orientation Ontology" . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . + . + "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . + "http://purl.obolibrary.org/obo/PROCO_$1"^^ . + . + "false"^^ . + . + . + . + "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . + . + "false"^^ . + "00020007"^^ . + . + . + "http://www.kegg.jp/"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + "false"^^ . + . + "https://github.com/Radiobiology-Informatics-Consortium/RBO"^^ . + "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references reactions."^^ . + . + . + . + "false"^^ . + . + "https://civicdb.org/"^^ . + "^MMP\\d+.\\d+$"^^ . + . + "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . + . + . + . + "EDDA Study Designs Taxonomy" . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital snapshot is a single-time output of the microenvironment (including basement membranes and the vascular network), any cells contained within, and essential metadata. Cells may include phenotypic data."^^ . + . + "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . + "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . + "https://www.expasy.org/prosite/"^^ . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . + . + . + _:N218fe6712b8d48939ba7aa2d08418b48 . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "GlycoEpitope" . + . + "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . + . + . + . + . + "false"^^ . + "None"^^ . + "http://purl.obolibrary.org/obo/BSPO_$1"^^ . + . + "^[A-Z]C\\d{1,3}$"^^ . + . + . + "^[0-9]{4}$"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/sra"^^ . + . + "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . + . + "00000022"^^ . + . + "https://github.com/obophenotype/biological-spatial-ontology"^^ . + . + . + . + . + . + . + "^bsg-[dscp]?\\d{6}$"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . + "http://gpmdb.thegpm.org/"^^ . + "The Ontology for Parasite Lifecycle (OPL) models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium."^^ . + . + "MNEST029358"^^ . + "false"^^ . + . + "false"^^ . + "false"^^ . + "Identifier for a species in iNaturalist"^^ . + . + . + "0000022"^^ . + . + "http://www.upol.cz/en/"^^ . + . + . + . + . + . + "Xenbase" . . - "0000055"^^ . - . - . - . + . + . + . + . + . + "^SM\\d{5}$"^^ . + "0000411"^^ . + . + . + . + . + . + . + . + . + "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . + . + . + . + . + . + "NOR00681"^^ . + . + . + . + . + . + . + "0001"^^ . + "^\\d+$"^^ . + . + . + . + . + "http://www.nbrc.nite.go.jp/e/index.html"^^ . + . + . + . + "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . + . + "^[A-Z]{2}\\d+$"^^ . + "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . + . + . + . + "Molecule role (INOH Protein name/family name ontology)" . + . + . + "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars."^^ . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/protein"^^ . + . + . + "false"^^ . + . + "Castor bean ontology" . + . + . + "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . + . + "http://www.genome.jp/kegg/drug/environ.html"^^ . + "Getty Thesaurus of Geographic Names" . + . + . + . + . + . + "false"^^ . + . + "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "GenBank" . + "https://wiki.zfin.org/display/general/Anatomy+Atlases+and+Resources"^^ . + . + . + . + . + "http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id=$1"^^ . + . + "^Q[A-Z0-9]+$"^^ . + "Cell line databases/resources"^^ . + . + "https://stemcells.nindsgenetics.org?line=$1"^^ . + . + . + . + . + "Genomic Epidemiology Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Performance Summary Display Ontology (PSDO) (pronounced \"pseudo\" or \"sudo\") is an application ontology about charts, tables, and graphs that are used to communicate performance information to employees and teams in organizations. PSDO's domain focus is on healthcare organizations that use performance summary displays in clinical dashboards and feedback interventions for healthcare professionals and teams. The displays commonly show information about the quality of care and health outcomes that has been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is not peer-reviewed."^^ . + "Electron Microscopy Data Bank" . + . + "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . + "http://sideeffects.embl.de/"^^ . + . + . + . + "Laboratory of Systems Pharmacology Compound" . + "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + . + . + "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . + . + . + . + . + . + . + "https://biopragmatics.github.io/providers/sdis/$1"^^ . + . + . + . + . + . + . + . + "https://genome.ucsc.edu/"^^ . + "The Animal Transcription Factor DataBase (AnimalTFDB) classifies TFs in sequenced animal genomes, as well as collecting the transcription co-factors and chromatin remodeling factors of those genomes. This collections refers to transcription factor families, and the species in which they are found."^^ . + "^\\d+$"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/dbvar"^^ . + . + . + . + . + . + . + "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . + . + . + . + . + . + . + "https://www.humanbehaviourchange.org/"^^ . + . + "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . + . + . + . + . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . + "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . + . + . + "^\\w+$"^^ . + "^[0-9]+-[0-9]+$"^^ . + . + . + . + . + "https://disprot.org/"^^ . + . + "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . + "https://www.kyinno.com/"^^ . + . + "https://signor.uniroma2.it/"^^ . + . + . + . + . + "false"^^ . + "Trish Whetzel" . + "^\\d{7}$"^^ . + . + . + "https://knowledge.lonza.com"^^ . + "false"^^ . + . + . + . + "The Lexicon is a foundational database with comprehensive drug product and disease nomenclature information. It includes drug names, drug product information, disease names, coding systems such as ICD-9-CM and NDC, generic names, brand names and common abbreviations. A comprehensive list of standard or customized disease names and ICD-9 codes is also included."^^ . + "Genomics of Drug Sensitivity in Cancer" . + . + "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + . + . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. This collections references inhibitors."^^ . + . + . + . + . + "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . + . + "9-1-1 Complex"^^ . + . + . + "https://ifaa.unifr.ch/"^^ . + . + . + . + "^P\\w+$"^^ . + . + "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . + . + . + "https://www.inaturalist.org/taxa/$1"^^ . + "^\\w+$"^^ . + . + . + "https://fairsharing.org/$1" . + "NLXFUNC covers terms for cognitive function."^^ . + "https://www.arraymap.org"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^ENSG\\d{11}$"^^ . + . + "^rs[0-9]+$"^^ . + . + . + "^urn\\:nbn\\:[A-Za-z_0-9]+\\:([A-Za-z_0-9]+)-[A-Za-z_0-9]+$"^^ . + . + . + . + . + "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . + . + . + . + . + . + . + "http://wodaklab.org/iRefWeb/"^^ . + "Polygenic Score Catalog" . + . + . + "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . + . + "Protein Structural Change Database" . + . + . + . + "https://lncipedia.org"^^ . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . + . + . + "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . + . + . + "102l"^^ . + "LGCEDe-S-000002244"^^ . + . + . + . + . + "100810"^^ . + . + . + "false"^^ . + . + "bioRxiv" . + . + "GR:0080039"^^ . + . + . + . + . + . + "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + "Cell line collections"^^ . + . + . + "^\\w+$"^^ . + "http://amigo.geneontology.org/amigo/term/GO:$1"^^ . + . + . + "^MIR:000\\d{5}$"^^ . + "25512"^^ . + . + . + . + . + . + . + . + "https://panoramaweb.org"^^ . + "MGnify Analysis" . + "false"^^ . + . + . + . + . + "false"^^ . + . + "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . + . + . + "the FAIR Cookbook" . + . + . + . + . + . + . + . + . + "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . + . + . + . + . + . + . + "false"^^ . + "7499841"^^ . + "^COG\\d+$"^^ . + . + . + . + . + "GitLab is The DevOps platform that empowers organizations to maximize the overall return on software development by delivering software faster and efficiently, while strengthening security and compliance. With GitLab, every team in your organization can collaboratively plan, build, secure, and deploy software to drive business outcomes faster with complete transparency, consistency and traceability."^^ . + . + . + "false"^^ . + . + "http://vegbank.org/cite/$1"^^ . + . + . + . + . + . + "http://cicblade.dep.usal.es:8080/APID/"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "YAL001C"^^ . + . + . + . + "101775319"^^ . + . + . + . + . + . + . + . + . + "SRS086444"^^ . + . + . + "Vertebrate Taxonomy Ontology" . + . + . + "developed by ICARDA - Dec 2018"^^ . + . + "Confidence Information Ontology" . + . + "MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms. Each entry in MACiE consists of an overall reaction describing the chemical compounds involved, as well as the species name in which the reaction occurs. The individual reaction stages for each overall reaction are listed with mechanisms, alternative mechanisms, and amino acids involved."^^ . + . + "^PD\\d+$"^^ . + . + . + . + "0000512"^^ . + . + "Apollo Structured Vocabulary" . + . + . + . + "53504"^^ . + "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . + . + "ProGlycProt" . + . + "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/PLO_$1"^^ . + . + . + . + . + . + . . - . - "Web Annotation Ontology" . - "https://scholar.google.com/"^^ . - . - "A formal represention for drug-drug interactions knowledge."^^ . - . - . - "false"^^ . - . - "^\\w+$"^^ . - "Ruili Huang" . - . - . - "LNCipedia" . - . - "ST000900"^^ . - . - "WikiPathways" . - _:N8f018e94918f4ace800449033ce895e0 . - . - "https://github.com/Novartis/hpath"^^ . - . - . - . - . - . - . - . - . - . - . - . - . + "false"^^ . + . + "https://biocyc.org/gene?id=$1"^^ . + "Input data and analysis results for the paper \"Topology of synaptic connectivity constrains neuronal stimulus representation, predicting two complementary coding strategies (https://www.biorxiv.org/content/10.1101/2020.11.02.363929v2 )."^^ . + . + "cd00400"^^ . + . + . + . + "PeptideAtlas Dataset" . + . + "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . + "EcoPortal" . + . + . + . + . + . + . + . + . + . + . + "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . + . + . + . + "https://github.com/PHI-base/phipo"^^ . + . + . + . + "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . + . + . + "http://linkedlifedata.com/resource/umls/id/$1"^^ . + "https://www.cropontology.org/rdf/CO_347:$1"^^ . + . + "http://www.cathdb.info/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "SIGNOR Relation" . + . + . + . + "DEF"^^ . + . + . + "Online Mendelian Inheritance in Animals is a a database of genes, inherited disorders and traits in animal species (other than human and mouse)."^^ . + "Epilepsy and Seizure Ontology" . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . + . + "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + . + . . - . - "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . - "0002902"^^ . - . - . - "Clytia hemisphaerica Development and Anatomy Ontology" . - . - . - . - "EU Clinical Trials" . + . + . + . + . + . + . + . + . + "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . + . + . + . + . + . + . + . + . + . + . + "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . + "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . + "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . + . + "0000101"^^ . + . + . + . + . + . + . + . + "DP00003"^^ . + . + . + . + . + . + . + . + "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "NIF Standard Ontology: Cognitive Function" . + "https://panoramaweb.org/$1.url"^^ . + "The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host and Vector Genomics Resource (VEuPathDB; https://veupathdb.org). The VEuPathDB ontology was previously named the EuPathDB ontology prior to EuPathDB joining with VectorBase.The ontology was built based on the Ontology of Biomedical Investigations (OBI) with integration of other OBO ontologies such as PATO, OGMS, DO, etc. as needed for coverage. Currently the VEuPath ontology is primarily intended to be used for support of the VEuPathDB sites. Terms with VEuPathDB ontology IDs that are not specific to VEuPathDB will be submitted to OBO Foundry ontologies for subsequent import and replacement of those terms when they are available."^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^rs\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://ncim.nci.nih.gov/"^^ . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "46977"^^ . + "Five Stars of Online Research Articles Ontology" . + . + . + "Drosophila Genomics Resource Center" . + . + . + . + . + "http://www.ebi.ac.uk/efo"^^ . + "1968"^^ . + . + . + . + "WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and other nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. This collection references WormBase-accessioned entities."^^ . + . + . + "50885"^^ . + . + "^\\d+$"^^ . + . + "^\\d+$"^^ . + . + "HIP000030660"^^ . + "^\\d+$"^^ . + . + "http://browser.planteome.org/amigo"^^ . + . + . + . + . + "The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance."^^ . + "false"^^ . + . + . + "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . + "https://bioregistry.io/registry/$1"^^ . + "^CPX-[0-9]+$"^^ . + "false"^^ . + "PS214100"^^ . + . + . + . + . + "http://www.knapsackfamily.com/KNApSAcK/"^^ . + . + . + . + "PTHR12345"^^ . + . + . + . + . + . + . + "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "https://www.w3.org/TR/owl-features/"^^ . + . + "^NOR\\d+$"^^ . + "false"^^ . + "^\\d{7}$"^^ . + "13GS"^^ . + "PomBase manages gene and phenotype data related to Fission Yeast. FYECO contains experimental conditions relevant to fission yeast biology. The FYECO namespace shows up in data ingests from PomBase."^^ . + . + . + "http://xmlns.com/foaf/0.1/$1"^^ . + . + . + . + . + . + "false"^^ . + "CharProt is a database of biochemically characterized proteins designed to support automated annotation pipelines. Entries are annotated with gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession."^^ . + "false"^^ . + "https://github.com/phenoscape/taxrank"^^ . + "EasyChair Topic" . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . + . + . + . + "http://www.mirbase.org/"^^ . + . + . + . + . + . + . + "false"^^ . + "MarCat" . + . + . + "has provider formatter" . + . + . + "https://pharmacodb.ca/datasets/$1"^^ . + . + "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . + . + . + . + . + . + . + . + . + . + "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + . + . + "1-18"^^ . + "ND50028"^^ . + . + . + "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . + . + "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . + . + . + . + . + . + "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . + . + . + "^PASS\\d{5}$"^^ . + . + . + _:Nff3094148bfc4aa9b3c4139865a0b3ef . + . + "Human Induced Pluripotent Stem Cells Initiative" . + . + . + . + . + . + "^\\d+$"^^ . + . + "DepMap Cell Lines" . + . + . + . + . + . + . + "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . + . + . + "https://biopragmatics.github.io/providers/sfam/$1"^^ . + . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with metazoa genomes."^^ . + "true"^^ . + . + "https://pfam.xfam.org/"^^ . + "090924"^^ . + . + "https://web.expasy.org/cellosaurus/"^^ . + . + "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NDDF"^^ . + . + . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . "SEED Reactions" . - . - . - . - "^[0-9]{1,7}$"^^ . - . - . - "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . - . - . - . - . - . - . - "0000630"^^ . - "^\\w+\\_\\d+(\\.\\d+)?$"^^ . - "false"^^ . - "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . - "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . - . - . - . - "^PKDB[0-9]{5}$"^^ . - . - . - "false"^^ . - . - "http://sabiork.h-its.org/"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . - "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^HIT\\d{9}(\\.\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . - . - "false"^^ . - . - "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . - "Collection"^^ . - . - . - . - . - . - . - . - "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - . - . - "^[A-Za-z0-9\\-\\_]+$"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "The spectra hash code (SPLASH) is a unique and non-proprietary identifier for spectra, and is independent of how the spectra were acquired or processed. It can be easily calculated for a wide range of spectra, including Mass spectroscopy, infrared spectroscopy, ultraviolet and nuclear magnetic resonance."^^ . - "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . - . - . - . - . - "false"^^ . - "Ontology for General Medical Science" . - "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . - "Nucleic Acids Phylogenetic Profiling" . - . - . - . - "602"^^ . - . - . + . + . + . + . + _:N89103e87a8814343a7ff5df839493a26 . + "^\\d+$"^^ . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . + . + . + . + . + . + "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . + . + "http://www.w3.org/2002/07/owl#$1"^^ . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/"^^ . + . + . + . + . + . + . + . + "https://github.com/OPMI/opmi"^^ . + . + . + . + "^K[0-9]+$"^^ . + . +_:Nbfb93ee5742149ae8c093731302fd738 "Thorsten Heinrich" . + . + . + . + "false"^^ . + . + "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . + . + "false"^^ . + "https://www.bindingdb.org"^^ . + . + "false"^^ . + . + "Cell line collections"^^ . + . + . + "true"^^ . + . + . + . + "The BioSample Database stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. It includes reference samples, such as cell lines, which are repeatedly used in experiments. Accession numbers for the reference samples will be exchanged with a similar database at NCBI, and DDBJ (Japan). Record access may be affected due to different release cycles and inter-institutional synchronisation."^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://repo.napdi.org/study/$1"^^ . + . + . + "http://rgd.mcw.edu/"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . + "0005067"^^ . + . + . + . + . + "Metabolic Encyclopedia of metabolic and other pathways" . + . + "100101"^^ . + . + "P10636"^^ . + . + . + . + . + "http://www.nlm.nih.gov/medlineplus/"^^ . + . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . + . + "Dataset"^^ . + . + . + . + . + . + "Blue Brain Project Topological sampling Knowledge Graph" . + "false"^^ . + . + "0005147"^^ . + . + "ModelSEED is a platform for creating genome-scale metabolic network reconstructions for microbes and plants. As part of the platform, a biochemistry database is managed that contains reactions unique to ModelSEED as well as reactions aggregated from other databases or from manually-curated genome-scale metabolic network reconstructions."^^ . + . + . + "Human Dermatological Disease Ontology" . + "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . + "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . + "PTM-0450"^^ . + . + . + . + "International Histocompatibility Workshop cell lines" . + "https://github.com/IHCC-cohorts/GECKO"^^ . + "http://www.clo-ontology.org"^^ . + _:Na4993da9f93f43338e0547ea8674d1c5 . + . + . + . + . + . + "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . + "50943"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "1000100"^^ . + "Digital Object Identifier" . + . + . + . + . + . + . + . + "https://models.physiomeproject.org/exposure/$1"^^ . + "Software Heritage is the universal archive of software source code."^^ . + . + . + . + . + . + "Computational and Informatics Resources for Glycoscience" . + "109082"^^ . + "has canonical" . + . + . + . + . + "^(doi\\:)?\\d{2}\\.\\d{4}.*$"^^ . + "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . + . + "National Microbiome Data Collaborative" . + . + . + . + "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . + "Protein modification" . + "C0001"^^ . . - "https://www.ebi.ac.uk/citexplore/"^^ . - . - . - . - . - . - . - . - "false"^^ . - "201022999"^^ . - . - . - . - "http://isbndb.com/search-all.html?kw=$1"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . - . - . - . - "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . - . - . - . - . - . - . - . - . - "^(\\w+)?\\d+$"^^ . - "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "FOOD00020"^^ . - . - . - . - . - . - . - . - . - . - "UniProt Cross-ref database" . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . - . - "174"^^ . - . - . - . - "^G\\d+$"^^ . - . - . - "https://www.animalgenome.org"^^ . - . - . - "^\\d{5}$"^^ . - . - . - "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - "^TA\\d+$"^^ . - "CATH Protein Structural Domain Superfamily" . - . - . - . - . - "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . - "0000205"^^ . - . - "Vertebrate Taxonomy Ontology" . - . - . - . - . - "Human Protein Atlas tissue profile information" . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "ArachnoServer" . - . - "^Gm\\d+$"^^ . - "false"^^ . - . - "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . - "Gene Expression Ontology" . - "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . - . - . - . - . - . - . - "A_24_P98555"^^ . - . - . - . - . - . - . - "Apollo Structured Vocabulary" . - . - "Eukaryotic Promoter Database" . - . - "^\\w+$"^^ . - . - . + . + . + . + "0001417"^^ . + . + . + . + . + . + _:N74ef5b212f444f4b82e6b6c6048084b4 . + "https://www.metanetx.org/chem_info/$1"^^ . + . + . + . + . + "^rxn\\d+$"^^ . + . + . + . + "A registry of life science prefxes"^^ . + . + "http://www.human-phenotype-ontology.org/"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^\\d{6}$"^^ . + . + . + . + "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . + . + "https://github.com/OPL-ontology/OPL"^^ . + . + . + "Ontology"^^ . + . + "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . + . + . + . + . + . + "1484"^^ . + "Contributor Role Ontology" . + . + . + . + . + "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . + "ACH-000001"^^ . + . + "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . + "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . + . + . + "http://gmd.mpimp-golm.mpg.de/"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "SPAR Ontologies" . + . + . + . + . + . + "F-SNP" . + . + . + . + . + "false"^^ . + . + . + . + "GeneDB" . + . + "false"^^ . + . + . + . + . + . + "Cell line databases/resources"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "NONCODE v3" . + . + "Human Developmental Stages" . + . + . + . + "Anne Morgat" . + . + . + . + . + "An ontology of phenotypes covering microbes"^^ . + "http://img.jgi.doe.gov/"^^ . + . + . + . + . + "http://webapps2.ucalgary.ca/~groupii/"^^ . + . + . + . + . + . + "PAR:0116"^^ . + . + . + "^((HGNC|hgnc):)?\\d{1,5}$"^^ . + . + "http://virtualflybrain.org/reports/$1"^^ . + . + "http://elm.eu.org/"^^ . + "Observational Medical Outcomes Partnership" . + . + . + . + "https://www.ebi.ac.uk/pdbe/emdb"^^ . + . + "https://www.geonames.org/$1"^^ . + "^\\d{8}$"^^ . + "Description of Plant Viruses" . + . + . + "https://www.discoverx.com/products-applications/cell-lines"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_324:$1"^^ . + . + "https://www.ebi.ac.uk/GOA/"^^ . + "145"^^ . + . + "false"^^ . + . + . + . + . + . + . + "https://scicrunch.org/scicrunch/interlex/dashboard"^^ . + "http://compbio.cs.queensu.ca/F-SNP/"^^ . + . + "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . + . + . + . + . + "^\\d{6}$"^^ . + "false"^^ . + "https://www.mlcommons.org/mlc-id/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "http://jjj.biochem.sun.ac.za/models/"^^ . + . + "http://phylomedb.org/"^^ . + . + . + . + "^DBCAT\\d+$"^^ . + "FlyBase Reference Report" . + . + . + "Sebastian Koehler" . + "^\\d{7}$"^^ . + . + "https://xmetdb.org"^^ . + . + . + . + . + "^PRO_[0-9]{10}$"^^ . + . + "http://purl.obolibrary.org/obo/EPO_$1"^^ . + "Bob Thacker" . + "PTN000000026"^^ . + . + . + "https://flowrepository.org/"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references individual peptides through spectra."^^ . + "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . + "http://exac.broadinstitute.org/transcript/$1"^^ . + . + . + "^[0-9]{15}[0-9X]{1}$"^^ . + . + . + . + . + . + . + . + "The database of Annotated regulatory Binding Sites (from orthologous promoters), ABS, is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography."^^ . + . + "http://www-bionet.sscc.ru/sitex/"^^ . + . + "https://github.com/obophenotype/fungal-anatomy-ontology/"^^ . + . + . + "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . + . + "^.+$"^^ . + "http://www.bioguo.org/AnimalTFDB/family_index.php"^^ . + "PR000001"^^ . + . + . + . + . + . + "http://www.begdb.com"^^ . + . + . + . + "false"^^ . + . + . + . + "Cell line databases/resources"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "http://www2.idac.tohoku.ac.jp/dep/ccr/"^^ . + . + . + . + . + "WGS-95-1333"^^ . + "false"^^ . + . + . + "http://www.pathbase.net"^^ . + . + "MobiDB is a database of protein disorder and mobility annotations."^^ . + . + "https://web.expasy.org/abcd/"^^ . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + "NOAA Fisheries Species Directory" . + "https://genelab-data.ndc.nasa.gov/genelab/"^^ . + "http://bcrj.org.br/celula/$1"^^ . + . + "EDAM Data" . + . + "0000093"^^ . + "false"^^ . + . + . + . + . + "6017782"^^ . + "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . + . + . + . + . + . + "PicTar" . + "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . + . + "http://www.atol-ontology.com"^^ . + . + "^(D|PP|R|T|H|X|AI)?\\d+$"^^ . + . + . + . + . + . + "The GPCR-LIgand DAtabase (GLIDA) is a GPCR-related chemical genomic database that is primarily focused on the correlation of information between GPCRs and their ligands. It provides correlation data between GPCRs and their ligands, along with chemical information on the ligands. This collection references ligands."^^ . + . + . + "^\\d{7}$"^^ . + . + "Scopus is the largest abstract and citation database of peer-reviewed literature: scientific journals, books and conference proceedings. \nDelivering a comprehensive overview of the world's research output in the fields of science, technology, medicine, social sciences, and arts \nand humanities, Scopus features smart tools to track, analyze and visualize research."^^ . + "Intrinsically Disordered proteins with Extensive Annotations and Literature" . + . + "MatrixDB" . + "http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi"^^ . + "http://umbbd.ethz.ch/"^^ . + . + . + "An ontology to describe entities related to prescription of drugs"^^ . + . + . + . + . + . + "0002005"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + "1398574"^^ . + . + . + . + "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . + "Metabolomics Workbench Project" . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "Beet Ontology ontology" . + . + . + . + . + . + . + . + . + "NIF Standard Ontology: Subcellular Entities" . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-6790/A-GEOD-6790.adf.txt"^^ . + . + . + "http://www.antirrhinum.net/"^^ . + "Rodent Unidentified Gene-Encoded Large Proteins" . + . + . + . + . + . + "http://www.conoserver.org/"^^ . + "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . + "https://pharmacodb.ca/tissues"^^ . + . + . + . + "Search Tool for Interactions of Chemicals" . + . + . + "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . + . + . + "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "https://github.com/obophenotype/developmental-stage-ontologies/wiki/HsapDv"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0278"^^ . + . + . + . + . + . + "Japan Consortium for Glycobiology and Glycotechnology Database" . + "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . + "JSTOR (Journal Storage) is a digital library containing digital versions of historical academic journals, as well as books, pamphlets and current issues of journals. Some public domain content is free to access, while other articles require registration."^^ . + . + "The Drug Ontology" . + . + . + . + . + "https://github.com/rsc-ontologies/rsc-cmo"^^ . + . + "HD+118-001"^^ . + . + . + . + "false"^^ . + "IMGT/HLA human major histocompatibility complex sequence database" . + . + . + . + "false"^^ . + "ProtoNet ProteinCard" . + . + . + "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . + "https://www.eurofir.org"^^ . + . + . + . + . + "Protein covalent bond" . + "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . + . + "^\\w+$"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + "Linear motifs are short, evolutionarily plastic components of regulatory proteins. Mainly focused on the eukaryotic sequences,the Eukaryotic Linear Motif resource (ELM) is a database of curated motif classes and instances."^^ . + . + . + "^DP\\d{5}r\\d{3}$"^^ . + "Arabidopsis Small RNA Project" . + . + . + . + . + . + "^[a-zA-Z0-9 +#'*]+$"^^ . + . + . + "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . + . + . + . + "Event (INOH pathway ontology)" . + "authoredBy"^^ . + . + "false"^^ . + . + "48439"^^ . + "false"^^ . + . + . + "^TTHERM\\_\\d+$"^^ . + "false"^^ . + "false"^^ . + "Plant Growth and Development Stage" . + . + "BioNumbers" . + "456789"^^ . + . + . + . + . + "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . + . + . + . + . + . + . + . + . + "100101"^^ . + "Experimental condition ontology" . + . + . + . + "5621"^^ . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + "true"^^ . + . + "https://www.abmgood.com/Cell-Biology.html"^^ . + . + . + . + . + . + . + . + . + . + "RXN-14904"^^ . + . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=XCO:$1"^^ . + . + "Yvonne Bradford" . + . + . + . + . + "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . + "Sanger Cell Model Passports" . + "http://www.w3.org/ns/oa#$1"^^ . + . + "true"^^ . + "0100002"^^ . + . + . + . + . + . + "https://prefixcommons.org/?q=$1" . + "GitLab" . + "2679240"^^ . + . + . + . + "The Prescription of Drugs Ontology" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OHD_$1"^^ . + . + . + . + . + "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . + "http://genolist.pasteur.fr/SubtiList/"^^ . + "https://www.va.gov/health"^^ . + "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . + . + . + . + . + . + . + . + . + . + "https://w3id.org/hso"^^ . + "Gm00047"^^ . + . + "^\\d+$"^^ . + . + . + . + "Database of Arabidopsis Transcription Factors" . + . + . + . + . + "https://sitem.herts.ac.uk/aeru/vsdb"^^ . + . + . + . + "http://purl.org/dc/terms/$1"^^ . + . + "false"^^ . + . + . + . + "PhenX Toolkit" . + "https://medlineplus.gov/genetics/condition"^^ . + . + "false"^^ . + . + . + "^AT\\d+$"^^ . + . + . + . + . + . + . + "https://www.disprot.org"^^ . + . + . + . + "https://pharmacodb.ca/cell_lines"^^ . + "https://www.getty.edu/research/tools/vocabularies/tgn/"^^ . + . + . + "http://purl.obolibrary.org/obo/ZECO_$1"^^ . + "PGOHUM00000289843"^^ . + "https://cropontology.org/ontology/CO_340/Cowpea"^^ . + . + . + . + "^\\d+$"^^ . + "0000253"^^ . + "http://www.jcm.riken.go.jp/"^^ . + . + . + . + . + . + "RGD Disease_Ontology" . + . + "identifierPattern"^^ . + "^\\d{3}$"^^ . + . + "true"^^ . + . + . + . + "3000887619"^^ . + . + . + "ACC-1"^^ . + . + "EDAM Topic" . + . + . + . + . + . + "false"^^ . + . + "Cell line collections"^^ . + "146421"^^ . + "false"^^ . + . + . + "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . + . + . + . + "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . + "https://bioportal.bioontology.org/"^^ . + . + "Identifiers.org namespace" . + . + "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . + . + . + . + . + "https://repeatsdb.org/"^^ . + . + . + . + . + "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . + "http://www.homd.org/index.php"^^ . + . + . + . + "603903"^^ . + . + . + "PolBase" . + . + "b97957"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "Protein Affinity Reagents" . + . + "^M\\d{4}$"^^ . + . + "false"^^ . + . + . + . + "Luis A. Gonzalez-Montana" . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + . + . + . + . + . + . + _:N62e97b7f4c3648b4a1ab89e34dcbe1a0 . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . + " Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . + . + . + . + "http://www.nlm.nih.gov/mesh/"^^ . + "CryptoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + "Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms."^^ . + "NIF Standard Ontology: Qualities" . + "Natural Product Activity and Species Source Database" . + . + . + "^\\d{6}$"^^ . + . + . + . + . + "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . + "http://www.narcis.nl"^^ . + . + . + . + "http://www.mgc.ac.cn/VFs/"^^ . + "The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative."^^ . + . + . + "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . . - "HMDB00001"^^ . - "false"^^ . - . - "0000080"^^ . - . - . - "false"^^ . - . - "^PWY\\w{2}\\-\\d{3}$"^^ . - "AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System was designed to organize and distribute genomic data and annotations for a large international community. This collection references the transcript report, which describes genomic location, sequence and exon information."^^ . - . - . - "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . - . - "https://caninecommons.cancer.gov/#/study/$1"^^ . - "VCell Published Models" . - "Provenance, Authoring, and Versioning Vocabulary" . - "false"^^ . - . - . - . - . - . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - . - . - . - "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein."^^ . - . - "M94112"^^ . - . - "http://www.genoscope.cns.fr/agc/microscope"^^ . - "Pharmacogenetics and Pharmacogenomics Knowledge Base" . - . - . - . - . - . - . - . - . - . - . - "0000088"^^ . - . - . - . - "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." . - . - . - . - "http://www.swisslipids.org/#/"^^ . - "https://www.genome.jp/kegg/glycan/"^^ . - . - "Unipathway" . - "CategorialBibliometricData"^^ . - . - . - . - . - "MetaNetX reaction" . - . - . - . - . - . - "0807.4956v1"^^ . - "^MIR:001\\d{5}$"^^ . - . - "^C?\\d+$"^^ . - "LINCS Protein" . - . - . - "https://code.google.com/p/epidemiology-ontology/"^^ . - . - . - . - "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . - "^(MNXM\\d+|BIOMASS|WATER)$"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - "Teleost taxonomy ontology" . - . - . - . - . - "http://www.informatics.jax.org/searches/AMA.cgi?id=MA:$1"^^ . - . - . - . - . - . - . - . - . - . - . - "UniRule" . - . -_:N63e482e1c00245d2abd0b0b2fbb19710 "Jonathan Bard" . - . - . - "Genotype Ontology" . - . - . - . - "false"^^ . - . - . - . - "https://www.gleif.org/"^^ . - . - . - "https://icd.who.int/browse10"^^ . - . - "false"^^ . - "http://addgene.org/"^^ . - . - . - . - . - "Yuki Yamagata" . - . - . - . - . - "false"^^ . - "An ontology of histopathological morphologies used by pathologists to classify/categorise animal lesions observed histologically during regulatory toxicology studies. The ontology was developed using real data from over 6000 regulatory toxicology studies donated by 13 companies spanning nine species."^^ . - . - . - . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - . - "^\\d{7}$"^^ . - "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . - "false"^^ . - . - . - . - . - . - . - . - "1174"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - . - . - "Colin Batchelor" . - . - "CTD Gene" . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . - . - . - . - . - "http://www.informatics.jax.org/accession/MGI:$1"^^ . - "^\\d{7}$"^^ . - "Cell line collections"^^ . - . - "^\\d+$"^^ . - . + . + . + . + . + . + . + "false"^^ . + . + . + . + "https://www.cropontology.org/rdf/CO_358:$1"^^ . + . + "^[A-Z]{2}[A-Z0-9][0-9]{5}$"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "The International Classification of Diseases for Oncology (ICD-O) is a domain-specific extension of the International Statistical Classification of Diseases and Related Health Problems for tumor diseases"^^ . + . + . + "^P\\d{5}$"^^ . + . + . + . + "Ontology about C. elegans and other nematode phenotypes"^^ . + . + . + . + "4007166"^^ . + . + . + "e999"^^ . + . + . + . + "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . + . + . + . + . + . + . + "HGNC Gene Group" . + . + . + "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . + "Cancer Data Standards Registry and Repository" . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://europepmc.org/article/CBA/$1"^^ . + . + . + . + . + . + . + . + "https://www.uniprot.org/unirule/$1"^^ . + . + . + . + . + "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . + . + . + . + . + "Fission Yeast Phenotype Ontology" . + . + . + "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . + . + . + "^\\d+$"^^ . + "http://cerevisiae.oridb.org/details.php?id=$1"^^ . + . + "false"^^ . + . + . + "0000041"^^ . + "Gramene Reference" . + . + . + . + "https://www.ebi.ac.uk/merops"^^ . + "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . + "https://www.nextprot.org/"^^ . "Selventa Complexes" . - . - . - . - . - . - . - . - . - . - "canal"^^ . - . - "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information."^^ . - "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . - . - "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . - "https://cellbank.snu.ac.kr/english"^^ . - "false"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://cancer.sanger.ac.uk/cosmic/"^^ . - . - . - "https://aopwiki.org/"^^ . - "HUMAN16963"^^ . - . - . - "https://cells.ebisc.org/$1"^^ . - . - . - . - "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . - . - "http://purl.obolibrary.org/obo/GSSO_$1"^^ . - . - . - . - . - "M1"^^ . - "MULT_4_VAR1_bovine"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "https://github.com/obophenotype/provisional_cell_ontology"^^ . - "31623"^^ . - . - . - "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . - "chebi" . - "Epilepsy Ontology" . - "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . - . - . - "The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The CCDS set is calculated following coordinated whole genome annotation updates carried out by the NCBI, WTSI, and Ensembl. The long term goal is to support convergence towards a standard set of gene annotations."