From 01bb86e08491c94537f2aa8126140f423f4bf7fb Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 17 Oct 2023 01:09:15 +0000 Subject: [PATCH] =?UTF-8?q?=F0=9F=93=AE=20Automatically=20update?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- docs/_data/curation.yml | 18 + docs/img/bibliography_years.svg | 198 +- docs/img/bioregistry_coverage.svg | 2850 +- docs/img/bioregistry_coverage_bar.svg | 1030 +- docs/img/bioregistry_coverage_bar_short.svg | 2 +- docs/img/external_overlap.svg | 2360 +- docs/img/has_attribute.svg | 644 +- docs/img/providers.svg | 10 +- docs/img/regex_report.svg | 2 +- docs/img/xrefs.svg | 310 +- exports/contexts/bioregistry.rpm.json | 4 + exports/rdf/bioregistry.jsonld | 184678 ++++++++------- exports/rdf/bioregistry.nt | 96588 ++++---- exports/rdf/bioregistry.ttl | 22 + exports/rdf/schema.jsonld | 340 +- exports/rdf/schema.nt | 224 +- exports/registry/registry.json | 26 + exports/registry/registry.tsv | 2 + exports/registry/registry.yml | 22 + exports/tables/summary.tex | 8 +- .../data/external/aberowl/processed.json | 10 +- .../data/external/aberowl/raw.json | 2 +- .../data/external/agroportal/processed.json | 3 +- .../data/external/agroportal/raw.json | 3 +- .../data/external/biolink/processed.json | 4 +- .../data/external/biolink/raw.yaml | 4 +- .../data/external/bioportal/curation.tsv | 2 +- .../data/external/bioportal/processed.json | 43 +- .../data/external/bioportal/raw.json | 46 +- .../data/external/ecoportal/curation.tsv | 2 +- .../data/external/ecoportal/processed.json | 2 - 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", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "AnVIL DRS" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": { - "@id": "https://registry.identifiers.org/registry/drs.anv0" - }, - "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://www.genome.gov/" - }, - "https://bioregistry.io/schema/#0000005": "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082", - "https://bioregistry.io/schema/#0000006": "https://data.terra.bio/ga4gh/drs/v1/objects/$1", - "https://bioregistry.io/schema/#0000008": "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$", - "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000024": "https://data.terra.bio/ga4gh/drs/v1/objects/", - "https://bioregistry.io/schema/#0000027": { - "@id": "https://data.terra.bio/ga4gh/drs/v1/objects/v2_1b0f158a-86e2-3887-b990-89e3cf2d9082" - }, - "https://bioregistry.io/schema/#0000029": { - "@value": "drsanv0" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/biocontext/PO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" - } - }, - { - "@id": "https://registry.identifiers.org/registry/myco.lepra", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/biocontext/LRG", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/biocontext/rdfs", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/biocontext" - } - }, - { - "@id": "https://cropontology.org/ontology/CO_337", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/cropoct" - } - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/ENVO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://bioregistry.io/collection/0000010", - "@type": "https://bioregistry.io/schema/#0000003", - "http://purl.org/dc/elements/1.1/creator": { - "@id": "https://orcid.org/0000-0003-4423-4370" - }, - "http://purl.org/dc/elements/1.1/description": { - "@value": "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" - }, - "http://purl.org/dc/terms/hasPart": [ + "@id": "https://bioregistry.io/registry/mosaic" + }, { - "@id": "https://bioregistry.io/registry/civic.sid" + "@id": "https://bioregistry.io/registry/lspci" }, { - "@id": "https://bioregistry.io/registry/chebi" + "@id": "https://bioregistry.io/registry/kegg.rclass" }, { - "@id": "https://bioregistry.io/registry/uniprot" + "@id": "https://bioregistry.io/registry/pina" }, { - "@id": "https://bioregistry.io/registry/go" + "@id": "https://bioregistry.io/registry/mirnest" }, { - "@id": "https://bioregistry.io/registry/pombase" + "@id": "https://bioregistry.io/registry/hcao" }, { - "@id": "https://bioregistry.io/registry/civic.vid" + "@id": "https://bioregistry.io/registry/asap" }, { - "@id": "https://bioregistry.io/registry/interpro" + "@id": "https://bioregistry.io/registry/epo" }, { - "@id": "https://bioregistry.io/registry/civic.did" + "@id": "https://bioregistry.io/registry/drsanv0" }, { - "@id": "https://bioregistry.io/registry/ensembl" + "@id": "https://bioregistry.io/registry/funderregistry" }, { - "@id": "https://bioregistry.io/registry/orphanet.ordo" + "@id": "https://bioregistry.io/registry/bmrb.restraint" }, { - "@id": "https://bioregistry.io/registry/civic.eid" + "@id": "https://bioregistry.io/registry/co_324" }, { - "@id": "https://bioregistry.io/registry/brenda" + "@id": "https://bioregistry.io/registry/csp" }, { - "@id": "https://bioregistry.io/registry/mgi" + "@id": "https://bioregistry.io/registry/dctypes" }, { - "@id": "https://bioregistry.io/registry/civic.tid" + "@id": "https://bioregistry.io/registry/ricecyc" }, { - "@id": "https://bioregistry.io/registry/pharmgkb.drug" + "@id": "https://bioregistry.io/registry/prints" }, { - "@id": "https://bioregistry.io/registry/ecocyc" + "@id": "https://bioregistry.io/registry/fbtc" }, { - "@id": "https://bioregistry.io/registry/panther.node" + "@id": "https://bioregistry.io/registry/massbank" }, { - "@id": "https://bioregistry.io/registry/orphanet" + "@id": "https://bioregistry.io/registry/idocovid19" }, { - "@id": "https://bioregistry.io/registry/bacdive" + "@id": "https://bioregistry.io/registry/cell_model_passport" }, { - "@id": "https://bioregistry.io/registry/pdb" + "@id": "https://bioregistry.io/registry/pubmed" }, { - "@id": "https://bioregistry.io/registry/hgnc" + "@id": "https://bioregistry.io/registry/yeastract" }, { - "@id": "https://bioregistry.io/registry/civic.aid" + "@id": "https://bioregistry.io/registry/brenda.ligand" }, { - "@id": "https://bioregistry.io/registry/ucsc" + "@id": "https://bioregistry.io/registry/asrp" }, { - "@id": "https://bioregistry.io/registry/gnomad" + "@id": "https://bioregistry.io/registry/sssom" }, { - "@id": "https://bioregistry.io/registry/civic.gid" + "@id": "https://bioregistry.io/registry/amphx" }, { - "@id": "https://bioregistry.io/registry/bto" + "@id": "https://bioregistry.io/registry/iceberg.ime" }, { - "@id": "https://bioregistry.io/registry/rhea" + "@id": "https://bioregistry.io/registry/4dn.replicate" }, { - "@id": "https://bioregistry.io/registry/zfin" + "@id": "https://bioregistry.io/registry/bitterdb.rec" }, { - "@id": "https://bioregistry.io/registry/agrkb" + "@id": "https://bioregistry.io/registry/abcam" }, { - "@id": "https://bioregistry.io/registry/panther.family" + "@id": "https://bioregistry.io/registry/nlx.br" }, { - "@id": "https://bioregistry.io/registry/pharmgkb.disease" + "@id": "https://bioregistry.io/registry/uniprot.chain" }, { - "@id": "https://bioregistry.io/registry/sgd" + "@id": "https://bioregistry.io/registry/biomodels.teddy" }, { - "@id": "https://bioregistry.io/registry/reactome" + "@id": "https://bioregistry.io/registry/aspgd.locus" }, { - "@id": "https://bioregistry.io/registry/brenda.ligand" + "@id": "https://bioregistry.io/registry/icd10cm" }, { - "@id": "https://bioregistry.io/registry/brenda.ligandgroup" + "@id": "https://bioregistry.io/registry/prosite" }, { - "@id": "https://bioregistry.io/registry/ena.embl" + "@id": "https://bioregistry.io/registry/galen" }, { - "@id": "https://bioregistry.io/registry/wormbase" + "@id": "https://bioregistry.io/registry/bold.taxonomy" }, { - "@id": "https://bioregistry.io/registry/flybase" + "@id": "https://bioregistry.io/registry/bcbc" }, { - "@id": "https://bioregistry.io/registry/eupath" + "@id": "https://bioregistry.io/registry/co_334" }, { - "@id": "https://bioregistry.io/registry/pharmgkb.gene" + "@id": "https://bioregistry.io/registry/go.gpi" }, { - "@id": "https://bioregistry.io/registry/chembl" + "@id": "https://bioregistry.io/registry/sedml.language" }, { - "@id": "https://bioregistry.io/registry/rgd" + "@id": "https://bioregistry.io/registry/seed" }, { - "@id": "https://bioregistry.io/registry/px" + "@id": "https://bioregistry.io/registry/dbd" }, { - "@id": "https://bioregistry.io/registry/pmc" + "@id": "https://bioregistry.io/registry/grid" }, { - "@id": "https://bioregistry.io/registry/pharmgkb.pathways" + "@id": "https://bioregistry.io/registry/oma.protein" }, { - "@id": "https://bioregistry.io/registry/panther.pthcmp" + "@id": "https://bioregistry.io/registry/sheepqtldb" }, { - "@id": "https://bioregistry.io/registry/gbif" + "@id": "https://bioregistry.io/registry/dso" }, { - "@id": "https://bioregistry.io/registry/panther.pathway" - } - ], - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Global Biodata Coalition - Global Core Biodata Resources" - } - }, - { - "@id": "https://bioregistry.io/registry/scr", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/description": "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.", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "SciCrunch Registry" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "@id": "https://bioregistry.io/registry/mamo" + }, { - "@id": "https://bioregistry.io/metaregistry/rrid/resolve/SCR" + "@id": "https://bioregistry.io/registry/cbioportal" }, { - "@id": "https://fairsharing.org/FAIRsharing.kj4pvk" - } - ], - "http://www.w3.org/ns/dcat#keyword": [ + "@id": "https://bioregistry.io/registry/nlx.sub" + }, { - "@value": "rrid" + "@id": "https://bioregistry.io/registry/unii" }, { - "@value": "nih initiative" + "@id": "https://bioregistry.io/registry/rebase" }, { - "@value": "life science" + "@id": "https://bioregistry.io/registry/xao" }, { - "@value": "neurobiology" + "@id": "https://bioregistry.io/registry/gc" }, { - "@value": "interactive portal" - } - ], - "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://scicrunch.org/browse/resourcedashboard" - }, - "https://bioregistry.io/schema/#0000005": "022586", - "https://bioregistry.io/schema/#0000006": "http://scicrunch.org/resolver/SCR_$1", - "https://bioregistry.io/schema/#0000008": "^\\d+$", - "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000023": { - "@value": "scicrunch" - }, - "https://bioregistry.io/schema/#0000024": "http://scicrunch.org/resolver/SCR_", - "https://bioregistry.io/schema/#0000027": { - "@id": "http://scicrunch.org/resolver/SCR_022586" - }, - "https://bioregistry.io/schema/#0000029": { - "@value": "scr" - } - }, - { - "@id": "https://registry.bio2kg.org/resource/imgthla", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" - } - }, - { - "@id": "https://registry.identifiers.org/registry/nasc", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://bioregistry.io/registry/mgnify.samp", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/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. 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This collection references samples.", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "MGnify Sample" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "@id": "https://bioregistry.io/registry/ogms" + }, { - "@id": "https://bioregistry.io/metaregistry/n2t/resolve/mgnify.samp" + "@id": "https://bioregistry.io/registry/gramene.reference" }, { - "@id": "https://registry.identifiers.org/registry/mgnify.samp" - } - ], - "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://www.ebi.ac.uk/metagenomics" - }, - "https://bioregistry.io/schema/#0000005": "SRS086444", - "https://bioregistry.io/schema/#0000006": "https://www.ebi.ac.uk/metagenomics/samples/$1", - "https://bioregistry.io/schema/#0000008": "^[A-Z]+[0-9]+$", - "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000024": "https://www.ebi.ac.uk/metagenomics/samples/", - "https://bioregistry.io/schema/#0000027": { - "@id": "https://www.ebi.ac.uk/metagenomics/samples/SRS086444" - }, - "https://bioregistry.io/schema/#0000029": { - "@value": "mgnify.samp" - } - }, - { - "@id": "http://www.wikidata.org/entity/P665", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/wikidata" - } - }, - { - "@id": "http://aber-owl.net/ontology/CRO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/aberowl" - } - }, - { - "@id": "https://fairsharing.org/FAIRsharing.9gqfpm", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" - } - }, - { - "@id": "https://registry.identifiers.org/registry/modeldb.concept", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/OVAE", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/ARO", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioportal" - } - }, - { - "@id": "https://orcid.org/0000-0002-6443-9376", - "http://www.w3.org/2000/01/rdf-schema#label": [ + "@id": "https://bioregistry.io/registry/rrrc" + }, { - "@value": "Jennifer Smith" + "@id": "https://bioregistry.io/registry/ornaseq" }, { - "@value": "Jennifer R Smith" - } - ], - "http://xmlns.com/foaf/0.1/mbox": { - "@value": "jrsmith@mcw.edu" - } - }, - { - "@id": "https://registry.identifiers.org/registry/exac.gene", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://registry.identifiers.org/registry/covid19", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://bioregistry.io/registry/xml", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/description": "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.", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/bioregistry" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Extensible Markup Language" - }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "@id": "https://bioregistry.io/registry/ppr" + }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/xml" + "@id": "https://bioregistry.io/registry/plasmodb" }, { - "@id": "https://fairsharing.org/FAIRsharing.b5cc91" - } - ], - "http://www.w3.org/ns/dcat#keyword": { - "@value": "subject agnostic" - }, - "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://www.w3.org/TR/xml/" - }, - "https://bioregistry.io/schema/#0000005": "lang", - "https://bioregistry.io/schema/#0000006": "http://www.w3.org/XML/1998/namespace#$1", - "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000024": "http://www.w3.org/XML/1998/namespace#", - 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SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, - "http://usefulinc.com/ns/doap#GitRepository": { - "@id": "https://github.com/EBISPOT/OBAN" - }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Open Biomedical Annotations" + "@value": "Simple Knowledge Organization System eXtension for Labels" }, - "http://www.w3.org/2004/02/skos/core#exactMatch": [ + "http://www.w3.org/ns/dcat#keyword": [ { - "@id": "https://bioregistry.io/metaregistry/biolink/resolve/OBAN" + "@value": "semantic web" }, { - "@id": "https://bioregistry.io/metaregistry/biocontext/OBAN" + "@value": "data model" + }, + { + "@value": "skos" + }, + { + "@value": "metadata" } ], - "http://www.w3.org/ns/dcat#keyword": { - "@value": "ontology" - }, "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://github.com/EBISPOT/OBAN" - }, - "https://bioregistry.io/schema/#0000005": "provenance", - "https://bioregistry.io/schema/#0000006": "http://purl.org/oban/$1", - "https://bioregistry.io/schema/#0000008": "^\\w+$", - "https://bioregistry.io/schema/#0000010": { - "@id": "https://raw.githubusercontent.com/EBISPOT/OBAN/master/ontology/oban_core.owl" + "@id": "http://www.w3.org/2008/05/skos-xl#" }, + "https://bioregistry.io/schema/#0000005": "literalForm", + "https://bioregistry.io/schema/#0000006": "http://www.w3.org/2008/05/skos-xl#$1", "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000024": "http://purl.org/oban/", + "https://bioregistry.io/schema/#0000024": "http://www.w3.org/2008/05/skos-xl#", "https://bioregistry.io/schema/#0000027": { - "@id": "http://purl.org/oban/provenance" + "@id": "http://www.w3.org/2008/05/skos-xl#literalForm" }, "https://bioregistry.io/schema/#0000029": { - "@value": "oban" + "@value": "skosxl" } }, { - "@id": "https://orcid.org/0000-0003-4614-562X", + "@id": "https://orcid.org/0000-0003-1321-3956", "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Pierre Grenon" + "@value": "Al Kikhney" }, "http://xmlns.com/foaf/0.1/mbox": { - "@value": "pierre.grenon@ifomis.uni-saarland.de" - } - }, - { - "@id": "https://registry.identifiers.org/registry/seed", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/miriam" - } - }, - { - "@id": "https://www.ebi.ac.uk/ols4/ontologies/colao", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/ols" - } - }, - { - "@id": "https://bioregistry.io/metaregistry/n2t/resolve/uspto", - "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/n2t" + "@value": "a.kikhney@embl-hamburg.de" } }, { - "@id": "https://fairsharing.org/FAIRsharing.wkdjpb", + "@id": "https://bartoc.org/en/node/20430", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/bartoc" } }, { - "@id": "https://fairsharing.org/FAIRsharing.7q4gsz", + "@id": "http://oid-info.com/get/2.16.840.1.113883.6.340", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/hl7" } }, { - "@id": "https://bioregistry.io/registry/genpept", + "@id": "https://bioregistry.io/registry/geogeo", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/description": "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank.", + "http://purl.org/dc/terms/description": "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. 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While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). 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Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have 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 supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf", + "http://purl.org/dc/terms/description": "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, - "http://usefulinc.com/ns/doap#GitRepository": { - "@id": "https://github.com/Display-Lab/psdo" - }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Performance Summary Display Ontology" + "@value": "Sensitive Data Ontology" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { - "@id": "http://www.ontobee.org/ontology/PSDO" - }, - { - "@id": "http://aber-owl.net/ontology/PSDO" - }, - { - "@id": "https://bioportal.bioontology.org/ontologies/PSDO" - }, - { - "@id": "https://www.ebi.ac.uk/ols4/ontologies/psdo" - }, - { - "@id": "https://www.obofoundry.org/ontology/psdo" - } - ], - "http://www.w3.org/ns/dcat#keyword": [ - { - "@value": "ontology" + "@id": "http://aber-owl.net/ontology/SENSO" }, { - "@value": "obo" + "@id": "https://bioportal.bioontology.org/ontologies/SENSO" } ], + "http://www.w3.org/ns/dcat#keyword": { + "@value": "ontology" + }, "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://github.com/Display-Lab/psdo" + "@id": "https://github.com/DataONEorg/sem-prov-ontologies" }, - "https://bioregistry.io/schema/#0000005": "0000055", - "https://bioregistry.io/schema/#0000006": "http://purl.obolibrary.org/obo/PSDO_$1", - "https://bioregistry.io/schema/#0000008": "^\\d{7}$", + "https://bioregistry.io/schema/#0000005": "00000003", + "https://bioregistry.io/schema/#0000006": "http://purl.dataone.org/odo/SENSO_$1", + "https://bioregistry.io/schema/#0000008": "^\\d+$", "https://bioregistry.io/schema/#0000010": { - "@id": "http://purl.obolibrary.org/obo/psdo.owl" + "@id": "http://aber-owl.net/media/ontologies/SENSO/1/senso.owl" }, "https://bioregistry.io/schema/#0000012": false, - "https://bioregistry.io/schema/#0000017": [ - { - "@id": "https://bioregistry.io/registry/stato" - }, - { - "@id": "https://bioregistry.io/registry/ro" - }, - { - "@id": "https://bioregistry.io/registry/iao" - }, - { - "@id": "https://bioregistry.io/registry/bfo" - } - ], "https://bioregistry.io/schema/#0000019": { - "@id": "https://orcid.org/0000-0002-9117-9338" + "@id": "https://orcid.org/0000-0002-0381-3766" }, - "https://bioregistry.io/schema/#0000024": "http://purl.obolibrary.org/obo/PSDO_", + "https://bioregistry.io/schema/#0000024": "http://purl.dataone.org/odo/SENSO_", "https://bioregistry.io/schema/#0000027": { - "@id": "http://purl.obolibrary.org/obo/PSDO_0000055" + "@id": "http://purl.dataone.org/odo/SENSO_00000003" }, "https://bioregistry.io/schema/#0000029": { - "@value": "psdo" + "@value": "senso" } }, { - "@id": "http://aber-owl.net/ontology/EHDA", + "@id": "https://fairsharing.org/FAIRsharing.d95034", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/aberowl" + "@id": "https://bioregistry.io/metaregistry/fairsharing" } }, { - "@id": "https://bioregistry.io/registry/cmecs", - "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/description": "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. 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This registry was previously known as Prefix Commons and was available at https://prefixcommons.org." - }, - "http://purl.org/dc/terms/hasPart": [ + "@id": "https://registry.bio2kg.org/resource/kegg.pathway" + }, { - "@id": "https://registry.bio2kg.org/resource/dbest" + "@id": "https://registry.bio2kg.org/resource/reactome" }, { - "@id": "https://registry.bio2kg.org/resource/eo" + "@id": "https://registry.bio2kg.org/resource/wbls" }, { - "@id": "https://registry.bio2kg.org/resource/kegg.genome" + "@id": "https://registry.bio2kg.org/resource/rna_sstrand" }, { - "@id": "https://registry.bio2kg.org/resource/wikipathways" + "@id": "https://registry.bio2kg.org/resource/kegg.genome" }, { - "@id": "https://registry.bio2kg.org/resource/pass2" + "@id": "https://registry.bio2kg.org/resource/gnd" }, { - "@id": "https://registry.bio2kg.org/resource/iuphar.family" + "@id": "https://registry.bio2kg.org/resource/gold" }, { - "@id": "https://registry.bio2kg.org/resource/mirnest" + "@id": "https://registry.bio2kg.org/resource/fbdv" }, { - "@id": "https://registry.bio2kg.org/resource/smpdb" + "@id": "https://registry.bio2kg.org/resource/cutg" }, { - "@id": "https://registry.bio2kg.org/resource/kegg.glycan" + "@id": "https://registry.bio2kg.org/resource/pfam" }, { - "@id": "https://registry.bio2kg.org/resource/chemidplus" + "@id": "https://registry.bio2kg.org/resource/aceview.worm" }, { - "@id": "https://registry.bio2kg.org/resource/biomodels" + "@id": "https://registry.bio2kg.org/resource/treefam" }, { - "@id": "https://registry.bio2kg.org/resource/hdr" + "@id": "https://registry.bio2kg.org/resource/compluyeast2dpage" }, { - "@id": "https://registry.bio2kg.org/resource/ncit" + "@id": "https://registry.bio2kg.org/resource/cl" }, { - "@id": "https://registry.bio2kg.org/resource/zfin" + "@id": "https://registry.bio2kg.org/resource/bindingdb" }, { - "@id": "https://registry.bio2kg.org/resource/greengenes" + "@id": "https://registry.bio2kg.org/resource/hgnc" }, { - "@id": "https://registry.bio2kg.org/resource/macie" + "@id": "https://registry.bio2kg.org/resource/chickenqtldb" }, { - "@id": "https://registry.bio2kg.org/resource/jcsd" + "@id": "https://registry.bio2kg.org/resource/noncode" }, { - "@id": "https://registry.bio2kg.org/resource/goa" + "@id": "https://registry.bio2kg.org/resource/rvd" }, { - "@id": "https://registry.bio2kg.org/resource/hbvar" + "@id": "https://registry.bio2kg.org/resource/modeldb" }, { - "@id": "https://registry.bio2kg.org/resource/unists" + "@id": "https://registry.bio2kg.org/resource/spbase" }, { - "@id": "https://registry.bio2kg.org/resource/genetree" + "@id": "https://registry.bio2kg.org/resource/pdbsum" }, { - "@id": "https://registry.bio2kg.org/resource/gramene.po" + "@id": "https://registry.bio2kg.org/resource/ivdb" }, { - "@id": "https://registry.bio2kg.org/resource/pid" + "@id": "https://registry.bio2kg.org/resource/doi" }, { - "@id": "https://registry.bio2kg.org/resource/atc" + "@id": "https://registry.bio2kg.org/resource/nmpdr" }, { - "@id": "https://registry.bio2kg.org/resource/flybase.est" + "@id": "https://registry.bio2kg.org/resource/ensembl" }, { - "@id": "https://registry.bio2kg.org/resource/ma" + "@id": "https://registry.bio2kg.org/resource/rnao" }, { - "@id": "https://registry.bio2kg.org/resource/pharmgkb.pathways" + "@id": "https://registry.bio2kg.org/resource/pmap.substratedb" }, { - "@id": "https://registry.bio2kg.org/resource/cath" + "@id": "https://registry.bio2kg.org/resource/interfil" }, { - "@id": "https://registry.bio2kg.org/resource/sep" + "@id": "https://registry.bio2kg.org/resource/taxonomy" }, { - "@id": "https://registry.bio2kg.org/resource/snornalbmedb" + "@id": "https://registry.bio2kg.org/resource/asrp" }, { - "@id": "https://registry.bio2kg.org/resource/swo" + "@id": "https://registry.bio2kg.org/resource/rnajunction" }, { - "@id": "https://registry.bio2kg.org/resource/neurolex" + "@id": "https://registry.bio2kg.org/resource/uniparc" }, { - "@id": "https://registry.bio2kg.org/resource/kegg.disease" + "@id": "https://registry.bio2kg.org/resource/pdbj" }, { - "@id": "https://registry.bio2kg.org/resource/dailymed" + "@id": "https://registry.bio2kg.org/resource/doqcs.model" }, { - "@id": "https://registry.bio2kg.org/resource/string" + "@id": "https://registry.bio2kg.org/resource/protonet.proteincard" }, { - "@id": "https://registry.bio2kg.org/resource/niaest" + "@id": "https://registry.bio2kg.org/resource/bionumbers" }, { - "@id": "https://registry.bio2kg.org/resource/nucleardb" + "@id": "https://registry.bio2kg.org/resource/mirbase.mature" }, { - "@id": "https://registry.bio2kg.org/resource/maizegdb" + "@id": "https://registry.bio2kg.org/resource/intenz" }, { - "@id": "https://registry.bio2kg.org/resource/ratmap" + "@id": "https://registry.bio2kg.org/resource/imgt.ligm" }, { - "@id": "https://registry.bio2kg.org/resource/splicenest" + "@id": "https://registry.bio2kg.org/resource/pubmed" }, { - "@id": "https://registry.bio2kg.org/resource/superfamily" + "@id": "https://registry.bio2kg.org/resource/4dxpress" }, { - "@id": "https://registry.bio2kg.org/resource/rapdb" + "@id": "https://registry.bio2kg.org/resource/arachnoserver" }, { - "@id": "https://registry.bio2kg.org/resource/hgvbase" + "@id": "https://registry.bio2kg.org/resource/so" }, { - "@id": "https://registry.bio2kg.org/resource/plasmodb" + "@id": "https://registry.bio2kg.org/resource/signaling-gateway" }, { - "@id": "https://registry.bio2kg.org/resource/ro" + "@id": "https://registry.bio2kg.org/resource/drugbank" }, { - "@id": "https://registry.bio2kg.org/resource/ensembl.plant" + "@id": "https://registry.bio2kg.org/resource/pdbligand" }, { - "@id": "https://registry.bio2kg.org/resource/rnajunction" + "@id": "https://registry.bio2kg.org/resource/pathguide" }, { - "@id": "https://registry.bio2kg.org/resource/drugbank" + "@id": "https://registry.bio2kg.org/resource/icdo" }, { - "@id": "https://registry.bio2kg.org/resource/neuromorpho" + "@id": "https://registry.bio2kg.org/resource/genenote" }, { - "@id": "https://registry.bio2kg.org/resource/homd.seq" + "@id": "https://registry.bio2kg.org/resource/ehdaa" }, { - "@id": "https://registry.bio2kg.org/resource/eugenes" + "@id": "https://registry.bio2kg.org/resource/kegg.gene" }, { - "@id": "https://registry.bio2kg.org/resource/imgt.primerdb" + "@id": "https://registry.bio2kg.org/resource/jcm" }, { - "@id": "https://registry.bio2kg.org/resource/chemspider" + "@id": "https://registry.bio2kg.org/resource/bioportal" }, { - "@id": "https://registry.bio2kg.org/resource/img.taxon" + "@id": "https://registry.bio2kg.org/resource/pmp" }, { - "@id": "https://registry.bio2kg.org/resource/ehdaa" + "@id": "https://registry.bio2kg.org/resource/scop" }, { - "@id": "https://registry.bio2kg.org/resource/spike" + "@id": "https://registry.bio2kg.org/resource/citexplore" }, { - "@id": "https://registry.bio2kg.org/resource/addgene" + "@id": "https://registry.bio2kg.org/resource/isfinder" }, { - "@id": "https://registry.bio2kg.org/resource/giardiadb" + "@id": "https://registry.bio2kg.org/resource/fbcv" }, { - "@id": "https://registry.bio2kg.org/resource/tied" + "@id": "https://registry.bio2kg.org/resource/protcom" }, { - "@id": "https://registry.bio2kg.org/resource/loqate" + "@id": "https://registry.bio2kg.org/resource/hssp" }, { - "@id": "https://registry.bio2kg.org/resource/pazar" + "@id": "https://registry.bio2kg.org/resource/pathwaycommons" }, { - "@id": "https://registry.bio2kg.org/resource/vz" + "@id": "https://registry.bio2kg.org/resource/macie" }, { - "@id": "https://registry.bio2kg.org/resource/kegg.compound" + "@id": "https://registry.bio2kg.org/resource/datf" }, { - "@id": "https://registry.bio2kg.org/resource/pharmgkb.disease" + "@id": "https://registry.bio2kg.org/resource/ccds" }, { - "@id": "https://registry.bio2kg.org/resource/alfred" + "@id": "https://registry.bio2kg.org/resource/mirnest" }, { - "@id": "https://registry.bio2kg.org/resource/aphidbase" + "@id": "https://registry.bio2kg.org/resource/bgee" }, { - "@id": "https://registry.bio2kg.org/resource/lipidmaps" + "@id": "https://registry.bio2kg.org/resource/ratmap" }, { - "@id": "https://registry.bio2kg.org/resource/arrayexpress" + "@id": "https://registry.bio2kg.org/resource/alfred" }, { - "@id": "https://registry.bio2kg.org/resource/pride" + "@id": "https://registry.bio2kg.org/resource/matrixdb" }, { - "@id": "https://registry.bio2kg.org/resource/fsnp" + "@id": "https://registry.bio2kg.org/resource/cdd" }, { - "@id": "https://registry.bio2kg.org/resource/innatedb" + "@id": "https://registry.bio2kg.org/resource/panther" }, { - "@id": "https://registry.bio2kg.org/resource/mampol" + "@id": "https://registry.bio2kg.org/resource/niaest" }, { - "@id": "https://registry.bio2kg.org/resource/xco" + "@id": "https://registry.bio2kg.org/resource/kegg.reaction" }, { - "@id": "https://registry.bio2kg.org/resource/s_mart_db" + "@id": "https://registry.bio2kg.org/resource/vz" }, { - "@id": "https://registry.bio2kg.org/resource/geneannot" + "@id": "https://registry.bio2kg.org/resource/intact" }, { - "@id": "https://registry.bio2kg.org/resource/fbbt" + "@id": "https://registry.bio2kg.org/resource/pid" }, { - "@id": "https://registry.bio2kg.org/resource/subtilist" + "@id": "https://registry.bio2kg.org/resource/tair.protein" }, { - "@id": "https://registry.bio2kg.org/resource/pirsf" + "@id": "https://registry.bio2kg.org/resource/sbo" }, { - "@id": "https://registry.bio2kg.org/resource/homologene" + "@id": "https://registry.bio2kg.org/resource/hmdb" }, { - "@id": "https://registry.bio2kg.org/resource/kegg.gene" + "@id": "https://registry.bio2kg.org/resource/kegg.compound" }, { - "@id": "https://registry.bio2kg.org/resource/ygob" + "@id": "https://registry.bio2kg.org/resource/fma" }, { - "@id": "https://registry.bio2kg.org/resource/sabiork.ec" + "@id": "https://registry.bio2kg.org/resource/gendis" }, { - "@id": "https://registry.bio2kg.org/resource/gnd" + "@id": "https://registry.bio2kg.org/resource/tcdb" }, { - "@id": "https://registry.bio2kg.org/resource/wikipedia" + "@id": "https://registry.bio2kg.org/resource/wbbt" }, { - "@id": "https://registry.bio2kg.org/resource/biosystems" + "@id": "https://registry.bio2kg.org/resource/rhea" }, { - "@id": "https://registry.bio2kg.org/resource/paleodb" + "@id": "https://registry.bio2kg.org/resource/archdb" }, { - "@id": "https://registry.bio2kg.org/resource/pr" + "@id": "https://registry.bio2kg.org/resource/mp" }, { - "@id": "https://registry.bio2kg.org/resource/datf" + "@id": "https://registry.bio2kg.org/resource/isbn" }, { - "@id": "https://registry.bio2kg.org/resource/grsdb" + "@id": "https://registry.bio2kg.org/resource/cgd" }, { - "@id": "https://registry.bio2kg.org/resource/peroxibase" + "@id": "https://registry.bio2kg.org/resource/prodom" }, { - "@id": "https://registry.bio2kg.org/resource/cdd" + "@id": "https://registry.bio2kg.org/resource/mesh" }, { - "@id": "https://registry.bio2kg.org/resource/wormpep" + "@id": "https://registry.bio2kg.org/resource/brenda" }, { - "@id": "https://registry.bio2kg.org/resource/pdbligand" + "@id": "https://registry.bio2kg.org/resource/ipi" }, { - "@id": "https://registry.bio2kg.org/resource/pmp" + "@id": "https://registry.bio2kg.org/resource/pharmgkb.gene" }, { - "@id": "https://registry.bio2kg.org/resource/nasc" + "@id": "https://registry.bio2kg.org/resource/virushostdb" }, { - "@id": "https://registry.bio2kg.org/resource/omim" + "@id": "https://registry.bio2kg.org/resource/img.taxon" }, { - "@id": "https://registry.bio2kg.org/resource/glycomedb" + "@id": "https://registry.bio2kg.org/resource/gramene.po" }, { - "@id": "https://registry.bio2kg.org/resource/insdc" + "@id": "https://registry.bio2kg.org/resource/mpi" }, { - "@id": "https://registry.bio2kg.org/resource/pfam" + "@id": "https://registry.bio2kg.org/resource/chemdb" }, { - "@id": "https://registry.bio2kg.org/resource/icdo" + "@id": "https://registry.bio2kg.org/resource/dbd" }, { - "@id": "https://registry.bio2kg.org/resource/ensembl.fungi" + "@id": "https://registry.bio2kg.org/resource/propreo" }, { - "@id": "https://registry.bio2kg.org/resource/clinicaltrials" + "@id": "https://registry.bio2kg.org/resource/pharmgkb.disease" }, { - "@id": "https://registry.bio2kg.org/resource/uniparc" + "@id": "https://registry.bio2kg.org/resource/insdc" }, { - "@id": "https://registry.bio2kg.org/resource/bionumbers" + "@id": "https://registry.bio2kg.org/resource/snap" }, { - "@id": "https://registry.bio2kg.org/resource/vbrc" + "@id": "https://registry.bio2kg.org/resource/cgnc" }, { - "@id": "https://registry.bio2kg.org/resource/treefam" + "@id": "https://registry.bio2kg.org/resource/wormbase" }, { - "@id": "https://registry.bio2kg.org/resource/panther" + "@id": "https://registry.bio2kg.org/resource/pathoplant" }, { - "@id": "https://registry.bio2kg.org/resource/miriam.resource" + "@id": "https://registry.bio2kg.org/resource/pride" }, { - "@id": "https://registry.bio2kg.org/resource/smart" + "@id": "https://registry.bio2kg.org/resource/t3db" }, { - "@id": "https://registry.bio2kg.org/resource/emap.ontology" + "@id": "https://registry.bio2kg.org/resource/aphidbase" }, { - "@id": "https://registry.bio2kg.org/resource/gendr" + "@id": "https://registry.bio2kg.org/resource/rebase" }, { - "@id": "https://registry.bio2kg.org/resource/wbphenotype" + "@id": "https://registry.bio2kg.org/resource/tair.gene" }, { - "@id": "https://registry.bio2kg.org/resource/ligandexpo" + "@id": "https://registry.bio2kg.org/resource/psi.mi" }, { "@id": "https://registry.bio2kg.org/resource/ensembl.bacteria" }, { - "@id": "https://registry.bio2kg.org/resource/hmdb" - }, - { - "@id": "https://registry.bio2kg.org/resource/cgnc" + "@id": "https://registry.bio2kg.org/resource/sao" }, { - "@id": "https://registry.bio2kg.org/resource/propreo" + "@id": "https://registry.bio2kg.org/resource/po" }, { - "@id": "https://registry.bio2kg.org/resource/uniprot.kw" + "@id": "https://registry.bio2kg.org/resource/teddy" }, { - "@id": "https://registry.bio2kg.org/resource/modeldb" + "@id": "https://registry.bio2kg.org/resource/iuphar.family" }, { - "@id": "https://registry.bio2kg.org/resource/mimodb" + "@id": "https://registry.bio2kg.org/resource/chemspider" }, { - "@id": "https://registry.bio2kg.org/resource/uniprot" + "@id": "https://registry.bio2kg.org/resource/eropmoscow" }, { - "@id": "https://registry.bio2kg.org/resource/fma" + "@id": "https://registry.bio2kg.org/resource/pharmvar" }, { - "@id": "https://registry.bio2kg.org/resource/imex" + "@id": "https://registry.bio2kg.org/resource/peroxibase" }, { - "@id": "https://registry.bio2kg.org/resource/cryptodb" + "@id": "https://registry.bio2kg.org/resource/wikipedia" }, { - "@id": "https://registry.bio2kg.org/resource/rgap" + "@id": "https://registry.bio2kg.org/resource/cazy" }, { - "@id": "https://registry.bio2kg.org/resource/door" + "@id": "https://registry.bio2kg.org/resource/pirsf" }, { - "@id": "https://registry.bio2kg.org/resource/teddy" + "@id": "https://registry.bio2kg.org/resource/evoc" }, { - "@id": "https://registry.bio2kg.org/resource/pmdb" + "@id": "https://registry.bio2kg.org/resource/ygob" }, { - "@id": "https://registry.bio2kg.org/resource/taxrank" + "@id": "https://registry.bio2kg.org/resource/bto" }, { - "@id": "https://registry.bio2kg.org/resource/pharmgkb.drug" + "@id": "https://registry.bio2kg.org/resource/rex" }, { - "@id": "https://registry.bio2kg.org/resource/snomedct" + "@id": "https://registry.bio2kg.org/resource/string" }, { - "@id": "https://registry.bio2kg.org/resource/hamap" + "@id": "https://registry.bio2kg.org/resource/rapdb" }, { - "@id": "https://registry.bio2kg.org/resource/sabiork.reaction" + "@id": "https://registry.bio2kg.org/resource/stitch" }, { - "@id": "https://registry.bio2kg.org/resource/spdo" + "@id": "https://registry.bio2kg.org/resource/chebi" }, { - "@id": "https://registry.bio2kg.org/resource/aceview.worm" + "@id": "https://registry.bio2kg.org/resource/ligandexpo" }, { - "@id": "https://registry.bio2kg.org/resource/dip" + "@id": "https://registry.bio2kg.org/resource/eugenes" }, { "@id": "https://registry.bio2kg.org/resource/trnadbce" }, { - "@id": "https://registry.bio2kg.org/resource/cco" - }, - { - "@id": "https://registry.bio2kg.org/resource/bykdb" + "@id": "https://registry.bio2kg.org/resource/pubchem.bioassay" }, { - "@id": "https://registry.bio2kg.org/resource/noncode" + "@id": "https://registry.bio2kg.org/resource/4dn" }, { - "@id": "https://registry.bio2kg.org/resource/come" + "@id": "https://registry.bio2kg.org/resource/nucleardb" }, { - "@id": "https://registry.bio2kg.org/resource/rouge" + "@id": "https://registry.bio2kg.org/resource/geneloc" }, { - "@id": "https://registry.bio2kg.org/resource/ccd" + "@id": "https://registry.bio2kg.org/resource/ncbi.protein" }, { - "@id": "https://registry.bio2kg.org/resource/norine" + "@id": "https://registry.bio2kg.org/resource/eggnog" }, { - "@id": "https://registry.bio2kg.org/resource/opb" + "@id": "https://registry.bio2kg.org/resource/clinicaltrials" }, { - "@id": "https://registry.bio2kg.org/resource/genecards" + "@id": "https://registry.bio2kg.org/resource/flymine" }, { - "@id": "https://registry.bio2kg.org/resource/do" + "@id": "https://registry.bio2kg.org/resource/nembase" }, { - "@id": "https://registry.bio2kg.org/resource/cutg" + "@id": "https://registry.bio2kg.org/resource/kegg.brite" }, { - "@id": "https://registry.bio2kg.org/resource/so" + "@id": "https://registry.bio2kg.org/resource/plasmodb" }, { - "@id": "https://registry.bio2kg.org/resource/icd" + "@id": "https://registry.bio2kg.org/resource/swissmodel" }, { - "@id": "https://registry.bio2kg.org/resource/mao" + "@id": "https://registry.bio2kg.org/resource/maizegdb" }, { - "@id": "https://registry.bio2kg.org/resource/tgma" + "@id": "https://registry.bio2kg.org/resource/sdap" }, { - "@id": "https://registry.bio2kg.org/resource/mmdb" + "@id": "https://registry.bio2kg.org/resource/pazar" }, { - "@id": "https://registry.bio2kg.org/resource/pathwaycommons" + "@id": "https://registry.bio2kg.org/resource/phylomedb" }, { - "@id": "https://registry.bio2kg.org/resource/tair.locus" + "@id": "https://registry.bio2kg.org/resource/esldb" }, { - "@id": "https://registry.bio2kg.org/resource/pandit" + "@id": "https://registry.bio2kg.org/resource/tao" }, { - "@id": "https://registry.bio2kg.org/resource/bind" + "@id": "https://registry.bio2kg.org/resource/hbvar" }, { - "@id": "https://registry.bio2kg.org/resource/clo" + "@id": "https://registry.bio2kg.org/resource/cellimage" }, { - "@id": "https://registry.bio2kg.org/resource/molmovdb" + "@id": "https://registry.bio2kg.org/resource/gendr" }, { - "@id": "https://registry.bio2kg.org/resource/tair.gene" + "@id": "https://registry.bio2kg.org/resource/greengenes" }, { - "@id": "https://registry.bio2kg.org/resource/sdap" + "@id": "https://registry.bio2kg.org/resource/world2dpage" }, { - "@id": "https://registry.bio2kg.org/resource/vo" + "@id": "https://registry.bio2kg.org/resource/pass2" }, { - "@id": "https://registry.bio2kg.org/resource/ivdb" + "@id": "https://registry.bio2kg.org/resource/kegg.glycan" }, { - "@id": "https://registry.bio2kg.org/resource/nmpdr" + "@id": "https://registry.bio2kg.org/resource/subtiwiki" }, { - "@id": "https://registry.bio2kg.org/resource/antweb" + "@id": "https://registry.bio2kg.org/resource/alzgene" }, { - "@id": "https://registry.bio2kg.org/resource/vbase2" + "@id": "https://registry.bio2kg.org/resource/csa" }, { - "@id": "https://registry.bio2kg.org/resource/scop" + "@id": "https://registry.bio2kg.org/resource/paleodb" }, { - "@id": "https://registry.bio2kg.org/resource/vectorbase" + "@id": "https://registry.bio2kg.org/resource/ensembl.protist" }, { - "@id": "https://registry.bio2kg.org/resource/sheepqtldb" + "@id": "https://registry.bio2kg.org/resource/echobase" }, { - "@id": "https://registry.bio2kg.org/resource/wbbt" + "@id": "https://registry.bio2kg.org/resource/sgd.pathways" }, { - "@id": "https://registry.bio2kg.org/resource/hgnc" + "@id": "https://registry.bio2kg.org/resource/redfly" }, { - "@id": "https://registry.bio2kg.org/resource/dictybase" + "@id": "https://registry.bio2kg.org/resource/napp" }, { - "@id": "https://registry.bio2kg.org/resource/fao" + "@id": "https://registry.bio2kg.org/resource/p3db" }, { - "@id": "https://registry.bio2kg.org/resource/mycobank" + "@id": "https://registry.bio2kg.org/resource/clo" }, { - "@id": "https://registry.bio2kg.org/resource/img.gene" + "@id": "https://registry.bio2kg.org/resource/topdb" }, { - "@id": "https://registry.bio2kg.org/resource/dbprobe" + "@id": "https://registry.bio2kg.org/resource/tgma" }, { - "@id": "https://registry.bio2kg.org/resource/ydpm" + "@id": "https://registry.bio2kg.org/resource/bykdb" }, { - "@id": "https://registry.bio2kg.org/resource/nmr" + "@id": "https://registry.bio2kg.org/resource/omim" }, { - "@id": "https://registry.bio2kg.org/resource/roleo" + "@id": "https://registry.bio2kg.org/resource/irefweb" }, { - "@id": "https://registry.bio2kg.org/resource/sabiork.kinetic" + "@id": "https://registry.bio2kg.org/resource/astd" }, { - 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"@id": "https://fairsharing.org/FAIRsharing.beb855", + "@id": "https://bioregistry.io/metaregistry/go/resolve/EnsemblMetazoa", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/go" } }, { - "@id": "https://registry.bio2kg.org/resource/img.taxon", + "@id": "https://bioregistry.io/metaregistry/biocontext/UMBBD.COMPOUND", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/prefixcommons" + "@id": "https://bioregistry.io/metaregistry/biocontext" } }, { - "@id": "https://bioregistry.io/registry/drduke", + "@id": "http://aber-owl.net/ontology/MOP", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/aberowl" + } + }, + { + "@id": "https://registry.identifiers.org/registry/p3db.site", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/miriam" + } + }, + { + "@id": "https://bioregistry.io/registry/fcsfree", "@type": "https://bioregistry.io/schema/#0000001", - "http://purl.org/dc/terms/description": "identifier for chemicals linked to information on occurrence in plants", + "http://purl.org/dc/terms/description": "Cell line databases/resources", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical" + "@value": "Fetal Calf Serum-Free Database" }, "http://www.w3.org/2004/02/skos/core#exactMatch": { - "@id": "http://www.wikidata.org/entity/P10074" + "@id": "https://bioregistry.io/metaregistry/cellosaurus/resolve/FCS-free" }, "http://xmlns.com/foaf/0.1/homepage": { - "@id": "https://phytochem.nal.usda.gov/phytochem/search/list" + "@id": "https://fcs-free.org" }, - "https://bioregistry.io/schema/#0000005": "19", - "https://bioregistry.io/schema/#0000006": "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1", + "https://bioregistry.io/schema/#0000005": "240-17-488-3-4-12", + "https://bioregistry.io/schema/#0000006": "https://fcs-free.org/fcs-database?$1", "https://bioregistry.io/schema/#0000012": false, - 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Gyori" + }, + "http://xmlns.com/foaf/0.1/mbox": { + "@value": "benjamin_gyori@hms.harvard.edu" } }, { - "@id": "https://fairsharing.org/FAIRsharing.azqskx", + "@id": "https://bioregistry.io/metaregistry/biocontext/ARRAYEXPRESS.PLATFORM", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/biocontext" } }, { - "@id": "https://fairsharing.org/FAIRsharing.zhwa8x", + "@id": "https://registry.bio2kg.org/resource/cco", "http://purl.org/dc/terms/isPartOf": { - "@id": "https://bioregistry.io/metaregistry/fairsharing" + "@id": "https://bioregistry.io/metaregistry/prefixcommons" } }, { - "@id": "https://orcid.org/0000-0003-3562-7869", + "@id": "https://bioregistry.io/registry/zfin", + "@type": "https://bioregistry.io/schema/#0000001", + "http://purl.org/dc/terms/description": "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN.", + "http://purl.org/dc/terms/isPartOf": { + "@id": "https://bioregistry.io/metaregistry/bioregistry" + }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "General Enquiries" + "@value": "Zebrafish Information Network Gene" }, - "http://xmlns.com/foaf/0.1/mbox": { - "@value": "depod@embl.de" + "http://www.w3.org/2004/02/skos/core#exactMatch": [ + { + "@id": "http://www.wikidata.org/entity/P3870" + }, + { + "@id": "https://registry.identifiers.org/registry/zfin" + }, + { + "@id": "https://fairsharing.org/FAIRsharing.ybxnhg" + }, + { + "@id": "https://bioregistry.io/metaregistry/ncbi/resolve/ZFIN" + }, + { + "@id": "https://www.uniprot.org/database/DB-0113" + }, + { + "@id": "https://bioregistry.io/metaregistry/n2t/resolve/zfin" + }, + { + "@id": "https://bioregistry.io/metaregistry/biocontext/ZFIN" + }, + { + "@id": "https://bioregistry.io/metaregistry/rrid/resolve/ZIRC" + }, + { + "@id": "https://registry.bio2kg.org/resource/zfin" + }, + { + "@id": "https://www.re3data.org/repository/r3d100010421" + }, + { + "@id": "https://bioregistry.io/metaregistry/go/resolve/ZFIN" + } + ], + "http://www.w3.org/ns/dcat#keyword": [ + { + "@value": "embryo" + }, + { + "@value": "genomics" + }, + { + "@value": "developmental biology" + }, + { + "@value": "zebrafish" + }, + { + "@value": "antibody" + }, + { + "@value": "research" + }, + { + "@value": "genetics" + }, + { + "@value": "pathology" + }, + { + "@value": "zebrafish line" + }, + { + "@value": "gene" + }, + { + "@value": "expressed sequence tag" + }, + { + "@value": "genome" + }, + { + "@value": "cdna" + }, + { + "@value": "fish" + }, + { + "@value": "adult" + }, + { + "@value": "animal physiology" + } + ], + "http://xmlns.com/foaf/0.1/homepage": { + "@id": "http://zfin.org" + }, + "https://bioregistry.io/schema/#0000005": "ZDB-GENE-041118-11", + "https://bioregistry.io/schema/#0000006": "http://zfin.org/$1", + "https://bioregistry.io/schema/#0000008": "^ZDB\\-\\w+\\-\\d+\\-\\d+$", + "https://bioregistry.io/schema/#0000012": false, + "https://bioregistry.io/schema/#0000019": { + "@id": "https://orcid.org/0000-0001-5831-7439" + }, + "https://bioregistry.io/schema/#0000023": { + "@value": "ZFIN" + }, + "https://bioregistry.io/schema/#0000024": "http://zfin.org/", + "https://bioregistry.io/schema/#0000027": { + "@id": "http://zfin.org/ZDB-GENE-041118-11" + }, + "https://bioregistry.io/schema/#0000029": { + "@value": "zfin" } } ] diff --git a/exports/rdf/bioregistry.nt b/exports/rdf/bioregistry.nt index 23816c31c..6e4a64ec8 100644 --- a/exports/rdf/bioregistry.nt +++ b/exports/rdf/bioregistry.nt @@ -1,48478 +1,48498 @@ -_:N107b1aebb90649278084a97fd9727b0c "WHO Collaborating Centre for Drug Statistics Methodology" . - "http://vocab.getty.edu/page/tgn/$1"^^ . - . - . - . - . - "modeldb" . - . - "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."^^ . - . - "interaction" . - . - . - "Conferences in EasyChair"^^ . - . - . - . - . - . - "funderregistry" . - "sequence" . - . - . - . - . - . - "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."^^ . - . - . - "ontology" . - "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"^^ . - "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO="^^ . - "false"^^ . - . - . - . - . - . - . - "animal husbandry" . - . - . - . - . - . - "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . - . - . - . - "Dataset"^^ . - . - "bioinformatics" . - . - . - "https://neurovault.org/images/"^^ . - . - . - . - "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . - . - . - . - . - . - . - . - . - "ontology" . - . - . - "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."^^ . - . - . - "http://purl.bioontology.org/ontology/HOIP/HOIP_"^^ . - . - . - . - "Database of Genomic Structural Variation - Variant" . - . - . - . - . - . - . - . - "dmba" . - . - . - . - . - . - "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . - . - . - "J0705A10"^^ . - "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . - . - . - "https://bioregistry.io/proteomicsdb.protein:"^^ . - . - . - "https://radlex.org/RID/$1"^^ . - . - . - "Dublin Core Types" . - . - "metabolomics" . - "Degradome Database" . - "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . - . - "false"^^ . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . - . - . - . - . - . - . - "ordb" . - "https://sorgerlab.github.io/famplex/"^^ . - . - . - . - "NONCODE v4 Transcript" . - . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId="^^ . - . - "http://www.bindingdb.org/compact/"^^ . - . - _:N805816e4756c44619cdb57e0f012fd3c . - . - . - "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . - . - "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"^^ . - "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."^^ . - "VHOG_RETIRED" . - . - "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"^^ . - . - . - . - . -_:N9e87a13b66ee4814aa6f9ba33e193e09 "Crop Ontology Helpdesk" . - "https://depmap.org/portal/cell_line/"^^ . - . - "phenotype" . - "ontology" . - . - . - "false"^^ . - . - . - . - . - "fyeco" . - "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."^^ . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "ontology" . - . - . - . - "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam="^^ . - . - . - "proteomics" . - . - . - "gene" . - . - . - . - . - "https://w3id.org/oc/meta/$1"^^ . - . - "ecg" . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID="^^ . - "^[a-zA-Z0-9-_]+$"^^ . - . - . - "natural science" . - . - . - "Chris Grove" . - . - "Jörg Overmann" . - "MGnify Sample" . - . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"^^ . - . - . - . - "ontology" . - . - . - . - . - . - . - . - "^\\w+$"^^ . - . - "^jRCT\\w?\\d+$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - . - "http://edamontology.org/operation_"^^ . - . - . - "false"^^ . - "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . - "Chemical Information Ontology" . - "0010039"^^ . - . - . - . - "false"^^ . - "Candida Genome Database" . - . - . - "dna" . - "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID="^^ . - . - . - . - "http://www.coloncanceratlas.org/search_cell_line?cell_line="^^ . - . - "YRC PDR" . - "rs121909098"^^ . - . - . - "false"^^ . - . - "https://cropontology.org/rdf/CO_330:$1"^^ . - . - . - . - . - . - "subject agnostic" . - "protein" . - "community care" . - . - . - "life science" . - "false"^^ . - . - . - . - "Raimond Winslow" . - . - . - . - "https://scicrunch.org/resolver/RRID:$1_$2" . - . - . - . - _:N226ad9bb06704cbfb4da47042ff528b0 . - . - . - . - . - "^LBCTR\\d+$"^^ . - "foodb.food" . - . - "https://www.confident-conference.org/index.php/Event:$1"^^ . - . - . - "genome" . - "tetrahymena thermophila" . - . - . - "pride" . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - "0000001"^^ . - "obo" . - "Event (INOH pathway ontology)" . - . - . - . - . - . - "life science" . - "genomics" . - . - . - . - "agriculture" . - . - . - "seinet" . - . - . - "dna" . - . - . - "240-17-488-3-4-12"^^ . - . - . - . - "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."^^ . - . - "https://w3id.org/reproduceme#$1"^^ . - . - . - "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID="^^ . - "true"^^ . - . - . - . - . - "jkissing@uga.edu" . - . - "false"^^ . - "human disease model" . - . - "cdpd" . - "http://tables.pseudogene.org/[?species_name]/$1"^^ . - . - . - "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid="^^ . - "drug repositioning" . - . - "false"^^ . - "http://linkedlifedata.com/resource/umls/id/"^^ . - . - . - . - . - . - . - "kclb" . - "immds"^^ . - "hms.lincs.antibody" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "^\\d{4,}$"^^ . - . - . - . - "^\\d{8}$"^^ . - "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."^^ . - "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."^^ . - "disease" . - "false"^^ . - "00620027"^^ . - "biomedical science" . - "http://purl.obolibrary.org/obo/EHDAA_"^^ . - . - . - . - . - . - "false"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "cdao" . - . - . - . - . - . - "^C\\d+$"^^ . - "RETIRED_EHDAA2" . - . - . - "AspGD Protein" . - . - . - "false"^^ . - . - "GeneTree" . - . - "false"^^ . - "protein" . - "Monique Zahn" . - . - . - . - . - "breeding" . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - "cath.superfamily" . - . - "co_370" . - "ERM00000044"^^ . - "obo" . - . - . - . - "parasitology" . - . - . - . - . - . - . - . - "pathway" . - . - "Manually curated collections of resources stored in the bioregistry"^^ . - . - . - "PubChem_Compound_CID" . - . - "0000215"^^ . - . - . - . - "model organism" . - "dna" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "5112"^^ . - . - . - . - "bioinformatics" . - . - . - . - . - . - . - . - "ken.sd.hsu@gmail.com" . - . - "wgs84" . - "^\\d{7}$"^^ . - . - . - . - "structure" . - . - . - "^\\d+$"^^ . - . - . - "https://bioregistry.io/combine.specifications:"^^ . - "^[A-Za-z_0-9]+$"^^ . - "false"^^ . - . - "ontology" . - "consulting" . - . - . - . - "true"^^ . - "^\\d+$"^^ . - "https://drugs.ncats.io/drug/"^^ . -_:N8b0188fd98fb4f68a9d1f2d2f5c39af7 "helpdesk@cropontology-curationtool.org" . - . - . - "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . - "molecular microbiology" . - "UniRule" . - "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."^^ . - . - "SwissProt" . - "false"^^ . - "bioactivities" . - . - "ClinVar Submission" . - . - "278"^^ . - "IUPHAR_LIGAND" . - . - . - . - "^MTBLS\\d+$"^^ . - . - "Ardan Patwardhan" . - . - "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."^^ . - . - . - . - . - "https://www.genome.jp/virushostdb/"^^ . - . - "ghr" . - . - . - "NIF Standard Ontology: Molecules" . - "obo" . - "MicrosporidiaDB" . - "stap" . - . - . - "knowledge and information systems" . - "dna" . - "MGnify Project" . - "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . - "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid="^^ . - . - . - "Human Reference Atlas Common Coordinate Framework Ontology" . - . - . - "Gene Expression Analysis Resource" . - . - "true"^^ . - . - . - . - . - . - . - . - "taxon" . - . - "Oryzabase Stage" . - . - . - . - . - "vita" . - . - "http://www.ebi.ac.uk/efo/EFO_$1"^^ . - "Torsten Schwede" . - . - "3000887619"^^ . - . - "ontology" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods"^^ . - . - . - . - . - . - "false"^^ . - "NIF Standard Ontology: Chemical" . - "https://www.genenames.org/cgi-bin/gene_symbol_report?match="^^ . - . - . - . - . - . - . - . - "3966782"^^ . - . - . - "Sensitive Data Ontology" . - "addgene" . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - . - . - "ontology" . - . - . - . - . - "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . - . - "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . - "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . - . - . - . - . - . - "http://www.w3.org/1999/02/22-rdf-syntax-ns#"^^ . - . - "OSR0818"^^ . - "http://iflastandards.info/ns/fr/frbr/frbrer/$1"^^ . - "mutant" . - . - . - . - . - "^\\d{7}$"^^ . - . - "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data."^^ . - "mpidb" . - "cell biology" . - "^\\d+$"^^ . - . - "Liz Allen" . - . - "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid="^^ . - . - "FAIRsharing" . - . -_:Ncbaba8be38314faa87e015c819d05226 "psidev-gps-dev@lists.sourceforge.net" . - . - "ega.dataset" . - "Mutant Mouse Resource and Research Centers" . - "Digital Object Identifier" . - _:N3a54fd90c5844e92bd4fa6b0242dba3d . - "life science" . - . - . - "bioregistry.schema" . - . - "^[A-Z0-9]+$"^^ . - . - . - "false"^^ . - . - . - "Uberon Property" . - "comparative genomics" . - "identifier for a fungus taxon in Index Fungorum"^^ . - . - . - . - . - . - "chemspider" . - "https://bioregistry.io/bpdb:"^^ . - "has canonical prefix" . - . - . - . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - "zebrafish" . - "cls" . - . - . - . - "NLXQUAL" . - . - "https://purl.dataone.org/odo/SALMON_"^^ . - . - "model" . - . - . - "icd9" . - . - "http://www.geneontology.org/formats/oboInOwl#"^^ . - . - "Golm Metabolome Database (GMD) provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools. This collection references metabolite information, relating the biologically active substance to metabolic pathways or signalling phenomena."^^ . - . - "^[0-9]+$"^^ . - . - "Human Endogenous Retrovirus Database" . - . - . - . - . - . - . - . - "^K\\d+$"^^ . - . - "A repository for the TSV-based, decentralized, community-curated curation of terms, properties, and relations that get turned into OBO, OWL, and OBO Graph JSON."^^ . - . - . - . - "false"^^ . - "http://www.radiomics.org/RO/"^^ . - . - "false"^^ . - . - . - "00000008"^^ . - . - "^\\d{7}$"^^ . - "Topology Data Bank of Transmembrane Proteins" . - . - . - . - . - . - . - "http://purl.uniprot.org/isoforms/$1"^^ . - . - "false"^^ . - . - . - "A database containing predicted viral miRNA candidate hairpins."^^ . - "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . - "http://zinc15.docking.org/substances/$1"^^ . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . - . - . - . - "http://snomed.info/id/"^^ . - . - . - . - "6200"^^ . - . - . - "nlx.mol" . - "false"^^ . - . - . - "UniProtKB" . - . - "botany" . - . - . - "Sabine.Oesterle@sib.swiss" . - . - "false"^^ . - "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." . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . - "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . - . - "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . - "conferences" . - . - . - "false"^^ . - "http://geneontology.org/docs/gene-product-information-gpi-format/#$1"^^ . - . - . - "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . - . - . - "transcriptomics" . - . - . - . - . - . - "false"^^ . - . - "obo" . - "biology" . - "https://radlex.org/RID/"^^ . - "^v2_[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . - "francesco.vitali@ibba.cnr.it" . - "^\\d+$"^^ . - . - . - . - . - . - "false"^^ . - "Arabidopsis Information Portal" . - "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . - . - . - . - "genome" . -_:N5411953aa3da420b83011b159fcbf568 "Ian Davis" . - . - . - . - . - . - . - . - . - "rscheuermann@jcvi.org" . - "false"^^ . - . - . - "biochemistry" . - . - . - . - "Yoshiharu Y. Yamamoto" . - . - "^OSC\\d{4}$"^^ . - . - . - "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . - . - "clinical studies" . - . - . - . - . - . - "Li-San Wang" . - "VMH metabolite" . - "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . - "false"^^ . - . - . - "false"^^ . - "https://ssbd.riken.jp/database/dataset/$1"^^ . - . - . - . - . - "https://bio.tools/$1"^^ . - . - "false"^^ . - . - "RNA SSTRAND" . - . - "^PTM-\\d{4}$"^^ . - . - . - . - . - . - . - "http://www.xmetdb.org/xmetdb/protocol/"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "NucleaRDB is an information system that stores heterogenous data on Nuclear Hormone Receptors (NHRs). It contains data on sequences, ligand binding constants and mutations for NHRs."^^ . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation. This is a prefix for referencing identifiers in the minid test namespace. "^^ . - . - . - . - . - . - "https://gnomad.broadinstitute.org/variant/"^^ . - . - . - "^\\d+$"^^ . - "false"^^ . - . -_:N107b1aebb90649278084a97fd9727b0c "whocc@fhi.no" . - . - . - "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode="^^ . - . - "long-finned-pilot-whale"^^ . - . - "nucleardb" . - . - "PerkinElmer cell line collection" . - "wwpdb" . - "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)."^^ . - "OMIM Phenotypic Series" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a"^^ . - . - . - . - "false"^^ . - . - "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . - . - . - "^RC\\d+$"^^ . -_:Nb4de457f8e114f4e8c18616dab90271d "Plant Ontology Administrators" . - . - . - "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]"^^ . - . - "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . - "NIF Standard Ontology: Qualities" . - "https://bioregistry.io/genpept:"^^ . - "suzia@stanford.edu" . - . - . - . - . - . - . - "GlycomeDB" . - . - . - . - "togovar" . - . - . - "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)"^^ . - "health science" . - "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members."^^ . - . - . - . - . - . - "mouse strain" . -_:Nf48677cf113e42d591a86e42e6f53ee3 "Cynthia.Hake@cms.hhs.gov" . - "http://purl.obolibrary.org/obo/kestrelo_"^^ . - . - . - . - "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . - . - "obo" . - . - . - "00000443"^^ . - "true"^^ . - "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . - . - . - . - . - "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."^^ . - . - . - . - . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marref/#/records/"^^ . - "chemistry" . - . - "video resource" . - . - "KEGG Pathways Database" . - "subject agnostic" . - . - . - "https://www.brenda-enzymes.org/php/result_flat.php4?ecno="^^ . - "https://bioregistry.io/csd:"^^ . - "1"^^ . - . - . - . - . - . - . - "https://www.uniprot.org/database/" . - . - . - . - . - . - "https://mobidb.org/"^^ . - . - . - . - "Q5BJF6-3"^^ . - "Marie-Angélique Laporte" . - "life science" . - "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "19"^^ . - . - . - "^A\\d+$"^^ . - . - . - . - "Simple Knowledge Organization System eXtension for Labels" . - "50018"^^ . - "obo" . - . - "structure" . - . - . - "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . - "2d-page" . - . - . - . - . - . - "false"^^ . - "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . - "https://mediadive.dsmz.de/solutions/"^^ . - "Sirarat Sarntivijai" . - . - . - . - . - . - "Plant Transcription Factor Database" . - "ontology" . - . - . - . - . - "ontology" . - . - . - "germline" . - . - . - "life science" . - . - . - "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . - . - . - "74"^^ . - . - . - "https://glycopost.glycosmos.org/entry/"^^ . - "ENSG00000139618"^^ . - . - . - "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."^^ . - "obo" . - "dictybase.gene" . - . - . - "nlm" . - . - "chmo" . - . - . - "Structural Database of Allergenic Proteins" . - . - . - "Charles Ettensohn" . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . - . - "yetfasco" . - . - "obo" . - "mathematics" . - . - "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."^^ . - . - . - . - "http://purl.obolibrary.org/obo/SIBO_$1"^^ . - "nddf" . - "ovae" . - _:Nffb883398fd44d7f8657b94b6b3a1812 . - "^\\d{7}$"^^ . - "cas" . - "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id="^^ . - "ecology" . - . - . - . - . - "^\\d+$"^^ . - . - "genbank" . - . - . - "http://purl.obolibrary.org/obo/VO_$1"^^ . - . - "ontology" . - "0000000"^^ . - . - . - . - "^C\\d+$"^^ . - "xmetdb" . - _:N7f8648ca4c8c4d6b9724d8d656769f4d . - . - . - . - . - . - "Fission Yeast Phenotype Ontology" . - "https://gold.jgi.doe.gov/resolver?id="^^ . - . - . - . - "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . - "Xeni Kechagioglou" . - . - "structure" . - "life science" . - . - "iuphar.family" . - . - "961"^^ . - "alfred" . - "http://purl.obolibrary.org/obo/XCO_"^^ . - . - _:N38af8888972743f18aa7f0992b3702d3 . - "https://cellrepo.ico2s.org/repositories/"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FBdv_$1"^^ . - . - . - . - . - . - . - . - "Grant"^^ . - "ontology" . - . - "dinto" . - . - . - "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver."^^ . - . - . - "false"^^ . - "https://pb.apf.edu.au/phenbank/strain.html?id="^^ . - . - "gmd.analyte" . - "https://w3id.org/semapv/vocab/"^^ . - . - . - . - . - . - . - "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . - "Samuel Friedman" . - "bbtp" . - . - "phylogenetics" . - . - . - . - . - . - "https://biopragmatics.github.io/providers/bs/$1"^^ . - . - "civic.eid" . - . - "false"^^ . - . - . - . - "xco" . - . - . - . - "http://www.innatedb.ca/getGeneCard.do?id=$1"^^ . - "ontology" . - . - "KW-1273"^^ . - . - . - . - . - . - . - "MCDS_S_0000000001"^^ . - . - . - "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . - "ubprop" . - . - . - . - . - "^\\w+$"^^ . - "ontology" . - "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"^^ . - "^[A-Za-z_0-9]+$"^^ . - "LinkML" . - . - . - "The FAIRsharing Subject Ontology (SRAO) is an application ontology for the categorization of research disciplines across all research domains, from the humanities to the natural sciences. It utilizes multiple external vocabularies."^^ . - . - . - . - . - . - . - . - . - "An additional Japanese clinical trial registry"^^ . - . - . - . - . - "false"^^ . - . - "Structural Classification of Protein - Stable Domain Identifier" . - "NX_O00165"^^ . - . - "https://flowrepository.org/id/"^^ . - . - . - . - . - "obo" . - . - . - "structural biology" . - . - . - "umbbd.compound" . - "https://disprot.org/"^^ . - . - . - . - . - "gene" . - . - . - . - "Database of Sequence Tagged Sites" . - . - . - "^\\d+$"^^ . - . - . - . - "ahamosh@jhmi.edu" . - . - . - . - . - . - . - "SNOMED CT (International Edition)" . - . - . - . - . - "nmrcv" . - . - . - "pubmed" . - . - . - "http://purl.org/oban/$1"^^ . - . - . - . - . - . - . - "phosphopoint.kinase" . - . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - "mmp.db" . - . - "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . - "false"^^ . - "strain" . - . - . - . - "false"^^ . - . - "ehdaa2" . - . - "Sanger Cell Model Passports" . - . - . - "5621"^^ . - "^\\d{4}$"^^ . - . - "ddpheno" . - "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)."^^ . - . - "ontology" . - . - . - "Robert Druzinsky" . - "false"^^ . - "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . - "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/ECTO_"^^ . - . - . - "nmpdr" . - . - . - "https://www.gwascentral.org/phenotype/"^^ . - "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . - . - "http://purl.obolibrary.org/obo/OPL_$1"^^ . - "sedml.language" . - . - "babelon" . - "UniPathway Compound" . - "dna" . - "false"^^ . - . - . - . - "^\\w+$"^^ . - . - "false"^^ . - "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . - . - . - . - "SNOMEDCT_2005_07_31" . - . - . - . - "http://purl.obolibrary.org/obo/VariO_$1"^^ . - . - . - "scop.sun" . - . - . - . - . - "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . - . - "ontology" . - . - . - . - "co_320" . - . - . - . - . - "PWY-1042"^^ . - . - "^\\d+$"^^ . - . - . - "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . - . - . - . - . - . - "natural science" . - . - . - . - "dcterms" . - . - . - . - . - . - "^\\d+$"^^ . - "uniprot.db" . - . - "507568"^^ . - . - . - . - . - . - . - . - . - . - . - . - "bioinformatics" . - . - . - . - "obo" . - "false"^^ . - "egon.willighagen@maastrichtuniversity.nl" . - . - . - . - "SLCTR/2023/010"^^ . - . - . - . - . - . - "Cell line databases/resources"^^ . - "Rosa2"^^ . - . - . - . - . - . - . - . - . - . - "life science" . - . - . - . - "biochemistry" . - . - "ontology" . - . - . - "IPD-IMGT/HLA" . - . - . - . - . - . - "false"^^ . - "Livestock Product Trait Ontology" . - . - "subtiwiki" . - . - "veNOG12876"^^ . - . - . - "http://purl.obolibrary.org/obo/NIF_CELL_"^^ . - "pathway" . - "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . - "ontology" . - "anatomy" . - "false"^^ . - . - . - . - . - . - "eukaryotic" . - . - "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . - . - . - "true"^^ . - . - "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . - . - . - "dna" . - . - "AnVIL DRS" . - "An ontology to describe entities related to prescription of drugs"^^ . - "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . - . - . - . - "vertebrate" . - . - "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . - . - . - . - . - . - "SP_SL" . - "interaction" . - . - . - "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q="^^ . - . - "catalog" . - . - "UniGene" . - . - "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)"^^ . - . - . - . - . - . - "Gene Expression Ontology"^^ . - . - "false"^^ . - . - "false"^^ . - . - "virology" . - . - . - . - . - . - . - . - "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . - . - . - . - . - "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id="^^ . - "http://repository.topdownproteomics.org/proteoforms/"^^ . - . - "http://www.w3.org/ns/odrl/2/$1"^^ . - . - . - "false"^^ . - "^(\\d+)|(\\w+)$"^^ . - "Cellosaurus identifeirs for publications, like Pubmed"^^ . - . - "arxiv" . - "basic science" . - "epidemiology" . - . - . - . - . - . - "false"^^ . - "go.ref" . - . - . - . - "SED-ML data format" . - "worfdb" . - . - "false"^^ . - . - . - . - . - . - "ANOVA"^^ . - . - . - . - "orphanet" . - "98346"^^ . - "xl" . - . - . - . - "http://opendata.inra.fr/ATOL/ATOL_$1"^^ . - "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . - . - . - "health sciences" . - "entrez" . - . - . - "http://dictybase.org/gene/"^^ . - . - "ontology" . - "NA06985"^^ . - . - . - . - _:N56d4e713323645afb58017bd33f565ae . - "https://www.ebi.ac.uk/intact/search?query="^^ . - . - "protein" . - . - . - . - . - . - . - "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . - "nrfc" . - "The REPRODUCE-ME ontology is an extension of the PROV-O and the P-Plan ontology to describe a complete path of a scientific experiment. It expresses the REPRODUCE-ME Data Model using the OWL2 Web Ontology Language (OWL2). It provides a set of classes and properties to represent a scientific experiment including its computational and non-computational steps to track the provenance of results. It describes a complete path of a scientific experiment considering the use-case of biological imaging and microscopy experiments, computational experiments, including Jupyter notebooks and scripts. It describes an experiment and its data, agents, activities, plans, steps, variables, instruments, materials, and settings required for its reproducibility."^^ . - . - . - . - . - "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources." . - . - . - . - . - . - . - . - "ClinVar Record" . - . - "pathway" . - "false"^^ . - . - "Sigma Aldrich is a life sciences supply vendor."^^ . - . - . - "http://purl.obolibrary.org/obo/ONS_"^^ . - . - . - . - "DirectiveInformationContentEntity"^^ . - "d.a59037e8"^^ . - "false"^^ . - . - . - . - "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term="^^ . - "^\\d*$"^^ . - . - . - . - . - . - "0000001"^^ . - . - . - . - . - "dwelter.ontologist@gmail.com" . - . - . - "ontology" . - . - . - "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . - "The 4D Nucleome Data Portal hosts data generated by the 4DN Network and other reference nucleomics data sets. The 4D Nucleome Network aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases."^^ . - . - "true"^^ . -_:N56d4e713323645afb58017bd33f565ae "tim.vandermeersch@gmail.com" . - . - "^T3D\\d+$"^^ . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "false"^^ . - . - . - . - "^\\d{8}$"^^ . - "^\\d+$"^^ . - "anatomy" . - "The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more."^^ . - "^000\\d{5}$"^^ . - "0001998"^^ . - . - . - "BioCyc collection of metabolic pathway databases" . - "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . - . - "http://purl.obolibrary.org/obo/AGRO_$1"^^ . - "Alan Bridge" . - "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id="^^ . - . - . - "Integrated Resource for Domestic Dog" . - "cgrove@caltech.edu" . - . - "http://elm.eu.org/elms/elmPages/$1.html"^^ . - . - . - . - . - . - "https://bioregistry.io/metaregistry/$1"^^ . - . - "true"^^ . - "metabolite" . - . - "https://www.ebi.ac.uk/QuickGO/GProtein?ac="^^ . - . - . - . - . - . - . - "Endogenous Regulatory OligoPeptide knowledgebase-Moscow" . - . - "^\\d+$"^^ . - . - . - . - "^\\d+$"^^ . - "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."^^ . - . - . - . - . - . - "https://www.cellbiolabs.com/search?keywords=$1"^^ . - . - . - "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . - . - . - "structure" . - . - "bind" . - "https://pubchem.ncbi.nlm.nih.gov/classification/#hid="^^ . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - "272"^^ . - "PRIDE Project" . - . - . - . - . - . - "Frédéric Bastian" . - . - . - . - . - . - "Ontology of Biological Attributes" . - "biodiversity" . - "Mauno Vihinen" . - . - . - "false"^^ . - "biochemistry" . - . - "http://gmd.mpimp-golm.mpg.de/Analytes/"^^ . - "Name Reaction Ontology" . - "The responsible person for a resource" . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . - . - "protein" . - "true"^^ . - "Unified Medical Language System Atomic Unique Identifier" . - . - . - . - . - "https://pathbank.org/view/"^^ . - . - "dbSNP Reference SNP number" . - "Jacqueline Campbell" . - . - . - . - . - . - "cellular neuroscience" . - . - "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . - "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . - . - "isanchez@cnb.csic.es" . - "msigdb" . - . - . - . - "obo" . - . - "John Westbrook" . - . - "983"^^ . - . - . - "drugs" . - "The allele registry provides and maintains identifiers for genetic variants"^^ . - . - . - . - "false"^^ . - . - . - . - "darc" . - "Fernanda Farinelli" . - "trans" . - . - "false"^^ . - "Biological Spatial Ontology" . - . - . - . - . - "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."^^ . - . - . - . - "data management" . - . - . - . - . - "flopo" . - . - . - . - "5fce9b7300001250"^^ . - "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"^^ . - . - . - . - . - "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . - . - "http://nava.liacs.nl/cgi-bin/nava.py?id="^^ . - "rx00408"^^ . - . - . - "ChEMBL" . - . - . - . - "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references Drosophila data."^^ . - . - "https://scicrunch.org/resolver/RRID:AGSC_"^^ . - . - . - "zachll@umich.edu" . - "Human Gene Mutation Database" . - . - "http://purl.org/spar/c4o/"^^ . - . - . - . - "ontology" . - . - "health" . - . - . - "http://purl.obolibrary.org/obo/PGDSO_"^^ . - "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . - . - "obo" . - "obo" . - . - "false"^^ . - "OpenAlex is a fully open catalog of the global research system that describes scholarly entities and how those entities are connected to each other."^^ . - "senso" . - . - . - . - . - "23159291"^^ . - . - "genetics" . - "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . - "https://www.fisheries.noaa.gov/species/"^^ . - . - "Maciej Antczak" . - "false"^^ . - . - . - "https://bioregistry.io/p3db.site:"^^ . - . - "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . - "https://morpheus.gitlab.io/models/"^^ . - "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - "http://purl.obolibrary.org/obo/PPO_$1"^^ . - "obo" . - . - . - . - "^[a-z][a-z]/[0-9]+$"^^ . - . - "GWAS Catalog" . - . - "arrayexpress.platform" . - "fibroblast" . - "http://www.sasbdb.org/data/"^^ . - . - "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1"^^ . - . -_:Nf7d4794e396447a1b92c7061cea44e79 "Crop Ontology Helpdesk" . - "ontology" . - "ORPHA" . - "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . - . - . - . - "obo" . - "20003"^^ . - "genetics" . - . - "false"^^ . - "pfam.clan" . - . - . - . - "50-00-0"^^ . - . - . - "GRIN URL" . - . - . - "Jeffrey Grethe" . - . - . - . - "^\\d{5}$"^^ . - . - . - . - "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . - . - . - . - . - . - . - . - "NXP" . - . - . - "^\\d+$"^^ . - . - . - . - "UPLOC" . - . - . - "structure" . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - "ComplexPortal" . - "false"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "Health Data Research Innovation Gateway" . - . - . - . - . - . - . - "John Garavelli" . - "https://www.storedb.org/store_v3/study.jsp?studyId="^^ . - "true"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary."^^ . - . - . - "false"^^ . - "false"^^ . - "20560"^^ . - "https://cropontology.org/rdf/CO_365:$1"^^ . - "gecko" . - . - . -_:N5e00e918e8a94b1dac10f0dde02fe9dd "wbug@ncmir.ucsd.edu" . - . - . - . - "atcvet" . - "http://purl.obolibrary.org/obo/FBbt_$1"^^ . - . - . - . - "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . - "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . - . - "nsrrc" . - "taxonomy" . - . - "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors."^^ . - . - "has local unique identifier example" . - . - "PAp00000009"^^ . - "https://publons.com/researcher/"^^ . - . - . - "developmental biology" . - "RePORTER is an electronic tool that allows users to search a repository of both intramural and extramural NIH-funded research projects and access publications and patents resulting from NIH funding."^^ . - "Disease Class" . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - "MHC Restriction Ontology" . - "https://medical-data-models.org/forms/$1"^^ . - . - . - "life sciences" . - . - . - . - . - "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1"^^ . - "https://run.biosimulations.org/simulations/"^^ . - "Clinical measurement ontology" . - . - . - . - . - "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . - "An ontology covering the taxonomy of teleosts (bony fish)"^^ . - "http://purl.obolibrary.org/obo/WBPhenotype_"^^ . - . - "https://doulix.com/constructs/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://sideeffects.embl.de/drugs/"^^ . - . - "Genomic Epidemiology Ontology" . - . - "https://bioregistry.io/registry/"^^ . - . - . - "CIViC Disease" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . - . - "Metabolic Encyclopedia of metabolic and other pathways" . - . - . - "https://www.kegg.jp/entry/$1"^^ . - . - "Alan Wood's Pesticides" . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . - "protein" . - . - "epidemiology" . - . - "MaizeGDB Locus" . - . - "beiresources" . - . - . -_:N27ef8028e2244489bf142e7a8b5cc089 "Crop Ontology Helpdesk" . - . - . - . - "structure" . - "phylogeny" . - . - . - . - "Experimental data table management software to make research data accessible and available for reuse with minimal effort on the part of the data provider. Designed to manage experimental data tables in an easy way for users, ODAM provides a model for structuring both data and metadata that facilitates data handling and analysis. It also encourages data dissemination according to FAIR principles by making the data interoperable and reusable by both humans and machines, allowing the dataset to be explored and then extracted in whole or in part as needed."^^ . - "mmusdv" . - . - "protein" . - . - . - . - "false"^^ . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])_.*|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*)$"^^ . - "BioSystems" . - "proteomics" . - . - . - "agriculture" . - "https://www.webelements.com/$1"^^ . - . - "SNP to Transcription Factor Binding Sites" . - "^XB\\-\\w+\\-\\d+$"^^ . - "cordis.project" . - "Southwestern Environmental Information Network" . - . - . - . - "rebec" . - "obo" . - . - . - "plant" . - . - . - . - "cell line" . - . - . - "Disease Drivers Ontology" . - "^\\d{7}$"^^ . - . - . - "SABIO Reaction Kinetics" . - "EOL Secretariat" . - . - . - . - "pso" . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_qual_"^^ . - "health science" . - . - . - . - . - "0002533"^^ . - "anatomy" . - "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . - . - . - "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA="^^ . - "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . - . - . - . - "^\\w+$"^^ . - . - . - "jesper.friis@sintef.no" . - . - "neuroscience" . - "nstd102"^^ . - . - "^\\d+$"^^ . - . - . - "rat model" . - "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database"^^ . - _:N2e5ebba17dfe4820a58407ea4cde60df . - "true"^^ . - . - . - "Stefan Kuhn" . - "aap-1"^^ . - . - "false"^^ . - . - . - "huang@southalabama.edu" . - . - . - . - "^\\d+$"^^ . -_:N618fd1ab6a6a4e379c6d1f4f1cd3173d "helpdesk@cropontology-curationtool.org" . - . - . - . - "homd.seq" . - "panther.pathway" . - . - "101"^^ . - "GOLD metadata" . - . - . - . - . - . - "kyinno" . - "voss@gbv.de" . - . - "https://www.storedb.org/store_v3/download.jsp?fileId="^^ . - . - . - "Publishing Roles Ontology" . - . - . - "obo" . - . - "biomedical science" . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - "life science" . - . - . - . - . - "^\\w+_COVID19_[-\\w]+$"^^ . - "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."^^ . - . - "ontology" . - . - . - . - "http://purl.obolibrary.org/obo/IAO_$1"^^ . -_:N0402b08463784fa0bcdbaac63beec045 "Allotrope Foundation" . - . - . - . - . - . - . - . - . - . - . - "013681"^^ . - . - "http://www.bindingdb.org/compact/$1"^^ . - . - "swiss-model" . - . - . - . - . - . - "http://www.ebi.ac.uk/cmpo/CMPO_$1"^^ . - "https://terminology.hl7.org/CodeSystem-v3-"^^ . - . - . - . - . - "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"^^ . - "http://purl.obolibrary.org/obo/MRO_"^^ . - . - . - . - . - . - . - "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . - "obo" . - . - . - "nextprot.family" . - "^\\d+$"^^ . - . - . - "msaier@ucsd.edu" . - . - . - . - "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."^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references compounds."^^ . - . - . - . - "hescriva@obs-banyuls.fr" . - "protonet.proteincard" . - . - . - . - "Sharkipedia Species" . - . - . - . - . - "glycomics" . - . - "life science" . - "9606117"^^ . - "Rodent Unidentified Gene-Encoded Large Proteins" . - . - . - . - . - "Curation of Neurodegeneration Supporting Ontology" . - . - . - . - . - "ontology" . - . - . - "gxa.expt" . - . - . - "1"^^ . - "false"^^ . - "plant" . - "obo" . - "disease" . - . - . - . - . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "John Graybeal" . - "2679240"^^ . - . - . - . - . - . - . - "caripark@iastate.edu" . - "http://www.drugtargetontology.org/dto/DTO_"^^ . - "vsdb" . - . - . - "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"^^ . - "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . - "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . - . - . - . - . - "protein" . - . - . - . - . - "systems biology" . - . - . - . - . - . - "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . - . - . - . - . - . - . - "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . - . - "data management" . - "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . - . - "Environmental conditions, treatments and exposures ontology" . - . -_:N5e5ef5c07ce54a41b7b91c5aada03718 "Crop Ontology Helpdesk" . - . - "microbiology" . - . - . - . - . - "https://civicdb.org/links/evidence/$1"^^ . - . - "http://purl.obolibrary.org/obo/SYMP_"^^ . - "enzymology" . - "variants" . - "false"^^ . - . - "ontology" . - "false"^^ . - . - . - "transcriptomics" . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - "G8944"^^ . - . - "https://hamap.expasy.org/unirule/"^^ . - . - . - "ECMDB00005"^^ . - . - . - . - . - . - . - "^RF\\d{5}$"^^ . - "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . - "https://www.kaggle.com/"^^ . - . - "schem" . - . - "software engineering" . - . - "001"^^ . - . - . - "urmas.koljalg@ut.ee" . - . - . - "SIGNOR Relation" . - "ontology" . - . - . - . - "false"^^ . - "chemical" . - . - "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases."^^ . - "The Identifiers.org Resolution Service provides consistent access to life science data using Compact Identifiers. Compact Identifiers consist of an assigned unique prefix and a local provider designated accession number (prefix:accession)." . - "63"^^ . - "Human Proteome Map" . - . - . - "comparative genomics" . - . -_:N9e87a13b66ee4814aa6f9ba33e193e09 "helpdesk@cropontology-curationtool.org" . - "slkbase" . - "^\\d{7}$"^^ . - "BindingDB is the first public database of protein-small molecule affinity data."^^ . - "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - . - . - "SNOMEDCT_US_2022_09_01" . - "ccle" . - . - "^\\d{8}$"^^ . - . - "vann" . - . - . - . - "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . - . - "NLXFUNC" . - "false"^^ . - . - . - . - . - . - . - "https://datacommons.org/browser/$1"^^ . - . - "co_366" . - "EcoPortal" . - "MSMEG_3769"^^ . - "false"^^ . - "addiehl@buffalo.edu" . - . - . - . - . - . - . - . - . - "biomedical science" . - . - . - "The Genomics of Drug Sensitivity in Cancer (GDSC) database is designed to facilitate an increased understanding of the molecular features that influence drug response in cancer cells and which will enable the design of improved cancer therapies."^^ . - . - "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . - "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . - . - . - . - "215"^^ . - . - "KEGG.EDRUG" . - "Mouse Developmental Stages" . - "clinical studies" . - "https://tools.ietf.org/rfc/rfc"^^ . - "mpid" . - "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . - "genomics" . - . - . - . - . - "D053716"^^ . - "ontology" . - . - . - "strain" . - . - . - "clo" . - "mim" . - "December 2019"^^ . - . - . - . - . - . - "^\\w{1,2}\\d+$"^^ . - "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . - . - "medical informatics" . - . - . - . -_:Nd2cf2107dfdb419d94a5e0f3473323b5 "helpdesk@cropontology-curationtool.org" . - "false"^^ . - "Nematode Expression Pattern DataBase" . - "Ontology of Organizational Structures of Trauma centers and Trauma systems" . - . - . - . - . - . - . - "dsm-iv" . - "structure" . - "https://www.datanator.info/gene/"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "quality" . - . - . - . - "eccode" . - . - . - "rna" . - "false"^^ . - "false"^^ . - "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace."^^ . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id="^^ . - "longevity" . - . - . - . - . - . - "0000389"^^ . - . - . - . - "ac" . - . - "zeco" . - "tritrypdb" . - "Ontological Interpretations for Web Property Graphs" . - "http://addgene.org/"^^ . - . - . - . - . - "Fossilworks Journal" . - . - . - "false"^^ . - . - . - . - . - . - "https://cropontology.org/rdf/CO_331:"^^ . - . - . - . - . - "false"^^ . - "dbvar.variants" . - . - "https://www.pharmvar.org/gene/$1"^^ . - . - "life science" . - "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . - "true"^^ . - . - . - "ontology" . - . - "MEROPS Family" . - . - "fplx" . - . - . - . - "ohmi" . - "National Library of Medicine Catalog" . - "Variable"^^ . - "1046"^^ . - . - . - . - . - "molecular chemistry" . - "RBR-6qvdftm"^^ . - . - . - "genetics" . - "EDAM Data" . - "ontology" . - . - . - . - "^Y[A-Z]{2}\\d+[CW]$"^^ . - "^\\d{7}$"^^ . - . - "https://biokb.lcsb.uni.lu/fact/$1"^^ . - . - . - "https://civicdb.org/links/variant_group/$1"^^ . - . - "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . - . - . - "gro-cpga" . - . - . - . - "http://purl.obolibrary.org/obo/HSO_"^^ . - . - "gnomad" . - "Global Biodata Coalition - Global Core Biodata Resources" . - . - . - "ev" . - . - . - . - . - . - . - "dna" . - "https://data.terra.bio/ga4gh/drs/v1/objects/"^^ . - . - "TB2:S1000"^^ . - . - "0000046"^^ . - . - "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . - . - . - "longevity" . - . - . - . - . - "anatomy" . - "BeAn 70563"^^ . - . - . - "medical informatics" . - . - "^CNP\\d{7}$"^^ . - "http://scop.berkeley.edu/sid="^^ . - . - "http://purl.obolibrary.org/obo/PdumDv_"^^ . - . - . - "fao" . - . - . - . - . - . - . - . - "ko00071"^^ . - . - "Ryan Brinkman" . - . - . - . - "true"^^ . - . - . - . - . - . - "ecyano.rule" . - . - . - "Cell line collections (Providers)"^^ . - . - . - . - . - . - . - . - . - "https://fcs-free.org/fcs-database?"^^ . - . - "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . - . - . - "protein" . - . - "Scholia Registry" . - . - . - . - "241"^^ . - . - "None"^^ . - "treefam" . - . - . - . - . - "Alayne Cuzick" . - . - . - . - . - . - . - "agro" . - . - . - . - "computational chemistry" . - "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . - . - . - "function" . - "obo" . - . - . - . - . - "false"^^ . - . - "Mouse Developmental Anatomy Ontology" . - . - . - "ISBN-10" . - "lschriml@som.umaryland.edu" . - "subject agnostic" . - "rmrich5@gmail.com" . - "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . - "ExO" . - . - . - . - . - . - "^ENSG\\d{11}$"^^ . - . - . - "Plant Stress Ontology" . - "https://purl.dataone.org/odo/SALMON_$1"^^ . - . -_:Nc2c3eeb40d884344b28b37273de129b2 "bgee@isb-sib.ch" . - "https://bio.tools/"^^ . - . - . - . - . - "false"^^ . - . - "HEPRO is an ontology of informational entities and processes related to health procedures and health activities."^^ . - "01467"^^ . - . - "false"^^ . - . - "Joshua Orvis" . - . - . - . - . - . - . - "uniprot.journal" . - "lars.holm.nielsen@cern.ch" . - . - . - "Reactome" . - . - "anatomy" . - . - . - "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."^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/REO_$11"^^ . - . - . - . - . - . - . - . - "Minimal Information About Anatomy ontology" . - . - "The Open Data Commons for Traumatic Brain Injury is a cloud-based community-driven repository to store, share, and publish traumatic brain injury research data."^^ . - "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . - "^\\d+$"^^ . - . - . - "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."^^ . - "false"^^ . - "CAL0003079"^^ . - . - "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . - . - . - "https://cellrepo.ico2s.org/repositories/$1"^^ . - . - . - "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI)."^^ . - . - . - "cell biology" . - "http://purl.obolibrary.org/obo/AISM_"^^ . - . - . - . - . - . - . - "pathway" . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl="^^ . - . - "http://repository.topdownproteomics.org/proteoforms/$1"^^ . - . - . - "http://www.w3.org/2001/XMLSchema#"^^ . - "https://biopragmatics.github.io/providers/peff/"^^ . - . - . - . - "https://www.sharkipedia.org/trends/"^^ . - "neurophysiology" . -_:Nd62b24d3a8fe48d892050a1d27e387a3 "mssohelp@meddra.org" . - . - . - "false"^^ . - . - "gene expression" . - "false"^^ . - . - . - . - . - . - . - "Sergio José Rodríguez Méndez" . - . - . - "https://odc-tbi.org/data/"^^ . - . - . - . - "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."^^ . - "ecolexicon" . - . - . - . - . - "false"^^ . - . - . - "inbred rat strain" . - . - . - . - "http://purl.obolibrary.org/obo/ECO_$1"^^ . - "5282"^^ . - "rnajunction" . - . - "co_359" . - "blast" . - . - "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)"^^ . - "life science" . - . - . - "https://neurovault.org/collections/$1"^^ . - . - . - . - . - "true"^^ . - "^\\d{8}$"^^ . - . - . - . - . - . - . - . - "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:"^^ . - "protein" . - . - . - "KEGG Genes" . - . - . - . - . - "1050"^^ . - . - . - . - . - . - . - . - "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . - . - "owl" . - . - . - "developmental biology" . - "false"^^ . - . - . - . - . - . - . - "pig" . - . - . - "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . - "https://doulix.com/constructs/$1"^^ . - "lincs.cell" . - "Data Commons" . - . - . - "Long Term Ecological Research Controlled Vocabulary" . - . - "mmsinc" . - . - "https://progenetix.org/services/ids/$1"^^ . - . - "ProtoNet ProteinCard" . - "The Crop Ontology (CO) current objective is to compile validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the multi-crop passport terms" . - "Mike Tyers" . - . - "orthology assignment" . - "tol" . - . - "microarray" . - "lotus" . - . - "false"^^ . - . - . - . - "^\\d{7}$"^^ . - "imsr_tac" . - "MGnify Analysis" . - . - . - "karr@mssm.edu" . - . - . - . - . - . - . - "https://scicrunch.org/scicrunch/interlex/view/ilx_"^^ . - . - "^\\d{6}$"^^ . - . - . - . - . - "Silvio Peroni" . - . - "https://www.nextprot.org/term/$1"^^ . - . - . - "Astrophysics Source Code Library" . - . - . - . - . - . - . - . - . - "0000001"^^ . - . - . - . - . - . - "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . - "zp" . - . - "ovarian" . - . - "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies."^^ . - "UP000005640"^^ . - . - . - . - . - "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . - . - . - "genomics" . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references kinase information."^^ . - . - . - . - "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles."^^ . - . - "^rs[0-9]+$"^^ . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/"^^ . - . - "Protein and Associated NucleotideDomains with Inferred Trees" . - . - "http://purl.uniprot.org/isoforms/"^^ . - "https://n2t.net/$1:" . - "0000009"^^ . - "false"^^ . - . - . - "true"^^ . - . - . - . - . - "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment."^^ . - . - . - "Enzo Life Sciences" . - . - . - . - . - . - "https://biopragmatics.github.io/providers/scomp/$1"^^ . - "false"^^ . - "helpdesk@cropontology-curationtool.org" . - "http://www.proteinatlas.org/$1"^^ . - "panorama" . - . - . - . - . - . - . - "00020134"^^ . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marcat/#/records/$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."^^ . - . - "omics" . - . - "http://purl.obolibrary.org/obo/LPT_$1"^^ . - . - . - . - "genome" . - . - "disorders" . - . - "http://purl.obolibrary.org/obo/PCO_$1"^^ . - . - "0058"^^ . - "botany" . - . - . - "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid="^^ . - "false"^^ . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "SwissLipid" . - "An organization" . - "ontology" . - . - . - "biology" . - . - . - "ontology" . - "social science" . - . - "nfdi4chem.ontocape" . - . - . - . - "CNP0171505"^^ . - "0002-1975-61"^^ . - "bioresource" . - . - . - . - . - "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . - . - . - . - . - . - . - . - . - "ppdb@gifu-u.ac.jp" . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - "chemistry" . - . - . - "https://gold.jgi.doe.gov/resolver?id=$1"^^ . -_:N61a3d10cbab946e29d82cb3fcd645550 "j@deltaflow.com" . - . - "Will Simpson" . - . - . - "life science" . - . - "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . - "allele" . - "obo" . - . - "0000054"^^ . - "false"^^ . - . - "gmd.gcms" . - . - . - . - . - "https://lincs.hms.harvard.edu/db/cells/$1"^^ . - . - "genomics" . - . - . - "03yrm5c26"^^ . - . - "http://www.kegg.jp/entry/"^^ . - . - . - . - "jiezheng@pennmedicine.upenn.edu" . - "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . - "topfind" . - "Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data."^^ . - . - . - "http://purl.obolibrary.org/obo/MMO_"^^ . - . - . - . - . - . - . - . - . - "genome" . - "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . - . - "http://multicellds.org/MultiCellDB/"^^ . - . - . - . - . - . - "obo" . - . - . - . - "false"^^ . - . - "SCC111"^^ . - "11478"^^ . - . - "100"^^ . - . - . - . - "00100037"^^ . - . - "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID="^^ . - "ontology" . - . - . - . - "virus" . - . - "false"^^ . - . - . - "human" . - "Metabolic Atlas" . - . - "19803"^^ . - "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."^^ . - . - . - . - "classification" . - . - . - "https://mednet-communities.net/inn/db/ViewINN.aspx?i="^^ . - . - "Research Resource Identifiers" . - "^\\d{7}$"^^ . - "imp10873"^^ . - . - . - "PomBase" . - . - . - . - . - "https://bioregistry.io/pmap.substratedb:"^^ . - "classification" . - . - "false"^^ . - . - "obo" . - "SBGN bricks represent biomolecular or biological concepts. BKO formally associates bricks with the concepts they represent. BKO includes terms that describe concepts, the template bricks representing these concepts, and categories that gather bricks in a broader way."^^ . - . - . - . - "^bt\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - "Human Induced Pluripotent Stem Cells Initiative" . - "cellular components" . - . - . - "Leszek Vincent" . - . - "familyName"^^ . - "0000609"^^ . - "CAA71118.1"^^ . - "http://purl.obolibrary.org/obo/VT_"^^ . - . - "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."^^ . - . - . - "Amazon Standard Identification Number" . - . - . - . - . - "1"^^ . - . - . - "polcaes@gmail.com" . - "transcriptomics" . - . - . - . - "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code="^^ . - . - . - . - . - "G02681"^^ . - "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . - . - . - "euclinicaltrials" . - . - . - . - . - . - . - "cheminformatics" . - . - . - . - . - . - . - "RPCEC00000423"^^ . - . - . - . - . - . - . - . - . - "Software Heritage is the universal archive of software source code."^^ . - . - . - . - . - . - . - . - . - . - . - "ontology" . - . - . - . - "^P\\d+$"^^ . - . - "molecular biology" . - . - . - . - . - . - . - "ProteomicsDB Peptide" . - . - "life science" . - "0000171"^^ . - . - . - "spbase" . - . - . - "irct" . - . - "MSV000082131"^^ . - "false"^^ . - . - "MF_01400"^^ . - . - "VEuPathDB ontology" . - . - . - "protein" . - "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. "^^ . - "FlowRepository" . - . - . - . - . - "https://www.genome.jp/virushostdb/$1"^^ . - "Dendritic cell" . - . - . - "functional genomics" . - . - . - "false"^^ . - "^[0-9]+(LR)?$"^^ . - . - . - "Uniprot ID" . - . - "0000022"^^ . - . - "21877"^^ . - . - . - "ontology" . - "exac.variant" . - . - . - "microbial" . - "wbbt" . - . - . - . - . - . - "http://metnetonline.org/browse_pathway2.php?pthID="^^ . - . - "http://purl.obolibrary.org/obo/VSMO_"^^ . - _:N618fd1ab6a6a4e379c6d1f4f1cd3173d . - . - "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."^^ . - . - . - . - "obo" . - . - . - . - . - "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."^^ . - . - . - . - "ontology" . - . - "BN000065"^^ . - "Proteomics data and process provenance" . - . - . - "https://e-cyanobacterium.org/models/model/$1"^^ . - . - . - . - "https://www.ribocentre.org/docs/"^^ . - "false"^^ . - "cro" . - . - . - . - "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . - . - "chebi" . - "Current Procedural Terminology" . - "EGAD00000000001"^^ . - . - . - . - . - . - . - . - . - "TAX" . - . - "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_"^^ . - . - "pharmacogenomics" . - . - . - . - "^\\d{7}$"^^ . - . - . -_:N62de8aa2a60e4ff4ab11da60480d7858 "cs@firstdatabank.com" . - . - "Langua aLimentaria Thesaurus" . - "Elvira Mitraka" . - . - "false"^^ . - "biomedical science" . - . - . - "Global Natural Products Social Molecular Networking Task" . - . - . - "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]"^^ . - "^MMP\\d+.\\d+$"^^ . - "false"^^ . - . - . - . - "https://mmp.sfb.uit.no/databases/marcat/#/records/"^^ . - . - . - . - "Ontology for the Anatomy of the Insect SkeletoMuscular system" . - . - "PANTHER Family" . - . - . - "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . - "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . - . - . - . - "biology" . - "oae" . - . - . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - "Aclame" . - "^[a-z]+(\\..*?)?$"^^ . - "http://vegbank.org/cite/$1"^^ . - . - "BM0456"^^ . - "https://europepmc.org/article/ppr/"^^ . - . - . - . - "mouse strain" . - . - "protein" . - . - "https://www.cancerrxgene.org/translation/Drug/$1"^^ . - "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains."^^ . - . - "life science" . - . - "Python"^^ . - . - . - . - . - "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."^^ . - . - . - "nicolas.matentzoglu@gmail.com" . - "NONCODE v3" . - "FlyBase Controlled Vocabulary" . - "http://purl.obolibrary.org/obo/GECKO_"^^ . - . - "0007114"^^ . - . - . - . - . - . - . - . - "lter" . - . - "Cell line collections (Providers)"^^ . - "https://gpcrdb.org/protein/$1"^^ . - . - "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - . - "PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them."^^ . - . - . - "https://ocid.ontochem.com/prefname?ocid=$1"^^ . - "transcriptomics" . - . - . - . - "cldb" . - . - "false"^^ . - . - "agriculture" . - . - . - "false"^^ . - . - . - "authorList"^^ . - "^[0-9\\-_]+$"^^ . - "hoip" . - "kegg.brite" . - "https://foodb.ca/foods/$1"^^ . - . - . - . - "ontology" . - . - . - . - "true"^^ . - "miRTarBase is a database of miRNA-target interactions (MTIs), collected manually from relevant literature, following Natural Language Processing of the text to identify research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments."^^ . - . - . - . - . - . - . - "mao" . - "icd9cm" . - . - "phrr" . - "https://www.uniprot.org/journals/"^^ . - "false"^^ . - . - "^\\d+-\\d+$"^^ . - "http://www.peptideatlas.org/PASS/"^^ . - "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . - . - . - . - . - . - . - "SNOMEDCT_US_2022_12_31" . - "false"^^ . - "36"^^ . - . - "knowledge and information systems" . - "Database of homology-derived secondary structure of proteins" . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . - . - . - . - "Virtual International Authority File" . - . - "post-translational modification" . - "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"^^ . - "false"^^ . - "false"^^ . - . - . - "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration."^^ . - . - "bioinformatics" . - "ab275461"^^ . - . - . - . - "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . - . - "obo" . - "false"^^ . - . - "http://purl.obolibrary.org/obo/VBO_"^^ . - . - . - "fairsharing.user" . - . - . - . - . - . - . - "protein" . - . - . - . - . - . - . - "https://europepmc.org/article/CBA/$1"^^ . - " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . - "^\\d+$"^^ . - . - "https://www.ncbi.nlm.nih.gov/pubmed/"^^ . - . - "Gi07796"^^ . - . - "false"^^ . - . - "gene" . -_:Na7f201c11d94490f8ca52133e1faab3c "J.Bard@ed.ac.uk" . - "false"^^ . - "Global Proteome Machine Database" . - . - "false"^^ . - "https://www.gwascentral.org/study/"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . - . - . - "life science" . - . - . - . - . - . - . - . - "http://pepbank.mgh.harvard.edu/interactions/details/"^^ . - . - "6017782"^^ . - . - . - . - . - . -_:N08e1f9097d1b4dae9796095cf1ebccef "helpdesk@cropontology-curationtool.org" . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . - "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."^^ . - "RGD" . - "LOC_Os01g49190.1"^^ . - "rna" . - "false"^^ . - . - "https://aopwiki.org/relationships/$1"^^ . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - "http://stitch.embl.de/interactions/$1"^^ . - . - "chictr" . - . - . - "false"^^ . - . - "http://www.ontobee.org/ontology/$1" . - . - . - . - . - . - . - "Nicole Vasilevsky" . - "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."^^ . - "BioTools" . - "ontology" . - "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . - "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . - . - . - "microbiology" . - . - "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."^^ . - . - . - . - . - . - "biology" . - "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . - . - "hpscreg" . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/LOGGERHEAD_"^^ . - "https://www.hipsci.org/lines/#/lines/$1"^^ . - "Ontology of Precision Medicine and Investigation" . - . - . - . - . - . - "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies."^^ . - . - "obo" . - . - . - . - "jcsd" . - "pcl" . - "false"^^ . - "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids."^^ . - . - . - "https://chemapps.stolaf.edu/jmol/jmol.php?model="^^ . - "Span" . - . - "false"^^ . - "ontology" . - . - . - . - "false"^^ . - "Arctic Data Center Academic Disciplines Ontology" . - "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)"^^ . - . - "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . - . - . - . - . - . - "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . - "Bio-Pesticides DataBase" . - . - . - . - "Hector Escriva" . - . - . - "CONSO00010"^^ . - . - . - "60025709"^^ . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "https://civicdb.org/links/gene/$1"^^ . - "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . - . - . - . - "4dn.replicate" . - "BDGP insertion DB" . - . - . - "aao" . - "biomedical science" . - "NBC00001"^^ . - "cell biology" . - "JCRB1355"^^ . - "^[0-9a-z_:\\.-]+$"^^ . - "genome" . - "0000004"^^ . - . - "ontology" . - "ico" . - . - "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."^^ . - . - "EU Clinical Trials" . - . - "http://purl.obolibrary.org/obo/MI_"^^ . - . - "https://cropontology.org/rdf/CO_359:"^^ . - . - "genome" . - . - "1351341"^^ . - . - . - . - "ontology" . - "MeDRA" . - . - "Datanator Reaction" . - . - "microbial" . - . - . - "clinical studies" . - . - . - . - . - . - "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . - "mirbase.family" . - . - . - . - . - . - . - . - . - "brain regions" . - . - . - . - . - "obo" . - "^BAMSC\\d+$"^^ . - . - . - "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]"^^ . - . - "^\\d{7}$"^^ . - . - . - . - "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . - . - . - . - . - . - "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . - . - "26957"^^ . - . - . - "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . - . - . - "elspeth@genenames.org" . - "https://eol.org/pages/$1"^^ . - "http://drugcentral.org/drugcard/$1"^^ . - "Issaku Yamada" . - . - . - "https://www.grid.ac/institutes/"^^ . - . - . - "kegg.rclass" . - "Human Pluripotent Stem Cell Registry" . - . - "image collection" . - "24801"^^ . - . - "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . - . - . - "ximbio" . - . - "Fahim Imam" . - . - "occupational medicine" . - . - . - . - . - . - "0000111"^^ . - "neurovault.collection" . - . - . - . - "273"^^ . - . - _:N824a8517c4d74a26874edd72d326307f . - . - . - . - . - "life science" . - . - . - . - "^[0-9]+$"^^ . - . - . - "The set of prefixes used in the Cellosaurus resource" . - . - "Property"^^ . - "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model."^^ . - . - "co_330" . - . - . - . - . - . - . - . - . - . - . - "ontology" . - "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."^^ . - . - . - . - "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."^^ . - . - . - "https://www.encodeproject.org/"^^ . - . - . - "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . - . - "2224"^^ . - . - . - . - . - "The Arabidopsis Information Resource" . - . - . - "ontology" . - . - . - . - "fairsharing" . - . - . - "^\\d+$"^^ . - "NIFEXT" . - . - "http://neuromorpho.org/neuron_info.jsp?neuron_name="^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/STATO_"^^ . - . - "ontology" . - . - . - "ontology" . - "^\\d{7}$"^^ . - "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."^^ . - "false"^^ . - "life science" . - . - . - "^\\d+$"^^ . - "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."^^ . - . - "tahh" . - "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_"^^ . - . - . - "SAMEA2397676"^^ . - . - "sequence" . - "nutritional science" . - "wos" . - . - "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . - . - . - . - . - . - "rbca.jackson@gmail.com" . - . - . - . - . - "Metabolites in the Xenobiotics Metabolism Database."^^ . - "http://biomodels.net/rdf/vocabulary.rdf#"^^ . - . - . - . - . - . - . - . - . - "Elementary Multiperspective Material Ontology" . - "0000001"^^ . - . - "MOSAiC Ontology" . - "genomics" . - "0000070"^^ . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . - . - . - "Cryo Electron Microscopy ontology" . - "http://purl.obolibrary.org/obo/ECO_"^^ . - . - "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . - "Cell line collections (Providers)"^^ . - . - "http://sideeffects.embl.de/se/"^^ . - . - . - . - "Comparative Data Analysis Ontology" . - . - "^Gm\\d+$"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "multicellds.collection" . - . - . - "http://purl.obolibrary.org/obo/CTO_$1"^^ . - . - "life science" . - "00000105"^^ . - . - "^[a-zA-Z0-9-]+$"^^ . - . - "^\\d{7}$"^^ . - "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals"^^ . - "obo" . - . - . - . - "^DG\\d+$"^^ . - "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "Elizabeth Arnaud" . - "^\\d+$"^^ . - . - . - . - . - "https://www.atcc.org/products/$1"^^ . - "A0TMC"^^ . - . - . - . - . - . - . - . - . - . - "health_care_quality_assessment"^^ . - . - . - "ontology" . - "protein" . - "anatomy" . - . - "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"^^ . - . - "dandi" . - . - . - . - "Database of small human noncoding RNAs" . - "dna" . - . - . - "Datanator Metabolite" . - . - "phismith@buffalo.edu" . - . - . - . - "BSU29180"^^ . - . - . - . - . - "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing."^^ . - "fly" . - . - . - . - . - . - "Toxin and Toxin Target Database" . - . - "^[A-Z0-9]+$"^^ . - "dc11" . - . - "uniprot.proteome" . - . - . - . - . - . - "Mosquito gross anatomy ontology" . - "http://www.cathdb.info/domain/$1"^^ . - . - "slctr" . - "small molecule" . - "^\\d{6}$"^^ . - . - "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"^^ . - . - . - . - "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "obo" . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE elements."^^ . - . - . - "Epilepsy and Seizure Ontology" . - "venom" . - . - . - . - . - "^BG\\d+$"^^ . - "glycomics" . - . - "BiGG Reaction" . - "false"^^ . - . - . - . - . - . - . - . - . - "Amanda Hicks" . - "http://purl.bioontology.org/ontology/IDODEN_"^^ . - "ontology" . - "genomics" . - . - . - "dna" . - "Brazilian Registry of Clinical Trials" . - "false"^^ . - . - . - . - . - . - . - . - "SASDAX8"^^ . - "Alistair Miles" . - "^[0-9]+$"^^ . - . - . - . - . - "ICDCM_2005" . - . - "0000109"^^ . - "^\\d+$"^^ . - . - . - . - "A subspace of Metabolic Atlas for compartment-specific records for metabolites."^^ . - "false"^^ . - . - "The bioRxiv is a preprint server for biology"^^ . - "http://solgenomics.net/phenome/locus_display.pl?locus_id="^^ . - . - "http://purl.obolibrary.org/obo/ENVO_$1"^^ . - . - . - "physiology" . - . - . - "Yvonne Bradford" . - "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"^^ . - "pathoplant" . - . - . - . - "rrrc" . - . - . - . - . - . - . - . - "experiment" . - "https://w3id.org/babelon/"^^ . - "DBCAT000600"^^ . - "0000091"^^ . - . - "https://bioregistry.io/spike.map:"^^ . - . - . - "MAR11851"^^ . - . - . - "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"^^ . - "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."^^ . - . - . - . - "false"^^ . - . - "https://icd.who.int/browse10/2019/en#/"^^ . - "http://purl.obolibrary.org/obo/CHIRO_"^^ . - . - . - "11303"^^ . - "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist="^^ . - . - . - . - . - . - "true"^^ . - . - "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . - . - . - . - . -_:N0b76c49429ac46d794bde4f27f024c25 "interhelp@ebi.ac.uk" . - "snap" . - . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references expressed sequence tag (EST) information."^^ . - . - "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . - . - "anatomy" . - "swisslipids" . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - "^\\d+$"^^ . - "false"^^ . - "structural biology" . - . - . - . - . - "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . - . - . - "HL7 V2 Code Systems" . - . - "EuroFir (European Food Information Resource Network), the world-leading European Network of Excellence on Food Composition Databank systems, is a partnership between 48 universities, research institutes and small-to-medium sized enterprises (SMEs) from 25 European countries."^^ . - . - "classification" . - "life science" . - . - . - . - . - "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . - . - "Plant Ontology" . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID="^^ . - . - "d4e2515"^^ . - . - . - . - "silvio.peroni@unibo.it" . - . - . - "life science" . - . - . - . - . - . - . - . - "antweb" . - "ontology" . - . - "SugarBind" . - "neuroscience" . - . - "gene" . - . - . - "tto" . - . - . - . - . - "https://civicdb.org/links/sources/"^^ . - . - . - . - . - . - "GitHub Issue" . - "farming systems research" . - "false"^^ . - . - . - . - . - . - "Phy000CLXM_RAT"^^ . - . - . - . - . - "epidemiology" . - "https://www.ncbi.nlm.nih.gov/homologene/"^^ . - "0000485"^^ . - . - "hepro" . - "ontology" . - . - . - "https://horizondiscovery.com/en/search?searchterm="^^ . - . - . - . - . - . - . - . - "A Semantic Web Rule Language Combining OWL and RuleML" . - . - . - . - . - "Dongsheng Cao" . - . - . - . - "biodiversity" . - "^L\\d+$"^^ . - . - . - . - "^\\w+\\_\\d+(\\.\\d+)?$"^^ . - "false"^^ . - . - "true"^^ . - "medical biotechnology" . - . - . - "ontology" . - . - . - . - _:Necdcf0cef45e47968707a7dee8f4a0d2 . - . - "CAS Registry Number" . - . - "https://openalex.org/$1"^^ . - . - . - _:Nb4de457f8e114f4e8c18616dab90271d . - . - "physiology" . - . - "https://europepmc.org/article/CBA/"^^ . - . - "genome" . - "functional genomics" . - "agriculture" . - . - "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . - . - . - . - . - . - . - "https://bioregistry.io/cellbank.australia:"^^ . - . - . - . - . - "aop" . - . - . - "Enzo Life Sciences is an antibody vendor."^^ . - . - . - . - . - . - "http://search.sisuproject.fi/#/variant/$1"^^ . - "A hierarchical classification of congenital heart disease "^^ . - . - "Daniel Schober" . - _:N8b0188fd98fb4f68a9d1f2d2f5c39af7 . - . - . - . - . - . - . - . - . - . - . - . - . - "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes."^^ . - . - . - . - . - "pass2" . - . - . - . - "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://purl.obolibrary.org/obo/HAO_"^^ . - "bao" . - "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . - "false"^^ . - . - . - . - "https://www.metabolome-express.org/datasetview.php?datasetid="^^ . - . - "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id="^^ . - _:Nf7d4794e396447a1b92c7061cea44e79 . - . - . - . - . - . - "false"^^ . - "NIF Standard Ontology: Subcellular Entities" . - . - . - . - . - . - "ricenetdb.protein" . - . - . - . - . - . - . - "dermatology" . - "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . - . - . - "Francesco Vitali" . - "Paragraph"^^ . - . - "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . - . - "0000050"^^ . - "https://civicdb.org/links/diseases/$1"^^ . - . - . - "165a"^^ . - . - . - . - . - "UMLSSG" . - . - . - "topics" . - . - "http://purl.obolibrary.org/obo/PSDO_"^^ . - . - . - . - . - "obo" . - . - "Signaling Pathways Project" . - . - . - "identifier for a scientific journal, in the UniProt database"^^ . - "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)"^^ . - . - "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"^^ . - . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - "FBcv" . - . - . - "Database of Escherichia coli Sequence and Function" . - "12e8LH"^^ . - . - . - . - . - . - "Jacqueline.Campbell@usda.gov" . - . - "Groundnut ontology" . - . - "disease model" . - "^LTS\\d{7}$"^^ . - . - "http://www.kegg.jp/entry/$1"^^ . - "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . - . - "glycoepitope" . - . - . - "The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications."^^ . - . - . - . - . - . - "false"^^ . - "Alexander Diehl" . - "life science" . - "pathways" . - "life science" . - "1cukA01"^^ . - . - "Wormpep" . - . - . - . - "Identifier for a place in iNaturalist"^^ . - . - . - "disease" . - "development" . - "David Blackburn" . - . - . - . - . - . - . - "^MNEST\\d+$"^^ . - . - . - "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"^^ . - . - . - "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . - . - "kristian.axelsen@sib.swiss" . - . - . - . - . - "false"^^ . - . - . - "true"^^ . - . - "https://bioregistry.io/tkg:"^^ . - "Platynereis Developmental Stages" . - . -_:N29700f95c1bf4501949b0ce8eb8684aa "Plant Ontology Administrators" . - "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . - "https://sed-ml.org/urns.html#language:"^^ . - "genome" . - "The Food Ontology" . - "vega" . - "small molecules" . - "biomedical science" . - "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . - "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . - . - . - . - . - "MIMPS" . - . - "faldo" . - . - "false"^^ . - . - "Regulation of Gene Expression Ontology" . - . - . - . - . - "https://www.uniprot.org/tissues/"^^ . - "^[CD]\\d+$"^^ . - "O08709"^^ . - "351"^^ . - . - . - . - . - "preprints" . - . - "small molecule" . - "ebf69ca24298b28b2361e7d43eb52d6c"^^ . - . - . - . - . - . - . - . - . - "echinobase" . - . - . - . - "^\\d+$"^^ . - . - . - "swrl" . - . - . - . - . - . - "http://purl.org/spar/c4o/$1"^^ . - . - "famplex" . - "http://purl.obolibrary.org/obo/LABO_$1"^^ . - . - . - "http://purl.obolibrary.org/obo/ADO_$1"^^ . - "Biolink Model Registry" . - "http://bigg.ucsd.edu/models/universal/metabolites/"^^ . - . - . - . - "human" . - . - . - . - . - . - . - . - "Common Anatomy Reference Ontology" . - . - . - "http://purl.obolibrary.org/obo/EMAPA_$1"^^ . - . - "false"^^ . - "ontology" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "493771"^^ . - . - . - . - "phosphosite.sitegroup" . - . - "^\\d+$"^^ . - . - "00100005"^^ . - . - "metabolomics" . - . - "A registry of life science prefxes"^^ . - . - . - "ontology" . - . - "https://w3id.org/faircookbook/"^^ . - . - "Mouse adult gross anatomy" . - . - . - . - . - "isni" . - "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species."^^ . - . - "agrovoc" . - "icdc" . - . - . - "neurology" . - . - . - . - . - "redfly" . - . - . - . - . - "Medical Dictionary for Regulatory Activities" . - "functional genomics" . - . - . - "https://gnomad.broadinstitute.org/variant/$1"^^ . - "BRENDA Tissue Ontology" . - "^AA\\d{4}$"^^ . - "ccds" . - "002678"^^ . - . - . - . - "vso" . - . - . - . - . - . - . - . - . - "dna" . - "false"^^ . - . - . - . - . - . - "false"^^ . - "true"^^ . - . - "Probability Distribution Ontology" . - . - . - . - . - "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . - "gene expression" . - . - . - . - . - "1242"^^ . - . - "biology" . - . - . - "^\\d{7}$"^^ . - . - . - "bykdb" . - . - "pseudogene.org" . - "informatics" . - . - . - . - "GlyTouCan" . - . - . - . - . - "^MIRT\\d{6}$"^^ . - "^\\d{8}$"^^ . - "false"^^ . - . - . - . - "ontology" . - "iRefWeb" . - . - . - . - . - . - . - "epidemiology" . - . - . - "http://purl.obolibrary.org/obo/DISDRIV_"^^ . - . - . - . - . - "SCC111"^^ . - . - . - "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D."^^ . - . - . - . - . - "Web Annotation Ontology" . - . - "false"^^ . - "http://purl.obolibrary.org/obo/LIPRO_"^^ . - "false"^^ . - "insdc" . - . - . - . - . - "protein" . - . - . - "stem cell" . - . - . - "false"^^ . - "Allergome" . - . - . - . - . - "false"^^ . - "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . - "Li7"^^ . - "Allotrope Merged Ontology Suite" . - "0000487"^^ . - "scopus.publication" . - . - . - . - "biology" . - "https://mobidb.org/$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - "http://www.w3.org/ns/oa#"^^ . - . - "000000012281955X"^^ . - "false"^^ . - "Blue Brain Project Topological sampling Knowledge Graph" . - "https://civicdb.org/links/assertions/$1"^^ . - . - "https://www.alzforum.org/mutations/$1"^^ . - "CHEMBL4303805"^^ . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. The PANTHER Pathway Component collection references specific classes of molecules that play the same mechanistic role within a pathway, across species. Pathway\r\ncomponents may be proteins, genes/DNA, RNA, or simple molecules. Where the identified component is a protein, DNA, or transcribed RNA, it is associated with protein sequences in the PANTHER protein family trees through manual curation."^^ . - "insdc.gca" . - . - "computer science" . - . - . - . - "2526"^^ . - . - . - . - "^[A-Z-a-z0-9]+$"^^ . - "seed.compound" . - "agriculture" . - . - "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . - . - . - . - "0000124"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "Structural Classification of Proteins - Unique Identifier" . - . - . - . - . - . - "http://vegbank.org/cite/"^^ . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/"^^ . - "An Affymetrix ProbeSet is a collection of up to 11 short (~22 nucleotide) microarray probes designed to measure a single gene or a family of genes as a unit. Multiple probe sets may be available for each gene under consideration."^^ . - . - "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . - "protein" . - . - "ArrayExpress Platform" . - . - "http://terminology.hl7.org/CodeSystem/v2-"^^ . - . - "false"^^ . - . - . - "http://www.narcis.nl/publication/RecordID/"^^ . - . - . - . - . - . - . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - . - . - "The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits."^^ . - . - . - . - . - . - . - "FlyBase Gene" . - "cpga" . - "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . - "false"^^ . - . - "gxa.gene" . - "Human Disease Ontology" . - . - "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."^^ . - . - "false"^^ . - . - "cheminformatics" . - "https://cropontology.org/rdf/CO_330:"^^ . - "DisProt region" . - . - "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . - "ontology" . - . - . - . - . - . - "COG0001"^^ . - "toxoplasma" . - "epidemiology" . - "obo" . - "phenotypes" . - "medicine" . - . - "false"^^ . - "CORDIS Article" . - . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - "obo" . - . - "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]"^^ . - "vmc" . - "sjwang@mcw.edu" . - . - . - . - _:Nf48677cf113e42d591a86e42e6f53ee3 . - "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . - . - "spdx" . - "viaf" . - "^\\d{7}$"^^ . - . - . - "Antibiotic Resistance Genes Database" . - "false"^^ . - . - "deepak.unni3@lbl.gov" . - "false"^^ . - . - . - . - . - . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/"^^ . - "NCIT" . - . - "imgt.hla" . - "https://amoebadb.org/amoeba/app/record/gene/"^^ . - "^\\d{7}$"^^ . - . - . - "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation."^^ . - . - . - . - . - . - "cpd15380"^^ . - . - "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . - . - . - . - . - "ontology" . - "phylogenetics" . - . - . - . - . - . - "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id="^^ . - . - . - "https://cropontology.org/rdf/CO_333:"^^ . - . - . - . - . - . - . - . - . - . - . - "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . - . - . - "pierre.grenon@ifomis.uni-saarland.de" . - . - "ontology" . - . - . - "Wikidata is a collaboratively edited knowledge base operated by the Wikimedia Foundation. It is intended to provide a common source of certain types of data which can be used by Wikimedia projects such as Wikipedia. Wikidata functions as a document-oriented database, centred on individual items. Items represent topics, for which basic information is stored that identifies each topic."^^ . - . - "FuncBase Fly" . - . - . - . - . - "http://purl.obolibrary.org/obo/MP_"^^ . - . - . - "^\\d{5}$"^^ . - . - . - . - "systems biology" . - "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . - . - . - "obo" . - "storedb.file" . - . - . - "ecto" . - . - . - "dna" . - . - "74"^^ . - "spp" . - . - . - . - . - . - . - "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."^^ . - . - . - . - "154022"^^ . - "pharmacogenomics" . - "https://jjj.bio.vu.nl/models/"^^ . - . - "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . - "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"^^ . - "PGS000018"^^ . - "false"^^ . - "false"^^ . - "MetaNetX chemical" . - "http://purl.obolibrary.org/obo/NCIT_$1"^^ . - "RNACentral" . - "biology" . - . - "dna" . - "anatomy" . - . - . - "mathematics" . - . - . - "regulation" . - "American Type Culture Collection" . - "61467"^^ . - "http://www.antweb.org/specimen.do?name="^^ . - "http://www.pantherdb.org/panther/family.do?clsAccession="^^ . - . - . - "10.1621/vwN2g2HaX3"^^ . - "aero" . - . - "gene" . - "culture" . - . - . - "https://www.cameo3d.org/sp/targets/target/"^^ . - "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . - "rexo" . - . - . - . - . - "Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation" . - "false"^^ . - "false"^^ . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID="^^ . - . - . - . - . - "laevis" . - "recombinase" . - . - "http://purl.obolibrary.org/obo/ERO_"^^ . - . - "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id="^^ . - . - "functional genomics" . - "Anne.Morgat@sib.swiss" . - . - "iNaturalist Observation" . - . - "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - _:N95d3105b2cdf4400a57957c9d02ead48 . - . - . - . - . - "2.16.840.1.113883.6.88" . - "ADM1"^^ . - . - . - "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . - . - . - "true"^^ . - . - "IUPHAR_LIGAND_ID" . - "^\\d+$"^^ . - "BEI Resources" . - "genome" . - "false"^^ . - "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1"^^ . - . - . - . - . - . - . - . - "EAWAG Biocatalysis/Biodegradation Database" . - . - . - . - . - . - "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)." . - . - . - . - . - "dto" . - "human" . - "nci.drug" . - . - . - . - "https://caninecommons.cancer.gov/#/study/"^^ . - "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . - . - . - . - "Plant Environment Ontology" . - . - "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . - "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . - . - "https://www.kegg.jp/entry/"^^ . - . - . - . - . - . - . - "SNOMEDCT_US" . - . - . - "comparative genomics" . - "Vocabulary of Interlinked Datasets" . - . - "Cell line collections (Providers)"^^ . - . - "Data Object Service" . - "Contributor Role Ontology" . - . - . - "^IID\\d+$"^^ . - . - "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 individual transcripts."^^ . - "ontology" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "http://www.w3.org/2003/11/swrl#$1"^^ . - "medicine" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - "mint" . - "false"^^ . - "918902"^^ . - . - . - . - . - . - "000410"^^ . - "strain" . - . - . - "https://www.obofoundry.org/ontology/$1" . - . - . - . - . - . - . - . - "physics" . - . - "https://knowledge.lonza.com/cell?id=$1"^^ . - . - "gene" . - "ICD9" . - "http://purl.obolibrary.org/obo/CARO_$1"^^ . - "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."^^ . - "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."^^ . - "data management" . - . - . - . - . - "https://bioregistry.io/metaregistry/biocontext/$1" . -_:N4e25957c43b8426f813f5579b8ff53d7 "Frédérick Giasson" . - . - . - "genome" . - . - "https://ximbio.com/reagent/"^^ . - . - "botany" . - "life science" . - "The set of prefixes used in the Cellosaurus resource"^^ . - "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . - . - . - . - . - "domain" . - . - "ontology" . - . - "https://urgi.versailles.inra.fr/gnpis/#result/term="^^ . - . - . - . - . - "false"^^ . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - "An organization" . - . - "MC" . - . - "ihw" . - . - "http://sabiork.h-its.org/newSearch?q="^^ . - . - "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."^^ . - . - "https://www.addexbio.com/productdetail?pid=$1"^^ . - . - . - "MAM01234c"^^ . -_:N7f8648ca4c8c4d6b9724d8d656769f4d "pierre.sprumont@unifr.ch" . - "Scopus affiliation ID" . -_:Ndd49303c904448229b8b238eb16b593d "BioModels.net team" . - . - . - . - . - . - "ontology" . - . - "inaturalist.user" . - . - . - "ClinVar Variation" . - "http://purl.obolibrary.org/obo/STATO_$1"^^ . - "life science" . - . - "false"^^ . - . - . - . - . - . - . - "ontology" . - . - "F11903"^^ . - . - . - . - "FlyMine Chromosome Band" . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "http://www.gramene.org/db/protein/protein_search?protein_id="^^ . - . - . - . - . - . - . - . - . - "GR_PROTEIN" . - . - "9861/3"^^ . - . - . - "registry" . - . - "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source."^^ . - . - . - . - . - . - "false"^^ . - "http://agroportal.lirmm.fr/ontologies/$1" . - . - . - . - . - "biology" . - . - "Pearl millet ontology" . - . - . - "https://bioregistry.io/odor:"^^ . - "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - "^D\\d+$"^^ . - . - . - . - . - . - "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?"^^ . - "RCV000033555.3"^^ . - . - . - "^\\d{7}$"^^ . - "https://www.datanator.info/metabolite/$1"^^ . - . - . - "An expanded example URL for a resource or metaresource." . - . - . - . - "botany" . - . - "Paolo Romano" . - . - "iresite" . - "model" . - . - . - "false"^^ . - . - . - . - . - "75"^^ . - . - "ontology" . - . - . - "^\\d+/.+$"^^ . - "sequence" . - . - . - . - "ribocentre" . - . - . - "Linear double stranded DNA sequences" . - . - "gene" . - . - . - . - "Sebastian Koehler" . - . - . - . - "ontology" . - "SRS086444"^^ . - . - . - . - "humIGHV025"^^ . - . - "obo" . - . - . - . - "SubtiWiki" . - . - . - . - . - "ontology" . - . - . - . - "vt" . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - . - . - . - . - . - . - . - "false"^^ . - "A comprehensive proteomics data and process provenance ontology."^^ . - "biomedical science" . - . - "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . - . - . - . - . - . - "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val="^^ . - "drug" . - . - . - "domain" . - . - . - . - "Babelon" . - "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]"^^ . - "^\\d+$"^^ . - "959"^^ . - "http://purl.obolibrary.org/obo/GNO_$1"^^ . - . - "GPIb_IX_V"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/WBPhenotype_$1"^^ . - . - . - . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . - . - "ConfIDent Event Series" . - . - . - "mmp.fun" . - "^\\d{7}$"^^ . - "kegg.module" . - "00000101"^^ . - "TreeFam" . - . - . - "fairsharing.organization" . - . - "https://bioregistry.io/panorama:"^^ . - . - "obo" . - . - . - . - . - . - . - . - . - "9008500"^^ . - . - . - "true"^^ . - . - . - "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."^^ . - . - . - "^TCTR\\d+$"^^ . - "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes."^^ . - . - "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."^^ . - . - "false"^^ . - . - . - "Symposium"^^ . - "Abdomen"^^ . - . - . - . - "0000001"^^ . - "false"^^ . - "http://www.t3db.org/toxins/$1"^^ . - . - "umls.st" . - . - . - . - . - "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . - . - "cell" . - "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . - "Rules are devised and tested by experienced curators using experimental data from manually annotated entries as templates. UniRule rules can annotate protein properties such as the protein name, function, catalytic activity, pathway membership, and subcellular location, along with sequence specific information, such as the positions of post-translational modifications and active sites."^^ . - "http://www.proteinmodelportal.org/query/uniprot/"^^ . - "Bgee is a database of gene expression patterns within particular anatomical structures within a species, and between different animal species. This collection refers to developmental stages."^^ . - . - . - "lang"^^ . - . - "27223"^^ . - . - "https://bioregistry.io/rebase:"^^ . - . - "^\\S+$"^^ . - . - . - "SNOMEDCT_US_2022_07_31" . - "^\\d{8}$"^^ . - "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object="^^ . - "^\\d{1,5}$"^^ . - . - . - . - "^[a-zA-Z0-9_-]{3,}$"^^ . - . - "https://www.ncbi.nlm.nih.gov/cdd?term="^^ . - "biochemistry" . - . - . - . - . - . - "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$"^^ . - . - "CharProt" . - . - . - "^GR\\:\\d+$"^^ . - . - . - "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . - . - . - . - . - . - . - "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id="^^ . - . - . - . - . - . - . - "^H\\d+$"^^ . - "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . - . - "false"^^ . - . - "^[0-9]+$"^^ . - "epio" . - "interlex" . - "jws" . - . - . - . - . - . - . - "http://www.receptors.org/nucleardb/proteins/$1"^^ . - . - "false"^^ . - . - . - "metagenomics" . - . - . - . - "Cell line collections (Providers)"^^ . - "https://www.gwascentral.org/marker/"^^ . - . - "AGROVOC is a multilingual and controlled vocabulary designed to cover concepts and terminology under FAO's areas of interest. It is the largest Linked Open Data set about agriculture available for public use and its greatest impact is through providing the access and visibility of data across domains and languages."^^ . - "G-Rich Sequences Database" . - "^\\d+$"^^ . - . - . - . - . - . - "NMR Restraints Grid" . - "2404"^^ . - . - . - . - "ppo" . - . - . - . - "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp="^^ . - . - . - "http://europepmc.org/articles/$1"^^ . - . - "Phenotype And Trait Ontology" . - "mixs" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "NHMRC Australian PhenomeBank" . - . - . - . - "https://www.abmgood.com/search?query="^^ . - "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - . - . - "rcb" . - . - . - . - . - "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]"^^ . - . - . - . - "cto" . - . - "BiGG Model" . - . - . - . - . - . - "false"^^ . - "social media" . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - "clinical LABoratory Ontology" . - . - "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:"^^ . - "phenomics" . - "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . - "gene" . - . - . - . - . - . - . - . - . - . - "https://www.gtexportal.org/home/gene/$1"^^ . - . - "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . - . - . - . - . - . - . - "Oryza Tag Line is a database that was developed to collect information generated from the characterization of rice (Oryza sativa L cv. Nipponbare) insertion lines resulting in potential gene disruptions. It collates morpho-physiological alterations observed during field evaluation, with each insertion line documented through a generic passport data including production records, seed stocks and FST information."^^ . - "UniProt Chain" . - . - "ontology" . - . - . - . - "sharkipedia.trait" . - . - . - . - . - "gno" . - . - . - . - "false"^^ . - . - . - . - . - "^SIGNOR-\\d+$"^^ . - . - . - "ontology" . - "kcris" . - . - . - "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."^^ . - . - . - . - . - "AU124"^^ . - "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."^^ . - . - . - . - "0000001"^^ . - "chemistry" . - "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."^^ . - . - . - "uberon"^^ . - . - . - . - . - "life science" . - "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . - "https://mediadive.dsmz.de/medium/$1"^^ . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - "vido" . - . - _:N11acbef7e61346bb88f3c99655fd742a . - . - . - . - . - "DBMET02292"^^ . - . - . - "worldavatar.compchem" . - "Cell line collections (Providers)"^^ . - . - "protein" . - . - . - . - "ontology" . - . - . - "LTS0004651"^^ . - . - . - . - . - . - . - "helpdesk@cropontology-curationtool.org" . - . - . - . - . - "frederic.bastian@unil.ch" . - . - . - . - "RiceNetDB Compound" . - "live animal" . - . - "false"^^ . - . - . - "sequence" . - "^[-A-Za-z0-9\\_]*$"^^ . -_:Ndd7978848d664705a828b97bdf16d069 "Pierre Sprumont" . - "cordis.article" . - . - . - "Drosophila Genomics Resource Center" . - "https://www.ncbi.nlm.nih.gov/nucleotide/"^^ . - . - "bams" . - . - . - . - . - . - . - . - . - . - "obo" . - "metagenomics" . - "AgroPortal" . - . - . - . - . - "fbql" . - "true"^^ . - . - . - . - . - "protein" . - . - "obo" . - "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . - "structure" . - "^\\d+$"^^ . - . - . - "60141"^^ . - . - "^NONHSAT\\d{6}$"^^ . - . - . - . - . - . - . - "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"^^ . - "SWISS-MODEL Repository" . - . - "annika.jahnke-bornemann@uni-hamburg.de" . - . - . - "virology" . - "ISO 3166-1 Country Code" . - "http://www.w3.org/ns/shacl#$1"^^ . - . - "false"^^ . - . - . - . - "http://www.w3.org/2004/02/skos/core#$1"^^ . - "^\\d+$"^^ . - . - . - "0019030"^^ . - "https://www.fishbase.ca/summary/"^^ . - . - "true"^^ . - . - "biomedical science" . - "http://purl.obolibrary.org/obo/RO_"^^ . - "^\\d{7}$"^^ . - "^\\d{7}$"^^ . - . - "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . - . - . - . - "repository" . - . - "Hilmar Lapp" . - . - . - . - "TubercuList" . - "haendel@ohsu.edu" . - "gabdank@stanford.edu" . - . - "tgv139393198"^^ . - "cath" . - . - "https://bionumbers.hms.harvard.edu/bionumber.aspx?id="^^ . - . - . - . - "kuiper@bio.ntnu.no" . - "KYinno cell lines" . - . - "animal genetics" . - "Cellular Phenotypes" . - . - . - . - "ontology" . - "regulation" . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - . - "hasOpenAccessRating"^^ . - . - . - . - . - "cryptodb" . - "^(MNXM\\d+|BIOMASS|WATER)$"^^ . - . - "KEGG_PATHWAY" . - . - "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."^^ . - "^\\d+$"^^ . - . - "false"^^ . - "structure" . - . - . - . - . - "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . - . - . - . - "Gramene Taxonomy" . - "https://www.internationalgenome.org/data-portal/sample/$1"^^ . - "^\\d{7}$"^^ . - . - "Scopus Work" . - . - . - . - "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_"^^ . - "false"^^ . - "Human Developmental Stages" . - . - "vhog" . - . - . - . - . - . - . - . - . - "cell lines" . - "biomedical science" . - . - "cgsc" . - . - "j.harry.caufield@gmail.com" . - . - . - "co_365" . - . - "COMBINE specifications" . - . - . - . - "David.Linke@catalysis.de" . - "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."^^ . - . - . - . - "https://bartoc.org/en/node/"^^ . - . - . - "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . - . - . - "Damion Dooley" . - "http://www.tcdb.org/search/result.php?tc=$1"^^ . - "^[\\w\\-:,]{3,64}$"^^ . - . - . - . - "1200"^^ . - . - "MPATH" . - . - "subject agnostic" . - . - . - . - "Observational Medical Outcomes Partnership" . - . - . - . - "metabolomics" . - . - . - "matrixdb.association" . - . - "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."^^ . - . - . - . - . - . - "RCB0002"^^ . - . - . - . - "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"^^ . - "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains"^^ . - "false"^^ . - . - . - "Luis A. Gonzalez-Montana" . - . - . - . - . - . - . - . - . - . - . - . - "1038233"^^ . - . - . - "gene" . - . - . - . - "noncodev4.gene" . - "life science" . - "true"^^ . - "true"^^ . - "http://purl.obolibrary.org/obo/TO_"^^ . - "^T[A-Z]\\d{7}$"^^ . - "0002959"^^ . - . - . - "^\\d{7}$"^^ . - . - "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"^^ . - . - . - "https://nanocommons.github.io/identifiers/registry#$1"^^ . - . - "^\\d{10}$"^^ . - . - "true"^^ . - . - . - . - "https://www.ebi.ac.uk/ega/datasets/"^^ . - "life science" . - . - . - . - . - "0000008"^^ . - . - "rdfs" . - . - "reaction" . - "mp" . - . - "ontology" . - "http://purl.obolibrary.org/obo/CIO_"^^ . - . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . - . - . - . - . - . - . - "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . - . - "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . - "ontology" . - . - . - . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . - . - . - . - . - . - "AT4G01080"^^ . - . - . - "false"^^ . - . - "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . -_:N9e98fa15e62c48f48e2f6b6195f1ae63 "INOH curators" . - "false"^^ . - . - "Environmental Molecular Sciences Laboratory Project" . - "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."^^ . - . - . - . - . - "protein" . - . - "false"^^ . - . - . - . - . - . - . - "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)."^^ . - . - . - "Oryzabase Reference" . - . - "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name="^^ . - . - "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . - . - . - . - . - . - . - . - "phenotype" . - "Lin Huang" . - . - . - . - "cog.category" . - "botany" . - . - . - "PubChem Cell Line" . - . - . - . - . - "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . - . - "https://archive.softwareheritage.org/browse/swh:"^^ . - . - . - . - "life science" . -_:N3a54fd90c5844e92bd4fa6b0242dba3d "Crop Ontology Helpdesk" . - "proteomics" . - . - . - . - "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."^^ . - "enviPath" . - . - . - . - . - . - "gramene.protein" . - . - . - . - . - . - . - . - . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . - "bcrc" . - . - . - . - "hannele.laivuori@helsinki.fi" . - "Matthias König" . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "noncodev3" . - . - "Raymond Lee" . - . - . - . - "ontology" . - "false"^^ . - "false"^^ . - . - "wikidata" . - "https://www.nextprot.org/term/"^^ . - . - "Legacy site for IETF RFC proposals"^^ . - . - . - . - . - . - . - "0005452"^^ . - . - . - . - "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1"^^ . - "false"^^ . - "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . - "Castor bean ontology" . - "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . - "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."^^ . - . - . - . - . - . - . - . - . - "112081"^^ . - "http://purl.obolibrary.org/obo/OHPI_$1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "life science" . - "Search the world's most comprehensive index of full-text books."^^ . - . - "false"^^ . - "MI0026471"^^ . - . - . - . - "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . - . - . - "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . - . - . - "developmental biology" . - . - . - "wb.rnai" . - . - "ontology" . - . - . - "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1"^^ . - "https://www.vmh.life/#metabolite/$1"^^ . - . - "KEGG ENVIRON (renamed from EDRUG) is a collection of crude drugs, essential oils, and other health-promoting substances, which are mostly natural products of plants. It will contain environmental substances and other health-damagine substances as well. Each KEGG ENVIRON entry is identified by the E number and is associated with the chemical component, efficacy information, and source species information whenever applicable."^^ . - . - "ecyano.entity" . - . - . - "agriculture" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/studies/"^^ . - "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . - "Semantic Web for Earth and Environment Technology Ontology" . - . - . - . - . - . - . - "false"^^ . - "http://www.genome.jp/dbget-bin/www_bget?cpd:"^^ . - "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."^^ . - . - . - . - . - . - "https://go.drugbank.com/salts/"^^ . - "^DBMET\\d+$"^^ . - "false"^^ . - . - . - "0000072"^^ . - "0000127"^^ . - . - . - "Banana ontology" . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - "https://cropontology.org/rdf/CO_343:$1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "BatchelorC@rsc.org" . - . - . - "http://purl.obolibrary.org/obo/ARO_$1"^^ . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - "faseb list" . - "vgnc" . - . - "SDY2614"^^ . - "life science" . - "https://www.disprot.org/$1"^^ . - . - "miRBase Families" . - . - "EchoBASE post-genomic database for Escherichia coli" . - . - "ISCW007415"^^ . - . - . - . - . - . - . - . - "http://www.w3.org/2002/07/owl#"^^ . -_:N7462add7e86d4deea995dffb95f5cd6b "helpdesk@cropontology-curationtool.org" . - "drsbello@gmail.com" . - "Korean Clinical Research Information Service" . - . - . - "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business."^^ . - . - . - . - "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"^^ . - . - "http://purl.obolibrary.org/obo/PO_"^^ . - . - . - . - . - "developmental biology" . - . - "genome" . - . - . - . - "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CDAO_$1"^^ . - "LINCS Cell" . - . - . - . - . - . - "clinvar" . - . - . - . - "http://purl.obolibrary.org/obo/RS_$1"^^ . - "richard@cyganiak.de" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "life science" . - . - . - "protein" . - . - . - . - . - . - . - . - . - "policy" . - . - . - . - . - "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)."^^ . - . - "bionumbers" . - "ontology" . - "cell biology" . - "H-InvDb Transcript" . - . - . - . - . - . - . - . - . - "rapdb.transcript" . - . - . - "http://www.informatics.jax.org/accession/MGI:$1"^^ . - . - . - . - "Terminology of Anatomy of Human Embryology" . - . - . - . - . - . - . - "https://proteinensemble.org/$1"^^ . - . - . - . - . - "mcro" . - . - "0000055"^^ . - . - . - "dna" . - . - "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . - "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . - "11002"^^ . - . - . - . - . - . - . - "evm" . - "jstor" . - "obo" . - "ecology" . - "ontology" . - . - "phylogenetics" . - . - "Identifier of an object from the ASTD database."^^ . - "health science" . - "structure" . - . - . - "^PS\\d{5}$"^^ . - "^[8-9]\\d{3}(/[0-3])?$"^^ . - "Aceview Worm" . - "trichdb" . - . - "https://www.biozol.de/en/product/"^^ . - "^OSR\\d{4}$"^^ . - "Search Tool for Retrieval of Interacting Genes/Proteins" . - . - . - "https://eds.gene.le.ac.uk/home.php?select_db=$1"^^ . - "http://purl.obolibrary.org/obo/KISAO_"^^ . - "false"^^ . - . - . - "Jeffrey A. Detras" . - . - "Gramene protein" . - . - "interaction" . - "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . - . - . - "hpo" . - . - "false"^^ . - . - "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)"^^ . - "false"^^ . - "FishBase" . - . - . - "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN="^^ . - . - . - . - . - . - . - "Software Heritage" . - "Vertebrate skeletal anatomy ontology."^^ . - "Fyler" . - "Carrine Blank" . - "Classification of Transcription Factors in Mammalia" . - . - . - . - . - . - "false"^^ . - . - . - "structure" . - . - "dan5@georgetown.edu" . - . - . - . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . - . - "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . - "FlyBase internal citation identifiers"^^ . - . - . - . - "^TC\\d+$"^^ . - "ontology" . - . - . - . - . - "zmp@ebi.ac.uk" . - "protein" . - . - "rnamod" . - . - . - . - . - "Enzyme Commission Code" . - . - "https://www.kaggle.com/$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OHMI_$1"^^ . - . - . - . - "Ensembl Protists" . - "false"^^ . - "Dictyostelium discoideum phenotype ontology" . - "aclame" . - . - "Neuroscience Multi-Omic BRAIN Initiative Data" . - . - "3hB06"^^ . - "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"^^ . - . - "W2741809807"^^ . - . - . - "^\\d+$"^^ . - . - "^\\d{7}$"^^ . - "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . - . - "gramene.gene" . - . - . - "VFDB Genus" . - . - . - . - "9-1-1 Complex"^^ . - . - . - "http://purl.obolibrary.org/obo/MAT_"^^ . - . - "ms" . - "pkdb" . - "medicinal chemistry" . - . - "false"^^ . - . - "0001021"^^ . - . - . - "support@bioontology.org" . - . - . - . - . - . - . - . - . - . - . - "protein" . - "http://purl.obolibrary.org/obo/UBERON_"^^ . - "Drug_Central" . - . - "Jianjiong Gao" . - . - . - . - . - . - . - . - . - "http://www.bioassayontology.org/bao#BAO_$1"^^ . - "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research."^^ . - . - . - . - . - . - . - "Mouse Tumor Biology Database" . - "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"^^ . - "epigenetics" . - "RepeatsDB Protein" . - . - "https://w3id.org/nfdi4cat/voc4cat_"^^ . - . - . - "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . - "ontology" . - . - "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . - "Medical Data Models" . - "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . - . - "0001807"^^ . - . - . - "102l"^^ . - . - "transcriptomics" . - . - "false"^^ . - "antibody" . - "http://purl.obolibrary.org/obo/EHDA_"^^ . - "false"^^ . - "comparative genomics" . - "https://www.wikidata.org/wiki/Property:"^^ . - . - "co_356" . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - "selventa" . - "life science" . - . - "http://www.weizmann.ac.il/molgen/loqate/gene/view/"^^ . - . - . - "https://bioregistry.io/gmd:"^^ . - . - . - . - . - . - . - "^\\d{3}$"^^ . - . - . - "sbo" . - . - "https://www.wikidata.org/wiki/Property:$1"^^ . - "MolMeDB" . - "false"^^ . - . - "http://purl.obolibrary.org/obo/BTO_"^^ . - . - . - . - "false"^^ . - . - "1-FEH+w3"^^ . - "E00002"^^ . - . - . - "An ontology of phenotypes covering microbes"^^ . - . -_:N5e00e918e8a94b1dac10f0dde02fe9dd "William Bug" . - "^\\d+$"^^ . - "evolutionary biology" . - "http://purl.obolibrary.org/obo/APO_"^^ . - "false"^^ . - . - . - . - . - . - "https://flowrepository.org/id/$1"^^ . - . - . - . - . - . - "760050"^^ . - . - "RDF"^^ . - "bel" . - . - . - . - . - . - . - "Stemcell Knowledge and Information Portal" . - "publons.publication" . - "ASPL0000349247"^^ . - "^\\d+$"^^ . - "NCIT_Thesaurus" . - "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . - "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . - "Costal and Marine Ecological Classification Standard" . - . - . - . - . - "https://www.datascienceontology.org/concept/$1"^^ . - . - "^\\d+$"^^ . - . - . - "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "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."^^ . - . - "true"^^ . - . - . - . - "biomedical science" . - "false"^^ . - "http://purl.obolibrary.org/obo/SWO_"^^ . - . - . - "Barley ontology" . - "obo" . - "nfdi4chem.cao" . - "Suggested Ontology for Pharmacogenomics" . - . - . - "protein" . - "subject agnostic" . - "AP00378"^^ . - . - . - "0000071"^^ . - . - . - . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . - . - . - . - . - "obo" . - . - . - . - . - . - . - "ontology" . - . - "hprd" . - "wikipathways.vocab" . - . - . - . - . - . - "true"^^ . - "Ensembl" . - "pathway" . - . - "TAIR Protein" . - . - "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . - "mark@gersteinlab.org" . - "rouge" . - . - . - "true"^^ . - "^\\d{7}$"^^ . - . - "embryo" . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . - . - . - . - "CADAFLAT00006211"^^ . - "1.10.8.10"^^ . - . - "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."^^ . - . - . - . - . - "structural biology" . - . - . - . - . - . - . - . - . - . - . - . - "ontology" . - "database" . - . - . - . - . - "GPCR Natural Variants database" . - "obo" . - "false"^^ . - . - "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . - . - "SM_UB-81"^^ . - . - . - . - "1000001"^^ . - . - "ALX-210-175"^^ . - . - . - "Human Protein Atlas tissue profile information" . - . - . - "false"^^ . - . - "Sheeba Samuel" . - . - . - . - . - "The ALlele FREquency Database" . - "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . - . - "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"^^ . - "medgen.gtr" . - "knowledge and information systems" . - "Gm00047"^^ . - . - "VEGA" . - . - "Genomics of Drug Sensitivity in Cancer" . - "Represent chemical entities having particular CHEBI roles"^^ . - . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized 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 metabolites."^^ . - "gsso" . - "International Classification of Diseases, 10th Revision, Procedure Coding System" . - "nucleotide" . - . - "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."^^ . - "geography" . - "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"^^ . - "true"^^ . - . - . - . - . - . - "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . - . - . - "LiceBase" . - . - . - "RNA ontology" . - . - . - "554"^^ . - . - "http://func.mshri.on.ca/yeast/genes/list_functional_scores/"^^ . - . - "molecular neuroscience" . - . - "false"^^ . - "Use this database to browse the CMECS classification and to get definitions for individual CMECS Units. This database contains the units that were published in the Coastal and Marine Ecological Classification Standard."^^ . - . - . - "medicine" . - "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"^^ . - . - . - "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."^^ . - . - . - "DDB_G0267522"^^ . - "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in 363 animal species (other than human and mouse and rats and zebrafish, which have their own resources)."^^ . - . - . - . - "genome" . - . - . - "AADB12"^^ . - . - . - . - . - . - . - . - . - "metnetdb" . - . - "http://ctdbase.org/detail.go?type=gene&acc="^^ . - . - . - . - . - . - "meghan.balk@gmail.com" . - "22RV1_12_2019"^^ . - . - "4D Nucleome Data Portal Biosource" . - . - . - . - . - "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . - . - "false"^^ . - "genomics" . - . - . - . - "http://purl.obolibrary.org/obo/OPL_"^^ . - . - . - "https://hpscreg.eu/cell-line/"^^ . - . - . - . - "Development Data Object Service" . - "erm" . - . - "00000014"^^ . - . - "life science" . - . - . - "false"^^ . - . - . - . - "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])?))$"^^ . - . - "Plant Phenology Ontology" . - . - . - "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . - . - "http://data.food.gov.uk/codes/foodtype/id/"^^ . - . - "Gene"^^ . - "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . -_:Nf48677cf113e42d591a86e42e6f53ee3 "Cynthia Hake" . - "Yeast Searching for Transcriptional Regulators and Consensus Tracking" . - . - . - "bioinformatics" . -_:Nc8087639f8dd4c109937179d880ccef7 "faldo@googlegroups.com" . - . - . - "ontology" . - . - . - . - . - "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12}$"^^ . - . - . - . - "^\\d{8}$"^^ . - "epidemiology" . - . - "interaction" . - "kushida@biosciencedbc.jp" . - . - "usageNote"^^ . - . - . - . - "SNOMED_CT" . - "ontology" . - . - . - . - . - . - "baoym@big.ac.cn" . - . - . - "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to proteins in Gramene."^^ . - . - . - . - "^([a-zA-Z]+-)?\\d+(\\.\\d)?$"^^ . - . - . - "kegg.environ" . - "https://chemkg.github.io/chemrof/$1"^^ . - . - . - . - "small molecule" . - . - "Mouse Developmental Anatomy Ontology with Theiler Stage" . - . - . - . - . - . - "^[0-9]+$"^^ . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . - . - . - "false"^^ . - "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)"^^ . - . - "gold standard" . - . - "false"^^ . - . - . - "life science" . - "National Science Foundation Award" . - "CHEBI" . - "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . - "National Drug Data File" . - . - . - . - "^\\d{7}$"^^ . - "metagenomics" . - "dawood@helix.nih.gov" . - . - "dna" . - . - . - . - "ontology" . - "^PD\\d+$"^^ . - "^c\\d+$"^^ . - . - . - "database" . - "T01B6.1"^^ . - . - "false"^^ . - . - "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . - . - . - . - "1"^^ . - . - "hancestro" . - . - . - "Miguel A. Fortuna" . - . - . - . - "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/FOBI_$1"^^ . - "https://bioregistry.io/kyinno:"^^ . - . - . - . - . - "https://github.com/semanticchemistry/semanticchemistry" . - . - "life science" . - . - "pato" . - "http://edamontology.org/data_"^^ . - . - . - . - . - "TC" . - . - . - "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)"^^ . - . - . - . - "swisslipids@isb-sib.ch" . - "https://www.ribocentre.org/docs/$1"^^ . - "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . - "Nikolaos Moustakas" . - "life science" . - . - . - "https://smpdb.ca/view/"^^ . - . - "Gs0000008"^^ . - . - "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"^^ . - . - . - . - "molecular biology" . - . - . - . - "computational biology" . - "EcoLexicon represents the conceptual structure of the specialized domain of the Environment in the form of a visual thesaurus. This thesaurus has been elaborated according to the theoretical premises of Frame-Based Terminology."^^ . - "true"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "MJoachimiak@lbl.gov" . - "https://models.physiomeproject.org/exposure/"^^ . - . - . - . - . - . - . - . - "obo" . - . - "social science" . - . - . - . - "pathway" . - . - "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$"^^ . - . - "life science" . - . - . - . - . - "^\\d+$"^^ . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - "https://bioregistry.io/kerafast:"^^ . - . - . - "NIAID ChemDB ID" . - . - . - . - . - . - "239287"^^ . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1="^^ . - "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . - "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . - "Accession number of an entry from the BIND database."^^ . - "life science" . - "Enrique Blanco" . - "http://www.pathoplant.de/detail.php?accNo="^^ . - "Identifiers.org" . - "http://purl.obolibrary.org/obo/EUPATH_"^^ . - "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO."^^ . - . - . - "The RNA Modification Database" . - "false"^^ . - "mimodb" . - . - . - . - . - . - "kegg.drug" . - "false"^^ . - . - "http://purl.obolibrary.org/obo/PLANA_"^^ . - "ontology" . - "Curated Drug-Drug Interactions Database - Drug" . - . - . - "hamap" . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - . - "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://purl.obolibrary.org/obo/NCBITaxon_$1"^^ . - . - . - . - "obstetrics" . - "Mark Engelstad" . - . - . - . - "Pathogen Host Interaction Phenotype Ontology" . - "https://www.worldwildlife.org/ecoregions/$1"^^ . - "false"^^ . - "life science" . - "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . - . - "Physico-chemical process" . - . - "^\\d{7}$"^^ . - . - "ontology" . - "^(ev\\:)?E\\d+$"^^ . - "DataCite Ontology" . - . - "https://plants.ensembl.org/id/"^^ . - . - . - . - . - . - . - . - . - . - "EBI-2307691"^^ . - . - . - . - . - . - . - "5277619"^^ . - . - . - . - . - . - "0005926"^^ . - . - . - "Beta Cell Genomics Ontology" . - "false"^^ . - "EMAPA_RETIRED" . - "http://modelseed.org/biochem/compounds/$1"^^ . - "^\\d{7}$"^^ . - . - "HsapDO:0000004"^^ . - . - . - . - . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id="^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "variation" . - "https://entomology.ca.uky.edu/content/"^^ . - . - . - "Xenopus Phenotype Ontology" . - . - . - "biology" . - . - . - . - . - . - "false"^^ . - . - . - . - "ygob" . - "https://repo.napdi.org/study/$1"^^ . - . - "genotype" . - "false"^^ . - "^MMP\\d+.\\d+$"^^ . - "Apollo Structured Vocabulary" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "75"^^ . - . - . - . - "UniProt Post-Translational Modification" . - "false"^^ . - . - "engelsta@ohsu.edu" . - . - . - . - "false"^^ . - . - "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."^^ . - "Alliance of Genome Resources Knowledge Base" . - . - "biology" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "^\\d+$"^^ . - "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . - "http://hawaii.eagle-i.net/i/"^^ . - "sequence" . - . - . - . - "1455"^^ . - . - . - . - . - . - . - "10004892"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "regulation" . - . - "drug repositioning" . - . - . - . - "statistics" . - "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . - "genomics" . - "massbank" . - "Meghan Balk" . - . - . - . - . - . - "research" . - . -_:Nf284f4107996471c8eac6209f8069992 "Julie Thompson" . - "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"^^ . - "nif_subcellular" . - . - . - . - . - . - . - "Genetic Testing Registry" . - "https://www.pirbright.ac.uk/node/$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."^^ . - "https://permalink.obvsg.at/"^^ . - . - . - "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . - . - "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . - . - "NM_006262"^^ . - . - . - "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id="^^ . - "UMLS CUI" . - "ontology" . - . - . - "obo" . - "false"^^ . - . - "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names."^^ . - "false"^^ . - "false"^^ . - . - "shacl" . - . - . - "genome" . - "1251"^^ . - "Kyoto Encyclopedia of Genes and Genomes" . - "Golm Metabolome Database GC-MS spectra" . - . - . - "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space."^^ . - . - . - . - "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . - . - . - . - "biodiversity" . - "^\\d+$"^^ . - . - . - "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."^^ . - . - "WGS84 Geo Positioning" . - . - "chiro" . - . - "protein" . - "^ST[0-9]{6}$"^^ . - . - "false"^^ . - "false"^^ . - . - "narcis" . - "C0001"^^ . - . - "^\\w{4}$"^^ . - "4544"^^ . - . - "genetics" . - "zea" . - "Paleobiology Database" . - . - . - . - . - . - "hagr.genage" . - . - "crossref.funder" . - "http://dictybase.org/gene/"^^ . - . - . - "^\\w+$"^^ . - . - . - . - . - "DSSTox substance" . - "genetic resource" . - . - . - . - . - "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored."^^ . - . - . - . - . - "life science" . - "Role Ontology" . - . - . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "robert.hoehndorf@kaust.edu.sa" . - . - "https://identifiers.org/$1:$2" . - . - . - . - "dcat" . - . - . - "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."^^ . - . - . - "European Searchable Tumour Line Database" . - . - . - . - "RXCUI" . - "0001"^^ . - . - . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/PLANA_$1"^^ . - "Foods in FooDB"^^ . - "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."^^ . - "chemistry" . - . - . - "Imanis Life Sciences cell line products" . - "https://w3id.org/mixs/"^^ . - . - . - "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."^^ . - "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."^^ . - . - . - . - "go.gpi" . - "protein" . - "ontology and terminology" . - . - . - "0000690"^^ . - "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "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."