^^ . - . - . - "false"^^ . - "false"^^ . - "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . - "Tom Gillespie" . - "Orphanet is a reference portal for information on rare diseases and orphan drugs. It’s aim is to help improve the diagnosis, care and treatment of patients with rare diseases."^^ . - "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . - . - . - . -_:N7c963f68a1fe42beadc6cc49111f5668 "Pantelis Topalis" . - . - . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - "61467"^^ . - . - "http://purl.obolibrary.org/obo/GENO_$1"^^ . - . - . - "56"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "688"^^ . - . - . - . - . - . - . - . - . - . - "http://modelseed.org/biochem/reactions/"^^ . - . - . - . - . - . - . - "https://www.hu-berlin.de/?set_language=en&cl=en"^^ . - "Ontology of Host Pathogen Interactions" . - "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . - . - . - "^\\d+$"^^ . - . - . - . - "Metabolite and Tandem Mass Spectrometry Database" . -_:Nb1c75d7f39034870890b7a86604e9033 "Jonathan Bard" . - . - . - . - . - . - "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes."^^ . - . - . - . - "PF11_0344"^^ . - "false"^^ . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "An application ontology built for beta cell genomics studies."^^ . - . - . - . - . - "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . - . - . - . - . - . - "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . + "^\\d{7}$"^^ . + . + "^A\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/intact/molecule/$1"^^ . + "false"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PDUMDV_$1"^^ . + . + . + . + . + "http://opencitations.net"^^ . + . + . + . + . + "https://ecmdb.ca"^^ . + "http://kinase.bioinformatics.tw/"^^ . + . + . + "http://mirtarbase.mbc.nctu.edu.tw/php/detail.php?mirtid=$1"^^ . + . + . + . + "MicroScope" . + . + "http://purl.obolibrary.org/obo/TXPO_$1"^^ . + . + . + . + "DrugBank Drug Category" . + "OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research."^^ . + . + . + "https://www.uniprot.org/diseases/$1"^^ . + "false"^^ . + "^GPM\\d+$"^^ . + "CHEBI" . + "http://bioassayontology.org"^^ . + . + . + . + . + . + . + "TF101014"^^ . + . + . + . + . + . + "http://www.whocc.no/atc_ddd_index/"^^ . + "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . + . + . + . + "http://www.imgt.org/ligmdb/view?id=$1"^^ . + . + . + . + . + . + . + "true"^^ . + . + . + "^virsi\\d+$"^^ . + "http://www.pseudogene.org"^^ . + "false"^^ . + "https://bioregistry.io/collection"^^ . + . + . + . + . + "rs17852708"^^ . + . + "false"^^ . + . + . + . + . + . + "https://www.datanator.info/gene/$1"^^ . + "http://environmentontology.org/"^^ . + . + . + "http://www.ebi.ac.uk/sbo/"^^ . + "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . + "https://www.metabolome-express.org/"^^ . + "http://aclame.ulb.ac.be/"^^ . + . + "http://omit.cis.usouthal.edu/"^^ . + . + . + "The pattern for identifiers in the given resource" . + . + . + . + . + . + "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . + "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + "false"^^ . + "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . + "^[1-9]\\d{0,5}$"^^ . + "Gs0000008"^^ . + . + . + "false"^^ . + . + . + "Genome Properties" . + "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . + . + . + "AKR-270"^^ . + "^\\w+\\_\\w+$"^^ . + . + . + "^\\d+$"^^ . + "Teleost taxonomy ontology" . + . + . + . "MycoBrowser leprae" . - . + . + "101"^^ . + . + . + . + "false"^^ . + . + "BLL"^^ . + . + . + "Gi07796"^^ . + . + "A database of fly neurons and pathways with an associated 3D viewer."^^ . + . + . + . + . + "true"^^ . + . + . + "https://portal.bluebrain.epfl.ch"^^ . + . + . + . + . + . + . + "Vocabulary of Interlinked Datasets" . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . + . + . + . + . + . + . + . + "4201PAT-CCTCC00348"^^ . + . + "^\\d+$"^^ . + "4005"^^ . + "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . + . + . + "FCB005"^^ . + . + . + . + . + . + "saddan"^^ . + . + "RSC3"^^ . + . + "273"^^ . + . + . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references development stage information."^^ . + "^\\d{8}$"^^ . + . + "https://www.swisslipids.org/#/entity/SLM:$1"^^ . + "Web Elements" . + . + . + . + . + . + . + "Tom Gillespie" . + . + . + "http://senselab.med.yale.edu/OdorDB"^^ . + . "false"^^ . - . - . - . - "Gramene Growth Stage Ontology" . - . - . - . - "^MINT\\-\\d{1,7}$"^^ . - . - . - . - . - . - "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . - . - . - "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . - . - "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . + . + "false"^^ . + . + . + . + . + "INSDC CDS" . + "1.1.1.1"^^ . + . + "http://isbndb.com/search-all.html?kw=$1"^^ . + "MetaNetX reaction" . + . + . + "https://github.com/semanticchemistry/semanticchemistry"^^ . + . + . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by tissue."^^ . + "90806"^^ . + "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . + . + . + . + . + . + "^MTBLS\\d+$"^^ . + . + . + "Plant Stress Ontology" . + . + . + "^\\d{7}$"^^ . + . + . + "The purpose of the joint FDA/USP Substance Registration System (SRS) is to support health information technology initiatives by generating unique ingredient identifiers (UNIIs) for substances in drugs, biologics, foods, and devices. The UNII is a non- proprietary, free, unique, unambiguous, non semantic, alphanumeric identifier based on a substance’s molecular structure and/or descriptive information."^^ . + "SM_UB-81"^^ . + "true"^^ . + "http://purl.obolibrary.org/obo/RNAO_$1"^^ . + "true"^^ . + . + . + . + . + . + . + "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . + "false"^^ . + "chebi"^^ . + . + . + "false"^^ . + . + . + . + "https://arxiv.org/"^^ . + . + "The [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies) are a suite of orthogonal and complementary OWL 2 ontologies that enable all aspects of the publishing process to be described in machine-readable metadata statements, encoded using RDF." . + . + . + "^Y[A-Z]{2}\\d+[CW]$"^^ . + . + . + "Sugar Kelp trait ontology"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.antirrhinum.net/"^^ . + "^\\d{8}$"^^ . + "0002-1975-61"^^ . + . + . + . + . + "http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "UniProt Archive" . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria marinum information."^^ . + . + . + . + "false"^^ . + . + "http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology"^^ . + "^GE\\d+$"^^ . + "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . + "http://purl.org/spar/bido/$1"^^ . + "^HGVST\\d+$"^^ . + . + . + . + . + . +_:N89103e87a8814343a7ff5df839493a26 "Pierre Sprumont" . + . + "http://oryzatagline.cirad.fr/"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + "968"^^ . + "PathBank" . + . + . + "Mechanism, Annotation and Classification in Enzymes" . + . + . + . + . + "Universal Natural Products Database" . + "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . + "^Gm\\d+$"^^ . + . + . + . + . + "https://odc-tbi.org/data/$1"^^ . + . + . + . + . + . + "true"^^ . + "false"^^ . + "Molecular Interaction Database" . + . + . + "Deepak Unni" . + . + . + . + "LRG_1"^^ . + . + . + . + . + . + . + "true"^^ . + "true"^^ . + . + "true"^^ . + "https://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php"^^ . + "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . + . + "false"^^ . + . + . + "Golm Metabolome Database GC-MS spectra" . + . . - . - "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . - " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . - . + . + "https://github.com/biobanking/biobanking"^^ . + . + "The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution."^^ . + "SubtiList serves to collate and integrate various aspects of the genomic information from B. subtilis, the paradigm of sporulating Gram-positive bacteria.\r\nSubtiList provides a complete dataset of DNA and protein sequences derived from the paradigm strain B. subtilis 168, linked to the relevant annotations and functional assignments."^^ . + . + "2701"^^ . + . + . + "false"^^ . + "Index Fungorum" . + . + . + . + . + . + . + . + "PWY3O-214"^^ . + "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000000"^^ . + "Human Endogenous Retrovirus Database" . + . + . + . + . + "http://bioportal.bioontology.org/ontologies/OPB"^^ . + "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . + . + "^[A-Za-z]+\\d+$"^^ . + "YeTFasCo" . + . + . + "^\\d+$"^^ . + . + . + . + . + . . - "InChIKey" . - . - . - . - . - . - . - "false"^^ . - "ASRP1423"^^ . - . - "https://www.google.com/patents/$1"^^ . - . - . - "https://proteininformationresource.org/resid/"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "300108/p3934_A-172"^^ . - . - . - . - . - . - "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . - . - . - "The International Harmonization of Nomenclature and Diagnostic criteria" . - . - "Affymetrix Probeset" . - . - "E-cyanobacterium rule" . - . - . - . - . - . - . - "^(SMP|PW)\\d+$"^^ . - "^D\\d+$"^^ . - . - "PubChem Cell Line" . - . - "4201PAT-CCTCC00348"^^ . - . - . - . - . - . - . - "The YDPM database serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition."^^ . - . - . - "^C\\d+$"^^ . - . - . - . - . - "false"^^ . - . - "Biolink Model Registry" . - "ECOCYC"^^ . - . - . + . + "0001079"^^ . + . + . + "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . + "Jennifer C. Giron" . + . + "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . + . + . + "https://www.doi.org/"^^ . + . + "FlyBase internal citation identifiers"^^ . + . + . + "GiardiaDB" . + . + . + . + . + . + . + "0001655"^^ . + "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^ . + "4776"^^ . + . + . + . + . + . + . + . + "Identifiers.org Ontology" . + "false"^^ . + . + . + . + . + . + "false"^^ . + "0000000"^^ . + "^[0-9]+$"^^ . + . + "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://vbrc.org/"^^ . + . + "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . + . + . + . + . + "https://github.com/allysonlister/swo"^^ . + . + . + . + "^\\d{7}$"^^ . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + . + "MULT_4_VAR1_bovine"^^ . + "Biomedical Informatics Research Network Lexicon" . + . + . + . + . + . + . + . + . + "The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts."^^ . + "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . + "^\\d{7}$"^^ . + . + "Tom Gillespie" . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + "https://cropontology.org/ontology/CO_337/Groundnut"^^ . + "http://lincsportal.ccs.miami.edu/datasets/"^^ . + . + . + . + "MIR:00000008"^^ . + . + . + . + . + . + "AberOWL" . + "^\\d{8}$"^^ . + "false"^^ . + . + . + . + . + "https://www.sigmaaldrich.com"^^ . + "https://www.ebi.ac.uk/miriam/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "NIF Standard Ontology" . + "FaBiO, the FRBR-aligned Bibliographic Ontology" . + . + . + "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . + . + . + "https://mmp.sfb.uit.no/databases/mardb/"^^ . + "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . + . + "https://www.gtexportal.org/home/gene/$1"^^ . + . + . + . + . + . + . + . + "Collection of European paediatric cardiac coding files"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . + . + "^CHEMBL\\d+$"^^ . + . + . + . + "P683" . + . + . + "TarBase stores microRNA (miRNA) information for miRNA–gene interactions, as well as miRNA- and gene-related facts to information specific to the interaction and the experimental validation methodologies used."^^ . + . + . + . + . + . + . + "M58335"^^ . + . + . + . + "true"^^ . + . + "https://w3id.org/oc/corpus"^^ . + . + . + . + "^\\d+$"^^ . + "DDB0016567"^^ . + "63250"^^ . + . + . + "Sol Genomics Network" . + . + . + . + . + "https://www.wikidata.org" . + . + "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . + . + . + "http://phenol-explorer.eu/foods/$1"^^ . + "https://www.rebuildingakidney.org/id/$1"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "http://microbialphenotypes.org"^^ . + . + . + "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . + . + . + "EcoliWiki from EcoliHub" . + "KEGG Compound" . + "https://web.expasy.org/variant_pages"^^ . + . + "false"^^ . + "false"^^ . . - . - . - "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . - . - "^IS\\w+(\\-\\d)?$"^^ . - . - . - "Cell line collections"^^ . - . - . - "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . - . - . - . - . - . - . - "ALIENSPECIES" . - . - . - "^HGVPM\\d+$"^^ . - . - _:N0ce5034e173846f0b47a46c42548ce15 . - "^\\d+$"^^ . - . - . - . - . - "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . - "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . - . - . - . - . - . - . - "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . - . - "Nematode Expression Pattern DataBase" . - . - . - . - "100101"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "https://github.com/obophenotype/planaria-ontology"^^ . + . + . + . + . + "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . + "https://github.com/OBOFoundry/COB"^^ . + . + . + . + . + . + "0000138"^^ . + "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . + . + . + . + "0000389"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "false"^^ . + . + "Panorama Public" . + "A formal ontology of phenotypes observed in fission yeast."^^ . + . + "https://www.ebi.ac.uk/ols" . + . + "Genomics Cohorts Knowledge Ontology" . + . + "UniProt Keywords" . + "^\\d+$"^^ . + "https://www.re3data.org/repository/$1" . + . + . + . + . + . + . + . + "false"^^ . + . + "https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10PCS"^^ . + . + "An ontology built for representating the organizational components of trauma centers and trauma systems."^^ . + "false"^^ . + . + . + . + . + . + . + . + "http://dictybase.org/gene/$1"^^ . + . + . + "https://mmp.sfb.uit.no/databases/marref/"^^ . + . + "bt0001"^^ . + "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . + . + . + "http://www.cbioportal.org"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "https://metazoa.ensembl.org/id/$1"^^ . + . + . + "https://gitlab.com/$1"^^ . + . + "https://cls.shop/"^^ . + . + "https://www.ebi.ac.uk/ols/ontologies/ordo"^^ . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/fbdv"^^ . + "Collembola Anatomy Ontology" . + "GCF_000005845.2"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "00023232"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/medgen/"^^ . + "false"^^ . + . + "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . + "0000190"^^ . + . + . + . + . + . + . + . + . + . + . + "The genome assembly database contains detailed information about genome assemblies for eukaryota, bacteria and archaea. The scope of the genome collections database does not extend to viruses, viroids and bacteriophage."^^ . + "https://idr.openmicroscopy.org"^^ . + . + . + . + "Sierra Moxon" . + . "An ontology of minimum information regarding potential drug-drug interaction information."^^ . - "true"^^ . - . - . - . - . - "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment."^^ . - . - . - . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-legacy-diseases.txt"^^ . - . - . - . - . - . - "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . - . - "K00001"^^ . - . - . - . - . - . - "GenBank" . - "101"^^ . - . - "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . - "0100002"^^ . - . - . - "1"^^ . - . - . - . - . - . - . - "true"^^ . - . - . - "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . - "^\\d+$"^^ . - . - . - "^\\d{7}$"^^ . - "^\\w+$"^^ . - . - . - . - . - "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . - . - . - . - . - . - "^EGAD\\d{11}$"^^ . - . - "Epidemiology Ontology" . - "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . + . + . + "Homologous Vertebrate Genes Database" . + . + . + . + . + . + . + . + "https://herv.img.cas.cz/s/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "240-17-488-3-4-12"^^ . + . + . + . + "18030"^^ . + "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . + . + . + . + "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . + . + . + "SCC111"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/"^^ . + "http://matrixdb.univ-lyon1.fr/"^^ . + . + . + . + . + . + "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . + . + . + "^[A-Z]\\d+(\\.[-\\d+])?$"^^ . + . + . + . + . + . + . + . + "false"^^ . + "0000001"^^ . + "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + "http://www.treefam.org/family/$1"^^ . + . + "Tom Gillespie" . + "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . + . + "http://arabidopsis.info/"^^ . + . + . + "PiroplasmaDB" . + . + "Ximbio" . + . + "http://dictybase.org/"^^ . + . + "^\\d{5}$"^^ . + . + . + . + . + "^\\d{9,9}$"^^ . + . + . + . + "Mathias Brochhausen" . + . + . + "Hepatitis C Virus Database" . + . + . + . + . + "https://giardiadb.org/giardiadb/"^^ . + "https://www.gwascentral.org/markers"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "UM-BBD Compound" . + . + . + . + "Veterans Administration National Drug File" . + . + . + . + . + . + . + "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . + . + . + . + "http://topdb.enzim.hu/"^^ . + "dsmz_mutz-id:ACC 291"^^ . + . + "http://www.psidev.info/groups/controlled-vocabularies"^^ . + . + "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . + "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . + . + . + "Open Researcher and Contributor" . + . + "Cell line collections"^^ . + . + . + "https://www.biozol.de/en/product/$1"^^ . + . + . + . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . + . + . + . + . + . + . + "4145692"^^ . + "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . + . + . + . + "AntiBodies Chemically Defined database" . + . + "https://www.ebi.ac.uk/chembl"^^ . + . + . + . + . + . + . + "An ontology of traits covering vertebrates"^^ . + . + "HGNC Symbol" . + "An ontology of Drosophila melanogaster developmental stages."^^ . + . + . + . + "https://bioportal.bioontology.org/ontologies/NPO"^^ . + "false"^^ . + . + "0000983"^^ . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/PSO_$1"^^ . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + . + "contributor"^^ . + . + . + "TRQ"^^ . + . + . + . + . + . + . + "https://cropontology.org/ontology/CO_325/Banana"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . + . + . + "Anvil" . + . + . + . + "false"^^ . + . + . + "100"^^ . + . + . + . + . + . + . + . + . + "NCBI dbSNP" . + "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . + . + . + . + "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . + . + . + "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . + . + . + "^\\d+$"^^ . + . + "https://github.com/HUPO-PSI/psi-mi-CV"^^ . + . + . +_:Nea857937d23a411e9c73d0450e3d7caa "Pantelis Topalis" . + . + . + "https://github.com/infectious-disease-ontology-extensions/ido-covid-19"^^ . + . + "UDB000691"^^ . + . + "0000001"^^ . + . + "nasa/kepler-exoplanet-search-results"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + . + "NCI Thesaurus" . + "https://www.geonames.org/export/codes.html"^^ . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/chembldb"^^ . + . + . + "SwissLipid" . + . + . + "AA0001"^^ . + . + . + . + . + . + "http://www.informatics.jax.org/searches/Phat.cgi?id=MP:$1"^^ . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . + "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . + . + . + "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . + . + . + "03307879"^^ . + . + . + . + . + "0000000"^^ . + "NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments."^^ . + "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . + "A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form."^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://publons.com/researcher"^^ . + . + . + . + . + . + . + . + . + . + . + . + "GabiPD (Genome Analysis of Plant Biological Systems Primary Database) constitutes a repository for a wide array of heterogeneous data from high-throughput experiments in several plant species. These data (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from different model or crop species, can be accessed through a central gene 'Green Card'."^^ . + . + . + . + "aap-1"^^ . + . + "^\\w+$"^^ . + "MIPF0000002"^^ . + . + . + . + . + . + . + "880798137"^^ . + . + . + . + "http://exac.broadinstitute.org/gene/$1"^^ . + . + . + "Anne Thessen" . + . + . + "https://developingmouse.brain-map.org/"^^ . + . + . + . + . + . + . + . + "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . + . + "http://purl.obolibrary.org/obo/UBERON_$1"^^ . + . + . +_:N74b5c109e3c245de9ba35c9a1b1d6b27 "chEBI" . + "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . + . + "2gc4E"^^ . + . + . + . + . + . + . + "AT1G01010"^^ . + "https://www.ncbi.nlm.nih.gov/genbank/"^^ . + "http://www.receptors.org/nucleardb/proteins/$1"^^ . + "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . + . + . + "RNAcentral" . + "HOMD Sequence Metainformation" . + . + . + . + . + . + . + . + "https://github.com/insect-morphology/lepao"^^ . + . + . + . + "Jim Balhoff" . + . + . + . + . + . + "https://apps.usgs.gov/thesaurus/thesaurus-full.php?thcode=3"^^ . + . + . + . + . + . + "GE86325"^^ . + . + . + . + . + "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . + . + . + "http://lisanwanglab.org/DASHR/entry/$1"^^ . + . + . + "^\\d+$"^^ . + . + "GXA Expt" . + . + . + . + . + . + "Oryzabase Mutant" . + . + . + . + . + . + . + "false"^^ . + "28"^^ . + "Liver Cancer Model Repository" . + . + . + . . - . - "Publishing Workflow Ontology" . - . - . - "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . - . - . - . - . - . - "RA01.0"^^ . - . - "^\\d{7}$"^^ . - . - "https://identifiers.org" . - . - . - "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . - "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . - "http://www.clo-ontology.org"^^ . - "false"^^ . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "^\\w+$"^^ . - . - . - . - . - . - . - "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . - . - . - "Open Tree of Life" . - . - . - . - "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . - "^GR\\_tax\\:\\d+$"^^ . - . - "The Morpheus model repository is an open-access data resource to store, search and retrieve unpublished and published computational models of spatio-temporal and multicellular biological systems, encoded in the MorpheusML language and readily executable with the Morpheus software.\n"^^ . - "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . - "NCBI PubChem database of bioassay records" . - . - . - . - . - . - . - . - "is deprecated" . - . + . + . + "NASA's GeneLab gathers spaceflight genomic data, RNA and protein expression, and metabolic profiles, interfaces with existing databases for expanded research, will offer tools to conduct data analysis, and is in the process of creating a place online where scientists, researchers, teachers and students can connect with their peers, share their results, and communicate with NASA."^^ . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . + . + . + "Integrated Genomic Resources of human Cell Lines for Identification" . + . + "377550"^^ . + . + "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . + "http://purl.obolibrary.org/obo/ICO_$1"^^ . + "https://cdno.info/"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "63189"^^ . + "SABIO-RK Reaction" . + "http://modelseed.org/"^^ . + . + . + . + . + . + . + "http://thebiogrid.org/"^^ . + . + . + "LINCS Small Molecule" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://github.com/FAIRsharing/subject-ontology"^^ . + . + "^(ev\\:)?E\\d+$"^^ . + "false"^^ . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . + . + . + . + . + "https://fairsharing.org/"^^ . + "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . + . + . + . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to quantitative trait loci identified in Gramene."^^ . + . + "The LifeWatch ERIC repository of semantic resources for the ecological domain." . + "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . + "3SBPLMKKVEVR"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "andreadega/systems-biology-compiler"^^ . + . + "http://drugcentral.org"^^ . + "http://www.psidev.info/MOD"^^ . + . + . + . + "WormBase RNAi" . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . + . + . + "false"^^ . + . + . + . + "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . + "false"^^ . + . + . + . + . + . + "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + . + . + "NeuroVault Image" . + . + . + "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . + . + . + . + . + . + . + . + . + "http://www.ymdb.ca"^^ . + "Lucas Leclere" . + . + . + . + . + . + . + . + "Charles Tapley Hoyt" . + . + . + . + . + . + . + "VCell Published Models" . + "57"^^ . + . + . + . + . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "^\\d+$"^^ . + "The Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . + . + . + . + . + "morpheus.lab/morpheus"^^ . + . + "https://molmedb.upol.cz/mol/$1"^^ . + . + "Unique Ingredient Identifier" . + . + "http://www.genecards.org/"^^ . + . + . + . + . + . + . + . + "H-InvDb Locus" . + "https://github.com/linikujp/OGSF"^^ . + . . - . - "^IM-\\d+(-?)(\\d+?)$"^^ . - . - . - "SIGNOR-252737"^^ . - . - . - . - . - . - . - . - . - . - . - . - . -_:N0ce5034e173846f0b47a46c42548ce15 "Pierre Sprumont" . - . + . + "ENSG00000026508"^^ . + . + . + . + "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . + . + . + . + . + . + . + . + . + . + . + "^C\\d{4}$"^^ . + "https://proteininformationresource.org/resid/"^^ . + . + . + . + "https://bacdive.dsmz.de/"^^ . + . + . + . + . + "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . + . + "http://fdasis.nlm.nih.gov/srs/srsdirect.jsp?regno=$1"^^ . + "CPX-263"^^ . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/GEO_$1"^^ . + "DBSALT001211"^^ . + . + "https://www.webelements.com/$1"^^ . + . + . + "The Cell Line Data Base (CLDB) is a reference information source for human and animal cell lines. It provides the characteristics of the cell lines and their availability through distributors, allowing cell line requests to be made from collections and laboratories."^^ . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + "Unified Phenotype Ontology" . + . + . + "^\\d{6,7}$"^^ . + . + . + . + . + . + . + . + "http://www.wikidata.org/entity/$1"^^ . + "Phenoscape Publication" . + . + . + . + . + . + . + . + . + . + "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . + . + "true"^^ . + . + . + . + . + . + . + "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . +_:N74ef5b212f444f4b82e6b6c6048084b4 "John Garavelli" . + . + . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . + . + "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . + . + . + . + . + "http://stormo.wustl.edu/ScerTF/details/$1"^^ . + "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . + . + "ConoServer" . + . + . + . + "false"^^ . + . . - "^\\d{7}$"^^ . - . - . - . - . - . - "false"^^ . - "Ensembl Gene" . - . - "UCSC Genome Browser" . - "03307879"^^ . - "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . - . - . - "^\\d+$"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . -_:Nc0ecb24abbb543e7b3a16d1ba11c38a8 "Marc Ciriello" . - . - . - "false"^^ . - . - . - . - . - . - . - "https://github.com/The-Sequence-Ontology/SO-Ontologies"^^ . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1"^^ . - . - "https://repo.napdi.org/"^^ . - . - "https://pfam.xfam.org/"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . - . - "Person"^^ . - . - . - "https://github.com/HajoRijgersberg/OM"^^ . - . - . - "http://matrixdb.univ-lyon1.fr/"^^ . - . - . - . - . - . - . - . - "http://wheat.pw.usda.gov"^^ . - . - "https://www.ncbi.nlm.nih.gov/gene"^^ . - . - "http://www.w3.org/ns/oa#$1"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/biomodels/"^^ . - "http://www.pseudogene.org"^^ . - . - "false"^^ . - . - "true"^^ . - "br/1"^^ . - . - "false"^^ . - _:N876775752ea24733b68c737a615f6f5c . - . - . - . - "Schema.org is a collaborative, community activity with a mission to create, maintain, and promote schemas for structured data on the Internet, on web pages, in email messages, and beyond."^^ . - "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . - . - "REPRODUCE-ME Ontology" . - . - . - "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . - . - . - . - "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . - . - . - . - . - . - . - "ILMN_129894"^^ . - "Curated Drug-Drug Interactions Database - Drug" . - . - . -_:Ne7bd6c7896fb4c08888ad9e245938067 "Animal Diversity Web technical staff" . - "http://obi-ontology.org"^^ . - "1009107926"^^ . - . - . - . - "false"^^ . - . - "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - "PRO_0000016681"^^ . - . - . - "false"^^ . - "Information for ligands in the BRENDA database."^^ . - "^\\d{7}$"^^ . - . - . - . - "Tom Gillespie" . - . - "http://www.begdb.com"^^ . - . - . - "ProDom" . - "^[A-Za-z0-9\\-\\/]+$"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "NeuroLex Dysfunction" . - . - . - . - . + . + . + . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "NIH RePORTER" . + "P01116"^^ . + . + . + . + "http://ecolexicon.ugr.es/en/index.htm"^^ . + "http://pkuxxj.pku.edu.cn/UNPD/"^^ . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . + . + . + . + "false"^^ . + "CHEBI" . + . + "0000590"^^ . + "MobiDB" . + "Epidemiology Ontology" . + . + . + . + . + . + . + . + "12929"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "Almost every product on our site has its own ASIN, a unique code we use to identify it. For books, the ASIN is the same as the ISBN number, but for all other products a new ASIN is created when the item is uploaded to our catalogue."^^ . + . + . + . + . + . + . + . + . + . + . + "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . + "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . + "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . + . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + . + . + . + . + "https://github.com/BgeeDB/homology-ontology"^^ . + "^\\d+$"^^ . + . + "http://www.gramene.org/"^^ . + "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . + "LL379-9"^^ . + . + "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . + "http://agroportal.lirmm.fr" . + . + . + . + . + . + . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "^[0-9]+$"^^ . + . + . + . + "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . + . + . + . + . + "^[SED]R[APRSXZ]\\d+$"^^ . + . + "The Bioinorganic Motif Database" . + "false"^^ . + . + "false"^^ . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . + . + . + . + . + . + "01001"^^ . + "https://proteinensemble.org/$1"^^ . + . + . + . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Phenotype."^^ . + . + "Functional Requirements for Bibliographic Records" . + . + . + . + . + "Imanis Life Sciences cell line products" . + . + . + "false"^^ . + "1000001"^^ . + . + . + . + . + "https://foodon.org/"^^ . + . + . + . + . + . + "G77500AY"^^ . + . + . + "IntAct Molecule" . + . + "Donny Winston" . + . + . + . + "true"^^ . + . + . + "http://www.brenda-enzymes.org"^^ . + . + . + "GWAS Central Study" . + "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . + "000000159"^^ . + . + . + . + . + . + "https://envipath.org/"^^ . + . + . + "MIMAT0046872"^^ . + . + "false"^^ . + . + "P29894"^^ . + . + . + "Regulation of Transcription"^^ . + . + . + . + . + . + . + "http://emouseatlas.org"^^ . + . + . + . + . + . + . + . + "http://www.w3.org/ns/shacl#$1"^^ . + . + . + . + . + . + . + . + . + . + . + "DragonDB DNA" . + . + . + . + . + "false"^^ . + . + . + . + "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . + "Bambara groundnut ontology" . + "G24361QY"^^ . + . + . + . + . + . + . + "AceView provides a curated sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These are aligned on the genome and clustered into a minimal number of alternative transcript variants and grouped into genes. In addition, alternative features such as promoters, and expression in tissues is recorded. This collection references C. elegans genes and expression."^^ . + . + . + . + . + . + . + "true"^^ . + "false"^^ . + . + . + . + . + . + . + "https://github.com/carrineblank/MicrO"^^ . + . + "https://github.com/obophenotype/c-elegans-phenotype-ontology"^^ . + . + . + . + . + "128011350"^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + "BindingDB is the first public database of protein-small molecule affinity data."^^ . + . + . + _:N77d13c0a01d940f5b35b8b27df76c01d . + "Datanator Reaction" . + . + . + . + . + . + . + . + . + . + . + . + "00103"^^ . + . + "0002058"^^ . + . + . + . + . + "https://bioregistry.io/$1:$2" . + . + "34"^^ . + . + "0019030"^^ . + . + . + . + "Wikidata Property" . + . + . + "Cell Line Database" . + . + . + "https://www.wormbase.org/db/seq/protein?name=$1"^^ . + . + . + "^[0-9]+$"^^ . + . + "false"^^ . + . + . + . + "10015919"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "Cephalopod Ontology" . + . + "^\\d+$"^^ . + . + . + . + "Regulation of Transcription Ontology" . + . + . + . + . + . + . + . + . + . + "^[a-z0-9]+$"^^ . + . + "Homologous Organ Groups" . + . + . + . + "http://purl.obolibrary.org/obo/CIDO_$1"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DUO_$1"^^ . + . + . + "The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis."^^ . + . + . + "LipidBank" . + . + . + "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . + . + . + . + "https://github.com/obophenotype/chiro"^^ . + . + "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . + "true"^^ . + . + . + "^\\d{7}$"^^ . + "VB.Ob.3736.GRSM125"^^ . + . + . + . + "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . + . + "VFDB Genus" . + "http://hpc-bioinformatics.cineca.it/fusion/main"^^ . + . + "^HIX\\d{7}(\\.\\d+)?$"^^ . + . + . + . + . "http://purl.obolibrary.org/obo/BFO_$1"^^ . - . - "ENSG00000026508"^^ . - . - "^\\w+(\\.\\d+)$"^^ . - "Amanda Hicks" . - . - "https://www.ebi.ac.uk/pride/archive/assays/$1"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://www.viprbrc.org/brc/home.do?decorator=vipr"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/PROCO_$1"^^ . - . - . - . - . - . - . - . - "0000088"^^ . - "^\\d{7}$"^^ . - . - "Chlamydia"^^ . - "Horizon Discovery cell line collection" . - . - . - "Platynereis Developmental Stages" . - "https://www.gwascentral.org/phenotype/$1"^^ . - "MultiCellDS Digital snapshot" . - . - . - . - . - . - "http://polbase.neb.com/"^^ . - "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "Paleobiology Database" . - . - "https://www.ebisc.org"^^ . - . - . - . - . - "Getty Thesaurus of Geographic Names" . - "http://www.sbgnbricks.org/"^^ . - "BioProject" . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "^\\d+$"^^ . - . - "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . - "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . - . - . - "A gazetteer constructed on ontological principles"^^ . - . - "CHEBI"^^ . - "http://purl.obolibrary.org/obo/OBCS_$1"^^ . - . - "Global LEI Index" . - "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . - "The cell line vocabulary inside FlyBase"^^ . - . - . - . - . - "NCI Metathesaurus" . - . - . - . - "Ontology Concept Identifiers" . - . - . - . - . - . - . - "false"^^ . - "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . - . - . - . - "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . - . - "Medical Subject Headings" . - "false"^^ . - "Functional Requirements for Bibliographic Records" . - . - . - . - . - . - . - . - "false"^^ . - "BioCyc collection of metabolic pathway databases" . - "36"^^ . - "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . - . - . - . - . - "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . - . - . - "^\\d+$"^^ . -_:N24d1369259724e22befc4951f66bc5b4 "Thorsten Heinrich" . - . - . - . - . - "0000400"^^ . - . - . - . - "spike00001"^^ . - . - . - . - "Genome Properties" . - . - "false"^^ . - . - "MicroScope" . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . - "false"^^ . - . - . - . - . - "true"^^ . - . - . - "false"^^ . - "An ontology of Drosophila melanogaster anatomy."^^ . - "http://purl.obolibrary.org/obo/MMO_$1"^^ . - . - "MMP3888430"^^ . - "^\\d{7}$"^^ . - "https://github.com/monarch-initiative/MAxO"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - "http://immunet.cn/bdb/"^^ . - . - . - . - . - "ENSG00000169174"^^ . - . - "false"^^ . - . - "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . - . - "^\\d+$"^^ . - "YeTFasCo" . - . - . - "^\\d+$"^^ . - . - "http://bacmap.wishartlab.com/"^^ . - "GLIDA Ligand" . - "PED00017e001"^^ . - "false"^^ . - . - . - "https://www.ebi.ac.uk/ega/datasets/$1"^^ . - "https://github.com/AnimalGenome/livestock-product-trait-ontology"^^ . - . - . - "Store DB" . - "GrainGenes" . - . - . - "Software Heritage is the universal archive of software source code."^^ . - . - . - . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + . + . + "25011"^^ . + . + "http://tuberculist.epfl.ch/"^^ . + . + . + . + . + "BiGG Compartment" . + "http://purl.obolibrary.org/obo/fbbt"^^ . + "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to individual transcripts."^^ . + . + "Liliana Andres Hernandez" . + "KIAA0001"^^ . + "13"^^ . + "true"^^ . + . + . + . + "Golm Metabolome Database Profile" . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + "http://www.aphidbase.com/aphidbase"^^ . + "http://purl.obolibrary.org/obo/BCO_$1"^^ . + . + . + "Michael Y Galperin" . + "Evidence ontology" . + "4"^^ . + "The UniProt Archive (UniParc) is a database containing non-redundant protein sequence information from many sources. Each unique sequence is given a stable and unique identifier (UPI) making it possible to identify the same protein from different source databases."^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/FIX_$1"^^ . + . + "http://purl.obolibrary.org/obo/ECAO_$1"^^ . + . + "^[A-Za-z-0-9_]+$"^^ . + . + "0000011"^^ . + . + . + . + . + "Drosophila development" . + . + "identifier for a fungus taxon in Index Fungorum"^^ . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . + "MultiCellDS collection" . + "^\\d+$"^^ . + . + . + . + . + . + "http://www.jcvi.org/charprotdb"^^ . + . + "The G protein-coupled receptor database (GPCRDB) collects, large amounts of heterogeneous data on GPCRs. It contains experimental data on sequences, ligand-binding constants, mutations and oligomers, and derived data such as multiple sequence alignments and homology models."