^^ . - "health science" . - . - "molmovdb" . - . - . - "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"^^ . - . - . - "https://www.nextprot.org/term/FA-"^^ . - . - . - . - . - . - . - . - . - "MIMAT0046872"^^ . - "http://purl.obolibrary.org/obo/NGBO_"^^ . - . - . - "Simple Knowledge Organization System" . - . - . - . - . - "false"^^ . - . - "biomedical science" . - . - "david.gloriam@sund.ku.dk" . - . - . - . - "http://purl.org/oban/"^^ . - "false"^^ . - "false"^^ . - "protein" . - "https://bioregistry.io/ligandexpo:"^^ . - "pid" . - "^[a-f0-9]+$"^^ . - . - . - . - "false"^^ . - "^[A-Z0-9*:]+$"^^ . - . - "biochemistry" . - . - "false"^^ . - . - "C023"^^ . - . - "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . - . - "microbiology" . - . - "umbbd.enzyme" . - . - . - "health science" . - . - "https://n2t.net" . - "The IUPAC International Chemical Identifier (InChI, see MIR:00000383) is an identifier for chemical substances, and is derived solely from a structural representation of that substance. Since these can be quite unwieldly, particularly for web use, the InChIKey was developed. These are of a fixed length (25 character) and were created as a condensed, more web friendly, digital representation of the InChI."^^ . - . - . - . - "^\\d{7}$"^^ . - . - "protein" . - . - . - . - . - . - . - . - "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . - . - "pdb" . - . - . - . - "^\\d{7}$"^^ . - . - "A database of GlycoMaps containing 2585 conformational maps."^^ . - . - . - "ontology" . - "http://purl.obolibrary.org/obo/MONDO_"^^ . - "^\\d{8}$"^^ . - . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . - . - . - "fbcv" . - . - . - "Asiyah Yu Lin" . - . - . - . - . - "obo" . - . - . - "false"^^ . - . - . - . - "https://www.arraymap.org/pgx:"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . - "LBCTR2023015204"^^ . - "mgnify.proj" . - . - . - "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web."^^ . - . - "Quantities, Units, Dimensions, and Types Ontology" . - . - . - . - . - . - "epso" . - . - . - . - . - "gene" . - "A0001"^^ . - . - "Erik van Nimwegen" . - . - . - "^([3-5][A-Z])\\w+[^A-Z][0-9]$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "https://chemapps.stolaf.edu/jmol/jmol.php?model=$1"^^ . - . - "nando" . - "physics" . - . - . - _:N4c3911b9ef174a30896482a25f2207f2 . - . - "^rx[0-9]{5}$"^^ . - "^CE\\d{5}$"^^ . - . - "SNP500Cancer" . - "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."^^ . - . - "ontoneo" . - . - . - . - . - . - . - "Simple Modular Architecture Research Tool" . - . - "bio.tools" . - "63189"^^ . - "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."^^ . - . - . - "http://genomics.senescence.info/genes/details.php?id="^^ . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid="^^ . - . - . - . - "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."^^ . - . - . - . - . - . - . - "ontology" . - . - . - "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . - . - . - . - . - . - . - . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . - . - . - . - "http://ecmdb.ca/compounds/"^^ . - "human" . - "http://phylomedb.org/?seqid="^^ . - . - . - "false"^^ . - . - . - "An ontology to represent genomics cohort attributes."^^ . - . - "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . - . - . - . - . - . - . - . - . - . - "unipathway" . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - "ontology" . - . - . - . - "Bioregistry Collections" . - "Life cycle stages for Medaka"^^ . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "subject" . - "macie" . - . - . - . - . - "Index Fungorum" . - . - . - "3D Metabolites" . - . - . - "Publication Provenance Prefixes" . - . - "false"^^ . - "040000"^^ . - . - "ontology" . - "ontology" . - "epidemiology" . - . - . - . - "false"^^ . - . - "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite."^^ . - . - . - . - _:Na7f201c11d94490f8ca52133e1faab3c . - "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . - "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . - "17:41223048"^^ . - "Leafsnap" . - . - . - "AN0097748"^^ . - . - . - "https://www.kegg.jp/entry/"^^ . - . - "Karel Berka" . - . - "https://www.ebi.ac.uk/miriam/main/resources/"^^ . - "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."^^ . - "ontology" . - . - . - . - . - "Prefix Commons" . - . - . - "genotype" . - . - . - "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . - . - "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . - . - . - . - . - "https://fairsharing.org/organisations/$1"^^ . - . - "http://purl.org/spar/scoro/$1"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "Metabolites in drugbank"^^ . - . - "false"^^ . - . - . - . - . - . - "MatrixDB Association" . - "false"^^ . - . - . - . - . - . - . -_:N7ead588b1f1a4386a2b710735d92b468 "J.Bard@ed.ac.uk" . - . - . - . - . - . - "Vertebrate Gene Nomenclature Committee" . - . - . - . - . - . - . - . - . - "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."^^ . - . - . - . - . - . - "bcp47" . - "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . - . - . - . - . - . - . - "GCA_000155495.1"^^ . - . - . - . - . - . - "erik.vannimwegen@unibas.ch" . - . - . - "CRISP" . - . - . - . - . - . - . - . - "977869"^^ . - . - . - . - . - "A vocabulary and ontology repository for agronomy and related domains." . - "rs" . - . - . - . - "knapsack" . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "The \"Codex General Standard for Food Additives\" (GSFA, Codex STAN 192-1995) sets forth the conditions under which permitted food additives may be used in all foods, whether or not they have previously been standardized by Codex. The Preamble of the GSFA contains additional information for interpreting the data. Users are encouraged to consult the Preamble when using this database."^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/ZP_"^^ . - "true"^^ . - "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . - "ISBN-13" . - . - . - . - . - . - "false"^^ . - . - . - . - "mo" . - "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."^^ . - "genetics" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "computational chemistry" . - . - . - . - . - . - "neuronames" . - "SNR17A"^^ . - . - . - . - "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers."^^ . - . - "Plant Trait Ontology" . - . - . - "http://purl.obolibrary.org/obo/DRON_$1"^^ . - "false"^^ . - . - . - "http://purl.org/linked-data/cube#"^^ . - . - "ontology" . - . - . - . - . - . - "false"^^ . - . - . - . - "OMA Protein" . - "ontology" . - . - . - . - . - "0000006"^^ . - . - . - "Biofactoid" . - . - "http://purl.obolibrary.org/obo/ECAO_$1"^^ . - "pathway" . - . - "http://purl.obolibrary.org/obo/CEPH_"^^ . - "ontology" . - . - . - "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID="^^ . - "Kyoto Encyclopedia of Genes and Genomes (KEGG) is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies."^^ . - . - . - "IDEAL provides a collection of knowledge on experimentally verified intrinsically disordered proteins. It contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments."^^ . - "^\\d+$"^^ . - . - . - "18125"^^ . - "https://pir.georgetown.edu/cgi-bin/ipcSF?id="^^ . - . - . - . - . - "pao" . - . - "TTHERM_00648910"^^ . - "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id="^^ . - "obo" . - "translational medicine" . - . - . - . - "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . - . - "pharmvar" . - . - . - "David Clunie" . - . - "https://vocab.org/vann/"^^ . - . - "rna" . - "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships."^^ . - "Small Angle Scattering Biological Data Bank" . - "Measurement method ontology" . - . - . - . - "4D Nucleome Data Portal Experiment Replicate" . - . - . - . - . - "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . - . - . - "classification" . - . - "http://purl.obolibrary.org/obo/MmusDv_$1"^^ . - . - . - "obo" . - "614"^^ . - "^\\d+$"^^ . - . - . - . - "preclinical studies" . - . - . - . - "0000002"^^ . - . - . - . - . - . - . - "dna" . - . - "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."^^ . - "0005250"^^ . - . - . - "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)"^^ . - . - . - "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."^^ . - "https://cropontology.org/rdf/CO_341:"^^ . - "sewilson@lbl.gov" . - "NLXORG" . - . - . - "PomBase" . - . - "systems biology" . - . - . - . - "protein" . - "disease" . - . - "Healthcare Organizations and Services Ontology" . - . - "identifier for chemicals linked to information on occurrence in plants"^^ . - . - . - "ontology" . - . - . - . - . - . - . - . - . - "drsc" . - . - "^[A-Za-z0-9]+$"^^ . - "dragondb.locus" . - . - . - . - . - "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . - "https://www.uniprot.org/unirule/"^^ . - . - "F45.21"^^ . - . - "ontology" . - . - "vbase2" . - "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . - . - "IHW09326"^^ . - "The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events"^^ . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/ATO_$1"^^ . - "^D\\d{4}$"^^ . - . - . - . - "civic.aid" . - "NP_012345"^^ . - "^\\d+$"^^ . - . - . - . - "https://bioregistry.io/d1id:"^^ . - "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . - . - "http://uri.neuinfo.org/nif/nifstd/oen_"^^ . - . - "https://biopragmatics.github.io/providers/sfam/"^^ . - "UniProt" . - "A public place to process, interpret and share GC/MS metabolomics datasets."^^ . - . - "http://purl.org/dc/terms/$1"^^ . - . - . - . - . - . - "ITMCTR2023000002"^^ . - "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . - . - . - "^\\d+$"^^ . - . - . - "1023371"^^ . - . - "https://www.cellosaurus.org/CVCL_$1"^^ . - "https://biopragmatics.github.io/providers/uniprot.ptm/"^^ . - . - "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . - "A_24_P98555"^^ . - . - . - "https://omim.org/MIM:PS$1"^^ . - "GenBank" . - . - . - . - "anatomy" . - "Christopher Baker" . - . - . - . - . - "PTPN1"^^ . - . - . - "An ontology supporting data modeling in WikiPathways"^^ . - "Yaroslav Halchenko" . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - "false"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - . - . - "genome" . - . - . - . - . - . - . - "4DN" . - "apo" . - . - . - "false"^^ . - . - . - . - . - "ontology" . - "http://purl.obolibrary.org/obo/FLU_"^^ . - . - . - . - . - . - . - "Ontology of Adverse Events" . - "http://purl.obolibrary.org/obo/MFMO_$1"^^ . - "0154"^^ . - "false"^^ . - "false"^^ . - "CUT"^^ . - . - . - "^S\\w+(\\.)?\\w+(\\.)?$"^^ . - . - . - . - . - . - . - "Japan Chemical Substance Dictionary" . - . - . - "ogms" . - "nsc" . - . - . - "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."^^ . - "molecular neuroanatomy resource" . - "RAP-DB Locus" . - "glycosciencesdb" . - . - "life science" . - . - "citlalli.mejiaalmonte@gmail.com" . - . - "Allotrope Merged Ontology Suite"^^ . - . - . - . - . - . - "life science" . - "0001655"^^ . - "voc4cat" . - . - . - . - . - . - "gfrishkoff@gsu.edu" . - . - . - "https://odc-tbi.org/data/$1"^^ . - "00042"^^ . - . - . - "robert.thacker@stonybrook.edu" . - "http://purl.org/spar/doco/$1"^^ . - "true"^^ . - "Langual stands for \"langua alimentaria\" or \"language of food\". it is an automated method for describing, capturing and retrieving data about food. the work on langual was started in the late 1970's by the center for food safety and applied nutrition (cfsan) of the united states food and drug administration as an ongoing co-operative effort of specialists in food technology, information science and nutrition. the thesaurus provides a standardized language for describing foods, specifically for classifying food products for information retrieval. langual is based on the concept that: - any food (or food product) can be systematically described by a combination of characteristics - these characteristics can be categorized into viewpoints and coded for computer processing - the resulting viewpoint/characteristic codes can be used to retrieve data about the food from external databases"^^ . - . - "false"^^ . - "life science" . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "biomedical science" . - "false"^^ . - "Yongqunh He" . - . - . - "false"^^ . - "human" . - "^\\d{7}$"^^ . - "NLXCHEM" . - . - "The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation."^^ . - "R00100"^^ . - "^\\d{7}$"^^ . - . - . - "ICD10WHO" . - . - . - . - "CRW_00469"^^ . - . - "dg.f82a1a" . - . - . - . - "mouse" . - "fossilworks.taxon" . - . - "false"^^ . - . - "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . - . - . - . - . - "Os01g0883800"^^ . - . - . - "nlx" . - "AB" . - . - "false"^^ . - . - . - "https://omim.org/MIM:"^^ . - "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."^^ . - . - . - "https://www.arraymap.org/pgx:$1"^^ . - . - "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"^^ . - "https://www.ebi.ac.uk/metagenomics/projects/"^^ . - "OBO in OWL" . - "VFDB Gene" . - . - . - . - _:Nc5efd8506e27413980b3c557b7d6565f . - "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id="^^ . - "LigandBox" . - "false"^^ . - "Database of the dielectric properties of biological tissues."^^ . - . - . - . - . - . - "https://polbase.neb.com/polymerases/$1#sequences"^^ . - . - "U49845"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/DINTO_$1"^^ . - . - . - . - "^[a-z0-9]{32,32}$"^^ . - . - . - . - "DRUGBANK_ID" . - . - . - . - "214100"^^ . - . - . - . - . - . - "biomedical science" . - "Getty Thesaurus of Geographic Names" . - "Christine Pourcel" . - . - "false"^^ . - "lincs.smallmolecule" . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . - "Novus Biologicals" . - . - . - . - . - . - . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . - "Molecular Signatures Database" . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "RepeatsDB Structure" . - . - "^COG\\d+$"^^ . - "microbiology" . - . - . - . - "obo" . - . - . - "LIPID MAPS" . - . - "00103"^^ . - "Marijane White" . - . - . - . - "foaf" . - . - . - . - . - . - "AA0001"^^ . - "E-cyanobacterium entity" . - "gene" . - . - . - . - . - . - "InterPro" . - "HEX1"^^ . - "aop.relationships" . - . - . - . - "rat" . - "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."^^ . - . - . - . - "biomedical science" . - . - . - . - "0000144"^^ . - . - "http://purl.obolibrary.org/obo/VT_$1"^^ . - "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - "false"^^ . - . - . - "secretariat@eol.org" . - "jcm" . - "Nathan Baker" . - "cultured cell" . - "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."^^ . - "GARD" . - . - "1058367"^^ . - . - . - . - . - "dna" . - . - . - "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . - "haiiu@dtu.dk" . - . - . - "^\\d+$"^^ . - "microbiome" . - "false"^^ . - "Resource Description Framework" . - . - "http://www.pathoplant.de/detail.php?accNo=$1"^^ . - . - "Database portal containing replicate experiments of different assays and samples"^^ . - . - . - . - "ontology" . - . - "^IPR\\d{6}$"^^ . - "false"^^ . - . - "covid19" . - "DDB0191090"^^ . - . - "40000617"^^ . - . - "co_360" . - "4776"^^ . - . - "^TS-\\d+$"^^ . - "asap" . - . - "Agricultural Online Access" . - . - . - . - . - . - . - . - "Thorsten Henrich" . - . - . - . - "https://www.enzolifesciences.com/$1"^^ . - "https://arxiv.org/abs/"^^ . - . - "disease" . - . - . - "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . - . - . - . - "false"^^ . - "https://bioregistry.io/flybrain.ndb:"^^ . - "WBPhenotype" . - "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions."^^ . - "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . - . - . - "PF11779"^^ . - . - "cazy" . - . - "baseDimensionEnumeration"^^ . - "otl" . - "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . - "druzinsk@uic.edu" . - . - . - "3SBPLMKKVEVR"^^ . - . - . - . - . - . - . - . - "http://ecoportal.lifewatch.eu" . - "https://w3id.org/sssom/$1"^^ . - . - "false"^^ . - . - "fbbi" . - "false"^^ . - "EB0170"^^ . - . - "Registry of Toxic Effects of Chemical Substances" . - . - . - . - "false"^^ . - "icdom:8500_3"^^ . - "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_="^^ . - . - . - . - "virushostdb" . - . - . - . - "pba" . - . - "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . - "Evidence ontology" . - . - "linguistics" . - . - "^\\d{7}$"^^ . - "kerafast" . - "apollosv" . - . - "Rudolf T. Pillich" . - . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - . - . - . - . - . - . - . - . - "obo" . - "Anne Morgat" . - . - . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . - . - . - . - . - . - "1-55516888-G-GA"^^ . - . - . - "ontology" . - . - "ICDO" . - "81944ba1-81d0-436e-8552-33d77a27834b"^^ . - "gene" . - . - "Research Resource Identification" . - "^\\d{5}$"^^ . - . - . - . - . - . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . - . - . - . - . - . - . - . - . - . - . - "Reaxys" . - . - "obo" . - . - "false"^^ . - . - "w.simpson@orcid.org" . - . - "pathway" . - . - "false"^^ . - . - . - . - "MetaNetX reaction" . - "col" . - . - "leafsnap" . - "http://www.kegg.jp/entry/$1"^^ . - "health science" . - . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . - . - "0002502"^^ . - "A person" . - . - . - . - "alteration" . - . - . - . - "http://edamontology.org/data_$1" . - . - . - . - . - . - . - "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure."^^ . - . - . - . - . - . - "IUPHAR_GPCR" . - . - . - "01625"^^ . - "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . - . - . - . - . - "ChemSpiderID" . - "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"^^ . - "^\\d{7}$"^^ . - "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."^^ . - . - . - . - "d.craik@imb.uq.edu.au" . - "alternative splicing" . - "false"^^ . - "life science" . - "Zhiliang Hu" . - "false"^^ . - . - . - . - "true"^^ . - . - . - . - "false"^^ . - . - "ato" . - . - "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The 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."^^ . - "Benjamin M. Gyori" . - "968"^^ . - . - . - . - . - . - . - . - "Microbial Conditions Ontology" . - . - "false"^^ . - "^\\d{7}$"^^ . - "https://catalog.hathitrust.org/Record/"^^ . - . - "0807.4956v1"^^ . - . - "obo" . - . - "developmental biology" . - . - "^\\d{5,6}$"^^ . - . - . - . - . - "exo" . - . - . - . - "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . - . - . - "igrhcellid" . - . - "^\\d+$"^^ . - "ontology" . - . - . - . - . - . - . - . - . - . - "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . - "http://purl.obolibrary.org/obo/OBCS_$1"^^ . - "Jennifer Smith" . - . - . - . - . - . - . - "128796-39-4"^^ . - "^\\d+$"^^ . - . - "false"^^ . - "ontology" . - . - "agsd" . - . - . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . - . - . - . - . - . - "life science" . - . - "SwissRegulon" . - . - "HGVPM623"^^ . - "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . - "Cephalopod Ontology" . - . - "Homology Ontology" . - . - . - . - . - "Human Protein Reference Database" . - . - . - . - "ontology and terminology" . - . - "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . - "https://bioregistry.io/discoverx:"^^ . - . - . - . - "false"^^ . - . - . - . - "come" . - "Developmental stages of the Zebrafish"^^ . - . - . - . - . - . - . - . - . - . - . - . - "HD+118-001"^^ . - "transcriptomics" . - "dhba" . - . - . - "Urmas Kõljalg" . - "9002859"^^ . - "Plant Growth and Development Stage" . - . - "metabolites" . - . - . - . - "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id="^^ . - . - "Peroxibase" . - "mgnify.samp" . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . - . - "^MF_\\d+$"^^ . - . - . - "MimoDB" . - "http://purl.obolibrary.org/obo/OAE_"^^ . - "RE" . - . - "fsnp" . - . - . - . - "structure" . - . - "http://purl.obolibrary.org/obo/SPD_$1"^^ . - . - . - . - "false"^^ . - . - "bel" . - . - . - . - "geonames.feature" . - . - . - "obo" . - "http://purl.obolibrary.org/obo/PROPREO_"^^ . - . - . - "data science" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "pathology" . - . - . - "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . - . - . - "https://sed-ml.org/urns.html#format:$1"^^ . - . - . - "obo" . - . - . - . - . - "true"^^ . - . - . - . - "http://purl.obolibrary.org/obo/COLAO_$1"^^ . - "KEGG_REACTION" . - . - "http://purl.obolibrary.org/obo/AEO_$1"^^ . - "0000106"^^ . - "false"^^ . - "has responsible" . - . - . - "pandit" . - "The OpenCitations Corpus is open repository of scholarly citation data made available under a Creative Commons public domain dedication (CC0), which provides accurate bibliographic references harvested from the scholarly literature that others may freely build upon, enhance and reuse for any purpose, without restriction under copyright or database law."^^ . - . - "^Os\\S+t\\d{7}-\\d{2}$"^^ . - . - . - . - . - "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id="^^ . - . - "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"^^ . - . - "Plasmodium Life Cycle" . - "349124"^^ . - . - . - . - . - "anatomy" . - "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."^^ . - "PiroplasmaDB" . - . -_:Nf7d4794e396447a1b92c7061cea44e79 "helpdesk@cropontology-curationtool.org" . - . - . - . - . - . - . - . - "UCSC Genome Browser" . - "58788"^^ . - . - . - "mriffle@u.washington.edu" . - . - "10007835"^^ . - "has alternative prefix" . - . - . - . - "https://depmap.org/portal/cell_line/$1"^^ . - "ontology" . - "epidemiology" . - . - "Platynereis stage ontology" . - . - . - "bioinformatics" . - . - "wicell" . - . - "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . - . - . - . - "biology" . - "life science" . - . - . - . - "http://www.wikidata.org/entity/$1"^^ . - . - . - . - . - "0002999"^^ . - "00573"^^ . - "Genomics Cohorts Knowledge Ontology" . - "pathway" . - . - . - "anatomy" . - . - "Gene Ontology Registry" . - . - "Cell line collections (Providers)"^^ . -_:N5b864b9d0d9e47e2b9877a5fcffa278f "NLM Customer Service" . - "https://cropontology.org/rdf/CO_323:$1"^^ . - . - . - "true"^^ . - . - . - . - . - . - "neurobiology" . - "^RBR-\\w+$"^^ . - . - "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada."^^ . - . - . - . - "NOR00681"^^ . -_:Nef1e0f2fdfb6453f867b6dc3d6aad05d "Crop Ontology Helpdesk" . - . - "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . - "ChEBI Data Sources" . - . - "http://geneontology.org/" . - . - . - . - . - . - "http://www.ontobee.org/" . - "vfdb.genus" . - "http://bitterdb.agri.huji.ac.il/Receptor.php?id="^^ . - . - . - "David Gloriam" . - . - "ArrayMap" . - . - . - . - "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . - "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]"^^ . - . - "https://www.inaturalist.org/taxa/$1"^^ . - . - . - . - . - "plo" . - . - . - . - . - "ORCID" . - . - . - . - . - . - "^N[0-9]{10}$"^^ . - . - "Protein Ensemble Database ensemble" . - . - "dna" . - "C0017565"^^ . - "dna" . - . - "UBPROP" . - . - . - . - "obo" . - . - "Tudor Oprea" . - "https://envipath.org/package/"^^ . - . - . - "NCBI Gene Expression Omnibus" . - . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - . - "napp" . - . - . - . - . - "gold standard" . - . - "Ontology for simulation, modelling, and optimization" . - . - . - "begdb" . - . - . - "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."^^ . - "tctr" . - . - "small molecule" . - "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."^^ . - . - . - "Molecular Modeling Database" . - "false"^^ . - . - "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis."^^ . - . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode="^^ . - . - . - "false"^^ . - . - . - . - "2gc4E"^^ . - . - . - "MedDRA" . - . - . -_:N27ef8028e2244489bf142e7a8b5cc089 "helpdesk@cropontology-curationtool.org" . - . - "PACTR202304525632216"^^ . - . - "Reactions in drugbank"^^ . - . - . - . - "0000547"^^ . - . - . - . - "life science" . - . - . - "rna" . - . - . - "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/TGMA_"^^ . - . - . - . - "http://purl.obolibrary.org/obo/CL_"^^ . - . - . - . - "Philippine Health Research Registry" . - . - . - "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . - . - . - . - . - "mutant mouse strain" . - . - "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . - . - . - "The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database."^^ . - . - . - . - . - "astrophysics and astronomy" . - "biology" . - . - . - . - . - . - . - . - . - "icf" . - . - . - "proteomicsdb.protein" . - . - "computational chemistry" . - "human disease" . - _:N9aafcf7456c84e55b289f755161257e1 . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - "mmdb" . - . - . - "European Genome-phenome Archive Study" . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - "ontology" . - . - . - . - . - . - . - "https://www.biozol.de/en/product/$1"^^ . - "false"^^ . - . - "adrien.coulet@loria.fr" . - "https://publons.com/researcher/$1"^^ . - . - . - . - . - "https://biopragmatics.github.io/providers/mba/"^^ . - . - . - "Network of Different Plant Genomic Research Projects" . - . - . - . - . - . - "false"^^ . - . - . - . - . - "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id="^^ . - "Cell Ontology" . - . - . - . - "^[0-9]*$"^^ . - . - . - "https://w3id.org/oc/oci/$1"^^ . - "false"^^ . - "http://ecmdb.ca/compounds/$1"^^ . - . - . - "Experimental condition ontology" . - . - "ontology" . - "false"^^ . - . - . - "^\\w+(\\.)?(\\d+)?$"^^ . - "false"^^ . - "dragondb.allele" . - . - "000009"^^ . - "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."^^ . - . - "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . - . - . - . - . - . - . - "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . - "false"^^ . - . - "obo" . - . - "metadata" . - "chemistry" . - . - . - . - . - . - . - "Jörg Wicker" . - . - . - . - . - "https://bartoc.org/en/node/$1"^^ . - . - "12929"^^ . - . - "ado" . - . - . - "glida.ligand" . - "registry" . - . - "13GS"^^ . - "structure" . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . - . - . - . - "anatomy" . - . - "ontology" . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - "enrique.blanco@crg.eu" . - . - . - . - . - "botany" . - . - . - . - . - . - "sty" . - "Sample processing and separation techniques" . - . - "https://metazoa.ensembl.org/id/"^^ . - "http://emmo.info/emmo#EMMO_"^^ . - . - . - . - "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . - "Human Dephosphorylation Database" . - . - . - . - . - . - "false"^^ . - "http://ascl.net/"^^ . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - "preclinical studies" . - "The FRBR-aligned Bibliographic Ontology (FaBiO) is an ontology for describing entities that are published or potentially publishable (e.g., journal articles, conference papers, books), and that contain or are referred to by bibliographic references."^^ . - "^\\d+$"^^ . - "false"^^ . - "AB_262044"^^ . - . - "http://metlin.scripps.edu/metabo_info.php?molid="^^ . - "0000001"^^ . - "developmental biology" . - . - . - . - . - "ror" . - . - . - . - . - . - "ensemblglossary" . - . - . - . - . - "embryonic stem cell" . - "http://www.interfil.org/details.php?id=$1"^^ . - . - "classification" . - . - . - . - "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"^^ . - . - . - "hrehm@mgh.harvard.edu" . - "false"^^ . - . - . - . - "^\\d+$"^^ . - "ontology" . - "people/11035"^^ . - "A type for entries in the Bioregistry's metaregistry." . - . - . - . - "biomaterial manufacture" . - . - "https://bioregistry.io/odam:"^^ . - . - . - . - "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."^^ . - . - . - "arraymap" . - . - . - "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . - "https://www.swisslipids.org/#/entity/SLM:"^^ . - . - . - . - . - . - "^([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+)$"^^ . - . - . - . - . - . - . - . - . - . - "proteomics" . - . - "cgd" . - "http://terminology.hl7.org/CodeSystem/v2-$1"^^ . - "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains."^^ . - . - "Cardiovascular Disease Ontology" . - . - "http://purl.obolibrary.org/obo/OBCS_"^^ . - "pathogen" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "A frontend to Wikidata"^^ . - . - "nmdc" . - . - . - "Broad Fungal Genome Initiative" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/MPIO_$1"^^ . - "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . - "neurondb" . - "http://purl.dataone.org/odo/SENSO_$1"^^ . - . - "botany" . - . - "https://www.ebi.ac.uk/biomodels/$1"^^ . - . - . - . - "life science" . - "^\\w+(\\.\\d+)$"^^ . - "false"^^ . - . - . - . - "emap" . - "scoro" . - . - . - "ERP004492"^^ . - . - . - . - "Molecular Interaction Database" . - . - . - "https://bioregistry.io/lgic:"^^ . - "nist" . - . - . - "0000029"^^ . - . - "Exposure ontology" . - . -_:N5e5ef5c07ce54a41b7b91c5aada03718 "helpdesk@cropontology-curationtool.org" . - . - . - "false"^^ . - "epidemiology" . - "ontology" . - "http://purl.obolibrary.org/obo/RO_$1"^^ . - . - . - "PDB ligand" . - . - . - "Alzforum_mut" . - . - . - . - "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . - . - . - . - . - . - . - "sasbdb" . - . - . - "gomf" . - . - "https://biopragmatics.github.io/providers/dhba/$1"^^ . - . - . - "wyeth@cmmt.ubc.ca" . - . - "false"^^ . - "true"^^ . - . - . - "comparative genomics" . - . - . - . - . - . - . - . - . - . - "false"^^ . - "HomologyRelation"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "bsu:BSU01340"^^ . - . - "https://www.imanislife.com/?s=$1"^^ . - "alignedWith"^^ . - . - . - . - . - . - "false"^^ . - . - . - "A0118748"^^ . - "COGs stands for Clusters of Orthologous Genes. The database was initially created in 1997 (Tatusov et al., PMID: 9381173) followed by several updates, most recently in 2014 (Galperin et al., PMID: 25428365). The current update includes complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera. The new features include ~250 updated COG annotations with corresponding references and PDB links, where available; new COGs for proteins involved in CRISPR-Cas immunity, sporulation, and photosynthesis, and the lists of COGs grouped by pathways and functional systems."^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - "https://purl.uniprot.org/uniprot/"^^ . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "A terminology for the skills necessary to make data FAIR and to keep it FAIR."^^ . - . - . - "http://purl.obolibrary.org/obo/PPO_"^^ . - . - . - "XML Schema Definition" . - . - . - . - "4447"^^ . - . - . - "pharmacodb.cell" . - . - "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."^^ . - . - . - "Ontology"^^ . - . - "hybrid" . - "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."^^ . - "^[A-Za-z0-9]+$"^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - "http://purl.obolibrary.org/obo/ZFA_"^^ . - . - . - . - "qudt" . - . - . - . - . - . - . - . - "viperdb" . - . - "https://odc-sci.org/data/$1"^^ . - . - . - . - "structrual bioinformatics" . - . - "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1"^^ . - . - . - . - "BAO" . - . - . - . - "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."^^ . - . - "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."^^ . - "dna" . - . - "true"^^ . - . - . - . - . - . - "PRO_0000016681"^^ . - "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . - "protein" . - . - . - "50583"^^ . - . - . - "genome" . - . - . - . - "pathway" . - . - "10531"^^ . - "biology" . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "002804"^^ . - . - . - . - . - "90806"^^ . - . - . - . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with fungal genomes."^^ . - . - "TogoVar" . - "Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.\nWikidata acts as central storage for the structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. "^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - "genome" . - "Blue Brain Project Knowledge Graph" . - . - "github.issue" . - . - "Mungbean ontology" . - "00020007"^^ . - "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."^^ . - "068078"^^ . - . - . - . - . - . - . - . - . - "90901"^^ . - . - . - "property" . - . - . - . - . - . - . - "AT1G73965"^^ . - "topdb" . - "https://world-2dpage.expasy.org/repository/"^^ . - "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid="^^ . - "organic chemistry" . - "Chemical Methods Ontology" . - . - "comparative genomics" . - . - . - . - . - . - . - "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - . - "grid.225360.0"^^ . - "http://igsn.org/$1"^^ . - . - . - "Chemical Component Dictionary" . - "Time Ontology in OWL" . - . - "domain" . - . - . - . - . - . - "true"^^ . - . - "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://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . - . - . - "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."^^ . - . - . - "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones."^^ . - . - "Jeffrey Wong" . - . - . - "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0="^^ . - . - "false"^^ . - . - . - "plant anatomy" . - "http://www.ebi.ac.uk/astd/geneview.html?acc="^^ . - "false"^^ . - . - . - . - . - "subject agnostic" . - "balhoff@renci.org" . - . - . - . - . - "Alvin Walker" . - "mycobank" . - . - "prefixcommons" . - "Social Insect Behavior Ontology" . - "snp2tfbs" . - "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - . - "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."^^ . - . - . - "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."^^ . - "03307879"^^ . - . - "BioGRID" . - . - . - "TC010103"^^ . - . - . - . - . - "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . - . - . - . - . - . - "nihreporter.project" . - . - . - . - . - . - "go" . - . - . - . - . - "ontology" . - . - . - . - . - . - "Andreas Ruepp" . - "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus="^^ . - "https://www.ebi.ac.uk/biosamples/sample/"^^ . - . - . - . - . - . - "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."^^ . - . - . - . -_:N2e5ebba17dfe4820a58407ea4cde60df "chEBI" . - . - "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . - "Nanbyo Disease Ontology" . - "pharmacogenomics" . - "support@bel.bio" . - . - . - "Gene Product Information Schema" . - . - . - "https://biopragmatics.github.io/providers/peff/$1"^^ . - "life science" . - . - "Henriette Harmse" . - . - "virology" . - . - . - "P12345"^^ . - . - "life science" . - . - "Contains information about cells and data sheets related to transfection."^^ . - . - . - "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId="^^ . - . - . - . - . - . - "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . - . - . - "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . - . - "repository" . - "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . - . - . - . - "WikiPathways" . - "Genome assembly database" . - . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - "proteomics" . - . - . - "obo" . - . - . - . - "false"^^ . - . - . - . - . - "^\\w{2,4}\\d{5}$"^^ . - . - . - "5.A.1.1.1"^^ . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - . - . - "bioinformatics" . - . - . - . - "g.gkoutos@bham.ac.uk" . - "linikujp@gmail.com" . - . - . - . - . - . - . - . - . - . - "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants."^^ . - "false"^^ . - "17254"^^ . - . - "ontology" . - "ontology" . - "dna" . - "Pankaj Jaiswal" . - "Berkeley Drosophila Genome Project EST database" . - . - "https://eol.org/pages/"^^ . - . - . - . - . - . - . - "vcell"^^ . - . - "false"^^ . - . - "http://topdb.enzim.hu/?m=show&id=$1"^^ . - . - . - "https://bioregistry.io/bacmap.map:"^^ . - "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'."^^ . - . - "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."^^ . - . - . - . - "true"^^ . - "1000"^^ . - . - "false"^^ . - "1a05"^^ . - "clustering" . - "1018"^^ . - . - . - . - . - . - . - "A comprehensive compendium of human long non-coding RNAs"^^ . - . - . - . - . - . - "obo" . - . - . - . - "publons.researcher" . - "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . - "YOR172W_571.0"^^ . - "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . - . - . - "ngbo" . - "2170610"^^ . - "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs."^^ . - "medicine" . - . - . - . - . - . - . - "fish" . - "The Python Package Index (PyPI) is a repository for Python packages."^^ . - "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."^^ . - . - . - "aaindex" . - "ensembl.protist" . - . - . - "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems."^^ . - "false"^^ . - "https://bdsc.indiana.edu/stocks/$1"^^ . - . - "false"^^ . - . - "Variation Modelling Collaboration" . - . - . - . - "cath.domain" . - . - . - . - "^\\d+$"^^ . - "CLV_MEL_PAP_1"^^ . - . - . - "^\\d{7}$"^^ . - . - "BacMap Biography" . - . - . - . - . - "grouping" . - . - "ontology" . - . - "false"^^ . - . - . - . - "MFO_0000001"^^ . - . - . - "chemistry" . - . - . - . - "100010"^^ . - "https://bioregistry.io/resolve/github/pull/"^^ . - . - "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . - . - "^PF\\d{5}$"^^ . - . - . - . - . - "^CLPUB\\d+$"^^ . - "ThoracicArtery"^^ . - . - . - . - "Peruvian Clinical Trial Registry" . - "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . - "^[1-9]\\d{0,11}$"^^ . - "Tb927.8.620"^^ . - . - . - . - "http://purl.obolibrary.org/obo/OGI_"^^ . - . - "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23"^^ . - . - "classification" . - . - "^\\d{8}$"^^ . - . - . - . - . - "nmr" . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "https://bioportal.bioontology.org/ontologies/$1" . - "obo" . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "KEGG_REACTION_CLASS" . - "molecular infection biology" . - "false"^^ . - . - "obo" . - "^ENSG\\d{11}$"^^ . - "03212fd7_abfd_4828_9c8e_62c293052d4b"^^ . - . - "RiceNetDB miRNA" . - "computational biology" . - "human" . - . - . - . - "IPP900099"^^ . - . - "^ENSGT\\d+$"^^ . - "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-"^^ . - . - "NIF Standard Ontology: External" . - . - . - . - "http://www.w3.org/ns/odrl/2/"^^ . - "ontology" . - "Health Canada Drug Identification Number" . - . - . - . - . - . - "phenotype" . - . - "datasubs@ebi.ac.uk" . - . - "agriculture" . - . - "http://purl.dataone.org/odo/ECSO_"^^ . - . - . - . - . - . - "nlfff" . - . - . - "Bio-MINDER Tissue Database" . - "false"^^ . - . - "Identifiers.org Ontology" . - . - . - . - . - . - . - "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="^^ . - . - "GWAS Central Phenotype" . - . - . - . - . - . - "3304"^^ . - "false"^^ . - . - . - "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities."^^ . - "http://purl.obolibrary.org/obo/HAO_$1"^^ . - "SNOMEDCT_US_2018_09_01" . - "co_335" . - . - "0400109"^^ . - "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . - "http://purl.obolibrary.org/obo/COVIDO_"^^ . - "life-cycle" . - . - . - . - "multicellds.cell_line" . - . - . - "bioproject" . - . - "^\\d{7}$"^^ . - "https://easychair.org/cfp/topic.cgi?tid="^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - . - "EcoliWiki from EcoliHub" . - . - . - . - "life science" . - . - . - . - "true"^^ . - "ProtClustDB" . - . - "http://purl.obolibrary.org/obo/HANCESTRO_"^^ . - "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . - . - . - "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."^^ . - . - "Zebrafish developmental stages ontology" . - . - . - "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . - "false"^^ . - "miw023@ucsd.edu" . - . - . - . - . - . - . - "Life cycle stages for Human"^^ . - . - . - "^\\d+$"^^ . - "relationships" . - . - "image" . - . - . - "rrid" . - "omit" . - "false"^^ . - "rna" . - . - "0000001"^^ . - . - "BiGG Metabolite" . - "tkg" . - "vendor" . - "false"^^ . - . - . - . - "Biotin_biosynthesis"^^ . - "INSDC CDS" . - . - . - "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name="^^ . - "false"^^ . - "Google Scholar Researcher" . - . - "^([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+)?$"^^ . - . - . - . - . - . - . - . - . - . - . - "Support Email" . - . - . - . - "small molecule" . - "NCBI Probe database Public registry of nucleic acid reagents" . - . - "R. Burke Squires" . - . - . - . - "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . - "ontology" . - . - . - . - "nathan.baker@pnnl.gov" . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . - "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . - "^Q[A-Z0-9]+$"^^ . - . - . - "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . - . - "preprints" . - . - "0278"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_chem_"^^ . - "NCITt" . - . - "George Gkoutos" . - "protein" . - . - . - "epigenetics" . - . - _:N9a58aee7324d447d80a82ed73e348c46 . - "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . - . - . - . - "^\\d+$"^^ . - . - "flybrain.ndb" . - "brycemecum@gmail.com" . - "rna" . - "A vocabulary for annotating vocabulary descriptions" . - . - . - . - . - . - . - . - . - "chemistry" . - . - . - . - "biology" . - "https://dbpedia.org/ontology/"^^ . - "n.lenovere@gmail.com" . - "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."^^ . - . - . - . - . - . - . - . - . - . - "sgd.pathways" . - . - "4"^^ . - "Decentralized Identifier" . - "edong@umich.edu" . - . - . - "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."^^ . - . - "bioinformatics" . - "^\\d+$"^^ . - "ontology" . - . - "false"^^ . - . - . - "IMGT/HLA human major histocompatibility complex sequence database" . - . - . - . - "https://bioregistry.io/ukprn:"^^ . - . - "false"^^ . - "https://www.metanetx.org/chem_info/"^^ . - . - "http://purl.obolibrary.org/obo/OVAE_$1"^^ . - "ligandexpo" . -_:N848769ba5c1f4a738b2435e71207d3ee "Josef Hardi" . - . - . - . - . - . - . - . - . - . - . - "French National Center for Scientific Research - Research Group Identifier" . - . - . - "false"^^ . - . - "reagent" . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - . - "false"^^ . - "Ath_AT1G01030.1"^^ . - . - "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"^^ . - . - "evolutionary biology" . - "true"^^ . - . - "https://lincs.hms.harvard.edu/db/antibodies/$1"^^ . - "http://www.w3.org/ns/shacl#"^^ . - . - . - . - "Mental Disease Ontology" . - . - "^\\d+$"^^ . - . - . - . - . - . - "ENST00000407236"^^ . - "door" . - . - "proteomics" . - . - "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$"^^ . - "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . - . - . - . - . - . - "National Center for Advancing Translation Sciences BioPlanet" . - . - . - . - . - "obo" . - . - "LOC_Os02g13300"^^ . - . - "nemo" . - . - . - . - "http://purl.obolibrary.org/obo/PLANP_$1"^^ . - "https://biopragmatics.github.io/providers/sdis/"^^ . - "protein" . - "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once."^^ . - . - . - . - . - . - "biochemistry" . - . - "^MSMEG\\w+$"^^ . - . - . - . - "https://www.ebi.ac.uk/gxa/experiments/"^^ . - "gdc" . - . - "humanities" . - "E5.11.2.0.0.0.4"^^ . - . - . - "ontoavida" . - "12345"^^ . - . - "CCLE_867"^^ . - "ontology" . - . - . - "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . - . - "cellosaurus" . - . - . - . - . - "developmental biology" . - . - "326705068"^^ . - "small molecule" . - . - "http://purl.obolibrary.org/obo/TADS_"^^ . - . - . - "emmo.cif" . - . - . - "YeTFasCo" . - . - . - . - "Jennifer L Harrow" . - . - . - . - "animal physiology" . - . - . - . - "https://shop.vbc.ac.at/vdrc_store/$1.html"^^ . - . - . - . - . - "carrine.blank@umontana.edu" . - "anatomy" . - . - . - "dna" . - . - . - . - . - . - . - . - "Veterinary Substances DataBase" . - "celia.michotey@inrae.fr" . - . - "https://bioregistry.io/medlineplus:"^^ . - . - . - . - . - "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC="^^ . - "Cross-linker reagents ontology" . - . - . - "bt0001"^^ . - . - "salamander" . - "pubchem.aid" . - . - . - . - "obo" . - "gudmap" . - . - "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . - . - . - "http://purl.obolibrary.org/obo/OBI_$1"^^ . - . - "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i="^^ . - "drugbank" . - . - . - . - . - . - "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . - "drugbank.salt" . - . - "http://www.pseudomonas.com/feature/show/?locus_tag="^^ . - . - "pictar-vert" . - . - . -_:N8b543b3ccc35445baa4f243e0b8deea9 "Crop Ontology Helpdesk" . - "ontology" . - . - . - . - "AcknowledgementCondition"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . - . - . - "Minimal Viable Identifier" . - . - "Jie Zheng" . - . - "https://registry.identifiers.org/registry/"^^ . - . - "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . - . - "0000000"^^ . - "life science" . - . - . - . - "false"^^ . - . - "inxight-drugs" . - . - "false"^^ . - . - "18030"^^ . - "false"^^ . - . - . - "6978836"^^ . - "opl" . - "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases."^^ . - . - "0002233"^^ . - "kronkcj@mail.uc.edu" . - "chemical" . - . - . - . - . - "Gene Ontology Registry" . - . - . - . - "life science" . - "ontology" . - "inxight" . - . - . - "^CH_\\d+$"^^ . - "Cell Lines Service" . - . - "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . - . - . - "classification" . - . - . - . - "Japan Consortium for Glycobiology and Glycotechnology Database" . - . - . - . - "computer science" . - . - "faseb list" . - . - "rapdb.locus" . - . - . - . - . - . - . - "wikipathways" . - . - . - . - . - . - "dispositions" . - "https://cropontology.org/rdf/CO_320:"^^ . - . - . - . - . - "0000093"^^ . - . - "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . - . - "https://bioregistry.io/ipi:"^^ . - "botany" . - "^e\\d+$"^^ . - "SCOP(e) concise classification string" . - . - . - "false"^^ . - . - . - . - . - . - "http://www.narcis.nl/publication/RecordID/$1"^^ . - . - . - . - "http://www.antweb.org/specimen.do?name=$1"^^ . - "biomedical science" . - "http://purl.obolibrary.org/obo/PW_$1"^^ . - . - "rxno" . - . - . - "subject agnostic" . - . - . - . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . - . - . - . - "NONCODE v4 Gene" . - "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)."^^ . - "protein" . - "ontology" . - "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 Marker."^^ . - . - . - . - . - . - . - "Cell line collections (Providers)"^^ . - "http://purl.obolibrary.org/obo/kestrelo_$1"^^ . - . - . - . - "4"^^ . - . - "NCI Drug Dictionary ID" . - "vto" . - "2649230"^^ . - . - . - . - . - "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains."^^ . - "Andrew G. McArthur" . - . - "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . - "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . - . - . - "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/"^^ . - . - "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . - . - . - "0000634"^^ . - "protein" . - "gtr" . - . - "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . - . - . - . - . - . - . - "CIViC variant" . - . - "http://purl.obolibrary.org/obo/OMO_"^^ . - . - "SP_VAR" . - "0459895"^^ . - "ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "life science" . - . - . - . - "obo" . - . - . - . - . - . - "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . - . - . - . - "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively."^^ . - "http://purl.obolibrary.org/obo/TO_$1"^^ . - "clinicaltrial" . - . - . - "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. "^^ . - . - . - . - . - . - "77"^^ . - "life sciences" . - . - "opmi" . - . - . - . - . - . - "https://www.storedb.org/?STOREDB:DATASET"^^ . - . - . - . - "MMSL_CODE" . - "pathway" . - "^\\d+$"^^ . - . - . - . - . -_:N5ee7902ef2b64c548828599daaf0d737 "helpdesk@eionet.europa.eu" . - "pwo" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/DUO_"^^ . - "jax" . - . - . - "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." . - "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . - "s_mart_db" . - "Clinical Trial Registries" . - "Yeast Intron Database v4.3" . - "siren" . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . - . - "DBCOND0066902"^^ . - . - . - "preclinical studies" . - . - "http://sideeffects.embl.de/drugs/$1"^^ . - . - . - . - "https://www.re3data.org/repository/$1" . - "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "hgmd" . - "genepio" . - "false"^^ . - . - . - . - "protein" . - . - . - "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"^^ . - "gaoj@mskcc.org" . - "gene" . - "https://www.abmgood.com/search?query=$1"^^ . - . - . - "false"^^ . - "leen.vandepitte@vliz.be" . - . - "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . - "obo" . - . - . - "true"^^ . - . - . - "peteremidford@yahoo.com" . - . - . - "European Collection of Authenticated Cell Culture" . - . - . - "obo" . - . - "Antimicrobial Peptide Database" . - . - "^\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/PLANP_"^^ . - . - . - "https://metacyc.org/compound?orgid=META&id=$1"^^ . - . - "anatomy" . - . - "http://bacmap.wishartlab.com/organisms/"^^ . - . - . - "NCI Metathesaurus" . - "molmedb" . - . - . - . - . - . - "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . - "agriculture" . - . - "^\\d{7}$"^^ . - . - . - . - "interaction" . - "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . - . - "life science" . - . - . - "genome" . - . - . - . - "https://cropontology.org/rdf/CO_325:$1"^^ . - . - "physical geography" . - . - . - "https://spdx.org/licenses/"^^ . - . - "Val Wood" . - . - . - "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . - "false"^^ . - "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . - "uniprot.isoform" . - . - "Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a \"peer\"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. "^^ . - "protein" . - "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . - . - . - . - . - . - "Metabolite and Tandem Mass Spectrometry Database" . - . - . - . - . - "environmental science" . - . - . - . - "genome" . - . - "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1"^^ . - . - . - "psipar" . - . - "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . - "molecule" . - . - "Citlalli Mejía-Almonte" . - "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . - . - "^\\d{7}$"^^ . - "GlycoPOST" . - "HL7 V2 Code Systems" . - . - "lpt" . - . - "tissue" . - . - . - . - . - . - "bbkg" . - "biomodels.kisao" . - . - . - . - . - . - "BioPortal Prefixes" . - . - . - "developmental biology" . - . - "biomedical science" . - "ontology" . - "http://purl.obolibrary.org/obo/MA_"^^ . - "8"^^ . - . - "https://www.emsl.pnnl.gov/project/"^^ . - "dna" . - "https://biosimulators.org/simulators/$1"^^ . - "Cell Signaling Technology Pathways" . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - "Rebuilding a Kidney" . - . - . - . - "https://biopragmatics.github.io/providers/cvx/"^^ . - . - . - "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format."^^ . - . - . - . - . - . - "cheminformatics" . - . - . - "true"^^ . - "^\\d+$"^^ . - "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . - . - . - . - . - "diseasesdb" . - "ecn" . - . - . - "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . - "false"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - "http://exac.broadinstitute.org/variant/"^^ . - . - "^\\d+$"^^ . - "dailymed" . - . - . - . - . - . - . - . - . - . - "obo" . - "VFG2154"^^ . - "co_324" . - . - "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . - . - "https://lincs.hms.harvard.edu/db/sm/"^^ . - . - . - . - . - "http://cutdb.burnham.org/relation/show/"^^ . - "protein" . - . - . - . - "S7000002168151102"^^ . - . - . - . - . - "IMGT/PRIMER-DB" . - . - "gene expression" . - "protein" . - . - . - . - . - . - "false"^^ . - . - "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . - . - "https://www.cellosaurus.org/CVCL_"^^ . - . - . - "ecology" . - "ontology" . - . - . - . - . - . - . - . - . - "drug-drug interactions" . - "life science" . - "umls.sty" . - . - . - . - . - . - . - . - . - "ontology" . - . - . - . - . - . - . -_:N3cc0025ca3d24a2dafbd5de44f56b1e2 "info@wikidata.org" . - . - . - "gateway" . - . - "100810"^^ . - "http://purl.obolibrary.org/obo/TADS_$1"^^ . - . - "^EDI_\\d+$"^^ . - . - . - "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."^^ . - . - . - . - "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."^^ . - . - . - "^\\d{4}-\\d+-\\d+-\\d+$"^^ . - "^\\d{7}$"^^ . - "cl" . - . - "SpBase" . - . - . - . - . - "MetaCyc" . - . - "do" . - _:N5411953aa3da420b83011b159fcbf568 . - . - "false"^^ . - . - . - "Process Chemistry Ontology" . - "^\\d+$"^^ . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id="^^ . - "ontology and terminology" . - "Small Molecule Pathway Database" . - . - . - . - "classification" . - . - . - . - "false"^^ . - . - . - "SPAR Ontologies" . - "environmental science" . - . - "true"^^ . - . - "ricenetdb.mirna" . - . - "AHR"^^ . - . - . - . - "false"^^ . - . - . - . - . - "Pfam Clans" . - . - . - . - "Mass spectrometry ontology" . - . - . - . - . - "biomedical science" . - . - "Flybase Cell Line" . - "648028003"^^ . - . - . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . - . - . - . - "Zoë May Pendlington" . - . - . - "semapv" . - . - "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . - . - . - "human" . - "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . - . - "false"^^ . - . - . - "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . - "false"^^ . - . - "Web of Science ID (work)" . - . - . - . - . - . - . - "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . - "Ligand Expo" . - "prints" . - . - . - . - . - . - "obo" . - . - "The Cell Cycle DB" . - "Terms from the source appear in the target resource" . - . - . - . - "gene" . - . - "ctri" . - . - . - "molecule" . - . - . - . - . - . - "psychiatry" . - . - . - . - . - "http://purl.obolibrary.org/obo/AEO_"^^ . - . - "computational biology" . - . - . - . - . - "ontology" . - "^\\d{7}(_\\d)?$"^^ . - . - "mzspec" . - "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."^^ . - "phenotyping" . - . - "false"^^ . - . - "Saccharomyces Genome Database" . - . - . - "http://genomics.senescence.info/diet/details.php?id=$1"^^ . - . - . - "obo" . - . - "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . - "http://www.ecogene.org/gene/$1"^^ . - "e.arnaud@cgiar.org" . - "false"^^ . - "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#"^^ . - "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . - . - "Tiffany J. Callahan" . - . - . - . - . - . - "62"^^ . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - . - "CGH Data Base" . - . - "https://www.re3data.org/repository/$1"^^ . - "https://bioregistry.io/dragondb.locus:"^^ . - "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . - . - "http://purl.obolibrary.org/obo/TTO_$1"^^ . - "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place."^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "gene" . - . - . - . - . - . - "MMP743597.11"^^ . - "genomics" . - . - "nucleotide" . - . - . - . - "edam.data" . - "Mouse Brain Atlas" . - . - . - . - . - "life science" . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist="^^ . - . - . - "obo" . - "https://www.rhea-db.org/rhea/"^^ . - "https://rnaloops.cs.put.poznan.pl/search/details/$1"^^ . - "canal"^^ . - . - . - . - . - . - . - "sharesAuthorInstitutionWith"^^ . - . - "Virtual Fly Brain" . - . - "transcript" . - . - "obo" . - "ontology" . - "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . - "dbprobe" . - . - . - . - . - "Annika Jahnke-Bornemann" . - . - . - "602"^^ . - . - . - "RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases."^^ . - "sequence" . - "^DP\\d{5}$"^^ . - . - "ThermoFisher is a life sciences supply vendor."^^ . - . - "Global Research Identifier Database" . - . - . - "proteomics" . - . - . - . - . - . - "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."^^ . - . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "046-19"^^ . - . - "Software"^^ . - . - . - "MCDS_C_0000000001"^^ . - "Orthology Ontology" . - . - . - "^\\w+$"^^ . - "henriette007@ebi.ac.uk" . - . - . - . - . - . - "Biological Imaging Methods Ontology" . - . - "ICEberg cis-integrative and mobilizable element" . - . - "_space_group_symop.operation_xyz"^^ . - . - . - "translation_language"^^ . - "metascience" . - . - "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . - "MTBLS1"^^ . - . - . - "true"^^ . - . - "^\\d+$"^^ . - . - . - "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . - . - . - . - "https://www.wormbase.org/db/seq/protein?name=$1"^^ . - . - "^FB\\d{8}$"^^ . - "has identifier space owner" . - . - . - . - "^\\d+$"^^ . - "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . - "FHIR External Terminologies" . - "https://www.mlcommons.org/mlc-id/"^^ . - . - "upheno" . - . - "life sciences" . - . - . - . - . - "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . - . - "asrp" . - . - "Prefix Commons" . - "genome" . - "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."^^ . - . - . - . - . - "has URI pattern" . - . - "deletion" . - . - . - . - . - . - "biomedical science" . - . - "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . - "https://rnacentral.org/rna/"^^ . - "cvdo" . - "obo" . - . - . - . - "life science" . - . - . - . - "obo" . - "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)"^^ . - . - . - "http://purl.obolibrary.org/obo/LPT_"^^ . - . - "https://cropontology.org/rdf/CO_340:"^^ . - . - . - . - . - "Josh Moore" . - . - "false"^^ . - "false"^^ . - "http://bactibase.hammamilab.org/"^^ . - . - . - . - "rdf" . - . - "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id="^^ . - . - . - . - . - . - "obo" . - . - . - "obo" . - . - . - "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . - . - . - "ontology" . - . - . - . - "Q-2958"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - "KEGG Enzyme" . - "structural bioinformatcs" . - "^\\d+$"^^ . - "0004"^^ . - "pfam" . - . - "genomics" . - "alignment" . - . - "ncbigene" . - "pubchem.assay" . - "0011140"^^ . - "16333295"^^ . - "false"^^ . - . - . - "repository" . - . -_:N50de7bbebb744373b98eaefc287f558e "Pat Brooks" . - . - "drugs" . - . - "taxonomy" . - "mgilson@health.ucsd.edu" . - . - . - . - . - "Laia Subirats" . - . - . - . - "Yeast Intron Database v3" . - . - . - . - . - . - . - "classification" . - . - . - . - "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."^^ . - "http://sweetontology.net/matrMineral/"^^ . - "false"^^ . - . - . - "JRBC Cell Bank" . - "http://www.cazy.org/$1.html"^^ . - . - . - . - "Terminologia Histologica" . - . - . - "go.rule" . - . - "false"^^ . - "^\\d{7}$"^^ . - "forest management" . - "false"^^ . - . - "scpd" . - . - . - . - . - . - . - "true"^^ . - . - . - "false"^^ . - . - "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . - . - . - . - . - "life science" . - "chembl.target" . - "MNXR101574"^^ . - "food chemistry" . - . - "http://exac.broadinstitute.org/gene/"^^ . - . - . - "ScerTF" . - . - "huge" . - . - "Laurent Duret" . - . - . - . - "ontology" . - "0001290"^^ . - "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . - . - "false"^^ . - "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$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."^^ . - . - . - . - . - "Functional Requirements for Bibliographic Records Entity-Relationship Model" . - "ontology" . - "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . - "The NIST Chemistry WebBook provides users with easy access to chemical and physical property data for chemical species through the internet. The data provided in the site are from collections maintained by the NIST Standard Reference Data Program and outside contributors. Data in the WebBook system are organized by chemical species."^^ . - . - . - "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners."^^ . - . - "ali.syed@kaust.edu.sa" . - "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)"^^ . - "software and information systems" . - "200906038218908385"^^ . - "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . - . - . - "^HGVM\\d+$"^^ . - . - . - . - . - "lonza" . - "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."^^ . - "cohd" . - "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."^^ . - . - . - "obo" . - . - "true"^^ . - . - . - "Crop Ontology Curation Tool" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "animal model" . - "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"^^ . - . - . - . - "contributor"^^ . - "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]"^^ . - "interaction" . - "false"^^ . - . - . - . - . - . - "earth science" . - . - . - . - . - . - . - "biomedical science" . - . - . - "40592-R001-100"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/EPO_$1"^^ . - "NanoParticle Ontology" . - . - . - "storedb.dataset" . - "https://bioregistry.io/$1:$2" . - . - "false"^^ . - "gocc" . - "life science" . - . - . - . - "^[1-9]\\d{5}$"^^ . - "culture" . - "^JCGG-STR\\d{6}$"^^ . - "https://cells.ebisc.org/"^^ . - "false"^^ . - "DBPedia Ontology" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "DB-0174"^^ . - . - . - . - . - . - . - "Anita Bandrowski" . - "Christopher Mull" . - . - "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."^^ . - . - . - "false"^^ . - . - "false"^^ . - . - "false"^^ . - . - "obo" . - . - . - . - "helpdesk@cropontology-curationtool.org" . - "https://bioregistry.io/metaregistry/ncbi/"^^ . - . - "http://purl.obolibrary.org/obo/EMAP_"^^ . - . - "Charles Tapley Hoyt" . - . - . - . - . - . - "identifier of a compound in the UniChem database"^^ . - . - . - . - "PubMed" . - . - "dgrc" . - . - "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . - . - . - . - "life science" . - . - . - . - . - "Leszek@missouri.edu" . - "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . - . - . - . - . - . - "https://www.probes-drugs.org/compound/$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . - . - "CorrDB" . - . - . - "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. This collection refers to pathway information."^^ . - "false"^^ . - "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id="^^ . - . - "metascience" . - . - . - . - . - . - . - "https://datacommons.org/browser/"^^ . - . - . - . - . - "An ontology of core ecological entities" . - "^\\d{7}$"^^ . - . - . - "inchi" . - . - . - "false"^^ . - "^[0-9]+$"^^ . - . - "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://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . - "go.resource" . - . - "false"^^ . - "expression" . - "https://bioregistry.io/resolve/github/issue/"^^ . - "https://bioregistry.io/p3db.protein:"^^ . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - "^[0-9]+:[0-9]+$"^^ . - . - . - . - . - . - "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . - . - "systems biology" . - . - "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."^^ . - . - . - "http://avis.princeton.edu/pixie/viewgraph.php?graphID="^^ . - "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."^^ . - "MIRBASE_FAMILY" . - . - . - "pharmacogenomics" . - . - . - "https://reporter.nih.gov/project-details/$1"^^ . - . - "false"^^ . - "obo" . - "BP100000"^^ . - . - "http://isbndb.com/search-all.html?kw=$1"^^ . - . - . - "Symptom Ontology" . - . - . - . - "resid" . - "https://hamap.expasy.org/unirule/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/FOVT_$1"^^ . - "genome" . - . - . - . - . - "fig|306254.1.peg.183"^^ . - . - . - . - . - "^\\w+$"^^ . - . - "obo" . - . - . - . - "TAO_RETIRED" . - "^PAp[0-9]{8}$"^^ . - "nmr" . - "ga4ghdos" . - . - "false"^^ . - "https://licebase.org/?q="^^ . - . - "https://www.uniprot.org/proteomes/$1"^^ . - . - . - . - . - "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . - . - "http://foodb.ca/compounds/$1"^^ . - . - . - . - . - . - "domain" . - . - . - . - . - "biodiversity" . - . - . - "https://w3id.org/BCI-ontology#"^^ . - "translational medicine" . - . - . - . - "protein" . - . - . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. This collection references groups of genes that have been organised as families."^^ . - . - "BIOMD" . - . - "co_339" . - "Roman Laskowski" . - . - "DSSTox_Generic_SID" . - "https://www.rrrc.us/Strain/?x="^^ . - . - "ncats.drug" . - "Canadian Drug Product Database" . - "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value="^^ . - "false"^^ . - "The Ageing Gene Database" . - . - . - . - . - "business administration" . - "false"^^ . - . - "http://www.w3.org/2000/01/rdf-schema#"^^ . - "obo" . - . - . - . - . - "16S rRNA gene database" . - "embryonic stem cell" . - "uniprot.database" . - "^DBCOND\\d+$"^^ . - "gene" . - . - "^T\\d{3}$"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . - . - . - . - . - "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://bioregistry.io/metaregistry/ncbi/$1"^^ . - . - . - "fbdv" . - . - . - . - "FaceBase Data Repository" . - . - . - . - . - . - "https://grants.nih.gov/stem_cells/registry/current.htm?ID="^^ . - . - . - "false"^^ . - "life science" . - . - . - "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . - "laml_tcga_pub"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - "http://zinc15.docking.org/substances/"^^ . - "Pierre-Marie Allard" . - . - "owlstar" . - . - . - "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."^^ . - . - "false"^^ . - . - "ehdaa" . - . - . - "5046"^^ . - . - "false"^^ . - . - "^(VT)?\\d{7}$"^^ . - "M77F7JM"^^ . - . - "http://www.fairsharing.org/ontology/subject/SRAO_$1"^^ . - . - "life science" . - "YMDB00001"^^ . - . - . - "comparative genomics" . - "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships."^^ . - "biodiversity" . - . - . - "MESH" . - . - . - "4685"^^ . - "The Behaviour Change Intervention Ontology" . - "Terminology for Description of Dynamics" . - . - . - . - . - . - . - . - . - "dashr.expression" . - "gene" . - . - . - . - "genome" . - . - "http://www.begdb.com/index.php?action=oneMolecule&state=show&id="^^ . - "false"^^ . - "http://exac.broadinstitute.org/gene/$1"^^ . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "reaction" . - "A vendor of antibodies and other biologics"^^ . - "botany" . - . - . - "906801"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TTO_"^^ . - . - "^[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}$"^^ . - . - . - "brenda" . - . - . - . - . - "anatomy" . - "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers."^^ . - "false"^^ . - . - "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes."^^ . - . - "chemistry" . - . - "VIRsiRNA" . - . - . - "langual" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://fairsharing.org/$1"^^ . - . - "miRBase pre-miRNA" . - . - "FoodOn is a comprehensive and easily accessible global farm-to-fork ontology about food that accurately and consistently describes foods commonly known in cultures from around the world. It is a consortium-driven project built to interoperate with the The Open Biological and Biomedical Ontology Foundry library of ontologies."^^ . - . - . - "BioSimulators is a registry of containerized simulation tools that support a common interface. The containers in BioSimulators support a range of modeling frameworks (e.g., logical, constraint-based, continuous kinetic, discrete kinetic), simulation algorithms (e.g., CVODE, FBA, SSA), and modeling formats (e.g., BGNL, SBML, SED-ML)."^^ . - . - . - "David Linke" . - . - . - . - . - "chebi"^^ . - "^\\d+$"^^ . - . - "Cell Signaling Technology Antibody" . - . - "SBML RDF Vocabulary" . - . - "IUPHARfam" . - . - . - "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."^^ . - . - "obo" . - . - . - "21393"^^ . - . - . - . - "protein" . - "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."^^ . - . - . - "life science" . - "Physico-chemical methods and properties" . - . - "molecular microbiology" . - "ontology" . - "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."^^ . - . - . - . - "http://viaf.org/viaf/$1"^^ . - . - . - . - . - . - . - "protein complexes" . - "Animal Genome Size Database" . - "Michael Y Galperin" . - "https://medlineplus.gov/genetics/condition/$1"^^ . - . - "bartoc" . - "ontology" . - "http://purl.obolibrary.org/obo/NGBO_$1"^^ . - . - . - . - "RiceNetDB Protein" . - "false"^^ . - . -_:N2e5ebba17dfe4820a58407ea4cde60df "chebi-help@ebi.ac.uk" . - . - . - "http://www.w3.org/ns/shex#"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . - . - . - . - "http://cerevisiae.oridb.org/details.php?id=$1"^^ . - . - "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment."^^ . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "data analysis service" . - . - . - "research" . - "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."^^ . - . - "6"^^ . - "ontology" . - . - "genomics" . - "Yuki Yamagata" . - . - "RF00230"^^ . - . - . - "2019-08-03_00000089_1"^^ . - "https://www.ncbi.nlm.nih.gov/books/"^^ . - "orth" . - "aceview.worm" . - "BitterDB Receptor" . - "http://www.ymdb.ca/compounds/$1"^^ . - . - "http://www.pharmgkb.org/gene/$1"^^ . - "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . - . - . - . - "mesh.vocab" . - . - "John-Marc Chandonia" . - . - "obo_rel" . - "A subspace of Metabolic Atlas for reactions."^^ . - . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - "International Standard Name Identifier" . - "^\\d+$"^^ . - "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . - . - . - "structure" . - "life science" . - "agb@ebi.ac.uk" . - . - "environmental science" . - . - . - "EJH014"^^ . - . - "Current Dental Terminology" . - . - . - "Dr Paul Schofield" . - . - . - . - "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id="^^ . - . - "ChecklistBank" . - "0001"^^ . - "false"^^ . - . - "MESHPP" . - . - "cell lines" . - . - . - "8497"^^ . - "4DN" . - "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant."^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . - "A Database of Human Hemoglobin Variants and Thalassemias" . - "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."^^ . - . - . - . - "Database of Arabidopsis Transcription Factors" . - . - "false"^^ . - "false"^^ . - . - . - . - "ontology" . - "false"^^ . - . - . - . - "false"^^ . - "ontology" . - . - "false"^^ . - . - "oboinowl" . - . - . - "false"^^ . - . - . - . - "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)."^^ . - . - . - . - "life science" . - . - . - . - . - "http://purl.obolibrary.org/obo/MAXO_"^^ . - . - . - "genomics" . - "erv" . - "Spectra Hash Code" . - . - . - . - "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."^^ . - . - . - "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . - "pdbsum" . - . - . - . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . - . - "biomedical science" . - . - . - "Metabolomics Standards Initiative Ontology" . - "http://purl.obolibrary.org/obo/PECO_$1"^^ . - . - . - . - "Ontology for Chemical Kinetic Reaction Mechanisms" . - "http://pombe.oridb.org/details.php?id=$1"^^ . - "TTD Target" . - . - "0000088"^^ . - . - . - "The integrated microbial genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI (DoE Joint Genome Institute) microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. This datatype refers to taxon information."^^ . - . - . - . - . - . - . - "phylogenetics" . - . - "false"^^ . - "https://prosite.expasy.org/"^^ . - "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . - "^\\d+$"^^ . - "1801.012"^^ . - . - . - . - "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . - "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . - "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3))."^^ . - "Human Metabolome Database" . - . - "502930"^^ . - "2200934"^^ . - . - . - "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."^^ . - . - "Life cycle stages for Platynereis dumerilii"^^ . - . - "Relation Ontology" . - . - "http://purl.bioontology.org/ontology/NDDF/$1"^^ . - . - . - . - "^\\d+$"^^ . - "1868"^^ . - . - . - "ino" . - . - . - "sdap" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OAE_$1"^^ . - "https://ssbd.riken.jp/database/dataset/"^^ . - "obo" . - "false"^^ . - . - . - . - "Metabolic Atlas Metabolite" . - . - . - . - . - "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . - . - "ZEA_0015177"^^ . - . - . - . - "Frederic Bastian" . - "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . - "https://ror.org/$1"^^ . - . - . - . - . - . - . - "eugenes" . - . - . - . - "Sheng-Da Hsu" . - . - . - . - . - . - "SNOMEDCTCT" . - . - . - . - "https://thebiogrid.org/interaction/$1"^^ . - . - . - "National Swine Resource and Research Center" . - . - . - . - "cdna" . - . - . - . - "Phenoscape Publication" . - . - . - . - . - "https://doi.org/$1"^^ . - "computer science" . - . - . - "chemistry" . - "model" . - . - . - "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."^^ . - . - . - . - . - . - "mutant strain" . - . - . - . - "taxonomy" . - "SKIP001214"^^ . - "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . - . - "0000088"^^ . - "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id="^^ . - . - . - . - "has resource example" . - . - . - . - "TR0000001"^^ . - "classification" . - . - "https://www.sharkipedia.org/traits/$1"^^ . - _:N19ba2f4b49e149989c007cb1324ae430 . - "obo" . - . - "ProtoNet Cluster" . - "false"^^ . - "worldavatar.kin" . - "Primate Brain Atlas" . - "arachnoserver" . - . - . - "http://purl.obolibrary.org/obo/DERMO_$1"^^ . - "Cell line collections (Providers)"^^ . - "^\\w+$"^^ . - "Chemistry resources"^^ . - . - "eaglei" . - "22-46615880-T-C"^^ . - . - . - "reagents" . - "^\\w+$"^^ . - . - . - . - "Database of Quantitative Cellular Signaling: Model" . - . - "Database for Prokaryotic Operons" . - "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . - "selventa" . - . - . - . - . - . - . - . - "ASRP1423"^^ . - "brenda.ligandgroup" . - "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . - . - "Chemical Analysis Ontology" . - . - "false"^^ . - "^\\d+$"^^ . - "genetics" . - . - "alejandra.gonzalez.beltran@gmail.com" . - . - "Cu.me.I1"^^ . - . - . - . - . - "medicine" . - . - . - . - . - . - "nicole@tislab.org" . - "https://gitlab.com/"^^ . - . - . - . - . - . - . - . - . - "preclinical studies" . - "Hazardous Substances Data Bank" . - . - "ontology" . - . - . - . - . - . - "life science" . - "dhowe@zfin.org" . - . - "miRNA Target Prediction at EMBL" . - "https://www.thermofisher.com/antibody/product/$1"^^ . - "MESHC" . - "UK Higher Education Statistics Agency" . - "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."^^ . - . - . - . - "nb2018006591"^^ . - . - "false"^^ . - "myco.marinum" . - . - . - . - . - . - "tgma" . -_:Nde452a2f59d5417986ed5e9498c51a7e "mejino@u.washington.edu" . - . - "earth science" . - "National Uniform Claim Committee Characteristic" . - "false"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/$1_$2" . - . - "ontology" . - . - . - . - . - "https://caninecommons.cancer.gov/#/study/$1"^^ . - . - "Collection of cell lines by Tohoku University. This includes transplantable animal cell lines, such as Yoshida sarcoma and rat ascites hepatoma (AH series) cell lines as well as human, murine cell lines and hybridoma cells."^^ . - "biopragmatics/bioregistry"^^ . - "KC-0979"^^ . - "umbbd.rule" . - . - "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . - "Silvio C.E. Tosatto" . - . - . - . -_:N5bba3595235448e1831c635d87c3b184 "Heinrich Herre" . - . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . - "life science" . - . - "^\\d+$"^^ . - . - . - . - . - "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . - . - . - . - . - . - "ndex" . - . - . - "http://purl.obolibrary.org/obo/HOM_$1"^^ . - . - . - . - "developmental biology" . - "envo" . - . - "CellBank Australia" . - . - . - "phosphosite.protein" . - . - . - "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . - "^\\d{7}$"^^ . - "^[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}$"^^ . - "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."^^ . - . - "Jessica Kissinger" . - "hgnc.genegroup" . - . - "https://scicrunch.org/resolver/RRID:$1"^^ . - "alzgene" . - . - . - . - "^\\w\\d+$"^^ . - . - . - "true"^^ . - . - "viralzone" . - "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"^^ . - . - . - . - . - "protocol" . - . - . - . - . - . - "smid" . - "false"^^ . - "^TTDS\\d+$"^^ . - "genetics" . - . - . - . - "spider" . - "Indications and other conditions in drugbank"^^ . - . - . - . - "NeuroMorpho" . - . - "protein" . - . - . - "flybase" . - . - "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."^^ . - "virology" . - . - . - . - "structure" . - . - . - "Austrian Library Network" . - "gitlab" . - . - . - "http://purl.obolibrary.org/obo/ADO_"^^ . - . - . - "help@emdatabank.org" . - "http://purl.obolibrary.org/obo/COVOC_"^^ . - . - "ncbigi" . - . - . - . - . - . - . - . - . - . - "subject agnostic" . - "European Paediatric Cardiac Codes" . - . - "false"^^ . - . - "Crystallographic Information Framework" . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - "cellopub" . - . - "false"^^ . - "interaction" . - . - . - . - "medicine" . - . - . - "genomics" . - . - . - "http://www.innatedb.ca/getGeneCard.do?id="^^ . - . - . - . - . - . - "hog" . - "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . - . - . - "structure" . - "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"^^ . - . - . - "false"^^ . - "https://phytochem.nal.usda.gov/phytochem/chemicals/show/"^^ . - "aellenhicks@gmail.com" . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/GENO_"^^ . - . - . - "T06648"^^ . - "obo" . - . - . - . - . - . - "saddan"^^ . - . - "true"^^ . - . - . - . - . - "mouse" . - "Mondo Disease Ontology" . - "https://ximbio.com/reagent/$1"^^ . - . - . - "ASKEM Epidemiology Prefixes" . - . - . - "life science" . - "https://www.cancerrxgene.org/translation/Drug/"^^ . - "mauno.vihinen@med.lu.se" . - "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Compound archives chemical structures and records."^^ . - . - "http://purl.obolibrary.org/obo/ONTOAVIDA_"^^ . - . - "small molecule" . - "jonrkarr@gmail.com" . - "^FR\\-FCM\\-\\w{4}$"^^ . - "enzyme" . - "fyler" . - . - "false"^^ . - "uniprot.location" . - . - . - . - "ICARDA - TDv5 - Sept 2018"^^ . - "An ontology to standardize research output of nutritional epidemiologic studies."^^ . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "LG Chemical Entity Detection Dataset (LGCEDe)" . - "obo" . - . - . - . - . - . - . - . - "co_345" . - . - . - "S1"^^ . - . - . - . - . - . - "Antibiotic resistance genes and mutations"^^ . - . - . - . - . - . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - "dna" . - "biosample" . - . - . - . - . - . - "^\\d{6}$"^^ . - "microsporidia" . - . - . - . - "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."^^ . - . - . - "morpheus.lab/morpheus"^^ . - "population genetics" . - "0000728"^^ . - "D00001"^^ . - . - . - . - . - . - . - . - "Database of human Major Histocompatibility Complex" . - . - "http://purl.obolibrary.org/obo/NOMEN_"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Asset Description Metadata Schema Vocabulary" . - "fr" . - "0221"^^ . - . - . - . - "http://purl.obolibrary.org/obo/HABRONATTUS_"^^ . - . - "CATH superfamily" . - "biomedical science" . - . - "^\\d+$"^^ . - . - . - "InterLex is a dynamic lexicon, initially built on the foundation of NeuroLex (PMID: 24009581), of biomedical terms and common data elements designed to help improve the way that biomedical scientists communicate about their data, so that information systems can find data more easily and provide more powerful means of integrating data across distributed resources and datasets. InterLex allows for the association of data fields and data values to common data elements and terminologies enabling the crowdsourcing of data-terminology mappings within and across communities. InterLex provides a stable layer on top of the many other existing terminologies, lexicons, ontologies, and common data element collections and provides a set of inter-lexical and inter-data-lexical mappings. "^^ . - . - "taxonomy" . - . - . - "false"^^ . - . - . - . - "immunology" . - . - "http://purl.obolibrary.org/obo/GNO_"^^ . - . - "https://omabrowser.org/oma/hog/HOG:"^^ . - . - . - "An identifier for a resource or metaresource." . -_:N824a8517c4d74a26874edd72d326307f "futo@stanford.edu" . - . - "NCATS Drugs" . - . - . -_:Nb01e8f454a334f6aa890c77212852321 "bioportal" . - "life science" . - . - . - . - . - . - "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . - . - "oct 2016"^^ . - . - "^A\\d{6}$"^^ . - "life science" . - . - "CHEBI"^^ . - "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . - . - "false"^^ . - "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . - "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . - "https://aopwiki.org/relationships/"^^ . - . - . - . - . - . - "dna" . - . - "structural biology" . - . - . - . - . - . - . - . - "reproduceme" . - . - . - . - . - . - . - "false"^^ . - "false"^^ . - "rna" . - . - "false"^^ . - . - "false"^^ . - "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."^^ . - . - "Chris Stoeckert" . - . - . - "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?"^^ . - "https://www.nextprot.org/db/entry/$1"^^ . - . - . - . - . - "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . - "wikidata" . - . - "span" . - "DECIPHER CNV Syndromes" . - . - . - "project management" . - . - . - . - . - . - . - . - "^[0-9X\\-]+$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/FBcv_"^^ . - . - "false"^^ . - . - "mcourtot@gmail.com" . - "false"^^ . - "The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation."^^ . - "genetic material" . - . - . - "sequence" . - . - "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . - "DAP000773"^^ . - . - . - "http://purl.obolibrary.org/obo/OBIB_"^^ . - "https://www.vmh.life/#reaction/"^^ . - . - . - . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . - "Biomedical Informatics Research Network Lexicon" . - . - "The Amphioxus Development and Anatomy Ontology" . - . - . - "false"^^ . - "alayne.cuzick@rothamsted.ac.uk" . - . - . - "^\\d+$"^^ . - "false"^^ . - . - "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . - . - . - . - "hmdb" . - . - . - . - "BirdBase" . - "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . - "false"^^ . - "gramene.ref" . - . - "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."^^ . - . - "gene" . - . - "1174"^^ . - . - "https://cropontology.org/rdf/CO_336:$1"^^ . - . - . - "http://purl.obolibrary.org/obo/OPMI_$1"^^ . - . - . - "ontology" . - . - "demographics" . - . - . - . - . - . - . - "Antony Williams" . - "https://www.proteomicsdb.org/#human/proteinDetails/"^^ . - . - "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . - "456789"^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - "tissue" . - "BTO" . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - "FBbt_root" . - . - . - . - "https://semanticscience.org/resource/CHEMINF_$1" . - "lindsey.anderson@pnnl.gov" . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - . - "false"^^ . - . - "protein" . - . - . - "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . - . - "https://www.ebi.ac.uk/arrayexpress/arrays/"^^ . - "^P\\w+$"^^ . - . - "extraction_set"^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . - . - "sao" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://eds.gene.le.ac.uk/home.php?select_db="^^ . - . - . - "^\\w+$"^^ . - . - "Cooperative Patent Classification" . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - . - . -_:Na7f201c11d94490f8ca52133e1faab3c "Jonathan Bard" . - "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."^^ . - "https://cropontology.org/rdf/CO_356:$1"^^ . - . - "https://panoramaweb.org/$1.url"^^ . - "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."^^ . - . - . - "hölzel" . - . - "taxrank" . - . - . - "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . - . - . - "nextprot" . - "1.10.10.200"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name="^^ . - . - "PKDB00198"^^ . - . - . - . - "L000001"^^ . - "taxid" . - "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - . - "false"^^ . - "277.9"^^ . - . - . - "debio" . - . - . - "ontology" . - . - . - . - "app-d678n-tottori"^^ . - . - "Integrative and Conjugative Element Ontology" . - . - . - . - . - "obo" . - "false"^^ . - "evan@epatters.org" . - . - . - "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - "true"^^ . - . - "false"^^ . - . - "20021"^^ . - . - "rnao" . - . - . - . - . - . - . - . - "classification" . - "data management" . - . - . - "ceph" . - . - "protein" . - . - "false"^^ . - "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . - . - "false"^^ . - "clinical studies" . - "https://www.biorxiv.org/content/10.1101/"^^ . - . - "false"^^ . - "Assembling the Fungal Tree of Life - Taxonomy" . - "UCR00513"^^ . - . - . - . - . - . - . - . - . - . - "nb100-56351"^^ . - "zebrafish" . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . -_:N3a54fd90c5844e92bd4fa6b0242dba3d "helpdesk@cropontology-curationtool.org" . - . - "0000199"^^ . - . - . - . - "orchard@ebi.ac.uk" . - . - "^\\d{3}\\w(\\w|\\d_)\\d{4}X$"^^ . - . - "life science" . - "false"^^ . - . - . - "^[0-9a-zA-Z]{8}$"^^ . - . - "microbial" . - "Bacterial Tyrosine Kinase Database" . - "0000138"^^ . - . - . - "clustering" . - "phenx" . - . - . - . - . - . - . - . - . - . - "https://www.cellbiolabs.com/search?keywords="^^ . - . - . - "pathway" . - . - "PesticideInfo chemical ID" . - . - . - . - . - "false"^^ . - "FDB002100"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . - . - "false"^^ . - . - . - "https://labsyspharm.github.io/lspci/$1"^^ . - "http://birdgenenames.org/cgnc/GeneReport?id="^^ . - . - "systems biology" . - . - . - . - "life science" . - . - . - . - "4000027"^^ . - . - "ontology" . - . - "relationships" . - . - . - . - . - . - . - . - "ModelDB concept" . - . - "false"^^ . - "HS000015122"^^ . - . - . - . - . - "false"^^ . - . - "21552"^^ . - . - . - . - . - "zhu@iastate.edu" . - "P01116"^^ . - . - "https://pubchem.ncbi.nlm.nih.gov/element/"^^ . - "3dmet" . - . - . - . - "8000221"^^ . - "https://uts.nlm.nih.gov/uts/umls/semantic-network/"^^ . - . - "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."^^ . - . - "AC00963334"^^ . - . - "umls.cui" . - . - _:N9e98fa15e62c48f48e2f6b6195f1ae63 . - "http://aber-owl.net" . - . - "Food-Drug interactions automatically extracted from scientific literature"^^ . - . - "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . - . - "pathway" . - . - . - "Pazar Transcription Factor" . - . - . - . - . - . - "false"^^ . - . - . - "6b1"^^ . - "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . - . - . - . - . - "NIHhESC-10-0083"^^ . - . - "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID="^^ . - . - "donny@polyneme.xyz" . - . - "subject agnostic" . - "https://doi.org/"^^ . - . - . - "https://www.uniprot.org/diseases/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/VIDO_"^^ . - . - "phenotype" . - "mirbase.mature" . - . - "ontology" . - "Apple Ontology" . - . - . - . - "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/gtr/conditions/"^^ . - "obo" . - "genomics" . - "life science" . - . - . - . - "2381/12775"^^ . - . - "pathway" . - . - "The MGED Ontology (MO) provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data."^^ . - . - . - . - "https://bioregistry.io/ppdb:"^^ . - . - . - . - "functional genomics" . - . - . - "HBG284870"^^ . - . - . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - "91005"^^ . - "The pattern for identifiers in the given resource" . - "project management" . - . - . - . - . - . - "https://cropontology.org/rdf/CO_326:"^^ . - "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2)."^^ . - . - . - . -_:Ndd7978848d664705a828b97bdf16d069 "pierre.sprumont@unifr.ch" . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "European Registry of Materials" . - . - . - "SitEx" . - "rna" . - "0000062"^^ . - "genome" . - . - "false"^^ . - . - . - . - "AphidBase Transcript" . - "Developing Human Brain Atlas" . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/MIRNAO_"^^ . - "1374"^^ . - "NIF Standard Ontology: Neurolex" . - . - . - . - . - . - "re3data" . - "dsm5" . - . - "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."^^ . - . - . - "01001"^^ . - . - . - . - "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . - . - "PMID" . - . - . - "An ontology of prokaryotic phenotypic and metabolic characters"^^ . - . - "Sebastien Moretti" . - . - . - . - "http://sabiork.h-its.org/newSearch?q=ecnumber:"^^ . - . - "Wasila Dahdul" . - . - "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . - . - "false"^^ . - "^[0-9]{4}$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "Pigeonpea ontology" . - . - "life science" . - "http://purl.obolibrary.org/obo/XPO_"^^ . - . - "1466"^^ . - . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "biomagresbank" . - . - . - . - . - . - "sequence" . - "10153"^^ . - . - . - "obo" . - "biodiversity" . - "false"^^ . - . - "http://www.w3.org/2000/01/rdf-schema#$1"^^ . - . - . - . - "^[\\w\\-.]{3,}$"^^ . - . - . - . - . - . - . - "obo" . - . - . - "mmo" . - "pandey@jhmi.edu" . - "http://hpc-bioinformatics.cineca.it/fusion/cell_line/"^^ . - "SNOMEDCT_US_2020_03_01" . - . - . - . - . - . - . - . - . - . - "Oryzabase Gene" . - "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."^^ . - "assays" . - . - . - . - . - "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource."^^ . - . - . - . - "subject agnostic" . - "bibliometrics" . - "DrugBank Target v4" . - . - . - "small molecule" . - "https://archive.gramene.org/db/ontology/search?id=GR_tax:"^^ . - . - . - . - "LMPR0102010012"^^ . - . - "p3db.protein" . - "DTXSID2021028"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"^^ . - "registry" . - "International repository of Adverse Outcome Pathways."^^ . - "Obstetric and Neonatal Ontology" . - "false"^^ . - "http://purl.obolibrary.org/obo/MC_$1"^^ . - . - "ardb" . - . - . - . - "KEGG Metagenome" . - "^PD\\d{6}$"^^ . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . - . - . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . - . - . - "0000031"^^ . - . - . - . - "190000021540"^^ . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/GENEPIO_"^^ . - . - . - "bdgp.insertion" . - . - . - "00000099"^^ . - . - . - "false"^^ . - "^\\w.+$"^^ . - . - . - "DICOM Controlled Terminology"^^ . - . - . - "NCI2004_11_17" . - "cell biology" . - "HGNC gene symbol" . - . - "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . - . - . - . - . - . - . - "Wheat ontology" . - . - . - . - . - . - . - . - . - . - . - "https://glytoucan.org/Structures/Glycans/$1"^^ . - . - . - "Guide to Pharmacology Ligand" . - . - "0000013"^^ . - . - "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."^^ . - . - . - . - . - . - . - _:N3cc0025ca3d24a2dafbd5de44f56b1e2 . - "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0="^^ . - . - . - . - . - "ZFA description."^^ . - . - . - . - "false"^^ . - "https://rism.online/$1"^^ . - "structure" . - "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . - . - . - "discoverx" . - "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . - "Jennifer C. Giron" . - . - . - . - . - "hoso" . - "Petra Fey" . - "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."^^ . - . - "false"^^ . - "ASPL0000349247"^^ . - . - . - "ontology" . - . - "http://purl.obolibrary.org/obo/AMPHX_"^^ . - . - . - "http://viroligo.okstate.edu/main.php?vid="^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "life science" . - "false"^^ . - . - "gene" . - . - "obo" . - . - "biomedical science" . - "SNOMEDCT_US_2020_09_01" . - . - "Selventa Families" . - . - . - . - . - "http://purl.obolibrary.org/obo/DOID_$1"^^ . - "https://bioregistry.io/skm:"^^ . - "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . - "molecules" . - . - "- 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."^^ . - "K00001"^^ . - "false"^^ . - . - "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . - . - "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . - . - . - . - . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . - "inn" . - . - . - . - . - . - "Ontology for vector surveillance and management" . - . - . - "MIRIAM Legacy Registry Identifier" . - . - . - . - "false"^^ . - . - . - "PseudoGene" . - "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."^^ . - "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)."^^ . - . - "NAD%20biosynthesis"^^ . - . - . - . - . - . - . - . - "database management" . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . - "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . - . - . - . - . - . - . - "^\\d{4}$"^^ . - "false"^^ . - . - . - "personalized medicine" . - . - . - "https://cropontology.org/rdf/CO_326:$1"^^ . - . - . - . - . - "gene" . - "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://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . - . - . - . - . - . - "microbiology" . - . - "agriculture" . - . - "false"^^ . - . - . - "25782"^^ . - "false"^^ . - . - . - "SIDER Drug" . - "genomics" . - "nlx.qual" . - "ontology" . - . - "false"^^ . - . - . - "^\\w{1,3}$"^^ . - . - . - "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . - . - "EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications)."^^ . - . - "Alzheimer Gene Database" . - . - "^\\d{7}$"^^ . - . - "^\\d+$"^^ . - . - . - "627"^^ . - . - . - "false"^^ . - . - . - . - "gene" . - "4DNESWX1J3QU"^^ . - . - . - . - . - "ontology" . - "ontology" . - . - . -_:N61a3d10cbab946e29d82cb3fcd645550 "Julian Seidenberg" . - . - . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . - . - . - . - . - . - "false"^^ . - "false"^^ . - "https://pypi.org/project/$1"^^ . - . - . - . - "60316"^^ . - . - "a.kikhney@embl-hamburg.de" . - . - "panther.pthcmp" . - "PAV is a lightweight ontology for tracking provenance, authorship, and versioning. It specializes the W3C provenance ontology PROV-O in order to describe authorship, curation and digital creation of online resources."^^ . - "uniprot.chain" . - "false"^^ . - "^(Q|P)\\d+$"^^ . - . - . - . - "^\\w+$"^^ . - . - "0000025"^^ . - . - "19333"^^ . - "idr" . - "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . - . - . - . - "data management" . - "ontology" . - "KEGG.COMPOUND" . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - . - "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains."^^ . - "https://athena.ohdsi.org/search-terms/terms/$1"^^ . - . - . - . - "^[SCTAGMNU]\\d+$"^^ . - "VB.Ob.3736.GRSM125"^^ . - "odc.sci" . - "obo" . - . - "nih initiative" . - . - . - "systems biology" . - "GR_QTL" . - "eggNOG" . - "Cellosaurus Registry" . - "biochemistry" . - . - . - . - . - . - . - . - "DrugBank Reaction" . - . - . - . - . - . - . - . - . - "esldb" . - . - . - "https://rrid.site" . - . - . - . - "ccle.cell" . - . - "animal genetics" . - . - "single nucleotide polymorphism" . - . - . - . - . - "ontology" . - . - . - "chemistry" . - . - . - . - . - . - "^MAM\\d{5}\\w$"^^ . - . - . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis="^^ . - . - . - . - . - . - . - . - . - "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . - . - . - "ontology" . - . - "false"^^ . - "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "dashr" . - "false"^^ . - . - "ontology" . - . - . - . - "ctcae" . - "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . - . - . - . - . - "molecular dynamics" . - . - "life science" . - "synthetic biology" . - . - . - . - . - . - . - . - . - "STRING (Search Tool for Retrieval of Interacting Genes/Proteins) is a database of known and predicted protein interactions.\r\nThe interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic Context, High-throughput Experiments,(Conserved) Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable."^^ . - . - . - "anatomy" . - . - . - "anatomy" . - . - "^[0-9]{12}$"^^ . - . - "botany" . - "Eukaryotic Promoter Database" . - . - . - . - "false"^^ . - . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1"^^ . - "^\\w+$"^^ . - "false"^^ . - . - . - . - . - . - _:N29700f95c1bf4501949b0ce8eb8684aa . - . - . - "CA981206459"^^ . - "^\\d+$"^^ . - . - . - "Evan Patterson" . - . - . - "oai:cwi.nl:4725"^^ . - . - . - "sbml.level-3.version-2"^^ . - "Discourse Elements Ontology" . - . - . - . - "10020.2"^^ . - "https://ecocyc.org/gene?id=$1"^^ . - "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . - . - "http://phenol-explorer.eu/foods/"^^ . - . - . - . - . - . - "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . - "bioinformatics" . - . - . - "http://open-services.net/ns/core#"^^ . - "https://www.biocatalogue.org/services/"^^ . - . - . - . - "Jennifer C. Girón" . - . - . - . - . - . - . - "MobiDB is a database of protein disorder and mobility annotations."^^ . - "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data."^^ . - . - . - . - . - "Protein covalent bond" . - "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid="^^ . - . - "biosimulators" . - . - "https://goldbook.iupac.org/terms/view/"^^ . - . - . - "CCDC Number" . - "mass spectrometry" . - . - "genome" . - . - . - "violinnet" . - "European Food Information Resource Network" . - . - "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . - . - . - . - . - . - . - "http://www.bind.ca/Action?identifier=bindid&idsearch="^^ . - . - "^CHEMBL\\d+$"^^ . - "https://pharmacome.github.io/conso/"^^ . - . - . - . - "090701"^^ . - . - "false"^^ . - . - "false"^^ . - "https://omia.org/OMIA$1"^^ . - . - "Software Package Data Exchange License" . - "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?"^^ . - . - . - . - . - . - . - "Funding, Research Administration and Projects Ontology" . - "gene" . - "structure" . - . - "784"^^ . - . - . - . - . - . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . - . - "http://emmo.info/emmo/cif-core#$1"^^ . - . - "046"^^ . - . - . - . - . - "obo" . - . - . - "Geographical Entity Ontology" . - "Horizon Discovery cell line collection" . - "glycomapsdb" . - "biology" . - "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."^^ . - "pmap.substratedb" . - . - "Laboratory of Systems Pharmacology Compound" . - . - "http://purl.org/dc/elements/1.1/"^^ . -_:Nd59148a3af5b498cbb0a2d1ceae31300 "loinc@regenstrief.org" . - . - . - "EUCTR" . - . - . - . - . - "edda" . - "environmental science" . - . - . - . - . - . - . - "gene expression" . - . - . - . - . - . - "biomedical science" . - . - "protein" . - . - . - "4892"^^ . - . - . - "true"^^ . - . - . - . - "biology" . - . - . - "mutation" . - _:N62de8aa2a60e4ff4ab11da60480d7858 . - . - "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."^^ . - . - . - . - . - . - . - . - . - "dentistry" . - . - . - . - . - . - "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . - . - "f.quaglia@ibiom.cnr.it" . - . - "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . - "false"^^ . - . - "0000-0002-5355-2576"^^ . - . - "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."^^ . - . - . - "2023-503698-40-00"^^ . - "shex" . - . - . - "http://purl.obolibrary.org/obo/ICEO_"^^ . - . - . -_:Nd2cf2107dfdb419d94a5e0f3473323b5 "Crop Ontology Helpdesk" . - "151022"^^ . - "101"^^ . - . - . - "false"^^ . - "Identifiers.org Ontology"^^ . - . - "obo" . - . - "false"^^ . - . - . - "https://bioregistry.io/iceberg.ime:"^^ . - . - . - "https://glyconavi.org/hub/?id=$1"^^ . - . - . - "ontology" . - . - "msio" . - "TIGR00010"^^ . - . - "https://www.jax.org/strain/$1"^^ . - "https://www.fao.org/fishery/en/species/$1"^^ . - . - . - "Next Generation Biobanking Ontology" . - . - . - . - "^\\d+$"^^ . - "uniprot.kw" . - . - . - . - . - . - . - "om" . - . - . - . - . - . - . - . - "0010034"^^ . - . - "NLX" . - . - "10015919"^^ . - "ontology" . - . - . - "^\\d+$"^^ . - "https://bioregistry.io/metaregistry/go/"^^ . - . - "biomedical science" . - "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . - . - . - . - . - . - "rfc" . - . - . - "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . - . - "cthoyt@gmail.com" . - . - . - . -_:Nd2da98853435498c95a99ab2d84381d1 "Crop Ontology Helpdesk" . - . - . - "^\\d{7}$"^^ . - . - "http://purl.obolibrary.org/obo/REX_$1"^^ . - "18"^^ . - "^\\d+$"^^ . - . - "https://www.inaturalist.org/observations/$1"^^ . - . - "^\\d{7}$"^^ . - "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . - . - . - "EMLSAT00000003403"^^ . - "^[0-9]+\\.[0-9]+$"^^ . - . - . - . - "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . - "false"^^ . - "AKR"^^ . - . - . - . - . - . - . - . - "knowledge and information systems" . - . - "degradome" . - "NCBI Taxonomy" . - . - "http://purl.org/spar/datacite/$1"^^ . - . - "traditional medicine" . - . - . - "classification" . - . - "dashr@lisanwanglab.org" . - . - . - "AB0"^^ . - "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."^^ . - "S000002493"^^ . - . - . - "MMAR_2462"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . - . - . - "topalis@imbb.forth.gr" . - . - "377550"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FBSP_"^^ . - . - . - "false"^^ . - . - . - "HsapDv" . - "https://cropontology.org/rdf/CO_370:$1"^^ . - . - "false"^^ . - . - . - . - "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . - "NIFSTD is a base namespace (like obo:) which houses many other prefixes. Sometimes NIFSTD prefixed identifiers appear undifferentiated, but usually if it shows up it means that another prefix definition is missing when serializing."^^ . - . - "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . - "false"^^ . - . - . - . - . - "gmelin" . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])|([0-9][A-Za-z0-9]{3})$"^^ . - . - "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . - "BCRTi001-A"^^ . - . - . - . - . - . - . - . - "https://flybase.org/reports/FBtc$1"^^ . - . - . - . - "kegg.enzyme" . - . - . - "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId="^^ . - . - . - . - "Lindsay.Cowell@utsouthwestern.edu" . - . - . - "mutation" . - . - "agriculture" . - "ped.ensemble" . - . - . - . - . - . - . - "https://cropontology.org/rdf/CO_322:"^^ . - "imaging" . - "^\\w\\d+$"^^ . - . - "STOREDB at University of Cambridge" . -_:Nd59148a3af5b498cbb0a2d1ceae31300 "LOINC Support" . - . - "http://www.ymdb.ca/compounds/"^^ . - . - "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . - "https://www.diseasesdatabase.com/ddb$1.htm"^^ . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - "Encyclopedia of Life" . - . - "^\\d+\\w?$"^^ . - . - "false"^^ . - . - "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." . - . - . - . - "monique.zahn@sib.swiss" . - "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . - . - . - . - . - "00000000"^^ . - . - . - "SNOMEDCT_US_2019_09_01" . - . - "Philip Strömert" . - "bioinformatics" . - "rtecs" . - . - . - . - "^[A-Z-_0-9]+$"^^ . - "051"^^ . - "ddanat" . - . - . - . - . - . - . - "Michael Riffle" . - . - . - . - . - "^[1-9][0-9]{3,6}$"^^ . - . - "lipro" . - "MAO:0000061"^^ . - "^PPR\\d+$"^^ . - "2005080"^^ . - . - "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . - . - . - "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . - . - . - "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . - "Software ontology" . - . - . - . - . - "ontology and terminology" . - "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)"^^ . - . - "Human developmental anatomy, timed version" . - "scr" . - . - "26753"^^ . - . - "baeverma@jcvi.org" . - . - "ontology" . - . - "BioSchemas" . - . - . - . - . - "Egon Willighagen" . - "ontology and terminology" . - "http://purl.obolibrary.org/obo/PO_$1"^^ . - . - . - "pr" . - . - . - . - . - . - "false"^^ . - "MCDS_S_0000000001"^^ . - . - . - . - "biomedical science" . - "https://massbank.jp/RecordDisplay?id=$1"^^ . - . - . - . - "interaction" . - "^\\d+$"^^ . - "http://biocyc.org/getid?id="^^ . - . - . - "taxonomy" . - . - . - . - "^PWY\\w{2}\\-\\d{3}$"^^ . - "http://data.crossref.org/fundingdata/funder/10.13039/"^^ . - "Codon Usage Tabulated from GenBank" . - . - "biomedical science" . - . - "Mammalian Phenotype Ontology" . - "tair.protein" . - "obo" . - "gene expression" . - . - . - . - "false"^^ . - . - . - . - "YAL001C"^^ . - . - . - "^\\d+$"^^ . - "infectious disease medicine" . - . - . - "PMC" . - "090201"^^ . - . - . - . - "^\\d+$"^^ . - . - "Food Classification and Description System" . - . - . - "npo" . - . - "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . - . - . - . - . - . - "false"^^ . - "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . - . - . - . - . - "obo" . - "glycomics" . - . - . - . - . - . - "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . - "structure" . -_:Na59b29921d6c49bc83dc307084549278 "Usha Mahadevan" . - "KEGG Module" . - "biomedical science" . - . - "http://sweetontology.net/matrMineral/$1"^^ . - "developmental biology" . - "Affymetrix Probeset" . - "classyfire" . - . - . - "false"^^ . - "^[0-9]{15}[0-9X]{1}$"^^ . - "4779"^^ . - . - "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam="^^ . - . - . - "^\\d+$"^^ . - "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"^^ . - "HIT000195363"^^ . - . - "http://purl.obolibrary.org/obo/GEO_"^^ . - "Document Components Ontology" . - "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum="^^ . - . - "ontology" . - . - . - "RC00001"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "biomedical science" . - . - . - . - . - . - . - "STUDY1040"^^ . - . - "OMOP" . - . - . - . - "0000095"^^ . - "co_326" . - . - _:Nf02a9133fb1b401fb2f49f9946084afa . - . - . - . - . - "elvira@imbb.forth.gr" . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . - . - . - "true"^^ . - . - . - . - "1398574"^^ . - "http://www.dpvweb.net/dpv/showdpv.php?dpvno="^^ . - . - . - "Handle" . - . - . - . - . - . - . - "earth science" . - . - . - . - . - "FlyBase Qualifiers" . - . - "systems biology" . - . - . - . - "Bill Hogan" . - "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . - . - . - "Terry.Hayamizu@jax.org" . - "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . - . - . - . - . - . - . - "itiswebmaster@itis.gov" . - "^[0-9a-z]{24,24}$"^^ . - . - "oryzabase.reference" . - . - "biolegend" . - . - "ontology" . - "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 smegmatis information."^^ . - "marine ecology" . - "burkesquires@gmail.com" . - . - . - "obo" . - . - "https://fairsharing.org/" . - . - . - . - . - . - "OrthoDB" . - "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"^^ . - . - . - . - "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . - "^\\d+$"^^ . - . - . - "ontology" . - . - . - "70"^^ . - "1484"^^ . - . - "obo" . - . - . - "HMS-LINCS" . - "ukprns" . - . - . - . - "^WB[A-Z][a-z]+\\d+$"^^ . - . - "epigenetics" . - . - "Study inside StoreDB"^^ . - "9001411"^^ . - . - . - . - . - "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . - . - "environmental science" . - . - "openalex" . - . - . - "http://en.wikipedia.org/wiki/"^^ . - "iECABU_c1320"^^ . - "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG)."^^ . - "SNHG3"^^ . - . - . - "MultiCellDS" . - "^NX_\\w+$"^^ . - "ubio.namebank" . - . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . - . - "1000290"^^ . - "botany" . - . - "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."^^ . - . - . - "pigqtldb" . - . - "biro" . - "life science" . - "ccrid" . - "https://bioregistry.io/treebase:"^^ . - . - "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID="^^ . - . - . - . - "linkml" . - . - . - "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . - . - "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . - . - . - . - . - "false"^^ . - "http://csbl.bmb.uga.edu/DOOR/operon.php?id="^^ . - . - . - . - "UniProt Cross-ref database" . - "true"^^ . - . - . - . - "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."^^ . - . - "janna.hastings@gmail.com" . - "proteomics" . - . - . - . - . - . - . - . - "http://www.w3.org/2001/XMLSchema#$1"^^ . - "false"^^ . - . - "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . - . - "2.7.1.1"^^ . - . - "https://www.kazusa.or.jp/rouge/gfpage/"^^ . - "mathematics" . - . - _:N5ee7902ef2b64c548828599daaf0d737 . - . - . - . - . - "http://func.mshri.on.ca/fly/genes/list_functional_scores/"^^ . - "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . - . - . - . - . - "ontology" . - . - "Progenetix" . - . - "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."^^ . - . - "epidemiology" . - . - . - . - "INN_ID" . - . - . - "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . - "false"^^ . - . - "metatlas.reaction" . - "life science" . - "http://www.pathwaycommons.org/pc/record2.do?id="^^ . - . - . - . - . - . - . - "Steven E. Wilson" . - "Database of Quantitative Cellular Signaling: Pathway" . - . - "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . - "USA National Service Center Number" . - . - "^NCT\\d{8}$"^^ . - . - . - . - "NCBITaxonomyID" . - "http://purl.org/vocab/frbr/core#"^^ . - . - "Troy Pells" . - "biomedical science" . - "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . - "M94112"^^ . - "PM0012345"^^ . - . - "0000038"^^ . - "http://bioportal.bioontology.org/ontologies/"^^ . - . - . - "dna" . - . - . - "A Systematic Annotation Package for Community Analysis of Genomes" . - . - . - . - . - "sepio" . - "15000"^^ . - "dg.4503" . - . - "identifiers.namespace" . - . - . - . - "subject agnostic" . - "obo" . - . - . - . - . - "53504"^^ . - . - . - "taxonomy" . -_:N9aafcf7456c84e55b289f755161257e1 "yingqin@rti.org" . - . - "Michael Witt" . - . - . - . - "gnpis" . - . - . - "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . - "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . - _:N1ee708fba9894af0bfe9c04bade98c46 . - "life science" . - . - . - . - . - . - . - "false"^^ . - . - "world2dpage" . - . - . - . - . - . - . - "SECONDARY_CAS_RN" . - . - . - "chemical in the database supplied by Pesticide Action Network North America"^^ . - . - "false"^^ . - "ChEMBL" . - "computational biology" . - . - "Yam ontology" . - "true"^^ . - . - . - . - . - "Sigma Aldrich" . - . - . - "https://repo.napdi.org/study/"^^ . - "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . - "interaction" . - . - . - "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . - "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."^^ . - . - . - . - . - "Morpheus model repository" . - "Models developed with the Virtual Cell (VCell) software prorgam."^^ . - . - "27267"^^ . - . - . - "metabolomics" . - . - . - . - "Call for paper topics in EasyChair"^^ . - . - . - . - "taxonomy" . - . - . - . - . - "Rice Metabolic Pathways" . - "https://w3id.org/babelon/$1"^^ . - "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . - "ctd.gene" . - "https://biofactoid.org/document/$1"^^ . - "DragonDB Protein" . - "life science" . - . - . - . - . - "genome" . - . - . - . - . - . - "pathway" . - . - "^LGCEDe-S-\\d{9}$"^^ . - . - "Circular double stranded DNA sequences composed" . - . - "derivatives%2Fthiocyclam%20hydrochloride"^^ . - . - "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . - . - . - "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."^^ . - "skip" . - . - "mw.project" . - . - "https://www.uniprot.org/proteomes/"^^ . - . - "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+"^^ . - . - . - "genetics" . - . - "^[\\w\\d\\.-]*$"^^ . - . - "Don Gilbert" . - . - . - . - . - . - "enzyme" . - "UP" . - . - . - . - . - "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . - "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . - . - "false"^^ . - "glytoucan" . - . - "false"^^ . - . - "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . - . - . - . - . - . - . - . - . - "GrassBase provides an interactive guide to nomenclature for the whole grass family. It provides lists of over 60,000 names for any given genus, geographical region or genus within a geographical region, helps find the accepted name, synonyms and distribution for any given name, and gives a desription for each species."^^ . - . - . - . - . - "Nicolas Matentzoglu" . - . - "classification" . - . - "William Hayes" . - . - . - . - . - . - . - . - "false"^^ . - . - "CTX" . - "^\\d{7}$"^^ . - . - . - . - . - "pathguide" . - . - . - . - . - . - . - . - . - "virsirna" . - . - . - . - "false"^^ . - . - "BT20_BREAST"^^ . - . - "https://www.ebi.ac.uk/chembl/compound/inspect/"^^ . - . - . - . - "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.kazusa.or.jp/rouge/gfpage/$1"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - "http://purl.bioontology.org/ontology/CSP/"^^ . - "false"^^ . - . - "RL3R1_HUMAN"^^ . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - "idot" . - . - . - "allyson.lister@oerc.ox.ac.uk" . - . - "false"^^ . - . - . - . - "https://pharmacodb.ca/tissues/"^^ . - . - "biology" . - . - "http://www.probonto.org/ontology#PROB_"^^ . - . - . - . - "re3data" . - "molecule" . - "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons."^^ . - . - . - . - "ENSG00000136147"^^ . - . - . - "http://purl.obolibrary.org/obo/TXPO_$1"^^ . - . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - "https://bartoc.org/en/node/$1" . - . - . - . - . - . - . - . - "^CPX-[0-9]+$"^^ . - . - "Zebrafish Phenotype Ontology" . - "false"^^ . - . - "database" . - "anatomy" . - "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . - . - . - . - . - "phosphopoint.protein" . - . - . - "true"^^ . - "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_"^^ . - . - . - "cpt" . - . - "ontology" . - "GE86325"^^ . - "biomedical science" . - "Ontology of Microbial Phenotypes" . - "bioinformatics" . - "ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "multicellds" . - . - . - . - . - . - . - "^\\d{6,7}$"^^ . - . - . - . - "false"^^ . - "subject agnostic" . - "^CHEMBL\\d+$"^^ . - . - . - . - . - "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln="^^ . - . - "MESH_DESCRIPTOR_UI" . - "false"^^ . - . - "https://bioregistry.io/geonames.feature:"^^ . - . - "mgnify.analysis" . - . - . - . - . - "interaction" . - . - "Animal natural history and life history" . - . - "https://data.terra.bio/ga4gh/drs/v1/objects/$1"^^ . - "classification" . - . - "SMID-DB" . - . - . - "Catalog of purchasable reagents and building blocks"^^ . - . - . - "https://biopragmatics.github.io/providers/pba/"^^ . - . - "E. coli Metabolite Database" . - . - "dragondb.protein" . - . - "false"^^ . - "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/ZFA_$1"^^ . - . - . - . - "dbg2introns" . - "Cell Version Control Repository" . - . - . - . - . - . - "oryzabase.mutant" . - "P3DB Protein" . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - "The YEast Intron Database (version 4.3) contains information on the spliceosomal introns of the yeast Saccharomyces cerevisiae. It includes expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors. The data are displayed on each intron page. This is an updated version of the previous dataset, which can be accessed through [MIR:00000460]."^^ . - . - . - . - "UMLS_ICD9CM_2005_AUI" . - . - "false"^^ . - . - . - "LL379-9"^^ . - "earth science" . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "life science" . - . - . - "Loggerhead nesting" . - "^\\d+$"^^ . - . - . - "https://labsyspharm.github.io/lspci/"^^ . - "http://www.kegg.jp/entry/"^^ . - . - . - "hypercldb" . - . - . - . - "http://purl.enanomapper.org/onto/ENM_"^^ . - "REFSEQ_PROT" . - . - "NIF Gross Anatomy" . - "obo" . - . - . - "false"^^ . - . - . - "anatomy" . - . - "scopus" . - . - . - . - "MRA-253"^^ . - . - "life science" . - . - "0000198"^^ . - . - . - "46977"^^ . - "mosaic" . - . - . - "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . - "true"^^ . - "PTM-0450"^^ . - . - "false"^^ . - "false"^^ . - "fypo" . - "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted."^^ . - "signaling-gateway" . - "luana.licata@gmail.com" . - "phipo" . - . - . - "eropmoscow" . - . - . - . - . - . - . - "CAA71118.1"^^ . - . - "Gene Normal Tissue Expression" . - . - . - " http://edamontology.org" . - . - . - . - "hms.lincs.cell" . - . - . - . - "https://bioregistry.io/mirex:"^^ . - "fluticasone"^^ . - . - . - "Regulation of Gene Expression"^^ . - "ATTC" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org)."^^ . - . - "false"^^ . - "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "human genetics" . - . - . - . - . - "http://zfin.org/$1"^^ . - . - . - . - . - "Mathias Uhlen" . - "https://pubchem.ncbi.nlm.nih.gov/bioassay/"^^ . - "Woody Plant Ontology ontology" . - "PK-DB an open database for pharmacokinetics information from clinical trials as well as pre-clinical research. The focus of PK-DB is to provide high-quality pharmacokinetics data enriched with the required meta-information for computational modeling and data integration. "^^ . - . - . - . - "false"^^ . - . - "PGOHUM00000289843"^^ . - . - . - "mKIAA4200"^^ . - . - "MINID Test" . - . - "uniprot/swiss-prot" . - "health science" . - "false"^^ . - "EcoCyc" . - . - . - . - . - "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . - "https://www.ebi.ac.uk/ena/data/view/"^^ . - . - "protein" . - . - . - . - . - . - . - . - "https://cls.shop/"^^ . - . - . - . - . - . - . - . - . - . - . - "Uberon" . - . - "^ITMCTR\\d+$"^^ . - . - . - . - "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . - . - "https://assets.nemoarchive.org/$1"^^ . - "Oryza Tag Line" . - . - . - . - . - . - "coconut" . - . - "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . - . - . - . - . - "http://igsn.org/"^^ . - . - . - . - "repec" . - . - "cells" . - "UniPathway Reaction" . - . - . - . - . - . - . - . - . - . - "obo" . - "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."^^ . - "https://www.ncbi.nlm.nih.gov/genome/"^^ . - . - . - . - . - . - "ark" . - . - . - "PubChem CID" . - . - . - . - . - "Ali Syed" . - . - . - . - "Scientific Event Ontology" . - . - . - . - "http://www.ifomis.org/bfo/1.1/snap#$1"^^ . - . - "psdo" . - "false"^^ . - "^\\d{7}$"^^ . - . - "false"^^ . - "00000021"^^ . - . - . - . - "0000685"^^ . - "https://www.sharkipedia.org/traits/"^^ . - . - "SL-0002"^^ . - "Genetic Code" . - "NCI" . - . - . - . - . - . - "https://www.internationalgenome.org/data-portal/sample/"^^ . - "https://www.langual.org/langual_thesaurus.asp?termid="^^ . - . - . - . - . - "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"^^ . - "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . - . - . - . - "controlled vocabularies" . - . - "KEGG LIGAND" . - . - . - . - . - . - "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . - "37"^^ . - . - . - "http://www.geneontology.org/formats/oboInOwl#$1"^^ . - . - . - "Resource" . - . - . - "phenomics" . - . - "https://www.ebi.ac.uk/ols4/ontologies/$1" . - . - . - . - . - . - . - "anatomy" . - . - . - . - . - . - . - . - "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."^^ . - "NCBI Registry" . - . - "PXD000440"^^ . - "Brassica ontology" . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "Philipp.Bucher@sib.swiss" . - . - "reaxys" . - . - "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . - . - "biology" . - "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="^^ . - "false"^^ . - "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "^[EL]D[SG]-\\d+$"^^ . - "rna" . - . - . - "http://ctdbase.org/detail.go?type=chem&acc="^^ . - . - "http://func.mshri.on.ca/mouse/genes/list_functional_scores/"^^ . - . - "pubchem.cell" . - . - "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."^^ . - . - "hammer"^^ . - . - . - . - . - . - "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 structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . - "aeon" . - . - "omiabis" . - "^A[A-Z]+\\d+$"^^ . - "peco" . - "false"^^ . - "http://purl.obolibrary.org/obo/OlatDv_$1"^^ . - "DASHR expression" . - "https://bacteria.ensembl.org/id/"^^ . - . - "data governance" . - "NodeShape"^^ . - "ontology" . - "false"^^ . - . - "oma.hog" . - . - . - "http://www.conoserver.org/?page=card&table=protein&id="^^ . - . - . - "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . - . - . - . - . - "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . - "structrual bioinformatics" . - . - "j.detras@cgiar.org" . - "https://mediadive.dsmz.de/solutions/$1"^^ . - . - . - . - . - "http://www.whocc.no/atc_ddd_index/?code="^^ . - . - . - . - . - . -_:N640b18da69e24f0fb18c32598a428ad3 "bert.van.nuffelen@tenforce.com" . - . - . - . - . - . - . - . - . - "The ECMDB is an expertly curated database containing extensive metabolomic data and metabolic pathway diagrams about Escherichia coli (strain K12, MG1655). This database includes significant quantities of “original” data compiled by members of the Wishart laboratory as well as additional material derived from hundreds of textbooks, scientific journals, metabolic reconstructions and other electronic databases. Each metabolite is linked to more than 100 data fields describing the compound, its ontology, physical properties, reactions, pathways, references, external links and associated proteins or enzymes."^^ . - "ARP-1513"^^ . - . - "casspc" . - "obo" . - . - . - . - . - . - . - "0000639"^^ . - "ontology" . - . - . - "ontology" . - . - "life science" . - . - . - "Information for ligand groups (chemical classes)."^^ . - . - . - . - . - . - . - . - "data integration" . - . - . - "^[A-Z_a-z]+$"^^ . - . - . - "false"^^ . -_:N805816e4756c44619cdb57e0f012fd3c "Rafael Gonçalves" . - . - . - "0110974"^^ . - "http://scipion.i2pc.es/ontology/CRYOEM_$1"^^ . - . - . - . - . - . - . - . - . - . - . - "4005"^^ . - "Rfam database of RNA families" . - . - . - "unpd" . - "^\\d+$"^^ . - "false"^^ . - . - . - . - "protein" . - "ontology" . - . - "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan."^^ . - . - . - . - . - "liumeng94@sjtu.edu.cn" . - "http://purl.obolibrary.org/obo/RXNO_"^^ . - . - "Cell line collections (Providers)"^^ . - "ontology" . - . - "symp" . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . - . - "genetics" . - "protein" . - "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . - "pseudogene" . - "subject agnostic" . - _:Ndd7978848d664705a828b97bdf16d069 . - "Curated Drug-Drug Interactions Database - Interaction" . - "SPU_000001"^^ . - . - . - . - "ontology" . - "http://purl.obolibrary.org/obo/MFO_$1"^^ . - "Clinical Trials Ontology" . - . - . - "peptideatlas" . - . - . - "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."^^ . - "mirEX" . - . - . - . - . - . - . - "ligea" . - "biology" . - . - . - . - . - "https://e-cyanobacterium.org/bcs/rule/"^^ . - . - "omics" . - . - . - . - . - . - "http://www.genomesize.com/result_species.php?id=$1"^^ . - . - "Lutz Fischer" . - "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . - "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . - "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."^^ . - "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . - . - . - . - . - "biomedical science" . - "Search Tool for Interactions of Chemicals" . - . - . - . - . - . - "Conserved Domain Database at NCBI" . - "http://purl.obolibrary.org/obo/OBA_$1"^^ . - . - . - "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."^^ . - . - . - . - "https://www.uniprot.org/arba/"^^ . -_:Ne79eba7c8d2944bba4b664305e5179ca "maria.herrero@kcl.ac.uk" . - . - "functional genomics" . - . - . - . - "bioinformatics" . - "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."^^ . - . - "http://purl.uniprot.org/annotation/"^^ . - "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . - "molecules" . - "^[A-Z0-9]{4}$"^^ . - . - "nsv3875336"^^ . - . - . - "https://bioregistry.io/abs:"^^ . - . - . - "micro" . - . - "false"^^ . - . - . - . - . - . - . - . - . - "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . - . - . - . - . - "jupp@ebi.ac.uk" . - "1664"^^ . - . - . - "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F"^^ . - "false"^^ . - "has responsible" . - . - "LOC_Os01g49190"^^ . - . - "^\\d{7}$"^^ . - "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:"^^ . - . - . - . - "epidemiology" . - . - "protein" . - "rs11603840"^^ . - . - . - "urn:nbn:fi:tkk-004781"^^ . - . - "http://purl.obolibrary.org/obo/CDAO_"^^ . - . - "biology" . - . - "PhosphoSite Protein" . - . - . - "life sciences" . - . - . - "cell biology" . - "false"^^ . - . - "Sorghum ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - "Selventa legacy disease namespace used with the Biological Expression Language"^^ . - "rex" . - "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1"^^ . - "Foundational Model of Anatomy" . - . - "ontology" . - "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid="^^ . - "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "botany" . - . - . - "C138986"^^ . - . - "URS0000759CF4"^^ . - . - "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."^^ . - . - "chemistry" . - "OMA HOGs" . - "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."^^ . - "classification" . - "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . - . - . - "^[A-Za-z0-9\\-\\_]+$"^^ . - "person" . - "false"^^ . - . - . - . - "false"^^ . - "March 2017 version "^^ . - . - . - . - . - "ontology" . - "48439"^^ . - "284196006"^^ . - . - . - . - . - . - . - "^[dp]\\.[a-z0-9]{8}$"^^ . - "GM17027"^^ . - . - . - "comparative genomics" . - . - "daniel.gautheret@u-psud.fr" . - . - "life science" . - . - . - "life science" . - . - "^[a-z_A-Z]+$"^^ . - . - "http://purl.obolibrary.org/obo/ZECO_$1"^^ . - "http://purl.obolibrary.org/obo/ORNASEQ_"^^ . - . - "false"^^ . - "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."^^ . - "ICEberg integrative and mobilizable element" . - . - . - "Database of biopesticides maintained by the University of Hertfordshire "^^ . - "75121530"^^ . - . - "true"^^ . - . - . - "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."^^ . - "https://www.ndexbio.org/viewer/networks/$1"^^ . - "life science" . - "AGRICOLA_ID" . - . - . - . - . - . - . - . - "life science" . - "fly" . - "http://purl.obolibrary.org/obo/OMP_$1"^^ . - "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="^^ . - . - . - . - "http://jcggdb.jp/idb/jcggdb/"^^ . - "200282"^^ . - . - "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . - . - . - . - . - . - . - "PR00001"^^ . - . - . - "life science" . - . - . - . - . - . - "rxn00001"^^ . - . - . - "0000019"^^ . - . - . - . - . - "tair.locus" . - . - "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . - . - . - "false"^^ . - "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id="^^ . - . - . - "disprot.region" . - "social and behavioural science" . - . - "muamith@utmb.edu" . - . - . - . - "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."^^ . - . - "Yeast Metabolome Database" . - . - . - . - . - . - "faseb list" . - . - . - . - . - . - "SYMP" . - . - "FooDB Food" . - "0000008"^^ . - "NCIt" . - "KEGG-path" . - . - "wd" . - . - "0000509"^^ . - "PASS01237"^^ . - "https://cropontology.org/rdf/CO_339:$1"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "SIGNOR" . - "https://plants.ensembl.org/id/$1"^^ . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/HOM_"^^ . - . - "^\\d{7}$"^^ . - "life science" . - . - . - "QJ51RV02"^^ . - "https://scicrunch.org/resolver/RRID:NXR_$1"^^ . - "false"^^ . - . - . - . - "A nomenclatural ontology for biological names" . - . - . - "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."^^ . - "false"^^ . - . - . - . - "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"^^ . - . - "virology" . - . - "http://jcggdb.jp/idb/jcggdb/$1"^^ . - "genome" . - . - . - "obo" . - "taxonomy" . - . - "0000712_1"^^ . - . - "https://aopwiki.org/stressors/"^^ . - . - "animal" . - . - . - . - . -_:Nef1e0f2fdfb6453f867b6dc3d6aad05d "helpdesk@cropontology-curationtool.org" . - . - . - "nextdb" . - "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."^^ . - "MMP3312982.2"^^ . - . - . - . - "http://purl.obolibrary.org/obo/TGMA_$1"^^ . - . - "false"^^ . - . - . - . - "https://sciflection.com/"^^ . - "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."^^ . - "http://purl.uniprot.org/annotation/VAR_$1"^^ . - "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . - . - "caps" . - "http://purl.obolibrary.org/obo/OBA_"^^ . - . - . - . - . - . - "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . - "Amos Bairoch" . - . - . - . - "http://purl.obolibrary.org/obo/AISM_$1"^^ . - . - "http://purl.dataone.org/odo/SENSO_"^^ . - . - . - "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."^^ . - . - "agriculture" . - . - . - . - . - . - . - "https://www.gtexportal.org/home/gene/"^^ . - . - . - "molecular biology" . - . - . - . - "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"^^ . - . - . - . - "false"^^ . - . - "pain medicine" . - . - "ontology" . - . - . - . - . - . - "https://cropontology.org/rdf/CO_345:$1"^^ . - "Christophe Dunand" . - "ettensohn@cmu.edu" . - . - "false"^^ . - "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC."^^ . - "false"^^ . - . - "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type"^^ . - "true"^^ . - . - . - . - "bibliometrics" . - . - . - . - "174"^^ . - . - "^001\\d{5}$"^^ . - . - "goeco" . - . - . - "false"^^ . - . - . - "Immune Epitope Database" . - . - . - . - "^\\d{7}$"^^ . - . - . - "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID="^^ . - . - "vdrc" . - "life science" . - . - . - "sgd" . - . - "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid="^^ . - "false"^^ . - . - "^[A-Za-z0-9]+$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "300165/p13898_2106T"^^ . - . - "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . - . - . - "Terminologia Embryologica" . - "sider.drug" . - "sabiork.reaction" . - . - . - "LGCEDe-S-000002244"^^ . - . - . - . - . - . - "Association-Rule-Based Annotator" . - . - "bigg.compartment" . - . - "Environment Ontology" . - . - . -_:N62de8aa2a60e4ff4ab11da60480d7858 "First DataBank Customer Support" . - "An anatomical and developmental ontology for cephalopods"^^ . - "ontology" . - "ontology" . - "diapriid@gmail.com" . - . - "NeuronDB" . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - . - . - . - "https://drs.microbiomedata.org/objects/$1"^^ . - . - "bfo" . - . - "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1"^^ . - "xuo" . - "true"^^ . - "http://www.alzgene.org/geneoverview.asp?geneid="^^ . - . - . - "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:"^^ . - . - . - . - . - . - . - . - . - "niaid.chemdb" . - . - . - . - . - . - . - "mim.ps" . - . - . - . - . - "^\\d+$"^^ . - . - . - "CGNC" . - . - . - . - "International Classification of Diseases for Oncology" . - "protein" . - . - "CLPUB00496"^^ . - "confident.series" . - . - . - "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea."^^ . - "developmental biology" . - "genomics" . - . - "^(T0\\d+|\\w{3,5})$"^^ . - "A language for validating RDF graphs against a set of conditions"^^ . - . - . - . - "^\\d+$"^^ . - "ontology" . - . - "https://vcell.org/biomodel-$1"^^ . - "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . - "Higher-level classifications of COG Pathways"^^ . - . - "caloha" . - . - . - "CHEMBL465070"^^ . - "4900"^^ . - "life science" . - . - "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$"^^ . - "https://biopragmatics.github.io/providers/schem/"^^ . - . - . - "IntAct protein interaction database" . - . - . - "cabri" . - "ontology" . - . - "NIF Dysfunction" . - . - . - "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . - "MNEST029358"^^ . - "false"^^ . - "yeastintron" . - . - "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . - "Open Researcher and Contributor" . - . - "G00054MO"^^ . - . - . - . - "dce" . - . - . - . - "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."^^ . - . - . - . - "Radiomics Ontology" . - "false"^^ . - . - . - . - . - . - . - . - . - "Online Mendelian Inheritance in Man" . - . - . - . - . - "structure" . - . - "FAIR* Reviews Ontology" . - . - . - . - "Cell Line Database" . - . - . - . - . - . - "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . - "http://n2t.net/ark:$1"^^ . - . - . - . - . - "false"^^ . - "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - . - . - . - . - . - . - . - "ZDB-GENE-041118-11"^^ . - . - "bibliometrics" . - . - "https://reaxys.emolecules.com/cgi-bin/more?vid="^^ . - . - . - "lbctr" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/AAO_$1"^^ . - "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections."^^ . - "structure" . - "life science" . - "Polbase is a database of DNA polymerases providing information on polymerase protein sequence, target DNA sequence, enzyme structure, sequence mutations and details on polymerase activity."^^ . - . - "EHDAA:2185"^^ . - . - "metabolites" . - "Viral Bioinformatics Resource Center" . - . - . - "biology" . - "cell line" . - . - . - . - . - . - "http://www.tcdb.org/search/result.php?tc="^^ . - . - . - . - . - . - "obo" . - . - . - . - "life science" . - "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots."^^ . - . - "ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with Microarray Gene Expression Data (MGED) recommendations.This collection references the specific platforms used in the generation of experimental results."^^ . - . - "co_350" . - "Human Ancestry Ontology" . - . - "environmental science" . - . - "true"^^ . - . - . - "gene" . - . - "Pierre-Alain Binz" . - "^(5?)\\d{7}$"^^ . - . - . - "nlx.cell" . - . - "SNOMEDCT_US_2021_03_01" . - . - . - . - . - . - . - . - "chemical" . - "echobase" . - . - . - . - "false"^^ . - "PjrpzUIAAAAJ"^^ . - . - . - . - . - . - "http://www.w3.org/ns/shex#$1"^^ . - . - "biolink" . - "ucas" . - . - "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . - . - . - "https://www.ebi.ac.uk/pride/archive/projects/"^^ . - . - . - "chemistry" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "PIRSF000100"^^ . - . - "https://civicdb.org/links/assertions/"^^ . - "RO_proposed_relation" . - . - . - "NITE Biological Research Center (NBRC) provides a collection of microbial resources, performing taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. A catalogue is maintained which states strain nomenclature, synonyms, and culture and sequence information."^^ . - . - . - . - "biomedical science" . - . - . - . - "oharb@pcbi.upenn.edu" . - . - . - "http://sabiork.h-its.org/reacdetails.jsp?reactid="^^ . - . - "NIF Standard Ontology: Brain Regions" . - . - "relations" . - . - "00000098"^^ . - "^\\d{7}$"^^ . - . - "http://purl.obolibrary.org/obo/ZFS_"^^ . - "false"^^ . - . - "20090303"^^ . - . - . - "^\\d+$"^^ . - "http://purl.obolibrary.org/obo/CL_$1"^^ . - "FunderRegistry" . - . - . - "false"^^ . - . - . - "omim" . - "3000045"^^ . - . - . - "Genatlas" . - . - "http://purl.obolibrary.org/obo/CHEMINF_"^^ . - "Ontology Lookup Service" . - . - . - . - . - "0007133"^^ . - . - "apaonto" . - . - . - "false"^^ . - "rxnorm" . - . - "^bkc[0-9]*$"^^ . - . - "Physical Medicine and Rehabilitation" . - "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . - . - "subject" . - . - "^\\w+$"^^ . - . - "true"^^ . - . - "Cell line databases/resources"^^ . - . - . - "false"^^ . - "inchikey" . - "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."^^ . - . - . - "blast" . - "r3d100014165" . - "biostudies" . - . - "GL50803_102438"^^ . - . - . - . - "0000504"^^ . - "mesh.2012" . - "pathway" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . - . - "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . - . - "subject agnostic" . - "PubMed" . - "text mining" . - . - . - . - "gene" . - . - . - . - "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . - "dsmz" . - . - "false"^^ . - . - "iso15926" . - "tropicalis" . - . - . - . - . - . - . - . - "E-cyanobacterium Experimental Data" . - "Tohoku University cell line catalog" . - . - "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . - "PA447218"^^ . - "false"^^ . - "T039"^^ . - "false"^^ . - "https://bioregistry.io/metaregistry/"^^ . - . - "FR-FCM-ZYGW"^^ . - . - . - . - . - "http://edamontology.org/format_"^^ . - . - "^\\d{7}$"^^ . - "knowledge graph" . - "icdo" . - "^\\d{7}$"^^ . - . - "hydrogeology" . - . - . - . - . - "MultiCellDS Digital snapshot" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PR_"^^ . - . - "^\\d{7}$"^^ . - . - . - "Population and Community Ontology" . - "unite" . - . - . - . - . - . - . - "false"^^ . - "classification" . - . - . - . - "https://bioregistry.io/cadsr:"^^ . - . - . - . - . - "https://www.thermofisher.com/antibody/product/"^^ . - . - . - "ised" . - . - "olatdv" . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_organ_"^^ . - . - . - "0000574"^^ . - . - . - . - . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"^^ . - "obo" . - "henrich@embl.de" . - . - . - . - . - "Compluyeast-2D-DB" . - . - . - "Reference Sequence Collection" . - "^\\d+$"^^ . - . - "social and behavioural science" . - "https://www.ncbi.nlm.nih.gov/books/$1"^^ . - "Virus-HostDB" . - "earth science" . - . - . - . - . - . - . - "EcoLexicon" . - "molbase.sheffield" . - . - . - . - . - "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . - . - . - "tngb" . - "wwf.ecoregion" . - "^\\d+$"^^ . - . - . - "false"^^ . - "idoden" . - . - . - . - "true"^^ . - . - . - . - . - "protein" . - . - . - . - . - . - . - "Leen Vandepitte" . - "https://www.flymine.org/flymine/report/ChromosomeBand/"^^ . - "Mathematical modeling ontology" . - "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:"^^ . - . - "10595"^^ . - "rdb20@pitt.edu" . - . - "Vital Sign Ontology" . - "medicine" . - . - . - . - . - "Human Proteome Map Peptide" . - "ArrayGroup"^^ . - . - "fungorum" . - . - "drosophila" . - "TransportDB" . - . - . - "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . - "ontology" . - . - . - . - . - . - "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . - . - "false"^^ . - . - . - "Imke Tammen" . - . - . - . - . - "https://grch38.togovar.org/variant/$1"^^ . - . - . - "HMS LINCS Cell" . - "http://www.jcvi.org/charprotdb/index.cgi/view/"^^ . - "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes."^^ . - . - "obo" . - . - "PharmacoDB Cells" . - "https://arxiv.org/abs/$1"^^ . - . - "BioPortal" . - "ecology" . - . - . - "Google Patents" . - . - "genomics" . - . - "Robert Court" . - . - . - "irgsp" . - . - "Cell Cycle Ontology" . - "life science" . - "Erik.Segerdell@cchmc.org" . - . - "false"^^ . - . - "PDC000351"^^ . - . - . - "^[0-9]+$"^^ . - "transyt" . - . - "SMP" . - "false"^^ . - "Martin Ramirez" . - "false"^^ . - . - . - "biodiversity" . - . - . - . - "vo" . - "gene" . - . - "false"^^ . - . - "ido" . - "casent0106247"^^ . - "ecology" . - "cho"^^ . - . - . - . - . - . - "31"^^ . - . - . - "http://purl.obolibrary.org/obo/BFO_$1"^^ . - "biomedical science" . - "true"^^ . - . - "http://www.lipidmaps.org/data/LMSDRecord.php?LMID="^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . - . - . - . - . - . - . - . - "NLXSUB" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "samuel.friedman@cammlab.org" . - . - . - "fivestars" . - . - . - . - "depod" . - . - . - . - "^[A-Z]{6}(\\d{2})?$"^^ . - "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"^^ . - . - . - "Influenza Virus Database" . - . - "UDB000691"^^ . - "https://www.wormbase.org/get?name=$1"^^ . - "https://www.cbioportal.org/study/summary?id=$1"^^ . - . - "false"^^ . - . - . - . - . - . - "true"^^ . - "http://aber-owl.net/ontology/$1/#/Browse/" . - . - . - . - . - . - "proteomics" . - "https://www.xenbase.org/entry/"^^ . - . - . - . - "SpliceNest" . - . - . - "animal husbandry" . - . - "chemdb" . - . - "false"^^ . - . - "MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data."^^ . - "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . - . - . - "Pathogen Transmission Ontology" . - "^[A-Za-z0-9\\/]+$"^^ . - . - "expression" . - . - . - "owl" . - "wormbase" . - . - "/53355/cl010066723"^^ . - . - . - . - "^DBCAT\\d+$"^^ . - . - . - . - . - . - "0000000"^^ . - . - . - "5013"^^ . - . - . - . - "http://purl.obolibrary.org/obo/ONE_"^^ . - . - "xao" . - . - "^\\S+$"^^ . - . - . - "semantic web" . - . - . - . - . - "obo" . - . - . - . - "false"^^ . - "KEGG DRUG" . - . - . - . - "Vienna Drosophila Resource Center" . - . - . - "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . - . - "^\\d+$"^^ . - . - "10343835"^^ . - . - "false"^^ . - . - . - . - . - "nkos" . - "^.+$"^^ . - . - . - . - . - . - "wujm@bjmu.edu.cn" . - "ontologies" . - "knowledge and information systems" . - . - . - "false"^^ . - . - . - . - . - "aspgd.locus" . - . - "empiar" . - . - . - "^PGS[0-9]{6}$"^^ . - . - "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . - . - . - . - . - . - "^DBSALT\\d{6}$"^^ . - "PF00004"^^ . - . - . - . - . - . - . - "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:"^^ . - . - . - "International Nonproprietary Names" . - . - "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "https://www.wormbase.org/species/c_elegans/rnai/"^^ . - . - . - "http://www.proglycprot.org/detail.aspx?ProId="^^ . - . - . - "strain" . - . - "genomic" . - . - "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . - . - . - . - "CHEMBL3307800"^^ . - "https://www.scopus.com/authid/detail.uri?authorId=$1"^^ . - . - "mmp.cat" . - . - "runBioSimulations" . - "false"^^ . - . - "https://cropontology.org/rdf/CO_357:"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FIDEO_"^^ . - . - "atmospheric science" . - . - "false"^^ . - "dna" . - . - . - "http://purl.obolibrary.org/obo/CDNO_"^^ . - . - "^\\w+$"^^ . - . - "mouse" . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"^^ . - "data visualization" . - . - "sharkipedia.trend" . - . - "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"^^ . - . - . - . - . - . - . - "tao" . - "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . - "false"^^ . - "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . - . - . - "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . - . - . - "00000180"^^ . - "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . - . - . - . - "life science" . - "STOREDB at University of Cambridge" . - "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . - "National Xenopus Resource" . - . - . - . - "enzyme" . - . - . - . - "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession="^^ . - . - "skos" . - . - "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."^^ . - "astd" . - . - . - . - "http://purl.obolibrary.org/obo/EPIO_$1"^^ . - "DB-0174" . - "https://bioregistry.io/diseasesdb:"^^ . - . - . - . - . - "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."^^ . - "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."^^ . - "false"^^ . - "cell types" . - . - "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . - "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . - "https://www.ebi.ac.uk/gxa/genes/$1"^^ . - "Daniel C. Berrios" . - . - "http://purl.obolibrary.org/obo/FOVT_"^^ . - . - "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . - "has reviewer" . - . - "13"^^ . - . - . - . - "^ACTRN\\d+$"^^ . - "Fetal Calf Serum-Free Database" . - "nucleic acid" . - . - . - . - . - "Tobias Schulze" . -_:Ne90ee8fed2df407b9c43d887d8abdc38 "slarson@ncmir.ucsd.edu" . - . - . - . - . - . - . - "ST000900"^^ . - . - "metascience" . - . - _:N5d69a50234384603b72e609a9e54e2b4 . - "^HIX\\d{7}(\\.\\d+)?$"^^ . - . - "primary health care" . - . - . - . - . - . - . - . - . - "17503"^^ . - "biochemistry" . - . - . - . - . - . - "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . - "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."^^ . - . - . - "Human Intermediate Filament Database" . - . - . - . - "COlleCtion of Open Natural ProdUcTs" . - . - "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . - "^\\w+$"^^ . -_:N17cb05833e8648b0b00adfc7b9e48962 "vlee@ebi.ac.uk" . -_:N5bba3595235448e1831c635d87c3b184 "heinrich.herre@imise.uni-leipzig.de" . - "^\\d+$"^^ . - "false"^^ . - "biomaterial supply resource" . - . - . - "rgd" . - . - . - . - . - . - "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . - . - "https://www.uniprot.org/keywords/$1"^^ . - . - . - . - . - "ontology" . - . - . - "anatomy" . - . - . - . - . - "http://purl.obolibrary.org/obo/MI_$1"^^ . - . - . - . - "Simon Cox" . - "biogrid.interaction" . - . - . - . - "mf" . - "WD_Entity" . - . - . - . - "atol" . - "http://aber-owl.net/ontology/$1" . - . - . - . - . - "anatomy" . - "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id="^^ . - . - "schober@imbi.uni-freiburg.de" . - "metadata" . - "The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc."^^ . - . - . - "knockout" . - "protein" . - "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . - . - . - "^[A-Z][a-z][0-9]+$"^^ . - "frim1"^^ . - . - "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."^^ . - . - . - "D0001"^^ . - . - "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . - . - "^FDB\\d+$"^^ . - . - . - . - . - . - . - "Chemspider" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . - . - . - . - "http://purl.obolibrary.org/obo/SBO_"^^ . - . - . - . - "Dengue Fever Ontology" . - . - "0000001"^^ . - . - . - . - "https://bioregistry.io/ecoliwiki:"^^ . - "https://bioregistry.io/chemspider:"^^ . - . - . - . - . - . - "Tick Anatomy Ontology" . - "pylebail@rennes.inra.fr" . - "false"^^ . - "^\\d{7}$"^^ . - . - "https://web.www.healthdatagateway.org/dataset/$1"^^ . - . - . - . - "research" . - . - . - . - . - . - . - "Open Citation Identifier" . - "http://sideeffects.embl.de/se/$1"^^ . - "false"^^ . - "BioStudies database" . - "http://purl.obolibrary.org/obo/ONE_$1"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MCRO_"^^ . - "CutDB" . - . - "Tissue List" . - . - "^[0-9]+$"^^ . - . - . - "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science."^^ . - "Defunct vaccine information source from the He Lab"^^ . - . - . - . - . - "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"^^ . - . - . - "paxdb.protein" . - . - . - "c0000005"^^ . - . - . - "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . - . - "estdab" . - . - "gene" . - . - . - . - . - . - . - . - "BitterDB is a database of compounds reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. This collection references receptors."^^ . - . - "The Molecular INTeraction database (MINT) stores, in a structured format, information about molecular interactions by extracting experimental details from work published in peer-reviewed journals."^^ . - . - "^\\d{7}$"^^ . - . - . - . - "C. elegans Gross Anatomy Ontology" . - "comparative genomics" . - . - . - . - . - "c.dudek@tu-braunschweig.de" . - "https://www.scopus.com/sourceid/"^^ . - . - "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id="^^ . - "^\\d+$"^^ . - . - . - . - . - "Medaka fish anatomy and development" . - . - . - . - "false"^^ . - "cstr" . - . - . - . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - . - . - . - "STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB)."^^ . - . - . - . - . - . - . - . - "https://grch38.togovar.org/variant/"^^ . - . - "^SD\\d+$"^^ . - . - . - . - "ontology" . - . - . - "rna" . - . - "http://purl.obolibrary.org/obo/ATO_"^^ . - . - "http://purl.obolibrary.org/obo/MAO_$1"^^ . - "ontology" . - . - "mondo" . - "obo" . - "obo" . - . - "0000038"^^ . - . - "^\\w+$"^^ . - . - "merops.entry" . - . - . - "arrayexpress" . - "myco.smeg" . - . - . - . - . - . - . - "Federica Quaglia" . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - . - . - . - "structural bioinformatics" . - . - . - . - "false"^^ . - "chemistry" . - "gene expression" . - "A database for Triticeae and Avena references."^^ . - . - "data management" . - . - . - . - "GlycoEpitope" . - . - . - "cogs@ncbi.nlm.nih.gov" . - . - "http://purl.obolibrary.org/obo/TRANS_"^^ . - . - . - . - "protein" . - "^\\w+\\d+$"^^ . - . - . - . - "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id="^^ . - "false"^^ . - . - . - . - . - . - . - . - "00000268"^^ . - . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . - . - . - . - . - "ontology" . - "false"^^ . - . - "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid="^^ . - "Intrinsically Disordered Proteins Ontology" . - "https://www.kegg.jp/entry/$1"^^ . - . - "^\\d+$"^^ . - . - . - . - "https://www.cameo3d.org/sp/targets/target/$1"^^ . - . - . - . - . - . - "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters"^^ . - "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)."^^ . - . - . - . - . - "Fungal gross anatomy" . - . - . - . - . - . - . - . - "systems biology" . - . - . - "Gene Ontology Causal Assembly Model" . - . - "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)."^^ . - . - . - . - . - . - . - . - . - . - . - "covoc" . - . - "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"^^ . - "ontology" . - "ontology" . - "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."^^ . - . - . - . - "antibodies" . - "http://www.allergome.org/script/dettaglio.php?id_molecule="^^ . - . - "dna" . - . - . - . - . - . - . - . - "ontology" . - "ontology" . - . - . - . - . - "miriam.resource" . - . - . - . - . - . - "http://www.iresite.org/IRESite_web.php?page=view&entry_id="^^ . - . - "https://www.ebi.ac.uk/interpro/set/pfam/"^^ . - . - . - "https://cropontology.org/rdf/CO_338:$1"^^ . - . - . - "SUBSET_SIREN" . - . - "http://purl.obolibrary.org/obo/BFO_"^^ . - . - "timrobertson100@gmail.com" . - "konigmatt@googlemail.com" . - "false"^^ . - "clement.jonquet@inrae.fr" . - . - "The COVID-19 Infectious Disease Ontology" . - . - . - . - . - "chemistry" . - . - . - . - . - . - "anatomy" . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_res_"^^ . - "gbif" . - . - . - . - "^[0-9\\.]+$"^^ . - "ontology" . - . - "pmdb" . - "ForwardStrandPosition"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PAO_$1"^^ . - . - . - . - . - . - "KNApSAcK" . - "protclustdb" . - . - . - "pesticideinfo" . - . - . - . - . - "Minimum PDDI Information Ontology" . - . - . - . - . - . - . - . - . - "false"^^ . - "protein" . - "http://scicrunch.org/resolver/SCR_"^^ . - "11"^^ . - "https://cropontology.org/rdf/CO_321:$1"^^ . - . - . - "NCI Thesaurus (NCIt) provides reference terminology covering vocabulary for clinical care, translational and basic research, and public information and administrative activities, providing a stable and unique identification code."^^ . - "^DB-\\d{4}$"^^ . - . - . - "mpath" . - "National Microbial Pathogen Data Resource" . - "CAID" . - . - "Ceri Van Slyke" . - "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://bioregistry.io/polbase:"^^ . - "expression" . - "false"^^ . - . - . - "mathias.uhlen@scilifelab.se" . - . - "http://aims.fao.org/aos/agrovoc/c_"^^ . - . - . - . - . - . - . - "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . - . - . - "http://vocabularies.bridgedb.org/ops#"^^ . - . - . - . - "genome" . - . - "https://bioregistry.io/dragondb.allele:"^^ . - . - "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . - . - . - . - "0000013"^^ . - . - . - . - . - . - "Adverse Event Reporting Ontology" . - "https://www.ebi.ac.uk/pdbsum/"^^ . - . - . - . - . - . - . - . - . - . - "Zebrafish anatomy and development ontology" . - . - . - . - . - . - . - . - "false"^^ . - . - "International Standard Serial Number" . -_:N8b543b3ccc35445baa4f243e0b8deea9 "helpdesk@cropontology-curationtool.org" . - "true"^^ . - . - "false"^^ . - "biomedical science" . - "^\\d{7}$"^^ . - "ontology" . - "https://www.ebi.ac.uk/metabolights/"^^ . - . - . - "0000052"^^ . - . - "false"^^ . - "agriculture" . - "DRSC05221"^^ . - "lei" . - . - "MarFun" . - . - . - . - . - . - . - . - "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . - . - . - "ZINC1084"^^ . - . - . - . - "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . - "The data cube vocabulary" . - "NLXOEN" . - . - . - . - . - . - "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops."^^ . - "HGVM15354"^^ . - . - "small molecule" . - . - . - "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."^^ . - . - "ontology" . - . - . - . - . - "oba" . - . - "https://cropontology.org/rdf/CO_365:"^^ . - . - . - . - . - . - . - "c"^^ . - . - "Gramene Gene" . - . - . - . - . - . - . - "rpcec" . - "GenPept" . - "data management" . - "classification" . - . - . - "false"^^ . - . - "epidemiology" . - "1h68"^^ . - "registry" . - . - . - "https://www.ebi.ac.uk/chembl/entity/$1"^^ . - "regulation" . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . - "Matúš Kalaš" . - . - . - . - "genetics" . - . - . - "iao" . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "obo" . - . - "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="^^ . - . - . - "NIF Standard Ontology: Cell Types" . - . - "merops.inhibitor" . - . - . - "EDAM Format" . - . - "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . - . - . - "http://purl.obolibrary.org/obo/OGSF_$1"^^ . - "^RPCEC\\d+$"^^ . - "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:"^^ . - "preclinical studies" . - "^\\d{7}$"^^ . - . - . - "false"^^ . - "genetics" . - . - . - . - "^ENST\\d{11}$"^^ . - . - . - "TA14985"^^ . - "enzo" . - . - . - . - . - "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."^^ . - . - . - "dct" . - "sphn" . - . - . - . - . - "Philippe Le Mercier" . - . - "TVAG_386080"^^ . - . - . - "false"^^ . - . - . - "0000590"^^ . - "^\\d+$"^^ . - . - . - . - . - "mosquito" . - . - . - "^\\d{7}$"^^ . - . - "Alzheimer's Disease Ontology" . - "https://ssbd.riken.jp/database/project/"^^ . - "careerPrizeMoney"^^ . - "Drosophila gross anatomy" . - "structure" . - . - . - "^[A-Z\\-]+$"^^ . - . - "genome" . - "http://purl.obolibrary.org/obo/YPO_$1"^^ . - "false"^^ . - . - "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . - "obo" . - . - . - "http://www.pharmgkb.org/disease/$1"^^ . - . - . - . - . - "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . - . - . - . - "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data."^^ . - "0001079"^^ . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . - "genetics" . - "zebrafish line" . - . - . - "Stacia R Engel" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "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."^^ . - "false"^^ . - . - "Human developmental anatomy, abstract" . - . - . - . - . - . - "Clair Kronk" . - "https://bioregistry.io/beiresources:"^^ . - . - . - "functional genomics" . - . - . - . - . - "Philip.Stroemert@tib.eu" . - "WormBase RNAi" . - . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - "false"^^ . - . - . - "life science" . - "LOC_Os02g13300"^^ . - "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . - "genomics" . - "false"^^ . - . - "Ion Channel Electrophysiology Ontology" . - . - . - . - "iclc" . - . - "GeneCards" . - . - " 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."^^ . - "snornabase" . - . - "go.chebi" . - . - "^[1-9]\\d*$"^^ . - "false"^^ . - . - . - "KEGG Drug" . - "^[A-Za-z0-9]+$"^^ . - "subject agnostic" . - . - "^\\d{7}$"^^ . - "false"^^ . - "H-InvDb Protein" . - . - . - . - "mice" . - "^[0-9]+$"^^ . - . - . - . - . - . - . - . - . - . - . - "Chlamydia"^^ . - . - "^\\d+$"^^ . - "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id="^^ . - . - . - "bmrb" . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - "obo" . - . - . - . - . - . - . - "false"^^ . - . - . - "DrugBank Salts" . - "vasilevs@ohsu.edu" . - . - . - . - . - . - . - "translational medicine" . - . - . - . - . - . - . - . - . - . - . - . - . - "genome" . - . - "RNAloops" . - . - . - . - . - . - "ontology" . - . - "false"^^ . - . - . - . - "^\\w+$"^^ . - "http://ddinter.scbdd.com/ddinter/drug-detail/"^^ . - "http://plugins.biogps.org/cgi-bin/wp.cgi?id="^^ . - . - "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."^^ . - . - . - "ICD9CM_2006" . - . - "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . - . - . - "jrsmith@mcw.edu" . - . - "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . - . - "false"^^ . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "obo" . - . - "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . - . - "P23298"^^ . - . - . - "https://datanator.info/reaction/"^^ . - . - . - . - . - . - . - . - . - "Christine.Pourcel@u-psud.fr" . - . - . - . - "small molecule" . - "GOLD genome" . - "Bambara groundnut ontology" . - . - . - . - "cellrepo" . - . - "life science" . - . - . - . - . - "life science" . - "GWAS Central Study" . - . - . - . - "ICD-11" . - "^SCV\\d+(\\.\\d+)?$"^^ . - "life science" . - "drugbank.bioentity" . - "0007807"^^ . - . - "Homologous Organ Groups" . - "Integrated Microbial Genomes Taxon" . - . - . - "NCBI_GeneID" . - "cryoem" . - "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)"^^ . - . - . - . - . - "cryopreserved" . - "http://www.wikipathways.org/instance/$1"^^ . - "Genomic Data Commons Data Portal" . - . - . - "https://www.metanetx.org/comp_info/$1"^^ . - . - . - "geology" . - . - . - . - "Intelligence Task Ontology" . - "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."^^ . - . - "biomedical science" . - . - "true"^^ . - "https://bioregistry.io/dragondb.dna:"^^ . - . - "10001-101"^^ . - . - . - "FAO/WHO_standards" . - "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . - "false"^^ . - "rbrinkman@bccrc.ca" . - . - "tsc" . - "biochemistry" . - . - . - . - . - . - . - "MetaNetX/MNXref integrates various information from genome-scale metabolic network reconstructions such as information on reactions, metabolites and compartments. This information undergoes a reconciliation process to minimise for discrepancies between different data sources, and makes the data accessible under a common namespace. This collection references cellular compartments."^^ . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/probe/?term="^^ . - . - . - . - "https://bioregistry.io/metaregistry/scholia/"^^ . - "glycosciences.db" . - . - "https://www.e-cyanobacterium.org/bcs/entity/"^^ . -_:N17cb05833e8648b0b00adfc7b9e48962 "Vivian Lee" . - . - "behavior" . - "Heidi L. Rehm" . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/MSIO_"^^ . - . - . - . - . - . - . - . - "Ontology of Physics for Biology" . - . - . - . - "scop" . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - . - . - "admin@envipath.org" . - "The main contact person for a registry" . - "obo" . - "ogms/OMRE" . - "Beilstein" . - "http://drugcentral.org/drugcard/"^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - "rnavdb" . - "adriano.rutz@ik.me" . - . - . - "biochemistry" . - . - "https://pubchem.ncbi.nlm.nih.gov/cell/"^^ . - . - . - "genomics" . - . - . - . - . - . - . - "ontology" . - . - . - "salmon" . - "0000400"^^ . - . - . - . - . - "https://portal.issn.org/resource/ISSN/$1"^^ . - . - . - . - . - "virgen" . - . - "omrse" . - . - "false"^^ . - "protein" . - . - . - "https://progenetix.org/services/ids/"^^ . - . - . - . - . - "neuroscience" . - . - "^\\d{7}$"^^ . - _:N4de731d6bf7c472ab6146634b077278a . - . - "animal" . - . - . - "http://www.treefam.org/family/$1"^^ . - "obo" . - . - "Model Card Report Ontology" . - . - "^\\d+$"^^ . - . - . - . - "^\\w+$"^^ . - "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . - . - . - . - "ontology" . - "^\\d+$"^^ . - . - . - "DailyMed" . - . - . - . - . - "cito" . - . - . - . - . - "https://www.novusbio.com/products/"^^ . - . - "ontology" . - . - "http://purl.obolibrary.org/obo/KISAO_$1"^^ . - . - "^\\d+$"^^ . - . - "arXiv" . - . - . - . - . - . - . - . - . - . - "ChemBank" . - . - . - . - . - "human" . - . - . - . - "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)."^^ . - . - . - "0000208"^^ . - . - . - . - . - "Basic Formal Ontology" . - . - . - "https://bioregistry.io/dashr.expression:"^^ . - . - "go.model" . - . - "https://civicdb.org/links/variant/"^^ . - "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . - . - . - "MIRBASEM" . - . - "sequence" . - "bioinformatics" . - "protein" . - . - . - . - . - . - "https://www.storedb.org/?"^^ . - "false"^^ . - . - "ordo.orphanet@inserm.fr" . - . - "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . - "false"^^ . - . - "Information Artifact Ontology" . - . - . - . - . - "johnbeverley2021@u.northwestern.edu" . - "xlmod" . - . - . - "population genetics" . - . - . - . - . - . - . - . - "http://classyfire.wishartlab.com/tax_nodes/C"^^ . - . - "ontology" . - . - "K"^^ . - . - . - . - . - "false"^^ . - . - . - "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . - "mammalian" . - "false"^^ . - . - . - . - . - . - . - . - "protein" . - . - . - "Kidney and Urinary Pathway Ontology" . - . - "^\\d{7}$"^^ . - "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . - "PDBsum; at-a-glance overview of macromolecular structures" . - . - "Pierre Grenon" . - . - . - . - "NCBI Bookshelf" . - . - "http://purl.obolibrary.org/obo/RoleO_$1"^^ . - "MMP02954345.1"^^ . - "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . - "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."^^ . - . - . - . - . - . - . - . - "Reaxys" . - . - . - . - . - . - "cjmungall@lbl.gov" . - . - "0002005"^^ . - "Signaling Gateway" . - . - "SABIO-RK EC Record" . - . - "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . - "The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities."^^ . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "zenodo.record" . - . - . - "^\\d{7}$"^^ . - . - . - . - "Echinobase" . - . - . - "https://www.disprot.org/idpo/IDPO:$1"^^ . - . - . - . - "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . - . - "0001927"^^ . - "This is the Agilent SurePrint G3 Human GE v2 8x60k Microarray, Agilent design ID 039494, GridName 039494_D_F_20120628. Probe layout is 1 x 1 x 384 rows x 164 cols, which is different from a similar ADF A-GEOD-16699 (1 x 1 x 328 rows x 192 cols). Version 2 of this array contains long intergenic non-coding RNA (lincRNA) probes designed to the human catalog of lincRNAs from the Broad Institute, along with an update of mRNA content when compared to version 1. Probes were designed using GRCh37 assembly of the human genome. Annotation of probes came from the following database: RefSeq Build 50, Ensembl Release 52, Unigene Build 216, GenBank (April 2009), Broad Institute Human lincRNA catalog (Nov 2011), Broad Institute TUCP transcripts catalog (Nov 2011). Probe annotation was taken from A-GEOD-16699."^^ . - . - "loggerhead" . - "^\\d{7}$"^^ . - . - . - "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."^^ . - . - "TripleExpression"^^ . - "https://biopragmatics.github.io/providers/dhba/"^^ . - "false"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ARO_"^^ . - . - . - "cytology" . - "Oat ontology" . - "^\\w{2,3}(-\\w+)?$"^^ . - . - "reactome" . - . - . - "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."^^ . - "molecules" . - "obo" . -_:Naaf3719147764fc2a918e626bdcc3b06 "helpdesk@cropontology-curationtool.org" . - . - "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . - "molecular infection biology" . - "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations"^^ . - "OBO Foundry" . - . - . - "http://purl.obolibrary.org/obo/OVAE_"^^ . - . - "microbiology" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ENVO_"^^ . - "life science" . - . - . - . - . - . - "ontology" . - . - . - . - "^[A-Z0-9]{6,7}$"^^ . - . - . - "biomedical science" . - . - . - . - . - . - . - "uniprot.ptm" . - . - "idog" . - "neurobiology" . - "Daniel Sonenshine" . - . - . - "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\"."