^^ . + . + . + "https://www.ebi.ac.uk/gxa/"^^ . + . + . + . + . + . + "https://registry.identifiers.org/registry?query=\"MIR:$1\""^^ . + . + . + . + . + . + . + "Dimension"^^ . + . + . + "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . + . + . + . + "0000062"^^ . + . + . + "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "0000632"^^ . + . + . + "https://www.python.org/psf/"^^ . + "MIRIAM Registry resource" . + . + "false"^^ . + "BioPortal Prefixes" . + . + . + "false"^^ . + "Call for paper topics in EasyChair"^^ . + . + . + . + . + "Genome properties is an annotation system whereby functional attributes can be assigned to a genome, based on the presence of a defined set of protein signatures within that genome."^^ . + . + . + . + "AN0097748"^^ . + . + . + "104674"^^ . + . + "SIGNOR-252737"^^ . + . + . + . + . + . + . + "http://kim.bio.upenn.edu/software/ornaseq.shtml"^^ . + . + . + . + . + "Melanoma Molecular Map Project Biomaps" . + . + "Candida Genome Database" . + . + . + . + . + . + . + . + . + "447860"^^ . + . + . + . + . + "ClinVar Submission" . + . + "http://www.jstor.org/"^^ . + . + . + . + . + . + . + . + "https://morpheus.gitlab.io/models/$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + "https://ratmine.mcw.edu/ontology/disease/"^^ . + . + "http://qudt.org/schema/qudt#$1"^^ . + "^[a-z_A-Z0-9]+$"^^ . + . + . + . + "https://www.google.com/patents/$1"^^ . + "Gene Ontology Annotation Database" . + . + . + . + "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . + . + . + . + . + . + . + . + . + . + . + "https://www.w3.org/2004/02/skos/"^^ . + . + . + "^\\d+$"^^ . + "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "https://github.com/obophenotype/porifera-ontology"^^ . + . + "false"^^ . + . + "Fly taxonomy" . + "false"^^ . + "https://open.med.harvard.edu/wiki/display/eaglei/Ontology"^^ . + . + . + . + "Cell Biolabs cell line products" . + "http://www.mesquiteproject.org/ontology/Habronattus/index.html"^^ . + "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . + "0000027"^^ . + . + "https://www.cropontology.org/rdf/CO_339:$1"^^ . + . + "https://hamap.expasy.org/"^^ . + "Danielle Welter" . + . + . + "Reaxys eMolecules" . + . + . + . + . + . + . + . + . + "https://github.com/evidenceontology/evidenceontology/"^^ . + . + . + . + "The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication."^^ . + "NeuroVault Collection" . + . + . + "http://purl.obolibrary.org/obo/ARO_$1"^^ . + "https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0085-x"^^ . + "false"^^ . + . + . + "https://www.signalingpathways.org/index.jsf"^^ . + . + "Non-Coding RNA Ontology" . + "^CE\\d{5}$"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "Activity Streams" . + "Carrine Blank" . + "Semantic Web for Earth and Environment Technology Ontology" . + . + "Human Proteome Map Peptide" . + "The European Environment Information and Observation Network (Eionet) is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries. The EEA is responsible for developing Eionet and coordinating its activities together with National Focal Points (NFPs) in the countries. This terminology supports those efforts."^^ . + "1009107926"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "http://www.disease-ontology.org"^^ . + "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . + . + "false"^^ . + . + . + "0000050"^^ . + . + . + "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/MMUSDV_$1"^^ . + . + . + . + . + . + . + . + . + "0002927"^^ . + "Signaling Pathways Project" . + . + . + "https://restraintsgrid.bmrb.io/NRG/MRGridServlet"^^ . + "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . + . + . + "false"^^ . + . + . + . + "^[1-9][0-9]*$"^^ . + . + . + . + "Tom Gillespie" . + . + . + . + . + . + . + . + "false"^^ . + . + "^[A-Za-z_0-9]+$"^^ . + . + "^\\d{7}$"^^ . + . + . + . + "PD10000"^^ . + "NCATS Drugs" . + . + . + . + . + "true"^^ . + . + . + . + "Nathan Baker" . + . + "Robert Hoehndorf" . + . + . + . + . + "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . + . + . + . + . + . + . + "A database-specific registry supporting curation in the Gene Ontology" . + "http://www.semantic-systems-biology.org/apo"^^ . + "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . + . + . + "NONCODE v4 Gene" . + . + . + . + . + . + . + . + . + . + . + . + "^BSU\\d{5}$"^^ . + "false"^^ . + "veNOG12876"^^ . + . + "0000423"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://biological-expression-language.github.io/"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "Clement Jonquet" . + . + . + . + "^\\d+$"^^ . + . + . + "http://ascl.net/$1"^^ . + . + . + "The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology terms to describe the molecular function, biological process, and subcellular localization of gene products."^^ . + "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . + "R-BTA-418592"^^ . + . + . + "Telethon Network of Genetic Biobanks" . + "^\\d+$"^^ . + . + "^GPST[0-9]{6}$"^^ . + . + . + . + "http://bitterdb.agri.huji.ac.il/dbbitter.php"^^ . + . + . + . + . + . + . + "DANDI works with BICCN and other BRAIN Initiative awardees to curate data using community data standards such as NWB and BIDS, and to make data and software for cellular neurophysiology FAIR (Findable, Accessible, Interoperable, and Reusable).\nDANDI references electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data.\nThese data will help scientists uncover and understand cellular level mechanisms of brain function. Scientists will study the formation of neural networks, how cells and networks enable functions such as learning and memory, and how these functions are disrupted in neurological disorders."^^ . + . + . + . + . + . + . + "Vertebrate Genome Annotation Database" . + . + "Darren Natale" . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + "CQG5"^^ . + "MSV000082131"^^ . + . + . + . + . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . + "false"^^ . + "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . + "https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html"^^ . + . + "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . + . + . + . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + . + . + "234"^^ . + "Chickpea ontology" . + "Homeodomain Research" . + . + . + "true"^^ . + . + . + . + . + "http://www.cellsignal.com/products/$1.html"^^ . + . + "Diseases Database" . + . + . + . + "0002233"^^ . + . + . + . + "10194"^^ . + "MarFun" . + "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . + "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . + . + "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . + "https://www.brenda-enzymes.de/ligand.php"^^ . + "Defines terms and relations necessary for interoperation between epidemic models and public health application software that interface with these models"^^ . + . + . + . + . + "https://www.cropontology.org/rdf/CO_341:$1"^^ . + . + . + "http://www.geneontology.org/cgi-bin/references.cgi"^^ . + . + "0000012b-5661-2f63-2f73-b43980000000"^^ . + "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . + . + . + "https://www.ncbi.nlm.nih.gov/gtr/"^^ . + . + . + "PASS01237"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + "Alan Wood's Pesticides" . + . + . + . + "https://aopwiki.org/"^^ . + . + "Genetics Home Reference" . + . + "E-cyanobacterium Experimental Data" . + . + . + "false"^^ . + . + "^\\d+$"^^ . + "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + . + "A download link for the given resource" . + . + . + . + "false"^^ . + . + . + "4544"^^ . + . + "ADA"^^ . + . + . + . + . + . + . + . + "Web Annotation Ontology" . + . + "The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance. The Anatomical Therapeutic Chemical (ATC) classification system and the Defined Daily Dose (DDD) is a tool for exchanging and comparing data on drug use at international, national or local levels."^^ . + . + . + . + . + . + . + "^PED\\d{5}e\\d{3}$"^^ . + "https://ega-archive.org/"^^ . + . + . + "PA131"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + "DataCite Ontology" . + . + . + . + _:N53c97813ee374354bc16b388728eb62a . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Nathan Edwards" . + . + "https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=MMO:0000000"^^ . + . + . + . + "false"^^ . + . + . + "https://github.com/obophenotype/ctenophore-ontology"^^ . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + "0000449"^^ . + " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . + . + . + . + . + . + . + "^MMP\\d+.\\d+$"^^ . + "^\\d+$"^^ . + "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . + . + . + . + . + . + . + . + "http://www.inoh.org"^^ . + . + . + "10.1621/vwN2g2HaX3"^^ . + "http://purl.obolibrary.org/obo/ERO_$1"^^ . + "1046"^^ . + . + "http://dictybase.org/"^^ . + . + . + . + . + "http://europepmc.org/"^^ . + "10595"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . + . + "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . + . + . + . + "WBRNAi00086878"^^ . + . + . + . + . + "http://umbbd.ethz.ch/"^^ . + . + "^\\w{14}$"^^ . + . + "false"^^ . + . + . + . + . + . + . + "SAMEA2397676"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "http://github.com/ga4gh/data-object-service-schemas"^^ . + . + . + . + . + "false"^^ . + . + "A type for entries in the Bioregistry's metaregistry." . + . + . + . + . + . + . + . + . + . + . + . + . + "PubChem Cell Line" . + . + . + . + . + . + "http://www.geosamples.org/"^^ . + . + . + "http://purl.uniprot.org/uniprot/$1"^^ . + . + . + . + . + . + "false"^^ . + "IPR016380"^^ . + "^NCT\\d{8}$"^^ . + . + . + "https://www.re3data.org" . + . + . + "^[A-Za-z]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "90901"^^ . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . + . + . + . + . + "0000049"^^ . + . + "Paleobiology Database" . + . + "^\\d+$"^^ . + "^L\\d+$"^^ . + . + . + "^\\w+(\\-|\\.|\\w)*$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "https://www.metanetx.org/equa_info/$1"^^ . + . + . + . + . + . + . + . + "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . + . + . + . + . + "DB14938"^^ . + "false"^^ . + . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway"^^ . + . + . + "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id=$1"^^ . + "Cube db" . + . + "^\\d+$"^^ . + "A nomenclatural ontology for biological names" . + . + . + . + . + . + "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . + . + "4D Nucleome Data Portal Experiment Replicate" . + . + "Person"^^ . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + "https://www.aepc.org/european-paediatric-cardiac-coding"^^ . + "87"^^ . + . + . + "https://reporter.nih.gov/project-details/$1"^^ . + "^\\d+$"^^ . + . + "0000055"^^ . + . + . + "Val Wood" . + . + . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/bto/terms?obo_id=BTO:$1"^^ . + . + . + . + . + . + "http://bigg.ucsd.edu/models/$1"^^ . + "https://bioregistry.io"^^ . + . + . + . + "https://www.ebi.ac.uk/ipd/estdab/"^^ . + "false"^^ . + . + "http://purl.org/vocab/frbr/core#$1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "http://ccr.coriell.org/"^^ . + . + "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + . + "^[1-9]\\d*$"^^ . + . + . + . + "false"^^ . + . + "Life cycle stages for Mus Musculus"^^ . + "false"^^ . + . + . + . + . + . + . + . + "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . + "100000001"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "G. Thomas Hayman" . + . + . + . + "MMP02954345.1"^^ . + . + . + "^MGYA\\d+$"^^ . + "MetaNetX compartment" . + "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . + . + "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . + . + . + "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . + . + . + . + "false"^^ . + . + . + . + "349124"^^ . + . + "http://biomodels.net/rdf/vocabulary.rdf"^^ . + . + . + . + . + "Ensembl Plants" . + "true"^^ . + . + "Virtual Fly Brain" . + "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . + . + . + . + . + "https://www.addexbio.com/productshow?id=4"^^ . + . + . + . + "https://www.w3.org/ns/dcat"^^ . + "false"^^ . + "1a24"^^ . + "CH_001923"^^ . + . + . + . + . + . + . + . + . + "https://github.com/PRIDE-Utilities/pride-ontology"^^ . + . + . + "00620027"^^ . + "http://sabiork.h-its.org/"^^ . + "^EDI_\\d+$"^^ . + . + "http://www.cropontology.org/ontology/CO_327/Pearl%20millet"^^ . + . + . + . + . + . + . + "https://www.kaggle.com/$1"^^ . + . + "PA146123006"^^ . + . + . + "IA"^^ . + . + "false"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . + . + . + "An ontology that provides a structured vocabulary written of document components, both structural (e.g., block, inline, paragraph, section, chapter) and rhetorical (e.g., introduction, discussion, acknowledgements, reference list, figure, appendix)."^^ . + . + "Resources mentioned in \"Sharing biological data: why, when, and how\"" . + "IPI"^^ . + . + "^[A-Z][a-z][0-9]+$"^^ . + . + . + "https://ximbio.com/reagent/$1"^^ . + . + . + "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by the EBI Functional Genomics Team."^^ . + "F0001"^^ . + . + . + . + "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . + . + . + "037727"^^ . + . + . + . + . + "Panorama is a freely-available, open-source repository server application for targeted mass spectrometry assays that integrates into a Skyline mass spec workflow. It makes links to the Proteomics Exchange when possible."^^ . + "82"^^ . + . + . + . + "EDAM Format" . + "Mark Engelstad" . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + . + . + . + . + . + . + . + "^[0-9]+$"^^ . + "Jackson Laboratories Strain" . + "The International Classification of Diseases is the international standard diagnostic classification for all general epidemiological and many health management purposes."^^ . + . + . + . + . + . + "http://neuinfo.org/"^^ . + . + "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . + "Food-Biomarker Ontology" . + . + . + "Canadian Drug Product Database" . + . + . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . + . + . + . + "^\\d{6}$"^^ . + . + . + . + "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . + "^\\d+$"^^ . + "^\\d+$"^^ . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + "ArrayExpress Platform" . + . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + "Environmental conditions, treatments and exposures ontology" . + "false"^^ . + . + . + "National Experimental Cell Resource Sharing Platform" . + . + . + "^\\w{2,4}\\d{5}$"^^ . + "https://sitem.herts.ac.uk/aeru/bpdb/index.htm"^^ . + . + . + . + "595"^^ . + "^ECMDB\\d+$"^^ . + "false"^^ . + . + . + . + . + . + "http://edamontology.org/operation_$1"^^ . + . + . + . + . + "44259"^^ . + . + "SSF57615"^^ . + "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "TTD Drug" . + "^\\d+$"^^ . + . + . + . + . + . + . + "http://www.yeastrc.org/pdr/"^^ . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . + . + . + . + . + "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . + "https://github.com/VEuPathDB-ontology/MIRO"^^ . + . + . + . + "UniProt Resource" . + "SABIO-RK EC Record" . + "https://topfind.clip.msl.ubc.ca"^^ . + "Full implementation of the DRS 1.1 standard with support for persistent identifiers. Open source DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + "false"^^ . + "CAA71118.1"^^ . + . + "ftp://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "LinkML" . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "M0001"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . + "false"^^ . + "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . + "Annotated Regulatory Binding Sites" . + . + . + "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references mutant strain information."^^ . + . +_:N87132ab790ed47c0856798958c4f76c4 "Daniel Sonenshine" . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "Elucidating the mechanism of toxicity is crucial in drug safety evaluations. TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.\n\nThe TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry from UBERON, Cell Ontology, NCBI Taxon, ChEBI, Gene Ontology, PATO, OGG, INOH, HINO, NCIT, DOID and Relational ontology (RO). The lower layer contains toxicological terms.\n\nIn applied work, we have developed a prototype of TOXPILOT, a TOXic Process InterpretabLe knOwledge sysTem. TOXPILOT provides visualization maps of the toxic course, which facilitates capturing the comprehensive picture for understanding toxicity mechanisms. A prototype of TOXPILOT is available: https://toxpilot.nibiohn.go.jp"^^ . + "0000021"^^ . + . + "http://microsporidiadb.org/micro/"^^ . + "http://mirtarbase.mbc.nctu.edu.tw/"^^ . + . + . + . + . + "https://cmecscatalog.org/cmecs"^^ . + . + . + "http://www.geneontology.org/formats/oboInOwl#$1"^^ . + . + "false"^^ . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . + . + "^cpd\\d+$"^^ . + . + "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "NMR-instrument specific component of metabolomics investigations" . + . + . + "00073"^^ . + "Sigma Aldrich is a life sciences supply vendor."^^ . + . + "Richard Cyganiak" . + . + . + "false"^^ . + . + . + . + . + . "https://pubchem.ncbi.nlm.nih.gov"^^ . - "Dongsheng Cao" . - . - . - . - . - . - . - . - "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . - "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . - . - "https://www-snorna.biotoul.fr/"^^ . - . - . - . - . - . - . - "^casent\\d+(\\-D\\d+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - . + . + "^\\d{7}$"^^ . + . + . + "http://www-deletion.stanford.edu/YDPM/"^^ . + . + . + . + . + . + . + . + . + . + . + "https://fair-research.org"^^ . + "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "International Medical Device Regulators Forum" . + . + . + "AberOWL is a framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services to provide access to specific biological datasets." . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "https://animaldiversity.org/accounts/$1"^^ . + "FBgn0011293"^^ . + "false"^^ . + . + "http://www.antirrhinum.net/"^^ . + . + . + . + "false"^^ . + . + "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . + . + . + . + . + . + . + . + . + . + . + "^[A-Z0-9]{5}\\d+$"^^ . + . + . + "https://www.ebi.ac.uk/uniparc/"^^ . + . + "The Food Ontology" . + . + . + . + "Scholarly Contributions and Roles Ontology" . + "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "false"^^ . + "https://swissmodel.expasy.org"^^ . + . + . + . + . + . + "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . + . + . + . + "^PTM-\\d{4}$"^^ . + "https://github.com/The-Sequence-Ontology/SO-Ontologies"^^ . + . + . + . + "R00100"^^ . + . + . + "National Center for Advancing Translation Sciences BioPlanet" . + . + . + "http://bigg.ucsd.edu/universal/metabolites"^^ . + . + . + . + "HomoloGene" . + "SitEx" . + . + "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . + "GO Chemicals" . + . + "http://www.yeastgenome.org/"^^ . + . + . + "E. coli Metabolite Database" . + "0010039"^^ . + "https://lincs.hms.harvard.edu/db/sm/$1"^^ . + "https://www.uniprot.org/database/DB-$1" . + . + . + "The responsible person for a resource" . + . + "0471491039"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . + . + . + "171"^^ . + . + . + . + "HIT000195363"^^ . + "17254"^^ . + "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . + . + . + . + . + . + . + . + . + "http://www.gramene.org/"^^ . + "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "https://www.biocatalogue.org/services/$1"^^ . + . + . + . + "https://www.flymine.org/come"^^ . + . + . + "false"^^ . + "HsapDO:0000004"^^ . + . + . + . + "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . + . + . + . + "hasOpenAccessRating"^^ . + . + . + "TOKU-E Cell-culture Database" . + "https://bams1.org"^^ . + . + "http://www.gramene.org/"^^ . + . + . + . + . + "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . + . + . + . + . + . + . + . + . + . + "https://github.com/CTDbase/exposure-ontology"^^ . + . + "http://www.antweb.org/specimen.do?name=$1"^^ . + . + "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . + . + . + _:N5bf3769b744f4926a943b3bade8a7223 . + . + . + . + . + . + . + "https://www.crossref.org/"^^ . + . + . + . + . + . + "^\\w+(\\.)?\\d+$"^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . + . + . + . + "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . + . + "http://www.animaldiversity.org"^^ . + "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . + . + . + "false"^^ . + . + "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . + . + . + . + . + . + "0000046"^^ . + . + "github" . + . + "K"^^ . + . + . + . + . + . + . + "https://cryptodb.org/cryptodb/"^^ . + . + "Ontology of Microbial Phenotypes" . + "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . + "C0017565"^^ . + . + "Represent chemical entities having particular CHEBI roles"^^ . + "http://purl.obolibrary.org/obo/AISM_$1"^^ . + . + . + . + . + "Unimod protein modification database for mass spectrometry" . + . + "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . + . + . + . + . + . + "EG10173"^^ . + . + . + "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . + "http://flybase.org/"^^ . + "false"^^ . + . + "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . + . + . + "http://n2t.net/ark:$1"^^ . + "DrugBank Target v4" . + "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . + "FAIRsharing" . + "1058367"^^ . + "117"^^ . + "https://www.metanetx.org/comp_info/$1"^^ . + . + "false"^^ . + . + . + . + . + "h_aktPathway"^^ . + . + . + . + . + . + . + . "^\\d{7}$"^^ . - . - . - . - . - . - . - "false"^^ . - . - "https://mmp.sfb.uit.no/databases/marfun"^^ . - . - . - . - "http://purl.obolibrary.org/obo/OHD_$1"^^ . - "Common Bean ontology" . - . - . - . - . - . - "Expression"^^ . - . - "NCBI Registry" . - "Protein Ontology" . - . - . - . - . - . - "^\\d{7}$"^^ . - "^\\d+$"^^ . - "http://www.atol-ontology.com"^^ . - "miRNA Target Prediction at EMBL" . - . - . - . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.enanomapper.net/"^^ . - . - . + . + . + . + "^PWY\\w{2}\\-\\d{3}$"^^ . + . + . + "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . + . + "cl3603"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://www.gwascentral.org/marker/$1"^^ . + . + . + . + "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . + . + . + . + . + "false"^^ . + . + . + "https://psidev.info/sepcv"^^ . + . + . + "https://VirtualFlyBrain.org"^^ . + . + . + "chebi" . + . + . + . + . + . + "^\\d+$"^^ . + "Shapes Constraint Language" . + "https://www.metanetx.org/"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "Sickle Cell Disease Ontology" . + . + "351"^^ . + . + "NONCODE v4 Transcript" . + "http://purl.obolibrary.org/obo/OGSF_$1"^^ . + . + "bsu:BSU01340"^^ . + "PED00017e001"^^ . + . + . + "^\\d{7}$"^^ . + "false"^^ . + "Lynn Schriml" . + . + "DUO is an ontology which represent data use conditions."^^ . + "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . + "https://www.ebi.ac.uk/chebi/"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . . - "https://github.com/SDG-InterfaceOntology/sdgio"^^ . - . - . - . - . - . - . - "FooDB Compound" . - . - . - "https://co.mbine.org/specifications/$1"^^ . - "https://www.eurofir.org"^^ . - . - . - . - . - "90000018"^^ . - . - . - . -_:N141173d7fe154477b6ac646d37cf2451 "Matthew Brush" . - . - "https://www.w3.org/TR/rdf-schema/"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Analytes are subjected to a gas chromatograph coupled to a mass spectrometer, which records the mass spectrum and the retention time linked to an analyte. This collection references GC-MS spectra."^^ . - . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . - . - . - . - . - "true"^^ . - . - "DDB_G0267522"^^ . - "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . - . - "https://www.biozol.de/en"^^ . - . - . - "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . - "http://www.wikipathways.org/instance/$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "Intelligence Task Ontology" . - "false"^^ . - . - . - . - "https://www.cropontology.org/rdf/CO_321:$1"^^ . + . + . + "https://www.opengalen.org"^^ . + . + . + . + . + . + "http://pax-db.org/"^^ . + . + . + . + . + . + . + . + . + "Q0VCA6"^^ . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . + "Online Mendelian Inheritance in Man" . + . + . + . + . + . + "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . + . + . + . + . + "FuncBase Fly" . + . + . + . + . + . + "The cell line vocabulary inside FlyBase"^^ . + "https://www.cellbiolabs.com/search?keywords=$1"^^ . + . + "Mutant Mouse Resource and Research Centers" . + . + . + "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . + . + . + . + . + . + . + "https://www.rebuildingakidney.org/"^^ . + "http://purl.obolibrary.org/obo/RS_$1"^^ . + . + "https://n2t.net/$1:$2" . + "https://www.ebi.ac.uk/ega/datasets/$1"^^ . + . + . + . + "Gene Regulation Ontology" . + . + "OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genome sequences. It identifies orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. This collection references groupings of orthologs."^^ . + . + "chromium"^^ . + "^\\d+$"^^ . + . + . + "^MIMAT\\d{7}$"^^ . + . + "EMD-1001"^^ . + . + . + . + . + . + . + "EU Clinical Trials" . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "Cell line collections"^^ . + "http://ctdbase.org/"^^ . + "Cell line collections"^^ . + . + "https://github.com/"^^ . + . + . + . + . + . + . + . + "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . + . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . + . + "Cancer Staging Terms" . + . + . + . + . + . + "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . + . + "ASPL0000349247"^^ . + . + "grid.225360.0"^^ . + . + "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. \n\nThe GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples."^^ . + "^[0-9]+\\.[0-9]+$"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "The [Alliance of Genome Resources](https://www.alliancegenome.org/about-us) creates identifiers for several biological entity types including genes, other sequence features, constructs, morpholinos, TALENs, CRISPRs, variants, alleles, genotypes, strains, environments and experiments, phenotype annotations, expression annotations, disease annotations, interactions, and variant annotations.\n\nThe Alliance of Genome Resources was founded by the following Model Organism databases and the Gene Ontology Consortium and distributes high-quality, curated knowledge about several model organisms in a single, unified location:\n\n- [ZFIN](https://zfin.org) - Zebrafish Information Network\n- [WormBase](https://wormbase.org)\n- [MGI](https://www.mgi.org) - Mouse Genome Informatics\n- [RGD](https://rgd.mcw.edu) - Rat Genome Database\n- [SGD](https://www.yeastgenome.org) - Saccharomyces Genome Database\n- [FlyBase](https://flybase.org)\n- [Xenbase](https://www.xenbase.org)"^^ . + "https://www.disprot.org/ontology"^^ . + "http://www.mirbase.org/"^^ . + "https://zenodo.org/record/$1"^^ . + . + . + "Ontology for Parasite LifeCycle" . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . + . + . + . + "careerPrizeMoney"^^ . + . + "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . + . + . + . + . + "true"^^ . + . + . + . + . + "Marijane White" . + . + "false"^^ . + "false"^^ . + . + "The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. It uses a defined classification for catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalysed by an enzyme."^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + "PK-DB" . + "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . + . + . + . + "https://www.biocarta.com/"^^ . + . + "^\\d{7}$"^^ . + . + "^P(X|R)D\\d{6}$"^^ . + . + "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . + . + . + . + . + . + . + . + "http://aber-owl.net/ontology/$1" . + . + . + "http://www.chemspider.com/"^^ . + . + "false"^^ . + "Daniel C. Berrios" . + "false"^^ . + . + . + "NINDS Human Cell and Data Repository" . + . + . + "^\\d{7}$"^^ . + . + "Reactome" . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "https://pharmacome.github.io/conso/$1"^^ . + . + "PubChem Element" . + "Rice ontology" . + . + . + "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + . + . . - . - "Database of homology-derived secondary structure of proteins" . - "Xenopus Anatomy Ontology" . - . - . - "http://ecoportal.lifewatch.eu/ontologies/$1" . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "KEGG LIGAND" . - . - . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/OBIB_$1"^^ . - . - "^C\\d+$"^^ . - "^[a-z_A-Z0-9]+$"^^ . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "TubercuList knowledge base" . - . - . - "^\\w{4}$"^^ . - "https://www.genome.jp/kegg/reaction/"^^ . - . - . - "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . - . - . - . - "http://www.genome.jp/kegg/disease/"^^ . - "http://purl.obolibrary.org/obo/FBbi_$1"^^ . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "Zach Landis-Lewis" . - . - . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . - "https://portal.issn.org"^^ . - "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . - . - "ev:E00032"^^ . - . - . - "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . - . - . - . - . - . - . - "SL-0002"^^ . - . - . - . - . - . - . - . - . - "Pearl millet ontology" . - . - "https://www.dataone.org"^^ . - "PED00037"^^ . - "false"^^ . - . - . - . - "A database-specific registry supporting curation in the Gene Ontology" . - . - . - "Scholia Registry" . - "false"^^ . - . - . - . - . - . - . - . - "PANTHER Pathway" . - . - . - . - "http://www.genenames.org"^^ . - "0000027"^^ . - . - "0000079"^^ . - . - . - . - . - "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - . - . - "https://www.ebi.ac.uk/arrayexpress/"^^ . - . - . - "This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes."^^ . - . - "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=$1&action=view"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "contributor"^^ . - . - . - . - . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/index-eng.jsp"^^ . - . - . - "PS214100"^^ . - "ERP004492"^^ . - . - . - "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . - "http://www.uniprot.org/"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "LigandBook" . - "http://purl.obolibrary.org/obo/IAO_$1"^^ . - . - . - "https://github.com/information-artifact-ontology/ontology-metadata"^^ . - . - . - . - "^\\d{8}$"^^ . - "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . - . - . - "https://github.com/enpadasi/Ontology-for-Nutritional-Studies"^^ . - "http://purl.obolibrary.org/obo/$1_$2" . - . + . + "P00266"^^ . + "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . + "COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer"^^ . + "http://www.w3.org/ns/dcat#$1"^^ . + "^\\d+$"^^ . + . + "http://trace.ddbj.nig.ac.jp/bioproject/"^^ . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . + . + "Fernanda Farinelli" . + . + "https://co.mbine.org/standards/"^^ . + "^\\d+$"^^ . + "Online Mendelian Inheritance in Animals" . + . + . + . + . + . + "Coriell Institute for Medical Research" . + "Cellosaurus identifeirs for publications, like Pubmed"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + "https://www.ebi.ac.uk/gwas/studies/$1"^^ . + . + . + . + _:Nab1e039fd9a3451dbad75da2e0d784fa . + "An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies."^^ . + "^\\d{7}$"^^ . + . + . + "Molecular Signatures Database" . + "false"^^ . + "https://www.cropontology.org/rdf/CO_360:$1"^^ . + . + . + . + . + . + . + . + "0000140"^^ . + . + "ChEBI Data Sources" . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "The Environment Ontology is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations."^^ . + . + . + . + . + "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . + . + . + . + . + . + . + . + . + "JCGG-STR008690"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + "0000001"^^ . + . + . + . + "https://icahn.mssm.edu/"^^ . + . + "http://umbbd.ethz.ch/"^^ . + "^DDInter\\d+$"^^ . + "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . + . + . + . + . + . + . + "090803"^^ . + "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . + . + . + . + . +_:N5bf3769b744f4926a943b3bade8a7223 "SEP developers via the PSI and MSI mailing lists" . + "^KW-\\d{4}$"^^ . + . + . + . + . + . + . + . + . + . + . + "ProDom" . + "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "Epilepsy Ontology" . + "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references wild strain information."^^ . + "^[A-Za-z0-9\\/]+$"^^ . + . + . + . + . + . + "false"^^ . + . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . + . + . + . + . + . + . + . + . + "https://run.biosimulations.org/simulations/$1"^^ . + . + "Spectral Database for Organic Compounds" . + . + . + "1"^^ . + . + . + . + . . - "^[a-z]+(\\..*?)?$"^^ . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . - . - . - "Charles Ettensohn" . - . - . - . - . + . + "5277619"^^ . + . + "https://aopwiki.org/stressors/$1"^^ . + . + . + "^((ENS[FPTG]\\d{11}(\\.\\d+)?)|(FB\\w{2}\\d{7})|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?)|([A-Z_a-z0-9]+(\\.)?(t)?(\\d+)?([a-z])?))$"^^ . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . + . + "https://bioregistry.io/metaregistry/biocontext/$1" . + . + . + . + . + "XUO" . + . + . + "https://www.ncbi.nlm.nih.gov/assembly/$1"^^ . + "http://bis.zju.edu.cn/ricenetdb"^^ . + . + . + "https://biolink.github.io/biolink-model/"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "https://cropontology.org/ontology/CO_365/Fababean"^^ . + . + . + "false"^^ . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . + "true"^^ . + "^ILMN_\\d+$"^^ . + "true"^^ . + . + . + . + . + "^\\d{1,5}$"^^ . + . + "Guide to Pharmacology Ligand" . + "http://func.mshri.on.ca/fly"^^ . + . + "Genetree displays the maximum likelihood phylogenetic (protein) trees representing the evolutionary history of the genes. These are constructed using the canonical protein for every gene in Ensembl."^^ . + . + . + "false"^^ . + . + "ThermoFisher is a life sciences supply vendor."^^ . + . + . + . + . + . + "http://edamontology.org"^^ . + . + . + . + . + . + "http://4dx.embl.de/4DXpress"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "The World Register of Marine Species (WoRMS) provides an authoritative and comprehensive list of names of marine organisms. It includes synonyms for valid taxonomic names allowing a more complete interpretation of taxonomic literature. The content of WoRMS is administered by taxonomic experts."^^ . + . + "^\\w+$"^^ . + "false"^^ . + . + "CoVoc Coronavirus Vocabulary" . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . + . + . + . + . + . + "false"^^ . + "http://braininfo.rprc.washington.edu/"^^ . + . + . + . + "Google Books" . + . + "CNBG_0001"^^ . + . + . + "OTTHUMG00000169812"^^ . + "https://github.com/EBISPOT/amphx_ontology"^^ . + "^\\d{4}$"^^ . + . + . + "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . + . + . + "https://bioregistry.io/collection/$1"^^ . + "false"^^ . + . + . + . + . + "ChEMBL" . + . + "PROSITE" . + . + . + . + "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . + . + "^\\d+$"^^ . + . + . + "http://polbase.neb.com/"^^ . + . + . + . + . + . + . + . + . + "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . + . + . + . + . + . + . + . + "Data Catalog" . + . + "http://plasmodb.org/plasmo/"^^ . + "https://www.cropontology.org/rdf/CO_365:$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . + "false"^^ . + . + . + . + . + "Curated Drug-Drug Interactions Database - Drug" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://w3id.org/linkml/$1"^^ . "http://mint.bio.uniroma2.it/mint/search/inFrameInteraction.do?interactionAc=$1"^^ . - "Marijane White" . - "0107180"^^ . - "https://bioregistry.io/metaregistry/$1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins."^^ . - . - . - "http://purl.bioontology.org/ontology/STY/$1"^^ . - "https://metacyc.org/compound?orgid=META&id=$1"^^ . - "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . - . - . - . - . - . - . - . - . - . - . - . -_:Ne13938b012994aa0ba4cf64b8ee0d5d4 "Jonathan Bard" . - "false"^^ . - "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . - "Cell line collections"^^ . - . - "ATL98012"^^ . - "https://www.cropontology.org/rdf/CO_359:$1"^^ . - . - . - . - . - . - . - . - . - . - "National Drug File - Reference Terminology" . - . - . - "00000000"^^ . - . - . - . - "LCL-2085"^^ . - "https://www.addexbio.com/productdetail?pid=$1"^^ . - . - . - "The human DEPhOsphorylation Database (DEPOD) contains information on known human active phosphatases and their experimentally verified protein and nonprotein substrates. Reliability scores are provided for dephosphorylation interactions, according to the type of assay used, as well as the number of laboratories that have confirmed such interaction. Phosphatase and substrate entries are listed along with the dephosphorylation site, bioassay type, and original literature, and contain links to other resources."^^ . - "https://bgee.org/"^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - "Cell line collections"^^ . - . - . - "PRIDE Controlled Vocabulary" . - "http://intron.ucsc.edu/yeast4.3/"^^ . - . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "^[a-z0-9\\_]+$"^^ . - "PRIDE Project" . - . - "false"^^ . - "http://www.orpha.net/ORDO/Orphanet_$1"^^ . - . - "Activity Streams is an open format specification for activity stream protocols, which are used to syndicate activities taken in social web applications and services, similar to those in Facebook's, Instagram's, and Twitter's. The standard provides a general way to represent activities."^^ . - . + . + . + "false"^^ . + "https://cropontology.org/ontology/CO_338/Chickpea"^^ . + . + "Python"^^ . + "Continuous Automated Model Evaluation" . + . + . + "false"^^ . + "oct 2016"^^ . + . + . + . + . + "http://www.evocontology.org/"^^ . + . + . + . + . + . + . + "SNP to Transcription Factor Binding Sites" . + . + . + "HMS LINCS Compound" . + . + . + . + . + . + "http://www.plantontology.org"^^ . + . + "https://reactome.org/content/detail/$1"^^ . + . + . + "https://www.ebisc.org"^^ . + "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . + . + "1755"^^ . + "https://hpscreg.eu/"^^ . + . + "https://www.nextprot.org/"^^ . + . + . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . + . + . + . + . + . + . + . + "https://cordis.europa.eu/"^^ . + . + . + . + "https://hamap.expasy.org/unirule/$1"^^ . + . + . + . + . + . + . + . + "http://rgd.mcw.edu/rgdweb/ontology/search.html"^^ . + . + . + . + "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . + . + . + . + . + "CHEBI" . + . + "PTPN1"^^ . + . + "https://doulix.com/biomodules/$1"^^ . + . + "Golm Metabolome Database Analyte" . + . + . + . + . + . . - . - "NIF Dysfunction" . - "Environment Ontology for Livestock" . - . - "https://icd.who.int/"^^ . - . - "https://www.cropontology.org/rdf/CO_323:$1"^^ . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . - . - . - . - . - . - "JRC Data Catalogue" . - . - "bioregistry"^^ . - . - . - . - "DragonDB Locus" . - "false"^^ . - . - "The Intelligence Task Ontology (ITO) provides a comprehensive map of machine intelligence tasks, as well as broader human intelligence or hybrid human/machine intelligence tasks."^^ . - . - "false"^^ . - "^[A-Za-z]+\\d+$"^^ . - . - . - . - . - "^GPST[0-9]{6}$"^^ . - . - . - "^\\d+$"^^ . - . - "https://www.gwascentral.org/phenotypes"^^ . - . - . - . - . - . - . - . - "http://www.w3.org/ns/shacl#$1"^^ . - "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . - "http://www.orpha.net/consor/"^^ . - _:Neb3cb9b18833405fb91839f2f128d866 . - . - . - . - . - . - "^\\w{2,4}\\d{5}$"^^ . - . - . - . - . - . - . - "http://www.jcvi.org/charprotdb"^^ . - . - . - "true"^^ . - . - . - . - . - "http://lincsportal.ccs.miami.edu/datasets/"^^ . - "false"^^ . - . - . + . + . + "http://www.kupkb.org/"^^ . + . + "It is a simple ontology to describe sequence feature positions and regions as found in GFF3, DBBJ, EMBL, GenBank files, UniProt, and many other bioinformatics resources"^^ . + "^\\d{7}$"^^ . + "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . + . + . + . + . + . + . + "201022999"^^ . + "Human Pluripotent Stem Cell Registry" . + . + . + "eVOC (Expressed Sequence Annotation for Humans)" . + . + "false"^^ . + . + . + . + . + "AGRICOLA (AGRICultural OnLine Access) serves as the catalog and index to the collections of the National Agricultural Library, as well as a primary public source for world-wide access to agricultural information. The database covers materials in all formats and periods, including printed works from as far back as the 15th century."^^ . + . + . + "RiceNetDB Compound" . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . + . + . + "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . + . + "false"^^ . + "http://www.guidetopharmacology.org/GRAC/LigandListForward?database=all"^^ . + . + . + . + "0001927"^^ . + "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/thornton-srv/databases/MACiE/index.html"^^ . + "http://aber-owl.net" . + "http://cellimagelibrary.org/images/$1"^^ . + . + . + . + . + . + . + . + "3hB06"^^ . + "false"^^ . + . + . + "Gazetteer" . + "MCDS_S_0000000001"^^ . + . + . + . + . + "^WB[A-Z][a-z]+\\d+$"^^ . + "Zebrafish Phenotype Ontology" . + . + . + "REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data."^^ . + . + . + "http://europepmc.org/articles/$1"^^ . + . + . + . + . + "http://func.mshri.on.ca/mouse/"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + "Unipathway" . + "http://www.pazar.info/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^G\\d+$"^^ . + . + . + . + "false"^^ . + . + . + . + . +_:Ncf9a92a673f44ee6b9624d114fb8704c "Plant Ontology Administrators" . + "Encyclopedia of DNA Elements" . + . + "https://orcid.org/$1"^^ . + "false"^^ . + . + "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^JCGG-STR\\d{6}$"^^ . + . + . + . + . + "The Brenda tissue ontology is a structured controlled vocabulary eastablished to identify the source of an enzyme cited in the Brenda enzyme database. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms."^^ . + . + . + . + "Unified Medical Language System Atomic Unique Identifier" . + . + . + . + "false"^^ . + "http://www.wikigenes.org/"^^ . + _:Naab6944c589a4e388b5102c114aedfe1 . + . + . + . + "^r3d\\d{9,9}$"^^ . + . + . + . + . + . + "http://multicellds.org/MultiCellDB.php"^^ . + . + . + . + "https://ocid.ontochem.com/prefname?ocid=$1"^^ . + . + . + "false"^^ . + . + . + "ECOLI:CYT-D-UBIOX-CPLX"^^ . + . + . + "0459895"^^ . + "O08709"^^ . + "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . + . + . + "2244"^^ . + "UniRule" . + . + . + . + "false"^^ . + . + "An ontology for the characterisation of the roles of agents – people, corporate bodies and computational agents in the publication process. These agents can be, e.g. authors, editors, reviewers, publishers or librarians."^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . + "Network Data Exchange" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . + . + . + . + . + . + "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . + . + "https://rnacentral.org/rna/$1"^^ . + "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . + . + "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . + . + "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . + "TA14985"^^ . + "https://www.ncbi.nlm.nih.gov/books"^^ . + . + "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery."^^ . + "The Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease"^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + "false"^^ . + . + "1023371"^^ . + "false"^^ . + "^\\w+$"^^ . + . + . + . + . + . + "https://gen3.theanvil.io"^^ . + . + . + . + . + . + "602"^^ . + . + . + . + . + . + . + . + "enviPath" . + . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references rules."^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "The Signaling Pathways Project is an integrated 'omics knowledgebase based upon public, manually curated transcriptomic and cistromic (ChIP-Seq) datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Our goal is to create a resource where scientists can routinely generate research hypotheses or validate bench data relevant to cellular signaling pathways."^^ . + . + . + "Probability Distribution Ontology" . + . + . + "false"^^ . + . + "The post-translational modifications used in the UniProt knowledgebase (Swiss-Prot and TrEMBL). The definition of the post-translational modifications usage as well as other information is provided in the following format"^^ . + "The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins."^^ . + . + "Raymond Lee" . + "false"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . + . + . + "78073"^^ . + "https://www.ebi.ac.uk/biomodels/"^^ . + "00000000"^^ . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/SEP_$1"^^ . + "false"^^ . + . + . + "Gene Expression Ontology"^^ . + "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . + . + . + "^(MNXR\\d+|EMPTY)$"^^ . + . + . + . +_:Nb4b44e0828c943bfbebdd12972a19af7 "Thorsten Heinrich" . + . + . + . + . + . + . + . + . + . + . + . + "http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en"^^ . + . + . + "^\\w+$"^^ . + . + . + . + . + . + "CADAFLAT00006211"^^ . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + . + . + "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . + . + "lectins/172"^^ . + "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . + "^\\d+$"^^ . +_:N1c1286af71f04954ae8d36f0142abbb3 "David Blackburn" . + . + . + "An ontology that enables the metadata properties of the DataCite Metadata Schema Specification (i.e., a list of metadata properties for the accurate and consistent identification of a resource for citation and retrieval purposes) to be described in RDF."^^ . + . + "https://datanator.info/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "https://www.hu-berlin.de/?set_language=en&cl=en"^^ . + . + . + . + . + "^.*?--%3E.*?$"^^ . + "2224"^^ . + . + . + . + . + . + "^[0-9a-zA-Z]+$"^^ . + . + "090701"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "GOLD genome" . + . + . + . + . + "817732"^^ . + "0000019"^^ . + . + . + "Logical Observation Identifiers Names and Codes" . + . + . + . + . + . + . + "^GLDS-\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://github.com/biolink/biolink-model" . + "^PROB_c\\d+$"^^ . + . + "https://www.w3.org/TR/rdf-schema/"^^ . + . + . + "title"^^ . + . + . + . + . + "Protein Ontology" . + "^\\d+$"^^ . + "^[A-Za-z0-9]+$"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . + . +_:N01ec5917f175401382cf32118f4788a1 "Jonathan Bard" . + "International Standard Serial Number" . + . + . + "http://purl.obolibrary.org/obo/SYMP_$1"^^ . + . + . + . + . + . + . + . + . + . + "https://www.ndexbio.org/viewer/networks/$1"^^ . + . + "false"^^ . + "Classification of Transcription Factors in Mammalia" . + "http://www.atol-ontology.com"^^ . + "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides locus information in RAP-DB."^^ . + . + "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . + "https://www.vmh.life/"^^ . + . + . + "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . + . + "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . + . + . + . + . + . + . + "osa-miR446"^^ . + . + . + "Novus Biologicals" . + . + . + . + "Phenotype And Trait Ontology" . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + "A*01:01:01:01"^^ . + . + "false"^^ . + . + . + "http://ifomis.org/bfo/"^^ . + "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . + . + . + . + "https://www.ebi.ac.uk/miriam/main/$1"^^ . + "0003463"^^ . + . + . + "992"^^ . + . + . + . + "Clinical measurement ontology" . + . + "PeptideAtlas" . + "TTD Target" . + . + "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . + . + "PIR Superfamily Classification System" . + . + . + "0000001"^^ . + "National Drug Data File" . + "AKR"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "https://www.uniprot.org"^^ . + . + . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "CPD-10330"^^ . + . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . + . + . + "http://jaxmice.jax.org/strain/$1.html"^^ . + . + . + . + . + . + . + . + . . - . - . - . - "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . - . - . - "http://www.genome.jp/kegg/drug/environ.html"^^ . - . - "Paragraph"^^ . - . - . - . - . - . - "Compositional Dietary Nutrition Ontology" . - . - . - . - . - . - . - . - . - "COG0001"^^ . - . - "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . - . - . - . - . - . - . - . - "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . - . - . - "GLIDA GPCR" . - . - . - . - . - "false"^^ . - . - . - "decimal"^^ . - . - . - . - . - . + . + "Rat Genome Database qTL" . + . + "^\\d+$"^^ . + "https://bitbucket.org/hegroup/ogg"^^ . + . + "https://www.scopus.com"^^ . + "http://jcggdb.jp/idb/jcggdb/$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "T06648"^^ . + . + . + . + "false"^^ . + "^T3D\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + "Human Protein Reference Database" . + . + "http://www.drugbank.ca/biodb/bio_entities/$1"^^ . + . + "https://biopragmatics.github.io/debio/$1"^^ . + . + . + . + "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . + . + "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . + . + . + . + . + . + . + . + "^PA\\w+$"^^ . + . + "false"^^ . + . + "https://www.ebi.ac.uk/gxa/genes/$1"^^ . + "false"^^ . + . + "SMP0000219"^^ . + . + "false"^^ . + . + . + "Minimum Anformation About a Phylogenetic Analysis Ontology" . + "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . + "false"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . + . + . + "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . + . + . + . + . + . + . + . + . + . + . + "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . + . + "https://github.com/geneontology/go-ontology"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "Cluster of orthologous genes" . + . + "http://environmentontology.github.io/gaz/"^^ . + "false"^^ . + . + . + . + . + . + "http://www.fludb.org/"^^ . + . + . + . + . + . + . "https://www.aapc.com"^^ . - . - . - . - "An ontology of physico-chemical methods and properties."^^ . - . - . - . - . - "00056"^^ . - "https://panoramaweb.org/$1.url"^^ . - . - "http://purl.obolibrary.org/obo/OGSF_$1"^^ . - "https://www.opengalen.org"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "^\\d+$"^^ . - "https://spdx.org/licenses/$1"^^ . - . - . - . - . - "Xenbase" . - . - . - . - . - . - . - . - "Ensembl Plants" . - "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . - . - . - . - . - . - . - "Fossilworks Taxon" . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - "Animal TFDB Family" . - . - . - . - . - "http://sabiork.h-its.org/"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "iNaturalist Taxonomy" . - "^(imp|gen)\\d{5}$"^^ . - "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . - . - . - "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . - "https://omim.org/phenotypicSeries/$1"^^ . - . - . - "^\\w+$"^^ . - "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . - . - . - "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . - "Malaria Ontology" . - "Database of Escherichia coli Sequence and Function" . - . - . - "International Geo Sample Number" . - . - . - "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . - . + . + . + "0000319"^^ . + "^\\d+$"^^ . + "false"^^ . + . + . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . + "^\\d{7}$"^^ . + "BitterDB Receptor" . + . + . + "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . + . + "^\\d{7}$"^^ . + "https://w3id.org/reproduceme/research"^^ . + "Microarray experimental conditions" . + . + . + . + . + . + . + . + "The Drug-Drug Interactions Ontology" . + . + . + . + "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . + "https://www.ebi.ac.uk/intact/"^^ . + . + . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . + . + . + . + "Funding, Research Administration and Projects Ontology" . + "Software Heritage" . + "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . + . + . + . + "https://github.com/obophenotype/provisional_cell_ontology"^^ . + . + . + "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Antibiotic Resistance Genes Database" . + "https://www.nlm.nih.gov/research/umls/rxnorm/sourcereleasedocs/mmsl.html"^^ . + . + . + . + . + "SNR17A"^^ . + . + "BiGG Model" . + . + "https://www.ncbi.nlm.nih.gov/nucest"^^ . + . + . + . + . + " http://edamontology.org" . + . + "https://www.uniprot.org/journals/$1"^^ . + . + . + . + "Adrien Rougny" . + "https://scicrunch.org/browse/resourcedashboard"^^ . + . + "WikiGenes" . + "^\\d{5}$"^^ . + "true"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . + . + "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https%3A%2F%2Fai-strategies.org%2Fontology%2F$1"^^ . + "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Gene Ontology Causal Assembly Model" . + . + "Bgee family" . + . + . + . + . + . + . + . + "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . + . + . + . + "^[A-Za-z-0-9]+$"^^ . + "true"^^ . + . + "http://purl.obolibrary.org/obo/TO_$1"^^ . + "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . + "FishBase" . + . + . +_:N727c7ef1cd614439b275141a746eb837 "WikiData Support" . + . + . + "ANOVA"^^ . + "EST database maintained at the NCBI." . + . + "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . + "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . + "https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo"^^ . + . + . + . + "http://www.candidagenome.org/"^^ . + . + . + . + . + . + . + "ToxoDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + . + "http://purl.obolibrary.org/obo/FBdv_$1"^^ . + . + . + "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . + . + . + "Terminology of Anatomy of Human Embryology" . + . + . + . + "STOREDB at University of Cambridge" . + . + "74"^^ . + . + . + "http://rdfs.org/ns/void#$1"^^ . + . + "Animal Genome Sheep QTL" . + . + "Mike Tyers" . + . + . + "46"^^ . + . + "cpd15380"^^ . + . + . + . + . + . + . + . + . + . + "Human Ancestry Ontology" . + "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . + . + . + . + . + . + . + "Gene Ontology Database references" . + . + . + "false"^^ . + . + . + . + . + . + . + . . - . - . - . - "RiceNetDB miRNA" . - . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - . - "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . - . - . - "International Classification of Diseases, 11th Revision" . - . - . - . - . - . - . - . - . - "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . - . - . - "Unimod protein modification database for mass spectrometry" . - . - . - . - . - . - . - . - . - . - . - "L000001"^^ . - . - "true"^^ . - "http://www.t3db.org/"^^ . - "The Vaccine Ontology (VO) is a biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine annotation, integrate various vaccine data, and support computer-assisted reasoning. VO supports basic vaccine R&D and clincal vaccine usage. VO is being developed as a community-based ontology with support and collaborations from the vaccine and bio-ontology communities."^^ . - "false"^^ . - "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . - . - . - . - "Collection of European paediatric cardiac coding files"^^ . - . - . - "Sea lice (Lepeophtheirus salmonis and Caligus species) are the major pathogens of salmon, significantly impacting upon the global salmon farming industry. Lice control is primarily accomplished through chemotherapeutants, though emerging resistance necessitates the development of new treatment methods (biological agents, prophylactics and new drugs). LiceBase is a database for sea lice genomics, providing genome annotation of the Atlantic salmon louse Lepeophtheirus salmonis, a genome browser, and access to related high-thoughput genomics data. LiceBase also mines and stores data from related genome sequencing and functional genomics projects."^^ . - . - . - . - "The VIRsiRNA database contains details of siRNA/shRNA which target viral genome regions. It provides efficacy information where available, as well as the siRNA sequence, viral target and subtype, as well as the target genomic region."^^ . - "Universal Spectrum Identifier" . - . - . - "Pathway ontology" . - . - "http://www.w3.org/ns/activitystreams#$1"^^ . - . - "Gender, Sex, and Sexual Orientation Ontology" . - "false"^^ . - . - . - . + . + "true"^^ . + . + "AP011135"^^ . + . + "false"^^ . + . + . + "0007807"^^ . + . + "^PAR:\\d+$"^^ . + . + "sbgn.er.level-1.version-1.2"^^ . + "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . + "https://flybase.org/reports/FBtc$1"^^ . + "http://tfclass.bioinf.med.uni-goettingen.de"^^ . + . + . + "Cell line collections"^^ . + "Reagent Ontology" . + . + . + . + . + "false"^^ . + . + "OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE). "^^ . + "https://fairsharing.org/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://bioregistry.io/schema/#$1"^^ . + . + "false"^^ . + . + "Fyler" . + . + . + . + "Bgee organ" . + . + "1000"^^ . + . + . + "http://edamontology.org"^^ . + "false"^^ . + . + . + . + "^EB\\d+$"^^ . + "Ontology for the Anatomy of the Insect SkeletoMuscular system" . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "http://pid.nci.nih.gov/"^^ . + "ViralZone" . + . + . + . + . + . + . + "1018"^^ . + . + . + . + . + . + . + . + . + . + "InChI" . + . + . + . + "^PR[0-9]{6}$"^^ . + . + . + . + . + "SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web"^^ . + "false"^^ . + . + . + . + . + "^RC\\d+$"^^ . + . + . + . + . + "9781584885658"^^ . + . + . + "The Coriell Cell Repositories provide essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing cell cultures and DNA derived from cell cultures. These collections, supported by funds from the National Institutes of Health (NIH) and several foundations, are extensively utilized by research scientists around the world."^^ . + . + . + . + . + "oai:cwi.nl:4725"^^ . + "^\\d+$"^^ . + . + "http://purl.obolibrary.org/obo/FBcv_$1"^^ . + . + "http://purl.obolibrary.org/obo/MAT_$1"^^ . + "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA expression."^^ . + . + "26"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl?language=en"^^ . + . + "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . + . + . + . + . + . + "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . + "^MINT\\-\\d{1,7}$"^^ . + . + "false"^^ . + . + . + . + "https://www.arraymap.org/pgx:$1"^^ . + "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . + "Zebrafish Information Network Gene" . + "false"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . + . + . + . + . + . . - . - . - . -_:N1ba6405f9f084822bd133523fd7c1e55 "Onard Mejino" . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - "Cell line collections"^^ . - . - "https://github.com/OpenBEL/resource-generator/blob/master/datasets/selventa-protein-families.txt"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . - . - "^\\w+$"^^ . - . - . - . - . - "BiGG Compartment" . - "Reagent Ontology" . - . - . - "false"^^ . - . - "http://www.phosphosite.org/homeAction.do"^^ . - . - . - . - "https://tripod.nih.gov/bioplanet/"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "Human Pluripotent Stem Cell Registry" . - . - "https://www.wikidata.org/wiki/Property:$1"^^ . - "https://lincs.hms.harvard.edu/db/sm/$1"^^ . - . - . - . - "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . - "BioGRID Interactions" . - . - "http://www.cabri.org/"^^ . - . - "MOL000160"^^ . - "http://www.genome.jp/kegg/catalog/org_list3.html"^^ . - "0000339"^^ . + . + "^\\w+$"^^ . + "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . + "^(ENSFM|ENSGTV:)\\d+$"^^ . + . + "5.1"^^ . + "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . + . + . + "Tribolium Genome Database -- Insertion" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.unimod.org/"^^ . + . + . + _:Neeb545bd1981481a87d11abe1a29209a . + . + . + . + . + . + . + . + . + "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + "https://morpheus.gitlab.io/"^^ . + . + "PS00001"^^ . + "false"^^ . + . + "MedlinePlus Health Topics" . + . + "^\\w+$"^^ . + . + . + "0001157"^^ . + "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . + . + . + . + "PA447218"^^ . + "http://psb.kobic.re.kr/STAP/refinement/"^^ . + . + . + . + . + "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . + "LinJ.20.0070"^^ . + . + "false"^^ . + "78"^^ . + . + . + . + "https://commonchemistry.cas.org/detail?ref=$1"^^ . + . + . + . + . + . + . + "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . + . + "C023"^^ . + . + . + . + "false"^^ . + "http://cdb.ics.uci.edu/"^^ . + . + "^\\d{7}$"^^ . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + "false"^^ . + . + "https://www.eionet.europa.eu/gemet/en/themes/"^^ . + "Transcription Factor Database" . + . + . + "1"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + "DIDs are an effort by the W3C Credentials Community Group and the wider Internet identity community to define identifiers that can be registered, updated, resolved, and revoked without any dependency on a central authority or intermediary."^^ . + . + . + . + "Assembly" . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "^[A-Z]+[A-Z-0-9]{2,}$"^^ . + . + . + "The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs."^^ . + "Viral Bioinformatics Resource Center" . + . + . + "false"^^ . + . + "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite. Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours."^^ . + . + . + . + "https://www.pgscatalog.org/pgs/$1"^^ . + "https://biopragmatics.github.io/debio"^^ . + . + "false"^^ . + "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . + "DBPedia Ontology" . + . + "977869"^^ . + "http://proconsortium.org"^^ . + . + "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/VSAO_$1"^^ . + "false"^^ . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + . + . + . + . + . + . + "https://smid-db.org/smid/$1"^^ . + "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . + "Xenopus Anatomy Ontology" . + . + . + . + . + . + "https://jcoin.datacommons.io"^^ . + . + . + "false"^^ . + . + . + . + "https://metabolome.cgfb.u-bordeaux.fr/"^^ . + . + . + . + . + "SchemaDefinition"^^ . + . + . + . + . + "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . + . + . + "Karen Eilbeck" . + "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . + "false"^^ . + "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . + . + "false"^^ . + . + "https://www.ebi.ac.uk/intact/interaction/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://sorgerlab.github.io/famplex/"^^ . + "An experimental run, served thrugh the ENA"^^ . + "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . + . + . + . + "https://bioregistry.io/metaregistry/go/$1"^^ . + . + "false"^^ . + . + . + "false"^^ . + "http://func.mshri.on.ca/yeast"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . + . + "false"^^ . + "10531"^^ . + "https://cropontology.org/ontology/CO_334/Cassava"^^ . + . + "^\\d+$"^^ . + "Long Term Ecological Research Controlled Vocabulary" . + "http://arabidopsis.org/index.jsp"^^ . + . + "001"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "https://github.com/OpenLHS/LABO"^^ . + . + "EcoliWiki is a wiki-based resource to store information related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. This collection references genes."^^ . + "false"^^ . + . + . + "Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis."^^ . + . + . + . + "Ontology of Genetic Susceptibility Factor" . + . + . + . + . + . + . + . + "https://mouse.brain-map.org"^^ . + . + . + . + . + "false"^^ . + . + "REBASE restriction enzyme database" . + . + "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . + "Contains entries for various database identifiers" . + "https://bioregistry.io/registry/$1" . + "Tissue List" . + . + "ENVO" . + "version 2019 - pvs"^^ . + . + . + "None"^^ . + "false"^^ . + "https://github.com/SciCrunch/NIF-Ontology"^^ . + . + . + . + . + "4447"^^ . + "CAL0003079"^^ . + . + "false"^^ . + . + "^([A-H,Y]|[A-H, Y]\\d{2}|[A-H, Y]\\d{2}[A-Z]|[A-H, Y]\\d{2}[A-Z]\\d{1,3}|[A-H, Y]\\d{2}[A-Z]\\d{1,3}(\\/)?\\d{2,})$"^^ . + . + "RL3R1_HUMAN"^^ . + "^\\d+$"^^ . + . + . + . + . + "OSC1416"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "Variation Ontology" . + . + . + . + . + . + "http://www.pharmgkb.org/"^^ . + "^\\d{7}$"^^ . + . + "http://db-mml.sjtu.edu.cn/ICEberg/browse_result.php?type=fam&fam_id=$1"^^ . + "http://urgi.versailles.inra.fr/Genefarm/"^^ . + . + . + . + . + . + . + . + . + . + . + "P0DP23"^^ . + "http://purl.obolibrary.org/obo/AGRO_$1"^^ . + "http://cellimagelibrary.org/"^^ . + . + "0000001"^^ . + "^\\d{7}$"^^ . + "Simple Knowledge Organization System" . + "BitterDB Compound" . + . + . + . + . + "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . + . + . + . + . + "false"^^ . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . + . + "RepeatsDB Protein" . + . + . + . + . + . + . . - . - . - . - . - . - . - . - . - . - . - . - . - . - "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . - . - . - . - . - . - . - "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . - . - . - "Signaling Network Open Resource" . - . - . - . - "CL0192"^^ . - . - . - . - . - "https://neurovault.org/images/$1"^^ . + . + "http://topdb.enzim.hu/?m=show&id=$1"^^ . + . + "^\\d{7}$"^^ . + . + "00000098"^^ . + . + . + "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . + "JRC Data Catalogue" . + . + . + . + . + "Gerhard Mayer" . + . + . + . + . + . + . + . + . + . + . + . + "SwissRegulon" . + . + . + . +_:N77d13c0a01d940f5b35b8b27df76c01d "Jonathan Bard" . + . + . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + "^[a-zA-Z0-9-_]+$"^^ . + . + . + "http://www.homd.org/index.php"^^ . + . + . + . + . + . + . + "^\\w+_COVID19_[-\\w]+$"^^ . + . + . + "Ontology for General Medical Science" . + . + "GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the \"Pathogen Genomics\" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed."^^ . + "http://pantree.org/"^^ . + . + . + . + "Bacillus subtilis genome sequencing project" . + "436605"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://data.bloodpac.org/."^^ . + . + "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . + . + . + . + "Small Angle Scattering Biological Data Bank" . + . + . + . + . + "53504"^^ . + . + "http://www.receptome.org"^^ . + . + . + "false"^^ . + . + . + "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . + "Clare Pilgrim" . + "false"^^ . + . + . + "https://www.ebi.ac.uk"^^ . + . + . + "Foundational Model of Anatomy" . + . + . + "arXiv" . + . + . + . + . + "GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest."^^ . + . + . + . + . + . + . + "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . + . + . + . + . + . + "Q5BJF6-3"^^ . + . + . + "International Standard Book Number" . + "^\\d+$"^^ . + . + . + . + . + "Bibliometric Data Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "614"^^ . + . + . + . + "GitHub is an online host of Git source code repositories."^^ . + . + "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . + "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . + . + . + . + . + . + . + . + "/12345/fk1234"^^ . + "9002859"^^ . + . + . + "^10.\\w{4}/\\w{10}$"^^ . + . + . + . + "https://flowrepository.org/id/$1"^^ . + . + . + "https://books.google.com/books?id=$1"^^ . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references reactions."^^ . + . + . + . + . diff --git a/exports/rdf/bioregistry.ttl b/exports/rdf/bioregistry.ttl index 606a942ef..41530db1f 100644 --- a/exports/rdf/bioregistry.ttl +++ b/exports/rdf/bioregistry.ttl @@ -249,8 +249,7 @@ bioregistry.schema:0000022 a rdf:Property ; rdfs:domain bioregistry.schema:0000002 ; rdfs:range bioregistry.schema:0000020 . -orcid:0000-0001-9439-5346 rdfs:label "Benjamin Gyori", - "Benjamin M. Gyori" ; +orcid:0000-0001-9439-5346 rdfs:label "Benjamin M. Gyori" ; dcterms:contributor bioregistry:bko, bioregistry:casspc, bioregistry:cordis.project, @@ -5207,7 +5206,7 @@ bioregistry:gno a bioregistry.schema:0000001 ; foaf:homepage "https://gnome.glyomics.org/"^^xsd:string ; bioregistry.schema:0000005 "10004892"^^xsd:string ; bioregistry.schema:0000006 "http://purl.obolibrary.org/obo/GNO_$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d{8}$"^^xsd:string ; + bioregistry.schema:0000008 "^(\\d{8}|(\\w+\\d+\\w+))$"^^xsd:string ; bioregistry.schema:0000012 false ; bioregistry.schema:0000019 orcid:0000-0001-5168-3196 . @@ -8740,7 +8739,7 @@ bioregistry:npo a bioregistry.schema:0000001 ; bioregistry.schema:0000005 "1731"^^xsd:string ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 false ; - bioregistry.schema:0000019 [ rdfs:label "Nathan Baker" ] . + bioregistry.schema:0000019 orcid:0000-0002-5892-6506 . bioregistry:nuclearbd a bioregistry.schema:0000001 ; rdfs:label "NucleaRDB" ; @@ -9841,19 +9840,6 @@ bioregistry:phenolexplorer a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . -bioregistry:phenx a bioregistry.schema:0000001 ; - rdfs:label "PhenX Toolkit" ; - dc:description "A Web-based catalog of recommended measurement protocols"^^xsd:string ; - dcterms:isPartOf bioregistry.metaresource:bioregistry ; - skos:exactMatch aberowl:PHENX, - bioportal:PHENX, - fairsharing:FAIRsharing.y5jcwa ; - foaf:homepage "https://www.phenxtoolkit.org/"^^xsd:string ; - bioregistry.schema:0000005 "130502"^^xsd:string ; - bioregistry.schema:0000006 "https://www.phenxtoolkit.org/protocols/view/$1"^^xsd:string ; - bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; - bioregistry.schema:0000012 false . - bioregistry:phosphopoint.kinase a bioregistry.schema:0000001 ; rdfs:label "PhosphoPoint Kinase" ; dc:description "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^xsd:string ; @@ -13403,6 +13389,8 @@ orcid:0000-0002-5316-1399 rdfs:label "Sebastian Koehler" . orcid:0000-0002-5714-991X rdfs:label "Chris Stoeckert" . +orcid:0000-0002-5892-6506 rdfs:label "Nathan Baker" . + orcid:0000-0002-6020-5919 rdfs:label "Elizabeth Arnaud" . orcid:0000-0002-6379-8932 rdfs:label "Laurel Cooper" . @@ -14085,6 +14073,8 @@ aberowl:TEDDY dcterms:isPartOf bioregistry.metaresource:aberowl . aberowl:TGMA dcterms:isPartOf bioregistry.metaresource:aberowl . +aberowl:TIME dcterms:isPartOf bioregistry.metaresource:aberowl . + aberowl:TO dcterms:isPartOf bioregistry.metaresource:aberowl . aberowl:TRANS dcterms:isPartOf bioregistry.metaresource:aberowl . @@ -16023,6 +16013,8 @@ bioportal:TEDDY dcterms:isPartOf bioregistry.metaresource:bioportal . bioportal:TGMA dcterms:isPartOf bioregistry.metaresource:bioportal . +bioportal:TIME dcterms:isPartOf bioregistry.metaresource:bioportal . + bioportal:TRANS dcterms:isPartOf bioregistry.metaresource:bioportal . bioportal:TTO dcterms:isPartOf bioregistry.metaresource:bioportal . @@ -17915,6 +17907,8 @@ biolink:isni dcterms:isPartOf bioregistry.metaresource:biolink . biolink:issn dcterms:isPartOf bioregistry.metaresource:biolink . +biolink:linkml dcterms:isPartOf bioregistry.metaresource:biolink . + biolink:medgen dcterms:isPartOf bioregistry.metaresource:biolink . biolink:metacyc.reaction dcterms:isPartOf bioregistry.metaresource:biolink . @@ -20825,6 +20819,15 @@ bioregistry:dbest a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^([A-Z]+)?\\d+(\\.\\d+)?$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:dbo a bioregistry.schema:0000001 ; + rdfs:label "DBPedia Ontology" ; + dc:description "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + foaf:homepage "https://dbpedia.org/ontology"^^xsd:string ; + bioregistry.schema:0000005 "careerPrizeMoney"^^xsd:string ; + bioregistry.schema:0000006 "https://dbpedia.org/ontology/$1"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:dbsnp a bioregistry.schema:0000001 ; rdfs:label "NCBI dbSNP" ; dc:description "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^xsd:string ; @@ -21753,6 +21756,16 @@ bioregistry:goeco a bioregistry.schema:0000001 ; bioregistry.schema:0000005 "IPI"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:google.book a bioregistry.schema:0000001 ; + rdfs:label "Google Books" ; + dc:description "Search the world's most comprehensive index of full-text books."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + skos:exactMatch wikidata:P675 ; + foaf:homepage "https://books.google.com"^^xsd:string ; + bioregistry.schema:0000005 "qafeQTWIWmcC"^^xsd:string ; + bioregistry.schema:0000006 "https://books.google.com/books?id=$1"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:google.patent a bioregistry.schema:0000001 ; rdfs:label "Google Patents" ; dc:description "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^xsd:string ; @@ -21826,6 +21839,16 @@ bioregistry:gtr a bioregistry.schema:0000001 ; bioregistry.schema:0000012 false ; bioregistry.schema:0000018 bioregistry:mondo . +bioregistry:hathitrust a bioregistry.schema:0000001 ; + rdfs:label "Hathi Trust Digital Library" ; + dc:description "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + foaf:homepage "https://www.hathitrust.org"^^xsd:string ; + bioregistry.schema:0000005 "008893080"^^xsd:string ; + bioregistry.schema:0000006 "https://catalog.hathitrust.org/Record/$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:hgnc.genegroup a bioregistry.schema:0000001 ; rdfs:label "HGNC Gene Group" ; dc:description "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^xsd:string ; @@ -22358,6 +22381,16 @@ bioregistry:kupo a bioregistry.schema:0000001 ; bioregistry.schema:0000012 true ; bioregistry.schema:0000018 bioregistry:cl . +bioregistry:langual a bioregistry.schema:0000001 ; + rdfs:label "Langua aLimentaria Thesaurus" ; + dc:description "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + foaf:homepage "https://www.langual.org"^^xsd:string ; + bioregistry.schema:0000005 "B2067"^^xsd:string ; + bioregistry.schema:0000006 "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^xsd:string ; + bioregistry.schema:0000008 "^B\\d+$"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:lincs.smallmolecule a bioregistry.schema:0000001 ; rdfs:label "LINCS Small Molecule" ; dc:description "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^xsd:string ; @@ -22371,6 +22404,17 @@ bioregistry:lincs.smallmolecule a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^LSM-\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:linkml a bioregistry.schema:0000001 ; + rdfs:label "LinkML" ; + dc:description "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + skos:exactMatch biolink:linkml ; + foaf:homepage "https://linkml.io/linkml-model/docs/SchemaDefinition/"^^xsd:string ; + bioregistry.schema:0000005 "SchemaDefinition"^^xsd:string ; + bioregistry.schema:0000006 "https://w3id.org/linkml/$1"^^xsd:string ; + bioregistry.schema:0000012 false ; + bioregistry.schema:0000019 orcid:0000-0002-6601-2165 . + bioregistry:lipidmaps a bioregistry.schema:0000001 ; rdfs:label "LIPID MAPS" ; dc:description "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^xsd:string ; @@ -23285,6 +23329,19 @@ bioregistry:pharmacodb.tissue a bioregistry.schema:0000001 ; bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:phenx a bioregistry.schema:0000001 ; + rdfs:label "PhenX Toolkit" ; + dc:description "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + skos:exactMatch aberowl:PHENX, + bioportal:PHENX, + fairsharing:FAIRsharing.y5jcwa ; + foaf:homepage "https://www.phenxtoolkit.org/"^^xsd:string ; + bioregistry.schema:0000005 "130502"^^xsd:string ; + bioregistry.schema:0000006 "https://www.phenxtoolkit.org/protocols/view/$1"^^xsd:string ; + bioregistry.schema:0000008 "^\\d+$"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:phipo a bioregistry.schema:0000001 ; rdfs:label "Pathogen Host Interaction Phenotype Ontology" ; dc:description "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^xsd:string ; @@ -23831,6 +23888,18 @@ bioregistry:thermofisher a bioregistry.schema:0000001 ; bioregistry.schema:0000006 "https://www.thermofisher.com/antibody/product/$1"^^xsd:string ; bioregistry.schema:0000012 false . +bioregistry:time a bioregistry.schema:0000001 ; + rdfs:label "Time Ontology in OWL" ; + dc:description "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars."^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + skos:exactMatch aberowl:TIME, + bioportal:TIME, + fairsharing:FAIRsharing.hw3bh2 ; + foaf:homepage "https://www.w3.org/TR/owl-time/"^^xsd:string ; + bioregistry.schema:0000005 "DateTimeDescription"^^xsd:string ; + bioregistry.schema:0000006 "http://www.w3.org/2006/time#$1"^^xsd:string ; + bioregistry.schema:0000012 false . + bioregistry:tkg a bioregistry.schema:0000001 ; rdfs:label "Tohoku University cell line catalog" ; dc:description "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^xsd:string ; @@ -24963,6 +25032,8 @@ fairsharing:FAIRsharing.hpvbxb dcterms:isPartOf bioregistry.metaresource:fairsha fairsharing:FAIRsharing.hsbpq3 dcterms:isPartOf bioregistry.metaresource:fairsharing . +fairsharing:FAIRsharing.hw3bh2 dcterms:isPartOf bioregistry.metaresource:fairsharing . + fairsharing:FAIRsharing.i1F3Hb dcterms:isPartOf bioregistry.metaresource:fairsharing . fairsharing:FAIRsharing.j0ezpm dcterms:isPartOf bioregistry.metaresource:fairsharing . @@ -28913,6 +28984,8 @@ wikidata:P6689 dcterms:isPartOf bioregistry.metaresource:wikidata . wikidata:P671 dcterms:isPartOf bioregistry.metaresource:wikidata . +wikidata:P675 dcterms:isPartOf bioregistry.metaresource:wikidata . + wikidata:P6778 dcterms:isPartOf bioregistry.metaresource:wikidata . wikidata:P683 dcterms:isPartOf bioregistry.metaresource:wikidata . @@ -31497,10 +31570,6 @@ bioregistry:iao a bioregistry.schema:0000001 ; bioregistry:xpo ; bioregistry.schema:0000019 orcid:0000-0002-2999-0103 . -orcid:0000-0002-6601-2165 rdfs:label "Chris Mungall" ; - dcterms:contributor bioregistry:insdc.run, - bioregistry:wwf.ecoregion . - bioregistry:pcl a bioregistry.schema:0000001 ; rdfs:label "Provisional Cell Ontology" ; dc:description "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^xsd:string ; @@ -31529,6 +31598,10 @@ bioregistry:pcl a bioregistry.schema:0000001 ; bioregistry:uberon ; bioregistry.schema:0000019 orcid:0000-0002-7073-9172 . +orcid:0000-0002-6601-2165 rdfs:label "Chris Mungall" ; + dcterms:contributor bioregistry:insdc.run, + bioregistry:wwf.ecoregion . + bioregistry:ecto a bioregistry.schema:0000001 ; rdfs:label "Environmental conditions, treatments and exposures ontology" ; dc:description "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^xsd:string ; @@ -32296,6 +32369,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:cp, bioregistry:credit, bioregistry:datacite, + bioregistry:dbo, bioregistry:dbvar.study, bioregistry:dbvar.variant, bioregistry:ddinter.interaction, @@ -32348,12 +32422,14 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:go.resource, bioregistry:goche, bioregistry:goeco, + bioregistry:google.book, bioregistry:graingenes.reference, bioregistry:graingenes.symbol, bioregistry:gramene.reference, bioregistry:grassbase, bioregistry:gsfa, bioregistry:gtr, + bioregistry:hathitrust, bioregistry:hba, bioregistry:hms.lincs.compound, bioregistry:hog, @@ -32369,6 +32445,8 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:kegg.dgroup, bioregistry:kegg.rclass, bioregistry:kupo, + bioregistry:langual, + bioregistry:linkml, bioregistry:lncipedia, bioregistry:lonza, bioregistry:lpt, @@ -32408,6 +32486,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:pfr, bioregistry:pharmacodb.dataset, bioregistry:pharmacodb.tissue, + bioregistry:phenx, bioregistry:pictar, bioregistry:ppdb, bioregistry:ppr, @@ -32447,6 +32526,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:tgn, bioregistry:th, bioregistry:thermofisher, + bioregistry:time, bioregistry:tkg, bioregistry:ubprop, bioregistry:umls.aui, @@ -32704,6 +32784,7 @@ bioregistry.metaresource:biolink a bioregistry.schema:0000002 ; biolink:isbn, biolink:isni, biolink:issn, + biolink:linkml, biolink:medgen, biolink:metacyc.reaction, biolink:mirbase, @@ -33142,6 +33223,7 @@ bioregistry.metaresource:wikidata a bioregistry.schema:0000002 ; wikidata:P665, wikidata:P6689, wikidata:P671, + wikidata:P675, wikidata:P6778, wikidata:P683, wikidata:P685, @@ -34503,6 +34585,7 @@ bioregistry.metaresource:bioportal a bioregistry.schema:0000002 ; bioportal:TAXRANK, bioportal:TEDDY, bioportal:TGMA, + bioportal:TIME, bioportal:TRANS, bioportal:TTO, bioportal:TXPO, @@ -34824,6 +34907,7 @@ bioregistry.metaresource:aberowl a bioregistry.schema:0000002 ; aberowl:TAXRANK, aberowl:TEDDY, aberowl:TGMA, + aberowl:TIME, aberowl:TO, aberowl:TRANS, aberowl:TTO, @@ -35545,6 +35629,7 @@ bioregistry.metaresource:fairsharing a bioregistry.schema:0000002 ; fairsharing:FAIRsharing.hmgte8, fairsharing:FAIRsharing.hpvbxb, fairsharing:FAIRsharing.hsbpq3, + fairsharing:FAIRsharing.hw3bh2, fairsharing:FAIRsharing.i1F3Hb, fairsharing:FAIRsharing.j0ezpm, fairsharing:FAIRsharing.j0fa1d, @@ -38391,6 +38476,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:dbg2introns, bioregistry:dbgap, bioregistry:dbmhc, + bioregistry:dbo, bioregistry:dbprobe, bioregistry:dbsnp, bioregistry:dbvar.study, @@ -38646,6 +38732,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:gold, bioregistry:gold.genome, bioregistry:gold.meta, + bioregistry:google.book, bioregistry:google.patent, bioregistry:google.scholar, bioregistry:gorel, @@ -38679,6 +38766,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:hamap, bioregistry:hancestro, bioregistry:hao, + bioregistry:hathitrust, bioregistry:hba, bioregistry:hcao, bioregistry:hcpcs, @@ -38815,6 +38903,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:kupo, bioregistry:kyinno, bioregistry:labo, + bioregistry:langual, bioregistry:lbo, bioregistry:lei, bioregistry:lepao, @@ -38831,6 +38920,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:lincs.protein, bioregistry:lincs.smallmolecule, bioregistry:linguist, + bioregistry:linkml, bioregistry:lipidbank, bioregistry:lipidmaps, bioregistry:lipro, @@ -39371,6 +39461,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:th, bioregistry:thermofisher, bioregistry:tigrfam, + bioregistry:time, bioregistry:tkg, bioregistry:tngb, bioregistry:to, diff --git a/exports/rdf/schema.jsonld b/exports/rdf/schema.jsonld index 1f644bcfd..9c8142866 100644 --- a/exports/rdf/schema.jsonld +++ b/exports/rdf/schema.jsonld @@ -13,167 +13,173 @@ }, "@graph": [ { - "@id": "https://bioregistry.io/schema/#0000016", + "@id": "https://bioregistry.io/schema/#0000019", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" + "@value": "The responsible person for a resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has canonical" + "@value": "has responsible" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "https://bioregistry.io/schema/#0000020" } }, { - "@id": "https://bioregistry.io/schema/#0000002", + "@id": "https://bioregistry.io/schema/#0000001", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's metaregistry." + "@value": "A type for entries in the Bioregistry's registry." }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Registry" + "@value": "Resource" } }, { - "@id": "https://bioregistry.io/schema/#0000007", + "@id": "https://bioregistry.io/schema/#0000016", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." + "@value": "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" }, "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000002" + "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has resolver formatter" + "@value": "has canonical" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000006", + "@id": "https://bioregistry.io/schema/#0000011", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." + "@value": "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has provider formatter" + "@value": "provides for" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000001", - "@type": "http://www.w3.org/2000/01/rdf-schema#Class", + "@id": "https://bioregistry.io/schema/#0000006", + "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's registry." + "@value": "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." + }, + "http://www.w3.org/2000/01/rdf-schema#domain": { + "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Resource" + "@value": "has provider formatter" + }, + "http://www.w3.org/2000/01/rdf-schema#range": { + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000022", + "@id": "https://bioregistry.io/schema/#0000012", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The main contact person for a registry" + "@value": "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." }, "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000002" + "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has responsible" + "@value": "is deprecated" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@id": "http://www.w3.org/2001/XMLSchema#boolean" } }, { - "@id": "https://bioregistry.io/schema/#0000011", + "@id": "https://bioregistry.io/schema/#0000017", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." + "@value": "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "provides for" + "@value": "depends on" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000008", + "@id": "https://bioregistry.io/schema/#0000018", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The pattern for identifiers in the given resource" + "@value": "Terms from the source appear in the target resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has pattern" + "@value": "appears in" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000017", + "@id": "https://bioregistry.io/schema/#0000007", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" + "@value": "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." }, "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "https://bioregistry.io/schema/#0000002" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "depends on" + "@value": "has resolver formatter" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000005", + "@id": "https://bioregistry.io/schema/#0000022", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "An identifier for a resource or metaresource." + "@value": "The main contact person for a registry" }, "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "https://bioregistry.io/schema/#0000002" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has example" + "@value": "has responsible" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@id": "https://bioregistry.io/schema/#0000020" } }, { - "@id": "https://bioregistry.io/schema/#0000018", + "@id": "https://bioregistry.io/schema/#0000010", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "Terms from the source appear in the target resource" + "@value": "A download link for the given resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "appears in" + "@value": "has download URL" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { @@ -193,71 +199,65 @@ } }, { - "@id": "https://bioregistry.io/schema/#0000010", + "@id": "https://bioregistry.io/schema/#0000008", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A download link for the given resource" + "@value": "The pattern for identifiers in the given resource" }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has download URL" + "@value": "has pattern" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000012", + "@id": "https://bioregistry.io/schema/#0000005", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." + "@value": "An identifier for a resource or metaresource." }, "http://www.w3.org/2000/01/rdf-schema#domain": { "@id": "https://bioregistry.io/schema/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "is deprecated" + "@value": "has example" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#boolean" + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000019", - "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", + "@id": "https://bioregistry.io/schema/#0000002", + "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "The responsible person for a resource" - }, - "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000001" + "@value": "A type for entries in the Bioregistry's metaregistry." }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "has responsible" - }, - "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@value": "Registry" } }, { - "@id": "https://bioregistry.io/schema/#0000020", + "@id": "https://bioregistry.io/schema/#0000003", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A person" + "@value": "A type for entries in the Bioregistry's collections" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Person" + "@value": "Collection" } }, { - "@id": "https://bioregistry.io/schema/#0000003", + "@id": "https://bioregistry.io/schema/#0000020", "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "A type for entries in the Bioregistry's collections" + "@value": "A person" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Collection" + "@value": "Person" } } ] diff --git a/exports/rdf/schema.nt b/exports/rdf/schema.nt index 83bd23a87..44de5941c 100644 --- a/exports/rdf/schema.nt +++ b/exports/rdf/schema.nt @@ -1,77 +1,77 @@ - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + "Terms from the source appear in the target resource" . + . + . + . + "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . . - "has download URL" . + "The main contact person for a registry" . + . + "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . + "has reviewer" . + "The pattern for identifiers in the given resource" . . - . - . - "A type for entries in the Bioregistry's metaregistry." . - . - "is deprecated" . - . - "appears in" . - . - . - . + "An identifier for a resource or metaresource." . "has canonical" . - . - . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + "The reviewer of a prefix" . . - "A type for entries in the Bioregistry's collections" . - "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - . - "The responsible person for a resource" . - . - . - "Terms from the source appear in the target resource" . + "A download link for the given resource" . . - . - "has example" . - . - "provides for" . - "The main contact person for a registry" . - "has responsible" . - "has responsible" . - . - . - . - "A type for entries in the Bioregistry's registry." . - . - . - "has reviewer" . - . - . + "The responsible person for a resource" . + . + . + . "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix" . "Registry" . + "has provider formatter" . + . + . + "A type for entries in the Bioregistry's collections" . + . . + . + . . - "has provider formatter" . - "The pattern for identifiers in the given resource" . - "Resource" . + . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + "Collection" . . - "Person" . - . - . - . - . + "A type for entries in the Bioregistry's metaregistry." . + . + "depends on" . + "has responsible" . . + . + . + . + . + "has resolver formatter" . + . + "is deprecated" . + . . - "An identifier for a resource or metaresource." . + . + "has download URL" . + . + . + . + "has responsible" . + "Person" . + "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . . - . - "A download link for the given resource" . . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - . - "depends on" . - "A property whose subject is a resource that denotes if it is still available and usable? Currently this is a blanket term for decommissioned, unable to locate, abandoned, etc." . - "A person" . - "Collection" . + . + "Resource" . + . + "provides for" . + . + "has example" . . - . - "has resolver formatter" . - . + . + . "has pattern" . - . - "For resources that do not create their own controlled vocabulary, this relation should be used to point to a different resource that it uses. For example, CTD's gene resource provides for the NCBI Entrez Gene resource." . - "The reviewer of a prefix" . + "appears in" . + "A person" . + "A type for entries in the Bioregistry's registry." . + . + . diff --git a/exports/registry/registry.json b/exports/registry/registry.json index a9275e259..ca4fe9277 100644 --- a/exports/registry/registry.json +++ b/exports/registry/registry.json @@ -2388,9 +2388,9 @@ "orcid": "0000-0002-2118-035X" }, "contributor": { - "email": null, + "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", - "name": "Benjamin Gyori", + "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way.", @@ -3671,6 +3671,15 @@ "name": "Chemical Information Ontology", "pattern": "^\\d{6}$", "preferred_prefix": "CHEMINF", + "providers": [ + { + "code": "semanticscience", + "description": "Legacy URLs before conversion of CHEMINF to OBO PURLs", + "homepage": "http://semanticscience.org", + "name": "Semantic Science", + "uri_format": "http://semanticscience.org/resource/CHEMINF_$1" + } + ], "repository": "https://github.com/semanticchemistry/semanticchemistry", "uri_format": "http://purl.obolibrary.org/obo/CHEMINF_$1", "version": "2.0" @@ -4836,7 +4845,7 @@ "coconut": { "comment": "@mSorok is the dev of the resource, hope I got it right!", "contributor": { - "email": null, + "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" @@ -4953,7 +4962,7 @@ }, "col.taiwan": { "contributor": { - "email": null, + "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" @@ -5155,7 +5164,7 @@ "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", - "name": "Benjamin Gyori", + "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020).", @@ -5945,6 +5954,20 @@ "pattern": "^\\d+$", "preferred_prefix": "dbmhc" }, + "dbo": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki.", + "example": "careerPrizeMoney", + "homepage": "https://dbpedia.org/ontology", + "name": "DBPedia Ontology", + "preferred_prefix": "dbo", + "uri_format": "https://dbpedia.org/ontology/$1" + }, "dbprobe": { "description": "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.", "example": "1000000", @@ -6093,7 +6116,8 @@ "name": "Dublin Core Metadata Vocabulary", "preferred_prefix": "dcterms", "synonyms": [ - "dc.terms" + "dc.terms", + "dct" ], "uri_format": "http://purl.org/dc/terms/$1" }, @@ -9652,7 +9676,7 @@ }, "fossilworks.journal": { "contributor": { - "email": null, + "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" @@ -9677,7 +9701,7 @@ }, "fossilworks.taxon": { "contributor": { - "email": null, + "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" @@ -10877,6 +10901,9 @@ "download_obo": "http://purl.obolibrary.org/obo/gno.obo", "download_owl": "http://purl.obolibrary.org/obo/gno.owl", "example": "10004892", + "example_extras": [ + "G99373GG" + ], "homepage": "https://gnome.glyomics.org/", "license": "CC BY 4.0", "mappings": { @@ -10887,9 +10914,28 @@ "ontobee": "GNO" }, "name": "Glycan Naming and Subsumption Ontology", - "pattern": "^\\d{8}$", + "pattern": "^(\\d{8}|(\\w+\\d+\\w+))$", "preferred_prefix": "GNO", + "providers": [ + { + "code": "gno.structure", + "description": "GNOme structure browser", + "homepage": "https://gnome.glyomics.org/StructureBrowser.html", + "name": "GNOme Structure Viewer", + "uri_format": "https://gnome.glyomics.org/StructureBrowser.html?focus=$1" + }, + { + "code": "gno.composition", + "description": "GNOme composition browser", + "homepage": "https://gnome.glyomics.org/CompositionBrowser.html", + "name": "GNOme Composition Browser", + "uri_format": "https://gnome.glyomics.org/CompositionBrowser.html?focus=$1" + } + ], "repository": "https://github.com/glygen-glycan-data/GNOme", + "synonyms": [ + "gnome" + ], "uri_format": "http://purl.obolibrary.org/obo/GNO_$1", "version": "1.10.0" }, @@ -11142,6 +11188,23 @@ "preferred_prefix": "gold.meta", "uri_format": "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1" }, + "google.book": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Search the world's most comprehensive index of full-text books.", + "example": "qafeQTWIWmcC", + "homepage": "https://books.google.com", + "mappings": { + "wikidata": "P675" + }, + "name": "Google Books", + "preferred_prefix": "google.book", + "uri_format": "https://books.google.com/books?id=$1" + }, "google.patent": { "description": "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.", "example": "US4145692", @@ -11726,6 +11789,21 @@ "uri_format": "http://purl.obolibrary.org/obo/HAO_$1", "version": "2021-03-05" }, + "hathitrust": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world.", + "example": "008893080", + "homepage": "https://www.hathitrust.org", + "name": "Hathi Trust Digital Library", + "pattern": "^\\d+$", + "preferred_prefix": "hathitrust", + "uri_format": "https://catalog.hathitrust.org/Record/$1" + }, "hba": { "contributor": { "email": "cthoyt@gmail.com", @@ -14372,6 +14450,21 @@ "uri_format": "http://purl.obolibrary.org/obo/LABO_$1", "version": "2021-06-08" }, + "langual": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases", + "example": "B2067", + "homepage": "https://www.langual.org", + "name": "Langua aLimentaria Thesaurus", + "pattern": "^B\\d+$", + "preferred_prefix": "langual", + "uri_format": "https://www.langual.org/langual_thesaurus.asp?termid=$1" + }, "lbo": { "contact": { "email": "caripark@iastate.edu", @@ -14648,6 +14741,30 @@ "repository": "https://github.com/github/linguist", "uri_format": "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1" }, + "linkml": { + "comment": "Closes #508", + "contact": { + "email": "cjmungall@lbl.gov", + "github": "cmungall", + "name": "Chris Mungall", + "orcid": "0000-0002-6601-2165" + }, + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks.", + "example": "SchemaDefinition", + "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", + "mappings": { + "biolink": "linkml" + }, + "name": "LinkML", + "preferred_prefix": "linkml", + "uri_format": "https://w3id.org/linkml/$1" + }, "lipidbank": { "description": "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.", "example": "BBA0001", @@ -14795,7 +14912,7 @@ "orcid": "0000-0003-0443-9902" }, "contributor": { - "email": null, + "email": "adriano.rutz@ik.me", "github": "adafede", "name": "Adriano Rutz", "orcid": "0000-0003-0443-9902" @@ -15777,6 +15894,13 @@ "pattern": "^\\d+$", "preferred_prefix": "MGI", "providers": [ + { + "code": "mgi.marker", + "description": "MGI Marker", + "homepage": "http://www.informatics.jax.org/marker", + "name": "MGI Marker", + "uri_format": "http://www.informatics.jax.org/marker/MGI:$1" + }, { "code": "bioentitylink", "description": "MGD through BioEntity Link", @@ -17645,6 +17769,15 @@ "name": "NCI Thesaurus", "pattern": "^C\\d+$", "preferred_prefix": "NCIT", + "providers": [ + { + "code": "evs", + "description": "Links to a no-longer existing OWL file", + "homepage": "https://ncit.nci.nih.gov/ncitbrowser/", + "name": "Legacy NCBI OWL", + "uri_format": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1" + } + ], "repository": "https://github.com/NCI-Thesaurus/thesaurus-obo-edition", "synonyms": [ "NCI", @@ -18115,7 +18248,7 @@ "contributor": { "email": "benjamin_gyori@hms.harvard.edu", "github": "bgyori", - "name": "Benjamin Gyori", + "name": "Benjamin M. Gyori", "orcid": "0000-0001-9439-5346" }, "description": "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding.", @@ -18794,10 +18927,10 @@ }, "npo": { "contact": { - "email": "nathan.baker@pnl.gov", - "github": null, + "email": "nathan.baker@pnnl.gov", + "github": "sobolevnrm", "name": "Nathan Baker", - "orcid": null + "orcid": "0000-0002-5892-6506" }, "description": "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.", "download_owl": "http://aber-owl.net/media/ontologies/NPO/31/npo.owl", @@ -18810,7 +18943,8 @@ }, "name": "NanoParticle Ontology", "pattern": "^\\d+$", - "preferred_prefix": "npo" + "preferred_prefix": "npo", + "repository": "https://github.com/sobolevnrm/npo" }, "nuclearbd": { "description": "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs.", @@ -20336,7 +20470,7 @@ }, "otol": { "contributor": { - "email": null, + "email": "meghan.balk@gmail.com", "github": "megbalk", "name": "Meghan Balk", "orcid": "0000-0003-2699-3066" @@ -21448,7 +21582,13 @@ "uri_format": "http://phenol-explorer.eu/foods/$1" }, "phenx": { - "description": "A Web-based catalog of recommended measurement protocols", + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants.", "download_owl": "http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl", "example": "130502", "homepage": "https://www.phenxtoolkit.org/", @@ -21460,6 +21600,9 @@ "name": "PhenX Toolkit", "pattern": "^\\d+$", "preferred_prefix": "phenx", + "synonyms": [ + "phenxtoolkit" + ], "uri_format": "https://www.phenxtoolkit.org/protocols/view/$1" }, "phipo": { @@ -24015,6 +24158,15 @@ "namespace_in_lui": true, "pattern": "^\\d{7}$", "preferred_prefix": "SBO", + "providers": [ + { + "code": "biomodels", + "description": "Provider for SBO at BioModels", + "homepage": "http://biomodels.net", + "name": "BioModels", + "uri_format": "http://biomodels.net/SBO/SBO_$1" + } + ], "repository": "https://github.com/EBI-BioModels/SBO", "uri_format": "https://www.ebi.ac.uk/sbo/main/SBO:$1", "version": "2021-08-28" @@ -25498,6 +25650,36 @@ "name": "Software ontology", "pattern": "^\\d{7}$", "preferred_prefix": "SWO", + "providers": [ + { + "code": "ebi", + "description": "The EBI's old SWO URIs before switching over to OBO PURLs", + "homepage": "http://www.ebi.ac.uk/swo/license", + "name": "Legacy EBI SWO", + "uri_format": "http://www.ebi.ac.uk/swo/SWO_$1" + }, + { + "code": "ebi.efo", + "description": "The EBI's old SWO URIs before switching over to OBO PURLs", + "homepage": "http://www.ebi.ac.uk/efo/swo/", + "name": "Legacy EBI SWO", + "uri_format": "http://www.ebi.ac.uk/efo/swo/SWO_$1" + }, + { + "code": "ebi.license", + "description": "The EBI's old SWO URIs before switching over to OBO PURLs", + "homepage": "http://www.ebi.ac.uk/swo/license", + "name": "Legacy EBI SWO", + "uri_format": "http://www.ebi.ac.uk/swo/license/SWO_$1" + }, + { + "code": "ebi.data", + "description": "The EBI's old SWO URIs before switching over to OBO PURLs", + "homepage": "http://www.ebi.ac.uk/swo/data", + "name": "Legacy EBI SWO", + "uri_format": "http://www.ebi.ac.uk/swo/data/SWO_$1" + } + ], "repository": "https://github.com/allysonlister/swo", "uri_format": "http://purl.obolibrary.org/obo/SWO_$1", "version": "1.7" @@ -25664,6 +25846,15 @@ "name": "The Arabidopsis Information Resource", "pattern": "^\\d+$", "preferred_prefix": "tair.locus", + "providers": [ + { + "code": "thalemine", + "description": "Data mining on aradopsis", + "homepage": "https://bar.utoronto.ca/thalemine", + "name": "ThaleMine", + "uri_format": "https://bar.utoronto.ca/thalemine/portal.do?externalids=$1" + } + ], "uri_format": "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1" }, "tair.protein": { @@ -25932,6 +26123,26 @@ ], "uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1" }, + "time": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.", + "download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl", + "example": "DateTimeDescription", + "homepage": "https://www.w3.org/TR/owl-time/", + "mappings": { + "aberowl": "TIME", + "bioportal": "TIME", + "fairsharing": "FAIRsharing.hw3bh2" + }, + "name": "Time Ontology in OWL", + "preferred_prefix": "time", + "uri_format": "http://www.w3.org/2006/time#$1" + }, "tkg": { "contributor": { "email": "cthoyt@gmail.com", @@ -27364,6 +27575,13 @@ "pattern": "^\\d+$", "preferred_prefix": "viaf", "providers": [ + { + "code": "viaf.https", + "description": "A duplicate endpoint over HTTPS", + "homepage": "http://viaf.org", + "name": "VIAF (https)", + "uri_format": "https://viaf.org/$1" + }, { "code": "scholia", "description": "Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other information in Wikidata.", @@ -28009,6 +28227,13 @@ "pattern": "^WB[A-Z][a-z]+\\d+$", "preferred_prefix": "WormBase", "providers": [ + { + "code": "wormbase.c_elegans", + "description": "Pages describing C. Elegans genes.", + "homepage": "http://www.wormbase.org", + "name": "WormBase C. Elegans Gene Portal", + "uri_format": "http://www.wormbase.org/species/c_elegans/gene/$1" + }, { "code": "bioentitylink", "description": "WormBase through BioEntity Link", diff --git a/exports/registry/registry.tsv b/exports/registry/registry.tsv index 09b4aa537..08b7d43a1 100644 --- a/exports/registry/registry.tsv +++ b/exports/registry/registry.tsv @@ -323,6 +323,7 @@ dbest EST database maintained at the NCBI. https://www.ncbi.nlm.nih.gov/nucest " dbg2introns DBG2 Introns http://webapps2.ucalgary.ca/~groupii/ The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank. ^\w{1,2}\.(\w{1,2}\.)?[A-Za-z0-9]+$ Cu.me.I1 http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1 False DBG2INTRONS dbg2introns dbg2introns dbgap Database of Genotypes and Phenotypes https://www.ncbi.nlm.nih.gov/projects/gap The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype. ^phs[0-9]{6}(.v\d+.p\d+)?$ phs000768.v2.p1 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1 False DBGAP dbgap dbgap dbmhc Database of human Major Histocompatibility Complex https://www.ncbi.nlm.nih.gov/gv/mhc/ Cell line databases/resources ^\d+$ 48439 True dbMHC +dbo DBPedia Ontology https://dbpedia.org/ontology This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki. careerPrizeMoney https://dbpedia.org/ontology/$1 False dbprobe NCBI Probe database Public registry of nucleic acid reagents https://www.ncbi.nlm.nih.gov/sites/entrez?db=probe The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities. ^\d+$ 1000000 https://www.ncbi.nlm.nih.gov/probe/?term=$1 False DBPROBE 2719 dbprobe dbprobe dbprobe dbsnp NCBI dbSNP https://www.ncbi.nlm.nih.gov/snp/ The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. ^rs\d+$ rs121909098 https://www.ncbi.nlm.nih.gov/snp/$1 False dbSNP dbSNP 1106 dbsnp dbsnp dbsnp r3d100010652 dbSNP dbvar.study Database of Genomic Structural Variation - Study https://www.ncbi.nlm.nih.gov/dbvar Studies in dbVar. nstd102 https://www.ncbi.nlm.nih.gov/dbvar/studies/$1 dbvar.studies False @@ -330,7 +331,7 @@ dbvar.variant Database of Genomic Structural Variation - Variant https://www.ncb dc Dublin Core https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. contributor http://purl.org/dc/terms/$1 False DC dc DC dcterms dc_cl Dendritic cell http://www.dukeontologygroup.org/Projects.html ^\d{7}$ 0000003 Lindsay.Cowell@utsouthwestern.edu http://purl.obolibrary.org/obo/DC_CL_$1 True DC_CL dc_cl dcat Data Catalog https://www.w3.org/ns/dcat DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web Dataset http://www.w3.org/ns/dcat#$1 False DCAT dcat DCAT -dcterms Dublin Core Metadata Vocabulary https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. title http://purl.org/dc/terms/$1 dc.terms False dcterms dcterms DCTERMS +dcterms Dublin Core Metadata Vocabulary https://www.dublincore.org/specifications/dublin-core/dcmi-terms/ This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. title http://purl.org/dc/terms/$1 dc.terms|dct False dcterms dcterms DCTERMS dctypes Dublin Core Types https://dublincore.org/specifications/dublin-core/dcmi-terms/ This document is an up-to-date specification of all metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes. Collection http://purl.org/dc/dcmitype/$1 False dctypes ddanat Dictyostelium discoideum anatomy http://dictybase.org/ A structured controlled vocabulary of the anatomy of the slime-mold Dictyostelium discoideum ^\d{7}$ 0000006 pfey@northwestern.edu http://purl.obolibrary.org/obo/DDANAT_$1 False DDANAT DDANAT DDANAT ddanat ddanat DDANAT ddanat ddinter.drug Curated Drug-Drug Interactions Database - Drug http://ddinter.scbdd.com Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety. ^DDInter\d+$ DDInter20 oriental-cds@163.com http://ddinter.scbdd.com/ddinter/drug-detail/$1 False @@ -572,7 +573,7 @@ gmd.gcms Golm Metabolome Database GC-MS spectra http://gmd.mpimp-golm.mpg.de/ Go gmd.profile Golm Metabolome Database Profile http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. GMD's metabolite profiles provide relative metabolite concentrations normalised according to fresh weight (or comparable quantitative data, such as volume, cell count, etc.) and internal standards (e.g. ribotol) of biological reference conditions and tissues. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 10b38aaf-b977-4950-85b8-f4775f66658d http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1 False GMD.PROFILE gmd.profile gmd.profile gmd.ref Golm Metabolome Database Reference Substance http://gmd.mpimp-golm.mpg.de/ Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. Since metabolites often cannot be obtained in their respective native biological state, for example organic acids may be only acquirable as salts, the concept of reference substance was introduced. This collection references reference substances. ^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$ 8cf84adb-b4db-4807-ac98-0004247c35df http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1 False GMD.REF gmd.ref gmd.ref gmelin Gmelins Handbuch der anorganischen Chemie https://link.springer.com/bookseries/562 The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s. ^[1-9][0-9]{3,6}$ 1466 False 1004 P1578 -gno Glycan Naming and Subsumption Ontology https://gnome.glyomics.org/ An ontology for glycans based on GlyTouCan, but organized by subsumption. ^\d{8}$ 10004892 nje5@georgetown.edu http://purl.obolibrary.org/obo/GNO_$1 False GNO GNO gno gno GNO +gno Glycan Naming and Subsumption Ontology https://gnome.glyomics.org/ An ontology for glycans based on GlyTouCan, but organized by subsumption. ^(\d{8}|(\w+\d+\w+))$ 10004892 nje5@georgetown.edu http://purl.obolibrary.org/obo/GNO_$1 gnome False GNO GNO gno gno GNO gnpis GnpIS https://urgi.versailles.inra.fr/gnpis/ GnpIS is an integrative information system focused on plants and fungal pests. It provides both genetic (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. ^[A-Za-z0-9]+$ AY109603 https://urgi.versailles.inra.fr/gnpis/#result/term=$1 False GNPIS gnpis gnpis r3d100012647 go Gene Ontology http://geneontology.org/ The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. ^\d{7}$ 0032571 suzia@stanford.edu http://amigo.geneontology.org/amigo/term/GO:$1 gobp|gobpid|gocc|goccid|gomf|gomfid False GO GO GO GO 1176 go go go go GO go GO P686 go.model Gene Ontology Causal Assembly Model http://www.geneontology.org/gocam GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform. 5fce9b7300001250 http://noctua.geneontology.org/editor/graph/gomodel:$1 False @@ -590,6 +591,7 @@ gold.meta GOLD metadata http://www.genomesonline.org/cgi-bin/GOLD/index.cgi "- D Please, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace. The GOLD (Genomes OnLine Database)is a resource for centralized monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references metadata associated with samples." ^Gm\d+$ Gm00047 http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 False GOLD.META gold.meta gold.meta +google.book Google Books https://books.google.com Search the world's most comprehensive index of full-text books. qafeQTWIWmcC https://books.google.com/books?id=$1 False P675 google.patent Google Patents https://www.google.com/patents/ Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date. ^[A-Z]{2,4}\d+([A-Z])?([0-9])?$ US4145692 https://www.google.com/patents/$1 patent False GOOGLE.PATENT Patent google.patent google.patent google.scholar Google Scholar Researcher https://scholar.google.com/ Google Scholar provides a simple way to broadly search for scholarly literature. You can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. PjrpzUIAAAAJ False gorel GO Relations http://geneontology.org/docs/ontology-relations/ Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO. ^\d{7}$ 0002005 ftp://ftp.geneontology.org/pub/go/ontology/extensions/gorel.owl False @@ -623,6 +625,7 @@ habronattus Habronattus courtship http://www.mesquiteproject.org/ontology/Habron hamap High-quality Automated and Manual Annotation of microbial Proteomes https://hamap.expasy.org/ HAMAP is a system that identifies and semi-automatically annotates proteins that are part of well-conserved and orthologous microbial families or subfamilies. These are used to build rules which are used to propagate annotations to member bacterial, archaeal and plastid-encoded protein entries. ^MF_\d+$ MF_01400 https://hamap.expasy.org/unirule/$1 False HAMAP 2766 hamap hamap hamap HAMAP hancestro Human Ancestry Ontology https://github.com/EBISPOT/ancestro Human ancestry ontology for the NHGRI GWAS Catalog ^\d{4}$ 0290 danielle.welter@uni.lu http://purl.obolibrary.org/obo/HANCESTRO_$1 False HANCESTRO HANCESTRO hancestro hancestro HANCESTRO hao Hymenoptera Anatomy Ontology http://hymao.org A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants) ^\d{7}$ 0000187 diapriid@gmail.com http://purl.obolibrary.org/obo/HAO_$1 False HAO HAO HAO hao hao HAO +hathitrust Hathi Trust Digital Library https://www.hathitrust.org Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. ^\d+$ 008893080 https://catalog.hathitrust.org/Record/$1 False hba Human Brain Atlas https://human.brain-map.org A controlled vocabulary to support the study of transcription in the human brain ^\d+$ 4005 https://raw.githubusercontent.com/obophenotype/uberon/master/source-ontologies/allen-hba.obo False hcao Human Cell Atlas Ontology https://www.humancellatlas.org Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas. False hcao hcpcs Healthcare Common Procedure Coding System https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo HCPCS is a collection of standardized codes that represent medical procedures, supplies, products and services. The codes are used to facilitate the processing of health insurance claims by Medicare and other insurers. G8944 False HCPCS HCPCS @@ -772,6 +775,7 @@ taxonomic class with which they are associated." ^C\d{8}$ C00000001 http://www. kupo Kidney and Urinary Pathway Ontology http://www.kupkb.org/ ^\d{7}$ 0001009 True kyinno KYinno cell lines https://www.kyinno.com/ Cell line collections KC-0979 https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf False KYinno labo clinical LABoratory Ontology https://github.com/OpenLHS/LABO LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents. ^\d{7}$ 0000124 paul.fabry@usherbrooke.ca http://purl.obolibrary.org/obo/LABO_$1 False LABO LABO labo labo LABO +langual Langua aLimentaria Thesaurus https://www.langual.org "Langual stands for ""langua alimentaria"" or ""language of food"". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases" ^B\d+$ B2067 https://www.langual.org/langual_thesaurus.asp?termid=$1 False lbo Livestock Breed Ontology http://bioportal.bioontology.org/ontologies/LBO A vocabulary for cattle, chicken, horse, pig, and sheep breeds. ^\d{7}$ 0000487 caripark@iastate.edu https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.owl https://github.com/AnimalGenome/livestock-breed-ontology/raw/master/current_release/lbo.obo False LBO LBO LBO lbo lei Global LEI Index https://www.gleif.org/ Established by the Financial Stability Board in June 2014, the Global Legal Entity Identifier Foundation (GLEIF) is tasked to support the implementation and use of the Legal Entity Identifier (LEI). The foundation is backed and overseen by the LEI Regulatory Oversight Committee, representing public authorities from around the globe that have come together to jointly drive forward transparency within the global financial markets. GLEIF is a supra-national not-for-profit organization headquartered in Basel, Switzerland. ^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$ HWUPKR0MPOU8FGXBT394 https://www.gleif.org/lei/$1 False lei lei lepao Lepidoptera Anatomy Ontology https://github.com/insect-morphology/lepao The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research. ^\d{7}$ 0000005 lagonzalezmo@unal.edu.co http://purl.obolibrary.org/obo/LEPAO_$1 False LEPAO LEPAO lepao lepao @@ -788,6 +792,7 @@ lincs.data LINCS Data http://lincsportal.ccs.miami.edu/datasets/ The Library of lincs.protein LINCS Protein http://lincs.hms.harvard.edu/db/proteins/ The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). It aims to collect and disseminate information relating to the fundamental principles of cellular response in humans to perturbation. This collection references proteins. ^\d+$ 200282 https://lincs.hms.harvard.edu/db/proteins/$1 False LINCS.PROTEIN lincs.protein lincs.protein lincs.smallmolecule LINCS Small Molecule http://lincsportal.ccs.miami.edu/SmallMolecules/ The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC). ^LSM-\d+$ LSM-6306 http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1 lincs False LINCS.SMALLMOLECULE lincs.smallmolecule lincs.smallmolecule linguist Linguist https://github.com/github/linguist Registry of programming languages for the Linguist program for detecting and highlighting programming languages. ^[a-zA-Z0-9 +#'*]+$ Python https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 False linguist +linkml LinkML https://linkml.io/linkml-model/docs/SchemaDefinition/ Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks. SchemaDefinition cjmungall@lbl.gov https://w3id.org/linkml/$1 False lipidbank LipidBank http://lipidbank.jp/index.html LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. ^\w+\d+$ BBA0001 http://lipidbank.jp/cgi-bin/detail.cgi?id=$1 False LIPIDBANK 2665 lipidbank lipidbank lipidbank lipidmaps LIPID MAPS http://www.lipidmaps.org The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. ^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$ LMPR0102010012 http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1 LIPID MAPS|LIPID_MAPS_class|LIPID_MAPS_instance False LIPIDMAPS 000564 2625 lipidmaps lipidmaps lipidmaps P2063 lipro Lipid Ontology An ontology representation of the LIPIDMAPS nomenclature classification. bakerc@unb.ca http://purl.obolibrary.org/obo/LIPRO_$1 True LIPRO LIPRO LIPRO lipro @@ -988,7 +993,7 @@ norine Nonribosomal Peptides Database http://bioinfo.lifl.fr/norine/ Norine is a novus Novus Biologicals https://www.novusbio.com A vendor of antibodies and other biologics nb100-56351 https://www.novusbio.com/products/$1 False npass Natural Product Activity and Species Source Database http://bidd.group/NPASS/ "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data. " ^NPC\d+$ NPC139585 False -npo NanoParticle Ontology https://bioportal.bioontology.org/ontologies/NPO An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. ^\d+$ 1731 nathan.baker@pnl.gov False NPO NPO +npo NanoParticle Ontology https://bioportal.bioontology.org/ontologies/NPO An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. ^\d+$ 1731 nathan.baker@pnnl.gov False NPO NPO nuclearbd NucleaRDB http://www.receptors.org/nucleardb/ NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs. ^\w+\_\w+$ prgr_human http://www.receptors.org/nucleardb/proteins/$1 False NUCLEARBD nuclearbd nuclearbd nucleotide Nucleotide https://www.ncbi.nlm.nih.gov/ The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. ^[a-zA-Z0-9_\.]+$ 880798137 https://www.ncbi.nlm.nih.gov/nuccore/$1 False nucleotide insdc oa Web Annotation Ontology http://www.w3.org/ns/oa The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture. sourceDateStart http://www.w3.org/ns/oa#$1 False OA oa OA @@ -1137,7 +1142,7 @@ pharmgkb.gene Pharmacogenetics and Pharmacogenomics Knowledge Base http://www.ph pharmgkb.pathways PharmGKB Pathways http://www.pharmgkb.org/ "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB Pathways are drug centric, gene based, interactive pathways which focus on candidate genes and gene groups and associated genotype and phenotype data of relevance for pharmacogenetic and pharmacogenomic studies." ^PA\d+$ PA146123006 http://www.pharmgkb.org/pathway/$1 False PHARMGKB.PATHWAYS 2650 pharmgkb.pathways pharmgkb.pathways pharmgkb.pathways P7001 phenolexplorer Phenol-Explorer http://www.phenol-explorer.eu/foods/ Phenol-Explorer is an electronic database on polyphenol content in foods. Polyphenols form a wide group of natural antioxidants present in a large number of foods and beverages. They contribute to food characteristics such as taste, colour or shelf-life. They also participate in the prevention of several major chronic diseases such as cardiovascular diseases, diabetes, cancers, neurodegenerative diseases or osteoporosis. ^\d+$ 75 http://phenol-explorer.eu/foods/$1 False PHENOLEXPLORER phenolexplorer phenolexplorer r3d100012197 -phenx PhenX Toolkit https://www.phenxtoolkit.org/ A Web-based catalog of recommended measurement protocols ^\d+$ 130502 https://www.phenxtoolkit.org/protocols/view/$1 False PHENX PHENX +phenx PhenX Toolkit https://www.phenxtoolkit.org/ A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants. ^\d+$ 130502 https://www.phenxtoolkit.org/protocols/view/$1 phenxtoolkit False PHENX PHENX phipo Pathogen Host Interaction Phenotype Ontology https://github.com/PHI-base/phipo Ontology of species-neutral phenotypes observed in pathogen-host interactions. ^\d{7}$ 0000001 alayne.cuzick@rothamsted.ac.uk http://purl.obolibrary.org/obo/PHIPO_$1 False PHIPO PHIPO phipo phipo PHIPO phosphopoint.kinase PhosphoPoint Kinase http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1 False PHOSPHOPOINT.KINASE phosphopoint.kinase phosphopoint.kinase phosphopoint.protein PhosphoPoint Phosphoprotein http://kinase.bioinformatics.tw/ PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information. ^\w+$ AURKA http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0 False PHOSPHOPOINT.PROTEIN phosphopoint.protein phosphopoint.protein @@ -1376,6 +1381,7 @@ tgn Getty Thesaurus of Geographic Names https://www.getty.edu/research/tools/voc th Terminologia Histologica https://ifaa.unifr.ch/ The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia] H3.03.00.0.00007 False thermofisher Thermo Fisher Scientific https://www.thermofisher.com ThermoFisher is a life sciences supply vendor. OSR00185W https://www.thermofisher.com/antibody/product/$1 False tigrfam TIGR protein families http://www.jcvi.org/cgi-bin/tigrfams/Listing.cgi TIGRFAMs is a resource consisting of curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. ^TIGR\d+$ TIGR00010 https://www.ncbi.nlm.nih.gov/cdd?term=$1 False TIGRFAM 1141 tigrfam tigrfam +time Time Ontology in OWL https://www.w3.org/TR/owl-time/ Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars. DateTimeDescription http://www.w3.org/2006/time#$1 False TIME TIME tkg Tohoku University cell line catalog http://www2.idac.tohoku.ac.jp/dep/ccr/ Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells. ^\d+$ 0221 http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html False TKG tngb Telethon Network of Genetic Biobanks http://biobanknetwork.telethon.it/ Cell line collections ^\d+$ 67035 http://biobanknetwork.telethon.it/Sample/View?sampleId=$1 False TNGB to Plant Trait Ontology http://browser.planteome.org/amigo A controlled vocabulary to describe phenotypic traits in plants. ^\d{7}$ 0000630 jaiswalp@science.oregonstate.edu http://purl.obolibrary.org/obo/TO_$1 False TO TO TO PTO to to TO diff --git a/exports/registry/registry.yml b/exports/registry/registry.yml index 481ad680f..2db77e9fd 100644 --- a/exports/registry/registry.yml +++ b/exports/registry/registry.yml @@ -2371,9 +2371,9 @@ bko: name: Adrien Rougny orcid: 0000-0002-2118-035X contributor: - email: null + email: benjamin_gyori@hms.harvard.edu github: bgyori - name: Benjamin Gyori + name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe @@ -3639,6 +3639,12 @@ cheminf: name: Chemical Information Ontology pattern: ^\d{6}$ preferred_prefix: CHEMINF + providers: + - code: semanticscience + description: Legacy URLs before conversion of CHEMINF to OBO PURLs + homepage: http://semanticscience.org + name: Semantic Science + uri_format: http://semanticscience.org/resource/CHEMINF_$1 repository: https://github.com/semanticchemistry/semanticchemistry uri_format: http://purl.obolibrary.org/obo/CHEMINF_$1 version: '2.0' @@ -4772,7 +4778,7 @@ cob: coconut: comment: '@mSorok is the dev of the resource, hope I got it right!' contributor: - email: null + email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 @@ -4897,7 +4903,7 @@ cohd: repository: https://github.com/MIT-LCP/mimic-omop col.taiwan: contributor: - email: null + email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 @@ -5091,7 +5097,7 @@ cordis.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori - name: Benjamin Gyori + name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded @@ -5935,6 +5941,22 @@ dbmhc: name: Database of human Major Histocompatibility Complex pattern: ^\d+$ preferred_prefix: dbmhc +dbo: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: This ontology is generated from the manually created specifications + in the dbpedia mappings wiki. each release of this ontology corresponds to a new + release of the dbpedia data set which contains instance data extracted from the + different language versions of wikipedia. for information regarding changes in + this ontology, please refer to the dbpedia mappings wiki. + example: careerPrizeMoney + homepage: https://dbpedia.org/ontology + name: DBPedia Ontology + preferred_prefix: dbo + uri_format: https://dbpedia.org/ontology/$1 dbprobe: description: The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together @@ -6071,6 +6093,7 @@ dcterms: preferred_prefix: dcterms synonyms: - dc.terms + - dct uri_format: http://purl.org/dc/terms/$1 dctypes: description: This document is an up-to-date specification of all metadata terms @@ -9559,7 +9582,7 @@ foodon: version: '2022-02-01' fossilworks.journal: contributor: - email: null + email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 @@ -9580,7 +9603,7 @@ fossilworks.journal: uri_format: http://fossilworks.org/?a=referenceInfo&reference_no=$1 fossilworks.taxon: contributor: - email: null + email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 @@ -10787,6 +10810,8 @@ gno: download_obo: http://purl.obolibrary.org/obo/gno.obo download_owl: http://purl.obolibrary.org/obo/gno.owl example: '10004892' + example_extras: + - G99373GG homepage: https://gnome.glyomics.org/ license: CC BY 4.0 mappings: @@ -10796,9 +10821,22 @@ gno: ols: gno ontobee: GNO name: Glycan Naming and Subsumption Ontology - pattern: ^\d{8}$ + pattern: ^(\d{8}|(\w+\d+\w+))$ preferred_prefix: GNO + providers: + - code: gno.structure + description: GNOme structure browser + homepage: https://gnome.glyomics.org/StructureBrowser.html + name: GNOme Structure Viewer + uri_format: https://gnome.glyomics.org/StructureBrowser.html?focus=$1 + - code: gno.composition + description: GNOme composition browser + homepage: https://gnome.glyomics.org/CompositionBrowser.html + name: GNOme Composition Browser + uri_format: https://gnome.glyomics.org/CompositionBrowser.html?focus=$1 repository: https://github.com/glygen-glycan-data/GNOme + synonyms: + - gnome uri_format: http://purl.obolibrary.org/obo/GNO_$1 version: 1.10.0 gnpis: @@ -11056,6 +11094,20 @@ gold.meta: pattern: ^Gm\d+$ preferred_prefix: gold.meta uri_format: http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1 +google.book: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Search the world's most comprehensive index of full-text books. + example: qafeQTWIWmcC + homepage: https://books.google.com + mappings: + wikidata: P675 + name: Google Books + preferred_prefix: google.book + uri_format: https://books.google.com/books?id=$1 google.patent: description: Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents @@ -11655,6 +11707,21 @@ hao: repository: https://github.com/hymao/hao uri_format: http://purl.obolibrary.org/obo/HAO_$1 version: '2021-03-05' +hathitrust: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Hathitrust is a partnership of academic and research institutions, + offering a collection of millions of titles digitized from libraries around the + world. + example: 008893080 + homepage: https://www.hathitrust.org + name: Hathi Trust Digital Library + pattern: ^\d+$ + preferred_prefix: hathitrust + uri_format: https://catalog.hathitrust.org/Record/$1 hba: contributor: email: cthoyt@gmail.com @@ -14259,6 +14326,29 @@ labo: repository: https://github.com/OpenLHS/LABO uri_format: http://purl.obolibrary.org/obo/LABO_$1 version: '2021-06-08' +langual: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: 'Langual stands for "langua alimentaria" or "language of food". it + is an automated method for describing, capturing and retrieving data about food. + the work on langual was started in the late 1970''s by the center for food safety + and applied nutrition (cfsan) of the united states food and drug administration + as an ongoing co-operative effort of specialists in food technology, information + science and nutrition. the thesaurus provides a standardized language for describing + foods, specifically for classifying food products for information retrieval. langual + is based on the concept that: - any food (or food product) can be systematically + described by a combination of characteristics - these characteristics can be categorized + into viewpoints and coded for computer processing - the resulting viewpoint/characteristic + codes can be used to retrieve data about the food from external databases' + example: B2067 + homepage: https://www.langual.org + name: Langua aLimentaria Thesaurus + pattern: ^B\d+$ + preferred_prefix: langual + uri_format: https://www.langual.org/langual_thesaurus.asp?termid=$1 lbo: contact: email: caripark@iastate.edu @@ -14548,6 +14638,29 @@ linguist: preferred_prefix: linguist repository: https://github.com/github/linguist uri_format: https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1 +linkml: + comment: 'Closes #508' + contact: + email: cjmungall@lbl.gov + github: cmungall + name: Chris Mungall + orcid: 0000-0002-6601-2165 + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Linkml is a flexible modeling language that allows you to author schemas + in yaml that describe the structure of your data. additionally, it is a framework + for working with and validating data in a variety of formats (json, rdf, tsv), + with generators for compiling linkml schemas to other frameworks. + example: SchemaDefinition + homepage: https://linkml.io/linkml-model/docs/SchemaDefinition/ + mappings: + biolink: linkml + name: LinkML + preferred_prefix: linkml + uri_format: https://w3id.org/linkml/$1 lipidbank: description: LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins. @@ -14680,7 +14793,7 @@ lotus: name: Adriano Rutz orcid: 0000-0003-0443-9902 contributor: - email: null + email: adriano.rutz@ik.me github: adafede name: Adriano Rutz orcid: 0000-0003-0443-9902 @@ -15641,6 +15754,11 @@ mgi: pattern: ^\d+$ preferred_prefix: MGI providers: + - code: mgi.marker + description: MGI Marker + homepage: http://www.informatics.jax.org/marker + name: MGI Marker + uri_format: http://www.informatics.jax.org/marker/MGI:$1 - code: bioentitylink description: MGD through BioEntity Link homepage: https://bioentity.link/ @@ -17480,6 +17598,12 @@ ncit: name: NCI Thesaurus pattern: ^C\d+$ preferred_prefix: NCIT + providers: + - code: evs + description: Links to a no-longer existing OWL file + homepage: https://ncit.nci.nih.gov/ncitbrowser/ + name: Legacy NCBI OWL + uri_format: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#$1 repository: https://github.com/NCI-Thesaurus/thesaurus-obo-edition synonyms: - NCI @@ -17924,7 +18048,7 @@ nihreporter.project: contributor: email: benjamin_gyori@hms.harvard.edu github: bgyori - name: Benjamin Gyori + name: Benjamin M. Gyori orcid: 0000-0001-9439-5346 description: RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications @@ -18550,10 +18674,10 @@ npass: preferred_prefix: npass npo: contact: - email: nathan.baker@pnl.gov - github: null + email: nathan.baker@pnnl.gov + github: sobolevnrm name: Nathan Baker - orcid: null + orcid: 0000-0002-5892-6506 description: An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy. @@ -18567,6 +18691,7 @@ npo: name: NanoParticle Ontology pattern: ^\d+$ preferred_prefix: npo + repository: https://github.com/sobolevnrm/npo nuclearbd: description: NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding @@ -20153,7 +20278,7 @@ otl: uri_format: http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1 otol: contributor: - email: null + email: meghan.balk@gmail.com github: megbalk name: Meghan Balk orcid: 0000-0003-2699-3066 @@ -21240,7 +21365,13 @@ phenolexplorer: preferred_prefix: phenolexplorer uri_format: http://phenol-explorer.eu/foods/$1 phenx: - description: A Web-based catalog of recommended measurement protocols + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: A web-based catalog of recommended measurement protocols selected by + experts to include in studies with human participants. download_owl: http://aber-owl.net/media/ontologies/PHENX/16/phenx.owl example: '130502' homepage: https://www.phenxtoolkit.org/ @@ -21251,6 +21382,8 @@ phenx: name: PhenX Toolkit pattern: ^\d+$ preferred_prefix: phenx + synonyms: + - phenxtoolkit uri_format: https://www.phenxtoolkit.org/protocols/view/$1 phipo: contact: @@ -23817,6 +23950,12 @@ sbo: namespace_in_lui: true pattern: ^\d{7}$ preferred_prefix: SBO + providers: + - code: biomodels + description: Provider for SBO at BioModels + homepage: http://biomodels.net + name: BioModels + uri_format: http://biomodels.net/SBO/SBO_$1 repository: https://github.com/EBI-BioModels/SBO uri_format: https://www.ebi.ac.uk/sbo/main/SBO:$1 version: '2021-08-28' @@ -25305,6 +25444,27 @@ swo: name: Software ontology pattern: ^\d{7}$ preferred_prefix: SWO + providers: + - code: ebi + description: The EBI's old SWO URIs before switching over to OBO PURLs + homepage: http://www.ebi.ac.uk/swo/license + name: Legacy EBI SWO + uri_format: http://www.ebi.ac.uk/swo/SWO_$1 + - code: ebi.efo + description: The EBI's old SWO URIs before switching over to OBO PURLs + homepage: http://www.ebi.ac.uk/efo/swo/ + name: Legacy EBI SWO + uri_format: http://www.ebi.ac.uk/efo/swo/SWO_$1 + - code: ebi.license + description: The EBI's old SWO URIs before switching over to OBO PURLs + homepage: http://www.ebi.ac.uk/swo/license + name: Legacy EBI SWO + uri_format: http://www.ebi.ac.uk/swo/license/SWO_$1 + - code: ebi.data + description: The EBI's old SWO URIs before switching over to OBO PURLs + homepage: http://www.ebi.ac.uk/swo/data + name: Legacy EBI SWO + uri_format: http://www.ebi.ac.uk/swo/data/SWO_$1 repository: https://github.com/allysonlister/swo uri_format: http://purl.obolibrary.org/obo/SWO_$1 version: '1.7' @@ -25454,6 +25614,12 @@ tair.locus: name: The Arabidopsis Information Resource pattern: ^\d+$ preferred_prefix: tair.locus + providers: + - code: thalemine + description: Data mining on aradopsis + homepage: https://bar.utoronto.ca/thalemine + name: ThaleMine + uri_format: https://bar.utoronto.ca/thalemine/portal.do?externalids=$1 uri_format: http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1 tair.protein: banana: AASequence @@ -25710,6 +25876,30 @@ tigrfam: - https://ftp.ncbi.nlm.nih.gov/hmm/TIGRFAMs/license_and_availability.txt - https://github.com/biopragmatics/bioregistry/issues/366 uri_format: https://www.ncbi.nlm.nih.gov/cdd?term=$1 +time: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Owl-time is an owl-2 dl ontology of temporal concepts, for describing + the temporal properties of resources in the world or described in web pages. the + ontology provides a vocabulary for expressing facts about topological (ordering) + relations among instants and intervals, together with information about durations, + and about temporal position including date-time information. time positions and + durations may be expressed using either the conventional (gregorian) calendar + and clock, or using another temporal reference system such as unix-time, geologic + time, or different calendars. + download_owl: http://aber-owl.net/media/ontologies/TIME/2/time.owl + example: DateTimeDescription + homepage: https://www.w3.org/TR/owl-time/ + mappings: + aberowl: TIME + bioportal: TIME + fairsharing: FAIRsharing.hw3bh2 + name: Time Ontology in OWL + preferred_prefix: time + uri_format: http://www.w3.org/2006/time#$1 tkg: contributor: email: cthoyt@gmail.com @@ -27169,6 +27359,11 @@ viaf: pattern: ^\d+$ preferred_prefix: viaf providers: + - code: viaf.https + description: A duplicate endpoint over HTTPS + homepage: http://viaf.org + name: VIAF (https) + uri_format: https://viaf.org/$1 - code: scholia description: Scholia is a service that creates visual scholarly profiles for topic, people, organizations, species, chemicals, etc using bibliographic and other @@ -27802,6 +27997,11 @@ wormbase: pattern: ^WB[A-Z][a-z]+\d+$ preferred_prefix: WormBase providers: + - code: wormbase.c_elegans + description: Pages describing C. Elegans genes. + homepage: http://www.wormbase.org + name: WormBase C. Elegans Gene Portal + uri_format: http://www.wormbase.org/species/c_elegans/gene/$1 - code: bioentitylink description: WormBase through BioEntity Link homepage: https://bioentity.link/ diff --git a/exports/sssom/bioregistry.sssom.tsv b/exports/sssom/bioregistry.sssom.tsv index a5da5dc9f..f8cf8f789 100644 --- a/exports/sssom/bioregistry.sssom.tsv +++ b/exports/sssom/bioregistry.sssom.tsv @@ -2189,6 +2189,7 @@ bioregistry:gold.genome skos:exactMatch n2t:gold.genome sssom:HumanCurated bioregistry:gold.meta skos:exactMatch biocontext:GOLD.META sssom:HumanCurated bioregistry:gold.meta skos:exactMatch miriam:gold.meta sssom:HumanCurated bioregistry:gold.meta skos:exactMatch n2t:gold.meta sssom:HumanCurated +bioregistry:google.book skos:exactMatch wikidata:P675 sssom:HumanCurated bioregistry:google.patent skos:exactMatch biocontext:GOOGLE.PATENT sssom:HumanCurated bioregistry:google.patent skos:exactMatch miriam:google.patent sssom:HumanCurated bioregistry:google.patent skos:exactMatch n2t:google.patent sssom:HumanCurated @@ -2845,6 +2846,7 @@ bioregistry:lincs.smallmolecule skos:exactMatch biocontext:LINCS.SMALLMOLECULE s bioregistry:lincs.smallmolecule skos:exactMatch miriam:lincs.smallmolecule sssom:HumanCurated bioregistry:lincs.smallmolecule skos:exactMatch n2t:lincs.smallmolecule sssom:HumanCurated bioregistry:linguist skos:exactMatch miriam:linguist sssom:HumanCurated +bioregistry:linkml skos:exactMatch biolink:linkml sssom:HumanCurated bioregistry:lipidbank skos:exactMatch biocontext:LIPIDBANK sssom:HumanCurated bioregistry:lipidbank skos:exactMatch fairsharing:FAIRsharing.bdn9br sssom:HumanCurated bioregistry:lipidbank skos:exactMatch miriam:lipidbank sssom:HumanCurated @@ -5105,6 +5107,9 @@ bioregistry:tgma skos:exactMatch prefixcommons:tgma sssom:HumanCurated bioregistry:tigrfam skos:exactMatch biocontext:TIGRFAM sssom:HumanCurated bioregistry:tigrfam skos:exactMatch miriam:tigrfam sssom:HumanCurated bioregistry:tigrfam skos:exactMatch n2t:tigrfam sssom:HumanCurated +bioregistry:time skos:exactMatch bioportal:TIME sssom:HumanCurated +bioregistry:time skos:exactMatch fairsharing:FAIRsharing.hw3bh2 sssom:HumanCurated +bioregistry:time skos:exactMatch aberowl:TIME sssom:HumanCurated bioregistry:to skos:exactMatch aberowl:TO sssom:HumanCurated bioregistry:to skos:exactMatch agroportal:TO sssom:HumanCurated bioregistry:to skos:exactMatch biocontext:TO sssom:HumanCurated diff --git a/exports/tables/summary.tex b/exports/tables/summary.tex index fe7c9dea3..3de1a4fae 100644 --- a/exports/tables/summary.tex +++ b/exports/tables/summary.tex @@ -6,16 +6,16 @@ \toprule Category & Count \\ \midrule - Version & 0.5.67-dev \\ + Version & 0.5.68-dev \\ Registries Surveyed & 24 \\ Registries Aligned & 23 \\ - Prefixes & 1422 \\ - Synonyms & 396 \\ - Cross-registry Mappings & 6939 \\ + Prefixes & 1428 \\ + Synonyms & 399 \\ + Cross-registry Mappings & 6950 \\ Curated Mismatches & 25 \\ Collections and Contexts & 7 \\ Direct Contributors & 28 \\ - Total Contributors & 169 \\ + Total Contributors & 170 \\ \bottomrule \end{tabular} \end{table} diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index 61fd34683..155ca4a97 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -36525,6 +36525,12 @@ "repository": "https://github.com/github/linguist" }, "linkml": { + "biolink": { + "is_identifiers": false, + "is_obo": false, + "prefix": "linkml", + "uri_format": "https://w3id.org/linkml/$1" + }, "comment": "Closes #508", "contact": { "email": "cjmungall@lbl.gov", @@ -36542,6 +36548,9 @@ "example": "SchemaDefinition", "github_request_issue": 512, "homepage": "https://linkml.io/linkml-model/docs/SchemaDefinition/", + "mappings": { + "biolink": "linkml" + }, "name": "LinkML", "uri_format": "https://w3id.org/linkml/$1" }, @@ -64911,6 +64920,18 @@ "uri_format": "https://www.ncbi.nlm.nih.gov/cdd?term=$1" }, "time": { + "aberowl": { + "description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.", + "download_owl": "http://aber-owl.net/media/ontologies/TIME/2/time.owl", + "homepage": "https://www.w3.org/TR/owl-time/", + "name": "OWL-Time", + "prefix": "TIME", + "version": "2017" + }, + "bioportal": { + "name": "OWL-Time", + "prefix": "TIME" + }, "contributor": { "email": "cthoyt@gmail.com", "github": "cthoyt", @@ -64919,8 +64940,24 @@ }, "description": "Owl-time is an owl-2 dl ontology of temporal concepts, for describing the temporal properties of resources in the world or described in web pages. the ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. time positions and durations may be expressed using either the conventional (gregorian) calendar and clock, or using another temporal reference system such as unix-time, geologic time, or different calendars.", "example": "DateTimeDescription", + "fairsharing": { + "abbreviation": "TIME", + "description": "OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars.", + "id": "367", + "name": "OWL-Time", + "prefix": "FAIRsharing.hw3bh2", + "publications": [], + "subjects": [ + "Subject Agnostic" + ] + }, "github_request_issue": 505, "homepage": "https://www.w3.org/TR/owl-time/", + "mappings": { + "aberowl": "TIME", + "bioportal": "TIME", + "fairsharing": "FAIRsharing.hw3bh2" + }, "name": "Time Ontology in OWL", "uri_format": "http://www.w3.org/2006/time#$1" }, diff --git a/src/bioregistry/data/external/aberowl/curation.tsv b/src/bioregistry/data/external/aberowl/curation.tsv index d47cd809c..ca6e6b46d 100644 --- a/src/bioregistry/data/external/aberowl/curation.tsv +++ b/src/bioregistry/data/external/aberowl/curation.tsv @@ -199,7 +199,6 @@ DCM DICOM Controlled Terminology http://dicom.nema.org/medical/dicom/current/out DCMITYPE DCMI Type Vocabulary http://dublincore.org/documents/dcmi-type-vocabulary The DCMI Type Vocabulary provides a general, cross-domain list of approved terms that may be used as values for the Resource Type element to identify the genre of a resource DCO Dispedia Core Ontology www.dispedia.de Dispedia Core Ontology is a schema for information brokering and knowledge management in the complex field of rare diseases. On the one hand, the Dispedia schema uses semantic technologies to describe patients affected by rare diseases, and on the other hand, to record expertise concerning these particular diseases in machine-processable form. In addition to the differentiated attribution of facts to the individual need for information, Dispedia enables information brokering which adjusts to the type of recipient, its character as well as its personal attitude. The schema was initially geared to an exemplified disease, Amyotrophe Lateralsclerose (ALS). DCO-DEBUGIT DebugIT Core Ontology http://www.debugit.eu/index.php The Debugit Core Ontology (dco) covers the complete conceptual space of the domain of interest in the DebugIT project. It focuses on the management of antibiotics resistance within hospitals and infectious diseases to cover the clinical monitoring use cases. The ontology shall provide a semantic reference as logically defined classes in a formal and computer understandable format. It is supposed to formally represent all basic kinds of entities in the domain of interest, together with their invariant and context-independent properties. The ontology is therefore distinct from the representation of clinical knowledge as targeted by the DebugIT WP 4. Instead, it has a supportive semantic glue Function as it provides standardized and formally described meaning identifiers across the whole project, hence serving the Interoperability platform as well. -DCT DC Terms Specification of all metadata terms maintained by the Dublin Core Metadata Initiative. Included are the fifteen terms of the Dublin Core Metadata Element Set DDI Ontology for Drug Discovery Investigations http://purl.org/ddi/home The goal of DDI project is to develop an ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI). DDIEM Drug Database for Inborn Errors of Metabolism (DDIEM) Ontology http://ddiem.phenomebrowser.net/ DDIEM Ontology for the Drug Database for Inborn Errors of Metabolism. The DDIEM database is a database of therapeutic strategies and treatments for inborn errors of metabolism. These strategies are classified by mechanism and outcome using the DDIEM Ontology. The DDIEM database also includes descriptions of the phenotypes addressed by the treatment, together with drugs and procedures applied. DDIO Drug Drug Interaction Ontology Drug Drug Interaction Ontology @@ -932,7 +931,6 @@ TESTUDEM2222 TestUdeM2222 tfernandes Thiago THREELPH NeuroMorpho.Org three layers in subcortical regions A hierarchy of three layers that are most commonly referred to in subcortical regions. TIM Terra Interoperability Model https://github.com/DataBiosphere/terra-interoperability-model The Terra Interoperability Model captures a common set of concepts and relationships for biomedical research intended to facilitate and encourage data sharing and reuse. Its purpose is to enable researchers to find highly connected biomedical data in a federated search space and support interoperability among datasets. -TIME OWL-Time https://www.w3.org/TR/owl-time/ OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars. TIMEBANK Timebank Ontology https://w3id.org/timebank The Timebank Ontology is used to describe Timebank systems for Peer-to-Peer Service Exchange. A Timebank allows user to store virtual money, often called a Time Dollar, into a bank account. This virtual currency can be earned by helping fellow Timebank users and spent by requesting help from others. The main goal of the ontology is to facilitate the matching between helpers and requesters of help. TM-CONST Traditional Medicine Constitution Value Set https://sites.google.com/site/whoictm/home The value set for the Constitution property of the International Classification of Traditional Medicine (ICTM). TM-MER Traditional Medicine Meridian Value Sets https://sites.google.com/site/whoictm/home The meridian value set used in the International Classification of Traditional Medicine. diff --git a/src/bioregistry/data/external/agroportal/raw.json b/src/bioregistry/data/external/agroportal/raw.json index bb47cce30..358d5276a 100644 --- a/src/bioregistry/data/external/agroportal/raw.json +++ b/src/bioregistry/data/external/agroportal/raw.json @@ -1,7 +1,32 @@ [ { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/E-PHY", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -509,7 +534,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/CO_320", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -834,7 +884,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/INIA-RDM", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -2028,32 +2103,7 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/", - "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", - "administeredBy": { - "@id": "http://data.bioontology.org/metadata/User", - "@type": "@id" - }, - "flat": "http://data.bioontology.org/metadata/flat", - "group": { - "@id": "http://data.bioontology.org/metadata/Group", - "@type": "@id" - }, - "hasDomain": { - "@id": "http://data.bioontology.org/metadata/Category", - "@type": "@id" - }, - "name": "http://omv.ontoware.org/2005/05/ontology#name", - "ontologyType": { - "@id": "http://data.bioontology.org/metadata/OntologyType", - "@type": "@id" - }, - "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", - "viewOf": { - "@id": "http://data.bioontology.org/metadata/Ontology", - "@type": "@id" - }, - "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" + "@vocab": "http://data.bioontology.org/metadata/" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/CO_322", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -2117,7 +2167,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/FOBI", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -2353,7 +2428,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/PR", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -2594,7 +2694,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/ATC", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -3808,7 +3933,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/SAREF", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -4919,7 +5069,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/ONTOBIOTOPE", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -5070,7 +5245,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/SOIL", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -5130,7 +5330,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/CO_020", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -5372,7 +5597,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/GR-TAX", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -5705,7 +5955,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/AFEO", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -6655,7 +6930,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/DSW", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -6718,7 +7018,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/ASCOPAIN-T", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -6780,7 +7105,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/CO_121", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -8158,7 +8508,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/CASO", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -8572,7 +8947,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/FLOPO", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -10039,7 +10439,32 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/" + "@vocab": "http://data.bioontology.org/metadata/", + "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", + "administeredBy": { + "@id": "http://data.bioontology.org/metadata/User", + "@type": "@id" + }, + "flat": "http://data.bioontology.org/metadata/flat", + "group": { + "@id": "http://data.bioontology.org/metadata/Group", + "@type": "@id" + }, + "hasDomain": { + "@id": "http://data.bioontology.org/metadata/Category", + "@type": "@id" + }, + "name": "http://omv.ontoware.org/2005/05/ontology#name", + "ontologyType": { + "@id": "http://data.bioontology.org/metadata/OntologyType", + "@type": "@id" + }, + "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", + "viewOf": { + "@id": "http://data.bioontology.org/metadata/Ontology", + "@type": "@id" + }, + "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/MS2O", "@type": "http://data.bioontology.org/metadata/Ontology", @@ -11067,32 +11492,7 @@ }, { "@context": { - "@vocab": "http://data.bioontology.org/metadata/", - "acronym": "http://omv.ontoware.org/2005/05/ontology#acronym", - "administeredBy": { - "@id": "http://data.bioontology.org/metadata/User", - "@type": "@id" - }, - "flat": "http://data.bioontology.org/metadata/flat", - "group": { - "@id": "http://data.bioontology.org/metadata/Group", - "@type": "@id" - }, - "hasDomain": { - "@id": "http://data.bioontology.org/metadata/Category", - "@type": "@id" - }, - "name": "http://omv.ontoware.org/2005/05/ontology#name", - "ontologyType": { - "@id": "http://data.bioontology.org/metadata/OntologyType", - "@type": "@id" - }, - "summaryOnly": "http://data.bioontology.org/metadata/summaryOnly", - "viewOf": { - "@id": "http://data.bioontology.org/metadata/Ontology", - "@type": "@id" - }, - "viewingRestriction": "http://data.bioontology.org/metadata/viewingRestriction" + "@vocab": "http://data.bioontology.org/metadata/" }, "@id": "http://data.agroportal.lirmm.fr/ontologies/FOODIE", "@type": "http://data.bioontology.org/metadata/Ontology", diff --git a/src/bioregistry/data/external/biolink/curation.tsv b/src/bioregistry/data/external/biolink/curation.tsv index 9531d0636..beaa4c521 100644 --- a/src/bioregistry/data/external/biolink/curation.tsv +++ b/src/bioregistry/data/external/biolink/curation.tsv @@ -14,7 +14,6 @@ GOP http://purl.obolibrary.org/obo/go#$1 False True gpi https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#$1 False False gtpo https://rdf.guidetopharmacology.org/ns/gtpo#$1 False False KEGG.BRITE http://www.kegg.jp/entry/$1 False False -linkml https://w3id.org/linkml/$1 False False NBO-PROPERTY http://purl.obolibrary.org/obo/nbo#$1 False True NCIT-OBO http://purl.obolibrary.org/obo/ncit#$1 False True OBAN http://purl.org/oban/$1 False False diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index c1e81846d..b2326ccd6 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -141,7 +141,6 @@ DCAT-FDC Data Catalog Vocabulary (DCAT) DCCDFV Dublin Core Collection Description Frequency Vocabulary DCMITYPE DCMI Type Vocabulary DCO Dispedia Core Ontology -DCT DC Terms DDI Ontology for Drug Discovery Investigations DDIEM Drug Database for Inborn Errors of Metabolism (DDIEM) Ontology DEB Devices, Experimental scaffolds and Biomaterials Ontology @@ -643,7 +642,6 @@ TEST_CBI test_cbi TEST_IDKWHATIMDO Tanya TESTEX test1 TIM Terra Interoperability Model -TIME OWL-Time TIMEBANK Timebank Ontology TM-CONST Traditional Medicine Constitution Value Set TM-MER Traditional Medicine Meridian Value Sets diff --git a/src/bioregistry/data/external/fairsharing/curation.tsv b/src/bioregistry/data/external/fairsharing/curation.tsv index 635338b1f..3b425c931 100644 --- a/src/bioregistry/data/external/fairsharing/curation.tsv +++ b/src/bioregistry/data/external/fairsharing/curation.tsv @@ -300,7 +300,6 @@ FAIRsharing.hqyeb7 Fire Ontology FIRE The ontology of Fire was created in order FAIRsharing.hs43fc Fish Ontology FISHO This Fish Ontology is an ontology created as how the author views the fish structure following the book "The Diversity of Fishes: Biology, Evolution and Ecology" as the main reference, which covers one part of view on ichthyology, with an emphasis on diversity and adaptation. This ontology is created with the mindset of categorizing fish automatically based on the attributes and terms mined from the fish specimen. Most of the basic organization from this ontology follows Nelson's research due to its synthetic and broad approach, while recognizing that Nelson's conclusions are one of many alternative interpretations of the literature, which is mostly agreed by our main references, and many fish and fisheries researchers. Most of the classification used in this ontology is in no means completed and just following the recent classification provided by the books For now our work focused more on two group of fish which is early jawless fish, and advanced jawed fishes. The classification from both of this group are structured following the reference. FAIRsharing.htq39f COMODI COMODI An ontology to characterise differences in versions of computational models in biology FAIRsharing.hve0ac Matter Transfer Ontology TRANSMAT The Matter Transfer ontology is dedicated to matter transfer (eg O2, CO2, H2O) and mechanical properties of materials especially with respect to food, bacteria and packaging fields. -FAIRsharing.hw3bh2 OWL-Time TIME OWL-Time is an OWL-2 DL ontology of temporal concepts, for describing the temporal properties of resources in the world or described in Web pages. The ontology provides a vocabulary for expressing facts about topological (ordering) relations among instants and intervals, together with information about durations, and about temporal position including date-time information. Time positions and durations may be expressed using either the conventional (Gregorian) calendar and clock, or using another temporal reference system such as Unix-time, geologic time, or different calendars. FAIRsharing.hw5gr6 Regional Healthcare System Interoperability and Information Exchange Measurement Ontology HEIO The purpose of this ontology is to develop a model for regional healthcare system interoperability and information exchange quantification (measured by the electronic health information exchange (eHIE) indicator). The eHIE is hypothesized as a leading measure of regional healthcare system integration. A publication associated with this ontology is currently under review. FAIRsharing.IUZaXe ASLS - Land Surface classifiers land-surface Machine-readable representation of the classifiers described in chapter 7 Land Surface, by R.C. McDonald, R.F. Isbell and J.G. Speight, in Australian soil and land survey field handbook (3rd edn). Land surface is concerned mainly with surface phenomena affecting land use and soil development that have traditionally been noted at the point of soil observation. The data was converted from the print representation to this linked-data form by Linda Gregory and Simon J D Cox. FAIRsharing.j01xzz NeuroMorpho.Org species ontology NMOSP The species ontology of NeuroMorpho.Org was updated (OntoSearch v1.3) to map the new species and strains added in NeuroMorpho.Org v6.3 release. diff --git a/src/bioregistry/data/external/miriam/processed.json b/src/bioregistry/data/external/miriam/processed.json index 39ad1177e..bbf259745 100644 --- a/src/bioregistry/data/external/miriam/processed.json +++ b/src/bioregistry/data/external/miriam/processed.json @@ -8841,7 +8841,7 @@ }, "ror": { "deprecated": false, - "description": "ROR (Research Organization Registry) is a global, community-led registry of open persistent identifiers for research organizations. ", + "description": "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. 