^^ . - . - "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://cropontology.org/rdf/CO_325:"^^ . - . - "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id="^^ . - "BridgeDb Vocabulary" . - . - . - . - "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . - . - . - . - . - . - "qb" . - "Ontology for MicroRNA Target" . - . - . - . - . - . - "co_346" . - "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . - "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"^^ . - . - . - . - . - "meteorology" . - "ontology" . - . - . - . - . - . - . - "natural producs" . - "stefanie.seltmann@ibmt.fraunhofer.de" . - . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - "N21"^^ . - . - "CID" . - . - "dna" . - . - . - . - "myco.tuber" . - . - . - . - . - "https://omia.org/OMIA"^^ . - "http://purl.obolibrary.org/obo/NBO_"^^ . - "http://id.nlm.nih.gov/mesh/vocab#"^^ . - . - "gene mapping" . - "ensembl.plant" . - . - . - . - . - "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . - "http://xmlns.com/foaf/0.1/$1"^^ . - . - "Satya S. Sahoo" . - "thomas@luetteke-online.de" . - . - "https://biopragmatics.github.io/providers/bs/"^^ . - "obo" . - . - "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . - . - . - . - . - . - . - . - . - . - "Teleost taxonomy ontology" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "Genetics Home Reference" . - "knowledge and information systems" . - . - . - . - "mobidb" . - . - . - . - . - . - "AY209920"^^ . - . - . - . - . - . - . - . - . - "^PRJ[DEN][A-Z]\\d+$"^^ . - . - . - "anatomy" . - "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . - "An ontology of physico-chemical methods and properties."^^ . - . - "4DNSR73BT2A2"^^ . - "A type for entries in the Bioregistry's collections" . - "nucleotide" . - . - . - . - "https://modeldb.science/"^^ . - . - . - "^[A-Z-_0-9]+$"^^ . - . - . - . - . - . - . - . - "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies."^^ . - . - "false"^^ . - . - . - "protein" . - . - "^ACH-\\d+$"^^ . - "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)."^^ . - . - "enzymology" . - "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 Phenotype."^^ . - . - . - . - "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . - "https://www.yeastgenome.org/locus/$1"^^ . - . - "Chemical Entities of Biological Interest" . - . - . - . - . - . - "https://www.gwascentral.org/marker/$1"^^ . - . - . - "Comprehensive Resource of Mammalian protein complexes" . - . - "false"^^ . - . - "drug discovery" . - "microbial" . - . - . - . - . - "^\\d+$"^^ . - "408"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "ICD10" . - "ontology" . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "Documentation of the Phenoscape Curation Workflow"^^ . - "miro" . - "metabolomics" . - . - "^\\d+$"^^ . - . - "1000"^^ . - "post-transcriptional modification" . - . - . - . - . - "AMDEFA"^^ . -_:Na44780e2985848e985ef5412da5b9845 "hajo.rijgersberg@wur.nl" . - . - _:N2049abb829ed4f9d86c5fbb00ea6b058 . - . - . - "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . - "2"^^ . - . - . - "OGI.owl" . - "1354581"^^ . - "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . - . - . - . - . - . - . - . - "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . - . - . - "ontology" . - "Quinoa Ontology ontology" . - . - "patent" . - "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn="^^ . - "obo" . - "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."^^ . - "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . - " Christos Louis" . - . - . - . - "MetaCyc Reaction" . - . - "wormmart" . - . - . - . - . - . - . - "^[A-Za-z0-9\\-\\/]+$"^^ . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - . - . - . -_:Nb4de457f8e114f4e8c18616dab90271d "po-discuss@plantontology.org" . - . - . - "marine biology" . - . - . - . - . - "Sri Lanka Clinical Trials Registry" . - "MeSH 2012" . - "http://purl.obolibrary.org/obo/MOP_$1"^^ . - . - . - . - . - "tahe" . - . - . - . - "genome" . - "sprint" . - "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."^^ . - . - . - . - . - "A database-specific registry supporting curation in the Gene Ontology" . - "life science" . - "EST database maintained at the NCBI." . - . - . - . - "true"^^ . - "14"^^ . - "false"^^ . - . - . - . - "IRCT20080904001199N7"^^ . - . - . - "http://cutdb.burnham.org/relation/show/$1"^^ . - "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"^^ . - . - . - "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/"^^ . - . - "ontology" . - . - "provenance"^^ . - . - . - "^GE\\d+$"^^ . - "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records."^^ . - . - "0009089"^^ . - . - "https://bioregistry.io/elm:"^^ . - . - "14"^^ . - "false"^^ . - "false"^^ . - . - "Cell Line Ontology [derivative]" . - . - "lipidmaps" . - . - . - "Elspeth Bruford" . - . - "life science" . - . - "health science" . - . - "https://biopragmatics.github.io/providers/sdis/$1"^^ . - . - "protein" . - . - . - . - "pancreatic islet" . - . - . - . - . - . - "true"^^ . - "obo" . - . - . - "ybradford@zfin.org" . - "false"^^ . - . - . - "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . - . - "The Human Unidentified Gene-Encoded (HUGE) protein database contains results from sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - . - "^\\d+$"^^ . - . - "Chinese Clinical Trial Registry" . - . - . - "ontology" . - . - . - . - "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."^^ . - . - . - . - . - "ATCC" . - "false"^^ . - . - _:N93c2c94de4ce46f29e17ab0a916cf895 . - . - "allergen" . - . - . - "life science" . - . - . - . - . - . - . - "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."^^ . - . - "sperm" . - . - . - "Chemical Entity Materials and Reactions Ontological Framework" . - . - . - . - "International repository of Adverse Outcome Pathways."^^ . - "https://proteinensemble.org/"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "^C\\d+$"^^ . - "^C\\d+$"^^ . - . - "https://books.google.com/books?id=$1"^^ . - . - . - . - "glygen" . - . - . - . - . - . - . - . - . - . - . - . - "small molecule" . - "CTRI/2023/04/052053"^^ . - "false"^^ . - . - . - "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$"^^ . - "Polygenic Score Catalog" . - . - . - . - . - "1"^^ . - . - "UM-BBD_compID" . - . - . - . - "plana" . - . - . - . - . - "^KCT\\d+$"^^ . - . - "clinvar.record" . - "kegg.reaction" . - . - . - . - . - "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . - . - . - . - . - . - . - "13"^^ . - . - . - . - "obo" . - . - . - . - . - "CHEBIID" . - "informatics" . - . - "https://registry.bio2kg.org" . - . - . - . - "^\\d{6}$"^^ . - . - "prodom" . - . - . - "false"^^ . - . - "Pocketome" . - "true"^^ . - . - . - "https://lincs.hms.harvard.edu/db/antibodies/"^^ . - . - . - "NucleaRDB" . - "false"^^ . - . - . - . - . - "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . - . - "Basic Register of Thesauri, Ontologies & Classifications" . - . - . - "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id="^^ . - . - "obo" . - . - . - "1.1.1.1"^^ . - . - "Thomas Lütteke" . - "https://go.drugbank.com/indications/"^^ . - "International repository of Adverse Outcome Pathways."^^ . - . - . - "https://e-cyanobacterium.org/models/model/"^^ . - . - "development" . - "false"^^ . - . - . - . - . - . - . - . - . - "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . - . - . - . - "568815597"^^ . - "false"^^ . - . - . - . - "ontology" . - "obo" . - . - . - . - "https://www.wormbase.org/get?name="^^ . - "false"^^ . - . - . - "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.."^^ . - . - . - . - . - . - "2023"^^ . - "proteomics" . - . - "https://lincs.hms.harvard.edu/db/datasets/"^^ . - . - . - . - "https://data.4dnucleome.org/biosources/"^^ . - . - "https://easychair.org/cfp/$1"^^ . - . - . - . - . - "ConoServer" . - . - . - . - . - "structure" . - . - . - . - "false"^^ . - . - "life science" . - . - "aquaculture" . - . - "false"^^ . - . - . - "http://www.wikipathways.org/instance/"^^ . - . - "remote sensing" . - . - . - "https://glygen.org/glycan/$1"^^ . - "narcis.fernandez@gmail.com" . - . - . - . - . - "49"^^ . - . - . - . - . - . - . - . - . - "worms" . - . - . - . - "false"^^ . - . - "ECOCYC" . - . - . - . - "https://www.ebi.ac.uk/ena/browser/view/"^^ . - . - . - . - . - . - . - . - "medicine" . - "FAIRsharing Organization" . - "unipathway.reaction" . - . - . - "https://viralzone.expasy.org/"^^ . - "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . - "Selventa Complexes" . - "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."^^ . - . - . - "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."^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - "AURKA"^^ . - . - "srao" . - . - "25512"^^ . - . - "panther.node" . - . - . - "https://fungi.ensembl.org/id/"^^ . - "http://w3id.org/owlstar/"^^ . - "functional genomics" . - . - . - . - . - "BioContext contains modular JSON-LD contexts for bioinformatics data." . - . - . - "wikigenes" . - . - . - "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 protein information."^^ . - . - . - . - "biochemistry" . - . - . - . - . - "genomics" . - . - . - "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."^^ . - . - . - . - . - . - . - "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."^^ . - . - "http://purl.obolibrary.org/obo/PW_"^^ . - . - "http://purl.obolibrary.org/obo/MFO_"^^ . - . - . - . - . - "https://www.picb.ac.cn/limore/cellLines/single?para="^^ . - . - "GeoNames Feature Code" . - . - . - "hcpcs" . - . - . - . - "sebastien.moretti@sib.swiss" . - "ontology" . - . - "enzyme" . - . - . - "cell line" . - "DDB0016567"^^ . - . - . - "rna" . - "uniprot.var" . - "^\\d{5,}$"^^ . - . - "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://pubchem.ncbi.nlm.nih.gov/source/hsdb/"^^ . - "0011124"^^ . - . - . - . - "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . - "mutant" . - "LIPID_MAPS_class" . - "false"^^ . - . - "Electron Microscopy Public Image Archive" . - "false"^^ . - "repeatsdb.structure" . - "Leigh.Carmody@jax.org" . - . - "bibliography" . - . - . - . - . - . - . - . -_:N0402b08463784fa0bcdbaac63beec045 "more.info@allotrope.org" . - . - "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . - . - "DataNode"^^ . - . - "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . - . - . - . - . - . - "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . - . - . - . - . - . - . - . - "http://emmo.info/emmo/cif-core#"^^ . - . - . - . - "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."^^ . - . - "Pubchem" . - . - . - "https://vac.niaid.nih.gov/view?id="^^ . - . - "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."^^ . - . - . - . - "classification" . - . - . - . - . - . - "MedlinePlus Health Topics" . - "life science" . - "http://purl.obolibrary.org/obo/MIAPA_"^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/$1"^^ . - . - "inaturalist.place" . - . - . - . - . - . - "https://cropontology.org/rdf/CO_367:"^^ . - . - . - . - . - . - "false"^^ . - "gene" . - "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/"^^ . - . - "CSP2005" . - . - . - "090803"^^ . - "bibliography" . - . - . - "plant breeding" . - "life science" . - . - "false"^^ . - "false"^^ . - "michel.dumontier@gmail.com" . - "life science" . - . - "GXA Gene" . - . - . - . - "molecular chemistry" . - . - . - . - "false"^^ . - . - . - . - . - . - "gene" . - . - . - . - . - . - . - "https://repeatsdb.org/protein/"^^ . - "^[1-9]\\d*$"^^ . - . - "bmrb.restraint" . - "http://purl.obolibrary.org/obo/PCL_$1"^^ . - . - "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . - . - . - . - . - "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"^^ . - . - . - "http://purl.obolibrary.org/obo/SYMP_$1"^^ . - "Influenza Ontology" . - "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."^^ . - . - . - . - . - . - . - "physiology" . - "false"^^ . - "life science" . - . - "funcbase.fly" . - "Daniel Himmelstein" . - "stem cell" . - "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . - . - "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number."^^ . - "^\\w+$"^^ . - "Stress Knowledge Map" . - "http://w3id.org/nkos/"^^ . - . - "noaa.cameo" . - . - . - "pdb-ccd" . - . - . - "http://www.molbase.com/en/index.php?app=search&search_keyword="^^ . - "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . - "0001417"^^ . - . - . - . - . - . - "https://swbiodiversity.org/seinet/taxa/index.php?taxon="^^ . - . - "SIGNOR-252737"^^ . - "https://www.uniprot.org/uniref/$1"^^ . - "http://purl.obolibrary.org/obo/OMIABIS_"^^ . - "chemistry" . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . - . - "^\\d+(\\w+)?$"^^ . - "lbo" . - . - . - . - "817732"^^ . - . - "false"^^ . - . - . - . - "^S\\d+$"^^ . - . - . - "functional genomics" . - . - . - "http://www-bionet.sscc.ru/sitex/index.php?siteid="^^ . - . - . - "cmo" . - . - . - . - . - . - . - "http://exac.broadinstitute.org/transcript/"^^ . - . - "translational medicine" . - . - . - . - . - . - "false"^^ . - "false"^^ . - . - "Ontology about C. elegans and other nematode phenotypes"^^ . - "life science" . - . - . - "The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns."^^ . - "^\\d+$"^^ . - . - . - . - . - "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_func_"^^ . - "pathway" . - "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS)."^^ . - . - "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . - "91792"^^ . - . - . - "classification" . - . - . - . - . - . - "false"^^ . - "GeneAnnot: Microarray Gene Annotation" . - . - . - . - . - . - . - "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . - . - "Salk Institute for Biological Studies" . - "0002902"^^ . - "http://purl.obolibrary.org/obo/MSIO_$1"^^ . - "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . - "false"^^ . - . - "foodon" . - "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files."^^ . - . - "Ontology for Nutritional Epidemiology" . - "Identifiers.org Terms" . - . - . - . - . - "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . - "https://fairsharing.org/users/"^^ . - "Web Ontology Language" . - "false"^^ . - . - . - . - . - . - "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . - "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1"^^ . - . - . - . - . - . - "ndfrt" . - "^\\d+$"^^ . - "false"^^ . - "systems biology" . - . - "ontology" . - . - "structure" . - "General Formal Ontology" . - . - "Maria Gould" . - . - . - "Akhilesh Pandey" . - . - . - "biomedical science" . - . - "Stian Soiland-Reyes" . - "Simple Standard for Sharing Ontological Mappings" . - . - . - . - . - . - "diseases" . - . - . - "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."^^ . - "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . - . - "false"^^ . - "MatrixDB" . - "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "http://database.deepsolar.space:18080/dbs/nlfff/$1"^^ . - . - . - "TRQ"^^ . - . - . - . - . - . - "life science" . - . - . - "life science" . - . - . - . - . - . - . - "false"^^ . - "PRO" . - . - . - "^[a-z0-9\\-]+$"^^ . - . - "Animal Trait Ontology for Livestock" . - . - . - . - "http://purl.org/gc/"^^ . - . - "false"^^ . - . - . - "Rhea, the Annotated Reactions Database" . - . - "0024"^^ . - "^\\d+$"^^ . - "insdc.sra" . - . - . - . - . - . - . - "ontology" . - "PharmGKB Disease" . - . - . - . - . - . - . - . - "false"^^ . - "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://icd.who.int/browse10/2019/en#/$1"^^ . - . - . - "VirGen" . - "Citation Counting and Context Characterisation Ontology" . - . - "geodesy" . - "^([a-z]{3,5}_)?M\\d{5}$"^^ . - . - . - "National Center for Biotechnology Information Registry" . - . - . - . - "http://purl.obolibrary.org/obo/SO_"^^ . - . - "http://www.pocketome.org/files/$1.html"^^ . - . - . - "miapa" . - "kegg.glycan" . - "paleodb" . - "RiceNetDB Reaction" . - "false"^^ . - . - "nlx.inv" . - . - . - "false"^^ . - . - . - "sfam" . - "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family="^^ . - "structural biology" . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HEPRO_$1"^^ . - "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . - "Confidence Information Ontology" . - . - "http://purl.obolibrary.org/obo/INO_"^^ . - "drug" . - "^\\d+$"^^ . - "RXN-14904"^^ . - "https://mediadive.dsmz.de/medium/"^^ . - "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."^^ . - . - "false"^^ . - . - "Alberto Traverso" . - . - . - . -_:N865baaa49d124e84968635b53d7122b6 "j.bard@ed.ac.uk" . - . - . - "HGNC gene family" . - . - . - . - . - . - "57"^^ . - . - "KCT0008394"^^ . - . - . - "false"^^ . - . - "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."^^ . - "http://www.unimod.org/modifications_view.php?editid1="^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . - "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."^^ . - . - . - "small molecule" . - . - "https://www.scopus.com/affil/profile.uri?afid=$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Aquatic Sciences and Fisheries Information System" . - . - "alzheimer's disease" . - . - "5fde96bdc5f1aa9ff0cce18a"^^ . - . - . - "https://civicdb.org/links/variant/$1"^^ . - . - . - "Soybean ontology" . - "fbol" . - . - . - "false"^^ . - . - . - "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . - . - "https://biopragmatics.github.io/providers/diseaseclass/"^^ . - "physiology" . - "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - "ito" . - "eNanoMapper ontology" . - "true"^^ . - "9"^^ . - . - . - "obo" . - . - . - . - . - . - . - "Electrocardiogram Ontology" . - "ontology" . - "Emotion 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"^^ . - . - "https://registry.identifiers.org/registry?query=MIR:"^^ . - . - . - "https://bioregistry.io/cldb:"^^ . - . - "georgeta.bordea@u-bordeaux.fr" . - "false"^^ . - . - "KEGG Compound" . - . - . - . - . - . - . - . - . - "dbvar.studies" . - "false"^^ . - . - "uniprot.tissue" . - "http://purl.obolibrary.org/obo/OMRSE_"^^ . - "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."^^ . - . - "G. Thomas Hayman" . - "fernanda.dorea@sva.se" . - . - . - . - "life science" . - . - "animal husbandry" . - "molecular biology" . - "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature="^^ . - . - "tccd" . - . - "FB00000917"^^ . - "false"^^ . - . - . - . - . - . - "life science" . - "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."^^ . - . - . - . - "latitude"^^ . - "gene expression" . - "evolutionary biology" . - "dsm4" . - . - . - "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match."^^ . - . - "4QHKG"^^ . - . - "Human Medical Genetics" . - "Sabrina@tislab.org" . - "http://purl.obolibrary.org/obo/VHOG_$1"^^ . - "ddinter.drug" . - "unimod" . - "biomedical science" . - "small molecule" . - "^AB\\d+$"^^ . - "Decentralized Biomedical Ontology" . - . - . - "Gene Ontology Annotation Database" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CTENO_$1"^^ . - "obo" . - . - . - . - "ctd.chemical" . - . - . - . - . - "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . - . - . - . - . - . - "life science" . - . - . - "https://cropontology.org/rdf/CO_333:$1"^^ . - "genome" . - . - . - . - . - . - "true"^^ . - "Alpha Tom Kodamullil" . - . - . - "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . - . - . - . - . - "false"^^ . - . - "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"^^ . - "Snapshot" . - . - . - "DateTimeDescription"^^ . - "https://biopragmatics.github.io/providers/icepo/$1"^^ . - . - . - . - "civic.sid" . - . - . - "Vilma Hualla Mamani" . - . - "false"^^ . - "^UMIN\\d+$"^^ . - . - . - . - . - . - . - . - "genome" . - . - "polbase" . - . - "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "Common Bean ontology" . - . - . - "^\\S+$"^^ . - "immunology" . - "ChemIDplus" . - . - . - . - . - "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." . - . - . - . - . - . - "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.jcvi.org/charprotdb/index.cgi/view/$1"^^ . - . - . - "1"^^ . - "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."^^ . - . - . - . - . - "preclinical studies" . - "https://biomedit.ch/rdf/sphn-ontology/sphn#$1"^^ . - "foaf" . - "https://www.glycoepitope.jp/epitopes/"^^ . - . - . - "http://nava.liacs.nl/cgi-bin/nava.py?id=$1"^^ . - . - . - "plant" . - . - "http://metnetonline.org/browse_pathway2.php?pthID=$1"^^ . - . - "nlx.br" . - . - . - . - . - . - "^CAL\\d{7}$"^^ . - "Cell line collections (Providers)"^^ . - . - . - . - . - . - . - . - "http://genomics.senescence.info/genes/details.php?id=$1"^^ . - . - . - . - "smr@stowers.org" . - . - "M1"^^ . - . - . - . - "nif.dysfunction" . - . - "reactions" . - . - . - "Selventa Chemicals" . - "Plant Anatomy Ontology" . - "https://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - "0000108"^^ . - . - "PTN000000026"^^ . - . - "Ontology of RNA Sequencing" . - . - . - "false"^^ . - "ontology and terminology" . - "Data Science Ontology" . - "ontology" . - "Ambystoma Genetic Stock Center" . - "http://purl.obolibrary.org/obo/BCO_"^^ . - "Bernd Müller" . - "life science" . - . - . - "odc.tbi" . - "Catalogue of Life" . - . - . - . - . - "statistics" . - . - . - . - "true"^^ . - . - . - . - . - "Idan Gabdank" . - . - . - "UTRdb" . - "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis"^^ . - . - . - . - . - "sov:WRfXPg8dantKVubE3HX8pw"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "life science" . - . - . - . - "46"^^ . - . - "life science" . - "http://purl.org/spar/cito/"^^ . - . - . - "Universal Natural Products Database" . - "preclinical studies" . - "Literature references in Gramene"^^ . - . - . - . - "false"^^ . - "https://civicdb.org/links/molecular_profile/$1"^^ . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CLYH_"^^ . - . - "0000618"^^ . - "WGS-95-1333"^^ . -_:Ne90ee8fed2df407b9c43d887d8abdc38 "Stephen Larson" . - "life science" . - "http://uri.neuinfo.org/nif/nifstd/nlx_dys_"^^ . - "^\\d+$"^^ . - "false"^^ . - . - "ChemSpider" . - "COSMIC Gene" . - . - "GLIDA GPCR" . - "http://purl.obolibrary.org/obo/ICO_"^^ . - . - "Semanticscience Integrated Ontology" . - "bacdive" . - . - . - . -_:Nc2c3eeb40d884344b28b37273de129b2 "Bgee team" . - . - . - . - . - . - . - "ontology" . - . - . - "database" . - "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid="^^ . - "movie" . - . - . - . - . - "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."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "https://bioregistry.io/pscdb:"^^ . - . - . - "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."^^ . - "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . - "aeo" . - . - . - . - . - . - . - . - "false"^^ . - "ABE-0009634"^^ . - . - . - . - "RIKEN Bioresource Center Cell Bank" . - . - "^\\d{7}$"^^ . - . - "graingenes.reference" . - . - . - . - . - "https://w3id.org/seo#$1"^^ . - . - . - "https://biopragmatics.github.io/debio/$1"^^ . - . - . - . - . - . - . - . - . - "ontology" . -_:N40de88241fe445dc8d11e9c9b635f056 "Chebi Administrators" . - . - . - . - "false"^^ . - "https://aopwiki.org/events/"^^ . - "100"^^ . - "http://vbrc.org/gene_detail.asp?gene_id="^^ . - "O80725"^^ . - "classification" . - . - . - "taxonomy" . - . - "false"^^ . - . - . - . - . - . - "meetings" . - . - . - . - . - . - "^E\\d+$"^^ . - . - . - . - "maxneal@gmail.com" . - . - . - "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . - . - . - "bioinformatics" . - . - "drug discovery" . - . - "http://swissregulon.unibas.ch/query/"^^ . - "Rosemary Shrestha" . - "^T3\\d+$"^^ . - "bioinformatics" . - . - . - . - . - "false"^^ . - "100000000000001"^^ . - . - . - "wormbase" . - . - . - "https://senselab.med.yale.edu/ModelDB/ModelList?id="^^ . - . - "Ontology for Biomedical Investigations" . - . - "NDFI4Chem Collection" . - . - . - "ALA"^^ . - . - "qtl" . - "materials informatics" . - . - . - "Gene Regulation Ontology" . - . - . - "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."^^ . - . - . - "hesa" . - "^EMD-\\d{4,5}$"^^ . - . - . - . - "ShiBASE" . - "obo" . - . - "interaction" . - . - . - . - "PUBCHEM_CID" . - "hhe@ebi.ac.uk" . - . - . - . - . - . - . - "structure" . - . - . - "autdb" . - . - . - . - . - . - "OriDB Schizosaccharomyces" . - . - . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . -_:N08e1f9097d1b4dae9796095cf1ebccef "Crop Ontology Helpdesk" . - "odrl" . - . - "botany" . - . - . - "146421"^^ . - . - "data quality" . - "https://www.pombase.org/gene/"^^ . - . - "tcdb" . - . - "biomedical science" . - . - . - . - "genome" . - "wikidata" . - . - . - . - "https://bioregistry.io/leafsnap:"^^ . - . - "https://bioregistry.io/cst:"^^ . - "expression" . - . - . - . - . - . - . - "https://biopragmatics.github.io/providers/schem/$1"^^ . - . - . - "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . - . - "gobp" . - . - . - "EMD-1001"^^ . - . - . - "ontology" . - "09200010"^^ . - . - . - . - . - "Feature Type Thesaurus" . - . - "pgx" . - "false"^^ . - . - . - . - . - "Q9UKQ2"^^ . - "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . - "0000066"^^ . - . - . - . - "http://www.peptideatlas.org/PASS/$1"^^ . - "ndc" . - . - . - . - . - . - . - . - . - . - . - . - "iuphar.receptor" . - "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . - "false"^^ . - "http://www.co-ode.org/ontologies/galen#"^^ . - . - . - . - . - "true"^^ . - . - "International Genome Sample Resource" . - . - . - "lincs" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FBSP_$1"^^ . - . - . - "https://www.rhea-db.org/rhea/$1"^^ . - "bdsc" . - . - . - "http://www.vbase2.org/vgene.php?id=$1"^^ . - "biomedical science" . - . - . - "^PTN\\d{9}$"^^ . - . - "anatomy" . - "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."^^ . - "false"^^ . - . - "8639.1"^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FBdv_"^^ . - _:N56f74624ea2a452aaea72b619dca97d2 . - . - . - . - "silvio.tosatto@unipd.it" . - . - . - "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . - . - . - "entiminae@gmail.com" . - "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement."^^ . - . - . - . - . - . - "glyconavi" . - . - "endocrinology" . - . - "^\\d+$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MCO_"^^ . - "false"^^ . - . - . - . - . - "Dimension"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "VCell Published Models" . - "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . - "true"^^ . - "molecular dynamics" . - . - . - "https://www.nextprot.org/term/FA-$1"^^ . - . - . - "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . - . - . - . - "https://bioregistry.io/nbn:"^^ . - "refseq" . - . - . - "miRBase mature miRNA" . - . - . - . - . - "^DRSC\\d+$"^^ . - . - . - . - . - . - . - . - "vmhreaction" . - . - "Molecular Process Ontology" . - . - . - "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"^^ . - . - . - "diseaseclass" . - . - . - . - "0001885"^^ . - . - "false"^^ . - . - . - "dbvar.study" . - "http://purl.obolibrary.org/obo/GEO_$1"^^ . - "https://biopragmatics.github.io/providers/diseaseclass/$1"^^ . - . - "zoology" . - "^\\d{7}$"^^ . - . - "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.)."^^ . - "co_331" . - . - . - "https://www.ebi.ac.uk/biostudies/studies/"^^ . - "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix."^^ . - "health science" . - "https://www.yeastgenome.org/locus/"^^ . - "organ" . - "computational biology" . - "http://www.pharmgkb.org/disease/"^^ . - . - . - . - "ontology" . - . - . - . - "true"^^ . - "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "protein" . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - . - "ontology" . - "The Ontology of Coronavirus Infectious Disease (CIDO) is a community-driven open-source biomedical ontology in the area of coronavirus infectious disease. The CIDO is developed to provide standardized human- and computer-interpretable annotation and representation of various coronavirus infectious diseases, including their etiology, transmission, pathogenesis, diagnosis, prevention, and treatment."^^ . - . - "HPSI0114i-bezi_1"^^ . - "neurobiology" . - . - "biology" . - "false"^^ . - "^PR\\d{5}$"^^ . - "0000984"^^ . - . - . - "false"^^ . - . - "https://bioregistry.io/cazy:"^^ . - "life science" . - . - . - . - . - . - . - "10046"^^ . - . - "pgdso" . - "disprot" . - . - "statistics" . - . - . - "559"^^ . - . - "Unique Ingredient Identifier" . - "C12345"^^ . - . - "Application ontology for entities related to insecticide resistance in mosquitos"^^ . - "Marc Ciriello" . - . - "gwascentral.phenotype" . - . - "Catalytic Site Atlas" . - "Transport Systems Tracker" . - . - . - "trait" . - "0000139"^^ . - . - "wasila.dahdul@usd.edu" . - . - . - "1"^^ . - "d1id" . - "https://tree.opentreeoflife.org/taxonomy/browse?id="^^ . - "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://gitlab.com/$1"^^ . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_anat_"^^ . - . - . - "false"^^ . - . - "https://bioregistry.io/bmrb:"^^ . - . - "ABL1"^^ . - "obo" . - "Coronavirus Infectious Disease Ontology" . - "seed" . - . - . - . - . - "ATL98012"^^ . - . - "80001"^^ . - "CL0192"^^ . - . - . - "gene" . - . - . - . - . - "interaction" . - "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="^^ . - . - . - . - . - . - . - "false"^^ . - "anatomy" . - . - . - . - . - "http://purl.obolibrary.org/obo/DDANAT_"^^ . - "NIST" . - . - "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?"^^ . - . - "Ontology of Zebrafish Experimental Conditions"^^ . - . - . - . - "proteomics" . - "Dictybase Gene" . - . - . - . - . - . - "0000128"^^ . - "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys."^^ . - . - "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."^^ . - . - "1001"^^ . - . - . - "https://comptox.epa.gov/dashboard/"^^ . - "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."^^ . - . - "http://biohackathon.org/resource/faldo#"^^ . - . - . - . - "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . - "ontology" . - "https://cropontology.org/rdf/CO_321:"^^ . - . - . - . - "http://purl.org/spar/bido/"^^ . - . - . - "medicine" . - . - . - . - . - . - . - . - . - "hgnc.genefamily" . - "https://modeldb.science/$1"^^ . - "hilmar.lapp@duke.edu" . - "http://purl.obolibrary.org/obo/PR_$1"^^ . - "health science" . - . - . - . - . - . - "lutz.fischer@tu-berlin.de" . - "oceanography" . - "https://zenodo.org/record/"^^ . - "^NOR\\d+$"^^ . - . - "Clinical Trials Information System" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "ontology" . - . - . - "embryo" . - . - "false"^^ . - . - . - . - "dna" . -_:N698447d4b6454989b84712a255c0e38c "Michael J. Lincoln MD" . - . - . - "lipid" . - . - . - . - . - "90062901"^^ . - "ontology" . - . - . - . - "https://medical-data-models.org/forms/"^^ . - "^\\w+$"^^ . - . - . - . - . - "https://www.inaturalist.org/places/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/MFOEM_"^^ . - "false"^^ . - . - . - . - . - "nlx.func" . - _:N9e87a13b66ee4814aa6f9ba33e193e09 . - . - . - . - . - "small molecule" . - . - . - . - "https://euclinicaltrials.eu/app/#/view/"^^ . - . - "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan="^^ . - "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format."^^ . - "Mechanism, Annotation and Classification in Enzymes" . - . - "http://purl.obolibrary.org/obo/VBO_$1"^^ . - "Zenodo" . - . - . - . - . - . - . - "Homeostasis imbalance process ontology" . - . - . - . - . - . - . - . - "experimental plant" . - "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."^^ . - "Amphibian taxonomy" . - . - . - "http://www.w3.org/ns/prov#$1"^^ . - . - . -_:N10720e6ba83e4d6c8be7c875b1455193 "Michael Lincoln" . - . - . - "https://bioregistry.io/dbd:"^^ . - "N0000001662"^^ . - . - . - . - . - . - "http://www.w3.org/ns/dcat#"^^ . - "http://clipserve.clip.ubc.ca/topfind/proteins/"^^ . - "false"^^ . - . - . - . - . - "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page)."^^ . - . - "^\\d+$"^^ . - . - . - . - . - "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . - . - "0107180"^^ . - . - . - . - "PF3D7_1328700"^^ . - . - . - "bgee.stage" . - . - . - "dna" . - . - . - . - "chemical in the database supplied by National Oceanic and Atmospheric Administration"^^ . - . -_:N1e52be9bd7ce42428f19eb8361ffc581 "Intellectual.PropertyServices@ama-assn.org" . - . - "ukprn" . - . - "Bob Thacker" . - . - . - . - "xml" . - "https://cropontology.org/rdf/CO_346:"^^ . - . - "^\\d+$"^^ . - . - "virology" . - "medical informatics" . - . - . - "life sciences" . - "modeldb.concept" . - . - . - "TDR" . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://n2t.net/ark:"^^ . - . - . - . - . - . - . - "biofactoid" . - "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . - . - . - . - "The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion."^^ . - "^[A-Za-z_0-9]+$"^^ . - "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."^^ . - . - "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . - "biomedical science" . - . - . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - . - . - . - . - . - "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$"^^ . - "^\\d{7}$"^^ . - . - "^\\d{7}$"^^ . - . - "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species."^^ . - . - . - . - . - "co_327" . - "http://purl.obolibrary.org/obo/HP_"^^ . - "obo" . - . - . - . - . - . - "^\\d{7}$"^^ . - "structure" . - "http://www.fao.org/gsfaonline/additives/details.html?id="^^ . - . - . - . - "obo" . - . - . - "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . - "^\\d{8}$"^^ . - "Drivers of human diseases including environmental, maternal and social exposures."^^ . - "feature"^^ . - . - . - . - "CIP - potato ontology - december 2018"^^ . - . - "^[0-9]+$"^^ . - . - . - "medicine" . - . - . - "iro" . - . - "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf="^^ . - "est" . - . - . - . - . - . - "000017"^^ . - "molecular" . - . - . - "^AT\\d+$"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d{3}$"^^ . - . - . - "false"^^ . - . - . - . - . - "^\\d{5}$"^^ . - . - . - "ProDom" . - "pmc" . - . - . - . - . - . - . - "TF0001053"^^ . - . - . - "http://purl.obolibrary.org/obo/OMO_$1"^^ . - . - . - . - . - "Lipid"^^ . - . - . - . - . - "Shur-Jen Wang" . - . - . - . - . - "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . - . - . - "false"^^ . - . - "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . - . - . - . - "http://www.isni.org/isni/$1"^^ . - . - "sasap" . - "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . - "https://cropontology.org/rdf/CO_337:"^^ . - . - "subject agnostic" . - . - . - "Sciflection" . - "An ontology for the description of Drosophila melanogaster phenotypes."^^ . - . - "^\\d{7}$"^^ . - "Logical Observation Identifiers Names and Codes" . - . - "wawong@gmail.com" . - . - . - . - . - . - "P00024"^^ . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . - . - . - "http://purl.obolibrary.org/obo/ONTONEO_"^^ . - . - "insertion" . - . - . - . - . - . - "grouping" . - "CCDS13573.1"^^ . - . - . - . - . - "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"^^ . - "protein" . - . - . - . - . - . - "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."^^ . - "structure" . - . - "World Wildlife Fund Ecoregion" . - "ICEberg family" . - . - "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . - . - . - . - . - "Ax1"^^ . - . - "Coleoptera Anatomy Ontology" . - "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"^^ . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - "eugenes@iubio.bio.indiana.edu" . - "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" . - "0000252"^^ . - . - "^B\\d+$"^^ . - . - . - "1.1.1.1"^^ . - . - "0000101"^^ . - . - . - . - . - "David Mendez Lopez" . - . - "mouse" . - "^NRFC\\d+$"^^ . - "A database-specific registry supporting curation in the Gene Ontology"^^ . - "https://ligandbook.org/package/$1"^^ . - "DragonDB Locus" . - . - . - . - . - . - "^\\d+$"^^ . - "mba" . - . - "false"^^ . - "pathway" . - "bioinformatics" . - . - "https://civicdb.org/links/drugs/"^^ . - . - "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . - . - "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . - "enm" . - "http://purl.obolibrary.org/obo/BOOTSTREP_"^^ . - . - . - . - "https://go.drugbank.com/salts/$1"^^ . - . - . - . - "nucleotide" . - . - . - "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . - . - . - . - "ASTD" . - . - "100291"^^ . - . - . - "A Knowledge Resource for Innate Immunity Interactions and Pathways" . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "genome" . - . - . - "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . - . - "VSAO_0000183"^^ . - . - . - . - _:Ne79eba7c8d2944bba4b664305e5179ca . - "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."^^ . - . - "A type for entries in the Bioregistry's registry." . - . - "has prefix" . - "life science" . - . - . - "9781584885658"^^ . - . - "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . - . - "false"^^ . - . - . - "https://www.deciphergenomics.org/syndrome/$1"^^ . - . - "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms."^^ . - "100101"^^ . - "false"^^ . - "https://mmp.sfb.uit.no/databases/marfun/#/records/"^^ . - . - . - . - . - "Donny Winston" . - . - . - _:N27ef8028e2244489bf142e7a8b5cc089 . - . - . - . - . - "BioModels Database" . - . - . - . - "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . - . - . - "pathway" . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references sheep QTLs."^^ . - . - . - . - "^\\d+$"^^ . - "transcriptomics" . - "ontology" . - . - "ontology" . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$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."^^ . - "transgenic" . - . - . - . - . - . - . - . - "dna" . - . - . - . - . - . - "obo" . - _:N0b76c49429ac46d794bde4f27f024c25 . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . - . - "^SM\\d{5}$"^^ . - "false"^^ . - . - "51"^^ . - "brendanx@uw.edu" . - . - . - "molecular biology" . - "cell biology" . - "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."^^ . - . - "https://sumlineknowledgebase.com/?page_id="^^ . - . - . - . - "^\\d{7}$"^^ . - . - "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . - . - . - "CIAT Common bean trait dictionary - version August 2014"^^ . - "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://cropontology.org/rdf/CO_334:$1"^^ . - "bigg.metabolite" . - . - "http://purl.obolibrary.org/obo/SCDO_"^^ . - . - "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . - "NIST Chemistry WebBook" . - "Variation Ontology" . - "ontology" . - . - "The Antibiotic Resistance Genes Database (ARDB) is a manually curated database which characterises genes involved in antibiotic resistance. Each gene and resistance type is annotated with information, including resistance profile, mechanism of action, ontology, COG and CDD annotations, as well as external links to sequence and protein databases. This collection references resistance genes."^^ . - . - . - . - "protein" . - . - . - . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PROCO_$1"^^ . - . - . - . - . - . - "^UP\\d{9}$"^^ . - "biomedical science" . - . - . - . - "agriculture" . - . - . - . - . - . - "minid.test" . - . - . - "ontology" . - "https://id.loc.gov/authorities/$1"^^ . - . - . - "^\\d+$"^^ . - . - . - "^M\\d{4}$"^^ . - . - . - . - "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . - . - "https://www.metanetx.org/comp_info/"^^ . - . - "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . - . - . - . - "false"^^ . - "^\\d{7}$"^^ . - "developmental biology" . - "Núria Queralt Rosinach" . - . - "http://purl.obolibrary.org/obo/MFMO_"^^ . - "^[0-9]*$"^^ . - . - "http://purl.obolibrary.org/obo/PHIPO_"^^ . - . - . - "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. "^^ . - . - "https://horizondiscovery.com/en/search?searchterm=$1"^^ . - "false"^^ . - . - "OMIMPS" . - . - . - "OncoTree" . - "oborel" . - . - . - "https://github.com/"^^ . - "false"^^ . - . - . - . - "false"^^ . - "efo" . - . - . - . - . - . - "protein" . - "orcid" . - "d4akea1"^^ . - . - . - . - "life science" . - . - "chemistry" . - "http://purl.obolibrary.org/obo/FYPO_$1"^^ . - . - . - "false"^^ . - "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . - . - "rna" . - . - . - "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . - . - . - . - . - "hms.lincs.compound" . - "^\\d{7}$"^^ . - . - . - . - "false"^^ . - . - . - "FuncBase Human" . - "cadsr" . - . - "false"^^ . - . - . - "Gene Expression Ontology" . - . - . - . - . - . - "Nicolas Le Novere" . - . - "ElementNumber"^^ . - . - . - . - . - . - "functional genomics" . - . - . - . - . - . - . - "NIH RePORTER" . - "E13035"^^ . - . - "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId="^^ . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId="^^ . - . - "false"^^ . - . -_:N56f74624ea2a452aaea72b619dca97d2 "NLM Customer Service" . - "TreeBASE" . - . - . - . - "Mathias Brochhausen" . - "plant genetics" . - . - . - "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . - . - "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym="^^ . - "1458400"^^ . - "false"^^ . - "yid" . - "https://www.arabidopsis.org/servlets/TairObject?type=locus&name="^^ . - . - "Prefix.cc" . - . - "obo" . - . - "false"^^ . - . - "anatomy" . - "^\\d+$"^^ . - "117145750"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1"^^ . -_:Nd2da98853435498c95a99ab2d84381d1 "helpdesk@cropontology-curationtool.org" . - "subject agnostic" . - "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid="^^ . - "The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation."^^ . - . - . - . - "Genitourinary Development Molecular Anatomy Project" . - "MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, it provides information about diseases, conditions, and wellness issues using non-technical terms and language."^^ . - "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . - . - "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces."^^ . - "https://identifiers.org" . - "tanja.bekhuis@tcbinfosci.com" . - "^PED\\d{5}e\\d{3}$"^^ . - . - . - "taxonomy" . - . - "false"^^ . - "Bioregistry" . - "https://dandiarchive.org/dandiset/"^^ . - . - . - . - . - . - . - . - . - "^[0-9a-zA-Z]+$"^^ . - . - . - "agricola" . - "life science" . - . - . - . - "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . - . - "genetically modified pig" . - "owl" . - . - "pspub" . - "neurophysiology" . - . - . - . - . - "78073"^^ . - . - . - . - "eolife" . - "0000404"^^ . - . - . - . - . - . - "https://www.ebi.ac.uk/intact/interaction/"^^ . - "life science" . - . - . - "BQJCRHHNABKAKU"^^ . - "genpept" . - "obo" . - . - . - "true"^^ . - . - . - . - . - . - . - "irefweb" . - "cog.pathway" . - . - "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/MF_"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "atcc" . - . - . - . - "GO Relations" . - "http://www.ubio.org/browser/details.php?namebankID="^^ . - "mirTarBase" . - "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"^^ . - "Hannele Laivuori" . - . - . - . - . - . - . - . - . - . - . - "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . - "ontology" . - "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . - "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1"^^ . - "https://bioregistry.io/metaregistry/scholia/$1"^^ . - "F0001"^^ . - "Dylan McGagh" . - . - . - . - . - . - . - . - "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . - . - . - "ontology" . - . - . - . - "grid" . - . - "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."^^ . - . - . - . - . - . - "true"^^ . - "https://civicdb.org/links/variant_group/"^^ . - . - . - . - . - "umbbd.pathway" . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . - . - . - "^EG\\d+$"^^ . - . - "Abcam" . - "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"^^ . - "true"^^ . - "https://web.expasy.org/cellosaurus/" . - "ViolinNet" . - "Vir-Mir db" . - . - . - . - . - . - . - "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"^^ . - . - "ensembl.fungi" . - . - . - "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."^^ . - "UniProt Diseases" . - . - "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."^^ . - "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."^^ . - . - "false"^^ . - "gene" . - "SBGN Bricks data and ontology" . - . - . - . - "131392"^^ . - . - . - "https://www.novusbio.com/products/$1"^^ . - . - . - . - . - "00000532"^^ . - . - . - . - . - . - . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . - . - "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"^^ . - . - . - "1"^^ . - "10142"^^ . - . - "pepbank" . - . - . - "sugarbind" . - "Agronomy Vocabulary" . - . - . - . - . - "^\\d+$"^^ . - . - "oriental-cds@163.com" . - "hso" . - "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle"^^ . - "https://www.uniprot.org/keywords/"^^ . - "^\\d{7}$"^^ . - "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."^^ . - . - . - "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."^^ . - . - "http://www.case.edu/EpilepsyOntology.owl#$1"^^ . - . - . - "^D\\d+$"^^ . - . - "Scientific Information Retrieval and Exchange Network" . - . - "false"^^ . - "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . - . - "interaction" . - "^\\d{7}$"^^ . - . - . - . - "^PRI\\d*$"^^ . - . - "reaction" . - "^\\d+$"^^ . - . - . - . - "false"^^ . - . - . - "artificial intelligence" . - "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . -_:N56f74624ea2a452aaea72b619dca97d2 "custserv@nlm.nih.gov" . - "Malaria Ontology" . - . - "http://purl.obolibrary.org/obo/IDOMAL_"^^ . - . - . - "false"^^ . - . - . - "civic.vgid" . - "obo" . - . - . - . - . - . - "life science" . - . - . - "Dictyostelium discoideum anatomy" . - . - "true"^^ . - "false"^^ . - . - . - . - . - "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."^^ . - "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . - . - . - . - "imotdb" . - . - "protein" . - . - . - . - . - "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."^^ . - "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . - "biorxiv" . - . - . - . - . - . - "https://www.uniprot.org/database/"^^ . - . - . - . - . - . - . - "https://mips.helmholtz-muenchen.de/corum/?id="^^ . - "Open Data for Access and Mining" . - . - "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . - . - "agriculture" . - "http://purl.obolibrary.org/obo/GENO_$1"^^ . - "International Traditional Medicine Clinical Trial Registry" . - . - "chemistry" . - "http://purl.obolibrary.org/obo/GO_$1"^^ . - "^\\d+$"^^ . - . - . - . - "https://europepmc.org/article/CTX/"^^ . - . - "CHEBI" . - "Information for ligands in the BRENDA database."^^ . -_:N9aafcf7456c84e55b289f755161257e1 "PhenX Admin" . - "PeptideAtlas Dataset" . - "^C\\d{8}$"^^ . - . - "obo" . - . - . - . - . - "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . - . - . - . - . - . - . - "nif.grossanatomy" . - "osa-miR446"^^ . - "bindingdb" . - . - "Performance Summary Display Ontology" . - . - "life science" . - . - . - "co_333" . - "false"^^ . - . - . - "descriptor" . - "mcc" . - . - "0000079"^^ . - . - . - "obo" . - . - "false"^^ . - . - "^M[0-9]{4,}$"^^ . - . - . - "0000127"^^ . - "https://registry.identifiers.org/registry?query=MIR:$1"^^ . - . - . - "http://scop.berkeley.edu/sccs="^^ . - "171"^^ . - . - . - . - . - "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . - . - . - . - "Zach Landis-Lewis" . - "false"^^ . - . - . - . - "http://www.alzgene.org/geneoverview.asp?geneid=$1"^^ . - . - "life science" . - . - . - . - "slm" . - . - "131"^^ . - . - . - . - "0000255"^^ . - "OSC1416"^^ . - . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . - . - "LINCS Protein" . - "ontology" . - "Statistical Torsional Angles Potentials" . - "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . - . - . - . - "1981638"^^ . - . - . - . - . - . - "human" . - . - "The Bioregistry's meta-registry"^^ . - "adult" . - "biology" . - . - . - "4007166"^^ . - "dso" . - . - . - . - . - "false"^^ . - "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . - . - "FamPlex" . - "ontology" . - . - . - . - . - "ToxoDB" . - . - "genome" . - . - . - . - "^\\d+$"^^ . - . - . - . - "bioinformatics" . - "^\\d+$"^^ . - . - "Uber Anatomy Ontology" . - . - . - . - . - "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein="^^ . - "ontology" . - . - . - . - "anatomy" . - "^\\d+$"^^ . - . - "life science" . - "wmueller@gbf.de" . - . - . - . - . - "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . - . - "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . - "https://github.com/prefixcommons/biocontext" . - . - . - . - . - . - . - "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . - . - . - "Biological Expression Language" . - "2gc4"^^ . - . - . - . -_:N5d69a50234384603b72e609a9e54e2b4 "helpdesk@cropontology-curationtool.org" . - . - . - "Pan African Clinical Trials Registry" . - "anatomy" . - . - "C. elegans ORFeome cloning project" . - "http://purl.obolibrary.org/obo/IDO_"^^ . - . - "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections."^^ . - "flymine.chromosome" . - . - "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . - . - "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . - "https://pk-db.com/data/$1"^^ . - . - . - "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . - . - . - "structure" . - "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."^^ . - . - . - "mice" . - . - . - "http://www.depod.bioss.uni-freiburg.de/showp.php?gene="^^ . - . - . - . - "Illumina Probe Identifier" . - "ontology" . - . - . - . - "MycoBrowser leprae" . - . - . - . - . - "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . - "The Ontology of Genes and Genomes" . - . - . - "genetics" . - . - "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate."^^ . - . - "protein" . - . - . - . - . - "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . - . - . - "false"^^ . - "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . - "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm="^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/DUO_$1"^^ . - . - "eukaryotic Subcellular Localization database" . - . - . - "http://www.fairsharing.org/ontology/subject/SRAO_"^^ . - "false"^^ . - "appears in" . - . - . - . - . - . - "gene" . - "5"^^ . - . - . - "ontology" . - . - "^\\d{7}$"^^ . - "taxonomy" . - . - "immunology" . - . - "PANTHER Pathway" . - . - . - . - "protein" . - "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id="^^ . - "http://purl.org/ontology/bibo/"^^ . - "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . - . - . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - "David Brodbelt" . - "metabolomics" . - . - . - "comparative genomics" . - "The coding sequence or protein identifiers as maintained in INSDC."^^ . - "NMR-instrument specific component of metabolomics investigations" . - . - . - "life science" . - "false"^^ . - "ISO Object Identifier" . - "ortholog" . - "development" . - "Histopathology Ontology" . - . - . - . - . - "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and the recently described transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references ligands."^^ . - "linguist" . - . - "The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification."^^ . - . - "false"^^ . - "Japan Collection of Microorganisms" . - . - . - "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . - . - . - "cdt" . - . - "http://purl.obolibrary.org/obo/OMP_"^^ . - . - . - . - "15567"^^ . - "subject agnostic" . - "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . - . - . - . - . - "^\\d{7}$"^^ . - "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"^^ . - . - "cd00400"^^ . - "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/"^^ . - "co_341" . - "^\\d{7}$"^^ . - "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."^^ . - "gene" . - . - "https://www.ebi.ac.uk/ega/datasets/$1"^^ . - . - . - "doi" . - . - . - "MESHA" . - . - . - . - . - . - "ontology" . - "http://bigg.ucsd.edu/compartments/"^^ . - . - . - . - "NLXFUNC covers terms for cognitive function."^^ . - . - . - "http://purl.org/spar/pro/"^^ . - "http://www.humanproteomemap.org/protein.php?hpm_id="^^ . - . - . - . - . - . - "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan."^^ . - . - . - . - "false"^^ . - "alistair.miles@linacre.ox.ac.uk" . - . - "isrctn" . - "PELNAW"^^ . - . - . - . - . - "tads" . - . - . - "https://www.vmh.life/#metabolite/"^^ . - "^\\d+$"^^ . - "comparative genomics" . - "false"^^ . - "http://purl.obolibrary.org/obo/CMF_$1"^^ . - . - . - . - . - . - "FDB MedKnowledge encompasses medications approved by the U.S. Food and Drug Administration, and information on commonly-used over-the-counter and alternative therapy agents such as herbals, nutraceuticals and dietary supplements."^^ . - . - . - . - . - . - . - "Maria Taboada" . - "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . - . - "TriTrypDB" . - "^RCB\\d+$"^^ . - "biology" . - "obo" . - "false"^^ . - "chemical" . - . - . - . - "protein" . - "life science" . - "ctd.disease" . - . - "http://www.co-ode.org/ontologies/galen#$1"^^ . - "false"^^ . - "ontology" . - . - "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . - . - . - . - "1199"^^ . - . - "c0001"^^ . - "topics" . - "http://icd9cm.chrisendres.com/index.php?action=search&srchtext="^^ . - . - . - . - . - "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . - . - "true"^^ . - "Odor Molecules DataBase" . - "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id="^^ . - . - "Q13485"^^ . - . - . - . - . - "http://data.europa.eu/89h/"^^ . - . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - . - . - . - . - . - "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . - "https://bioregistry.io/abcam:"^^ . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/NCBITaxon_"^^ . - "environmental science" . - . - . - . - "MobiDB" . - . - "http://purl.obolibrary.org/obo/DINTO_"^^ . - . - "50943"^^ . - . - . - . - . - . - . - . - "International repository of Adverse Outcome Pathways."^^ . - . - "IRD Segment Sequence" . - "^\\d+$"^^ . - "false"^^ . - . -_:N7ead588b1f1a4386a2b710735d92b468 "Jonathan Bard" . - "obo" . - . - . - . - . - . - "TopFind" . - . - . - . - "Anatomical Therapeutic Chemical Classification System" . - . - . - "nmckenna@bcm.edu" . - "^B\\d{5}$"^^ . - . - . - . - "classification" . - "MGYA00002270"^^ . - "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . - . - "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno="^^ . - "mjyoder@illinois.edu" . - . - . - "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . - "John Beverly" . - "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . - . - "The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with CATH domains."^^ . - . - "obo" . - . -_:N80cd99ec595a4d0599dce7bf309e7f23 "agrovoc@fao.org" . - . - "^\\d+$"^^ . - . - . - . - "environmental science" . - "genedb" . - . - . - . - "https://www.scopus.com/authid/detail.uri?authorId="^^ . - . - . - . - . - . - "clao" . - . - "false"^^ . - . - "Virus' miRNA target" . - . - . - . - . - . - "http://modelseed.org/biochem/compounds/"^^ . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - "true"^^ . - . - . - "vsao" . - "life science" . - "ai10e-kctd13b"^^ . - . - . - . - "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . - . - "Glyma0021s00410"^^ . - . - . - . - "http://noctua.geneontology.org/editor/graph/gomodel:"^^ . - . - . - . - . - "phosphosite.residue" . - . - . - . - "http://arabidopsis.org/servlets/TairObject?accession=AASequence:"^^ . - . - . - . - . - "https://www.ebi.ac.uk/chembl/entity/"^^ . - . - "^SL-\\d+$"^^ . - . - . - "6472"^^ . - "Human Brain Atlas" . - . - . -_:N5a47e5d4a29a4e209ad7f089db31aeb3 "European Food Safety Authority" . - "chemical" . - . - "seed" . - "false"^^ . - . - . - "https://www.hipsci.org/lines/#/lines/"^^ . - "biomedical science" . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/OMIT_$1"^^ . - . - . - . - "rism" . - . - . - . - . - . - "genome" . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id="^^ . - . - . - . - "rebase" . - "rna" . - . - . - "http://www.receptors.org/nucleardb/proteins/"^^ . - . - . - "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . - . - "characterisation data heat" . - . - . - . - . - "true"^^ . - . - "lectins/172"^^ . - "biomedical science" . - "tigrfam" . - . - . - . - "biomedical science" . - . - "true"^^ . - . - . - "NONHSAG00001"^^ . - . - . - . - "false"^^ . - . - . - . - "^[A-Z]+[A-Z-0-9]{2,}$"^^ . - . - "false"^^ . - . - . - . - "obo" . - . - . - "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . - . - "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . - . - . - . - . - "http://www.wikidata.org/entity/"^^ . - "ontology" . - "life science" . - "ontology" . - . - "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . - . - . - "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . - . - . - "plant genetics" . - . - "PubChem Element" . - "decipher" . - "protein" . - . - "^MMAR\\_\\d+$"^^ . - "false"^^ . - . - "genome" . - "PK-DB" . - . - "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . - . - "ymdb" . - "LipidBank" . - . - . - "life science" . - . - "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)."^^ . - "phylogenomics" . - . - . - . - "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . - "data management" . - "Chicken Gene Nomenclature Consortium" . - . - . - . - . - . - "uniprot.keyword" . - "UR000124451"^^ . - "life science" . - . - "https://www.ebi.ac.uk/gwas/studies/"^^ . - . - . - . - . - . - . - . - . - . - "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . - . - . - . - "SNR17A"^^ . - "Paul Fabry" . - . - "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . - "https://www.worldwildlife.org/ecoregions/"^^ . - . - . - . - . - . - . - "MGgn0008978"^^ . - . - . - . - "drugcentral" . - . - "434"^^ . - "^\\d{7}$"^^ . - . - "mesh" . - . - "1829126"^^ . - . - . - "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."^^ . - "CASID" . - . - "false"^^ . - . - "developmental biology" . - . - . - "pseudomonas" . - "genetics" . - . - "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."^^ . - "Luis González-Montaña" . - . - "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . - "Cell line databases/resources"^^ . - "transposon family" . - . - "false"^^ . - "10087"^^ . - . - . - "Liliana Andres Hernandez" . - . - . - . - . - . - . - "rna" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "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."^^ . - "https://cropontology.org/ontology/$1" . - . - . - . - "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . - . - . - . - "Sunflower ontology" . - "deepak.unni3@gmail.com" . - . - "upper-level ontology" . - "glycomics" . - "comparative genomics" . - . - "immunology" . - . - . - . - . - . - "http://oid-info.com/get/$1" . - . - "structure" . - . - "sabiork.kineticrecord" . - . - "^\\d{7}$"^^ . - . - . - . - "fbrf" . - . - "2029"^^ . - . - . - "mat" . - . - . - "^\\d{7}$"^^ . - . - "1"^^ . - "GO-Causal Activity Models (GO-CAMs) use a defined “grammar” for linking multiple GO annotations into larger models of biological function (such as “pathways”) in a semantically structured manner. GO-CAMs are created by expert biocurators from the GO Consortium, using the Noctua Curation Platform."^^ . - . - . - "http://purl.obolibrary.org/obo/MS_"^^ . - . - . - . - . - . - . - . - . - . - . - . - "ecoliwiki" . - . - . - "^[0-9]{10}$"^^ . - "ontology" . - . - . - . - . - . - "animal physiology" . - "http://pax-db.org/#!protein/"^^ . - . - . - . - . - . - "Bioregistry" . - "false"^^ . - "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code="^^ . - "computer science" . - . - . - "false"^^ . - . - "false"^^ . - . - . - "^G\\d+$"^^ . - "gthayman@mcw.edu" . - . - . - "RxNorm" . - . - . - . - "ArrayExpress" . - . - "true"^^ . - . - . - "true"^^ . - . - . - . - . - "0005067"^^ . - . - . - . - "Molecular Interactions Controlled Vocabulary" . - "false"^^ . - . - . - . - "txpo" . - . - . - "false"^^ . - . - "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)."^^ . - . - . - . - "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "health science" . - "bio.tools" . - "Sue Bello" . - "Barry Smith" . - "genome" . - "https://assets.nemoarchive.org/"^^ . - . - . - . - . - . - . - "clinical veterinary medicine" . - . - . - "An identifier for a country in numeric format per ISO 3166-1"^^ . - "^\\d+$"^^ . - "xeni.kechagioglou@lifewatch.eu" . - . - "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . - . - "https://www.metanetx.org/chem_info/$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer."^^ . - "2244"^^ . - . - . - . - "DrugBank" . - . - . - "pathway" . - . - "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . - . - . - . - . - "https://s3.us-east-2.amazonaws.com/lg.cede/"^^ . - . - . - . - . - "obo" . - "false"^^ . - "emaps" . - "The Olfactory Receptor Database (ORDB) is a repository of genomics and proteomics information of olfactory receptors (ORs). It includes a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfactory receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs)."^^ . - . - . - . - . - "obo" . - "MLCommons Association" . - . - . - "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://modelseed.org/biochem/reactions/"^^ . - "0000001"^^ . - . - . - . - . - . - "46"^^ . - "health science" . - . - . - . - . - . - . - "unique identifiers" . - "false"^^ . - . - . - . - . - "Pol Castellano Escuder" . - . - "Provenance, Authoring, and Versioning Vocabulary" . - . - "false"^^ . - . - . - . - . - . - . - "K00973"^^ . - "PR000001"^^ . - "Vertebrate Genome Annotation Database" . - . - . - . - . - . - "David Osumi-Sutherland" . - . - "Database of RNA Junctions and Kissing loop Structures" . - . - "^\\d+$"^^ . - . - . - "false"^^ . - "ontology" . - . - "image" . - . - "FooDB compound" . - . - "Influenza Sequence and Epitope Database" . - . - . - . - . - . - "hssp" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "^[A-Z0-9]+$"^^ . - . - "human genetics" . - "http://purl.obolibrary.org/obo/REX_"^^ . - "scholia.resource" . - "orthodb" . - "true"^^ . - "http://w3id.org/nkos/$1"^^ . - . - . - . - "ecso" . - "chemistry" . - . - . - . - . - . - . - . - . - . - "subject agnostic" . - . - . - . - "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . - . - . - "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."^^ . - "https://bioregistry.io/reo:"^^ . - "Genotype Ontology" . - . - . - . - "ecocore" . - . - . - "pathway" . - . - "https://www.ncbi.nlm.nih.gov/nucest/"^^ . - . - . - "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://www.iclc.it/details/det_list.php?line_id="^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - . - "http://bigg.ucsd.edu/models/$1"^^ . - . - . - "BIND accession number" . - "http://www.isni.org/isni/"^^ . - "ontology" . - . - . - . - . - . - . - "https://aopwiki.org/aops/$1"^^ . - . - "metabolomics" . - . - . - . - "spd" . - . - _:Na59b29921d6c49bc83dc307084549278 . - . - "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . - "doi" . - . - . - . - . -_:Neb0864156da647c4b350d1c2d17e099a "Crop Ontology Helpdesk" . - . - . - . - . - . - "CoVoc Coronavirus Vocabulary" . - . - "false"^^ . - . - . - . - "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . - . - "^\\d+$"^^ . - . - "false"^^ . - . - "Olfactory Receptor Database" . - . - "cell regeneration" . - . - . - "ontology" . - "p3db.site" . - . - . - "co_357" . - "protein" . - "90000018"^^ . - . - . - . - . - . - "agriculture" . - "ecosystem science" . - "Epidemiology Ontology" . - "http://hdl.handle.net/$1"^^ . - "false"^^ . - "Chen Yang" . - . - . - "System Science of Biological Dynamics dataset" . - . - . - . - . - "Hepatitis C Virus Database Project" . - "snomedct" . - . - "life science" . - . - . - "SIDM01262"^^ . - "pathbank" . - . - . - . - . - . - . - . - . - "molecular biology" . - . - . - . - "Cell line collections (Providers)"^^ . - . - . - . - . - . - "MycoBrowser marinum" . - . - . - . - . - "13"^^ . - . - . - "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"^^ . - "0000390"^^ . - "5"^^ . - "https://lincs.hms.harvard.edu/db/cells/"^^ . - . - . - . - "lucas.leclere@obs-vlfr.fr" . - "ontology" . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . - . - "http://purl.obolibrary.org/obo/MOD_"^^ . - "6819"^^ . - "life science" . - . - . - . - . - "Unified Medical Language System Concept Unique Identifier" . - . - . - "life science" . - . - . - "ppr" . - . - "ontology" . - "https://www.bgee.org/gene/"^^ . - . - . - . - . - "http://purl.org/spar/pwo/"^^ . - "Guide to Pharmacology Target" . - . - . - "protein" . - . - . - . - . - . - "Drosophila RNAi Screening Center" . - . - . - "edeutsch@systemsbiology.org" . - "pharmacology" . - . - "metabolomics" . - "biomedical science" . - . - "natural science" . - "0000080"^^ . - "https://w3id.org/oc/meta/"^^ . - . - . - . - . - . - "0000890"^^ . - . - . - . - "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library"^^ . - . - . - . - "https://www.grid.ac/institutes/$1"^^ . - "icldb" . - "igsn" . - . - "subject agnostic" . - "dna" . - . - . - . - . - . - . - . - . - . - . - "http://usefulinc.com/ns/doap#"^^ . - "Higher order grouping of Pfam families"^^ . - "false"^^ . - . - . - . - . - "https://lobid.org/gnd/$1"^^ . - "chemistry" . - "flowrepository" . - . - "http://purl.unep.org/sdg/SDGIO_$1"^^ . - "data visualization" . - "structure" . - . - . - . - . - "pid.pathway" . - . - . - "protein" . - . - "CIViC Evidence" . - . - "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . - . - . - "https://bioregistry.io/cabri:"^^ . - "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id="^^ . - "International Classification of Diseases, 9th Revision, Clinical Modification" . - "STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons."^^ . - . - "agriculture" . - . - . - "bpeters@lji.org" . - . - . - "Fungal Nomenclature and Species Bank" . - "false"^^ . - "life science" . - "http://purl.obolibrary.org/obo/MmusDv_"^^ . - . - "subject agnostic" . - . - . - "vipr" . - . - . - "Neuro Behavior Ontology" . - . - . - . - "Selventa legacy complex namespace used with the Biological Expression Language"^^ . - . - . - "^[0-9]+$"^^ . - "false"^^ . - . - . - "false"^^ . - . - . - "life science" . - . - . - . - "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada."^^ . - . - "datanator.gene" . - . - . - . - . - . - . - . - "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . - _:N6d2a57bcd6da4511b6f2ea2a501201de . - . - . - . - . - . - "false"^^ . - . - "https://ontology.iedb.org/ontology/ONTIE_"^^ . - . - . - . - . - "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . - "gexo" . - . - "ontology" . - "Semantic Mapping Vocabulary" . - . - . - . - "Hymenoptera Anatomy Ontology" . - . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . - "^[a-z_A-Z0-9]+$"^^ . - . - "ontology" . - "ontology" . - . - . - . - . - "ontology" . - . - . - . - . - . - . - "phylogeny" . - "false"^^ . - . - . - . - . - "Multiple alignment" . - "^\\d{7}$"^^ . - . - . - . - "Electron Microscopy Data Bank" . - . - "BugBase Protocol" . - . - . - "false"^^ . - "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . - . - . - . - . - . - . - . - . - . - . - "https://animaldiversity.org/accounts/$1"^^ . - . - "brenda.ligand" . - . - . - . - . - "biomedical science" . - . - "MGI" . - . - . - . - . - . - . - "obo" . - . - "proteomics" . - "life science" . - . - "icepo" . - . - . - . - . - . - "obo" . - . - . - "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . - . - "ontology" . - "structure" . - "MM00040"^^ . - "https://www.worldcat.org/oclc/"^^ . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . - . - . - "FB" . - . - . - . - . - . - . - . - . - . - . - . - . - "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . - "false"^^ . - . - "life science" . - "dylan.mcgagh@magd.ox.ac.uk" . - "^\\d{7}$"^^ . - "https://disprot.org/$1"^^ . - . - . - "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . - . - "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . - "A pull request in any public repository on GitHub."^^ . - . - . - . - "helpdesk@cropontology-curationtool.org" . - . - . - . - . - . - "^\\d{8}$"^^ . - . - . - . - "obo" . - . - . - "genecards.geneannot" . - . - "DiscoverX cell line products" . - . - "cosmic.cell" . - "protein" . - . - "http://rdfs.org/ns/void#$1"^^ . - "Allyson Lister" . - . - "AllSomeInterpretation"^^ . - . - . - . - "health" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/AAO_"^^ . - . - "https://www.affymetrix.com/LinkServlet?probeset="^^ . - . - . - . - "ontology" . - . - "obo" . - . - . - "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . - . - . - "Paula Duek Roggli" . - "gorel" . - . - . - "emolecules" . - "false"^^ . - "https://www.rebuildingakidney.org/id/"^^ . - . - "PhylomeDB" . - . - . - . - "Salmon Ontology" . - "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . - . - . - . - "arba" . - . - "mfoem" . - . - "Bilateria anatomy" . - "obo" . - "vegbank" . - . - "https://models.physiomeproject.org/workspace/"^^ . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "LINCS Small Molecule" . - . - "2555646"^^ . - . - . - "http://purl.obolibrary.org/obo/NCIT_"^^ . - . - . - . - "http://purl.org/sig/ont/fma/fma$1"^^ . - "false"^^ . - . - "^[A-Z0-9]{6,7}$"^^ . - . - . - . - "ontology" . - "http://purl.obolibrary.org/obo/AEON_$1"^^ . - . - "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . - "http://purl.obolibrary.org/obo/DIDEO_"^^ . - . - . - "2004-2820"^^ . - . - . - . - "Physiome Model Repository workspace" . - "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . - . - "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . - . - . - "NCBI_gi" . - "pubchem.bioassay" . - "AT1402"^^ . - "taxonomy" . - "false"^^ . - . - . - . - . - . - . - . - . - "Protein Model Database" . - . - . - . - . - "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . - . - . - . - . - "false"^^ . - "https://www.uniprot.org/uniref/"^^ . - . - "^\\d+$"^^ . - . - "^[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}$"^^ . - . - "uniprot" . - . - . - "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . - "medicine" . - "false"^^ . - . - . - . - "^\\S+$"^^ . - . - "genome" . - "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . - . - . - . - "491187"^^ . - . - "scopus.affiliation" . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "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."^^ . - . - "345201101230312003"^^ . - . - "iobc" . - "BG11523"^^ . - . - "demographics" . - . - . - . - . - "false"^^ . - . - . - "https://biopragmatics.github.io/providers/msigdb/$1"^^ . -_:N612ccc06c1964e1ab2ea595e41a70881 "Matt Berriman" . - . - . - "phenotype" . - . - "http://autism.mindspec.org/GeneDetail/$1"^^ . - . - . - . - . - . - . - "ped" . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "00005643"^^ . - . - . - "obo" . - "gene" . - . - . - "Veterinary Nomenclature" . - . - . - "^FCB\\d{3}$"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "https://fairsharing.org/$1" . - . - "co_336" . - . - "https://hl7.org/fhir/us/"^^ . - . - . - . - . - . - "https://lobid.org/gnd/"^^ . - "UMLS Semantic Network The Semantic Network consists of (1) a set of broad subject categories, or Semantic Types, that provide a consistent categorization of all concepts represented in the UMLS Metathesaurus, and (2) a set of useful and important relationships, or Semantic Relations, that exist between Semantic Types."^^ . - . - . - "^BE\\d{7}$"^^ . - . - . - . - "obo" . - . - . - . - . - . - . - "268"^^ . - . - "8668"^^ . - . - . - . - "UniProtKB-SubCell" . - "genewiki" . - "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."^^ . - . - "nucleotide" . - "genetic construct" . - . - . - . - . - . - "neurodegeneration" . - . - . - "https://cropontology.org/rdf/CO_324:$1"^^ . - . - . - . - "Organization" . - "botany" . - "genome" . - . - "http://purl.obolibrary.org/obo/EHDAA2_"^^ . - "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . - . - "false"^^ . - . - . - "codelink" . - . - . - "siiraa@umich.edu" . - "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . - . - "ontology" . - . - "false"^^ . - . -_:N11acbef7e61346bb88f3c99655fd742a "pbrooks@hcfa.gov" . - "false"^^ . - "false"^^ . - . - . - "Ana Rath" . - . - . - "The Drug Ontology" . - "hao" . - . - . - . - . - . - . - "https://www.emsl.pnnl.gov/project/$1"^^ . - . - . - . - "FBgn0000015"^^ . - . - . - "Library of Congress Subject Headings" . - . - . - . - . - . - . - . - . - . - "SNOWMEDCT" . - . - . - "http://purl.obolibrary.org/obo/OlatDv_"^^ . - . - . - "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)"^^ . - "biomedical science" . - . - . - . - . - "github.pull" . - . - . - . - . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/"^^ . - "imke.tammen@sydney.edu.au" . - . - . - . - . - . - . - "https://purl.dataone.org/odo/SASAP_$1"^^ . - . - . - "botany" . - . - . - "pharmacogenomics" . - "sitex" . - . - . - "false"^^ . - . - . - . - . - "Erik Segerdell" . - . - "Sabrina Toro" . - . - "biosimulations" . - . - . - . - . - "https://bioregistry.io/n2t:"^^ . - . - . - . - . - . - . - "structure" . - . - . - . - . - "false"^^ . - . - "co_340" . - "^(MAM\\d{5}\\w)|(MAR\\d{5})$"^^ . - . - . - . - "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."^^ . - . - . - . - . - . - "http://www.ontology-of-units-of-measure.org/resource/om-2/"^^ . - . - "biology" . - . - . - "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID="^^ . - . - . - "^E(S|D)i\\d+-\\w$"^^ . - "0000003"^^ . - . - "trait" . - "^FOOD\\d+$"^^ . - "http://tuberculist.epfl.ch/quicksearch.php?gene+name="^^ . - "anatomy" . - "https://idr.openmicroscopy.org/search/?query=Name:idr"^^ . - "ftp://hgdownload.cse.ucsc.edu/goldenPath/"^^ . - "biochemistry" . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query="^^ . - . - . - . - "https://www.signalingpathways.org/datasets/dataset.jsf?doi="^^ . - . - "^SLCTR/\\d{4}/\\d+$"^^ . - "http://purl.obolibrary.org/obo/UO_"^^ . - "Anvil" . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/SOPHARM_"^^ . - . - "Cellosaurus Registry" . - . - . - . - . - "false"^^ . - . - "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid="^^ . - "structure" . - . - "APID Interactomes" . - . - . - . - . - . - . - . - . - "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g="^^ . - . - "Protein Ensemble Database" . - "life science" . - . - . - . - "systems biology" . - . - . - "obo" . - "https://pk-db.com/data/"^^ . - . - . - "^\\d+$"^^ . - "genome" . - "false"^^ . - "XUO" . - . - . - . - "Q0VCA6"^^ . - . - "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present."^^ . - . - . - . - . - "https://biopragmatics.github.io/providers/dmba/$1"^^ . - . - . - . - "Xenopus Anatomy Ontology" . - . - "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."^^ . - . - . - . - . - . - . - "pscdb" . - "mouse embryonic stem cell line" . - . - . - "structure" . - . - . - "nucleotide" . - . - "http://purl.obolibrary.org/obo/TAHH_$1"^^ . - . - . - "FxnI151FMs"^^ . - . - "chemistry" . - "protein" . - . - . - . - . - "http://ciliate.org/index.php/feature/details/$1"^^ . - . - "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes."^^ . - "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."^^ . - . - "bcio" . - "HIP000030660"^^ . - . - . - . - "A formal represention for drug-drug interactions knowledge."^^ . - . - "https://publons.com/publon/$1"^^ . - . - . - . - "16941567"^^ . - "life science" . - . - "^FB\\w{2}\\d{7}$"^^ . - "https://www.worldcat.org/oclc/$1"^^ . - . - "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]"^^ . - . - . - "Gemina Symptom Ontology" . - . - "gene" . - "^\\d{7}$"^^ . - "splicenest" . - . - . - . - "false"^^ . - . - "obo" . - "http://psb.kobic.re.kr/STAP/refinement1/result.php?search="^^ . - "structure" . - . - . - "biomedical science" . - . - . - "kegg.metagenome" . - . - . - "genomics" . - . - "Lycalopex_vetulus"^^ . - . - . - . - . - . - . - "jakkbl@gmail.com" . - . - "wosuid" . - "genomics" . - . - . - . - "NeuroNames" . - . - . - . - "botany" . - "Cell line collections (Providers)"^^ . - . - "bioinformatics" . - . - "false"^^ . - "http://purl.obolibrary.org/obo/VSAO_"^^ . - . - . - "agriculture" . - . - "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . - . - . - . - . - . - "https://entomology.ca.uky.edu/content/$1"^^ . - . - . - . - . - . - . - . - "ontology" . - . - . - "00050"^^ . - . - . - . - . - . - "nlx.chem" . - . - . - "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt="^^ . - "IUPAC Gold Book Compendium of Chemical Terminology" . - "nlx.org" . - "http://www.imgt.org/ligmdb/view?id="^^ . - . - . - "MO000027"^^ . - "https://biokb.lcsb.uni.lu/fact/"^^ . - "dommino" . - "0000288"^^ . - . - . - "Sequence-Structural Templates of Single-member Superfamilies" . - . - . - "obo" . - . - . - "^\\d+$"^^ . - "Database of Complete Genome Homologous Genes Families" . - . - . - "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . - . - "^EGAS\\d{11}$"^^ . - . - . - "gene expression" . - . - "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . - . - . - "NUI" . - . - "bibliometrics" . - "genomics" . - "life science" . - "http://www.candidagenome.org/cgi-bin/locus.pl?dbid="^^ . - . - "medicine" . - . - . - "Maize ontology" . - . - "biomedical science" . - "vendor" . - . -_:N11acbef7e61346bb88f3c99655fd742a "Patricia Brooks" . - . - "Nucleic Acids Phylogenetic Profiling" . - "bacmap.map" . - . - "sciflection" . - "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . - . - . - . - "1"^^ . - "https://bioregistry.io/jaxmice:"^^ . - . - "false"^^ . - . - . - "http://gmd.mpimp-golm.mpg.de/Spectrums/"^^ . - "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains."^^ . - "Proteomic Data Commons" . - . - "http://purl.obolibrary.org/obo/HEPRO_"^^ . - "NCBI Protein" . - . - . - "false"^^ . - . - . - "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . - . - "combine.specifications" . - . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "3075966"^^ . - . - . - "genome" . - . - . - . - . - . - . - . - "^MIMAT\\d{7}$"^^ . - . - . - "edam" . - . - . - . - . - . - "false"^^ . - "https://cropontology.org/rdf/CO_323:"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "https://www.checklistbank.org/dataset/$1"^^ . - . - "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information."^^ . - . - . - . - . - . - . - "ecocyc" . - "anatomy" . - "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales."^^ . - . - "clinical studies" . - "Regulatory Elements Database for Drosophila" . - . - "annethessen@gmail.com" . - "life science" . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "^\\d+$"^^ . - "cell cycle" . - "https://cropontology.org/rdf/CO_339:"^^ . - . - . - "Descriptive Ontology for Linguistic and Cognitive Engineering" . - "^\\d{7}$"^^ . - . - "pharmacodb.tissue" . - "variant" . - "proteins" . - "false"^^ . - . - . - "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"^^ . - . - . - . - . - . - "gene" . - . - . - . - "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . - . - "00001234"^^ . - "^[A-Z_]{3}[0-9]{4,}$"^^ . - "life science" . - "Transcription Factor Database" . - . - "https://glygen.org/glycan/"^^ . - . - "Harry E. Pence" . - . - . - . - . - "genomics" . - . - . - . - . - "biomedical science" . - . - . - . - . - . - . - . - . -_:N5a47e5d4a29a4e209ad7f089db31aeb3 "datex@efsa.europa.eu" . - "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . - . - "FAIRsharing User" . - . - . - "GR_GENE" . - . - "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."^^ . - . - . - "gene expression" . - . - "http://purl.obolibrary.org/obo/IAO_"^^ . - . - "protein" . - . - . - "post-translational modification" . - . - . - "unirule" . - "Database of Interacting Proteins" . - . - "false"^^ . - "funding agencies" . - . - "infectious disease medicine" . - . - "Dan Brickley" . - . - . - . - "false"^^ . - . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . - "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "^tgv[0-9]+$"^^ . - . - . - "ontology" . - . - . - "MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway."^^ . - "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . - "data_1664"^^ . - . - "^\\d{7}$"^^ . - . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - . - "^\\d+$"^^ . - . - "EDAM Operation" . - . - "^\\d+$"^^ . - "DDInter20"^^ . - "goa" . - "^\\w+$"^^ . - . - . - "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant."^^ . - . - "http://purl.obolibrary.org/obo/PDRO_"^^ . - "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."^^ . - "structure" . - . - . - "00000003"^^ . - "gdsc" . - . - "Anne Thessen" . - . - "opb" . - . - "genome" . - "Interlinking Ontology for Biological Concepts" . - "semantic web" . - . - . - . - _:N8b543b3ccc35445baa4f243e0b8deea9 . - . - "SNOMEDCT_US_2019_03_01" . - . - . - "ontology" . - . - "AT5G05330"^^ . - . - . - "mmmp:biomaps" . - "false"^^ . - "anatomy" . - . - . - . - . - "life science" . - . - "Swiss Personalized Health Network Schema" . - . - . - . - . - "0101963"^^ . - "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."