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The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.","created":"2019-06-11T14:17:26.654+0000","modified":"2019-06-11T14:17:26.654+0000","resources":[{"id":1332,"mirId":"MIR:00100600","urlPattern":"http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}","name":"YDPM at Stanford University School of Medicine","description":"YDPM at Stanford University School of Medicine","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"YAL001C","resourceHomeUrl":"http://www-deletion.stanford.edu/YDPM/","institution":{"id":1331,"name":"Stanford University School of Medicine, Stanford, California","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"YAL001C","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1333,"prefix":"wb.rnai","mirId":"MIR:00000466","name":"WormBase RNAi","pattern":"^WBRNAi\\d{8}$","description":"WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. 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This collection references ICE elements.","created":"2019-06-11T14:17:27.338+0000","modified":"2019-06-11T14:17:27.338+0000","resources":[{"id":1340,"mirId":"MIR:00100604","urlPattern":"http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}","name":"ICEberg element at Shanghai Jiaotong University","description":"ICEberg element at Shanghai Jiaotong University","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"100","resourceHomeUrl":"http://db-mml.sjtu.edu.cn/ICEberg/","institution":{"id":1339,"name":"State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"CN","countryName":"China"}},"location":{"countryCode":"CN","countryName":"China"},"deprecated":false,"deprecationDate":null}],"sampleId":"100","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1341,"prefix":"iceberg.family","mirId":"MIR:00000470","name":"ICEberg family","pattern":"^\\d+$","description":"ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. 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This collection refers to growth stage ontology information in Gramene.","created":"2019-06-11T14:17:36.384+0000","modified":"2019-06-11T14:17:36.384+0000","resources":[{"id":1438,"mirId":"MIR:00100649","urlPattern":"http://www.gramene.org/db/ontology/search?id=GRO:{$id}","name":"Gramene Growth Stage Ontology at Cold Spring Harbor","description":"Gramene Growth Stage Ontology at Cold Spring Harbor","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"0007133","resourceHomeUrl":"http://www.gramene.org/","institution":{"id":556,"name":"Cold Spring Harbor Laboratory, New York","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"0007133","namespaceEmbeddedInLui":true,"deprecated":false,"deprecationDate":null},{"id":1439,"prefix":"mgnify.samp","mirId":"MIR:00000510","name":"MGnify Sample","pattern":"^[A-Z]+[0-9]+$","description":"The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.","created":"2019-06-11T14:17:36.594+0000","modified":"2019-06-11T14:17:36.594+0000","resources":[{"id":1440,"mirId":"MIR:00100656","urlPattern":"https://www.ebi.ac.uk/metagenomics/samples/{$id}","name":"MGnify Sample","description":"MGnify Sample","official":false,"providerCode":"ebi","sampleId":"SRS086444","resourceHomeUrl":"https://www.ebi.ac.uk/metagenomics","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"SRS086444","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1441,"prefix":"ega.study","mirId":"MIR:00000511","name":"European Genome-phenome Archive Study","pattern":"^EGAS\\d{11}$","description":"The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.","created":"2019-06-11T14:17:36.823+0000","modified":"2019-06-11T14:17:36.823+0000","resources":[{"id":1442,"mirId":"MIR:00100657","urlPattern":"https://www.ebi.ac.uk/ega/studies/{$id}","name":"EGA Study at European Bioinformatics Institute","description":"EGA Study at European Bioinformatics Institute","official":true,"providerCode":"ebi","sampleId":"EGAS00000000001","resourceHomeUrl":"https://www.ebi.ac.uk/ega/studies","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1443,"mirId":"MIR:00100851","urlPattern":"https://www.omicsdi.org/dataset/ega/{$id}","name":"EGA Study through OmicsDI","description":"EGA Study through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"EGAS00000000001","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"EGAS00000000001","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1444,"prefix":"ega.dataset","mirId":"MIR:00000512","name":"European Genome-phenome Archive Dataset","pattern":"^EGAD\\d{11}$","description":"The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.","created":"2019-06-11T14:17:37.233+0000","modified":"2019-06-11T14:17:37.233+0000","resources":[{"id":1445,"mirId":"MIR:00100658","urlPattern":"https://www.ebi.ac.uk/ega/datasets/{$id}","name":"EGA Dataset at European Bioinformatics Institute","description":"EGA Dataset at European Bioinformatics Institute","official":true,"providerCode":"ebi","sampleId":"EGAD00000000001","resourceHomeUrl":"https://www.ebi.ac.uk/ega/dataset","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1446,"mirId":"MIR:00100852","urlPattern":"https://www.omicsdi.org/dataset/ega/{$id}","name":"EGA Dataset through OmicsDI","description":"EGA Dataset through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"EGAD00000000001","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"EGAD00000000001","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1453,"prefix":"pride.project","mirId":"MIR:00000515","name":"PRIDE Project","pattern":"^P(X|R)D\\d{6}$","description":"The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.","created":"2019-06-11T14:17:38.030+0000","modified":"2019-06-11T14:17:38.030+0000","resources":[{"id":1454,"mirId":"MIR:00100662","urlPattern":"https://www.ebi.ac.uk/pride/archive/projects/{$id}","name":"PRIDE Project at EBI","description":"PRIDE Project at EBI","official":true,"providerCode":"ebi","sampleId":"PXD000440","resourceHomeUrl":"https://www.ebi.ac.uk/pride/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1455,"mirId":"MIR:00100858","urlPattern":"https://www.omicsdi.org/dataset/pride/{$id}","name":"PRIDE Project through OmicsDI","description":"PRIDE Project through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"PXD000440","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"PXD000440","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1456,"prefix":"antibodyregistry","mirId":"MIR:00000516","name":"Antibody Registry","pattern":"^\\d{6}$","description":"The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.","created":"2019-06-11T14:17:38.379+0000","modified":"2019-06-11T14:17:38.379+0000","resources":[{"id":1458,"mirId":"MIR:00100664","urlPattern":"http://antibodyregistry.org/AB_{$id}","name":"Antibody Registry at University of California","description":"Antibody Registry at University of California","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"493771","resourceHomeUrl":"http://antibodyregistry.org/","institution":{"id":1457,"name":"Neuroscience Information Framework, University of California, San Diego, California","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"493771","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1459,"prefix":"mamo","mirId":"MIR:00000517","name":"Mathematical Modelling Ontology","pattern":"^MAMO_\\d{7}$","description":"The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.","created":"2019-06-11T14:17:38.625+0000","modified":"2019-06-11T14:17:38.625+0000","resources":[{"id":1460,"mirId":"MIR:00100665","urlPattern":"http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}","name":"MAMO through BioPortal","description":"MAMO through BioPortal","official":false,"providerCode":"bptl","sampleId":"MAMO_0000026","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/MAMO","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1461,"mirId":"MIR:00100758","urlPattern":"https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id}","name":"MaMO through OLS","description":"MaMO through OLS","official":false,"providerCode":"ols","sampleId":"MAMO_0000026","resourceHomeUrl":"https://www.ebi.ac.uk/ols/ontologies/mamo","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"MAMO_0000026","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1462,"prefix":"eo","mirId":"MIR:00000518","name":"Plant Environment Ontology","pattern":"^(P)?EO\\:\\d{7}$","description":"The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.","created":"2019-06-11T14:17:38.985+0000","modified":"2019-06-11T14:17:38.985+0000","resources":[{"id":1463,"mirId":"MIR:00100667","urlPattern":"http://archive.gramene.org/db/ontology/search?query=EO:{$id}","name":"Plant Environment Ontology through Gramene","description":"Plant Environment Ontology through Gramene","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"0007404","resourceHomeUrl":"http://archive.gramene.org/db/ontology/search_term?id=EO:0007359","institution":{"id":556,"name":"Cold Spring Harbor Laboratory, New York","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1464,"mirId":"MIR:00100668","urlPattern":"http://purl.bioontology.org/ontology/PECO/EO:{$id}","name":"Plant Environment Ontology through BioPortal","description":"Plant Environment Ontology through BioPortal","official":false,"providerCode":"bptl","sampleId":"0007404","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/PECO","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1465,"mirId":"MIR:00100669","urlPattern":"https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id}","name":"Plant Environment Ontology through OLS","description":"Plant Environment Ontology through OLS","official":false,"providerCode":"ols","sampleId":"0007404","resourceHomeUrl":"https://www.ebi.ac.uk/ols/ontologies/eo","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"0007404","namespaceEmbeddedInLui":true,"deprecated":false,"deprecationDate":null},{"id":1466,"prefix":"idot","mirId":"MIR:00000519","name":"Identifiers.org Terms","pattern":"^[A-Za-z]+$","description":"Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.","created":"2019-06-11T14:17:39.487+0000","modified":"2019-06-11T14:17:39.487+0000","resources":[{"id":1467,"mirId":"MIR:00100670","urlPattern":"https://biomodels.net/vocab/idot.rdf#{$id}","name":"IdoT via biomodels.net","description":"IdoT via biomodels.net","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"identifierPattern","resourceHomeUrl":"https://identifiers.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"identifierPattern","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1470,"prefix":"yeastintron","mirId":"MIR:00000521","name":"Yeast Intron Database v4.3","pattern":"^[A-Z0-9]+$","description":"The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].","created":"2019-06-11T14:17:39.906+0000","modified":"2019-06-11T14:17:39.906+0000","resources":[{"id":1471,"mirId":"MIR:00100673","urlPattern":"http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}","name":"Yeast Intron Database version 4.3 at Baskin School of Engineering","description":"Yeast Intron Database version 4.3 at Baskin School of Engineering","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"SNR17A","resourceHomeUrl":"http://intron.ucsc.edu/yeast4.3/","institution":{"id":1319,"name":"University of California, Santa Cruz","homeUrl":"https://www.ucsc.edu","description":"UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n","rorId":"https://ror.org/03s65by71","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"SNR17A","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1472,"prefix":"ardb","mirId":"MIR:00000522","name":"Antibiotic Resistance Genes Database","pattern":"^[A-Z_]{3}[0-9]{4,}$","description":"The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.","created":"2019-06-11T14:17:40.104+0000","modified":"2019-06-11T14:17:40.104+0000","resources":[{"id":1474,"mirId":"MIR:00100678","urlPattern":"http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id}","name":"ARDB at University of Maryland","description":"ARDB at University of Maryland","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"CAE46076","resourceHomeUrl":"http://ardb.cbcb.umd.edu/","institution":{"id":1473,"name":"Center for Bioinformatics and Computational Biology, University of Maryland, Maryland","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"CAE46076","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1475,"prefix":"proteomicsdb.protein","mirId":"MIR:00000524","name":"ProteomicsDB Protein","pattern":"^\\d+$","description":"ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.","created":"2019-06-11T14:17:40.344+0000","modified":"2019-06-11T14:17:40.344+0000","resources":[{"id":1477,"mirId":"MIR:00100680","urlPattern":"https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary","name":"Proteomics DB Protein at Center for Integrated Protein Science","description":"Proteomics DB Protein at Center for Integrated Protein Science","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"53504","resourceHomeUrl":"https://www.proteomicsdb.org/#human","institution":{"id":1476,"name":"Center for Integrated Protein Science, Munich,","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"DE","countryName":"Germany"}},"location":{"countryCode":"DE","countryName":"Germany"},"deprecated":false,"deprecationDate":null}],"sampleId":"53504","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1478,"prefix":"proteomicsdb.peptide","mirId":"MIR:00000525","name":"ProteomicsDB Peptide","pattern":"^\\d+$","description":"ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.","created":"2019-06-11T14:17:40.583+0000","modified":"2019-06-11T14:17:40.583+0000","resources":[{"id":1480,"mirId":"MIR:00100681","urlPattern":"https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/","name":"Proteomics DB Peptide at Center for Integrated Protein Science","description":"Proteomics DB Peptide at Center for Integrated Protein Science","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"53504","resourceHomeUrl":"https://www.proteomicsdb.org/#peptideSearch","institution":{"id":1479,"name":"Center for Integrated Protein Science, Munich","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"DE","countryName":"Germany"}},"location":{"countryCode":"DE","countryName":"Germany"},"deprecated":false,"deprecationDate":null}],"sampleId":"53504","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1481,"prefix":"hpm.protein","mirId":"MIR:00000526","name":"Human Proteome Map Protein","pattern":"^\\d+$","description":"The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.","created":"2019-06-11T14:17:40.825+0000","modified":"2019-06-11T14:17:40.825+0000","resources":[{"id":1482,"mirId":"MIR:00100682","urlPattern":"http://www.humanproteomemap.org/protein.php?hpm_id={$id}","name":"Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)","description":"Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"1968","resourceHomeUrl":"http://www.humanproteomemap.org/index.php","institution":{"id":1087,"name":"Institute of Bioinformatics, International Tech Park, Bangalore","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"IN","countryName":"India"}},"location":{"countryCode":"IN","countryName":"India"},"deprecated":false,"deprecationDate":null}],"sampleId":"1968","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1483,"prefix":"hpm.peptide","mirId":"MIR:00000527","name":"Human Proteome Map Peptide","pattern":"^\\d+$","description":"The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. 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This collection references the Record Report, based on RCV accession.","created":"2019-06-11T14:17:42.685+0000","modified":"2019-06-11T14:17:42.685+0000","resources":[{"id":1501,"mirId":"MIR:00100710","urlPattern":"http://www.ncbi.nlm.nih.gov/clinvar/{$id}/","name":"ClinVar Record at NCBI","description":"ClinVar Record at NCBI","official":false,"providerCode":"ncbi","sampleId":"RCV000033555.3","resourceHomeUrl":"http://www.ncbi.nlm.nih.gov/clinvar/","institution":{"id":26,"name":"National Center for Biotechnology Information","homeUrl":"https://www.ncbi.nlm.nih.gov/","description":"The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.","rorId":"https://ror.org/02meqm098","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"RCV000033555.3","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1502,"prefix":"mgnify.proj","mirId":"MIR:00000535","name":"MGnify Project","pattern":"^[A-Z]+[0-9]+$","description":"MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.","created":"2019-06-11T14:17:42.938+0000","modified":"2019-06-11T14:17:42.938+0000","resources":[{"id":1503,"mirId":"MIR:00100711","urlPattern":"https://www.ebi.ac.uk/metagenomics/projects/{$id}","name":"MGnify Project","description":"MGnify Project","official":false,"providerCode":"ebi","sampleId":"ERP004492","resourceHomeUrl":"https://www.ebi.ac.uk/metagenomics","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"ERP004492","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1504,"prefix":"euclinicaltrials","mirId":"MIR:00000536","name":"EU Clinical Trials","pattern":"^\\d{4}\\-\\d{6}\\-\\d{2}$","description":"The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.","created":"2019-06-11T14:17:43.129+0000","modified":"2019-06-11T14:17:43.129+0000","resources":[{"id":1506,"mirId":"MIR:00100712","urlPattern":"https://www.clinicaltrialsregister.eu/ctr-search/search?query={$id}","name":"EU Clinical Trials at European Medicines Agency","description":"EU Clinical Trials at European Medicines Agency","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"2008-005144-16","resourceHomeUrl":"https://www.clinicaltrialsregister.eu/","institution":{"id":1505,"name":"European Medicines Agency, London","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"2008-005144-16","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1507,"prefix":"google.patent","mirId":"MIR:00000537","name":"Google Patents","pattern":"^[A-Z]{2}\\d+([A-Z])?$","description":"Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.","created":"2019-06-11T14:17:43.371+0000","modified":"2019-06-11T14:17:43.371+0000","resources":[{"id":1509,"mirId":"MIR:00100714","urlPattern":"https://www.google.com/patents/{$id}","name":"Google Patents at Google","description":"Google Patents at Google","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"US4145692","resourceHomeUrl":"https://www.google.com/patents/","institution":{"id":1508,"name":"Google Incorporated","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"US4145692","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1510,"prefix":"uspto","mirId":"MIR:00000538","name":"USPTO","pattern":"^(D|PP|R|T|H|X|AI)?\\d+$","description":"The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. 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The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.","created":"2019-06-11T14:17:43.853+0000","modified":"2019-06-11T14:17:43.853+0000","resources":[{"id":1515,"mirId":"MIR:00100716","urlPattern":"https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC={$id}","name":"Cooperative Patent Classification at Espace","description":"Cooperative Patent Classification at Espace","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"A01M1/026","resourceHomeUrl":"https://worldwide.espacenet.com/classification","institution":{"id":1514,"name":"Espace, European Patent Office","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"A01M1/026","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1516,"prefix":"gwascentral.study","mirId":"MIR:00000540","name":"GWAS Central Study","pattern":"^HGVST\\d+$","description":"GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. 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This collection references a GWAS Central Study.","created":"2019-06-11T14:17:44.062+0000","modified":"2019-06-11T14:17:44.062+0000","resources":[{"id":1517,"mirId":"MIR:00100717","urlPattern":"https://www.gwascentral.org/study/{$id}","name":"GWAS Central Study at University of Leicester","description":"GWAS Central Study at University of Leicester","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"HGVST1828","resourceHomeUrl":"https://www.gwascentral.org/studies","institution":{"id":1079,"name":"Department of Genetics, University of Leicester, Leicester","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"HGVST1828","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1518,"prefix":"exac.variant","mirId":"MIR:00000541","name":"ExAC Variant","pattern":"^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$","description":"The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.","created":"2019-06-11T14:17:44.275+0000","modified":"2019-06-11T14:17:44.275+0000","resources":[{"id":1520,"mirId":"MIR:00100718","urlPattern":"http://exac.broadinstitute.org/variant/{$id}","name":"ExAC Variant at Exome Aggregation Consortium","description":"ExAC Variant at Exome Aggregation Consortium","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"22-46615880-T-C","resourceHomeUrl":"http://exac.broadinstitute.org/","institution":{"id":1519,"name":"Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"22-46615880-T-C","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1521,"prefix":"gwascentral.marker","mirId":"MIR:00000542","name":"GWAS Central Marker","pattern":"^HGVM\\d+$","description":"GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. 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This collection references a GWAS Central Marker.","created":"2019-06-11T14:17:44.511+0000","modified":"2019-06-11T14:17:44.511+0000","resources":[{"id":1522,"mirId":"MIR:00100719","urlPattern":"https://www.gwascentral.org/marker/{$id}","name":"GWAS Central Marker at University of Leicester","description":"GWAS Central Marker at University of Leicester","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"HGVM15354","resourceHomeUrl":"https://www.gwascentral.org/markers/","institution":{"id":1079,"name":"Department of Genetics, University of Leicester, Leicester","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"HGVM15354","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1555,"prefix":"bigg.metabolite","mirId":"MIR:00000556","name":"BiGG Metabolite","pattern":"^[a-z_A-Z0-9]+$","description":"BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references individual metabolotes.","created":"2019-06-11T14:17:47.850+0000","modified":"2019-06-11T14:17:47.850+0000","resources":[{"id":1556,"mirId":"MIR:00100733","urlPattern":"http://bigg.ucsd.edu/models/universal/metabolites/{$id}","name":"BiGG Metabolite at University of Cakifornia","description":"BiGG Metabolite at University of Cakifornia","official":false,"providerCode":"ucsd","sampleId":"12dgr161","resourceHomeUrl":"http://bigg.ucsd.edu/universal/metabolites","institution":{"id":190,"name":"University of California, San Diego","homeUrl":"https://ucsd.edu/","description":"is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.","rorId":"https://ror.org/0168r3w48","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"12dgr161","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1525,"prefix":"lincs.cell","mirId":"MIR:00000544","name":"LINCS Cell","pattern":"(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)","description":"The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. 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The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.","created":"2019-06-11T14:17:44.903+0000","modified":"2019-06-11T14:17:44.903+0000","resources":[{"id":1527,"mirId":"MIR:00100721","urlPattern":"http://lincsportal.ccs.miami.edu/cells/#/view/{$id}","name":"LINCS Portal","description":"LINCS Portal","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"LCL-2085","resourceHomeUrl":"http://lincsportal.ccs.miami.edu/cells/","institution":{"id":1526,"name":"University of Miami, BD2K-LINCS DCIC","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"LCL-2085","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1528,"prefix":"lincs.protein","mirId":"MIR:00000545","name":"LINCS Protein","pattern":"^\\d+$","description":"The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). 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UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.","created":"2019-06-11T14:17:48.502+0000","modified":"2019-06-11T14:17:48.502+0000","resources":[{"id":1562,"mirId":"MIR:00100736","urlPattern":"http://linkedlifedata.com/resource/umls/id/{$id}","name":"Unified Medical Language System at LinkedLifeData","description":"Unified Medical Language System at LinkedLifeData","official":true,"providerCode":"CURATOR_REVIEW","sampleId":"C0021390","resourceHomeUrl":"http://linkedlifedata.com/","institution":{"id":63,"name":"Linkedlifedata, Ontotext, Sofia","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"BG","countryName":"Bulgaria"}},"location":{"countryCode":"BG","countryName":"Bulgaria"},"deprecated":false,"deprecationDate":null}],"sampleId":"C0021390","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1565,"prefix":"emdb","mirId":"MIR:00000561","name":"Electron Microscopy Data Bank","pattern":"^EMD-\\d{4}$","description":"The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. 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The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).","created":"2019-06-11T14:17:49.428+0000","modified":"2019-06-11T14:17:49.428+0000","resources":[{"id":1571,"mirId":"MIR:00100740","urlPattern":"http://purl.bioontology.org/ontology/MEDDRA/{$id}","name":"MedDRA through BioPortal","description":"MedDRA through BioPortal","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"10015919","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/MEDDRA","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"10015919","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1572,"prefix":"dashr","mirId":"MIR:00000564","name":"DASHR","pattern":"^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$","description":"DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. 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The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition.","created":"2019-06-11T14:17:26.654+0000","modified":"2019-06-11T14:17:26.654+0000","resources":[{"id":1332,"mirId":"MIR:00100600","urlPattern":"http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist={$id}","name":"YDPM at Stanford University School of Medicine","description":"YDPM at Stanford University School of Medicine","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"YAL001C","resourceHomeUrl":"http://www-deletion.stanford.edu/YDPM/","institution":{"id":1331,"name":"Stanford University School of Medicine, Stanford, California","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"YAL001C","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1333,"prefix":"wb.rnai","mirId":"MIR:00000466","name":"WormBase RNAi","pattern":"^WBRNAi\\d{8}$","description":"WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. 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This collection references ICE elements.","created":"2019-06-11T14:17:27.338+0000","modified":"2019-06-11T14:17:27.338+0000","resources":[{"id":1340,"mirId":"MIR:00100604","urlPattern":"http://db-mml.sjtu.edu.cn/ICEberg/feature_page.php?ice_id={$id}","name":"ICEberg element at Shanghai Jiaotong University","description":"ICEberg element at Shanghai Jiaotong University","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"100","resourceHomeUrl":"http://db-mml.sjtu.edu.cn/ICEberg/","institution":{"id":1339,"name":"State Key Laboratory of Microbial Metabolism and School of Life Sciences &amp;amp;amp; Biotechnology, Shanghai Jiaotong University, Shanghai","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"CN","countryName":"China"}},"location":{"countryCode":"CN","countryName":"China"},"deprecated":false,"deprecationDate":null}],"sampleId":"100","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1341,"prefix":"iceberg.family","mirId":"MIR:00000470","name":"ICEberg family","pattern":"^\\d+$","description":"ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. 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This collection refers to growth stage ontology information in Gramene.","created":"2019-06-11T14:17:36.384+0000","modified":"2019-06-11T14:17:36.384+0000","resources":[{"id":1438,"mirId":"MIR:00100649","urlPattern":"http://www.gramene.org/db/ontology/search?id=GRO:{$id}","name":"Gramene Growth Stage Ontology at Cold Spring Harbor","description":"Gramene Growth Stage Ontology at Cold Spring Harbor","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"0007133","resourceHomeUrl":"http://www.gramene.org/","institution":{"id":556,"name":"Cold Spring Harbor Laboratory, New York","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"0007133","namespaceEmbeddedInLui":true,"deprecated":false,"deprecationDate":null},{"id":1439,"prefix":"mgnify.samp","mirId":"MIR:00000510","name":"MGnify Sample","pattern":"^[A-Z]+[0-9]+$","description":"The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the phylogenetic diversity as well as the functional and metabolic potential of a sample. Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. This collection references samples.","created":"2019-06-11T14:17:36.594+0000","modified":"2019-06-11T14:17:36.594+0000","resources":[{"id":1440,"mirId":"MIR:00100656","urlPattern":"https://www.ebi.ac.uk/metagenomics/samples/{$id}","name":"MGnify Sample","description":"MGnify Sample","official":false,"providerCode":"ebi","sampleId":"SRS086444","resourceHomeUrl":"https://www.ebi.ac.uk/metagenomics","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"SRS086444","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1441,"prefix":"ega.study","mirId":"MIR:00000511","name":"European Genome-phenome Archive Study","pattern":"^EGAS\\d{11}$","description":"The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Studies' which are experimental investigations of a particular phenomenon, often drawn from different datasets.","created":"2019-06-11T14:17:36.823+0000","modified":"2019-06-11T14:17:36.823+0000","resources":[{"id":1442,"mirId":"MIR:00100657","urlPattern":"https://www.ebi.ac.uk/ega/studies/{$id}","name":"EGA Study at European Bioinformatics Institute","description":"EGA Study at European Bioinformatics Institute","official":true,"providerCode":"ebi","sampleId":"EGAS00000000001","resourceHomeUrl":"https://www.ebi.ac.uk/ega/studies","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1443,"mirId":"MIR:00100851","urlPattern":"https://www.omicsdi.org/dataset/ega/{$id}","name":"EGA Study through OmicsDI","description":"EGA Study through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"EGAS00000000001","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"EGAS00000000001","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1444,"prefix":"ega.dataset","mirId":"MIR:00000512","name":"European Genome-phenome Archive Dataset","pattern":"^EGAD\\d{11}$","description":"The EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. This collection references 'Datasets'.","created":"2019-06-11T14:17:37.233+0000","modified":"2019-06-11T14:17:37.233+0000","resources":[{"id":1445,"mirId":"MIR:00100658","urlPattern":"https://www.ebi.ac.uk/ega/datasets/{$id}","name":"EGA Dataset at European Bioinformatics Institute","description":"EGA Dataset at European Bioinformatics Institute","official":true,"providerCode":"ebi","sampleId":"EGAD00000000001","resourceHomeUrl":"https://www.ebi.ac.uk/ega/dataset","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1446,"mirId":"MIR:00100852","urlPattern":"https://www.omicsdi.org/dataset/ega/{$id}","name":"EGA Dataset through OmicsDI","description":"EGA Dataset through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"EGAD00000000001","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"EGAD00000000001","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1453,"prefix":"pride.project","mirId":"MIR:00000515","name":"PRIDE Project","pattern":"^P(X|R)D\\d{6}$","description":"The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects.","created":"2019-06-11T14:17:38.030+0000","modified":"2019-06-11T14:17:38.030+0000","resources":[{"id":1454,"mirId":"MIR:00100662","urlPattern":"https://www.ebi.ac.uk/pride/archive/projects/{$id}","name":"PRIDE Project at EBI","description":"PRIDE Project at EBI","official":true,"providerCode":"ebi","sampleId":"PXD000440","resourceHomeUrl":"https://www.ebi.ac.uk/pride/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null},{"id":1455,"mirId":"MIR:00100858","urlPattern":"https://www.omicsdi.org/dataset/pride/{$id}","name":"PRIDE Project through OmicsDI","description":"PRIDE Project through OmicsDI","official":false,"providerCode":"omicsdi","sampleId":"PXD000440","resourceHomeUrl":"https://www.omicsdi.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"PXD000440","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1456,"prefix":"antibodyregistry","mirId":"MIR:00000516","name":"Antibody Registry","pattern":"^\\d{6}$","description":"The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information.","created":"2019-06-11T14:17:38.379+0000","modified":"2019-06-11T14:17:38.379+0000","resources":[{"id":1458,"mirId":"MIR:00100664","urlPattern":"http://antibodyregistry.org/AB_{$id}","name":"Antibody Registry at University of California","description":"Antibody Registry at University of California","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"493771","resourceHomeUrl":"http://antibodyregistry.org/","institution":{"id":1457,"name":"Neuroscience Information Framework, University of California, San Diego, California","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"493771","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1459,"prefix":"mamo","mirId":"MIR:00000517","name":"Mathematical Modelling Ontology","pattern":"^MAMO_\\d{7}$","description":"The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.","created":"2019-06-11T14:17:38.625+0000","modified":"2019-06-11T14:17:38.625+0000","resources":[{"id":1460,"mirId":"MIR:00100665","urlPattern":"http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/{$id}","name":"MAMO through BioPortal","description":"MAMO through BioPortal","official":false,"providerCode":"bptl","sampleId":"MAMO_0000026","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/MAMO","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1461,"mirId":"MIR:00100758","urlPattern":"https://www.ebi.ac.uk/ols/ontologies/mamo/terms?short_form={$id}","name":"MaMO through OLS","description":"MaMO through OLS","official":false,"providerCode":"ols","sampleId":"MAMO_0000026","resourceHomeUrl":"https://www.ebi.ac.uk/ols/ontologies/mamo","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"MAMO_0000026","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1462,"prefix":"eo","mirId":"MIR:00000518","name":"Plant Environment Ontology","pattern":"^(P)?EO\\:\\d{7}$","description":"The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies.","created":"2019-06-11T14:17:38.985+0000","modified":"2019-06-11T14:17:38.985+0000","resources":[{"id":1463,"mirId":"MIR:00100667","urlPattern":"http://archive.gramene.org/db/ontology/search?query=EO:{$id}","name":"Plant Environment Ontology through Gramene","description":"Plant Environment Ontology through Gramene","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"0007404","resourceHomeUrl":"http://archive.gramene.org/db/ontology/search_term?id=EO:0007359","institution":{"id":556,"name":"Cold Spring Harbor Laboratory, New York","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1464,"mirId":"MIR:00100668","urlPattern":"http://purl.bioontology.org/ontology/PECO/EO:{$id}","name":"Plant Environment Ontology through BioPortal","description":"Plant Environment Ontology through BioPortal","official":false,"providerCode":"bptl","sampleId":"0007404","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/PECO","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null},{"id":1465,"mirId":"MIR:00100669","urlPattern":"https://www.ebi.ac.uk/ols/ontologies/eo/terms?obo_id=EO:{$id}","name":"Plant Environment Ontology through OLS","description":"Plant Environment Ontology through OLS","official":false,"providerCode":"ols","sampleId":"0007404","resourceHomeUrl":"https://www.ebi.ac.uk/ols/ontologies/eo","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"0007404","namespaceEmbeddedInLui":true,"deprecated":false,"deprecationDate":null},{"id":1466,"prefix":"idot","mirId":"MIR:00000519","name":"Identifiers.org Terms","pattern":"^[A-Za-z]+$","description":"Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets.","created":"2019-06-11T14:17:39.487+0000","modified":"2019-06-11T14:17:39.487+0000","resources":[{"id":1467,"mirId":"MIR:00100670","urlPattern":"https://biomodels.net/vocab/idot.rdf#{$id}","name":"IdoT via biomodels.net","description":"IdoT via biomodels.net","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"identifierPattern","resourceHomeUrl":"https://identifiers.org/","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"identifierPattern","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1470,"prefix":"yeastintron","mirId":"MIR:00000521","name":"Yeast Intron Database v4.3","pattern":"^[A-Z0-9]+$","description":"The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460].","created":"2019-06-11T14:17:39.906+0000","modified":"2019-06-11T14:17:39.906+0000","resources":[{"id":1471,"mirId":"MIR:00100673","urlPattern":"http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName={$id}","name":"Yeast Intron Database version 4.3 at Baskin School of Engineering","description":"Yeast Intron Database version 4.3 at Baskin School of Engineering","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"SNR17A","resourceHomeUrl":"http://intron.ucsc.edu/yeast4.3/","institution":{"id":1319,"name":"University of California, Santa Cruz","homeUrl":"https://www.ucsc.edu","description":"UC Santa Cruz opened in 1965 with 650 students. During the 2018-2019 academic year, 16,983 undergraduate and 1,822 graduate students were enrolled.\n","rorId":"https://ror.org/03s65by71","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"SNR17A","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1472,"prefix":"ardb","mirId":"MIR:00000522","name":"Antibiotic Resistance Genes Database","pattern":"^[A-Z_]{3}[0-9]{4,}$","description":"The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes.","created":"2019-06-11T14:17:40.104+0000","modified":"2019-06-11T14:17:40.104+0000","resources":[{"id":1474,"mirId":"MIR:00100678","urlPattern":"http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term={$id}","name":"ARDB at University of Maryland","description":"ARDB at University of Maryland","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"CAE46076","resourceHomeUrl":"http://ardb.cbcb.umd.edu/","institution":{"id":1473,"name":"Center for Bioinformatics and Computational Biology, University of Maryland, Maryland","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"CAE46076","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1475,"prefix":"proteomicsdb.protein","mirId":"MIR:00000524","name":"ProteomicsDB Protein","pattern":"^\\d+$","description":"ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins.","created":"2019-06-11T14:17:40.344+0000","modified":"2019-06-11T14:17:40.344+0000","resources":[{"id":1477,"mirId":"MIR:00100680","urlPattern":"https://www.proteomicsdb.org/#human/proteinDetails/{$id}/summary","name":"Proteomics DB Protein at Center for Integrated Protein Science","description":"Proteomics DB Protein at Center for Integrated Protein Science","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"53504","resourceHomeUrl":"https://www.proteomicsdb.org/#human","institution":{"id":1476,"name":"Center for Integrated Protein Science, Munich,","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"DE","countryName":"Germany"}},"location":{"countryCode":"DE","countryName":"Germany"},"deprecated":false,"deprecationDate":null}],"sampleId":"53504","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1478,"prefix":"proteomicsdb.peptide","mirId":"MIR:00000525","name":"ProteomicsDB Peptide","pattern":"^\\d+$","description":"ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to the peptides identified for a given protein.","created":"2019-06-11T14:17:40.583+0000","modified":"2019-06-11T14:17:40.583+0000","resources":[{"id":1480,"mirId":"MIR:00100681","urlPattern":"https://www.proteomicsdb.org/#human/proteinDetails/{$id}/peptides/","name":"Proteomics DB Peptide at Center for Integrated Protein Science","description":"Proteomics DB Peptide at Center for Integrated Protein Science","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"53504","resourceHomeUrl":"https://www.proteomicsdb.org/#peptideSearch","institution":{"id":1479,"name":"Center for Integrated Protein Science, Munich","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"DE","countryName":"Germany"}},"location":{"countryCode":"DE","countryName":"Germany"},"deprecated":false,"deprecationDate":null}],"sampleId":"53504","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1481,"prefix":"hpm.protein","mirId":"MIR:00000526","name":"Human Proteome Map Protein","pattern":"^\\d+$","description":"The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. The project was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. The HPM contains direct evidence of translation of a number of protein products derived from human genes, based on peptide identifications of multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. The HPM portal provides data on individual proteins, as well as on individual peptide spectra. This collection references proteins.","created":"2019-06-11T14:17:40.825+0000","modified":"2019-06-11T14:17:40.825+0000","resources":[{"id":1482,"mirId":"MIR:00100682","urlPattern":"http://www.humanproteomemap.org/protein.php?hpm_id={$id}","name":"Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)","description":"Human Proteome Map Protein at Institute of Bioinformatics (Bangalore)","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"1968","resourceHomeUrl":"http://www.humanproteomemap.org/index.php","institution":{"id":1087,"name":"Institute of Bioinformatics, International Tech Park, Bangalore","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"IN","countryName":"India"}},"location":{"countryCode":"IN","countryName":"India"},"deprecated":false,"deprecationDate":null}],"sampleId":"1968","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1483,"prefix":"hpm.peptide","mirId":"MIR:00000527","name":"Human Proteome Map Peptide","pattern":"^\\d+$","description":"The Human Proteome Map (HPM) portal integrates the peptide sequencing result from the draft map of the human proteome project. 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This collection references the Record Report, based on RCV accession.","created":"2019-06-11T14:17:42.685+0000","modified":"2019-06-11T14:17:42.685+0000","resources":[{"id":1501,"mirId":"MIR:00100710","urlPattern":"http://www.ncbi.nlm.nih.gov/clinvar/{$id}/","name":"ClinVar Record at NCBI","description":"ClinVar Record at NCBI","official":false,"providerCode":"ncbi","sampleId":"RCV000033555.3","resourceHomeUrl":"http://www.ncbi.nlm.nih.gov/clinvar/","institution":{"id":26,"name":"National Center for Biotechnology Information","homeUrl":"https://www.ncbi.nlm.nih.gov/","description":"The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.","rorId":"https://ror.org/02meqm098","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"RCV000033555.3","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1502,"prefix":"mgnify.proj","mirId":"MIR:00000535","name":"MGnify Project","pattern":"^[A-Z]+[0-9]+$","description":"MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis.","created":"2019-06-11T14:17:42.938+0000","modified":"2019-06-11T14:17:42.938+0000","resources":[{"id":1503,"mirId":"MIR:00100711","urlPattern":"https://www.ebi.ac.uk/metagenomics/projects/{$id}","name":"MGnify Project","description":"MGnify Project","official":false,"providerCode":"ebi","sampleId":"ERP004492","resourceHomeUrl":"https://www.ebi.ac.uk/metagenomics","institution":{"id":2,"name":"European Bioinformatics Institute","homeUrl":"https://www.ebi.ac.uk","description":"At EMBL-EBI, we make the world’s public biological data freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. \nWe are part of the European Molecular Biology Laboratory (EMBL), an international, innovative and interdisciplinary research organisation funded by 26 member states and two associate member states.","rorId":"https://ror.org/02catss52","location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"ERP004492","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1504,"prefix":"euclinicaltrials","mirId":"MIR:00000536","name":"EU Clinical Trials","pattern":"^\\d{4}\\-\\d{6}\\-\\d{2}$","description":"The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population.","created":"2019-06-11T14:17:43.129+0000","modified":"2019-06-11T14:17:43.129+0000","resources":[{"id":1506,"mirId":"MIR:00100712","urlPattern":"https://www.clinicaltrialsregister.eu/ctr-search/search?query={$id}","name":"EU Clinical Trials at European Medicines Agency","description":"EU Clinical Trials at European Medicines Agency","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"2008-005144-16","resourceHomeUrl":"https://www.clinicaltrialsregister.eu/","institution":{"id":1505,"name":"European Medicines Agency, London","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"2008-005144-16","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1507,"prefix":"google.patent","mirId":"MIR:00000537","name":"Google Patents","pattern":"^[A-Z]{2}\\d+([A-Z])?$","description":"Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date.","created":"2019-06-11T14:17:43.371+0000","modified":"2019-06-11T14:17:43.371+0000","resources":[{"id":1509,"mirId":"MIR:00100714","urlPattern":"https://www.google.com/patents/{$id}","name":"Google Patents at Google","description":"Google Patents at Google","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"US4145692","resourceHomeUrl":"https://www.google.com/patents/","institution":{"id":1508,"name":"Google Incorporated","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"US4145692","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1510,"prefix":"uspto","mirId":"MIR:00000538","name":"USPTO","pattern":"^(D|PP|R|T|H|X|AI)?\\d+$","description":"The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. 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The CPC patent classification system has been used by EPO and USPTO since 1st January, 2013.","created":"2019-06-11T14:17:43.853+0000","modified":"2019-06-11T14:17:43.853+0000","resources":[{"id":1515,"mirId":"MIR:00100716","urlPattern":"https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC={$id}","name":"Cooperative Patent Classification at Espace","description":"Cooperative Patent Classification at Espace","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"A01M1/026","resourceHomeUrl":"https://worldwide.espacenet.com/classification","institution":{"id":1514,"name":"Espace, European Patent Office","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"A01M1/026","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1516,"prefix":"gwascentral.study","mirId":"MIR:00000540","name":"GWAS Central Study","pattern":"^HGVST\\d+$","description":"GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. 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This collection references a GWAS Central Study.","created":"2019-06-11T14:17:44.062+0000","modified":"2019-06-11T14:17:44.062+0000","resources":[{"id":1517,"mirId":"MIR:00100717","urlPattern":"https://www.gwascentral.org/study/{$id}","name":"GWAS Central Study at University of Leicester","description":"GWAS Central Study at University of Leicester","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"HGVST1828","resourceHomeUrl":"https://www.gwascentral.org/studies","institution":{"id":1079,"name":"Department of Genetics, University of Leicester, Leicester","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"HGVST1828","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1518,"prefix":"exac.variant","mirId":"MIR:00000541","name":"ExAC Variant","pattern":"^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$","description":"The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references variant information.","created":"2019-06-11T14:17:44.275+0000","modified":"2019-06-11T14:17:44.275+0000","resources":[{"id":1520,"mirId":"MIR:00100718","urlPattern":"http://exac.broadinstitute.org/variant/{$id}","name":"ExAC Variant at Exome Aggregation Consortium","description":"ExAC Variant at Exome Aggregation Consortium","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"22-46615880-T-C","resourceHomeUrl":"http://exac.broadinstitute.org/","institution":{"id":1519,"name":"Exome Aggregation Consortium (ExAC), Cambridge, Massachusetts","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"22-46615880-T-C","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1521,"prefix":"gwascentral.marker","mirId":"MIR:00000542","name":"GWAS Central Marker","pattern":"^HGVM\\d+$","description":"GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. 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This collection references a GWAS Central Marker.","created":"2019-06-11T14:17:44.511+0000","modified":"2019-06-11T14:17:44.511+0000","resources":[{"id":1522,"mirId":"MIR:00100719","urlPattern":"https://www.gwascentral.org/marker/{$id}","name":"GWAS Central Marker at University of Leicester","description":"GWAS Central Marker at University of Leicester","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"HGVM15354","resourceHomeUrl":"https://www.gwascentral.org/markers/","institution":{"id":1079,"name":"Department of Genetics, University of Leicester, Leicester","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"GB","countryName":"United Kingdom"}},"location":{"countryCode":"GB","countryName":"United Kingdom"},"deprecated":false,"deprecationDate":null}],"sampleId":"HGVM15354","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1555,"prefix":"bigg.metabolite","mirId":"MIR:00000556","name":"BiGG Metabolite","pattern":"^[a-z_A-Z0-9]+$","description":"BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. 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This collection references individual metabolotes.","created":"2019-06-11T14:17:47.850+0000","modified":"2019-06-11T14:17:47.850+0000","resources":[{"id":1556,"mirId":"MIR:00100733","urlPattern":"http://bigg.ucsd.edu/models/universal/metabolites/{$id}","name":"BiGG Metabolite at University of Cakifornia","description":"BiGG Metabolite at University of Cakifornia","official":false,"providerCode":"ucsd","sampleId":"12dgr161","resourceHomeUrl":"http://bigg.ucsd.edu/universal/metabolites","institution":{"id":190,"name":"University of California, San Diego","homeUrl":"https://ucsd.edu/","description":"is a public research university in San Diego, California.\nEstablished in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh-oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling approximately 30,000 undergraduate and 8,500 graduate students.","rorId":"https://ror.org/0168r3w48","location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"12dgr161","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1525,"prefix":"lincs.cell","mirId":"MIR:00000544","name":"LINCS Cell","pattern":"(^LCL-\\d+$)|(^LDC-\\d+$)|(^ES-\\d+$)|(^LSC-\\d+$)|(^LPC-\\d+$)","description":"The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. 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The metadata contains information provided by each LINCS Data and Signature Generation Center (DSGC) and the association with a tissue or organ from which the cells were derived, in many cases are also associated to a disease.","created":"2019-06-11T14:17:44.903+0000","modified":"2019-06-11T14:17:44.903+0000","resources":[{"id":1527,"mirId":"MIR:00100721","urlPattern":"http://lincsportal.ccs.miami.edu/cells/#/view/{$id}","name":"LINCS Portal","description":"LINCS Portal","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"LCL-2085","resourceHomeUrl":"http://lincsportal.ccs.miami.edu/cells/","institution":{"id":1526,"name":"University of Miami, BD2K-LINCS DCIC","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"LCL-2085","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1528,"prefix":"lincs.protein","mirId":"MIR:00000545","name":"LINCS Protein","pattern":"^\\d+$","description":"The HMS LINCS Database currently contains information on experimental reagents (small molecule perturbagens, cells, and proteins). 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UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank.","created":"2019-06-11T14:17:48.502+0000","modified":"2019-06-11T14:17:48.502+0000","resources":[{"id":1562,"mirId":"MIR:00100736","urlPattern":"http://linkedlifedata.com/resource/umls/id/{$id}","name":"Unified Medical Language System at LinkedLifeData","description":"Unified Medical Language System at LinkedLifeData","official":true,"providerCode":"CURATOR_REVIEW","sampleId":"C0021390","resourceHomeUrl":"http://linkedlifedata.com/","institution":{"id":63,"name":"Linkedlifedata, Ontotext, Sofia","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"BG","countryName":"Bulgaria"}},"location":{"countryCode":"BG","countryName":"Bulgaria"},"deprecated":false,"deprecationDate":null}],"sampleId":"C0021390","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1565,"prefix":"emdb","mirId":"MIR:00000561","name":"Electron Microscopy Data Bank","pattern":"^EMD-\\d{4}$","description":"The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. 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The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT).","created":"2019-06-11T14:17:49.428+0000","modified":"2019-06-11T14:17:49.428+0000","resources":[{"id":1571,"mirId":"MIR:00100740","urlPattern":"http://purl.bioontology.org/ontology/MEDDRA/{$id}","name":"MedDRA through BioPortal","description":"MedDRA through BioPortal","official":false,"providerCode":"CURATOR_REVIEW","sampleId":"10015919","resourceHomeUrl":"http://bioportal.bioontology.org/ontologies/MEDDRA","institution":{"id":5,"name":"National Center for Biomedical Ontology, Stanford","homeUrl":"CURATOR_REVIEW","description":"CURATOR_REVIEW","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"10015919","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null},{"id":1572,"prefix":"dashr","mirId":"MIR:00000564","name":"DASHR","pattern":"^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$","description":"DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. 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","official":true,"providerCode":"ror","sampleId":"03yrm5c26","resourceHomeUrl":"https://ror.org","institution":{"id":3270,"name":"California Digital Library","homeUrl":"https://www.cdlib.org/","description":"Organization information obtained from ROR API using ROR ID 'https://ror.org/03yrm5c26' with Wikidata IDs [Q5020447], and ISNI IDs [0000 0001 1957 5136]","rorId":null,"location":{"countryCode":"US","countryName":"United States"}},"location":{"countryCode":"US","countryName":"United States"},"deprecated":false,"deprecationDate":null}],"sampleId":"03yrm5c26","namespaceEmbeddedInLui":false,"deprecated":false,"deprecationDate":null}]}} \ No newline at end of file diff --git a/src/bioregistry/data/external/obofoundry/raw.yaml b/src/bioregistry/data/external/obofoundry/raw.yaml index ecba4f841..34a402ec4 100644 --- a/src/bioregistry/data/external/obofoundry/raw.yaml +++ b/src/bioregistry/data/external/obofoundry/raw.yaml @@ -1230,6 +1230,18 @@ ontologies: repository: https://github.com/semanticchemistry/semanticchemistry title: Chemical Information Ontology tracker: https://github.com/semanticchemistry/semanticchemistry/issues + usages: + - description: ChEMBL uses CHEMINF in the RDF download + examples: + - description: The RDF is provided as SPARQL endpoint by Maastricht University. + url: https://chemblmirror.rdf.bigcat-bioinformatics.org/ + user: https://www.ebi.ac.uk/chembl/ + - description: PubChem uses CHEMINF in their RDF representation + examples: + - description: Physicochemical properties are represented as classes that are + typed with CHEMINF classes + url: https://pubchem.ncbi.nlm.nih.gov/rest/rdf/descriptor/CID161282_Canonical_SMILES + user: https://pubchem.ncbi.nlm.nih.gov/ - activity_status: active build: checkout: git clone https://github.com/obophenotype/chiro.git diff --git a/src/bioregistry/data/external/re3data/curation.tsv b/src/bioregistry/data/external/re3data/curation.tsv index b8c646f9b..026b68409 100644 --- a/src/bioregistry/data/external/re3data/curation.tsv +++ b/src/bioregistry/data/external/re3data/curation.tsv @@ -396,7 +396,7 @@ r3d100010293 World Data Center for Cosmic Rays http://cidas.isee.nagoya-u.ac.jp/ r3d100010294 WDC for Ionosphere and Space Weather http://wdc.nict.go.jp/wdc_e.html National Institute of Information and Communications Technology (NICT) has taken charge of the WDC for Ionosphere. WDC for Ionosphere archives ionospheric data and metadata from approximately 250 stations across the globe. r3d100010295 Nobeyama Radio Polarimeters http://solar.nro.nao.ac.jp/norp/ Nobeyama Radio Polarimeters (NoRP) are observing the Sun with multiple frequencies in the microwave range. It is capable to obtain the total coming flux and the circular-polarization degree. r3d100010297 Cold and Arid Regions Science Data Center at Lanzhou http://card.westgis.ac.cn/ World Data System for Cold and Arid Regions(CARD) is a new scientific data sharing system which is established on the basis of the former World Data Center for Glaciology and Geocryology, Lanzhou and other data centers hosted by Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences. World Data System for Cold and Arid Regions is one of the constituents of World Data System. The data sharing system's main goals are to collect, manage and store the scientific data of Cold and Arid Regions area in China and provide the services for the scientific research of Cold and Arid Regions. -r3d100010299 World Data Center for Climate https://www.dkrz.de/up/systems/wdcc The mission of World Data Center for Climate (WDCC) is to provide central support for the German and European climate research community. The WDCC is member of the ISC's World Data System. Emphasis is on development and implementation of best practice methods for Earth System data management. Data for and from climate research are collected, stored and disseminated. The WDCC is restricted to data products. Cooperations exist with thematically corresponding data centres of, e.g., earth observation, meteorology, oceanography, paleo climate and environmental sciences. The services of WDCC are also available to external users at cost price. A special service for the direct integration of research data in scientific publications has been developed. The editorial process at WDCC ensures the quality of metadata and research data in collaboration with the data producers. A citation code and a digital identifier (DOI) are provided and registered together with citation information at the DOI registration agency DataCite. +r3d100010299 World Data Center for Climate https://wdc-climate.de The mission of World Data Center for Climate (WDCC) is to provide central support for the German and European climate research community. The WDCC is member of the ISC's World Data System. Emphasis is on development and implementation of best practice methods for Earth System data management. Data for and from climate research are collected, stored and disseminated. The WDCC is restricted to data products. Cooperations exist with thematically corresponding data centres of, e.g., earth observation, meteorology, oceanography, paleo climate and environmental sciences. The services of WDCC are also available to external users at cost price. A special service for the direct integration of research data in scientific publications has been developed. The editorial process at WDCC ensures the quality of metadata and research data in collaboration with the data producers. A citation code and a digital identifier (DOI) are provided and registered together with citation information at the DOI registration agency DataCite. r3d100010300 International Geodynamics and Earth Tide Service http://isdc.gfz-potsdam.de/igets-data-base/ IGETS is the International Geodynamics and Earth Tide Service of the International Association of Geodesy (IAG). The main objective of IGETS is to monitor temporal variations of the Earth gravity field through long‐term records from ground gravimeters, tiltmeters, strainmeters and other geodynamic sensors. IGETS continues the activities of the Global Geodynamics Project (GGP) to provide support to geodetic and geophysical research activities using superconducting gravimeter (SG) data within the context of an international network. Furthermore, IGETS continues the activities of the International Center for Earth Tides (ICET), in particular, in collecting, archiving and distributing Earth tide records from long series of gravimeters, tiltmeters, strainmeters and other geodynamic sensors. GFZ is the main Data Center and operates the IGETS data base of worldwide high precision SG records. EOST (Ecole et Observatoire des Sciences de la Terre, Strasbourg, France) is the secondary Data Center, The University of French Polynesia (Tahiti) and EOST (Strasbourg, France) are the two current Analysis Centers. @@ -1348,7 +1348,7 @@ The data come primarily from the imaging beamlines of the Helmholtz Center Geest r3d100011126 Integrated Digitized Biocollections https://www.idigbio.org/ The National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation. Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public r3d100011128 National Vegetation Survey Databank https://nvs.landcareresearch.co.nz/ The National Vegetation Survey (NVS) Databank is a physical archive and electronic databank containing records of over 121,000 vegetation survey plots - including data from over 25,000 permanent plots in New Zealand. The data can be explored online and requested for download. The NVS Databank provides data spanning more than 60 years of indigenous and exotic plant plot records from throughout New Zealand's terrestrial ecosystems. The physical archive includes plot sheets, maps, and photographs from many years of vegetation surveys. Purpose-built software for entering, validating and summarising data is available. NVS is accorded the status of a Nationally Significant database and upkeep and maintenance is supported by Core funding for Crown Research Institutes from the NZ Ministry of Business, Innovation and Employment. r3d100011129 Nanomaterial Registry https://nanomaterialregistry.net/Default.aspx The Nanomaterial Registry is a publicly available repository for curated research data on nanomaterials, including their physico-chemical characteristics and their interactions with biological and environmental systems. -r3d100011130 e!DAL - electronic Data Archive Library https://edal.ipk-gatersleben.de/ e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is "Plant Genomics and Phenomics Research Data Repository" [https://doi.org/10.1093/database/baw033]. +r3d100011130 e!DAL - electronic Data Archive Library https://edal.ipk-gatersleben.de/ !!! <<< this record is no longer maintained, please use https://www.re3data.org/repository/r3d100011876 or https://www.re3data.org/repository/r3d100011647 >>> !!!: e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is "Plant Genomics and Phenomics Research Data Repository" [https://doi.org/10.1093/database/baw033]. r3d100011131 Panel Study on Income Dynamics https://psidonline.isr.umich.edu/ A national study on socioeconomics and family health over lifetimes and across generations funded by National Science Foundation (NSF). It is the longest running longitudinal household survey in the world, started in 1968 with a nationally representative sample of over 18,000 individuals living in 5,000 families in the United States. It is recognizing the importance of the socioeconomic data, available on this website without cost to researchers and analysts. r3d100011132 Social Scientific Research Documentation Centre Repository https://openarchive.tk.mta.hu/ The Research Documentation Centre of the Centre for Social Sciences at the Hungarian Academy of Sciences provides information on and access to research conducted at the Centre. The metadata and many of the documents of the Research Documentation Centre (RDC) are available to all visitors. External researchers may ask for access to restricted collections r3d100011135 Integrated Public Use Microdata Series - International https://international.ipums.org/international/ IPUMS is the world's largest accessible collection of individual-level data on population, and is a collaboration of over 100 national statistical agencies. @@ -2244,7 +2244,7 @@ The component ‘LIAS names’ is a platform for managing taxonomic names and cl The LIAS portal contents, interfaces, and databases run on servers of the IT Center of the Bavarian Natural History Collections and are maintained there. 'LIAS names' and ‘LIAS light’ also deliver content data to the Catalogue of Life, acting as the Global Species Database (GSD) for lichens. LIAS gtm is a database for visualising the geographic distribution of lichen traits. LIAS is powered by the Diversity Workbench database framework with several interfaces for data management and publication. The LIAS long-term project was initiated in the early 1990s and has since been continued with funding from the DFG, the BMBF, and the EU. r3d100011873 Staatliche Naturwissenschaftliche Sammlungen Bayerns https://www.snsb.de/index.php/en/ The Bavarian Natural History Collections (Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB) are a research institution for natural history in Bavaria. They encompass five State Collections (zoology, botany, paleontology and geology, mineralogy, anthropology and paleoanatomy), the Botanical Garden Munich-Nymphenburg and eight museums with public exhibitions in Munich, Bamberg, Bayreuth, Eichstätt and Nördlingen. Our research focuses mainly on the past and present bio- and geodiversity and the evolution of animals and plants. To achieve this we have large scientific collections (almost 35,000,000 specimens), see "joint projects". r3d100011874 RefractiveIndex.INFO https://refractiveindex.info/ A database of optical constants of materials -r3d100011876 Plant Genomics and Phenomics Research Data Repository https://edal-pgp.ipk-gatersleben.de/ The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and the German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data [https://dx.doi.org/10.1093/database/baw033]. This covers in particular these cross-domain data sets that are not being published in central repositories because of its huge volume, unsupported data domain or scope, like image collections from plant phenotyping and microscopy, unassembled sequences, genotyping data, visualizations of complex morphological plant models, movies plant 3-D models, raw data from mass spectrometry, software, and documents. Accepted data is published as citable DOIs and core set of technical metadata is registered at DataCite. The used e!DAL-embedded Web frontend generates for each data set a landing page and supports an interactive exploration of available datasets. This long-term stable access to plant genomic and phenomic primary data records across domains and laboratories in one repository can empower researchers to reproduce already published analysis results as well as performing subsequent, advanced studies. +r3d100011876 Plant Genomics and Phenomics Research Data Repository https://edal-pgp.ipk-gatersleben.de/ The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents. r3d100011879 KNMI Data Platform https://dataplatform.knmi.nl/ KDP has replaced the KNMI Data Centre (KDC), which was turned off on the 27th of July 2020. Not only a change of name, but also a transition to new technologies. Initially, the KDP will be more primitive than KDC. To fulfill future ambitions, a digital KNMI transformation has been initiated. Part of this transition is the development of a new KDP as a successor of the KDC. All data on the KNMI Data Platform is free to use. For some datasets a service agreement is available, which is indicated on the page of the dataset. The KNMI Data platform provides access to KNMI data on weather, climate and seismology. Here you will find KNMI data on various subjects such as the most recent 10-minute observations, historical series, data about meteorological measuring stations, model calculations, earthquake data and satellite products. In addition to KNMI datasets, we also make datasets from other parties available, such as ECMWF, ECOMET, EUMETSAT and WMO. r3d100011880 CIAT Dataverse https://dataverse.harvard.edu/dataverse/CIAT The International Center for Tropical Agriculture (CIAT), a member of the CGIAR Consortium, believes that open access contributes to its mission of reducing hunger and poverty, and improving human nutrition in the tropics through research aimed at increasing the eco-efficiency of agriculture. Research data produced by CIAT and its Partners is distributed freely whenever possible. Kindly note that these datasets require proper citation and citation information is included with the metadata for each dataset. diff --git a/src/bioregistry/data/external/re3data/processed.json b/src/bioregistry/data/external/re3data/processed.json index ea6c3752a..e43ee7d1a 100644 --- a/src/bioregistry/data/external/re3data/processed.json +++ b/src/bioregistry/data/external/re3data/processed.json @@ -2966,7 +2966,7 @@ }, "r3d100010299": { "description": "The mission of World Data Center for Climate (WDCC) is to provide central support for the German and European climate research community. The WDCC is member of the ISC's World Data System. Emphasis is on development and implementation of best practice methods for Earth System data management. Data for and from climate research are collected, stored and disseminated. The WDCC is restricted to data products. Cooperations exist with thematically corresponding data centres of, e.g., earth observation, meteorology, oceanography, paleo climate and environmental sciences. The services of WDCC are also available to external users at cost price. A special service for the direct integration of research data in scientific publications has been developed. The editorial process at WDCC ensures the quality of metadata and research data in collaboration with the data producers. A citation code and a digital identifier (DOI) are provided and registered together with citation information at the DOI registration agency DataCite.", - "homepage": "https://www.dkrz.de/up/systems/wdcc", + "homepage": "https://wdc-climate.de", "name": "World Data Center for Climate", "prefix": "r3d100010299", "synonyms": [ @@ -10536,7 +10536,7 @@ } }, "r3d100011130": { - "description": "e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is \"Plant Genomics and Phenomics Research Data Repository\" [https://doi.org/10.1093/database/baw033].", + "description": "!!! <<< this record is no longer maintained, please use https://www.re3data.org/repository/r3d100011876 or https://www.re3data.org/repository/r3d100011647 >>> !!!: e!DAL stands for electronic Data Archive Library. It is a lightweight open source software software framework for publishing and sharing research data. e!DAL was developed based on experiences coming from decades of research data management and has grown towards being a general data archiving and publication infrastructure [https://doi.org/10.1186/1471-2105-15-214]. First research data repository is \"Plant Genomics and Phenomics Research Data Repository\" [https://doi.org/10.1093/database/baw033].", "homepage": "https://edal.ipk-gatersleben.de/", "name": "e!DAL - electronic Data Archive Library", "prefix": "r3d100011130" @@ -16257,7 +16257,7 @@ } }, "r3d100011876": { - "description": "The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and the German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data [https://dx.doi.org/10.1093/database/baw033]. This covers in particular these cross-domain data sets that are not being published in central repositories because of its huge volume, unsupported data domain or scope, like image collections from plant phenotyping and microscopy, unassembled sequences, genotyping data, visualizations of complex morphological plant models, movies plant 3-D models, raw data from mass spectrometry, software, and documents. Accepted data is published as citable DOIs and core set of technical metadata is registered at DataCite. The used e!DAL-embedded Web frontend generates for each data set a landing page and supports an interactive exploration of available datasets. This long-term stable access to plant genomic and phenomic primary data records across domains and laboratories in one repository can empower researchers to reproduce already published analysis results as well as performing subsequent, advanced studies.", + "description": "The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and German Plant Phenotyping Network (DPPN) has jointly initiated the Plant Genomics and Phenomics Research Data Repository (PGP) as infrastructure to comprehensively publish plant research data. This covers in particular cross-domain datasets that are not being published in central repositories because of its volume or unsupported data scope, like image collections from plant phenotyping and microscopy, unfinished genomes, genotyping data, visualizations of morphological plant models, data from mass spectrometry as well as software and documents.", "homepage": "https://edal-pgp.ipk-gatersleben.de/", "name": "Plant Genomics and Phenomics Research Data Repository", "prefix": "r3d100011876",