^^ . - . - . - "12"^^ . - "MAMpol005339"^^ . - "false"^^ . - "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"^^ . - "pancreatic islet function" . - . - "false"^^ . - . - "false"^^ . - . - . - . - . - "http://www.pharmgkb.org/gene/"^^ . - . - . - . - "Open Tree of Life" . - "chembl" . - . - . - . - . - . - . - . - . - "miriam"^^ . - . - . - "https://purl.uniprot.org/uniprot/$1"^^ . - "LexicalMatching"^^ . - "634515043"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "KIAA0001"^^ . - . - "ontology and terminology" . - . - . - "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . - "http://purl.obolibrary.org/obo/PSO_$1"^^ . - . - "mpjensen@buffalo.edu" . - . - "gnd" . - . - . - . - "ontology" . - "^A\\d{4}$"^^ . - . - . - . - . - "ClinVar Submitter" . - . - . - . - . - . - "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . - . - "unists" . - . - "0000030"^^ . - . - "Common Terminology Criteria for Adverse Events" . - . - . - "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)."^^ . - . - . - . - . - . - "ontology" . - . - . - . - "^\\d{7}$"^^ . - "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . - . - . - "ontology" . - "The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy."^^ . - . - . - "https://www.pharmvar.org/gene/"^^ . - . - . - "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound="^^ . - . - . - . - . - . - "did" . - "An ontology and inventory of geopolitical entities such as nations and their components (states, provinces, districts, counties) and the actual physical territories over which they have jurisdiction. We thus distinguish and assign different identifiers to the US in \"The US declared war on Germany\" vs. the US in \"The plane entered US airspace\"."^^ . - . - . - "^\\d+$"^^ . - . - . - "false"^^ . - . - "The S/MAR transaction DataBase" . - . - "ontie" . - . - . - . - . - "pgs" . - . - . - "312.33"^^ . - "ontology" . - "HMDB" . - . - "Data Catalog" . - "structure" . - "^\\d+$"^^ . - . - "ncbi.resource" . - . - . - . - . - . - . - "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . - "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . - "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . - "Wikidata Property" . - "http://purl.obolibrary.org/obo/CMO_$1"^^ . - . - . - . - . - . - . - "creeas@gmail.com" . - . - . - . - . - . - . - . - "ENSG00000169174"^^ . - . - "https://tools.ietf.org/rfc/rfc$1"^^ . - . - . - . - . - . - "biopixie" . - . - "cemo" . - . - . - . - . - "https://www.uniprot.org/tissues/$1"^^ . - . - . - . - . - "false"^^ . - "0000983"^^ . - "huanglin36@mail.sysu.edu.cn" . - "hdl" . - "poro" . - . - . - . - . - "Lars Holm Nielsen" . - "^(cd)?\\d{5}$"^^ . - . - . - "ERR436051"^^ . - . - . - . - . - "https://www.uniprot.org/locations/"^^ . - . - "REPRODUCE-ME Ontology" . - . - . - _:N10720e6ba83e4d6c8be7c875b1455193 . - . - . - "protein" . - . - . - . - . - . - . - "false"^^ . - . - . - "Cell line collections"^^ . - "genomics" . - . - "false"^^ . - "gaz" . - . - . - "https://medlineplus.gov/genetics/condition/"^^ . - . - "disorders" . - . - "Maciej.Antczak@cs.put.poznan.pl" . - "regulation" . - . - . - "false"^^ . - . - . - "cas_id" . - . - "aop.events" . - . - . - "https://www.cellbankaustralia.com/$1.html"^^ . - . - . - "^\\d{7}$"^^ . - . - "^\\d{7}$"^^ . - . - "0003"^^ . - "https://www.facebase.org/data/record/#1/isa:dataset/accession="^^ . - . - "http://snomed.info/id/$1"^^ . - . - . - . - "^\\d+$"^^ . - "co_343" . - . - "http://www-snorna.biotoul.fr/plus.php?id=$1"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - "Image Data Resource" . - "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID="^^ . - . - . - "TGME49_053730"^^ . - . - "faseb list" . - "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . - . - "26"^^ . - . - "Cell line collections (Providers)"^^ . - "http://opendata.inra.fr/ATOL/ATOL_"^^ . - . - "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."^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . - . - "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."^^ . - . - "http://www.w3.org/ns/oa#$1"^^ . - . - . - . - . - . - "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . - "Identifier for a species in iNaturalist"^^ . - . - . - . - . - . - "handle" . - . - . - . - . - "https://id.loc.gov/authorities/"^^ . - . - "chemistry" . - . - "false"^^ . - "prediction" . - "https://data.4dnucleome.org/biosources/$1"^^ . - "NLXCELL conatins cell types with a focus on neuron types."^^ . - "function" . - . - . - . - "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_"^^ . - . - . - "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . - . - . - "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . - "Xenobiotics Metabolism Database" . - . - "ontology" . - . - . - . - . - "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID="^^ . - . - "PANTHER Node" . - . - "VSAO_RETIRED" . - . - . - . - . - "Vendor for assays, cells, and antibodies"^^ . - "structure" . - "The UniProt Knowledgebase (UniProtKB) is a comprehensive resource for protein sequence and functional information with extensive cross-references to more than 120 external databases. Besides amino acid sequence and a description, it also provides taxonomic data and citation information."^^ . - . - . - . - . - . - . - . - "https://datalab.rwth-aachen.de/MINDER/resource/"^^ . - "https://ligandbook.org/package/"^^ . - . - "^[a-z0-9-]+$"^^ . - . - "protein"^^ . - "proteomics" . - . - "39421"^^ . - "International Classifications of Diseases" . - . - . - . - "obo" . - . - "imgt.primerdb" . - "chemistry" . - . - "gene" . - . - "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1"^^ . - . - "Banco de Celulas do Rio de Janeiro" . - . - . - "https://go.drugbank.com/reactions/"^^ . - . - . - . - "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc="^^ . - "false"^^ . - . - . - . - . - "http://purl.org/vocab/frbr/core#$1"^^ . - . - "https://openalex.org/"^^ . - "biomedical science" . - . - . - "perkinelmer" . - . - . - "http://purl.obolibrary.org/obo/IPR_$1"^^ . - . - "Open Biological and Biomedical Ontologies" . - . - "PdumDv" . - "ontology" . - "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . - . - . - "^\\d{7}$"^^ . - . - "life science" . - "bioinformatics" . - . - . - . - "http://www.noncode.org/NONCODERv3/ncrna.php?ncid="^^ . - . - . - "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="^^ . - "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . - . - . - . - . - . - "https://cropontology.org/rdf/CO_350:$1"^^ . - . - . - "RHEA" . - "^\\w+$"^^ . - "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . - "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . - . - . - . - "false"^^ . - . - . - "Plant Genome Network" . - . - "false"^^ . - . - . - "0000435"^^ . - . - "^[AMCST][0-9x][0-9]$"^^ . - "data management" . - . - . - . - . - . - . - . - "dna" . - . - "mampol" . - . - "protein" . - . - . - . - . - . - "biomedical science" . - . - "false"^^ . - . - "M58335"^^ . - "taxonomy" . - . - . - "false"^^ . - "^ML\\w+$"^^ . - "genome" . - . - . - "SABIO-RK" . - "nbo" . - . - . - . - . - "Progenetix" . - . - "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/"^^ . - . - . - . - . - . - . - . - . - "5UTR_107_ENST00000517291.2"^^ . - . - . - . - . - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . - . - "42840"^^ . - "gsfa" . - "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats."^^ . - "http://purl.obolibrary.org/obo/SIBO_"^^ . - . - . - "https://www.metanetx.org/equa_info/"^^ . - . - . - "true"^^ . - . - _:N7ead588b1f1a4386a2b710735d92b468 . - . - . - "ontology" . - . - . - . - . - . - "Selventa Diseases" . - . - "0000044"^^ . - . - . - "biology" . - "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . - "037727"^^ . - "term"^^ . - "https://www.checklistbank.org/dataset/3LR/taxon/"^^ . - . - "obo" . - . - "epidemiology" . - . - . - . - . - . - . - "HUGO Gene Nomenclature Committee" . - "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . - . - . - "false"^^ . - . - "metascience" . - "genome" . - "DragonDB DNA" . - "cvx" . - . - "http://www.kegg.jp/entry/"^^ . - . - "true"^^ . - . - . - . - . - "anatomy" . - . - . - "https://catalog.hathitrust.org/Record/$1"^^ . - . - "^[0-9A-Za-z\\-.]+$"^^ . - "54"^^ . - . - . - . - . - . - "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."^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "1"^^ . - . - . - . - . - . - . - . - . - . - "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio."^^ . - "pypi" . - . - . - . - "ChEMBL" . - "life science" . - . - . - "Datasets inside StoreDB"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . - . - "phenotype" . - "https://prefix.cc/$1" . - . - "ontology" . - "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . - . - . - "structure" . - . - "false"^^ . - . - "obo" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]"^^ . - . - "Nonribosomal Peptides Database" . - . - "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . - . - . - . - . - . - . - . - . - "anatomy" . - "^\\d{4}$"^^ . - . - . - "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."^^ . - . - "http://purl.obolibrary.org/obo/FAO_"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "https://w3id.org/oc/corpus/$1"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="^^ . - . - "Ensembl Glossary" . - . - . - . - "qtldb" . - . - . - . -_:N61f371b1d2fa4381a3fcd51f3dd48a97 "jamsden@us.ibm.com" . - . - "CAPS-DB" . - "Social Behavior in insects"^^ . - . - . - "^\\d+$"^^ . - . - "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . - "http://www.w3.org/2008/05/skos-xl#"^^ . - . - . - . - "transgenic" . - . - "false"^^ . - . - . - "mesh.2013" . - . - . - "http://purl.obolibrary.org/obo/CRO_$1"^^ . - . - "Minimum Anformation About a Phylogenetic Analysis Ontology" . - . - . - "https://comptox.epa.gov/dashboard/$1"^^ . - "bibliography" . - "larvae" . - "false"^^ . - . - . - . - "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . - . - . - . - . - . - "^YMDB\\d+$"^^ . - "false"^^ . - . - . - . - . - . - . - "SCV000151292"^^ . - "bko" . - . - "Database of Macromolecular Movements" . - "pride.project" . - "false"^^ . - "unichem" . - . - . - "https://bioregistry.io/wikigenes:"^^ . - . - . - "LNCipedia" . - "co_323" . - . - . - "oryzabase.stage" . - . - . - "1047874"^^ . - . - "expression" . - . - "4145692"^^ . - "HMS Library of Integrated Network-based Cellular Signatures Datasets" . - "obv" . - "false"^^ . - . - . - . - . - "T0599"^^ . - . - . - "false"^^ . - . - "ontology" . - "TA_H3"^^ . - . - "http://topdb.enzim.hu/?m=show&id="^^ . - . - "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . - . - . - . - . - . - . - . - "Jakob Voß" . - "4201PAT-CCTCC00348"^^ . - . - "obo" . - . - . - "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:"^^ . - . - "ontology" . - . - "DI-04240"^^ . - "omim.ps" . - . - "ADA"^^ . - . - . - "prefLabel"^^ . - . - "bacmap.biog" . - "CIViC Variant Group" . - "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . - . - "Protein Ontology" . - "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://purl.obolibrary.org/obo/ECAO_"^^ . - . - . - . - . - . - . - "ontology" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Glycan Naming and Subsumption Ontology" . - "Neil McKenna" . - "semantic web" . - . - . - . - . - "false"^^ . - . - "DI" . - . - "bspo" . - "^\\d+$"^^ . - . - . - . - . - . - "biomedical science" . - "mutant mouse repository" . - "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . - . - "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . - "ma" . - "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . - . - . - . - . - . - . - "M0001"^^ . - . - . - "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . - . - . - "environmental science" . - . - "e999"^^ . - "research" . - "https://purl.dataone.org/odo/MOSAIC_$1"^^ . - "https://cgap.nci.nih.gov/Pathways/BioCarta/"^^ . - "obo" . - . - "Yongqun Oliver He" . - "github" . - "abm" . - . - "virsi1909"^^ . - "medicine" . - . - "mirnest" . - . - "ontology" . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . - . - . - . - . - . - . - "161671"^^ . - "http://purl.obolibrary.org/obo/LBO_$1"^^ . - . - . - . - . - "https://cstr.cn/"^^ . - . - . - . - "false"^^ . - . - . - . - "http://purl.org/sig/ont/fma/fma"^^ . - . - "obo" . - . - "obo" . - "^\\d+$"^^ . - . - . - "Network Data Exchange" . - "genomics" . - . - "true"^^ . - . - . - . - "pathway" . - . - "false"^^ . - "subject agnostic" . - . - . - . - . - . - . - . - . - . - . - "The international standard for identifying health measurements, observations, and documents."^^ . - . - "enzyme" . - . - "adcad" . - "AAA35559"^^ . - "Jesper Friis" . - . - . - . - "fungidb" . - . - . - . - "contact@bacdive.de" . - . - "false"^^ . - "false"^^ . - . - "false"^^ . - "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."^^ . - . - "Gmelins Handbuch der anorganischen Chemie" . - "phytozome.locus" . - . - . - . - . - "0000253"^^ . - "http://purl.obolibrary.org/obo/OBIB_$1"^^ . - "f665230-5267"^^ . - . - "drsanv0" . - . - . - "http://pax-db.org/#!species/"^^ . - "proteomics" . - "kegg" . - "false"^^ . - "developmental biology" . - "http://qudt.org/schema/qudt#"^^ . - . - "Identifiers for proposals/projects at the Joint Genome Institute"^^ . - "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space"^^ . - . - "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . - . - . - "genotyping" . - . - . - . - . - "software engineering" . - . - . - . - . - . - "International Classification of Diseases, 10th Revision" . - "https://www.ncbi.nlm.nih.gov/medgen/"^^ . - "structure" . - . - . - "P10636"^^ . - "dna" . - . - . - . - . - "false"^^ . - . - . - "subject agnostic" . - "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."^^ . - . - "http://rebase.neb.com/rebase/enz/$1.html"^^ . - "Janna Hastings" . - "subject agnostic" . - . - . - "GrainGenes" . - . - "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . - "A controlled vocabulary to describe phenotypic traits in plants."^^ . - "fly" . - "medicine" . - "strain" . - . - . - . - . - . - . - . - . - "https://gudmap.org/id/$1"^^ . - . - "wdduncan@gmail.com" . - "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"^^ . - "montana.smith@pnnl.gov" . - "virus" . - "UPa" . - "ontology" . - . - . - . - . - . - . - "functional genomics" . - . - . - . - . - "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . - . - . - "false"^^ . - "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . - "UniProt Keywords" . - . - "http://purl.obolibrary.org/obo/EMAPA_"^^ . - . - . - . - . - . - . - . - . - . - "numpy"^^ . - "Rv1908c"^^ . - . - . - "biology" . - . - . - "E12768"^^ . - . - . - . - "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . - . - "EG10173"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "molecule" . - "ontology" . - "^\\d{7}$"^^ . - . - "ECGOntology" . - "andreas.ruepp@helmholtz-muenchen.de" . - "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . - "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . - . - "https://www.uniprot.org/arba/$1"^^ . - . - . - . - "UMLS Semantic Types Ontology" . - . - "protein" . - . - . - "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . - . - "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . - "https://uniresolver.io/#did:"^^ . - "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . - "obo" . - "andreas.ledl1@fhnw.ch" . - "false"^^ . - "false"^^ . - "ontology" . - "^\\d{9,9}$"^^ . - . - "sequence" . - "http://purl.obolibrary.org/obo/ZFS_$1"^^ . - . - "identifier for a chemical compound per EINECS or ELINCS"^^ . - . - "http://www.drugtargetontology.org/dto/DTO_$1"^^ . - . - "^PA\\w+$"^^ . - "dna" . - . - . - "1948"^^ . - "Ruili Huang" . - "Cotton ontology" . - "SR0000178"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "Eukaryotic Genes" . - . - . - . - . - "UPPRO" . - . - . - "^\\d+$"^^ . - "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . - "gene" . - . - . - . - "drug" . - "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."^^ . - . - "false"^^ . - "Amos.Bairoch@sib.swiss" . - "psychology" . - . - . - . - . - "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . - . - "mex" . - . - "GCF_000005845.2"^^ . - . - . - . - . - "Metabolomics Workbench Project" . - . - "iev" . - . - "^\\d+$"^^ . - "http://phylomedb.org/?seqid=$1"^^ . - "false"^^ . - "^\\d{7}$"^^ . - "Kerafast cell lines" . - . - "astrophysics and astronomy" . - . - . - . - "structure" . - "Database of Macromolecular Interactions" . - "Milton H. Saier, Jr." . - "false"^^ . - "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . - . - . - . - . - "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . - "mingxun.wang@cs.ucr.edu" . - "UPC04349"^^ . - "rbk" . - . - . - . - . - "Multum MediSource Lexicon" . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . - "life science" . - . - . - "http://purl.obolibrary.org/obo/HSO_$1"^^ . - "http://purl.obolibrary.org/obo/LABO_"^^ . - . - "^\\d+$"^^ . - . - . - "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - . - . - . - "cdno" . - "2200950"^^ . - "https://cropontology.org/rdf/CO_358:$1"^^ . - . - "chemistry" . - . - . - . - "^M\\d+$"^^ . - "Sofia Robb" . - . - "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . - "Linguist" . - "http://purl.obolibrary.org/obo/MMO_$1"^^ . - . - . - . - . - "development" . - . - "false"^^ . - "https://ror.org/"^^ . - . - "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . - "life science" . - . - . - . - "Wikidata Property" . - "dal.alghamdi92@gmail.com" . - "Swiss National Clinical Trials Portal" . - "CL070"^^ . - . - "0000254"^^ . - "http://purl.org/spar/datacite/"^^ . - . - . - "ncbitaxon" . - "ontology" . - . - . - . - . - . - . - "anatomy" . - . -_:N137416fe0fe14465a245cb8a86726e9d "The World Health Organization" . - . - . - "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project." . - . - "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . - . - "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . - . - . - . - "Subcellular Anatomy Ontology" . - "SNOMEDCT_US_2015_03_01" . - . - . - . - "false"^^ . - "^\\d+$"^^ . - "785"^^ . - "AY109603"^^ . - "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . - . - "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://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . - . - "false"^^ . - "Rat Strain Ontology" . - . - "mfo" . - "http://purl.obolibrary.org/obo/PORO_"^^ . - . - "Robert Hoehndorf" . - "322"^^ . - . - "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . - . - "ontology" . - "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . - . - . - . - . - "aging" . - . - . - . - "false"^^ . - "^GPST[0-9]{6}$"^^ . - . - . - . - . - . - . - "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . - "polysaccharide" . - "obo" . - . - . - "aro" . - "3905431"^^ . - "Plant Experimental Conditions Ontology" . - "^\\d+$"^^ . - "pathway" . - "July 2018"^^ . - . - . - "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . - "http://eugenes.org:7072/.bin/fbidq.html?"^^ . - . - "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."^^ . - . - "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/)."^^ . - . - "http://purl.obolibrary.org/obo/OHPI_"^^ . - . - "bioinformatics" . - "Resources mentioned in \"Sharing biological data: why, when, and how\"" . - . - . - "Sugar Kelp trait ontology" . - "0005"^^ . - "http://purl.obolibrary.org/obo/NBO_$1"^^ . - . - "http://purl.bioontology.org/ontology/VANDF/"^^ . - "Database of Genomic Structural Variation - Study" . - "ICD-10" . - . - . - . - "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://www.echinobase.org/entry/gene/showgene.do?method=display&geneId="^^ . - . - "small molecule" . - . - . - "ontology" . - . - . - . - . - "jgrethe@ucsd.edu" . - "genomics" . - . - . - "SM0000020"^^ . - . - . - . - . - "false"^^ . - . - . - "csp" . - "sopharm" . - . - . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . - . - . - . - "sequence" . - "earth science" . - . - . - "genome" . - . - . - "false"^^ . - "nbn" . - "false"^^ . - "https://civicdb.org/links/diseases/"^^ . - . - . - . - "0000062"^^ . - . - "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . - . - . - "cellimage" . - . - "shibase" . - . - "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)."^^ . - . - . - "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . - . - . - . - . - "ala"^^ . - . - "molecules" . - . - . - . - . - . - . - . - . - "ndf-rt" . - "http://purl.obolibrary.org/obo/FBcv_$1"^^ . - . - . - "epidemiology" . - . - . - "life science" . - . - . - "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"^^ . - . - "genetics" . - . - "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . - "hinv.locus" . - . - "0001056"^^ . - "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . - . - "UPISO" . - . - . - "obo" . - . - . - . - . - . - "neurobiology" . - . - "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."^^ . - . - . - . - "PhenX Toolkit" . - "Xenbase" . - "false"^^ . - . - "eol" . - "metagenomics" . - "http://www.hprd.org/protein/$1"^^ . - "^\\d+$"^^ . - . - . - "ACC-1"^^ . - "Reaxys eMolecules" . - . - "po" . - . - "ontology" . - . - "expression" . - "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID="^^ . - "The LifeWatch ERIC repository of semantic resources for the ecological domain." . - "31623"^^ . - "faseb list" . - "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName="^^ . - . - "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id="^^ . - . - . - "^\\d{7}$"^^ . - "ec-code" . - . - . - . - "genome" . - "http://fossilworks.org/?a=taxonInfo&taxon_no="^^ . - . - . - _:Nd2cf2107dfdb419d94a5e0f3473323b5 . - "https://www.aapc.com/codes/cpt-codes/"^^ . - "microarray" . - "688"^^ . - . - _:N4e25957c43b8426f813f5579b8ff53d7 . - . - . - . - . - . - . - . - . - "https://sciflection.com/$1"^^ . - . - "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . - "preclinical studies" . - . - "bdgp.est" . - . - "protein" . - . - . - . - "false"^^ . - "protein" . - . - "A user of FAIRsharing"^^ . - . - . - . - "https://bacteria.ensembl.org/id/$1"^^ . - "biomedical science" . - . - . - . - . - "dna" . - . - . - . - "^\\d{8}$"^^ . - . - . - "bernd.mueller@zbmed.de" . - "false"^^ . - . - "Database of structurally defined protein interfaces" . - "https://civicdb.org/links/molecular_profile/"^^ . - . - "false"^^ . - . - "ECMDB" . - . - "http://www.yeastract.com/view.php?existing=locus&orfname=$1"^^ . - . - "https://www.flymine.org/come/entry?gn=$1"^^ . - . - "ontology" . - . - . - . - "https://protists.ensembl.org/id/$1"^^ . - "swo" . - . - . - "anatomy" . - "SUM Breast Cancer Cell Line Knowledge Base" . - "funcbase.human" . - . - . - "23"^^ . - . - "lincs.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."^^ . - "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . - "stefan.kuhn@dmu.ac.uk" . - . - . - . - . - . - . - "https://civicdb.org/links/drugs/$1"^^ . - . - . - "^\\d{7}$"^^ . - . - "http://purl.obolibrary.org/obo/PCO_"^^ . - . - . - "MIRT000002"^^ . - "BIOMD0000000048"^^ . - "spectrometry" . - . - "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . - . - "Universal Spectrum Identifier" . - . - . - . - "https://bioregistry.io/cst.ab:"^^ . - . - . - . - . - . - "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . - "ISRCTN10175490"^^ . - "CAS_RN" . - . - . - "emsl.project" . - . - . - "^ECMDB\\d+$"^^ . - "Name-to-Thing" . - . - . - "http://purl.obolibrary.org/obo/GAZ_"^^ . - . - . - "false"^^ . - "https://scicrunch.org/resolver/RRID:IMSR_TAC_"^^ . - . - . - . - "Al Kikhney" . - . - . - "life science" . - . - . - . - . - . - . - "NIH Human Embryonic Stem Cell Registry" . - . - "gene" . - . - . - "https://orcid.org/$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."^^ . - . - . - "SchemaDefinition"^^ . - "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."^^ . - . - . - "Protein Structural Change Database" . - "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches)."^^ . - "false"^^ . - "metanetx.reaction" . - . - "xenbase" . - . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/"^^ . - "false"^^ . - . - "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . - . - "Citation Typing Ontology" . - . - "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."^^ . - . - "ligandbox" . - . - . - "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . - "0000048"^^ . - "iceberg.ime" . - "wosid" . - . - . - "21723"^^ . - . - . - "Cellular Microscopy Phenotype Ontology" . - "jcggdb" . - . - . - . - . - . - "alberto.traverso@maastro.nl" . - . - . - . - . - . - . - . - . - "chemical" . - . - "false"^^ . - . - . - . - "^JCRB\\d+$"^^ . - . - "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."^^ . - "metagenomics" . - . - . - "sequenced strain" . - . - . - "life science" . - "BAMSC981"^^ . - "biology" . - . - . - . - . - . - . - "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."^^ . - . - "true"^^ . - "metabolite" . - . - . - "asin" . - . - "^\\d+$"^^ . - "oryzabase.strain" . - . - . - . - . - "ontology" . - . - . - . - "ontology" . - . - . - . - . - . - "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."^^ . - . - . - . - "https://www.storedb.org/?STOREDB:DATASET$1"^^ . - . - . - . - "nif.cell" . - "http://oid-info.com/get/"^^ . - . - "genetics" . - "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . - "imsr.apb" . - . - "http://www.molmovdb.org/cgi-bin/morph.cgi?ID="^^ . - . - . - . - . - "221058"^^ . - "true"^^ . - . - . - "phenomics" . - . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PROCO_"^^ . - . - "go.chemical" . - "https://bioportal.bioontology.org/" . - . - . - . - "https://www.ensembl.org/id/$1"^^ . - . - . - . - . - "omid" . - "genomics" . - . - "obo" . - "MEROPS Clan" . - "0001017"^^ . - . - . - . - . - . - . - . - . - . - . - . - "28789"^^ . - . - "Panorama Public" . - . - . - . - . - . - . - . - "RiceNetDB Gene" . - "false"^^ . - . - . - "life science" . - . - . - . - "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"^^ . - . - "false"^^ . - . - . - . - . - . - . - "ZFIN" . - . - "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . - "BE0000048"^^ . - . - "epidemiology" . - . - "vw253@cam.ac.uk" . - . - "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"^^ . - "Clare Pilgrim" . - . - "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . - "metabolite" . - "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/"^^ . - "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . - . - "4140"^^ . - "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/"^^ . - . - "Research Organization Registry" . - "chebi" . - . - . - "ProbOnto, is an ontology-based knowledge base of probability distributions, featuring uni- and multivariate distributions with their defining functions, characteristics, relationships and reparameterisation formulae. It can be used for annotation of models, facilitating the encoding of distribution-based models, related functions and quantities."^^ . - . - . - . - . - "biomedical science" . - . - _:Nd62b24d3a8fe48d892050a1d27e387a3 . - "software engineering" . - . - . - . - "MSH" . - . - "^DDB_G\\d+$"^^ . - "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . - . - . - "4238"^^ . - . - . - "biocatalogue.service" . - "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . - "modularmassactionprimer"^^ . - "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . - . - "agriculture" . - "Metabolomics Workbench Study" . - "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . - . - . - . - . - . - "ppdb" . - "relationships" . - "multicellds.snapshot" . - "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID="^^ . - "false"^^ . - . - . - "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . - "ama-cpt" . - . - . - "Stephen Fisher" . - . - . - "UMR7315"^^ . - "^C?\\d+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - "alzforum.mutation" . - . - . - "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . - "false"^^ . - . - . - "gene" . - . - . - "obo" . - . - . - _:N698447d4b6454989b84712a255c0e38c . - . - . - . - "mutations" . - . - . - . - "https://aopwiki.org/aops/"^^ . - "false"^^ . - . - . - . - . - "biochemistry" . - "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . - . - . - . - . - "cooperl@oregonstate.edu" . - . - "pdbj" . - . - . - . - "http://www.onto-med.de/ontologies/gfo.owl#"^^ . - "AOPWiki (Key Event Relationship)" . - . - . - . - . - . - "false"^^ . - . - . - . - "knockout" . - . - . - "BOLD Systems taxon" . - "http://purl.obolibrary.org/obo/BSPO_"^^ . - "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$"^^ . - . - . - "iedb" . - "fetus" . - . - . - . - "false"^^ . - . - . - . - "botany" . - "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)" . - "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . - "false"^^ . - "^(STUDY|FILE|DATASET)\\d+$"^^ . - . - "CHEMONTID" . - "false"^^ . - "omics" . - . - . - "phylogenetics" . - "Cowpea ontology" . - . - . - . - "false"^^ . - . - "genomics" . - . - . - "bioinformatics" . - "m.a.laporte@cgiar.org" . - . - "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . - "PepBank Peptide Database" . - "biomedical science" . - . - . - . - "matrixdb" . - . - . - . - "ChiCTR2300070727"^^ . - . - . - "ontology" . - "radiology" . - "000000024"^^ . - . - . - "false"^^ . - . - . - . - . - . - "genome" . - "ontology" . - . - . - "100E"^^ . - "interaction" . - . - "anatomy" . - . - "https://web.expasy.org/cellosaurus/cellopub/"^^ . - . - "0116"^^ . - . - "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."^^ . - . - . - . - "The State of Alaska's Salmon and People Ontology" . - "The upper level ontology upon which OBO Foundry ontologies are built."^^ . - "false"^^ . - . - "cell reprogramming" . - . - . - . - "stem cell" . - . - . - . - "https://cropontology.org/rdf/CO_370:"^^ . - . - "mgiglio@som.umaryland.edu" . - . - . - . - "https://commonchemistry.cas.org/detail?cas_rn=$1"^^ . - . -_:N4de731d6bf7c472ab6146634b077278a "eVOC mailing list" . - "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . - . - "hpm.protein" . - "0000006"^^ . - "https://www.ncbi.nlm.nih.gov/sra/"^^ . - . - "http://purl.obolibrary.org/obo/VTO_$1"^^ . - "NIST Chemistry WebBook" . - . - . - "rna" . - "hoelzel" . - . - . - "false"^^ . - . - "ncbiprotein" . - . - . - . - "^\\d+$"^^ . - . - . - "Redistributor of bilogics and biomedical supplies"^^ . - "false"^^ . - "https://omim.org/MIM:PS"^^ . - . - "^\\d{5}$"^^ . - "EasyChair Call for Paper" . - . - . - "https://ensaiosclinicos.gov.br/rg/"^^ . - "ontology" . - . - "FaBiO, the FRBR-aligned Bibliographic Ontology" . - . - . - . - . - . - "Vertebrate Taxonomy Ontology" . - "MOL000160"^^ . - "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . - . - "ctis" . - "false"^^ . - "http://purl.org/obo/owlEOL_$1"^^ . - . - . - "gene" . - . - . - . - "MatrixDB stores experimentally determined interactions involving at least one extracellular biomolecule. It includes mostly protein-protein and protein-glycosaminoglycan interactions, as well as interactions with lipids and cations."^^ . - "obo" . - . - . - "^\\d+$"^^ . - "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . - . - . - . - "http://purl.obolibrary.org/obo/APOLLO_SV_"^^ . - "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . - "2966"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - . - "ensembl" . - "cell biology" . - "allergome" . - . - . - . - . - . - "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . - "innatedb" . - "^[1-9][0-9]*$"^^ . - "NLFFF Database" . - . - "FBtr0084214"^^ . - "ontology" . - . - . - . - . - . - . - . - "civic.gid" . - "^\\d{7}$"^^ . - . - . - "rna" . - . - "false"^^ . - . - . - . - "exac.transcript" . - . - . - . - "http://www.proteinatlas.org/"^^ . - "rna" . - . - . - . - . - . - "biology" . - . - . - "5601141"^^ . - "hipsci" . - "^WBRNAi\\d{8}$"^^ . - . - . - "protein" . - . - . - "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid="^^ . - "false"^^ . - . - "ontology" . - . - . - "scopus.eid" . - . - . - . - . - "interfil" . - "https://data.bloodpac.org/ga4gh/drs/v1/objects/"^^ . - . - . - . - "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]="^^ . - . - "Gene Ontology" . - "http://linkedlifedata.com/resource/umls/id/$1"^^ . - "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . - "^\\d+$"^^ . - . - "Biological Magnetic Resonance Data Bank" . - "https://herv.img.cas.cz/s/"^^ . - "false"^^ . - . - . - . - . - "Golm Metabolome Database" . - . - "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."^^ . - . - "chemical" . - . - "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . - "syoid" . - . - "1004" . - . - . - "life science" . - . - . - "Inge Jonassen" . - . - . - . - . - "taxonomy" . - "metascience" . - "http://bcrj.org.br/celula/"^^ . - . - "http://www.genome.jp/dbget-bin/www_bget?aaindex:"^^ . - . - "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#"^^ . - . - . - "tol.webproj" . - . - "schemaorg" . - . - "CHEMBL3467"^^ . - . - "Oral Health and Disease Ontology" . - . - "^[1-9][0-9]*$"^^ . - . - . - . - . - _:Nfd951b17478f477895aef1fdeccce346 . - . - "nje5@georgetown.edu" . - . - . - . - . - . - . - . - "false"^^ . - . - "life science" . - . - "transcriptomics" . - "ML0224"^^ . - . - "101775319"^^ . - "has local unique identifier pattern" . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . - "grsdb" . - "false"^^ . - "^\\d+$"^^ . - . - "https://pubchem.ncbi.nlm.nih.gov/substance/"^^ . - . - . - . - . - "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . - . - . - "1"^^ . - . - "http://www.phosphosite.org/proteinAction.do?id="^^ . - . - . - . - "dna" . - "^\\d{7}$"^^ . - "false"^^ . - "http://purl.obolibrary.org/obo/CARO_"^^ . - "img.taxon" . - . - "false"^^ . - . - . - "An ontology of Drosophila melanogaster anatomy."^^ . - . - "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . - . - . - "false"^^ . - . - . - . - "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."^^ . - . - . - "igsr" . - . - . - . - . - . - . - "protein" . - . - . - "genetics" . - . - "Studies in dbVar."^^ . - "http://purl.obolibrary.org/obo/TXPO_"^^ . - "gendis" . - . - "biodiversity" . - "bioinformatics" . - . - . - "EGID" . - "7345"^^ . - "false"^^ . - "Publons Researcher" . - "https://www.sharkipedia.org/species/"^^ . - . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/GOREL_$1"^^ . - "^GPM\\d+$"^^ . - "dna" . - . - "0000079"^^ . - "http://purl.org/spar/scoro/"^^ . - "mediadive.medium" . - "joerg.overmann@dsmz.de" . - . - _:N137416fe0fe14465a245cb8a86726e9d . - . - . - . - . - "false"^^ . - "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code="^^ . - . - . - . - . - . - . - "false"^^ . - "identifier for an organisation in author affiliations per Scopus"^^ . - . - "http://purl.obolibrary.org/obo/CIDO_"^^ . - . - . - . - "https://www.uniprot.org/database/$1" . - . - "duret@biomserv.univ-lyon1.fr" . - . - . - . - "geography" . - "ecology" . - . - . - . - "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/"^^ . - "http://exac.broadinstitute.org/transcript/$1"^^ . - . - . - . - "anatomy" . - "molecular biology" . - "OriDB Saccharomyces" . - . - "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . - "TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships. It includes phylogenetic trees and data matrices, together with information about the relevant publication, taxa, morphological and sequence-based characters, and published analyses. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, etc."^^ . - . - . - "embryonic stem cell" . - . - "abs" . - "https://w3id.org/oc/corpus/"^^ . - "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . - "ls-c35719-120"^^ . - . - "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name="^^ . - "^\\d+$"^^ . - "false"^^ . - . - "gene" . - "david.c.blackburn@gmail.com" . - "scopus.author" . - . - "Jackson Laboratories Strain" . - . - . - . - "ontology" . - "SEQF1003"^^ . - "http://tolweb.org/$1"^^ . - "NCBI Genome" . - "0000001"^^ . - "pathway" . - . - . - . - . - "0001009"^^ . - . - . - . - "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . - . - . - . - "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."^^ . - "obo" . - "Trish Whetzel" . - . - . - "biochemistry" . - . - "emmo" . - . - . - . - "http://purl.unep.org/sdg/SDGIO_"^^ . - . - "false"^^ . - . - "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . - . - "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."^^ . - "http://purl.obolibrary.org/obo/ZECO_"^^ . - "Person"^^ . - "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . - . - . - . - "gene function" . - . - . - . - "Protein Affinity Reagents" . - . - . - . - . - "Natural Product-Drug Interaction Research Data Repository" . - "natural science" . - "y3ax-8bq3-60"^^ . - . - . - . - . - . - . - "4685"^^ . - . - . - . - . - "transcriptomics" . - "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . - "protein" . - "bridgedb" . - "Porifera Ontology" . - "protein trap" . - . - . - . - "clinical studies" . - "National Academic Research and Collaborations Information System" . - . - . - . - . - . - ""^^ . - "Human Cell Atlas Ontology" . - "0000072"^^ . - "mop" . - . - "metatlas.metabolite" . - "Marcin Pawel Joachimiak" . - . - . - . - "ArachnoServer" . - . - . - "false"^^ . - . - "biomedical science" . - . - . - . - . - "Rutger Vos" . - "Cassava ontology" . - . - . - "ATOL (Animal Trait Ontology for Livestock) is an ontology of characteristics defining phenotypes of livestock in their environment (EOL). ATOL aims to: - provide a reference ontology of phenotypic traits of farm animals for the international scientificand educational - communities, farmers, etc.; - deliver this reference ontology in a language which can be used by computers in order to support database management, semantic analysis and modeling; - represent traits as generic as possible for livestock vertebrates; - make the ATOL ontology as operational as possible and closely related to measurement techniques; - structure the ontology in relation to animal production."^^ . - . - . - . - "LOTUS, actually, represents the most exhaustive resource of documented structure-organism pairs. Within the frame of current computational approaches in Natural Produts’s research and related fields, these documented structure-organism pairs should allow a more complete understanding of organisms and their chemistry."^^ . - . - . - "PhosphoSite Site Group" . - . - "^\\d{7}$"^^ . - . - . - . - "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."^^ . - . - "Probes and Drugs" . - . - . - . - "agronomy" . - . - . - "https://biopragmatics.github.io/providers/goche/"^^ . - . - . - . - . - . - . - . - . - . - "ontology" . - "false"^^ . - "ontology and terminology" . - . - . - . - "ontology" . - "ontology" . - . - "false"^^ . - . - "biomedical science" . - . - . - "BitterDB Compound" . - . - . - "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."^^ . - . - . - . - . - . - . - "drugs" . - . - "NeuroLex Anatomy" . - "SoyBase" . - . - . - "rfam" . - . - "neurology" . - . - . - . - "false"^^ . - . - "http://data.europa.eu/89h/$1"^^ . - "small molecule" . - . - . - . - . - "http://purl.obolibrary.org/obo/OHD_$1"^^ . - . - . - "life science" . - "PharmGKB Gene" . - . - . - . - . - "false"^^ . - . - "obo" . - "ontology" . - "A vocabulary for the catalysis disciplines" . - "github" . - . - . - . - . - "https://www.kazusa.or.jp/huge/gfpage/"^^ . - "OMIM" . - "proteomics" . - . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . - "Blake A Sweeney" . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "biomedical science" . - "MGD" . - . - . - . - . - . - "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . - "genetics" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "dna" . - "ontology" . - . - "infectious" . -_:N3cc0025ca3d24a2dafbd5de44f56b1e2 "WikiData Support" . - "https://www.wormbase.org/db/seq/protein?name="^^ . - "^[A-Za-z_0-9]+$"^^ . - . - "^\\d+$"^^ . - "false"^^ . - . - . - . - . - "http://purl.org/net/orth#"^^ . - . - . - . - . - . - . - "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."^^ . - "rbo" . - "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . - . - . - "0000057"^^ . - . - . - "regulation" . - . - . - "Web Elements" . - . - . - "false"^^ . - . - . - . - "http://www.hprd.org/protein/"^^ . - . - "General Standard for Food Additives Online Database" . - . - "life science" . - . - "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . - "008893080"^^ . - "ontology" . - "http://purl.org/cerif/frapo/$1"^^ . - . - . - . - "33607"^^ . - . - . - "^\\d{7,}$"^^ . - . - . - . - "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . - "global health" . - "GenProp0699"^^ . - . - . - . - "vmhgene" . - "classification" . - . - . - . - . -_:N4e25957c43b8426f813f5579b8ff53d7 "fred@fgiasson.com" . - "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . - . - "http://purl.bioontology.org/ontology/HCPCS/$1"^^ . - "receptome.family" . - "Brian Aevermann" . - "OASIS Open Services for Lifecycle Collaboration Core Vocabulary" . - . - "NCI Pathway Interaction Database: Pathway" . - "The Cambridge Stuctural Database (CSD) is the world's most comprehensive collection of small-molecule crystal structures. Entries curated into the CSD are identified by a CSD Refcode."^^ . - . - "^\\d+$"^^ . - "MSH2010_2010_02_22" . - . - . - "nucleotide" . - "0000546"^^ . - . - "thermofisher" . - . - . - . - "Potato ontology" . - . - "https://molmedb.upol.cz/mol/"^^ . - . - . - . - "protein structure" . - "dpo" . - "earth science" . - "pco" . - "biology" . - "eukaryota" . - . - "false"^^ . - . - . - . - . - . - "http://www.w3.org/ns/adms#"^^ . - . - "0000004"^^ . - "Cell Image Library" . - "00000001"^^ . - . - . - . - . - "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . - . - . - . - . - . - . - . - . - "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . - . - "structural biology" . - . - . - "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . - . - . - . - . - . - . - . - . - . - . - . - "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^ . - . - . - "protein" . - . - "00000674"^^ . - "^\\d{7}$"^^ . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/COVIDO_$1"^^ . - . - . - . - . - "ATCC number" . - "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id="^^ . - . - . - . - "small molecule" . - "htn" . - . - . - . - . - . - "true"^^ . - . - _:Nd2da98853435498c95a99ab2d84381d1 . - . - . - . - . - . - . - . - . -_:N38af8888972743f18aa7f0992b3702d3 "Allen Institute for Brain Science" . - . - . - . - "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid="^^ . - . - . - "0000024"^^ . - "^\\d+$"^^ . - . - "http://www.w3.org/ns/activitystreams#$1"^^ . - . - . - . - . - . - "ontology" . - . - . - "structure" . - "Brachiaria ontology" . - "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . - "minid" . - . - "bioactivities" . - "van_slyke@zfin.org" . - "Ekaterina Chuprikova" . - . - . - "https://www.pirbright.ac.uk/node/"^^ . - . - . - "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."^^ . - . - . - . - . - . - . - . - . - "FuncBase Yeast" . - "life science" . - . - . - . - "http://antibodyregistry.org/AB_$1"^^ . - . - . - "gene expression" . - "ontology" . - "database management" . - "plant breeding" . - "developmental biology" . - "false"^^ . - . - . - . - "metlin" . - . - "^WP\\d{1,5}(\\_r\\d+)?$"^^ . - "false"^^ . - "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - "applied microbiology" . - . - "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."^^ . - . - . - . - "Nicholas Furnham" . - "medicine" . - . - "katy@indiana.edu" . - . - . - "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . - . - . - . - "anatomy" . - . - . - . - . - "false"^^ . - "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . - "false"^^ . - . - . - . - . - . - . - "00000022"^^ . - . - . - . - "repeatsdb.protein" . - . - . - . - "Darren Natale" . - "https://www.kegg.jp/entry/$1"^^ . - . - "^UPI[A-F0-9]{10}$"^^ . - . - "oio" . - . - . - "LOTUS Initiative for Open Natural Products Research" . - . - "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . - . - "biomedical science" . - . - "Vitis ontology" . - . - . - . - . - . - . - . - "NCBI_Taxon_ID" . - . - . - . - "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 )."^^ . - "International Classification of Functioning, Disability and Health" . - . - "https://gudmap.org/id/"^^ . - "FBgn0011293"^^ . - "AAC"^^ . - . - . - "BioSample" . - "false"^^ . - "http://www.knapsackfamily.com/knapsack_core/information.php?word="^^ . - . - . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - "01406"^^ . - "agrkb" . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - "An ontology for dengue fever."^^ . - . - "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."^^ . - "medicine" . - . - . - . - "label"^^ . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_mol_"^^ . - . - . - . - . - . - . - . - . - . - . - . - "biology" . - "^\\d+$"^^ . - . - . - "prediction" . - "dictyBase" . - . - "pmp" . - "19757"^^ . - . - . - "Gerhard Mayer" . - "Signaling Network Open Resource" . - . - "biogrid" . - "skm" . - . - . - "social science" . - "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical" . - "http://cellimagelibrary.org/images/"^^ . - "http://scop.berkeley.edu/sunid=$1"^^ . - . - "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."^^ . - "virology" . - "false"^^ . - . - . - . - . - . - "European Genome-phenome Archive Dataset" . - "002368"^^ . - . - . - . - . - . - . - . - . - "Allergy"^^ . - "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . - "yoh@dartmouth.edu" . - . - "laia.subirats@gmail.com" . - . - . - . - "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"^^ . - . - . - "http://multicellds.org/MultiCellDB/"^^ . - . - "^\\d+$"^^ . - . - "lrg" . - . - . - . - "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . - . - . - . - . - "oclc" . - "^oai\\:cwi\\.nl\\:\\d+$"^^ . - . - . - . - . - "true"^^ . - . - . - . - . - . - . - . - "^\\d{6}$"^^ . - "https://animaldiversity.org/accounts/"^^ . - "agriculture" . - . - "Cell line collections (Providers)"^^ . - "^virsi\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "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"^^ . - "Teleost Anatomy Ontology" . - . - "ecacc" . - . - "loqate" . - . - . - "https://pdc.cancer.gov/pdc/study/"^^ . - "false"^^ . - . - "https://pharmacome.github.io/conso/$1"^^ . - . - . - . - . - "forest management" . - "primary health care" . - . - "false"^^ . - . - . - . - . - . - "https://w3id.org/reproduceme#"^^ . - "https://cropontology.org/rdf/CO_366:"^^ . - "ontology" . - . - "false"^^ . - "biology" . - . - . - "biomaterial" . - . - "CHEBI" . - . - "false"^^ . - . - "false"^^ . - . - . - "Wes Schafer" . - . - "http://www.pantree.org/node/annotationNode.jsp?id="^^ . - . - "^\\d+$"^^ . - . - "https://www.ebi.ac.uk/intact/interaction/$1"^^ . - . - . - . - . - "runbiosimulations" . - . - . - "false"^^ . - "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . - . - "false"^^ . - "PANTHER Pathway Component" . - . - . - "jfernand@um.es" . - . - "GeneDB" . - "Vaccine Ontology" . - . - "genome" . - . - "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . - "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . - . - . - . - . - . - "rnamods" . - . - . - . - . - "Activity Streams" . - . - "http://purl.obolibrary.org/obo/CRO_"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "ontology" . - . - "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . - . - . - . - "funcbase.mouse" . - "LG Chemical Entity Detection Dataset (LGCEDe) is only available open-dataset with molecular instance level annotations (i.e. atom-bond level position annotations within an image) for molecular structure images. This dataset was designed to encourage research on detection-based pipelines for Optical Chemical Structure Recognition (OCSR)."^^ . - . - . - "Identifier of a taxon or synonym in the Catalogue of Life"^^ . - . - "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]"^^ . - . - . - . - . - "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . - . - . - "sean@arabidopsis.org.uk" . - "preclinical studies" . - "0000086"^^ . - "^Rv\\d{4}(A|B|c)?$"^^ . - . - . - . - . - . - "kinetics" . - "bioinformatics" . - . - . - . - "https://w3id.org/aio/$1"^^ . - "systems biology" . - . - "DrugBank Drug Category" . - "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."^^ . - . - . - "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."^^ . - "https://www.google.com/patents/"^^ . - . - . - . - "PDB Structure" . - . - . - "life science" . - "classification" . - "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"^^ . - . - . - . - . - . - . - "molecular physical chemistry" . - "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . - "Cell line collections (Providers)"^^ . - . - . - _:Nc8087639f8dd4c109937179d880ccef7 . - "data model" . - . - . - . -_:N4de731d6bf7c472ab6146634b077278a "evoc@sanbi.ac.za" . - "Bibliometric Data Ontology" . - "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . - . - . - "protein" . - "false"^^ . - . - . - . - "uo" . - . - . - . - . - . - "This cooperative effort, which includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Chicago, focuses on the development of the comparative genomics environment called the SEED. It is a framework to support comparative analysis and annotation of genomes, and the development of curated genomic data (annotation). Curation is performed at the level of subsystems by an expert annotator, across many genomes, and not on a gene by gene basis. This collection references subsystems."^^ . - . - . - "MolMeDB is an open chemistry database about interactions of molecules with membranes. We collect information on how chemicals interact with individual membranes either from experiment or from simulations. "^^ . - "^\\d{7}$"^^ . - "genomics" . - "MEDRA" . - "ontology" . - . - "https://rfam.xfam.org/family/"^^ . - "life science" . - . - . - "genome" . - . - "^\\d{7}$"^^ . - . - "Variants in dbVar."^^ . - . - . - . - . - "^\\d+$"^^ . - "grassbase" . - "false"^^ . - . - . - "chembl" . - . - "structure" . - "biodiversity" . - . - . - "^[0-9]*$"^^ . - "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$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."^^ . - . - "LSM-6306"^^ . - . - . - "aop.stressor" . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . - . - . - . - . - "National Uniform Claim Committee Taxonomy" . - . - . - . - "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . - "mapping_justification"^^ . - . - . - . - . - "life science" . - . - . - . - . - "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . - "UBREL" . - . - . - . - . - "0002058"^^ . - "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/$1"^^ . - . - . - "The Molecular Modeling Database (MMDB) is a database of experimentally determined structures obtained from the Protein Data Bank (PDB). Since structures are known for a large fraction of all protein families, structure homologs may facilitate inference of biological function, or the identification of binding or catalytic sites."^^ . - . - . - "^\\d+$"^^ . - . - . - "https://bioregistry.io/metaregistry/go/$1"^^ . - . - "taxonomy" . - "Ascomycete phenotype ontology" . - . - . - . - . - . - . - "Rice annotation Project database" . - "life science" . - . - . - . - "ViralZone" . - . - . - "0000001"^^ . - "WWF" . - . - "false"^^ . - . - . - "http://purl.org/obo/owlEOL_"^^ . - "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."^^ . - . - "false"^^ . - . - . - "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . - . - . - . - "false"^^ . - . - "ProGlycProt" . - . - "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004)."^^ . - . - "panther.family" . - "https://www.cropontology.org" . - . - . - . - "elm" . - . - . - . - . - "UniRef" . - "LigandBook" . - . - . - . - "http://purl.jp/bio/4/id/$1"^^ . - . - . - . - . - . - . - . - "12969"^^ . - . - . - . - "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . - "ontology" . - . - "0000000"^^ . - . - . - "ontology" . - . - _:Ne90ee8fed2df407b9c43d887d8abdc38 . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . - "botany" . - . - . - . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . - "environmental science" . - . - . - . - "http://yeastrc.org/pdr/viewProtein.do?id="^^ . - "Terminology of Anatomy of Human Histology" . - "obo" . - . - "375364"^^ . - . - . - "false"^^ . - . - . - . - . - "clinical trials" . - "obo" . - "structure" . - . - "reaction" . - . - . - "NeuroVault Collection" . - . - . - . - "scop.sid" . - "bold.taxonomy" . - "^2-s2\\.0-\\d+$"^^ . - . - . - . - . - . - "DG00301"^^ . - "false"^^ . - . - . - . - . - . - . - "thesaurus" . - . - . - "https://pubchem.ncbi.nlm.nih.gov/compound/"^^ . - . - . - "ontology" . - . - . - . - "ypo" . - "https://bioregistry.io/collection/"^^ . - . - . - "cutg" . - . - "https://flybase.org/reports/FBrf$1"^^ . - "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . - "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . - "epidemiology" . - . - "https://cropontology.org/rdf/CO_322:$1"^^ . - . - . - "http://lisanwanglab.org/DASHR/entry/$1"^^ . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - . - "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . - "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . - . - . - "IPI"^^ . - . - . - . - "false"^^ . - "structure" . - "biomedical science" . - . - . - "https://bioschemas.org/profiles/"^^ . - . - . - "Pathway ontology" . - "false"^^ . - . - . - "https://w3id.org/linkml/$1"^^ . - . - "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . - . - . - . - . - . - . - . - "19-T4"^^ . - . - "neuromorpho" . - . - "TS-0285"^^ . - "Yeast Genome Order Browser" . - . - "00000001"^^ . - "http://vita.mbc.nctu.edu.tw/search.php?acc="^^ . - "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)."^^ . - . - "rna" . - . - . - . - . - "dna" . - . - . - . - . - "life science" . - . - "CATH Protein Structural Domain Superfamily" . - . - . - "http://purl.obolibrary.org/obo/ERO_$1"^^ . - . - . - "PA146123006"^^ . - "https://bioschemas.org/profiles/$1"^^ . - . - . - "ontology" . - . - "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc="^^ . - "^\\d+$"^^ . - . - . - "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . - . - . - . - . - . - "^PA\\d+$"^^ . - "HWUPKR0MPOU8FGXBT394"^^ . - "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."^^ . - . - "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . - . - "identifier for a source/publication venue (journal, conference, etc) in Scopus"^^ . - "Developing Mouse Brain Atlas" . - . - . - "^\\d{7}$"^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . - "basic research" . - . - . - "false"^^ . - "Food Interactions with Drugs Evidence Ontology" . - . - "cell lines" . - "dc.terms" . - . - . - . - . - . - "biocarta.pathway" . - . - . - . - "transportdb" . - . - "idoo" . - "http://purl.obolibrary.org/obo/OPMI_"^^ . - . - . - "false"^^ . - "PMCID" . - "neuroscience" . - . - _:Nde452a2f59d5417986ed5e9498c51a7e . - . - . - . - . - _:N1e52be9bd7ce42428f19eb8361ffc581 . - . - "Cotton ontology from CottonGen database - June 2019"^^ . - . - "maria.taboada@usc.es" . - "false"^^ . - "Tuan Amith" . - "1915"^^ . - . - "false"^^ . - . - . - . - . - . - . - "subtilist" . - . - . - . - . - "FOOD00020"^^ . - "anatomy" . - . - . - . - "104674"^^ . - . - . - "^\\w+$"^^ . - "FCB005"^^ . - . - . - "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."^^ . - . - "^[SED]R[APRSXZ]\\d+$"^^ . - . - "https://bioregistry.io/vdrc:"^^ . - . - . - "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"^^ . - "http://purl.obolibrary.org/obo/PLO_$1"^^ . - . - . - . - . - . - . - "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . - . - "17186"^^ . - . - "http://www.marinespecies.org/aphia.php?p=taxdetails&id="^^ . - "metagenomics" . - "402558626"^^ . - . - . - "tgn" . - . - "2-s2.0-0030770923"^^ . - . - . - . - . - . - . - "https://www.sharkipedia.org/trends/$1"^^ . - . - . - . - . - . - . - . - . - "obo" . - . - . - "https://rism.online/"^^ . - "protein" . - . - . - "has provider formatter" . - . - . - . - . - . - . - . - . - "Orphanet Rare Disease Ontology" . - "UM-BBD_reactionID" . - . - . - . - "reproduction" . - "false"^^ . - . - "neurolex" . - . - . - . - "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . - . - . - "https://w3id.org/semapv/vocab/$1"^^ . - "http://www.w3.org/XML/1998/namespace#"^^ . - . - . - "Cell line collections (Providers)"^^ . - . - "protein" . - "rgap" . - "angiology" . - "MagnitudeValueType"^^ . - . - "model" . - "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop="^^ . - . - "http://purl.obolibrary.org/obo/MF_$1"^^ . - "myco.lepra" . - . - . - . - . - . - "Rat Genome Database qTL" . - . - . - "false"^^ . - "biomedical science" . - . - "AS000060"^^ . - . - . - "Wikidata" . - . - . - . - . - . - . - "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."^^ . - . - "epo" . - . - "developmental biology" . - . - . - . - . - "ocid" . - . - . - "LCL-2085"^^ . - . - . - . - . - . - . - "phenomics" . - "0000858"^^ . - . - . - . - . - . - "ontology" . - . - "interpro" . - . - "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . - "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . - . - "scientist" . - . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - . - "dggr" . - . - . - "false"^^ . - "r.court@ed.ac.uk" . - "Cube db" . - . - "http://purl.obolibrary.org/obo/INO_$1"^^ . - . - . - . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . - . - . - . - "life science" . - "https://lincs.hms.harvard.edu/db/proteins/"^^ . - "obo" . - . - . - . - . - . - . - . - . - . - . - "ab-1-ha"^^ . - . - "https://bioregistry.io/ccdc:"^^ . - "false"^^ . - "true"^^ . - "tissue" . - . - "preclinical studies" . - . - . - "KEGG Genome" . - . - . - . - . - "life science" . - "NIF Standard Ontology: Cognitive Function" . - . - . - "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references individual reactions."^^ . - . - "false"^^ . - . - . - "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . - . - . - . - . - "karel.berka@upol.cz" . - . - . - . - "MIRIAM Registry collection" . - . - . - "^TIGR\\d+$"^^ . - . - "004435"^^ . - "false"^^ . - "dpv" . - "interaction" . - . - . - "MarDB" . - "blast" . - . - . - "4214"^^ . - "^(\\w){3}$"^^ . - "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . - . - "https://www.wwpdb.org/pdb?id=$1"^^ . - . - "glycomedb" . - "3517823"^^ . - . - . - . - . - "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"^^ . - "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. "^^ . - "Represents chemical kinetic reaction mechanisms."^^ . - . - . - . - "fbsp" . - "false"^^ . - "KEGG COMPOUND" . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID="^^ . - "smart" . - . - "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . - . - "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . - . - "CC2(C)C\\1CCC(C)/C=C/12"^^ . - "https://www.kegg.jp/entry/"^^ . - . - . - "C00000001"^^ . - "reactions" . - . - . - . - "^\\d+$"^^ . - "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . - "http://purl.obolibrary.org/obo/XAO_"^^ . - "ontology" . - "MESHCS" . - "http://purl.obolibrary.org/obo/PDRO_$1"^^ . - "^\\d{7}$"^^ . - . - "European Bank for induced pluripotent Stem Cells" . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . - . - . - . - . - "pathway" . - . - "AICARTRANSIMPCYCLO-CPLX"^^ . - "the FAIR Cookbook" . - . - "http://w3id.org/owlstar/$1"^^ . - "false"^^ . - "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."^^ . - . - . - . - "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . - "Eschmeyer's Catalog of Fishes" . - . - . - "https://www.datascienceontology.org/concept/"^^ . - . - . - . - "false"^^ . - . - . - "true"^^ . - . - "^\\d+$"^^ . - . - "life science" . - "SEED Compound" . - "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)."^^ . - . - "Wyeth W. Wasserman" . - . - . - . - "false"^^ . - . - . - "true"^^ . - . - . - "Yeast Deletion and the Mitochondrial Proteomics Project" . - "false"^^ . - . - . - "Homeodomain Research" . - . - . - . - "National Repository of Fish Cell Lines" . - . - . - "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . - "doqcs.model" . - . - . - . - . - "life science" . - "A-GEOD-50"^^ . - . - . - "gnps.task" . - . - . - "agriculture" . - . - "https://www.ebi.ac.uk/pdbe/entry/emdb/"^^ . - . - "genomics" . - "structure" . - . - . - "^\\d{4}-\\d{3}[\\dX]$"^^ . - . - "^(HOM)?\\d{7}$"^^ . - . - . - "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . - . - "0000000"^^ . - . - . - "mathematics" . - "false"^^ . - . - . - "^S\\d+$"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - "rnaloops" . - "false"^^ . - . - . - . - "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected."^^ . - "^CCDS\\d+\\.\\d+$"^^ . - "ontology" . - "Information about the C57BL/6J. Includes genetic background and disease data."^^ . - . - . - . - . - . - . - . - . - . - . - . - "http://standards.iso.org/iso/15926/part14/"^^ . - "http://www.nematodes.org/nembase4/cluster.php?cluster="^^ . - . - . - . - "^[a-z]+/[0-9]+$"^^ . - "sheepqtldb" . - . - "rna" . - "87"^^ . - "false"^^ . - . - . - "eo" . - . - "KEGG Glycan" . - "^GenProp\\d+$"^^ . - . - "P4355"^^ . - "agilent.probe" . - "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . - . - . - . - "obo" . - . - . - . - . - . - "None"^^ . - . - "info@hoelzel.de" . - . - . - . - . - . - "life science" . - . - . - "Cell line collections (Providers)"^^ . - . - "false"^^ . - . - "foodb.compound" . - "https://world-2dpage.expasy.org/repository/$1"^^ . - . - . - . - . - . - . - . - "Dublin Core Metadata Initiative Terms" . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . - . - . - "ricecyc" . - . - . - . - . - . - . - "http://exac.broadinstitute.org/variant/$1"^^ . - . - "IPI00000001"^^ . - "life science" . - . - "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . - "obo" . - "meetings" . - . - "The SEED;" . - . - "https://www.gwascentral.org/phenotype/$1"^^ . - "http://modelseed.org/biochem/reactions/$1"^^ . - . - . - . - "ontology" . - "true"^^ . - . - "5359"^^ . - . - . - "Doug Howe" . - "tissue" . - . - "Ctenophore Ontology" . - . - "https://smpdb.ca/view/$1"^^ . - . - . - . - . - . - . - . - "drugbank.condition" . - . - . - . - . - . - "biology" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/OGG_$1"^^ . - . - . - . - "toxicology" . - . - . - "Database of Genotypes and Phenotypes" . - . - . - "GitHub Pull Request" . - . - . - . - . - "small molecule" . - . - "biomedical science" . - . - . - . - . - . - . - "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . - "mir" . - . - "genome" . - . - "http://purl.obolibrary.org/obo/TRANS_$1"^^ . - "DrugBank Condition" . - . - . - . - . - . - "histology" . - . - "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1"^^ . - . - . - . - . - . - . - . - . - "nmr" . - . - . - . - "kinetics" . - . - . - . - . - "drug development" . - . - . - . - . - . - "LIPID_MAPS_instance" . - . - . - . - . - . - . - "https://www.fisheries.noaa.gov/species/$1"^^ . - . - "Mental Functioning Ontology" . - "DEF"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Genomic Distribution of structural Superfamilies" . - "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . - "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."^^ . - . - . - "false"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/ICEO_$1"^^ . - "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . - "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."^^ . - . - . - . - "structural biology" . - . - "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . - . - . - . - "insdc.run" . - . -_:N917df5114e6348d2a23df4152c26f3d5 "af8d@nih.gov" . - "false"^^ . - . - . - "hpa" . - . - "false"^^ . - . - . - "Systems Biology Ontology" . - . - . - "nlx.res" . - "medical informatics" . - . - . - . - "PPR103739"^^ . - "catalog" . - "http://purl.obolibrary.org/obo/MCRO_$1"^^ . - "^\\d{7}$"^^ . - . - . - "^\\d+$"^^ . - "ontology" . - . - . - . - "Protein Alignment organised as Structural Superfamily" . - "epidemiology" . - "57-27-2"^^ . - . - "genetic" . - . - "All geographical features in GeoNames are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes."^^ . - . - . - . - . - . - "small molecule" . - . - "ontology" . - . - . - . - . - . - . - "Schema.org" . - . - . - . - "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . - . - "BugBase Expt" . - "CIViC Molecular Profile" . -_:N38af8888972743f18aa7f0992b3702d3 "chinhda@alleninstitute.org" . - "http://purl.obolibrary.org/obo/FBbi_$1"^^ . - "gene" . - . - "drug metabolism" . - "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . - "false"^^ . - . - "neurobiology" . - . - . - . - "bioinformatics" . - "protein" . - "AGRO" . - . - . - . - . - . - "cst.ab" . - "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . - "^\\d{7}$"^^ . - . - . - "biomodels.teddy" . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - . - "https://scicrunch.org/resolver/RRID:NXR_"^^ . - . - . - . - . - "Metabolome Express" . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "AP011135"^^ . - . - . - "Gene Location" . - . - . - . - . - "http://purl.bioontology.org/ontology/NDDF/"^^ . - . - "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . - . - . - . - "false"^^ . - . - . - "Open Data Commons for Traumatic Brain Injury" . - . - "protein" . - "MaizeGDB" . - . - . - "http://purl.obolibrary.org/obo/BCO_$1"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "http://purl.org/net/orth#$1"^^ . - "0000069"^^ . - . - . - . - . - "https://ssbd.riken.jp/database/project/$1"^^ . - "1"^^ . - . - "Brendan MacLean" . - . - . - "gold.meta" . - . - . - . - . - . - "mirnao" . - . - . - . - . - . - . - "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . - "metabolite" . - . - "life science" . - "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id="^^ . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/dbvar/variants/"^^ . - "Health Canada Natural Product Number" . - . - . - "Mammalian Feeding Muscle Ontology" . - . - . - "false"^^ . - "false"^^ . - . - "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . - . - . - . - "BindingDB" . - . - "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."^^ . - . - . - "gabi" . - . - . - "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."^^ . - "metanetx.compartment" . - . - . - . - "BRIP1"^^ . - "https://www.iedb.org/reference/"^^ . - "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses."^^ . - "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."^^ . - . - . - . - . - "bioinformatics" . - . - "http://purl.obolibrary.org/obo/VIDO_$1"^^ . - "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."^^ . - _:Naaf3719147764fc2a918e626bdcc3b06 . - . - "structure" . - "P3DB Site" . - . - . - "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1"^^ . - . - . - . - . - "metadata" . - "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . - . - . - . - . - . - . - "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . - "ApiDB_PlasmoDB" . - . - . - . - . - . - . - "http://ascl.net/$1"^^ . - . - . - . - "IID00001"^^ . - "ontology" . - . - . - . - . - "https://biopragmatics.github.io/debio/"^^ . - . - . - . - "0000015"^^ . - "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . - . - "structure" . - . - . - "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."^^ . - . - "comparative genomics" . - "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"^^ . - "EAWAG Biocatalysis/Biodegradation Database" . - . - "dna" . - . - "https://rfam.xfam.org/family/$1"^^ . - "ontology" . - . - . - . - . - "life sciences" . - . - "false"^^ . - . - . - "C6155"^^ . - . - . - "cgd7_230"^^ . - . - . - "false"^^ . - . - . - . - "antibody" . - . - "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . - . - . - "B2067"^^ . - . - . - . - . - "classification" . - "jrc-eurl-ecvam-chemagora"^^ . - . - . - . - . - . - . - . - . - "Microbial Protein Interaction Database" . - "life science" . - . - "false"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . - "^\\d{4}$"^^ . - "http://purl.obolibrary.org/obo/VTO_"^^ . - "false"^^ . - . - . - . - "NXPFA" . - . - "protein" . - . - . - . - "taxonomy" . - . - . - "nickf@ebi.ac.uk" . - . - . - . - . - . - . - "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . - . - "^[A-Za-z0-9-]+$"^^ . - "ExAC Variant" . - "FBbt" . - "issn" . - . - . - . - . - . - "UMIN000049383"^^ . - "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . - "statistics" . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . - . - "The Drug-Drug Interactions Ontology" . - "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . - . - . - . - "obo" . - "ChEMBL-Targets" . - "obo" . - . - . - . - "S6"^^ . - . - . - . - . - "false"^^ . - . - . - . - "biomedical science" . - "0000586"^^ . - "Orientations of Proteins in Membranes Database" . - . - . - "chemistry" . - "Antibody Registry" . - . - "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . - . - . - . - . - "human" . - . - "botany" . - . - . - . - "life science" . - . - "ehda" . - . - "Jonathan Karr" . - "98"^^ . - "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId="^^ . - . - "http://purl.obolibrary.org/obo/CLAO_$1"^^ . - . - "mouse" . - . - . - . - . - . - . - "http://thebiogrid.org/"^^ . - "biology" . - . - . - "ontology" . - "^\\d{4,6}$"^^ . - . - "P0DP23"^^ . - . - . - . - "gene expression" . - "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . - "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."^^ . - "Gemeinsame Normdatei" . - "e0333"^^ . - . - . - . - . - "p.buttigieg@gmail.com" . - . - "population genetics" . - "36010371"^^ . - . - . - "bigg.model" . - "sequence" . - . - . - . - "ohd" . - . - "^\\d{7}$"^^ . - "0032571"^^ . - . - . - . - . - . - "https://spdx.org/licenses/$1"^^ . - "obo" . - "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . - . - . - . - . - . - "https://foodb.ca/foods/"^^ . - . - . - "false"^^ . - . - "congenic rat" . - "http://purl.obolibrary.org/obo/CHEBI_$1"^^ . - . - "ricenetdb.gene" . - . - . - _:Nc2d8d233b5dd4e92b1c37108a30c724a . - "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . - . - "US4145692"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "uniprot.taxonomy" . - "ontology" . - "^\\d+$"^^ . - . - . - . - "dna" . - "false"^^ . - "https://proteininformationresource.org/cgi-bin/resid?id="^^ . - . - . - . - . - "AT1G01030.1"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - . - "PaxDb Organism" . - "^\\d{6}$"^^ . - . - . - . - . - . - "bila" . - . - . - . - "http://purl.obolibrary.org/obo/OARCS_$1"^^ . - . - "false"^^ . - . - . - "A0014"^^ . - . -_:Naaf3719147764fc2a918e626bdcc3b06 "helpdesk cropontology" . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "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."^^ . - "1a24"^^ . - "snctp" . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - "^[A-Z0-9]+$"^^ . - . - "http://purl.bioontology.org/ontology/npo#NPO_"^^ . - "Golm Metabolome Database Profile" . - . - . - "araport" . - . - "Gene Ontology Rules" . - . - . - "ivdb" . - "https://hdl.handle.net/hdl:20.500.12633/"^^ . - "CRISP Thesaurus" . - "A modeling paradigm-specific registry of prefixes and their URL expansions" . - "ontology" . - . - . - "peroxibase" . - . - "false"^^ . - . - . - . - . - "https://cordis.europa.eu/project/id/$1"^^ . - . - "iceberg.cime" . - . - "0000010"^^ . - "http://www.wikidata.org/entity/$1" . - . - . - "false"^^ . - . - . - . - "snp500cancer" . - . - . - . - . - . - . - "UniRef90_P00750"^^ . - . - . - . - . - . - . - . - . - "ICEberg (Integrative and conjugative elements) is a database of integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome, and can carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. It contains details of ICEs found in representatives bacterial species, and which are organised as families. This collection references ICE families."^^ . - "mutant" . - . - . - "Tick Cell Biobank" . - . - "vaccine" . - . - "epidemiology" . - . - "CHEBI" . - . - "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . - "beta cell" . - . - "The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast)."^^ . - "life science" . - . - . - . - . - "dip" . - . -_:N93c2c94de4ce46f29e17ab0a916cf895 "J.Bard@ed.ac.uk" . - "Regulation of Transcription Ontology" . - . - "^\\w+$"^^ . - "wbls" . - "facebase" . - "false"^^ . - . - "anatomy" . - . - "false"^^ . - . - . - . - "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name="^^ . - "An alternative or synonymous prefix" . - . - . - . - "dicom" . - . - . - . - . - . - . - "louis@imbb.forth.gr" . - . - . - . - . - . - . - "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID="^^ . - "1044544"^^ . - "virology" . - . - . - . - . - "Cell line databases/resources"^^ . - . - . - . - "http://purl.obolibrary.org/obo/OGMS_$1"^^ . - . - "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."^^ . - "http://uri.neuinfo.org/nif/nifstd/"^^ . - . - "Pharmacogene Variation Consortium" . - "abcam" . - "Michelle Giglio" . - . - "false"^^ . - . - "0000001"^^ . - . - "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . - . - "IMGT, the international ImMunoGeneTics project, is a collection of high-quality integrated databases specialising in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species. IMGT/HLA is a database for sequences of the human MHC, referred to as HLA. It includes all the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. This collection references allele information through the WHO nomenclature."^^ . - "ontology" . - . - . - "^\\d{7}$"^^ . -_:Na59b29921d6c49bc83dc307084549278 "usha@molecularconnections.com" . - . - "obo" . - . - "false"^^ . - . - "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="^^ . - . - "mgi" . - "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"^^ . - . - "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . - . - . - . - . - . - . - "Unified Code for Units of Measure" . - "dna" . - . - "bel" . - . - . - . - . - "molecule" . - . - "https://purl.dataone.org/odo/SASAP_"^^ . - "^\\d+$"^^ . - . - "ontology" . - "false"^^ . - "true"^^ . - "Luana Licata" . - . - . - . - . - . - "Pseudomonas Genome Database" . - "sgn" . - . - "vendor" . - . - . - "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . - . - "EasyChair Topic" . - "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823"^^ . - . - . - . - . - . - "urgi-contact@versailles.inra.fr" . - . - "life science" . - . - "PR" . - . - "obo" . - . - "Medical Subject Headings Vocabulary" . - "false"^^ . - "cog" . - . - . - . - . - . - . - . - . - . - . - "https://www.pesticideinfo.org/chemical/"^^ . - "false"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - "drug discovery" . - . - "developmental biology" . - . - . - "^[0-9]+$"^^ . - . - "https://www.pombase.org/gene/$1"^^ . - . - . - . - . - . - . - . - "bido" . - "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."^^ . - "Food-Biomarker Ontology" . - . - . - . - "TrichDB" . - "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . - . - "false"^^ . - . - "^EP\\d{4}$"^^ . - . - "https://fcs-free.org/fcs-database?$1"^^ . - . - . - "Add"^^ . - . - "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . - . - . - "0000632"^^ . - . - "307"^^ . - . - . - "kegg.dgroup" . - "85163"^^ . - "MarRef" . - "life science" . - "classification" . - . - "yperez@ebi.ac.uk" . - . - "https://www.inaturalist.org/places/"^^ . - . - . - . - . - . - . - . - "gpmdb" . - . - . - . - . - . - . - . - . - "http://thebiogrid.org/$1"^^ . - . - "^\\w+$"^^ . - . - . - . - . - "Os01t0883800-02"^^ . - "https://biopragmatics.github.io/providers/cvx/$1"^^ . - "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . - . - "ontology" . - "http://europepmc.org/articles/"^^ . - . - . - "runBioSimulations is a platform for sharing simulation experiments and their results. runBioSimulations enables investigators to use a wide range of simulation tools to execute a wide range of simulations. runBioSimulations permanently saves the results of these simulations, and investigators can share results by sharing URLs similar to sharing URLs for files with DropBox and Google Drive."^^ . - . - . - "knowledge and information systems" . - "false"^^ . - . - "The NCATS BioPlanet is a comprehensive, publicly accessible informatics resource that catalogs all pathways, their healthy and disease state annotations, and targets within and relationships among them. The BioPlanet integrates pathway annotations from publicly available, manually curated sources subjected to thorough redundancy and consistency cross-evaluation via extensive manual curation. The browser supports interactive browsing, retrieval and analysis of pathways, exploration of pathway connections, and pathway search by gene targets, category, and availability of bioactivity assays."^^ . - "pav" . - . - . - "biomedical science" . - . - "seo" . - . - . - . - "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CVDO_"^^ . - . - . - . - . - . - . - . - . - . - . - "gmd" . - "436605"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid="^^ . - . - . + "Sanger Cell Model Passports" . + "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."^^ . + . + . + . + . + . + . + "preclinical studies" . + . + "4007166"^^ . + "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=$1"^^ . + . + . + . + . + . + . + . + . + . + "ecn" . + . +_:N81fe899ae37e4bc6870b3fdde5669e37 "Crop Ontology Helpdesk" . + . + . + "http://purl.obolibrary.org/obo/MMO_"^^ . + . + . + "false"^^ . + "biomedical science" . + . + . + . + "http://purl.obolibrary.org/obo/ZFS_"^^ . + . + . + "cellrepo" . + . + "ontology" . + "http://www.genome.jp/dbget-bin/www_bget?aaindex:"^^ . + . + "gobpid" . + . + . + . + . + . + . + "genome" . + . + "Plant Stress Ontology" . + . + . + . + . + "Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse" . + . + . + "https://mips.helmholtz-muenchen.de/corum/?id="^^ . + . + "https://eol.org/pages/$1"^^ . + . + . + . + . + . + "http://www.alzgene.org/geneoverview.asp?geneid="^^ . + . + "gene expression" . + . + . + "THE1B"^^ . + "PUBCHEM_CID" . + "Frederic Bastian" . + . + "obo" . + . + . + "ddinter.interaction" . + . + . + . + . + . + . + . + "http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/$1.html"^^ . + "life science" . + . + . + . + "https://molmedb.upol.cz/mol/"^^ . + "^\\d{7}$"^^ . + "Application ontology for entities related to insecticide resistance in mosquitos"^^ . + . + . + "ontology" . + . + . + . + "Gene Ontology Database references" . + "false"^^ . + . + "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."^^ . + . + . + . + . + . + . + . + "maria.gould@ucop.edu" . + . + "evolutionary biology" . + . + . + . + "http://purl.obolibrary.org/obo/PW_"^^ . + . + . + . + . + . + . + "Sheng-Da Hsu" . + "occ" . + "Bjoern Peters" . + . + . + "http://www.ontobee.org/" . + . + "Online Computer Library Center WorldCat" . + . + . + . + . + "17254"^^ . + "biochemistry" . + . + . + . + "Yasset Perez-Riverol" . + . + "Aceview Worm" . + . + . + . + . + "Animal TFDB Family" . + "http://exac.broadinstitute.org/transcript/$1"^^ . + "life science" . + . + . + . + . + . + . + . + "botany" . + "has alternative prefix" . + . + . + "TOKU-E Cell-culture Database" . + "Global Biodiversity Information Facility" . + . + "https://odc-sci.org/data/$1"^^ . + . + . + . + . + "genetic engineering" . + . + . + . + "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name="^^ . + . + . + "http://purl.obolibrary.org/obo/PW_$1"^^ . + "HBG284870"^^ . + "NCBI Probe database Public registry of nucleic acid reagents" . + . + . + "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . + "life science" . + "chemical" . + "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . + . + "cpd15380"^^ . + . + . + . + "Probes and Drugs" . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters (Submitter IDs). Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submitters (submitter ids) that submit the submissions (SCVs)."^^ . + . + "MMAR_2462"^^ . + . + "https://www.cropontology.org" . + "FlyBase Reference Report" . + . + . + . + "ontology" . + . + . + . + "A01M1/026"^^ . + . + . + "version 2019 - pvs"^^ . + . + "UPPRO" . + "iECABU_c1320"^^ . + . + . + . + . + . + "http://purl.bioontology.org/ontology/CSP/"^^ . + "^AB\\d+$"^^ . + . + . + . + . + "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . + "genetics" . + . + "https://biopragmatics.github.io/providers/hog/"^^ . + . + . + "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."^^ . + . + "https://www.probes-drugs.org/compound/$1"^^ . + "ontology" . + . + . + . + . + . + "^[0-9]+$"^^ . + . + . + . + . + . + . + . +_:N161c830f834442a4b8b33f16f6be7221 "pierre.sprumont@unifr.ch" . + . + . + "SPIKE Map" . + . + "Human Cell Atlas Ontology" . + "^rx[0-9]{5}$"^^ . + "GlycoEpitope" . + "transcriptomics" . + . + . + . + . + "anatomy" . + . + "The Ensembl glossary lists the terms, data types and file types that are used in Ensembl and describes how they are used."^^ . + . + . + . + _:N9e7c97749a6f4045a68fcff83d0fafd5 . + "Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases."^^ . + . + "00103"^^ . + "environmental science" . + "publishing" . + . + "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."^^ . + "clustering" . + . + . + "http://purl.obolibrary.org/obo/OBCS_$1"^^ . + . + . + "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br$1"^^ . + "false"^^ . + "small molecule" . + . + . + . + . + . + "gene expression" . + "life science" . + "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."^^ . + . + . + . + . + . + . + "http://www.pathoplant.de/detail.php?accNo="^^ . + "http://scop.berkeley.edu/sccs=$1"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_organ_"^^ . + . + . + "false"^^ . + "dna" . + . + "sbml.level-3.version-2"^^ . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id=$1"^^ . + . + . + . + . + . + . + "Yvonne Bradford" . + "http://matrixdb.univ-lyon1.fr//cgi-bin/current/newPort?type=association&value=$1&class=Association"^^ . + "P12345"^^ . + . + . . - "3403"^^ . - . - . - . - . - . - "identifier for an educational organization issued by the UK Register of Learning Providers"^^ . - . - "Academic Event Ontology" . - . - "The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data."^^ . - . - . - . - "^rxn\\d+$"^^ . - "^\\S+$"^^ . - "SNOMEDCTCT_2018_03_01" . - . - "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . - . - . - . - . - . - . - . - . - "rhea" . - "dna" . - "FMA_RETIRED" . - . - . - "S-EPMC6266652"^^ . - . - . - "false"^^ . - . - "otol" . - . - "http://www.cathdb.info/domain/"^^ . - . - . - . - . - . - _:N61a3d10cbab946e29d82cb3fcd645550 . - . - . - "true"^^ . - . - . - "global health" . - . - . - "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."^^ . - . - . - . - . - . - . - . - . - "bkc640"^^ . - . - "47419"^^ . - . - . - "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . - . - "ietf.language" . - . - . - . - "biomodels.db" . - "https://www.checklistbank.org/dataset/3LR/taxon/$1"^^ . - "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . - "Liver Cancer Model Repository" . + . + . + "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."^^ . + "AutDB" . + . + "ontology" . + . + "http://www.pantree.org/node/annotationNode.jsp?id="^^ . + . + . + "PDB_CHEM_ID" . + . + "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . + . + . + . + "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."^^ . + "https://vocab.lternet.edu/vocab/vocab/index.php?tema=$1"^^ . + . + "PharmGKB Disease" . + . + "http://www.pharmgkb.org/pathway/"^^ . + . + . + . + . + . + . + . + . + "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."^^ . + "http://www.w3.org/ns/prov#$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."^^ . + . + . + . + . + . + . + . + "life science" . + "https://civicdb.org/links/gene/$1"^^ . + . + "^\\d+$"^^ . + . + "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . + "fig|306254.1.peg.183"^^ . + . + . + . + "Cellosaurus identifeirs for publications, like Pubmed"^^ . + . + . + "http://lisanwanglab.org/DASHR/entry/"^^ . + . + . + "Wikidata Property" . + . + "^\\w+$"^^ . + . + "Ax1"^^ . + . + . + . + . + "classification" . + "pathway" . + . + "puro" . + "NLXFUNC" . + . + . + . + . + "rfam" . + . + "National Uniform Claim Committee Characteristic" . + . + . + "domain" . + . + "http://purl.obolibrary.org/obo/VBO_"^^ . + . + . + . + . + . + . + . + "iceberg.ime" . + . + . + . + . + . + . + "biomedical science" . + . + "MarCat" . + . + . + . + . + . + . + "eco" . + . + "http://purl.bioontology.org/ontology/HOIP/HOIP_$1"^^ . + . + . + . + . + . + . + . + "obo" . + . + . + . + . + "false"^^ . + . + . + "https://catalog.hathitrust.org/Record/"^^ . + . + . + . + . + "dictybase.gene" . + "false"^^ . + . + "Olfactory Receptor Database" . + "NLXQUAL covers qualities and dispositions similar to the Phenotype And Trait Ontology (PATO)."^^ . + "obo" . + "130502"^^ . + . + . + "life science" . + . + . + . + "^\\d+$"^^ . + "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."^^ . + "https://bioregistry.io/spike.map:"^^ . + . + "phylogenomics" . + . + . + "http://purl.org/linked-data/cube#"^^ . + . + "https://cropontology.org/rdf/CO_343:"^^ . + "taxonomy" . + . + "http://www.wikipathways.org/instance/"^^ . + "physiology" . + . + "nlx.func" . + "subject agnostic" . + . + . + . + . + . + . + . + . "Sugar Kelp trait ontology"^^ . - "statistics" . - . - . - . - . - . - "ucum" . - . - "structure" . - "pdbechem" . - . - . - "nextProt" . - . - "faseb list" . - . - . - "UniProtKB_VAR" . - "ontology" . - "ontology" . - . - "https://www.ensembl.org/id/"^^ . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FLU_$1"^^ . - . - "UM-BBD_pathwayID" . - . - "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . - "obo" . - . - . - . - "drugbank.target" . - "SubtiWiki is a scientific wiki for the model bacterium Bacillus subtilis. It provides comprehensive information on all genes and their proteins and RNA products, as well as information related to the current investigation of the gene/protein. \r\nNote: Currently, direct access to RNA products is restricted. This is expected to be rectified soon."^^ . - "^\\d+$"^^ . - . - "false"^^ . - "life science" . - . - "fma" . - "WBbt" . - . - . - "oid" . - . - . - "Tetrahymena Stock Center" . - . - "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."^^ . - . - . - . - "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)"^^ . - "KEGG Drug Group" . - . - "Saccharomyces genome database pathways" . - . - . - . - . - . - "srodriguez142857@gmail.com" . - "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . - "ontology" . - "TaxonomyID" . - "false"^^ . - "Fission Yeast Experimental Conditions Ontology" . - "http://oid-info.com/get/$1"^^ . - . - "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . - "false"^^ . - . - . - . - . - . - "https://www.biocatalogue.org/services/$1"^^ . - "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."^^ . - . - . - . - . - . - . - "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . - . - . - . - . - "uminctr" . - . - "false"^^ . - . - . - "http://pax-db.org/#!species/$1"^^ . - "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . - "life science" . - . - . - . + "https://www.beiresources.org/Catalog/cellBanks/$1.aspx"^^ . + "ontology" . + "The US National Cancer Institute (NCI) maintains and administers data elements, forms, models, and components of these items in a metadata registry referred to as the Cancer Data Standards Registry and Repository, or caDSR."^^ . + . + . + . + . + . + "VHOG_RETIRED" . + "^DDInter\\d+$"^^ . + "^\\d{7}$"^^ . + . + . + . + "NHMRC Australian PhenomeBank" . + . + . + "kegg_genomes" . + . + "false"^^ . + . + "nsrrc" . + . + "false"^^ . + "life science" . + . + . + . + . + . + . + . + "http://www.unimod.org/modifications_view.php?editid1="^^ . + . + "634515043"^^ . + . + . + "false"^^ . + "https://mediadive.dsmz.de/medium/$1"^^ . + "false"^^ . + . + "CRISP Thesaurus" . + . + "sequence" . + "d.a59037e8"^^ . + . + . + . + . + "animal physiology" . + . + . + "https://www.scopus.com/sourceid/$1"^^ . + "false"^^ . + "small molecule" . + . + "semantic web" . + "PubChem CID" . + . + . + . + . + . + "TR0000001"^^ . + . + "human" . + . + . + . + . + . + "DI-04240"^^ . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/PORO_"^^ . + . + . + . + . + "https://bioregistry.io/metaregistry/$1"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + "^[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}$"^^ . + . + "ontology" . + . + . + . + "Cell line databases/resources"^^ . + "false"^^ . + "2gc4E"^^ . + "RiceNetDB Reaction" . + . + . + . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4}\\d{8}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + . + . + "NONCODE v4 Transcript" . + . + . + "cryoem" . + . + "ppr" . + . + . + . + . + . + "An organization" . + "Ligand Expo is a data resource for finding information about small molecules bound to proteins and nucleic acids."^^ . + "RepeatsDB Structure" . + . + . + "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."^^ . + . + "http://www.humanproteomemap.org/protein.php?hpm_id=$1"^^ . + "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://purl.obolibrary.org/obo/OMIT_"^^ . + . + "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . + . + . + . + . + "The Semantic Mapping Vocabulary provides and defines terms used for creating and maintaining semantic mappings, in particular mapping metadata."^^ . + "Ontologies of diseases that integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms."^^ . + . + . + "FAIRsharing" . + . + "computational biology" . + . + . + . + "An ontology to standardize research output of nutritional epidemiologic studies."^^ . + . + "^\\d+$"^^ . + . + . + . + . + "dna" . + "WD_Entity" . + "e999"^^ . + . + "atcc" . + "http://func.mshri.on.ca/mouse/genes/list_functional_scores/$1"^^ . + . + . + "Andreas Ruepp" . + "^PDC\\d+$"^^ . + . + "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."^^ . + "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . + . + . + . + "civic.vgid" . + . + "https://cropontology.org/rdf/CO_321:"^^ . + . + . + . + . + "life science" . + . + "metaregistry" . + . + "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."^^ . + "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"^^ . + "false"^^ . + . + "scop.sunid" . + "wikipathways" . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + "preclinical studies" . + "protein" . + . + "^AA\\d{4}$"^^ . + "^([a-zA-Z]+-)?\\d+(\\.\\d)?$"^^ . + . + . + . + . + "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1"^^ . + . + "https://easychair.org/cfp/$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . "obo" . - . - . - . - . - . - . - _:N3abf7e22f0e74131a3b6b2ff255f1b2b . + . + . + . + . + . + . "Minimal Anatomical Terminology" . - . - . - . - . - "dna" . - "false"^^ . - . - "microbiology" . - "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . - "PTHR12345"^^ . - . - "false"^^ . - . - . - . - . - . - . - "^\\d{1,9}$"^^ . - . - "10194"^^ . - . - . - . - "obo" . - "obo" . - . - "SNCTP000005580"^^ . - . - . - . - . - "PA131"^^ . - "EGAS00000000001"^^ . - "false"^^ . - "^\\d+$"^^ . - . - "NITE Biological Resource Center" . - . - "CY077097"^^ . - . - "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)."^^ . - . - . - . - . - "small molecule" . - "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . - . - . - "TAIR Gene" . - "https://hl7.org/fhir/us/$1"^^ . - . - "adenovirus" . - . - . - . - . - . - "en-GB"^^ . - "http://purl.obolibrary.org/obo/MS_$1"^^ . - . - . - . - . - . - "^ERM[0-9]{8}$"^^ . - "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . - . - . - "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have been derived from clinical data using performance measures (aka metrics, process indicators, quality measures, etc). PSDO uses Basic Formal Ontology as its upper level ontology. This work is supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf"^^ . - "itis" . - "rs17852708"^^ . - "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . - "drugs" . - "^\\d+$"^^ . - . - . - "quantitative genetics" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PdumDv_$1"^^ . - . - . - . - . - . - "0000000"^^ . - "https://vac.niaid.nih.gov/view?id=$1"^^ . - . - "obo" . - "drks" . - . - . - . - . - . - . - . - "Ontology of Medically Related Social Entities" . - . - "agriculture" . - . - . - . - "john.garavelli@ebi.ac.uk" . - . - "^\\d+$"^^ . - . - . - "sabiork.compound" . - "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans."^^ . - . - . - . - . - . - . - . - . - . - . - . - "https://vectorbase.org/gene/$1"^^ . - . - . - . - . - . - "4349895"^^ . - "preclinical studies" . - . - . - . - . - . - . - . - . - "Feature Annotation Location Description Ontology " . - "https://run.biosimulations.org/simulations/$1"^^ . - . - "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . - . - . - . - . - . - "life science" . - . - "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.bioinfo.org/NONCODEv4/show_gene.php?id="^^ . - "ontology" . - . - "genome" . - "lcsh" . -_:N50de7bbebb744373b98eaefc287f558e "patricia.brooks2@cms.hhs.gov" . - . - "^\\d+$"^^ . - . - "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."^^ . - "health science" . - . - . - . - . - . - . - "ontology" . - . - . - "UPI000000000A"^^ . - . - . - . - . - . - . - "anatomy" . - . - "NCit" . - "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN="^^ . - "^\\d+$"^^ . -_:N9c76a2bea9b1468b8d223185d6d2be17 "GenBank Support" . - . - "http://purl.obolibrary.org/obo/MONDO_$1"^^ . - "^\\d+$"^^ . - "chemistry" . - . - "phylogenetics" . -_:Na44780e2985848e985ef5412da5b9845 "Hajo Rijgersberg" . - . - . - "https://herv.img.cas.cz/s/$1"^^ . - _:N5bba3595235448e1831c635d87c3b184 . - . - . - . - "subject agnostic" . - . - "biotools" . - . - . - . - . - . - . - . - "Sierra Moxon" . - . - . - . - . - "International Geo Sample Number" . - . - . - . - . - "Animal Genome Chicken QTL" . - "Vertebrate Homologous Organ Group Ontology" . - "HDAA2" . - . - "https://w3id.org/sssom/"^^ . - . - . - . - "kegg.disease" . - "Colin Batchelor" . - . - . - "obcs" . - "https://www.perkinelmer.com/searchresult?searchName="^^ . - . - "true"^^ . - . - . - "ESi007-A"^^ . - . - "ontology" . - . - . - "genome" . - . - . - . - "ensembl.metazoa" . - "Fly taxonomy" . - "proglyc" . - . - "teddy" . - "ontology" . - . - . - "https://drks.de/search/en/trial/"^^ . - . - . - . + . + "^\\d{7}$"^^ . + "false"^^ . + . + "Prefixes mentioned on the _external_ list on the FHIR [Code Systems](https://hl7.org/fhir/terminologies-systems.html) page. This list is mostly complete. Notably, some entries that have not been curated:\n\n- HGVS (see discussion at [#460](https://github.com/biopragmatics/bioregistry/issues/460))\n- [NUBC](http://www.nubc.org) (National Uniform Billing Committee) - could not find information about the terminology or its entries\n- [ICPC](http://www.ph3c.org/) (International Classification of Primary Care) _same_\n- [GTIN](https://www.gs1.org/standards/id-keys/gtin) (Global Trade Item Number) _same_\n- [MDC](https://www.iso.org/standard/37890.html) (Medical Device Codes) since that appears to be part of a larger ISO standard vocabulary that needs further investigation" . + "obo" . + . + . + "biodiversity" . + . + . + . + . + "https://archive.gramene.org/db/ontology/search?id=GR_tax:"^^ . + . + . + . + . + . + "http://aims.fao.org/aos/agrovoc/c_$1"^^ . + "" . + . + . + . + . + . + . + "data analysis" . + . + . + "00073"^^ . + "https://knowledge.lonza.com/cell?id="^^ . + . +_:Nad42f8f18c534f0cb3d3fdabcabf743f "WHO Collaborating Centre for Drug Statistics Methodology" . + . + . + . + . + "https://signor.uniroma2.it/relation_result.php?id=$1"^^ . + "Paula Duek Roggli" . + "Amos Bairoch" . + . + "geogeo" . + . + . + . + "goeco" . + "https://pharmacodb.ca/datasets/$1"^^ . + . + "http://purl.obolibrary.org/obo/SIBO_"^^ . + "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."^^ . + "ontology" . + "mammalian" . + "http://cutdb.burnham.org/relation/show/$1"^^ . + . + "EcoliWiki from EcoliHub" . + . + . + . + . + . + "MultiCellDS is data standard for multicellular simulation, experimental, and clinical data. A digital cell line is a hierarchical organization of quantitative phenotype data for a single biological cell line, including the microenvironmental context of the measurements and essential metadata."^^ . + . + "CHEMBL465070"^^ . + . + . + "protein" . + . + "medicinal chemistry" . + . + "Costal and Marine Ecological Classification Standard" . + . + "90901"^^ . + . + . + "^MTBLS\\d+$"^^ . + . + . + "^[0-9a-zA-Z]+$"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + "K00973"^^ . + . + . + "ontology" . + . + . + "IRD Segment Sequence" . + "^\\d+$"^^ . + "vandf" . + . + . + "A application driven Epilepsy Ontology with official terms from the ILAE."^^ . + "biomedical science" . + . + . + "Feature Annotation Location Description Ontology " . + . + . + "MGnify Sample" . + "false"^^ . + . + . "corrdb" . - "http://purl.obolibrary.org/obo/ECOCORE_"^^ . - "rutgeraldo@gmail.com" . - "https://amzn.com/"^^ . - . - "https://glycopost.glycosmos.org/entry/$1"^^ . - . - "Jason E. Stajich" . - . - "ChemIDplus" . - . - . - "Sequence Read Archive" . - "obo" . - "http://open-services.net/ns/core#$1"^^ . - . - . - "medlineplus" . - . - . - . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/VSAO_$1"^^ . - . - . - . - . - "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . - "^HIP\\d{9}(\\.\\d+)?$"^^ . - "true"^^ . - . - . - . - "6VDC956"^^ . - "transposon" . - . - . - "rna" . - . - "http://purl.obolibrary.org/obo/FOODON_$1"^^ . - . - . - "Ontology for Nutritional Studies" . - "^PA\\d+$"^^ . - . - . - . - . - "coriell" . - "MTHICD9_2006" . - . - . - "gene" . - "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)."^^ . - . - "subject agnostic" . - . - . - "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . - . - . - "px" . - "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession="^^ . - "https://www.ebi.ac.uk/metagenomics/analyses/"^^ . - . - . - "http://www.w3.org/ns/activitystreams#"^^ . - . - "Pathguide" . - "false"^^ . - . - "0000001"^^ . - . - . - . - . - . - . - . - . - "troy_pells@yahoo.ca" . - . - "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource."^^ . - . - . - "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . - . - . - . - . - . - . - . - . - "SFB_COVID19_MW286762"^^ . - "biomedical science" . - . - "life science" . - "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid="^^ . - . - . - "https://models.physiomeproject.org/exposure/$1"^^ . - . - . - . - . - . - "false"^^ . - . - . - "The Echinoderm Anatomy and Development Ontology" . - "true"^^ . - . - "false"^^ . - "life science" . - . - "65"^^ . - "false"^^ . - . - . - "https://www.rrrc.us/Strain/?x=$1"^^ . - . - . - . - "Ensembl Plants" . - . - . - "ncithesaurus" . - . - . - . - "http://ratmap.org/Showgene.php?gene_stable_id="^^ . - . - . - . - "doi"^^ . - . - . - . - "false"^^ . - . - . - . - "false"^^ . - "Data Use Ontology" . - . - "0000210"^^ . - "false"^^ . - "mod" . - . - . - . - . - . - "^\\d{4}$"^^ . - "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems."^^ . - . - . - . - "^(R)?PXD\\d{6}$"^^ . - "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."^^ . - . - "false"^^ . -_:N5ee7902ef2b64c548828599daaf0d737 "Eionet Helpdesk" . - . - "false"^^ . - . - . - "protocol" . - . - . - "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . - "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id="^^ . - . - . -_:N0b76c49429ac46d794bde4f27f024c25 "InterPro Help" . - . - . - . - . - "Molbase" . - . - . - . - . - "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . - "structure" . - "biomedical science" . - "^[\\d.]+$"^^ . - . - . - "EDAM Ontology" . - "radiology" . - . - "gene expression" . - . - "developmental biology" . - "cst" . - . - "doqcs.pathway" . - "functional genomics" . - "propreo" . - . - . - "false"^^ . - "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . - . - . - . - . - . - . - "ontology and terminology" . - . - . - . - . - "false"^^ . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - "false"^^ . - "drug" . - . - "^F\\d{4}$"^^ . - . - . - . - . - "false"^^ . - "https://biosimulators.org/simulators/"^^ . - . - "proco" . - "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . - . - . - . - "false"^^ . - . - . - . - . - "http://www.ontologyrepository.com/CommonCoreOntologies/"^^ . - "An issue in any public repository on GitHub."^^ . - . - . - "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ="^^ . - "ontology" . - . - . - "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . - . - . - "Sweet Potato ontology" . - . - "IPR016380"^^ . - . - . - . - . - . - _:Nc2c3eeb40d884344b28b37273de129b2 . - "The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records in order to obtain complete coverage of the sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view."^^ . - "https://bacdive.dsmz.de/strain/"^^ . - . - "https://web.www.healthdatagateway.org/dataset/"^^ . - . - . - . - . - . - "0000003"^^ . - "^[A-Za-z0-9]+$"^^ . - . - . - "pathogen" . - "https://www.abcam.com/$1.html"^^ . - "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."^^ . - . - . - . - . - "false"^^ . - . - . - "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . - . - "Carsten Linder" . - "atfdb.family" . - . - . - "false"^^ . - . - . - . - . - "jcrb" . - . - . - . - "false"^^ . - . - "Infectious Disease Ontology" . - "ValidatorDB" . - . - "obo" . - . - . - "classification" . - . - . - . - . - . - . - "Hs635"^^ . - . - "nucc.characteristic" . - "drugbank.category" . - "A controlled vocabulary to support the study of transcription in the primate brain"^^ . - . - . - . - . - "gpcrnava" . - "https://www.sharkipedia.org/species/$1"^^ . - . - "false"^^ . + . + . + . + . + "spider" . + . + "UP" . + . + . + . + "ncbiprotein" . + . + . + . + . + . + "Tick Anatomy Ontology" . + . + . + . + "00005643"^^ . + . + . + . + "0000062"^^ . + "mesh.2013" . + . + . + "0000252"^^ . + "handle" . + "Identifier for a species on the noaa fisheries website"^^ . +_:N4b239e856348428b86c8044d5a72bbff "datex@efsa.europa.eu" . + "biomedical science" . + . + . + "^\\d{7}$"^^ . + . + "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."^^ . + . + . + "false"^^ . + . + "RISM Online" . + . + . + . + "Bibliographic Reference Ontology" . + "ORPHA" . + . + . + "drugs" . + . + . + . + . + . + . + "bioregistry"^^ . + "obo" . + . + . + "false"^^ . + "chemistry" . + "VegBank" . + . + . + . + "0000519"^^ . + . + . + "http://www.case.edu/EpilepsyOntology.owl#"^^ . + . + . + . + "^LOC\\_Os\\d{1,2}g\\d{5}\\.\\d$"^^ . + . + "^\\d+$"^^ . + "http://purl.obolibrary.org/obo/ZEA_"^^ . + . + "^\\d{6}(\\/\\d+\\.\\d+\\.\\d+)?$"^^ . + . + . + "http://purl.org/spar/doco/$1"^^ . + . + "remote sensing" . + . + "https://biopragmatics.github.io/providers/dhba/"^^ . + . + "International Geo Sample Number" . + . + "^BSU\\d{5}$"^^ . + . + . + . + . + . + "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . + "54"^^ . + . + . + "C063233"^^ . + . + . + . + . + . + . + "one" . + . + . + . + . + . + "70"^^ . + "false"^^ . + "0000339"^^ . + . + . + "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . + "preclinical studies" . + . + . + . + "4685"^^ . + . + . + "worfdb" . + "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."^^ . + . + . + . + "https://rnaloops.cs.put.poznan.pl/search/details/$1"^^ . + . + . + . + . + "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . + . + . + "0000390"^^ . + "The pre-IND tracking number for submissions to the FDA"^^ . + "http://www-bionet.sscc.ru/sitex/index.php?siteid=$1"^^ . + . + . + "ontology and terminology" . + . + "rgd.qtl" . + . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/$1"^^ . + "http://www-snorna.biotoul.fr/plus.php?id="^^ . + "dbd" . + "life science" . + "http://purl.bioontology.org/ontology/VANDF/$1"^^ . + "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."^^ . + . + "social science" . + "graingenes.symbol" . + . + . + "ontology" . + . + "0000564"^^ . "A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry."^^ . - . - . - "http://purl.obolibrary.org/obo/MOD_$1"^^ . - . - . - . - "bco" . - . - . - . - . - "A collection of biological attributes (traits) covering all kingdoms of life. Interoperable with VT (vertebrate trait ontology) and TO (plant trait ontology). Extends PATO."^^ . - . -_:N40de88241fe445dc8d11e9c9b635f056 "chebi-help@ebi.ac.uk" . - . - . - . - . - "http://phenol-explorer.eu/foods/$1"^^ . - . - "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . - "false"^^ . - . - "genetics" . - . - . - . - . - . - "reagent" . - . - . - . - . - "https://www.pgscatalog.org/pgs/$1"^^ . - "^[0-9]+$"^^ . - "epidemiology" . - . - "9606"^^ . - . - . - "agriculture" . - . - "Cuban Registry of Clinical Trials" . - . - . - "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."^^ . - . - . - . - "life science" . - "cnrs" . - . - "uniprot.disease" . - . - . - . - "Lipid Ontology" . - . - . - . - . - . - "https://go.drugbank.com/indications/$1"^^ . - "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."^^ . - . - . - . - "IntellectualContribution"^^ . - . - . - "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name="^^ . -_:Neb0864156da647c4b350d1c2d17e099a "helpdesk@cropontology-curationtool.org" . - "metabolights" . - . - . - "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . - . - . - "false"^^ . - . - "https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#"^^ . - . + . + . + "^\\d{7}$"^^ . + . + "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+"^^ . + . + . + . + . + "^\\d{3}\\w(\\w|\\d_)\\d{4}X$"^^ . + . + "https://bioregistry.io/gmd:"^^ . + . + . + . + . + . + . + . + . + . + . + . + "obo" . + . + . + "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q="^^ . + . + . + "domain" . + "genome" . + . + . + "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "00023232"^^ . + "Cell line databases/resources"^^ . + "bdgp.est" . + "128796-39-4"^^ . + . + . + . + "SED-ML model format" . + . + "gene" . + . + "false"^^ . + . + . + "false"^^ . + . + "ontology" . + "^[0-9]*$"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]=$1"^^ . + . + "KEGG_DRUG_GROUP" . + . + . + "The PeptideAtlas Project provides a publicly accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools."^^ . + "false"^^ . + . + . + . + "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam="^^ . + . + . + . + . + "ECOLI:CYT-D-UBIOX-CPLX"^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + . . - . - "The International Harmonization of Nomenclature and Diagnostic criteria" . - . - . - . - . - . - . - . - . - "biomedical science" . - . - "Bgee organ" . - . - . - "^\\d{7}$"^^ . - . - . - . - . - "^\\d+$"^^ . - . - "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . - . - . - "true"^^ . - . - . - . - "scicrunch" . - "life science" . - . - . - . - "knockout" . - "oa" . - "false"^^ . - "http://purl.obolibrary.org/obo/SEPIO_"^^ . - "http://purl.obolibrary.org/obo/PATO_$1"^^ . - . - . - . - "https://pypi.org/project/"^^ . -_:Nf02a9133fb1b401fb2f49f9946084afa "vlee@ebi.ac.uk" . - "^\\d{7}$"^^ . - . - "https://www.ebi.ac.uk/intact/search?query=$1"^^ . - . - "false"^^ . - . - . - . - "^\\d+$"^^ . - . - "https://pharmacodb.ca/datasets/$1"^^ . - "inhand" . - "http://purl.org/pav/$1"^^ . - . - "false"^^ . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - "Collagen Mutation Database" . - . - . - . - "false"^^ . - "^F\\d+$"^^ . - "SNOMEDCTCT_2019_03_01" . - "UM-BBD_ruleID" . - "false"^^ . - "DataCollection"^^ . - "Telethon Network of Genetic Biobanks" . - . - "^[A-Z]C\\d{1,3}$"^^ . - . - . - . - . - . - . - . - . - . - . + "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:"^^ . + . + . + . + . + "life science" . + . + . + . + . + . + . + . + . + "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone="^^ . + "0000000"^^ . + . + . + "aop" . + . + "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . + . + "NCBI Taxonomy" . + "false"^^ . + . + "RIKEN Bioresource Center Cell Bank" . + . + "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_"^^ . + "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id="^^ . + "https://fungi.ensembl.org/id/"^^ . + . + "false"^^ . + . + . + . + "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."^^ . + . + . + "24867"^^ . + . + "taxrank" . + . + . + "ontology" . + . + . + . + "HGNC_GROUP" . + . + . + . + . + . + . + . + . + "false"^^ . + "bioinformatics" . + . + "structure" . + . + . + . + "dg5b0d" . + . + "NLXANAT covers anatomy terms. Almost all terms are also in Uberon."^^ . + . + . + . + "http://www.w3.org/2006/time#$1"^^ . + . + "An issue in any public repository on GitHub."^^ . + . + . + . + . + . + . + "The number of known protein sequences exceeds those of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. The Protein Model Portal (PMP) provides a single portal to access these models, which are accessed through their UniProt identifiers."^^ . + "health science" . + "^\\d+$"^^ . + "4214"^^ . + . + "BioData Catalyst" . + "^\\d+$"^^ . + . + . + "Blue Brain Project Knowledge Graph" . + . + "wormbase" . + . + . + . + . + . + "^\\w+$"^^ . + "^(\\d+)|(\\w+)$"^^ . + . + . + . + . + "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1"^^ . + . + "Identifier for an animal, plant, or microorganism from the fossilworks website"^^ . + . + . + . + . + . + . + . + . + . + "ado" . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cog/$1"^^ . + . + . + "Maciej Antczak" . + . + . + . + . + . + "Affymetrix Probeset" . + . + . + . + "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:$1"^^ . + . + . + "rapdb.locus" . + "false"^^ . + "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . + . + . + . + "Vilma Hualla Mamani" . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. In addition, HGNC also provides a unique numerical ID to identify gene families, providing a display of curated hierarchical relationships between families."^^ . + "Database of living organisms, taxonomic. \n The GBIF—the Global Biodiversity Information Facility—is international network and data infrastructure funded by the world's governments and aimed at providing anyone, anywhere, open access to data about all types of life on Earth."^^ . + . + . + . + . + "gene" . + . + . + . + . + . + "Cell line collections (Providers)"^^ . + "http://purl.obolibrary.org/obo/OBIB_"^^ . + . + . + "SpliceNest" . + "cgd7_230"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_qual_"^^ . + . + "http://purl.obolibrary.org/obo/VHOG_"^^ . + . + "PRIDE Project" . + . + . + . + "Neil McKenna" . + . + . + . + . + . + "mriffle@u.washington.edu" . + "linguistics" . + . + . + . + . + . + . + "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . + . + . + . + "srodriguez142857@gmail.com" . + "https://www.isrctn.com/"^^ . + "interaction" . + . + . + . + . + "life science" . + . + . + . + "^OSC\\d{4}$"^^ . + . + . + "false"^^ . + "0019171"^^ . + "biology" . + "structural bioinformatics" . + . + "http://stormo.wustl.edu/ScerTF/details/"^^ . + "bindingdb" . + . + . + . + . + . + "biodiversity" . + . + . + "http://purl.obolibrary.org/obo/HEPRO_"^^ . + "https://medical-data-models.org/forms/"^^ . + "virsirna" . + "chickenqtldb" . + . + . + "biomedical science" . + . + "http://purl.obolibrary.org/obo/EHDAA2_"^^ . + . + "^[A-Za-z0-9]+$"^^ . + . + "antibodies" . + "proteomics" . + . + . + . + . + . + . + "genomics" . + . + . + "false"^^ . + "false"^^ . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term="^^ . + "ASPL0000349247"^^ . + . + "false"^^ . + "MHC Restriction Ontology" . + . + . + "MCDS_S_0000000001"^^ . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + "n2t" . + . + "marine ecology" . + "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."^^ . + . + . + . + "Lentil Trait Dictionary in template v5 - ICARDA - July 2015"^^ . + . + . + . + . + . + . + "0000019"^^ . + . + . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . + . + "ontology" . + . + . + . + "UMLS Semantic Types Ontology" . + "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."^^ . + . + . + . + . + . + . + . + "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . + . + . + "genome" . + . + "biofactoid" . + . + "0290"^^ . + . + . + . + "apollosv" . + "epidemiology" . + . + . + "dcat" . + "false"^^ . + "https://goldbook.iupac.org/terms/view/"^^ . + "0007133"^^ . + . + . + "https://bioregistry.io/kyinno:"^^ . + "faseb list" . + . + . + . + "aeon" . + . + . + . + "life science" . +_:N7ddd4d39a93142dfb150e76ca0925d12 "Patricia Brooks" . + "0000001"^^ . + "GenBank" . + "ISBN-13" . + "PubChem Element" . + "http://purl.obolibrary.org/obo/TAHE_"^^ . + "false"^^ . + "wosuid" . + "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)." . + . + . + "^\\d+$"^^ . + "KEGG.EDRUG" . + "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."^^ . + "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al."^^ . + . + . + . + "^\\d+$"^^ . + . + "https://bioregistry.io/pscdb:"^^ . + . + "154022"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + "human" . + . + "10015919"^^ . + "https://www.biozol.de/en/product/$1"^^ . + "ontology" . + "^\\d+$"^^ . + . + "vo" . + "FlyBrain Neuron Database" . + "GPM32310002988"^^ . + . + . + "http://data.europa.eu/89h/$1"^^ . + "false"^^ . + . + . + "^FR\\-FCM\\-\\w{4}$"^^ . + "genome" . + . + . + . + "bioinformatics" . + "Database of Escherichia coli Sequence and Function" . + . + "unipathway.compound" . + . + "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . + . + . + "https://www.gbif.org/species/$1"^^ . + . + . + "false"^^ . + . + "GlycoEpitope is a database containing useful information about carbohydrate antigens (glyco-epitopes) and the antibodies (polyclonal or monoclonal) that can be used to analyze their expression. This collection references Glycoepitopes."^^ . + . + . + . + . + "AGR" . + "bactibase" . + . + "ontology" . + . + "structure" . + . + . + . + . + . + . + . + . + . + . + "glycomics" . + . + . + "Unique Ingredient Identifier" . + . + "Radiation Biology Ontology" . + . + "life science" . . - . - "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . - . - "hom" . - "false"^^ . - "1001"^^ . - . - . - . - . - "life science" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "biomedical science" . - "seed.reaction" . - . - . - "antibodies" . - . - "classification" . - . - . -_:N76f00e653b4248c9891b2f17b031ddbd "World Health Organization" . - . - . - . - . - "vfdb.gene" . - . - . - "The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions"^^ . + "^\\d{7}$"^^ . + . + . + "ontology and terminology" . + . + . + . + . + . + . + "subject agnostic" . + . + . + . + . + . + . + "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . + "http://purl.obolibrary.org/obo/OGSF_$1"^^ . + "P3DB Protein" . + . + "https://eds.gene.le.ac.uk/home.php?select_db=$1"^^ . + . + . + . + . + . + . + "virushostdb" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "^[a-z]+(\\..*?)?$"^^ . + "Gene Regulation Ontology" . + . + . + . + . + "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."^^ . + . + . + "62"^^ . + "genetics" . + "The pattern for identifiers in the given resource" . + . + "https://www.ebi.ac.uk/pride/archive/projects/$1"^^ . + "bel" . + . + . + . + "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query="^^ . + "fly" . + . + "genome" . + "International Fungal Working Group Fungal Barcoding." . + . + "^casent\\d+(\\-D\\d+)?$"^^ . + . + . + . + "SNOWMEDCT_US" . + "burkesquires@gmail.com" . + . + . + . + "oae" . + "http://uri.neuinfo.org/nif/nifstd/nlx_mol_$1"^^ . + . + . + . + . + . + "false"^^ . + "https://cropontology.org/rdf/CO_335:"^^ . + . + . + . + . + . + . + "bbkg" . + . + . + . + . + . + . + . + . + . + "gene function" . + "^[0-9\\-_]+$"^^ . + "false"^^ . + . + . + "SNOMEDCT_US_2019_09_01" . + . + . + "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." . + . + "repec" . + . + . + . + "http://purl.obolibrary.org/obo/OARCS_$1"^^ . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + "This document describes a vocabulary for annotating descriptions of vocabularies with examples and usage notes."^^ . + "nutritional science" . + . + . + . + "embryonic stem cell" . + . + . + . + "scopus.affiliation" . + "http://snomed.info/id/$1"^^ . + "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=$1"^^ . + "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://topdb.enzim.hu/?m=show&id="^^ . + . + . + "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."^^ . + "gene" . + . + . + "Ramona Walls" . + . + "https://spdx.org/licenses/"^^ . + . + . + . + "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id=$1"^^ . + . + . +_:N0f79c573c15a4405a1d8a67adb3a8e7a "BioModels.net team" . + . + "agriculture" . + . + . + "symp" . + "kristian.axelsen@sib.swiss" . + . + "Animal Genome Sheep QTL" . + . + . + . +_:N45e4474439d94b1c85c9d3a15c3a1d47 "helpdesk@cropontology-curationtool.org" . + . + "^\\d+$"^^ . + "meetings" . + . + "hancestro" . + . + . + "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . + . + . + "biodiversity" . + . + . + . + . + . + "true"^^ . + "false"^^ . + "Ontology of units of Measure" . + "abcam" . + . + . + "ontology" . + . + "The CDC's National Center of Immunization and Respiratory Diseases (NCIRD) developed and maintains the CVX (vaccine administered) code set. The table below has the most up to date values. It includes both active and inactive vaccines available in the US. CVX codes for inactive vaccines allow transmission of historical immunization records."^^ . + "urgi-contact@versailles.inra.fr" . + "subject agnostic" . + . + . + . + . + "structural biology" . + "57-27-2"^^ . + "https://www.ebi.ac.uk/intact/search?query="^^ . + . + . + "obo" . + "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop="^^ . + . + . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + "gnd" . + . + . + . + . + "ideal" . + "gene" . + . + . + . + . + "false"^^ . + . + "Structural Classification of Protein - Stable Domain Identifier" . + . + . + . + . + "1046"^^ . + "https://bio.tools/$1"^^ . + "gno" . + . + . + "dictyBase" . + . + "https://prefix.cc/" . + "pharmgkb.gene" . + . + . + . + "Genetics Home Reference" . + . + . + . + . + "biomedical science" . + "http://func.mshri.on.ca/yeast/genes/list_functional_scores/"^^ . + "obo" . + "genecards.genenote" . + "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . + . + . + . + . + . + . + "https://fairsharing.org/organisations/$1"^^ . + "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria smegmatis information."^^ . + . + . + "false"^^ . + . + . + "BioCyc collection of metabolic pathway databases" . + "ricenetdb.mirna" . + "^S\\d+$"^^ . + "disorders" . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/$1"^^ . + . + "https://coconut.naturalproducts.net/compound/coconut_id/"^^ . + "Leen Vandepitte" . + . + . + . + . + "^WP\\d{1,5}(\\_r\\d+)?$"^^ . + "4623"^^ . + "Neuro Behavior Ontology" . + . + . + . + . + . + "civic.sid" . + "addexbio" . + . + . + . + "CQG5"^^ . + "void" . + . + "mouse strain" . + . + . + . + . + . + "EMLSAT00000003403"^^ . + . + "1010"^^ . + . + . + "false"^^ . + . + . + . + . + . + "protein" . + . + "181" . + "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id="^^ . + . + "qudt" . + . + . + . + "MediaDive Medium" . + . + . + "dna" . + . + "https://data.terra.bio/ga4gh/drs/v1/objects/"^^ . + "0.7-123"^^ . + . + "DrugBank is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets."^^ . + . + . + . + . + . + . + "life science" . + . + . + "biology" . + . + "false"^^ . + "disease model" . + . + . + "5046"^^ . + . + . + . + "biomedical science" . + . + . + "http://purl.obolibrary.org/obo/PSO_"^^ . + "noncodev4.rna" . + "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound=$1"^^ . + . + "ontology" . + . + "agricola" . + . + "fossilworks.taxon" . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/datasets/genome/"^^ . + . + . + . + . + . + "https://www.phenxtoolkit.org/protocols/view/"^^ . + . + . + . + . + . + "hagr.gendr" . + . + . + "https://bioregistry.io/cghdb:"^^ . + . + . + . + . + . + "ICD9CM" . + . + . + . + . + . + . + . + . + "https://units-of-measurement.org/$1"^^ . + "leen.vandepitte@vliz.be" . + . + . + . + . + "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . + . + . + "siren" . + . + . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + . + "swrl" . + . + . + "htn" . + . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + . + . + . + "https://www.mlcommons.org/mlc-id/"^^ . + . + "life science" . + . + . + "gmd.gcms" . + . + "Database of validation results for ligands and non-standard residues in the Protein Data Bank."^^ . + . + . + "https://jjj.bio.vu.nl/models/"^^ . + . + "https://www.ncbi.nlm.nih.gov/clinvar/variation/"^^ . + . + "false"^^ . + . + . + . + "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . + . + . + "DP00003"^^ . + . + . + . + . + . + "aef4c195-9cf9-46db-a12a-7cfd1ff3eec3"^^ . + "false"^^ . + "Scientific research institute for neuroscience, genetics, immunology, plant biology and more."^^ . + . + "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."^^ . + . + . + "data management" . + . + . + "developmental biology" . + . + . + "https://envipath.org/package/$1"^^ . + . + "^\\d{4}-\\d{3}[\\dX]$"^^ . + . + . + "http://purl.obolibrary.org/obo/AAO_$1"^^ . + "MNXR101574"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://bioregistry.io/lrg:"^^ . + . + . + . + . + . + "pathway" . + . + "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . + "https://bioregistry.io/registry/"^^ . + "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "https://bioregistry.io/jaxmice:"^^ . + . + "mirnao" . + "small molecule" . + "A registry of life science prefxes"^^ . + . + . + . + . + "ontology" . + "ipi" . + . + "Genomics of Drug Sensitivity in Cancer" . + . + . + . + . + . + "obo" . + . + . + "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . + . + . + . + "data mining" . + "classification" . + "MedlinePlus Genetics contains detailed information about the effects of genetic variation on human health, covering more than 1,300 genetic conditions and 1,400 genes, all of the human chromosomes, and mitochondrial DNA (mtDNA)."^^ . + . + "false"^^ . + "life science" . + "GRIN provides National Genetic Resources Program (NGRP) personnel and germplasm users continuous access to databases for the maintenance of passport, characterization, evaluation, inventory, and distribution data important for the effective management and utilization of national germplasm collections."^^ . + . + . + . + "kegg.orthology" . + "false"^^ . + . + . + "A classification of the diverse roles performed in the work leading to a published research output in the sciences. Its purpose to provide transparency in contributions to scholarly published work, to enable improved systems of attribution, credit, and accountability."^^ . + . + "UM-BBD_reactionID" . + "http://standards.iso.org/iso/15926/part14/"^^ . + . + . + "citexplore" . + "regulation" . + . + . + "chemical" . + . + . + . + . + . + . + "exo" . + . + "^PTHR\\d{5}(\\:SF\\d{1,3})?$"^^ . + . + . + . + . + "0000138"^^ . + . + . + . + . + . + . + "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . + . + . + . + . + "NUI" . + . + "0000079"^^ . + . + . + . + "false"^^ . + "classification" . + "false"^^ . + . + . + . + . + . + . + "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . + "12e8LH"^^ . + "98034"^^ . + . + "allergome" . + "false"^^ . + "cdt" . + . + . + . + "http://www.w3.org/1999/02/22-rdf-syntax-ns#"^^ . + . + . + . + . + "https://lincs.hms.harvard.edu/db/proteins/"^^ . + . + "social and behavioural science" . + . + . + "The Biological Expression Language is a domain-specific language for describing causal, correlative, and associative relationships between a variety of biological agents."^^ . + . + "post-translational modification" . + "agriculture" . + "lschriml@som.umaryland.edu" . + . + . + . + "geneotype" . + . + . + . + _:N3b02556718da42d990354f82b5791ec2 . + . + "genetics" . + . + "^Os\\S+t\\d{7}-\\d{2}$"^^ . + "http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=$1&format=default"^^ . + . + . + . + . + . + . + . + "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."^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/TO_$1"^^ . + "https://lincs.hms.harvard.edu/db/sm/$1"^^ . + . + . + . + "helpdesk@cropontology-curationtool.org" . + "ontology" . + . + "cell biology" . + . + . + . + . + "ontie" . + "sequence" . + . + "false"^^ . + "plant" . + . + . + . + . + . + . + . + . + . + . + . + "ecosystem science" . + . + . + . + "BioTools is a registry of databases and software with tools, services, and workflows for biological and biomedical research."^^ . + "ACYPI000159"^^ . + "https://cgap.nci.nih.gov/Pathways/BioCarta/"^^ . + . + . + "https://www.metanetx.org/chem_info/"^^ . + . + . + "DBMET02292"^^ . + . + . + . + . + . + "false"^^ . . - . - . - "false"^^ . + . + "biochemistry" . + "^\\d{7}$"^^ . + . + . + . + "ato" . + . + . + . + "https://rpcec.sld.cu/en/trials/"^^ . + "KEGG_PATHWAY" . + . + "GrassBase" . + . + . + . + "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-$1"^^ . + . + . + . + . + "http://www.p3db.org/protein.php?id=$1&ref=0"^^ . + . + . + . + "obo" . + . + . + . + . + . + "The Mental Disease Ontology is developed to facilitate representation for all aspects of mental disease. It is an extension of the Ontology for General Medical Science (OGMS) and Mental Functioning Ontology (MF)."^^ . + . + "^\\d+$"^^ . + "https://cadsrapi.nci.nih.gov/cadsrapi4/GetXML?query=DataElement[@publicId=$1]"^^ . + . + "Matthias König" . + . + . + "https://www.uniprot.org/journals/"^^ . + . + . + . + . + . + . + . + . + . + . + "31623"^^ . + . + . + . + . + "CAMEO Chemicals ID" . + "LipidBank" . + . + . + "Medical Dictionary for Regulatory Activities Terminology" . + . + . + "false"^^ . + "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=$1"^^ . + . + "phytozome.locus" . + . + "KYinno cell lines" . + "epigenetics" . + . + "pathwaycommons" . + . + . + . + "The Ecosystem Ontology" . + . + . + . + . + . + . + . + "human disease" . + . + . + "E-MTAB-2037"^^ . + "database" . + "https://labsyspharm.github.io/lspci/"^^ . + . + . + "CALM1"^^ . + "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another."^^ . + . + "https://www.ebi.ac.uk/ols4" . + "admin@envipath.org" . + . + . + . + . + "phylogenetics" . + . + . + . + . + . + . + "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."^^ . + "pathway" . + . + . + . + "http://purl.obolibrary.org/obo/FIX_"^^ . + . + . + . + . + . + "protein" . + . + . + . + . + . + . + . + "http://purl.org/pav/"^^ . + . + . + "https://www.ebi.ac.uk/intact/search?query=$1"^^ . + "AT1402"^^ . + . + . + . + . + . + . + . + . + "stem cell" . + . + . + "dhba" . + "^\\d+$"^^ . + "https://bioregistry.io/bykdb:"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "ICD-O" . + . + "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages"^^ . + . + . + "Jennifer C. Girón" . + "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."^^ . + . + . + "https://nmrshiftdb.nmr.uni-koeln.de/molecule/"^^ . + . + . + "0000006"^^ . + . + . + "^.+$"^^ . + . + . + . + . + "rat model" . + . + . + . + "swiss-model" . + . + "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id="^^ . + . + . + "iso15926" . + . + . + . + "https://www.ncbi.nlm.nih.gov/books/$1"^^ . + . + . + . + . + . + . + . + . + "dron" . + . + . + . + "2649230"^^ . + . + "https://bartoc.org/" . + . + . + . + "^[A-Za-z0-9+\\-\\*=#$:().>/\\\\\\[\\]%]+$"^^ . + "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . + . + . + . + . + "tumor" . + . + . + "cryopreserved" . + _:N6d31f3e671ef4a46915145d8a044dbb3 . + . + . + . + . + "https://www.perkinelmer.com/searchresult?searchName="^^ . + . + "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\"."^^ . + "Sandra Orchard" . + . + . + "Berkeley Drosophila Genome Project EST database" . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + "PRO" . + . + . + "false"^^ . + "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . + . + "Asset"^^ . + . + . + "Genome Aggregation Database" . + . + "bugbase.expt" . + "alberto.traverso@maastro.nl" . + . + "false"^^ . + "false"^^ . + . + . + "nlx.cell" . + . + . + "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."^^ . + . + "dandi" . + . + . + . + "Pier Luigi Buttigieg" . + "000140" . + "http://purl.obolibrary.org/obo/CHIRO_$1"^^ . + . + . + . + "MediaDive Ingredient" . + . + . + . + . + "life science" . + . + . + "gene expression" . + . + . + . + . + . + . + "^[A-Z]+$"^^ . + . + . + "false"^^ . + . + "International Classification of Diseases, 10th Revision, Clinical Modification" . + . + . + . + . + . + . + "https://cropontology.org/rdf/CO_327:"^^ . + "https://www.ebi.ac.uk/chembl/target/inspect/"^^ . + . + . + . + . + . + "muamith@utmb.edu" . + . + . + . + "https://www.alzforum.org/mutations/"^^ . + . + . + . + "fishbase.species" . + "0000144"^^ . + "biomedical science" . + . + "false"^^ . + "obo" . + . + "troy_pells@yahoo.ca" . + . + . + . + . + "ontology" . + . + . + . + . + . + . + . + . + . + "life sciences" . + . + . + . + "ivdb" . + . + "Q9P0K8"^^ . + "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)"^^ . + "selventa" . + . + "American Type Culture Collection" . + "http://purl.obolibrary.org/obo/WBPhenotype_"^^ . + "http://www.kegg.jp/entry/$1"^^ . + "NIF Dysfunction" . + . + "ontology" . + . + "co_335" . + "arrayexpress" . + . + . + "0009089"^^ . + . + . + "false"^^ . + . + "https://www.wormbase.org/db/seq/protein?name="^^ . + . + . + . + . + "ontology" . + . + . + . + . + "https://chemkg.github.io/chemrof/"^^ . + . + "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)"^^ . + "http://www.fao.org/gsfaonline/additives/details.html?id=$1"^^ . + . + "https://www.ncbi.nlm.nih.gov/bioproject/?term="^^ . + . + . + . + . + . + "bioinformatics" . + . + "http://virtualflybrain.org/reports/$1"^^ . + . + . + . + "omim" . + "http://purl.obolibrary.org/obo/SPD_"^^ . + . + . + . + . + . + . + "ontoavida" . + . + "http://purl.obolibrary.org/obo/CIDO_$1"^^ . + . + "Protein Ensemble Database" . + . + . + . + . + . + . + "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . + . + "http://purl.obolibrary.org/obo/TAXRANK_$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + "http://bitterdb.agri.huji.ac.il/Receptor.php?id="^^ . + . + . + "^\\d+$"^^ . + . + . + . + "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."^^ . + "false"^^ . + "pathway" . + . + "^[A-Za-z]+\\/[0-9]+$"^^ . + . + "http://bigg.ucsd.edu/models/"^^ . + "obo" . + . + . + . + "https://biofactoid.org/document/$1"^^ . + "https://omia.org/OMIA$1"^^ . + . + "CAID" . + "ontology" . + "true"^^ . + . + . + . + . + "http://addgene.org/"^^ . + . + . + . + . + . + . + "life science" . + "nmrcv" . + "^\\d{7}$"^^ . + . + "uc001rvw.5"^^ . + . + . + . + . + "cordis.project" . + "epo" . + . + . + . + . + "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert=$1"^^ . + . + . + . + "false"^^ . + . + "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . + . + . + . + "The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. ENA is made up of a number of distinct databases that includes EMBL-Bank, the Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. This collection references Embl-Bank identifiers."^^ . + "^\\d+$"^^ . + "nsf.award" . + "http://www.bioinfo.org/NONCODEv4/show_gene.php?id="^^ . + . + "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021"^^ . + "health_care_quality_assessment"^^ . + . + . + . + "molecular dynamics" . + . + . + "radlex" . + . + "https://www.wormbase.org/get?name=$1"^^ . + "CCLE_867"^^ . + . + "Antibiotic resistance genes and mutations"^^ . + . + . + . + . + . + . + . + . + . + . + "lincs.cell" . + . + . + . + . + . + . + . + . + . + "MCDS_S_0000000001"^^ . + . + "health science" . + . + "life science" . + "structure" . + . + . + "wmueller@gbf.de" . + . + . + "metabolites" . + . + "https://rfam.xfam.org/family/"^^ . + . + "multicellds.collection" . + . + . + . + . + . + . + "mampol" . + . + . + . + . + . + "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId="^^ . + . + . + . + "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . + . + . + . + "r3d100010772"^^ . + "SSF57615"^^ . + . + . + . + "http://purl.org/dc/elements/1.1/"^^ . + . + . + "^GenProp\\d+$"^^ . + . + "^[a-z][a-z]/[0-9]+$"^^ . + . + . + . + . + . + . + . + . + "molecular biology" . + . + . + . + . + . + "protein" . + . + "ena.embl" . + . + "Benchmark Energy & Geometry Database" . + "statistics" . + . + "https://www.ebi.ac.uk/gxa/experiments/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/OMRSE_"^^ . + . + . + "taxonomy" . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "eff796f3-6195-11e5-8ac5-06603eb7f303"^^ . + "false"^^ . + "David Clunie" . + "Cell Line Database" . + . + "T3D0001"^^ . + . + . + "obo" . + "fungi" . + . + . + "Identifiers.org namespace" . + . + "Bill Duncan" . + "^[a-z][a-z]/06[1-9]*0[1-9][0-9]*$"^^ . + . + . + "Gi07796"^^ . + . + "The Plant Stress Ontology describes biotic and abiotic stresses that a plant may encounter."^^ . + "life science" . + "lang"^^ . + "^C\\d+$"^^ . + . + "Google Scholar Researcher" . + "Zebrafish anatomy and development ontology" . + . + . + . + . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + . + "NIA Mouse cDNA Project" . + . + "development" . + . + . + "2029"^^ . + . + . + . + "pubchem.substance" . + . + . + "bioschemas" . + "Metabolic Network Exchange Database" . + "http://bcrj.org.br/celula/"^^ . + . + "d1id" . + . + . + "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."^^ . + . + . + . + . + "https://www.inaturalist.org/places/"^^ . + . + "evm" . + . + "CIViC Source" . + . + "false"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/FBcv_$1"^^ . + "sewilson@lbl.gov" . + "datf" . + . + "anatomy" . + . + . + . + "transcriptomics" . + "^\\d{7}$"^^ . + . + . + . + "glycomedb" . + . + . + "000000021"^^ . + . + . + . + . + "life science" . + . + "false"^^ . + "17503"^^ . + "protein" . + . + . + "^\\d+$"^^ . + . + . + "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . + . + . + "DBCOND0066902"^^ . + "obo" . "https://bioregistry.io/wicell:"^^ . - . - "Ligand-Gated Ion Channel database" . - . - "http://ddinter.scbdd.com/ddinter/interact/"^^ . - . -_:N1ee708fba9894af0bfe9c04bade98c46 "Crop Ontology Helpdesk" . - . - . - "0000000"^^ . - "false"^^ . - . - . - . - . - "aging" . - "biosimulations" . - "http://www.orpha.net/ORDO/Orphanet_"^^ . - . - . - . - "Ensembl Bacteria" . - "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."^^ . - . - . - "ontology" . - . - . - . -_:N2049abb829ed4f9d86c5fbb00ea6b058 "Stephan Schurer" . - "Eukaryotic Linear Motif Resource" . - "gene prediction" . - . - . - . - . - "false"^^ . - . - "epd" . - . - "false"^^ . - "fideo" . - . - "Fernanda Dorea" . - "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . - "false"^^ . - . - . - . - "genecards" . - . - . - "subject agnostic" . - . - "http://purl.obolibrary.org/obo/TAO_$1"^^ . - "david.wishart@ualberta.ca" . - "000177759000002"^^ . - "organism supplier" . - "maxo" . - . - . - . - "Kristian Axelsen" . - "https://precision.fda.gov/uniisearch/srs/unii/"^^ . - . - "BioCarta Pathway" . - . - . - "^[a-zA-Z0-9\\-:#\\.]+$"^^ . - "1"^^ . - "http://purl.obolibrary.org/obo/GOREL_"^^ . - "BioGRID Interactions" . - . - . - . - . - . - . - . - "biology" . - "gene" . - . - . - . - "exac.gene" . - "Registry of Research Data Repositories" . - . - . - "dlxc" . - . - . - . - . - . - "genome" . - . - . - . - . - . - . - . - "https://bioregistry.io/hovergen:"^^ . - . - . - . - . - "^\\w+$"^^ . - "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . - . - . - . - "^\\d{6,8}$"^^ . - "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance"^^ . - . - . - "http://purl.obolibrary.org/obo/CTENO_"^^ . - . - "Encyclopedia of DNA Elements" . - "biomedical science" . - . - . - "^A_\\d+_.+$"^^ . - . - . - . - . - . - "fhir.implementation" . - . - "Rebecca Jackson" . - "^\\d{7}$"^^ . - "https://www.gwascentral.org/study/$1"^^ . - "FlyBase_Cell_line" . - "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO="^^ . - . - . - "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:"^^ . - "egon.willighagen@gmail.com" . - . - . - . - . - . - . - . - . - "https://sed-ml.org/urns.html#format:"^^ . - "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . - "Cell line databases/resources"^^ . - "rna" . - "data set" . - . - . - "Ontology of Arthropod Circulatory Systems" . - "https://cropontology.org/rdf/CO_334:"^^ . - . - . - . - "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . - . - . - "https://drs.microbiomedata.org/objects/"^^ . - . - . - . - "https://biopragmatics.github.io/providers/scomp/"^^ . - . - . - . - "PhosphoPOINT is a database of the human kinase and phospho-protein interactome. It describes the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. It also incorporates gene expression and uses gene ontology (GO) terms to annotate interactions. This collection references phosphoprotein information."^^ . - "false"^^ . - "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id="^^ . - . - . - . - "environmental science" . - "^\\d{7}$"^^ . - . - . - . - "https://umgear.org/p?id=$1"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FOBI_"^^ . - . - . - "clinicaltrials" . - "subject agnostic" . - "Laurel Cooper" . - "Hypertension Ontology" . - . - . - "^\\d{7}$"^^ . - "Health Canada Clinical Trials Database" . - "^2\\d{4}$"^^ . - "^\\d+$"^^ . - "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . - . - "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . - . - "biomedical science" . - "false"^^ . - . - . - . - "drug discovery" . - "https://pharmacodb.ca/cell_lines/"^^ . - . - "ontology" . - "noncodev4.rna" . - "chemistry" . - "SysBioCancer2022"^^ . - . - "ontology" . - . - . - . - . + . + . + . + "experiment" . + . + "botany" . + . + "The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer’s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data."^^ . + . + . + _:N17235b39f30847fc8a5e42bdd6482ff2 . + . + . + "ModelDB is a curated, searchable database of published models in the computational neuroscience domain. It accommodates models expressed in textual form, including procedural or declarative languages (e.g. C++, XML dialects) and source code written for any simulation environment."^^ . + "danbri@w3.org" . + . + . + "1000"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "Reactions in drugbank"^^ . + "Phenol-Explorer" . + . + "https://amzn.com/$1"^^ . + . + "^\\d+$"^^ . + . + . + . + "Ontology for Avida digital evolution platform" . + "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . + "Getty Thesaurus of Geographic Names" . + . + . + . + . + . + "icd9" . + . . - "https://stemcells.nindsgenetics.org?line="^^ . - . - . - "credit" . - "http://purl.obolibrary.org/obo/CTO_"^^ . - "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . - "false"^^ . - . - "^\\d+$"^^ . - . - "https://europepmc.org/article/ppr/$1"^^ . - "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name="^^ . - . - "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures)."^^ . - "pharmgkb.disease" . - "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . - "false"^^ . - . - . - . - . - . - . - . - "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . - . - . - "https://biopragmatics.github.io/providers/icepo/"^^ . - "000064"^^ . - . - . - "fishbase.species" . - "PA448710"^^ . - . - . - . - . - "oarcs" . - "^\\d{7}$"^^ . - . - "nikolaos.moustakas@catalysis.de" . - "life science" . - "ontology" . - "ABC"^^ . - . - "genomics" . - "genes" . - "https://registry.identifiers.org/registry/$1"^^ . - "HIX0004394"^^ . - . - . - . - "true"^^ . - "obo" . - . - "Leigh Carmody" . - . - . - "life science" . - "https://bioregistry.io/collection/$1"^^ . - "Ontology about the gross anatomy of the C. elegans"^^ . - "030719"^^ . - . - . - . - "A database of fly neurons and pathways with an associated 3D viewer."^^ . - . - "^\\d+$"^^ . - "google.patent" . -_:Nffb883398fd44d7f8657b94b6b3a1812 "adw_geeks@umich.edu" . - . - . - . - "PS" . - "life science" . - . - "http://aps.unmc.edu/AP/database/query_output.php?ID="^^ . - . - . - . - "ontology" . - . - . - . - . - . - "pdbe" . - . - . - . - . - "0000002"^^ . - . - . - . - . - . - . - "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."^^ . - . - . - "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . - . - . - . - . - . - . - . - "3305"^^ . - "^\\d+$"^^ . - . - . - . - . + . + . + . + "VMH reaction" . + . + "metabolomics" . + . + . + . + . + . + . + . + "UniProt Post-Translational Modification" . + "This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures. This issue of the database contains 17.024 entries (as of October 2007) of which 1350 are two-chain protein hetero-complexes, 7773 homodimers and 1589 are one-chain proteins parsed into two domains (domain structures)."^^ . + . + . + . + . . - "cognitive neuroscience" . - . - . - "^\\d+$"^^ . - "software engineering" . - . - . - . - . - "obo" . - . - . - "^\\d{7}$"^^ . - . - "BUNA790102"^^ . - . - . - . - . - "colonatlas" . - "^\\d+$"^^ . - . - . - "enzyme" . - . - . - . - "Xenbase" . - "false"^^ . - . - . - "bsg-000052"^^ . - "obo" . - "^[A-Za-z]+$"^^ . - . - _:N5e00e918e8a94b1dac10f0dde02fe9dd . - . - . - . - . - "http://purl.obolibrary.org/obo/TAO_"^^ . - . - . - . - . - . - "signor.relation" . - . - . - "genome" . - . - "eagle-i resource ontology" . - . - "biomedical science" . - "https://pharmacodb.ca/datasets/"^^ . - . - . - . - "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . - . - . - . - . - . - . - . - . - . - "SNOMEDCT_2010_1_31" . - "false"^^ . - "biosamples" . - "http://purl.org/dc/dcmitype/"^^ . - . - . - . - . - "BEI_Resources" . - . - . - . - . - . - "col.taiwan" . - . - "^[A-Za-z]+$"^^ . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - "http://purl.org/pav/"^^ . - . - "genetics" . - . - "Cell line databases/resources"^^ . - . - "dbest" . - . - . - . - . - . - "https://pharmacodb.ca/cell_lines/$1"^^ . - "http://www.radiomics.org/RO/$1"^^ . - . - . - "ARBA00000001"^^ . - "cell biology" . - . - . - "epigenomics" . - "traits" . - . - . - "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . - . - "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."^^ . - . - . - "genomics" . - "biosystems" . - . + . + "Datasets inside StoreDB"^^ . + "false"^^ . + . + . + . + . + "structure" . + . + . + "Cell line collections (Providers)"^^ . + "000410"^^ . + . + "David Mendez Lopez" . + . + . + . + . + "Selventa legacy protein family namespace used with the Biological Expression Language"^^ . + "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name=$1"^^ . + "gramene.growthstage" . + . + "false"^^ . + . + . + . + . + . + . + . + . + "life science" . + "gramene.protein" . + "Lonza" . + . + "OncoTree" . + "S6"^^ . + . + . + . + . + "Livestock Breed Ontology" . + . + . + . + . + "International Classification of Diseases, 11th Revision" . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + . + . + "^ACYPI\\d{6}(-RA)?$"^^ . + "true"^^ . + . + "biology" . + . + . + . + "^\\w+$"^^ . + "nhcdr" . + . + "cellular components" . + . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "developmental biology" . + "International Traditional Medicine Clinical Trial Registry" . + . + . + . + . + "false"^^ . + "TAO_RETIRED" . + . + . + "UK Universities and Colleges Admissions Service" . + "https://www.datascienceontology.org/concept/"^^ . + "Informed Consent Ontology" . + "agriculture" . + . + . + . + "https://bioregistry.io/geonames.feature:"^^ . + "Molbase" . + "paxdb.protein" . + "function" . + . + . + "Woody Plant Ontology ontology" . + . + . + "http://uri.neuinfo.org/nif/nifstd/$1"^^ . + . + . + . + . + "Bacterial Tyrosine Kinase Database" . + . + "Canadian Drug Product Database" . + "https://www.imanislife.com/?s=$1"^^ . + . + "http://purl.obolibrary.org/obo/RoleO_"^^ . + "database" . + "metabolomics" . + . + "A biological ontology to standardize and integrate Integrative and Conjugative Element (ICE) information and to support computer-assisted reasoning."^^ . + "biomedical" . + . + . + . + . + . + "false"^^ . + . + "Cell line collections (Providers)"^^ . + "19-T4"^^ . + "https://tools.ietf.org/rfc/rfc$1"^^ . + . + "co_321" . + . + . + . + "HDAA2" . + . + . + . + "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="^^ . + "pscdb" . + "VirOligo" . + . + . + . + . + . + "life science" . + . + . + . + . + "RF00230"^^ . + "Ontology for vector surveillance and management" . + . + . + . + . + . + "Reagent Ontology" . + "ontology" . + . + . + . + . + "ontology" . + "environmental science" . "Tetrahymena Genome Database" . - "false"^^ . - . - . - "https://discover.pennsieve.io/package/"^^ . - . - "ontology" . - . - "WP732"^^ . - "yuki.yamagata@riken.jp" . - . - "ontology" . - . - . - "biology" . - . - . - _:Na44780e2985848e985ef5412da5b9845 . - . - . - "http://www.w3.org/ns/dcat#$1"^^ . - "http://www.bioinfo.org/NONCODEv4/show_rna.php?id="^^ . - "go.chemicals" . - "4623"^^ . - . - "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)"^^ . - "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . - . - "Activity"^^ . - . - "http://antibodyregistry.org/AB_"^^ . - . - . - . - . - "maizegdb.locus" . - . - . - . - . - . - . - "obo" . - . - . - "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."^^ . - "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."^^ . - . - . - . - . - . - "GnpIS" . - . - . - . - "http://purl.org/linked-data/cube#$1"^^ . - "interaction" . - . - "Unified Phenotype Ontology" . - . - "biomedical science" . - "^\\d{7}$"^^ . - "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."^^ . - . - . - "population dynamics" . - . - "119514"^^ . - "rsk00410"^^ . - "0000140"^^ . - "structure" . - "biomedical science" . - . - . - "doi" . - . - "^\\d+$"^^ . - . - . - . - . - . - "zoology" . - . - . - "The BioCatalogue provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Registered services are monitored, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. BioCatalogue is free to use, for all."^^ . - . - . - . - . - . - . - "MMsINC" . - "mi" . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - "Genotype-Tissue Expression" . - "ontology" . - "structure" . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "Medical Action Ontology" . - . - "icd10" . - "WiCell Research Institute Cell Collection" . - "http://purl.obolibrary.org/obo/SWO_$1"^^ . - . - . - "kegg_genome" . - "abcd" . - "DeBiO" . - "^\\d+$"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "Cellosaurus" . - . - . - . - "false"^^ . - "BioData Catalyst" . - . - . - . - . - . - . - "metascience" . - "selventa" . - . - "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1"^^ . - "false"^^ . + . + "1466"^^ . + "http://purl.obolibrary.org/obo/EHDAA2_$1"^^ . + "MNXM1723"^^ . + . + . + . + . + . + . + "An ontology to describe entities related to prescription of drugs"^^ . + . + "structure" . + . + "neuroscience" . + . + . + . + . + . + "The microbial protein interaction database (MPIDB) provides physical microbial interaction data. The interactions are manually curated from the literature or imported from other databases, and are linked to supporting experimental evidence, as well as evidences based on interaction conservation, protein complex membership, and 3D domain contacts."^^ . + "ndex" . + "false"^^ . + "erv" . + . + . + . + . + . + _:N818b7e54347f4b79b69a5d8c44ba1463 . + . + . + . + "^D\\d{4}$"^^ . + . + "flu" . + . + . + "http://repository.topdownproteomics.org/proteoforms/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "Teleost Anatomy Ontology" . + "proteomics" . + . + "Rat Genome Database qTL" . + . + . + "Shur-Jen Wang" . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "gateway" . + . + "HomologyRelation"^^ . + . + . + "gene" . + "flybrain.ndb" . + "http://purl.obolibrary.org/obo/HOM_$1"^^ . + . + "small molecule" . + . + "false"^^ . + . + "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . + . + . + . + "gene" . + . + "false"^^ . + . + "biomedical science" . + . + "true"^^ . + "EHDAA2_RETIRED" . + "true"^^ . + "proteins" . + "https://n2t.net/$1:$2" . + . + "life science" . + "ontology" . + . + . + "https://www.gwascentral.org/phenotype/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . + . + . + "vertebrate" . + "HOSO is an ontology of informational entities and processes related to healthcare organizations and services."^^ . + . + "10595"^^ . + . + "ontology and terminology" . + . + . + . + . + . + "^\\d{7}$"^^ . + "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/"^^ . + . + "protein" . + . + . + "dip" . + . + "ricenetdb.reaction" . . - "false"^^ . - "false"^^ . - . - . - . - . - _:N5b864b9d0d9e47e2b9877a5fcffa278f . - . - "603903"^^ . - "ontology" . - "^TA\\d+$"^^ . - . - "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."^^ . - . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . - "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task="^^ . - "wikipedia.en" . - . - . - "SEED Reactions" . - . - "false"^^ . - . - "co_367" . - . - . - . - "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."^^ . - "https://pdc.cancer.gov/pdc/study/$1"^^ . - . - "false"^^ . - . - "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1"^^ . - . - "false"^^ . - "http://ciliate.org/index.php/feature/details/"^^ . - "GC06M052656"^^ . - . - "02069237"^^ . - . - "functional genomics" . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "ICD9CM_2005" . - "life science" . - "obo" . - . - "http://biobanknetwork.telethon.it/Sample/View?sampleId="^^ . - . - "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . - . - "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."^^ . - . - "https://www.ebi.ac.uk/ena/data/view/$1"^^ . - . + "disease" . + "personalized medicine" . + . + . + . + . + "0000079"^^ . + . + "268"^^ . + _:Na1ba3c668f924c12b186e383d49eb9a2 . + . + . + . + "^\\w+$"^^ . + "protein" . + . + . + . + . + . + . + . + . + . + . . - . - . - . - . - . - "DrugBank Metabolite" . - . - "gro" . - . - . - . - . - . - "http://pax-db.org/#!protein/$1"^^ . - "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . - "NCBIGene" . - . - . - . - "small molecule" . - . - "oostt" . - "inbred" . - . - "Datanator Gene" . - "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "model organism database" . - . - "http://purl.obolibrary.org/obo/AEON_"^^ . - . - . - . - . - "sider.effect" . - "false"^^ . - . - "cell line" . - . - "rna" . - "https://nanocommons.github.io/identifiers/registry#"^^ . - . - "High-quality Automated and Manual Annotation of microbial Proteomes" . - . - . - "false"^^ . - . - . - . - . - "^[1-9]\\d{0,6}$"^^ . - "database" . - "Banana Trait Dictionary in template 5 - Bioversity & IITA - April 2019"^^ . - . - . - "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . - "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases."^^ . - . - . - "Global LEI Index" . - "Gene Regulation Ontology" . - . - . - . - "molecular" . - "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid=$1"^^ . - "microRNA Ontology" . - . - . - . - . - . - "false"^^ . - . - . - "^10.\\w{4}/\\w{10}$"^^ . - . - . - . - . - . - . - . - . - . - "http://www.pharmgkb.org/pathway/$1"^^ . - "geo" . - "Ontology of Vaccine Adverse Events" . - "false"^^ . - . - . - "2afacf00-9a1d-4d80-8c32-69d3923d3913"^^ . - "ontology" . - . - . - . - . - "geogeo" . - "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM="^^ . - "software engineering" . - "sibo" . - . - . + "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0="^^ . + . + . + . + "scoro" . + . + "http://www.interfil.org/details.php?id="^^ . + . + . + . + "https://www.enzolifesciences.com/$1"^^ . + . + "nucleic acid" . + "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . + "http://www.scopus.com/record/display.url?origin=inward&eid="^^ . + . + "Topology Data Bank of Transmembrane Proteins" . "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object="^^ . - "obo" . - . - . - "false"^^ . - "https://doulix.com/biomodules/"^^ . - . - . - . - . - "WBRNAi00086878"^^ . - . - . - "registry" . - . - . - "pennsieve" . - "ccf" . - "life sciences" . - . - "90801"^^ . - "peptideatlas.dataset" . - "a.39.1.1"^^ . - . - "GitLab" . - "false"^^ . - "ReviewVersion"^^ . - "^SAM[NED](\\w)?\\d+$"^^ . - "false"^^ . - "false"^^ . - . - . - "https://www.genedb.org/gene/"^^ . - . - "DICOM Controlled Terminology" . - . - . - . - "bgee@sib.swiss" . - "https://www.uniprot.org/locations/$1"^^ . - . - . - . - "dlxb" . - . - . - . - . - "https://vectorbase.org/gene/"^^ . - . - "virology" . - . - . - . - . - . - "environmental science" . - . - "vario" . - "^\\d{7}$"^^ . - "botany" . - "false"^^ . - . - "biomedical science" . - . - "International Medical Device Regulators Forum" . - . - . - "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . - "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . - . - . - . - . - . - "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database."^^ . - . - "https://cryptodb.org/cryptodb/app/record/gene/"^^ . - . - "artificial intelligence" . - . - . - "gtex" . - . - . - . - "health science" . - . - "^\\d+$"^^ . - "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."^^ . - . - . - "Internet Standard -- IETF Request for Comments" . - . - . - "ligandbook" . - . - . - . - . - "KEGG_DGROUP" . - . - . - . - . - "false"^^ . + . + "false"^^ . + "Diagnostic and Statistical Manual of Mental Disorders (4th Edition)" . + . + . + "false"^^ . + . + . + "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"^^ . + "PGOHUM00000289843"^^ . + . + "MESHC" . + . + . + . + . + . + . + "stap" . + . + . + "olatdv" . + . + . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . + . + . + . + . + "https://gnomad.broadinstitute.org/variant/$1"^^ . + . + . + "bioinformatics" . + . + . + . + "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."^^ . + . + "fyler" . + . + "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . + "false"^^ . + . + . + . + . + . + . + "Selventa Families" . + . + "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . + . + . + "false"^^ . + . + "^[0-9]+$"^^ . + . + . +_:N17235b39f30847fc8a5e42bdd6482ff2 "yingqin@rti.org" . + . + . + . + "Chinese Clinical Trial Registry" . + . + "http://getentry.ddbj.nig.ac.jp/getentry/dad/$1"^^ . + "Paleobiology Database" . + "Aromatic"^^ . + "false"^^ . + . + . + "dbvar.study" . + . + . + "mirbase.family" . + . + . + "gene expression" . + . + . + . +_:Na0c300fd6bd246fc84f22a3874137663 "nospam@iandavis.com" . + . + "^K\\d+$"^^ . + . + "botany" . + . + . + "adriano.rutz@ik.me" . + . + "12345"^^ . + . + . + "https://bio.tools/"^^ . + "http://purl.org/net/orth#$1"^^ . + . + "BQJCRHHNABKAKU"^^ . + "false"^^ . + "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."^^ . + "false"^^ . + . + . + . + "obo" . + . + "CVCL" . + . + . + "0000210"^^ . + "chromium"^^ . + . + "47419"^^ . + "PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them."^^ . + "icf" . + . + "false"^^ . + . + "rcb" . + "inxight-drugs" . + "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."^^ . + "https://www.addexbio.com/productdetail?pid=$1"^^ . + . + "frbrer" . + "The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee."^^ . + "GeoNames" . + . + . + "clinvar.variant" . + . + . + . + "^HIX\\d{7}(\\.\\d+)?$"^^ . + . +_:N4fc383ac4b554144bf3019945d5dcd7d "Animal Diversity Web technical staff" . + . + "ukprns" . + . + "0000106"^^ . + . + . + "Gene Product Information Schema" . + "^\\d+$"^^ . + "hogenom" . + . + "E13035"^^ . + . + . + . + . + . + "pubchem.bioassay" . + . + . + "http://www.phosphosite.org/siteAction.do?id=$1"^^ . + . + "https://www.ncbi.nlm.nih.gov/probe/?term=$1"^^ . + . + . + . + "true"^^ . + . + . + . + "false"^^ . + . + . + . + . + "genome" . + "molecular biology" . + . + "David Gloriam" . + . + "http://www.w3.org/2004/02/skos/core#"^^ . + . + "obo" . + . + "HL7 External Code Systems are stored within the greater OID system" . + . + "life science" . + "false"^^ . + . + "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available."^^ . + "TC" . + "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."^^ . + "FooDB Food" . + . + "cheminformatics" . + "1:rev:309cf2674ee7a0749978cf8265ab91a60aea0f7d"^^ . + "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"^^ . + . + . + "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:"^^ . + . + "life science" . + "ctri" . + . + "https://portal.issn.org/resource/ISSN/"^^ . + . + . + . + "false"^^ . + "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."^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OMIABIS_$1"^^ . + . + . + "life science" . + "HMDB" . + . + . + . + . + "genomics" . + . + . + . + . + . + "RE" . + "^\\d{7}$"^^ . + . + . + "^\\d+$"^^ . + . + . + "https://biopragmatics.github.io/providers/sfam/"^^ . + "embryo" . + . + "ai10e-kctd13b"^^ . + "ENST00000407236"^^ . + . + "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1"^^ . + "jorvis@gmail.com" . + . + . + . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/GEO_"^^ . + "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . + . + "N21"^^ . + . + . + . + "ontology" . + . + . + . + . + . + . + "https://www.affymetrix.com/LinkServlet?probeset="^^ . + . + "1100107"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=$1"^^ . + "HUGO Gene Nomenclature Committee" . + . + "environmental science" . + . + . + "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=$1"^^ . + "person" . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . + "obo" . + "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + . + "CE28239"^^ . + . + . + "obo" . + . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + . + . + "A Drug Identification Number (DIN) is a computer-generated eight digit number assigned by Health Canada to a drug product prior to being marketed in Canada. It uniquely identifies all drug products sold in a dosage form in Canada and is located on the label of prescription and over-the-counter drug products that have been evaluated and authorized for sale in Canada."^^ . + . + "tgma" . + "ontology" . + . + . + "ontology" . + . + . + "biochemistry" . + . + "36"^^ . + "pfam" . + . + "Friend of a Friend" . + . + . + . + . + "aceview.worm" . + . + "^SMP\\d+$"^^ . + . + . + . + . + . + "http://ddinter.scbdd.com/ddinter/drug-detail/$1"^^ . + . + "brycemecum@gmail.com" . + . + "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val="^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "0001417"^^ . + . + "false"^^ . + "ATL98012"^^ . + . + . + . + . + . + . + "http://www.bioguo.org/AnimalTFDB/family.php?fam="^^ . + "true"^^ . + "International Classification of Functioning, Disability and Health" . + . + . + . + . + "pathway" . + "mfmo" . + "https://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatget.asp?spid="^^ . + . + . + . + . + "A Database of Human Hemoglobin Variants and Thalassemias" . + . + "^\\d{3}-\\d{3}-\\d$"^^ . + "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"^^ . + "subject agnostic" . + . + . + . + . + "true"^^ . + . + . + . + . + "gene" . + . + "Terminologia Histologica" . + . + "1174"^^ . + . + . + . + "false"^^ . + "A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma."^^ . + "^[0-9]+$"^^ . + . + . + . + "obo" . + . + . + . + "^EP\\d{4}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.dataone.org/odo/ECSO_$1"^^ . + "^\\d{7}$"^^ . + "obo" . + . + "https://euclinicaltrials.eu/app/#/view/"^^ . + "hso" . + "https://sciflection.com/"^^ . + . + "https://biomodels.net/vocab/idot.rdf#$1"^^ . + . + . + . + "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br"^^ . + "HMS LINCS Compound" . + . + . + . + . + "Anne.Morgat@sib.swiss" . + . + "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."^^ . + . + . + "protein" . + "microbiology" . + . + . + . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + . + . + "Molecular Interactions Controlled Vocabulary" . + . + "Shorthand representations of languages and their subtypes"^^ . + "https://www.hipsci.org/lines/#/lines/$1"^^ . + . + "obo" . + "PF11_0344"^^ . + "yid" . + . + "false"^^ . + "semantic web" . + "An ontology for representing the provenance of scientific claims and the evidence that supports them."^^ . + "9861/3"^^ . + "http://lincsportal.ccs.miami.edu/datasets/#/view/$1"^^ . + . + "https://registry.identifiers.org/registry/"^^ . + . + . + "The coding sequence or protein identifiers as maintained in INSDC."^^ . + . + . + . + . + . + . + . + . + . + . + "pancreas" . + . + . + . + "^[0-9]{9}$"^^ . + . + "breeding" . + . + . + . + "ygob" . + . + . + . + . + "http://www.cathdb.info/domain/$1"^^ . + . + . + . + . + "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . + "bootstrep" . + "datacite" . + "false"^^ . + . + . + . + "genome" . + . + "VFDB Genus" . + . + "false"^^ . + "global health" . + . + . + . + . + . + "MycoBrowser marinum" . + . + "E. coli Metabolite Database" . + . + "10b38aaf-b977-4950-85b8-f4775f66658d"^^ . + . + . + "proteomics" . +_:N7905bc80f2e64f5990160fb6972ac478 "faldo@googlegroups.com" . + "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#"^^ . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/cdd?term=$1"^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/CHMO_"^^ . + . + . + . + "hc.npn" . + . + . + . + "https://bartoc.org/en/node/$1"^^ . + . + "https://bioregistry.io/bmrb:"^^ . + "biology" . + "https://publons.com/researcher/$1"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line=$1"^^ . + . + "Dictybase Gene" . + "drsanv0" . + . + "emaps" . + . + . + . + . + . + "health science" . + . + "CharProt" . + . + "ontology" . + . + . + . + "mosquito" . + . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + . + . + . + "NCITt" . + "life science" . + "structure" . + "https://www.ncbi.nlm.nih.gov/datasets/genome/$1"^^ . + "ecmdb" . + . + . + . + . + "https://protists.ensembl.org/id/"^^ . + "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id="^^ . + . + "https://drks.de/search/en/trial/$1"^^ . + . + . + "obo" . + "false"^^ . + "life science" . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG$1"^^ . + "mpath" . + . + "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?$1"^^ . + . + . + "Chemical Entities of Biological Interest" . + "life science" . + . + . + . + "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . + "0000983"^^ . + . + "http://purl.obolibrary.org/obo/PR_$1"^^ . + . + "^\\d+$"^^ . + "social and behavioural science" . + . + . + . + . + . + "epidemiology" . + "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt="^^ . + . + "embryo" . + . + "ttd.drug" . + . + . + . + . + "false"^^ . + "http://sabiork.h-its.org/newSearch?q=ecnumber:$1"^^ . + "http://purl.obolibrary.org/obo/TADS_"^^ . + "false"^^ . + "biomedical science" . + "ontology" . + "Defunct vaccine information source from the He Lab"^^ . + . + . + . + . + . + . + . + . + . + . + "plana" . + "Pharmacogene Variation Consortium" . + "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."^^ . + "http://www.kegg.jp/entry/$1"^^ . + . + "ricecyc" . + . + . + . + "^[dp]\\.[a-z0-9]{8}$"^^ . + . + "CIAT Common bean trait dictionary - version August 2014"^^ . + "Mathematical modeling ontology" . + "http://purl.obolibrary.org/obo/UPHENO_"^^ . + "ontology" . + . + . + "http://purl.obolibrary.org/obo/kestrelo_"^^ . + . + . + . + "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + "metagenomics" . + "Foods in FooDB"^^ . + "gemet" . + . + . + . + "^DB-\\d{4}$"^^ . + "gmd.profile" . + "biomedical science" . + . + "life science" . + "obo" . + . + . + "cell lines" . + . + . + . + . + "http://phenol-explorer.eu/foods/$1"^^ . + "false"^^ . + . + . + . + . + . + . + "virgen" . + "CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information."^^ . + . + "false"^^ . + "foodb" . + . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp="^^ . + . + . + . + . + . + . + . + "emmo" . +_:N18d11baf84d04ccaa32fc6ed3f139ddd "Stephen Larson" . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references individual metabolites."^^ . + . + . + . + . + "vega" . + . + . + "18030"^^ . + . + "Redistributor of bilogics and biomedical supplies"^^ . + . + "PMC3084216"^^ . + . + "Genetic code, mitochontrial genetic code, and other linked information to NCBI taxonomy entries."^^ . + . + . + "WBls" . + . + "NCBITaxon" . + . + . + . + "dashr.expression" . + "^\\w+$"^^ . + . + . + . + "robert.thacker@stonybrook.edu" . + "bykdb" . +_:N9c645ce04f594b14a09661a17b0ccc23 "Crop Ontology Helpdesk" . + . + . + . + . + . + . + . + "https://s3.us-east-2.amazonaws.com/lg.cede/"^^ . + . + . + . + . + . + . + "false"^^ . + . + "phenotype" . + . + . + . + . + . + . +_:N947c2ef4044f49f18bd9f0caf7c87ee6 "American Medical Association" . + . + "http://purl.obolibrary.org/obo/EHDA_"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "plant genetics" . + "subject agnostic" . + . + . + "hypercldb" . + "asap" . + . + . + "ontology" . + "Sorghum TDv5 - Oct 2019"^^ . + . + . + . + "^\\d+$"^^ . + "false"^^ . + "false"^^ . + "BitterDB Receptor" . + . + . + . + "spbase" . + . + . + . + "biomedical science" . + "^\\d{8}$"^^ . + . + . + . + "0000111"^^ . + . + "UM-BBD_compID" . + . + . + "miriam" . + . + . + "biodiversity" . + "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "Regulation of Transcription"^^ . + . + _:N1902992fefc74b64a0200f6ba3d98584 . + . + . + . + . + . + . + "edam.topic" . + . + "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."^^ . + "subject agnostic" . + "2555646"^^ . + "subject agnostic" . + . + "https://data.terra.bio/ga4gh/drs/v1/objects/$1"^^ . + . + "ontology" . + . + . + . + . + . + "https://bioregistry.io/abcam:"^^ . + . + . + . + "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."^^ . + "genome" . + "botany" . + . + . + "https://www.pgscatalog.org/pgs/$1"^^ . + . + . + . + . + "false"^^ . +_:N6d31f3e671ef4a46915145d8a044dbb3 "rafael.goncalves@stanford.edu" . + "P10636"^^ . + "ValidatorDB" . + "RGD" . + "genetics" . + . + . + "1"^^ . + . + . + . + . + "Pierre Grenon" . + . + . + . + . + "UMLS" . + . + "obo" . + "life science" . + . + . + . + . + "http://www.iresite.org/IRESite_web.php?page=view&entry_id=$1"^^ . + . + . + . + "1257009"^^ . + "ontology" . + . + "false"^^ . + . + . + . + "0000127"^^ . + . + . + "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id=$1"^^ . + "National Bibliography Number" . + . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID=$1"^^ . + . + "159787"^^ . + "https://omabrowser.org/oma/hog/HOG:$1"^^ . + . + "0100010"^^ . + "ovae" . + . + . + . + . + . + "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=$1"^^ . + . + . + . + . + "dna" . + "dna" . + . + . + . + . + . + "a.kikhney@embl-hamburg.de" . + . + . + . + . + "https://www.worldwildlife.org/ecoregions/$1"^^ . + . + . + "https://www.datanator.info/metabolite/"^^ . + "subject agnostic" . + . + . + . + . + . + "^[-\\w]+(?:\\/[-\\w]+)(?:\\/\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b)$"^^ . + . + . + . + "false"^^ . + "Chris Grove" . + . + "kushida@biosciencedbc.jp" . + "http://www.gramene.org/db/protein/protein_search?protein_id="^^ . + "phenotype" . + "AY109603"^^ . + . + "https://www.cbioportal.org/study/summary?id=$1"^^ . + . + . + "tgd" . + . + . + "^.*/.*$"^^ . + "deficiency" . + "^\\d{1,5}$"^^ . + "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"^^ . + . + . + . + "life science" . + "ontology" . + "dna" . + "metatlas" . + . + "0000199"^^ . + . + . + "Selventa legacy complex namespace used with the Biological Expression Language"^^ . +_:N6d31f3e671ef4a46915145d8a044dbb3 "Rafael Gonçalves" . + "http://purl.obolibrary.org/obo/PLANP_$1"^^ . + "false"^^ . + . + "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence."^^ . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + "earth science" . + "anatomy" . + "^[A-Za-z]+$"^^ . + . + "Bioregistry" . + . + . + "hgnc.symbol" . + "5.A.1.1.1"^^ . + "^\\d+$"^^ . + . + . + . + . + "catalog" . + . + . + "bao" . + . + "bioinformatics" . + "violinID" . + . + . + . + "false"^^ . + . + "david.c.blackburn@gmail.com" . + . + . + . + . + "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . + . + . + "ISA1083-2"^^ . + . + . + . + "C0020004/4992"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "strain" . + "959"^^ . + . + . + . + . + . + "social science" . + "^\\w.+$"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_res_$1"^^ . + . + . + . + . + . + . + . + . + "mouse" . + . + "human" . + . + "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."^^ . + "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . + . + "protein" . + . + "false"^^ . + "j.detras@cgiar.org" . + . + . + . + . + "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"^^ . + "repository" . + . + "ECOCYC" . + . + "anzctr" . + . + "true"^^ . + "^[0-9]+$"^^ . + "kegg.genome" . + . + "cell lines" . + . + "Core Vocabulary defines the OSLC Core RDF vocabulary terms and resources, that have broad applicability across various domains."^^ . + . + . + . + "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."^^ . + "bcbc" . + "https://purl.uniprot.org/uniprot/"^^ . + "biomedical science" . + . + . + . + "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge."^^ . + . + . + . + . + . + "embryonic stem cell line" . + . + . + "alternative splicing" . + . + "Tissue List" . + "false"^^ . + . + . + "entiminae@gmail.com" . + . + "Plant Genome Network" . + . + "transgene" . + "SwissRegulon" . + "false"^^ . + . + "github.pull" . + . + . + . + . + "4D Nucleome Data Portal Biosource" . + "protein" . + . + . + "mirtarbase" . + "^\\d+$"^^ . + "Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts. Virus-Host DB covers viruses with complete genomes stored in 1) NCBI/RefSeq and 2) GenBank whose accession numbers are listed in EBI Genomes. The host information is collected from RefSeq, GenBank (in free text format), UniProt, ViralZone, and manually curated with additional information obtained by literature surveys."^^ . + . + . + "NIF Standard Ontology: External" . + . + . + "ascl" . + "NIST Chemistry WebBook" . + "Functional Requirements for Bibliographic Records" . + . + . + . + "3792"^^ . + . + "Marcin Pawel Joachimiak" . + . + . + "clinicaltrials" . + "false"^^ . + "^[0-9a-z]{24,24}$"^^ . + . +_:N8a1cf018ca2c4c11bf7f165adebf9721 "Plant Ontology Administrators" . + "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . + . + . + "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository"^^ . + "small molecule" . + . + . + . + . + "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID="^^ . + "metabolights" . + "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . + . + . + "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . + "structure" . + . + "https://www.worldcat.org/oclc/$1"^^ . + . + "protein" . + . + . + "Bgee gene" . + . "labo" . - . - . - . - . - "http://purl.obolibrary.org/obo/COB_"^^ . - . - . - . - "assays" . - "Metabolic Atlas Reaction" . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/ExO_"^^ . - . - . - "illumina.probe" . - . - . - "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . - . - "^\\d{3}$"^^ . - . - . - "http://purl.obolibrary.org/obo/OGMS_"^^ . -_:Nf02a9133fb1b401fb2f49f9946084afa "Vivian Lee" . - . - . - . - . - . - "false"^^ . - "Phenol-Explorer" . - "https://cropontology.org/rdf/CO_359:$1"^^ . - . - . - "http://www.hmdb.ca/metabolites/$1"^^ . - "0000194"^^ . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "obo" . - . - . - "^\\d{7}$"^^ . - "P683" . - . - "false"^^ . - "^PKDB[0-9]{5}$"^^ . - "merops.clan" . - . - . - . - . - . - . - . - . - "http://www.kegg.jp/entry/$1"^^ . - . - "447860"^^ . - . - . - . - "nutritional science" . - . - "structural biology" . - . - "MolBase" . - "https://glytoucan.org/Structures/Glycans/"^^ . - "antibody" . - . - . - "CASRAI Contributor Roles Taxonomy" . - "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"^^ . - . - . - . - . - . - . - . - "https://www.uniprot.org/unirule/$1"^^ . - . - "0000947"^^ . - . - . - "false"^^ . - . - _:N5a47e5d4a29a4e209ad7f089db31aeb3 . - . - "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q="^^ . - . - "nif.ext" . - "A01M1/026"^^ . - "NCITm" . - . - . - . - . - . - "dev.ga4ghdos" . - "gene" . - . - . - "http://purl.org/ontology/bibo/$1"^^ . - . - . - . - "ontology" . - "http://purl.obolibrary.org/obo/CMO_"^^ . - . - "Medaka Developmental Stages" . - . - "Lorenz Reimer" . - . - . - "agriculture" . - "ontology" . - . - . - "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. "^^ . - . - "Quality"^^ . - . - . - . - . - "preclinical studies" . - . - "metacyc.compound" . - . - . - . - . - "Simplified molecular-input line-entry system" . - "rna" . - . - "transposon insertion" . - "5HT3Arano"^^ . - . - "45539"^^ . - "http://bioinfo.lifl.fr/norine/result.jsp?ID="^^ . - . - "false"^^ . - "http://codes.iarc.fr/search.php?cx=009987501641899931167%3A2_7lsevqpdm&cof=FORID%3A9&ie=UTF-8&ie=ISO-8859-1&oe=ISO-8859-1&sa=&q="^^ . - . - . - "cheminf" . - . - . - "4.2.78"^^ . - . - . - "true"^^ . - "300108/p3934_A-172"^^ . - "https://www.gleif.org/lei/"^^ . - "immunogenetics" . - . - "gene expression" . - . - . - "Tribolium Genome Database -- Insertion" . - "plwhetzel@gmail.com" . - . - . - "^CHEMBL\\d+$"^^ . - . - "protein" . - . - . - . - "false"^^ . - . - "https://www.imanislife.com/?s="^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release."^^ . - "vendor" . - . - "https://www.ebi.ac.uk/miriam/main/$1"^^ . - . - . - "SSF57615"^^ . - "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"^^ . - . - . - . - "182"^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - "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."^^ . - . - . - . - "^\\d{7}$"^^ . - "subject agnostic" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "sdis" . - . - . - "lipidbank" . - "ontology" . - "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . - . - . - "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . - . - . - . - . - "iNaturalist User" . - . - "life science" . - "ENSG00000026508"^^ . - . - "NLXORG covers organisms."^^ . - "ega.study" . - . - . - . - "A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)" . - . - "regulation" . - . - "https://portal.issn.org/resource/ISSN/"^^ . - . - . - . - "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."^^ . - . - . - "PathBank" . - "12"^^ . - . - . - "https://sparontologies.github.io/fabio/current/fabio.html#$1"^^ . - . - . - . - . - "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - "Compositional Dietary Nutrition Ontology" . - "classification" . - . - "spike00001"^^ . - . - "dragondb.dna" . - . - . - "https://nmrshiftdb.nmr.uni-koeln.de/molecule/"^^ . - "false"^^ . - . - . - . - . - "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."^^ . - "http://www.icd9data.com/getICD9Code.ashx?icd9="^^ . - . + . + . + . + "^\\d+$"^^ . + "proteomics" . + . + . + "false"^^ . + "molecular neuroanatomy resource" . + "false"^^ . + . + . + "homd.taxon" . + . + . + . + . + "clinvar.variation" . + . + "http://purl.bioontology.org/ontology/NDDF/$1"^^ . + . + "false"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DUO_"^^ . + "qtldb" . + . + "Regulation of Gene Expression"^^ . + "AT4G01080"^^ . + "International Classification of Diseases, 9th Revision" . + . + . + . + . + . + . + . + . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/$1"^^ . + "sigmaaldrich" . + "The IRESite database presents information about experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract the eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure."^^ . + . + "The IUPAC International Chemical Identifier (InChI) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources. It is derived solely from a structural representation of that substance, such that a single compound always yields the same identifier."^^ . + "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . + . + . + . + . + . + . + . +_:Ne90637670289458180b3f4b6ec45ab94 "Crop Ontology Helpdesk" . + . + . + . + . + "pharmvar" . + . + "https://bioregistry.io/pmap.substratedb:"^^ . + . + . + . + "molmedb" . + "https://bioschemas.org/profiles/"^^ . + . + "^[a-z0-9-]+$"^^ . + . + "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)"^^ . + "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."^^ . + . + "human" . + "KEGG Environ" . + . + "true"^^ . + . + . + "dylan.mcgagh@magd.ox.ac.uk" . + . + . + "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID=$1"^^ . + "4D Nucleome Data Portal Experiment Replicate" . + . + . +_:N12491eabd3e44c84bef06eb91f048151 "Chebi Administrators" . + . + . + . + "ontology" . + . + . + . + "http://purl.obolibrary.org/obo/DDPHENO_"^^ . + . + . + . + . + . + "https://mged.sourceforge.net/ontologies/MGEDontology.php#"^^ . + "http://purl.obolibrary.org/obo/AMPHX_$1"^^ . + . + . + . + . + . + "Influenza Sequence and Epitope Database" . + . + "http://purl.org/spar/doco/"^^ . + "PhosphoSite Site Group" . + . + . + . + . + . + "people/11035"^^ . + . + "^\\d{7}$"^^ . + "SNOMEDCT_US_2019_03_01" . + "false"^^ . + . + "biology" . + . + . + "https://pubchem.ncbi.nlm.nih.gov/element/"^^ . + . + "http://purl.obolibrary.org/obo/WBls_"^^ . + "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . + . + . + "1948"^^ . + . + . + . + . + . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + "The pattern for expanded URIs in the given resource" . + . + . + . + "false"^^ . + "false"^^ . + . + "true"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "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"^^ . + . + . + . + "An ontology for glycans based on GlyTouCan, but organized by subsumption."^^ . + "https://ligandbook.org/package/$1"^^ . + . + . + . + . + "protein" . + . + . + . + . + . + "The academic event ontology, currently still in development and thus unstable, is an OBO compliant reference ontology for describing academic events such as conferences, workshops or seminars and their series. It is being developed as part of the [ConfIDent project](https://projects.tib.eu/confident/) to allow RDF representations of the academic events and series stored and curated in the [ConfIDent platform](https://www.confident-conference.org/index.php/main_page)."^^ . + . + . + . + "false"^^ . + . + . + . + . + "mw.study" . + "Christopher Mull" . + . + "GWAS Central Phenotype" . + "040000"^^ . + . + "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . + "false"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "Nonlinear Force-Free Field Three-Dimensional Magnetic Fields Data of Solar Active Regions Database"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + "MU9_3181"^^ . + "chemrof" . + "iNaturalist Taxonomy" . + "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#$1"^^ . + . + . + . + "3hB06"^^ . + . + . + "https://www.uniprot.org/diseases/$1"^^ . + "iso.3166" . + . + "Mental Functioning Ontology" . + . + "ontology" . + . "Bioregistry Metaregistry" . - . - . - . - . - "https://chem.nlm.nih.gov/chemidplus/rn/"^^ . - "http://usefulinc.com/ns/doap#$1"^^ . - "2000191"^^ . - . - . - "https://cropontology.org/rdf/CO_360:$1"^^ . - . - . - . - . - . - . - "http://purl.org/spar/deo/"^^ . - "^DIP(\\:)?\\-\\d{1,}[ENXS]$"^^ . - "^[1-9]\\d*$"^^ . - . - . - . - "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . - "neXtProt family" . - "^\\w{14}$"^^ . - . - . - "AberOWL" . - . - . - . -_:Nc2d8d233b5dd4e92b1c37108a30c724a "pbrooks@hcfa.gov" . - "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."^^ . - "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."^^ . - . - . - . - . - . - . - "true"^^ . - "http://sabiork.h-its.org/newSearch?q=$1"^^ . - . - . + . + . + "https://pubchem.ncbi.nlm.nih.gov/element/$1"^^ . + "drug" . + "^\\d{7}$"^^ . + . + . + . + . + . + "4145692"^^ . + . + . + "NCBI PubChem database of bioassay records" . + "A gazetteer constructed on ontological principles"^^ . + "^\\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."^^ . + . + . + . + . + "structural biology" . + "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases."^^ . + "life science" . + "genome" . + "false"^^ . + . + "rlwalls2008@gmail.com" . + . + . + . + . + . +_:N6336578d53d547a592544f1d65a18759 "The World Health Organization" . + "https://www.storedb.org/?$1"^^ . + "miRNA Target Prediction at EMBL" . + "false"^^ . + "false"^^ . + "true"^^ . + . + . + "Unified Code for Units of Measure" . + . + "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . + . + . + "Chemical Information Ontology" . + . + . + "life science" . + "Bacillus subtilis genome sequencing project" . + . + . + "http://open-services.net/ns/core#"^^ . + "Biotin_biosynthesis"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "0000026"^^ . + "AOPWiki (Key Event Relationship)" . + . + "^\\d{1,5}$"^^ . + . + . + . + "http://thebiogrid.org/"^^ . + . + "^CONSO\\d{5}$"^^ . + . + . +_:N81fe899ae37e4bc6870b3fdde5669e37 "helpdesk@cropontology-curationtool.org" . + "true"^^ . + "Resources mentioned in \"Sharing biological data: why, when, and how\"" . + . + "false"^^ . + "dr.shorthair@pm.me" . + . + "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample."^^ . + "biomedical science" . + "functional genomics" . + . + . + . + . + . + "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM="^^ . + . + "gene" . + "genome" . + . + . + "The data cube vocabulary" . + "An application ontology for use with miRNA databases."^^ . + . + . + . + . + "Fission Yeast Phenotype Ontology" . + . + . + "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . + . + "https://bioregistry.io/mesh.2012:"^^ . + . + . + . + . + . + "COG_Cluster" . + . + "false"^^ . + . + . + "Integrative and Conjugative Element Ontology" . + "biomedical science" . + "http://purl.obolibrary.org/obo/KISAO_"^^ . + . + . + . + "https://morpheus.gitlab.io/models/"^^ . + "0002902"^^ . + "https://www.xenbase.org/entry/$1"^^ . + . + . + . + . + "true"^^ . + . + "^G(PL|SM|SE|DS)\\d+$"^^ . + . + . + . + . + . + . + _:N4d553228bdc9474894f812f565b509c7 . + "Gene Regulation Ontology" . + "db-object-id"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/COB_"^^ . + . + "http://purl.org/spar/pwo/"^^ . + "Database for Prokaryotic Operons" . + . + . + . + . + . + "false"^^ . + "^\\d+$"^^ . + . + "Animal Genome Pig QTL" . + . + . + . + "http://oncotree.mskcc.org/api/tumorTypes/search/code/"^^ . + . + . + . + . + "31253.11.sciencedb.j00001.00123"^^ . + . + "http://id.who.int/icd/entity/"^^ . + . + . + "tokue" . + "gomf" . + "J0705A10"^^ . + "http://purl.obolibrary.org/obo/MA_$1"^^ . + . + "registry" . + "SubtiWiki" . + . + . + "false"^^ . + . + "cmecs" . + "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."^^ . + "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . + . + "http://www.wikidata.org/entity/"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "^[A-Za-z 0-9]+$"^^ . + "broad" . + . + . + . + . + . + . + . . - . - . - . - . - "topics" . - "false"^^ . - "drug discovery" . - . - . - . - . - . - . - . - . - "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)." . - . - "development" . - "false"^^ . - "http://dictybase.org/gene/$1"^^ . + "obo" . + "protein" . + "maize" . + . + "Pathway ontology" . + . + . + "bbtp" . + "Clair Kronk" . + "Medaka fish anatomy and development" . + "false"^^ . + . + "https://www.inaturalist.org/taxa/"^^ . + . + "http://data.crossref.org/fundingdata/funder/10.13039/"^^ . + . + . + "false"^^ . + . + . + . + . + . + "gramene.qtl" . + . + . + . + . + . + . + . + . + . + "ACC-1"^^ . + . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_mol_"^^ . + "The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence. This collection references projects."^^ . + . + . + "cell lines" . + "^\\d{7}$"^^ . + "PTM-0450"^^ . + . + . + . + . + . + "ViralZone" . + . + . + . + . + . + "https://cropontology.org/rdf/CO_356:$1"^^ . + "CRW_00469"^^ . + . + . + . + "structural bioinformatcs" . + "obo" . + . + . + . + . + . + "gxa.expt" . + . + . + "ppo" . + . + . + "fivestars" . + "meetings" . + "A controlled vocabulary to support the study of transcription in the human brain"^^ . + "cadsr" . + "geography" . + . + . + "qtl" . + "protein" . + "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."^^ . + "Cassava ontology" . + . + . + . + . + . + . + . + "5601141"^^ . + "classification" . + . + "false"^^ . + "false"^^ . + . + "https://www.confident-conference.org/index.php/Event_Series:"^^ . + . + . + . + "KEGG_REACTION_CLASS" . + . + "http://sabiork.h-its.org/newSearch?q=$1"^^ . + "MEDLINE" . + "Oat trait dictionary started by Oat Global (http://oatglobal.org/) and improved by NIAB and PepsiCo"^^ . + "2170610"^^ . + . + . + . + "false"^^ . + . + "http://www.innatedb.ca/getGeneCard.do?id="^^ . + . + . + . + "2022.07.08.499378"^^ . + . + . + . + "microbiology" . + . + . + . + "alignedWith"^^ . + "genomics" . + . + . + . + . + "Mammalia Polymorphism Database" . + . + "life science" . + "Cell line databases/resources"^^ . + . + . + "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."^^ . + . + "0002999"^^ . + . + . + "false"^^ . + "ProteomeXchange" . + . + . + . + "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."^^ . + "biomedical science" . + . + . + . + . + . + . + . + . + . + "sgd" . + . + . + "Cell line collections (Providers)"^^ . + . + . + "omics" . + . + "false"^^ . + . + . + . + . + "https://bioregistry.io/mirex:"^^ . + "false"^^ . + . + . + . + "cellopub" . + "https://europepmc.org/article/CBA/"^^ . + . + . + . + . + . + "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]"^^ . + "http://www.genome.jp/dbget-bin/www_bget?ec:"^^ . + . + . + . + . + "http://lisanwanglab.org/DASHR/entry/$1"^^ . + . + . + . + "obo" . + . + . + . + . + "small molecule" . + "http://www.geneontology.org/formats/oboInOwl#"^^ . + . + . + . + "false"^^ . + "ontology" . +_:N0d15b74d2231418f80502274c743eb89 "helpdesk@cropontology-curationtool.org" . + . + "https://www.storedb.org/?STOREDB:DATASET$1"^^ . + . + . + "Sabrina@tislab.org" . + . + "population genetics" . + . + . + . + . + . + "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."^^ . + "obo" . + . + . + . + "clinical decision support systems" . + . + . + . + . + . + "A structured controlled vocabulary of stage-specific anatomical structures of the developing human."^^ . + . + "Imanis Life Sciences cell line products" . + "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://genomics.senescence.info/genes/details.php?id=$1"^^ . + "P23298"^^ . + . + "omics" . + "http://purl.obolibrary.org/obo/BTO_"^^ . + . + . + . + . + . + "obo" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "http://www.knapsackfamily.com/knapsack_core/information.php?word="^^ . + . + "Internet Engineering Task Force Language Tag" . + "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."^^ . + . + . + . + "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g="^^ . + "egon.willighagen@gmail.com" . + "Metabolomics Workbench Study" . + "UniProt Subcellular Locations" . + "nmpdr" . + . + _:Nce56519a74584e27bab9646e3c0efa5e . + . + . + . + . + . + "https://www.alliancegenome.org/accession/$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + "health monitoring" . + "trnadbce" . + . + . + "biomagresbank" . + . + . + . + "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."^^ . + . + . + "false"^^ . + . + . + . + . + "051"^^ . + . + . + . + "idomal" . + . + "phylogenetics" . + "A manually curated resource for the representation and annotation of metabolic pathways"^^ . + . +_:N18d11baf84d04ccaa32fc6ed3f139ddd "slarson@ncmir.ucsd.edu" . + . + "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid="^^ . + . + . + "culture" . + . + "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."^^ . + . + . + . + . + . . - "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id="^^ . - . - . - "false"^^ . - "cmf" . - "0000060"^^ . - . - "loinc" . - . - . - "NCBITaxon" . - "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."^^ . - . - . - "David Wishart" . - . - . - . - . - . - "MassBank" . - . - . - . - "Protein Model Portal" . - "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."^^ . - . - "false"^^ . - . - . - . - . - . - "95-0166C6"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - . - "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://www.ebi.ac.uk/ega/studies/"^^ . - "marine biology" . - "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol="^^ . - . + "faseb list" . + . + . + . + . + "immunology" . + "structural biology" . + . + . + . + . + . + "https://biopragmatics.github.io/debio/"^^ . + . + . + . + . + "gianni.cesareni@torvergata.it" . + "iceberg.element" . + . + . + . + . + . + . + "genotype" . + . + "life science" . + "false"^^ . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "protein" . + . + . + "https://www.geonames.org/$1"^^ . + "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."^^ . + . + . + "ontology" . + . + . + . + . + "chebi" . + "computational chemistry" . + "ontology" . + . + "false"^^ . + "fbbt" . + "false"^^ . + "false"^^ . + . + "MMP743597.11"^^ . + . + . + . + "life science" . + "http://purl.obolibrary.org/obo/IPR_"^^ . + . + . + "DTXSID2021028"^^ . + . + . + . + . + _:N5601098de94f4d4fbeab59b9878b4d57 . + "obo" . + . +_:N0d15b74d2231418f80502274c743eb89 "Crop Ontology Helpdesk" . + . + "obo" . + . + "medicine" . + . + "https://biopragmatics.github.io/providers/dhba/$1"^^ . + . + . + "The Ontology of Immune Epitopes (ONTIE) is an effort to represent terms in the immunology domain in a formal ontology with the specific goal of representing experiments that identify and characterize immune epitopes."^^ . + . + . + . + "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=$1"^^ . + "ontology" . + "Pantelis Topalis" . + . + . + "Drosophila Phenotype Ontology" . + "http://www.pharmgkb.org/disease/"^^ . + . + "Uniprot ID" . + . + . + . + "genomics" . + "OMIM Phenotypic Series" . + . + . + . + "Ontology for General Medical Science" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "SIGNOR-252737"^^ . + "false"^^ . + "^((S\\d+$)|(Y[A-Z]{2}\\d{3}[a-zA-Z](\\-[A-Z])?))$"^^ . + "http://purl.obolibrary.org/obo/HTN_"^^ . + . + . + . + . + "alayne.cuzick@rothamsted.ac.uk" . + "genecards.geneannot" . + "GC06M052656"^^ . + "false"^^ . "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."^^ . - "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources."^^ . - . - . - . - "Jesualdo Tomás Fernández-Breis" . - . - . - "130502"^^ . - "http://vocab.getty.edu/page/tgn/"^^ . - "4DN"^^ . - . - . - "biozil" . - . - "BioAssay Ontology" . - . - . - . - "false"^^ . - "KEGG_RCLASS" . - "environmental science" . - "GN_G03681DA"^^ . - "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."^^ . - "ecmdb" . - . - "xenopus" . - . - . - . - . - . - "Pennsieve" . - . - "TCTR20230429001"^^ . - . - "http://www.chemspider.com/"^^ . + "The responsible person for a resource" . + "life science" . + . + "kinetics" . + . + . + . + "http://purl.org/oban/"^^ . + . + "0000062"^^ . + "inhibitors" . + . + "^\\d{7}$"^^ . + . + . + "aphidbase.transcript" . + "Progenetix" . + "FlyBase is the database of the Drosophila Genome Projects and of associated literature."^^ . + "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."^^ . + . + . + . + "biomedical science" . + . + . + . + . + . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/$1"^^ . + . + . + "Maciej.Antczak@cs.put.poznan.pl" . + . + . + . + "https://www.aapc.com/codes/cpt-codes/$1"^^ . + "informatics" . + . + . + "ontology" . + . + . + . + . + . + . + . + "hrehm@mgh.harvard.edu" . + . + . + . + . + "ontology" . + . + . + . + "http://purl.obolibrary.org/obo/ONE_"^^ . + . + . + . + "false"^^ . + . + "bioregistry.registry" . + . + . + . + . + "false"^^ . + . + "VSAO_0000183"^^ . + . + "Open Citation Identifier" . + "https://permalink.obvsg.at/$1"^^ . + "http://purl.obolibrary.org/obo/PRIDE_$1"^^ . + . + "Cross-linker reagents ontology" . + . + . + . + . + . + . + . + . + "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."^^ . + . + "INN_ID" . + . + "ncbi.genome" . + . + "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://purl.obolibrary.org/obo/TAO_$1"^^ . + "Software Heritage" . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid=$1"^^ . + . + "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)."^^ . + . + "AB" . + "http://pombe.oridb.org/details.php?id="^^ . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#"^^ . + "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."^^ . + "cordis.article" . + "SubstrateDB" . + . + . + . + . + "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id=$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/$1_$2" . + . + "01625"^^ . + "the FAIR Cookbook" . + . + "^\\w+$"^^ . + "cbioportal" . + . + . + "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:"^^ . + . + . + "tm.shah@cgiar.org" . + . + "derivatives%2Fthiocyclam%20hydrochloride"^^ . + . + "http://purl.obolibrary.org/obo/RXNO_$1"^^ . + "rna" . + . + . + "An ontology to represent medically relevant actions, procedures, therapies, interventions, and recommendations."^^ . + . + "https://www.ebi.ac.uk/metagenomics/samples/"^^ . + . + . + . . - "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . - . - "false"^^ . - . - . - "https://biopragmatics.github.io/providers/hba/$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."^^ . - "civic.vid" . - "false"^^ . - . - . - "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . + . + . + . + . + "MLCommons Association" . + . + . + "^\\d+$"^^ . + . + . + "FAIR* Reviews Ontology" . + "This collection contains various brain atlases from the Allen Institute." . + . + "http://swissregulon.unibas.ch/query/"^^ . + . + "idog" . + "^\\d+$"^^ . + "alteration" . + . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query="^^ . + "veterinary medicine" . + "NeuroMorpho" . + "http://arabidopsis.info/StockInfo?NASC_id="^^ . + . + . + . + . + "165a"^^ . +_:N0f79c573c15a4405a1d8a67adb3a8e7a "biomodels-net-support@lists.sf.net" . + . + . + . + "Database portal containing replicate experiments of different assays and samples"^^ . + . + . + . + "http://www.coloncanceratlas.org/search_cell_line?cell_line=$1"^^ . + "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref="^^ . + "false"^^ . + . + "oboformat" . + . + "inchikey" . + . + "pubchem.aid" . + . + "pirsf" . + . + . + "http://scop.berkeley.edu/sccs="^^ . + "Lycalopex_vetulus"^^ . + "100101"^^ . + "ontology" . + "Add"^^ . + "FHIR United States Implementation Guides" . + . + "protein" . + . + . + "http://purl.obolibrary.org/obo/MRO_$1"^^ . + "https://rpcec.sld.cu/en/trials/$1"^^ . + . + "M1"^^ . + . + "http://www.wikidata.org/entity/$1"^^ . + . + "stian@soiland-reyes.com" . + . + . + . + "katy@indiana.edu" . + . + "https://www.drugbank.ca/categories/$1"^^ . + . + "biology" . + "enm" . + "^\\d+$"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "992"^^ . + . + . + . + . + . + "xco" . + . + . + . + . + "fbol" . + . + . + "computer science" . + . + "https://www.ncbi.nlm.nih.gov/cdd?term="^^ . + "agro" . + . + . + . + . + . + "2008-005144-16"^^ . + "mediadive.solution" . + . + . + . + "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . + . + . + "medicinal chemistry" . + . + "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . + . + . + . + "false"^^ . + . + "Terry Hayamizu" . + "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. "^^ . + "https://www.thermofisher.com/antibody/product/"^^ . + "loqate" . + . + . + . + "https://icd.who.int/browse10/2019/en#/$1"^^ . + . + "false"^^ . + "PSI Extended File Format" . + . + "ontology" . + . + "false"^^ . + "biology" . + . + . + "0000254"^^ . + . + . + . + . + "false"^^ . + . + . + . + "COB brings together key terms from a wide range of OBO projects to improve interoperability."^^ . + . + . + . + . + . + . + "pathway" . + . + "AC119"^^ . + "genomics" . + . + "https://proteininformationresource.org/cgi-bin/resid?id="^^ . + . + . + . + . + . + "Linkml is a flexible modeling language that allows you to author schemas in yaml that describe the structure of your data. additionally, it is a framework for working with and validating data in a variety of formats (json, rdf, tsv), with generators for compiling linkml schemas to other frameworks."^^ . + . + "Vertebrate Breed Ontology" . + . + "ohd" . + . + . + . + . + "1981638"^^ . + . + . + . + "Brassica Trait Ontology (BRaTO) hosts trait information to describe brassica crop data. Terms are collected from various projects including OREGIN, RIPR (UK) and Rapsodyn (France). BRATO development is conducted by Earlham Institute (UK), Southern Cross University (Australia) and INRA (France)."^^ . + "https://doulix.com/constructs/"^^ . + . + . + . + "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets"^^ . + . + "^[a-z0-9]{32,32}$"^^ . + "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."^^ . + "http://www.pocketome.org/files/$1.html"^^ . + . + . + . + "58788"^^ . + . + . + . + . + . + . + . + "Current Dental Terminology" . + . + "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."^^ . + . + . + . + . + . + . + . + . + . + "ChemBank" . + "http://erop.inbi.ras.ru/result2.php?PepName="^^ . + . + . + . + . + "0000574"^^ . + . + . + . + . + . + "ehda" . + "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:$1"^^ . + "mp" . + . + "nicolas.matentzoglu@gmail.com" . + "OGI formalized the genomic element by defining an upper class 'genetic interval'.\n\nThe definition of 'genetic interval' is \"the spatial continuous physical entity which contains ordered genomic sets(DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic Acid Base Residue) on a chromosome or RNA molecule which must have a liner primary sequence sturcture.\" \n\nRelated paper:\n\n1. Yu Lin, Norihiro Sakamoto (2009) “Genome, Gene, Interval and Ontology” Interdisciplinary Ontology Vol.2 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2009. Page(s):25-34 (http://cdb-riken.academia.edu/LinYu/Papers/142399/Genome_Gene_Interval_and_Ontology)\nYu Lin, Hiroshi Tarui, Peter Simons (2009) “From Ontology for Genetic Interval(OGI) to Sequence Assembly – Ontology apply to next generation sequencing” Proceeding of the Semantic Web Applications and Tools for Life Science Workshop, Amsterdam, Nov.20th, 2009. (http://ceur-ws.org/Vol-559/Poster2.pdf)\nYu Lin, Peter Simons (2010) “DNA sequence from below: A Nominalist Approach” Interdisciplinary Ontology Vol.3 - Proceedings of the Second Interdisciplinary Meeting, Tokyo, Feb. 28th- Mar. 1st, 2010. (http://philpapers.org/rec/LINDSF)\n\n\n"^^ . + . + . + "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with plant genomes."^^ . + "http://purl.obolibrary.org/obo/GENEPIO_"^^ . + "oceanography" . + "^\\d+$"^^ . + . + "http://www.radiomics.org/RO/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ADH1"^^ . + . + . + "miriam"^^ . + . + . + "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . + . + . + . + . + . + . + . + . + . + . + . + "1kfv"^^ . + . + . + . + . + "https://icd.who.int/browse10/2019/en#/"^^ . + . + "RCB0002"^^ . + . + "v2_1b0f158a-86e2-3887-b990-89e3cf2d9082"^^ . + "col.taiwan" . + . + . + . + . + "minid" . + . + . + . + . + "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . + "57"^^ . + . + . + . + "^NOR\\d+$"^^ . + . + "life science" . + . + "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."^^ . + . + "Ontology about the gross anatomy of the C. elegans"^^ . + "Hilmar Lapp" . + . + . + . + "protein" . + "microbiology" . + "^\\d+$"^^ . + . + . + . + . + "Steven E. Wilson" . + . + . + "dg.anv0" . + "^\\d{7}$"^^ . + . + . + . + . + "ontology" . + . + . + . + "https://bioregistry.io/ukprn:"^^ . + "proteins" . + . + . + "imgt.hla" . + . + "xao" . + . + . + . + "reaction" . + . + . + "brenda.ligandgroup" . + . + . + "^[A-Za-z0-9]+$"^^ . + . + "https://cropontology.org/rdf/CO_334:"^^ . + "true"^^ . + . + . + . + . + "andreadega/systems-biology-compiler"^^ . + "https://cropontology.org/rdf/CO_350:$1"^^ . + "Amphibian gross anatomy" . + . + . + "http://purl.obolibrary.org/obo/RBO_$1"^^ . + . + . + . + "Time Ontology in OWL" . + "TAIR Protein" . + . + . + "shibase" . + "Alexander Diehl" . + . + "https://www.kaggle.com/$1"^^ . + . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis=$1"^^ . + . + . + "Cu.me.I1"^^ . + . + "MSMEG_3769"^^ . + . + "Golm Metabolome Database GC-MS spectra" . + . + . + . + "Cancer cell LInes GEne fusions portAl" . + . + . + "Flora Phenotype Ontology" . + . + . + "2381/12775"^^ . + . + "ARP-1513"^^ . + . + . + "false"^^ . + "101"^^ . + . + "topfind" . + . + . + . + "Scopus Publication" . + . + "chemistry" . + "bams" . + "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/$1"^^ . + . + . + . + . + "FBtr0084214"^^ . + . + . + . + "http://www.jcvi.org/mpidb/experiment.php?interaction_id="^^ . + . + . + . + . + . + . + "oboinowl" . + "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_$1"^^ . + . + . + . + "rs121909098"^^ . + "Gene Expression Analysis Resource" . + "T0599"^^ . + . + . + . + "dpv" . + . + "^\\d+$"^^ . + . + . + "KNApSAcK provides information on metabolites and the\ntaxonomic class with which they are associated."^^ . + . + "false"^^ . + . + . + "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)."^^ . + . + . + . + . + . + "https://www.sigmaaldrich.com/US/en/product/sigma/"^^ . + . + . + . + . + . + . + . + . + . + "Presents the new fast tracks for clinical research and observational studies on INDIGENOUS PEOPLE AND TRADITIONAL COMMUNITIES and on NEGLECTED TROPICAL DISEASES (NTDs). Fast-track can reduce the normal approval period for clinical trials to less than 48 hours, if the documentation, information and any mandatory changes requested are provided by the registrant."^^ . + . + "mouse" . + . + . + . + . + . + . + "snp500cancer" . + . + . + "^\\d+$"^^ . + "http://www.w3.org/ns/odrl/2/$1"^^ . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "hsapdv" . + . + . + "grin.taxonomy" . + "metabolite" . + . + . + "gene" . + "Pol Castellano Escuder" . + . + . + . + . + . + . + . + . + "PWY-1042"^^ . + . + . + "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)"^^ . + "ontology" . + . + . + "interaction" . + "medlineplus" . + . + . + "https://models.physiomeproject.org/workspace/"^^ . + . + "ontology" . + . + . "sourceDateStart"^^ . - . - "SNOMED" . - "storedb.study" . - "biochemistry" . - "SP_DI" . - . - . - . - . - . - . - . - . - "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. "^^ . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_inv_"^^ . - . - "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)."^^ . - "supfam" . - . - . - . - . - "biomedical science" . - . - "Dr. Alpha Tom Kodamullil" . - . - . - "sigmaaldrich" . - "false"^^ . - . - "Genomes Online Database" . - . - "^\\d{7}$"^^ . - "worm" . - . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/"^^ . - . - . - "zfa" . - "false"^^ . - . - . - "Bacillus subtilis genome sequencing project" . - "https://loinc.org/$1"^^ . - "sstoss" . + . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID=$1"^^ . + "limore" . + . + "The PSCDB (Protein Structural Change DataBase) collects information on the relationship between protein structural change upon ligand binding. Each entry page provides detailed information about this structural motion."^^ . + . + . + . + "https://www.abmgood.com/search?query="^^ . + "metabolites" . + . + . + "apaonto" . + "This database aims to record all published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP, FKBP10, LEPRE1 and PPIB genes."^^ . + "life science" . + . + . + . + . + . + . + . + "cell biology" . + . + . + "^\\d{7}$"^^ . + "http://pepbank.mgh.harvard.edu/interactions/details/"^^ . + "rna" . + "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)."^^ . + . + . + . + . + "wb.rnai" . + "^\\w+$"^^ . + "AnVIL DRS" . + "ontology" . + "ecg" . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. This collection refers to records using the HGNC symbol."^^ . + . + . + . + . + . + "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States."^^ . + . + "Sierra Moxon" . + . + . + "pathway" . + . + . + "false"^^ . + "false"^^ . + . + . + . + "WGS-95-1333"^^ . + . + . + . + . + "^CLPUB\\d+$"^^ . + . + "false"^^ . + . + "GenProp0699"^^ . + . + . + "SWRL enables Horn-like rules to be combined with an OWL knowledge base."^^ . + "false"^^ . + . + "https://bioregistry.io/odam:"^^ . + . + . + . + . + . + "rna" . + "https://disprot.org/$1"^^ . + . + . + . + . + . + . + . + "Zebrafish Phenotype Ontology" . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "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."^^ . + . + "earth science" . + . + . + . + "true"^^ . + "^\\d{7}$"^^ . + . + "Imke Tammen" . + "ontology" . + "false"^^ . + "phenxtoolkit" . + . + . + "classification" . + "pathway" . + "https://scicrunch.org/resolver/RRID:IMSR_TAC_$1"^^ . + "false"^^ . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + . + . + "false"^^ . + . + . + "Analyses of microbiome data within MGnify"^^ . + . + . + . + "^\\d{7}(_\\d)?$"^^ . + . + . + "https://www.geonames.org/recent-changes/featurecode/$1/"^^ . + "Basic Register of Thesauri, Ontologies & Classifications" . + . + "unigene" . + . + . + . + "gene expression" . + . + "Salk Institute for Biological Studies" . + . + "worldavatar.kin" . +_:Ncacac89b73af4494b2963250287dad6c "sschurer@med.miami.edu" . + . + "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + "http://purl.obolibrary.org/obo/HsapDv_$1"^^ . + "https://hpscreg.eu/cell-line/"^^ . + "IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI maintaisn a database of cross references between the primary data sources, it provides minimally redundant but complete sets of proteins for featured species, and it maintains stable and unique identifiers."^^ . + "TB2:S1000"^^ . + "true"^^ . + "http://purl.obolibrary.org/obo/PDRO_$1"^^ . + . + . + "https://bioregistry.io/metaregistry/prefixcommons/"^^ . + . + "gene expression" . + "National Drug File - Reference Terminology" . + . + "1426686"^^ . + "false"^^ . + . + . + . + "phrr" . + . + "classification" . + . + . + . + "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://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1"^^ . + "http://purl.obolibrary.org/obo/CLO_$1"^^ . + . + "http://sugarbind.expasy.org/$1"^^ . + . + "^\\d{1,2}\\-\\d+\\-[GATC]\\-[GATC]$"^^ . + "false"^^ . + "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value="^^ . + "^\\d{7}$"^^ . + . + . + . + "ocid" . + . + "Charles Ettensohn" . + . + . + . + "^\\d+$"^^ . + . + . + . + "idocovid19" . + . + . + . + "TCTR20230429001"^^ . + . + . + . + . + "SYMP" . + "AB_262044"^^ . + . + "0000088"^^ . + . + . + "smr@stowers.org" . + . + . + . + . + . + "sfam" . + . + . + "protein" . + . + "^\\d{7}$"^^ . + "Human developmental anatomy, abstract version" . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l=$1"^^ . + . + "false"^^ . + "^\\d{10}$"^^ . + . + "biomedical science" . + "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/$1"^^ . + . + . + . + . + . + "andreas.ruepp@helmholtz-muenchen.de" . + . + . + . + . + . + . + . + "Software"^^ . + "http://purl.obolibrary.org/obo/SOPHARM_"^^ . + . + . + "Semantic Mapping Vocabulary" . + . + "KEGG.COMPOUND" . + . + "false"^^ . . - . - . - . - "structure" . - . - . - . - "http://edamontology.org/format_$1"^^ . - . - . - . - "Rat Genome Database" . - "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"^^ . - . - "http://www.imgt.org/ligmdb/view?id=$1"^^ . - . - . - "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . - "matus.kalas@uib.no" . - . - . - . - "http://sugarbind.expasy.org/"^^ . - . - "false"^^ . - . - . - . - "Matthias Samwald" . - "r0001"^^ . - . - . - "A collection of ontologies relevant for chemistry.\n\nSkipped:\n- DOLCE (dead links)" . - "false"^^ . - . - "csd" . - . - "http://purl.obolibrary.org/obo/EMAP_$1"^^ . - . - . - "false"^^ . - . - "SMIDs (Small Molecule Identifiers) represent gene-style identifiers for small molecules newly identified in C. elegans and other nematodes. SMIDs aim to make life easier for describing biogenic small molecules in metabolomic and genomic applications. "^^ . - "^\\d{7}$"^^ . - . - . - . - . - "4dn.biosource" . - "false"^^ . - . - "100"^^ . - . - . - . - "ornaseq" . - . - "iNaturalist Taxonomy" . - . - . - "ChEBI" . - . - . - "^\\d+$"^^ . - "life science" . - . - . - "^\\d{7}$"^^ . - . - . - "HGVST1828"^^ . - . - . - . - . - . - . - "The Artificial Intelligence Ontology" . - . - "^\\w+$"^^ . - . - "28"^^ . - . - . - . - . - "so" . - . - . - "GT10"^^ . - "https://stemcells.nindsgenetics.org?line=$1"^^ . - . - "anatomy" . - . - . - . - . - "MIPModDB" . - "Ontologized MIABIS" . - "false"^^ . - "bioinformatics" . - . - . - . - "preclinical studies" . - . - "^\\d{7}$"^^ . - . - "agriculture" . - . - . - . - "false"^^ . - "^\\d+$"^^ . - "pgxbs-kftva5zv"^^ . - "false"^^ . - "bibliography" . - . - . - "uniprot.arba" . - "upa" . - . - "version Dec 2019"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "Gene"^^ . + . + "11303"^^ . + "ECGOntology" . + . + "mmmp.biomaps" . + . + "molecular chemistry" . + "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://modelseed.org/biochem/reactions/$1"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "msigdb" . + "splash" . + . + . + . + . + "gsfa" . + "An ontology of minimum information regarding potential drug-drug interaction information."^^ . + "cgnc" . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/PO_$1"^^ . + "http://degradome.uniovi.es/cgi-bin/protease/"^^ . + . + . + "https://bionumbers.hms.harvard.edu/bionumber.aspx?id="^^ . + . + "Microbial Conditions Ontology" . + "ontology" . + . + . + "Virus-HostDB" . + . + . + "https://mmp.sfb.uit.no/databases/marcat/#/records/"^^ . + "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id="^^ . + . + . + . + . + . + . + "Model format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + "ontology" . + . + "biomedical science" . + . + . + . + . + "^\\d+$"^^ . + "Morpheus model repository" . + . + "ontology" . + "https://purl.dataone.org/odo/SASAP_"^^ . + . + "The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies"^^ . + . + "http://viroligo.okstate.edu/main.php?vid="^^ . + . + "physiology" . + "false"^^ . + "Software Heritage is the universal archive of software source code."^^ . + . + "^[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}$"^^ . + . + . + . + . + "unpd" . + . + "false"^^ . + "BDGP insertion DB" . + . + "ontology" . + . + . + . + . + "gene" . + . + . + . + . + "^\\d+$"^^ . + "http://www.whocc.no/atc_ddd_index/?code=$1"^^ . + . + "false"^^ . + "https://bioregistry.io/nbn:"^^ . + . + . + . + . + "snp2tfbs" . + . "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an=$1"^^ . - "^(imp|gen)\\d{5}$"^^ . - . - "false"^^ . - . - "IC9CM" . - . - . - "hsa-mir-200a"^^ . - . - "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."^^ . - "ontology" . - "mouse" . - . - . - "ftp://hgdownload.cse.ucsc.edu/goldenPath/$1"^^ . - "37232"^^ . -_:N19ba2f4b49e149989c007cb1324ae430 "Stephan Schurer" . - "humanities" . - . - . - "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . - . - "plant" . - "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . - . - . - "false"^^ . - "^\\d+$"^^ . - . - "slime-mould" . - "^HMDB\\d+$"^^ . -_:N76f00e653b4248c9891b2f17b031ddbd "info@who.int" . - "Bill Duncan" . - . - "jla1@sanger.ac.uk" . - . - "protein" . - "https://bioregistry.io/metaregistry/prefixcommons/"^^ . - . - "embryo" . - . - . - . - "http://purl.obolibrary.org/obo/GSSO_"^^ . - "^\\w{1,2}\\d{8,10}$"^^ . - "ontology" . - . - . - . - . - . - "dna" . - . - . - "obo" . - "GlycoNAVI" . - . - "Veterans Administration National Drug File" . - . - . - "false"^^ . - "Mouse Genome Informatics" . - "0000460"^^ . - . - . - . - . - . - . - . - . - "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . - . - . -_:Nc2d8d233b5dd4e92b1c37108a30c724a "Patricia Brooks" . - . - . - "roman@ebi.ac.uk" . - "^\\d+$"^^ . - . - "EAWAG Biocatalysis/Biodegradation Database" . - "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . - "Biosapiens Protein Feature Ontology" . - "Registry" . - . - . - . - . - "Melanie Courtot" . - . - . - . - . - "^[0-9][A-Za-z0-9]{3}$"^^ . - "ClinicalTrials.gov" . - "obo" . - . - "false"^^ . - "PolBase" . - . - "http://scipion.i2pc.es/ontology/CRYOEM_"^^ . - "false"^^ . - . - . - "GrainGenes" . - . - . - "HOSO is an ontology of informational entities and processes related to healthcare organizations and services."^^ . - . - . - . - . - "false"^^ . - "obo" . - . - "protein" . - . - . - "G24361QY"^^ . - . - "7499841"^^ . - . - "ontology" . - "http://ecoliwiki.net/colipedia/index.php/$1:Gene"^^ . - . - . - . - . - . - . - "BIOZIL" . - . - "biomedical science" . - "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . - . - . - . - . - . - . - . - . - . - . - . - "obo" . - . - . - "Dalia Alghamdi" . - . - "Paula.Duek@sib.swiss" . + . + "^DBCOND\\d+$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/ARO_$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "PA448710"^^ . + "^\\d+$"^^ . + "80001"^^ . + "obo" . + "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"^^ . + "mosaic" . + "false"^^ . + "http://purl.obolibrary.org/obo/ERO_$1"^^ . + . + "DICOM Controlled Terminology" . + "ontology" . + . + . + "^[A-Z]+[0-9]+(\\.\\d+)?$"^^ . + "pharmacogenomics" . + "^[1-9][0-9]{3,6}$"^^ . + "false"^^ . + . + "^[a-z]+(\\..*?)?$"^^ . + "false"^^ . + "Ontology for simulation, modelling, and optimization" . + "UPa" . + . + . + "https://bioregistry.io/dragondb.allele:"^^ . + "ontology" . + . + . + . + "easychair.cfp" . + "false"^^ . + . + . + . + . + "SWISS-MODEL Repository" . + . + "Groundnut ontology" . + . + . + . + "bioregistry" . + "International Genome Sample Resource" . + . + . + . + . + . + "Monique Zahn" . + "live animal" . + . + . + . + "https://w3id.org/linkml/"^^ . + . + "biomedical science" . + . + "Mihail Anton" . + . + . + "0000138"^^ . + . + "648028003"^^ . + "KNApSAcK" . + . + . + . + . + . + "life science" . + "^(([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]+)$"^^ . + . + . + . + "obo" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "cst" . + "false"^^ . + "^\\w+$"^^ . + "http://phylomedb.org/?seqid=$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "http://aclame.ulb.ac.be/perl/Aclame/Genomes/mge_view.cgi?view=info&id=mge:"^^ . + . + "^\\d+$"^^ . + . + . + "Lucas Leclere" . + . + . + "4DNSR73BT2A2"^^ . + . + . + . + "protein" . + "data management" . + "https://grants.nih.gov/stem_cells/registry/current.htm?ID="^^ . + . + . + "doap" . + . + . + . + . + "anatomy" . + . + . + "false"^^ . + . + . + "^PS\\d{5}$"^^ . + . + . + . + "^\\d+$"^^ . + "https://www.ncbi.nlm.nih.gov/dbvar/studies/"^^ . + "UPI000000000A"^^ . + . + . + "ror" . + . + . + . + . + . + "^\\d+$"^^ . + "wb" . + "Danielle Welter" . + "Within the CIViC database, the disease should be the cancer or cancer subtype that is a result of the described variant. The disease selected should be as specific as possible should reflect the disease type used in the source that supports the evidence statement."^^ . + "biokc" . + "https://civicdb.org/links/diseases/"^^ . + . + . + "mipmod" . + . + "https://lincs.hms.harvard.edu/db/sm/"^^ . + . + "Q13485"^^ . + "Probability Distribution Ontology" . + . + . + . + . + "PGS000018"^^ . + . + . + "nutritional science" . + . + "0000001"^^ . + . + "ChEMBL-Targets" . + . + . + . + . + "^BE\\d{7}$"^^ . + . + . + . + "gene" . + "congenic rat" . + "life science" . + "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . + . + . + "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId="^^ . + . + . + "panther.pthcmp" . + "EasyChair Topic" . + . + . + . + "obo" . + "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . + . + . + "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry."^^ . + . + "1915"^^ . + "is deprecated" . + "gudmap" . + . + . + . + "false"^^ . + "knowledge and information systems" . + "https://www.dsmz.de/collection/catalogue/details/culture/"^^ . + . + "NCT00222573"^^ . + . + . + . + . + . + . + "http://www.chemspider.com/"^^ . + . + "https://ecocyc.org/gene?id="^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:N12491eabd3e44c84bef06eb91f048151 . + . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + "omo" . + . + "https://discover.pennsieve.io/package/$1"^^ . + . + . + . + "ontology" . + "http://emmo.info/emmo/cif-core#"^^ . + . + "scopus.eid" . + "false"^^ . + "true"^^ . + . + "protein" . + "false"^^ . + "An anatomical and developmental ontology for cephalopods"^^ . + . + . + . + . + . + "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . + "false"^^ . + "protein" . + . + . + "https://www.merckmillipore.com/catalogue/item/"^^ . + . + . + . + . + . + "^\\d{6}$"^^ . + . + . + "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No=$1"^^ . + . + . + . + "https://glyconavi.org/hub/?id=$1"^^ . + . + . + "genomics" . + . + "model" . + "PDB ligand" . + "1-FEH+w3"^^ . + . + . + . + . + . + "obo" . + . + "false"^^ . + "false"^^ . + . + "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . + . + "^[A-Za-z_0-9]+$"^^ . + . + . + . + "ucsc" . + "ontology" . + "ABC"^^ . + "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."^^ . + . + . + . + "Cell line databases/resources"^^ . + . + . + . + "clyh" . + "vso" . + . + . + . + "0000190"^^ . + . + . + . + . + . + "hagr.genage" . + . + "http://biocyc.org/getid?id="^^ . + . + "https://www.drugbank.ca/categories/"^^ . + . + . + . + "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."^^ . + "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . + . + "false"^^ . + "interaction" . + . + "Yiming Bao" . + . + "NLXQUAL" . + . + . + "false"^^ . + . + . + "gene" . + . + . "Cell line databases/resources"^^ . - "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . - . - "E-cyanobacterium rule" . - . - . - . - . - "dg5b0d" . - . - "obo" . - . - . - . - "transgene" . - . - . - . - . - . - . - "^VB\\.[A-Za-z][A-Za-z]\\..*$"^^ . - . - "^DI-\\d{5}$"^^ . - "^[A-Za-z_0-9]+$"^^ . - "false"^^ . - . - . - . - . - . - . - "false"^^ . - "^HIT\\d{9}(\\.\\d+)?$"^^ . - . - "UniProt Subcellular Locations" . - . - . - . - . - "structure" . - . - . - "https://www.alliancegenome.org/accession/"^^ . - "http://www.jcvi.org/mpidb/experiment.php?interaction_id="^^ . - . - . - . - . - . - . - "ZINC is not Commercial" . - "https://purl.dataone.org/odo/MOSAIC_"^^ . - . - . - . - . - "systems biology" . - "false"^^ . - "broad" . - "chemical biology" . - "botany" . - "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."^^ . - . - . - _:N61f371b1d2fa4381a3fcd51f3dd48a97 . - "false"^^ . - . - "false"^^ . - "The primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - . - "https://www.storedb.org/?$1"^^ . - "https://proteinensemble.org/$1"^^ . - . - . - . - "tcb" . - "http://purl.bioontology.org/ontology/HCPCS/"^^ . - . - "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . - "life science" . - . - . - . - . - . - . - . - "^(c|k)\\d{7}$"^^ . - . - "false"^^ . - . - . - "false"^^ . - "G protein-coupled receptor database" . - . - . - "health science" . - "https://biofactoid.org/document/"^^ . - "cghdb" . - . - . - "population genetics" . - . - . - "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . - . - . - . - . - . - "AAindex" . - . - . - . - "mmsl" . - . - . - . - "statistics" . - "civic.tid" . - . - . - . - "WikiPathways is a database of biological pathways maintained by and for the scientific community."^^ . - . - "Proteoform Atlas" . - . - "Pesticide Properties DataBase" . - . - . - . - . - . - . - . - "l.andres.hernandez.18@student.scu.edu.au" . - "3447"^^ . - . - "Rice ontology" . - . - "health science" . - "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."^^ . - "3771877"^^ . - . - "phylomedb" . - . - "https://ocid.ontochem.com/prefname?ocid="^^ . - "protein" . - "BioContext" . - . - . - . - . - "http://purl.obolibrary.org/obo/MOP_"^^ . - . - . - "structure" . - . - . - . - . - "3792"^^ . - . - . - . - "false"^^ . - "developmental biology" . - . - . - . - . - "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."^^ . - . - . - . - . - "ontology" . - "false"^^ . - . - "0000512"^^ . - . - . - . - . - "biomedical science" . - . - . - . - . - "anatomy" . - . - "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."^^ . - . - . - . - . - "Nucleotide" . - . - . - "Tom Gillespie" . + "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"^^ . + . + . + . + "obo" . + . + . + . + . + . + "sssom" . + . + . + . + "vipr" . + . + . + . + "An ontology based on PRO for describing the contributions that may be made, and the roles that may be held by a person with respect to a journal article or other publication (e.g. the role of article guarantor or illustrator)."^^ . + . + . + "^[a-zA-Z0-9_-]{3,}$"^^ . + . + . + "false"^^ . + . + "The Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology."^^ . + . + . + . + . + . + . + . + "pibase" . + "GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray" . + "http://purl.obolibrary.org/obo/REX_"^^ . + "true"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + "Classification of Transcription Factors in Mammalia" . + . + . + "registry" . + . + . + . + "GenDR is a database of genes associated with dietary restriction (DR). GenDR includes two datasets: 1) genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of DR; 2) genes robustly altered due to DR, derived from a meta-analysis of microarray DR studies in mammals"^^ . + "NIF Standard Ontology: Brain Regions" . + . + . + . + . + . + . + . + "false"^^ . + . + "ghr" . + . + . + . + . + . + "false"^^ . + . + "FlyBase Controlled Vocabulary" . + "https://www.pharmvar.org/gene/$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "https://lincs.hms.harvard.edu/db/cells/"^^ . + . + . + . + "OSR00185W"^^ . + . + . + . + . + "anatomy" . + . + . + "PTM" . + . + . + "http://dicom.nema.org/resources/ontology/DCM/"^^ . + "biology" . + . + . + . + . + . + "bido" . + . + . + "030719"^^ . + . + "strain" . + "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."^^ . + "life science" . + "https://bioregistry.io/ccdc:"^^ . + "https://cropontology.org/rdf/CO_365:$1"^^ . + . + . + . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/FBbt_$1"^^ . + . + . + . + . + "^(HOM)?\\d{7}$"^^ . + "epd" . + . + . + "https://ror.org/$1"^^ . + _:N7905bc80f2e64f5990160fb6972ac478 . + "0000187"^^ . + "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."^^ . + . + . + "biology" . + . + "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."^^ . + . + . + . + . + "environmental science" . + . + "CAE46076"^^ . + . + . + "https://www.worldcat.org/oclc/"^^ . + "protein" . + . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + "gene" . + "false"^^ . + . + . + "This document describes the XML Schema namespace. It also contains a directory of links to these related resources, using Resource Directory Description Language."^^ . + "Genome Properties" . + . + "transportdb" . + "epidemiology" . + . + "http://lincsportal.ccs.miami.edu/datasets/#/view/"^^ . + . + . + "9781584885658"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "funcbase.mouse" . + . + . + . + "classification" . + . + "false"^^ . + . + . + . + "sequence" . + . + . + . + . + . + . + . + . + "unipathway.reaction" . + . + "Beta Cell Genomics Ontology" . + "false"^^ . + "Swiss National Clinical Trials Portal" . + "Oat ontology" . + "Unified Medical Language System Atomic Unique Identifier" . + "obo" . + . + . + "caripark@iastate.edu" . + . + "atfdb.family" . + "Phy000CLXM_RAT"^^ . + . + . + "https://www.encodeproject.org/"^^ . + "0000005"^^ . + . + "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_"^^ . + . + "http://www.w3.org/ns/adms#$1"^^ . + "https://athena.ohdsi.org/search-terms/terms/"^^ . + . + . + . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . + . + "Rice Genome Annotation Project" . + . + "spd" . + . + "mouse" . + "ontology" . + "CAL0003079"^^ . + . + . + . + . + "^C\\d+$"^^ . + . + . + . + . + . + "obo" . + "https://scicrunch.org/resolver/RRID:$1"^^ . + . + . + . + "co_341" . + "0376"^^ . + . + . + "United States Patent and Trademark Office" . + . + . + . + "scretf" . + . + . + . + . + "thesaurus" . + "ontology" . + "^[a-z]+/[0-9]+$"^^ . + . + "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications."^^ . + "Developing Human Brain Atlas" . + . + "bibliography" . + "Publons publication" . + . + "seed.compound" . + "https://aopwiki.org/relationships/$1"^^ . + "dgrc" . + "true"^^ . + "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . + "Sequence types and features ontology" . + . + "bel" . + "ncro" . + . + "COVID-19 Surveillance Ontology" . + "ontology" . + . + . + . + . + "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . + . "http://purl.obolibrary.org/obo/RBO_"^^ . - . - . - . - "Reagent Ontology" . - "0000001"^^ . - "^KIAA\\d{4}$"^^ . - . - . - . - . - . - . - . - "false"^^ . + "GlycoMapsDB" . + "chebi"^^ . + "glida.ligand" . + . + . + . + . + "http://www.kegg.jp/entry/"^^ . + . + . + "biology" . + . + . + . + . + . + . + . + . + . + "rat" . + . + . + . + . + "biology" . + "hhe@ebi.ac.uk" . + "https://www.nextprot.org/term/$1"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/LABO_$1"^^ . + "http://w3id.org/owlstar/"^^ . + . + . + "0000044"^^ . + . + . + . + . + "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)"^^ . + . + . + . + . + "modularmassactionprimer"^^ . + "false"^^ . + . + . + . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID="^^ . + . + "human" . + . + . + . + "rutgeraldo@gmail.com" . + "^\\d{7}$"^^ . + . +_:Ndf03f6d8403c435dbcd86c77420d1bf0 "NLM Customer Service" . + . + . + . + . + . + "Publication Provenance Prefixes" . + . + . + . + . + . + . + . + "adult" . + . + "2005080"^^ . + . + . + . + . + "mutant mouse strain" . + . + . + "http://func.mshri.on.ca/mouse/genes/list_functional_scores/"^^ . + . + . + "miRBase pre-miRNA" . + "http://substrate.burnham.org/protein/annotation/$1/html"^^ . + . + "preclinical studies" . + . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID=$1"^^ . + "gene" . + "false"^^ . + "genome" . + "https://biosimulators.org/simulators/"^^ . + "false"^^ . + "ogms" . + . + "life science" . + . + . + "^[A-Za-z_0-9]+$"^^ . + . + "^R\\d+$"^^ . +_:N5601098de94f4d4fbeab59b9878b4d57 "LOINC Support" . + "CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes."^^ . + "ontology" . + . + "^\\d+$"^^ . + "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . + . + "cell cycle" . + . + "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "bgee.gene" . + . + "medicine" . + . + . + "http://purl.unep.org/sdg/SDGIO_$1"^^ . + "obo" . + "http://www.ncbi.nlm.nih.gov/clinvar?term=$1"^^ . + . + . + . + . + "miRBase Families" . +_:Naa71f4b9d1a3472aafbbf8cea9abd883 "Radiological Society of North America" . + "elvira@imbb.forth.gr" . + "radiomics" . + . + . + . + . + "VIPERdb" . + "http://purl.obolibrary.org/obo/IDO_$1"^^ . + "0000127"^^ . + . + "377550"^^ . + . + . + . + "Rice Metabolic Pathways" . + . + . + . + "an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems."^^ . + "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . + . + . + . + . + . + . + . + . + "Swiss Personalized Health Network Schema" . + "http://www.kegg.jp/entry/"^^ . + . + . + "obo" . + "pubchem.compound" . + "false"^^ . + "25512"^^ . + . + . + . + . + . + . + . + "http://biohackathon.org/resource/faldo#"^^ . + . + "http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=/netahtml/PTO/search-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN/"^^ . + "BioStudies database" . + . + "^\\d+$"^^ . + . + "RDF Schema provides a data-modelling vocabulary for RDF data. RDF Schema is an extension of the basic RDF vocabulary."^^ . + "Pierre-Marie Allard" . + . + . + "bkc640"^^ . + . + "oban" . + "Yeast Metabolome Database" . + . + . + . + . + . + . + "http://dictybase.org/gene/"^^ . + "gocc" . + "https://icd.codes/icd10cm/"^^ . + . + "MIMAT0046872"^^ . + "http://bacmap.wishartlab.com/organisms/"^^ . + . + "http://purl.obolibrary.org/obo/TRANS_$1"^^ . + . + . + . + "Veterinary Nomenclature" . + "ontology" . + . + . + . + . + . + "Encyclopedia of Life" . + "http://fossilworks.org/?a=referenceInfo&reference_no="^^ . + . + . + . + "scop.sun" . + . + . + "structure" . + . + . + . + "EcoLexicon" . + . + "ontology" . + . + "false"^^ . + "http://purl.obolibrary.org/obo/FOBI_"^^ . + "structure" . + . + "http://purl.obolibrary.org/obo/SYMP_$1"^^ . + "^\\d+$"^^ . + "loinc" . + "Person"^^ . + "false"^^ . + "ito" . + . + . + . + . + "18125"^^ . + "nbn" . + "Kids First" . + "^\\d{7}$"^^ . + "The localization and quantitation atlas of the yeast proteome" . + . + . + . + "obo" . + . + "https://tree.opentreeoflife.org/taxonomy/browse?id="^^ . + . + "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . + . + . + . + . + . + . + "https://mediadive.dsmz.de/ingredients/$1"^^ . + "neurolex" . + . + "DrugBank Target v4" . + . + . + . + . + "https://rnacentral.org/rna/$1"^^ . + . + "taxonomy" . + . + "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID=$1"^^ . + . + . + . + "https://www.uniprot.org/uniref/"^^ . + . + . + "mirTarBase" . + "smp-m3w9hbe"^^ . + . + "taxonomy" . + "^WB[A-Z][a-z]+\\d+$"^^ . + . + "physics" . + . + . + . + . + "The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology"^^ . + "https://www.ebi.ac.uk/ena/browser/view/"^^ . + . + "^(\\d{4}\\.\\d{2}\\.\\d{2}\\.)?\\d{6,8}(v\\d{1,3})?$"^^ . + "ontology" . + . + "http://mirbase.org/cgi-bin/mature.pl?mature_acc="^^ . + . + "violinId" . + . + . + "https://bioregistry.io/resolve/github/pull/"^^ . + . + "http://www.w3.org/2002/07/owl#$1"^^ . + . + . + . + "datanator.reaction" . + . + "CTD Disease" . + "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)."^^ . + . + "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."^^ . + . + "0000125"^^ . + "conso" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "PF3D7_1328700"^^ . + "protein" . + . + "cellular" . + "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=$1"^^ . + . + . + "63250"^^ . + . + "obo" . + . + "pig" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/COLAO_"^^ . + "funding agencies" . + . + . + . + . + . + "https://www.affymetrix.com/LinkServlet?probeset=$1"^^ . + . + . + . + "https://sitem.herts.ac.uk/aeru/ppdb/en/Reports/$1.htm"^^ . + "https://www.ncbi.nlm.nih.gov/research/cog/pathway/"^^ . + . + . + . + . + "harukin@protein.osaka-u.ac.jp" . + . + . +_:Nfa7ed40a90074ec19376c04d4c9a1c78 "mb4@sanger.ac.uk" . + . + . + . + . + "^([a-z]{3,5}_)?M\\d{5}$"^^ . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid="^^ . + "vendor" . + "metanetx.reaction" . + . + . + . + . + "inhand" . + . + . + "01406"^^ . + "Bioregistry" . + "taxonomy" . + "cell" . + . + . + "ontology" . + "false"^^ . + . + . + . + . + . + . + . + . + "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . + "false"^^ . + . + . + "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."^^ . + . + . + "ontology" . + "Non-Coding RNA Ontology" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "ontology" . + . + . + "life science" . + . + "genomics" . + . + "obo" . + . + "agriculture" . + . + "Hector Escriva" . + "false"^^ . + "polbase" . + . + . + . + . + . + "neuroscience" . + "http://www.treefam.org/family/$1"^^ . + . + "CRISP Thesaurus, 2006" . + . + . + "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term="^^ . + . + "false"^^ . + . + "MMP3888430"^^ . + . + . + . + . + . + . + . + . + . + . + "The Digital Object Identifier System is for identifying content objects in the digital environment."^^ . + "false"^^ . + "false"^^ . + "agriculture" . + . + . + . + "Life cycle stages for Platynereis dumerilii"^^ . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "https://europepmc.org/article/ppr/"^^ . + . + . + "^\\d+$"^^ . + . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data."^^ . + . + . + . + . + "false"^^ . + "gold standard" . + . + "0000040"^^ . + . + . + . + . + "PubMed Central" . + . + . + . + . + . + . + . + "4"^^ . + . + . + "^\\d+$"^^ . + . + . + "true"^^ . + "biomedical science" . + "A terminology for the skills necessary to make data FAIR and to keep it FAIR."^^ . + "^[0-9]*$"^^ . + "Sabine Oesterle" . + . + . + "ClinGen Allele Registry" . + "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID="^^ . + "http://www.begdb.com/index.php?action=oneMolecule&state=show&id="^^ . + . + . + . + "chemical biology" . + "https://civicdb.org/links/diseases/$1"^^ . + "pharmacology" . + . + "false"^^ . + . + "^G[0-9]{5}[A-Z]{2}$"^^ . + "EasyChair Call for Paper" . + "20021"^^ . + . + "0000001"^^ . + "primary health care" . + . + "topics" . + "http://noctua.geneontology.org/editor/graph/gomodel:"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + "ontology" . + . + "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/"^^ . + . + . + . + "BridgeDb Vocabulary" . + . + "treefam" . + . + . + "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."^^ . + "gramene.gene" . + "Symposium"^^ . + "3639"^^ . . - . - . - . - "small molecule" . - . - . - "hinv.transcript" . - . - . - . - . - . - "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"^^ . - . - "gmd.ref" . - "PyPI" . + . + . + . + . + "^\\d+$"^^ . + . + . + "^HIP\\d{9}(\\.\\d+)?$"^^ . + . + . + . + . + "meteorology" . + . + . + "Subcellular Anatomy Ontology" . + . + "Plant Environment Ontology" . + . + . + . + . + "cooperl@oregonstate.edu" . + . + . + . + "Golm Metabolome Database Reference Substance" . + . + "ENSFM00500000270089"^^ . + "GO Rules are a way of documenting the set of filters and reports that should apply to GAF annotation data. Some rules are expressed as SPARQL on a triplestore, some are code in the GAF parsing software, ontobio."^^ . . - . - . - . - . - . - . - "structure" . - . - . - "vz" . - . - . - . - "ontology" . - "ird.segment" . - . - "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group."^^ . - . - . - . - . - "R-BTA-418592"^^ . - . - . - . - "MediaDive Solution" . - . - "NameRXN" . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - "mirbase" . - "https://jrct.niph.go.jp/en-latest-detail/"^^ . - "ontology" . - . - "cco" . - "DSMZCellDive" . - "genomics" . - . - . - . - . - "false"^^ . - . -_:N95d3105b2cdf4400a57957c9d02ead48 "Albert Goldfain" . - "COG Pathways" . - . - "Archival Resource Key" . - . - "ontology" . - "0778"^^ . - "gene" . - "ontology" . - "fernanda.farinelli@gmail.com" . - . - "dictyBase" . - . - . - . - "MycoBrowser smegmatis" . - . - "https://www.ncbi.nlm.nih.gov/snp/"^^ . - . - . - "AY321118"^^ . - . - . - . - "cubedb" . - "^\\w+$"^^ . - . - . - . - . - "odor" . - . - . - . - . - . - "life science" . - . - "Shapes Constraint Language" . - . - "jorvis@gmail.com" . - "Agilent Probe" . - . - . - "^\\d+$"^^ . - . - . - . - . - "obo" . - . - . - "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes."^^ . - . - . - "ExAC Gene" . - . - . - . - "agriculture" . - . - "2c6s"^^ . - . - . - . - . - . - "marker" . - . - . - "Ontology about the development and life stages of the C. elegans"^^ . - . - . - . - . - . - . - . - "eupath" . - . - . - . - . - . - . - . - "immunology" . - . - . - . - "false"^^ . - "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . - . - . - . - "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id="^^ . - . - "Bgee family" . - "ontology" . - "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . - . - . - . - . - . - . - . - . - "ontology" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "biochemistry" . - . - . - . - . - . - . - "false"^^ . - . - . - "dna" . - . - "https://bioregistry.io/gard:"^^ . + "CADAFLAT00006211"^^ . + "David Craik" . + "^ENSGT\\d+$"^^ . + . + . + . + . + "1354581"^^ . + . + . + "ecology" . + . + . + . + "http://purl.obolibrary.org/obo/PLANP_"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . . - "immunology" . - . - "ro" . - . - "nucleotide" . - . - . - . - . - . - "J55.713G"^^ . - . - . - . - . - "depmap" . - "https://bioregistry.io/nsrrc:"^^ . - "^\\d{7}$"^^ . - "^R\\d+$"^^ . - . - . - "https://cropontology.org/rdf/CO_345:"^^ . - . - "BRAF"^^ . - "Person" . - "992"^^ . - "Sustainable Development Goals Interface Ontology" . - . - . - . - "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."^^ . - "nlx.anat" . - "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . - . - . - "^[1-9]\\d*$"^^ . - "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."^^ . - . - . - "pmid" . - . - . - . - "obo" . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/protein/$1"^^ . - "The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally."^^ . - "inaturalist.taxon" . - . - . - "drosophila" . - . - "bitterdb.cpd" . - . - "unigene" . - "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#"^^ . - "AgentIdentifierScheme"^^ . - "sharkipedia.species" . - . - . - . - "cell lines" . - "ShareLoc" . - . - . - "http://purl.obolibrary.org/obo/VO_"^^ . - . - . - "HGNC Gene Group" . - . - . - "International Histocompatibility Workshop cell lines" . - . - _:N917df5114e6348d2a23df4152c26f3d5 . - . - . - . - . - . - "^\\w+$"^^ . - "ontology" . - "false"^^ . - . - "https://bitbucket.org/"^^ . - . - "Bloomington Drosophila Stock Center" . - "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan=$1"^^ . - . - "https://www.datanator.info/gene/$1"^^ . - . - "^\\d+$"^^ . - . - . - . - . - "interaction" . - . - "false"^^ . - . - "MmusDv" . - . - . - . - "^\\d{7}$"^^ . - . - . - "gene" . - . - . - . - . - . - . - . - . - "^[a-zA-Z0-9_\\.]+$"^^ . - "comparative genomics" . - "cameo" . - . - . - "computational biology" . - "goldbook" . - . - . - . - "http://www.w3.org/ns/prov#"^^ . - . - . - . - "Chickpea ontology" . - . - "Ontology of rat strains"^^ . - . - "https://cropontology.org/rdf/CO_350:"^^ . - . - "http://purl.obolibrary.org/obo/ORNASEQ_$1"^^ . - . - . - . - "obo" . - . - . - . - . - . - . - "http://www.alanwood.net/pesticides/$1.html"^^ . - . - . - . - . + . + "ICD10WHO" . + "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . + "Jim Balhoff" . + . + . + "tkg" . + . + . + . + . + . + . + . + "human" . + "Terminology of Anatomy of Human Histology" . + . + "A*01:01:01:01"^^ . + . + . + . + . + . + . + "ACM1_HUMAN"^^ . + . + . + . + . + . + . + "property" . + . + . + "RDF"^^ . + . + . + . + . + "NeuroNames" . + . + "false"^^ . + . + "^\\d+$"^^ . + "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."^^ . + . + "immunology" . + "life science" . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "Bio-MINDER Tissue Database" . + "development" . + "^(MNXR\\d+|EMPTY)$"^^ . + "secondary_attack_rate"^^ . + . + "obo" . + "culture" . + "false"^^ . + "C. elegans phenotype" . + . + . + . + . + . + . + . + "ArchDB" . + . + . + . + . + . + . + . + "The tRNA Gene DataBase Curated by Experts \"tRNADB-CE\" was constructed by analyzing 927 complete and 1301 draft genomes of Bacteria and Archaea, 171 complete virus genomes, 121 complete chloroplast genomes, 12 complete eukaryote (Plant and Fungi) genomes and approximately 230 million DNA sequence entries that originated from environmental metagenomic clones."^^ . + . + "REPRODUCE-ME Ontology" . + "true"^^ . + . + "wbls" . . - "^\\d{7}$"^^ . - . - "structure" . - . - "sisu" . -_:Ne9d7876377624aa795c29d593ee4a373 "Edd Wilder-James" . - "https://www.google.com/patents/$1"^^ . - "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . - . - "^DRKS\\d+$"^^ . - "181" . - "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . - . - "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref"^^ . - "false"^^ . - . - . - . - "nasa/kepler-exoplanet-search-results"^^ . - . - . - . - "Cell line databases/resources"^^ . - . - "identifierPattern"^^ . - "false"^^ . - "ClinGen Allele Registry" . - . - . - "Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications."^^ . - "Kids First" . - . - . - . - . - "supply" . - . - . - . - "The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names."^^ . - "cteno" . - . - "life science" . - "^\\d+\\-\\d+\\-\\d+$"^^ . - "version control" . - . - "Geomames" . - "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."^^ . - . - . - . - . - . - "mhb120@gmail.com" . - . - . - . - "false"^^ . - "ontology" . - "http://www.humanproteomemap.org/spectrum.php?pep_id="^^ . - "bork@embl.de" . - . - "gene" . - . - . - "35742"^^ . - "corum" . - . - . - . - . - . - "false"^^ . - "http://purl.enanomapper.org/onto/ENM_$1"^^ . - . - . - "drugs" . - . - . - "true"^^ . - "false"^^ . - "E-MEXP-1712"^^ . - . - "NIH HIV Reagent Program" . - . - . - "Collection of many cell lines derived from human and other various animals, preserved by the RIKEN BioResource Research Center."^^ . - "agriculture" . - "Database of Aligned Ribosomal Complexes" . - . - . - _:Neb149b8fd9b444d5a596c99172b80614 . - "https://pharmacodb.ca/tissues/$1"^^ . - "http://bacmap.wishartlab.com/organisms/$1"^^ . - "00007294"^^ . - . - "interaction" . - . - . + "http://purl.obolibrary.org/obo/XAO_"^^ . + . + "ontology" . + "https://www.fishbase.ca/summary/$1"^^ . + . + . + "false"^^ . + "http://biocyc.org/getid?id=$1"^^ . + "This ontology represents the clinical findings and procedures used in the oral and maxillo-facial surgical domain"^^ . + "clinical studies" . + "wikigenes" . + . + . + . + . + . + "Platynereis Developmental Stages" . + . + . + "obo" . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "obo" . + . + . + . + "75"^^ . + . + . + . + "credit" . + . + . + . + "SABIO-RK EC Record" . + . + "http://zinc15.docking.org/substances/$1"^^ . + . + "false"^^ . + "1351341"^^ . + . + . + "ricenetdb.compound" . + . + . + . + "D00123"^^ . + "^\\d{8}$"^^ . + . + "IMGT/HLA human major histocompatibility complex sequence database" . + . + "data visualization" . + "RAP-DB Locus" . + "https://bioregistry.io/iceberg.cime:"^^ . + . + . + . + . + "false"^^ . + . + "Leszek Vincent" . + "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . + . + . + . + "interaction" . + . + . + . + "Nicolas Le Novère" . + . + "cell line" . + . + "^[a-z_A-Z]+$"^^ . + . + "MobiDB is a database of protein disorder and mobility annotations."^^ . + . + "pseudogene" . + . + . + . + . + "82"^^ . + . + . + . + . + . + . + "developmental biology" . + "false"^^ . + . + . + . + . + "Alzforum Mutations" . + "apo" . + . + "^\\d+$"^^ . + . + . + "0116"^^ . + . + . + . + . + "^HGVM\\d+$"^^ . + . + "GDS1234"^^ . + . + . + . + . + . + "true"^^ . + . + . + "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."^^ . + . + . + "transcriptomics" . + "http://opm.phar.umich.edu/protein.php?pdbid="^^ . + "Cell Version Control Repository" . + . + . + . + "http://www.wikipathways.org/instance/$1"^^ . + . . - . - . - "MMs00000001"^^ . - "^[WAICV]\\d{2,}$"^^ . - "protein" . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . - . - . - . - . - . - . - "false"^^ . -_:N930481746a634af6b35ac1a972a4d6a1 "Radiological Society of North America" . - . - . - "ModelDB" . - . - "true"^^ . - . - "https://bioregistry.io/tokue:"^^ . - "The International Medical Device Regulators Forum (IMDRF) is a forum of voluntary medical device regulators from around the world who have come together to build on the strong foundational work of the Global Harmonization Task Force on Medical Devices (GHTF), and to accelerate international medical device regulatory harmonization and convergence."^^ . - . - . - "functional genomics" . - . - . - . + . + "earth science" . + . + . + "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . + "^[A-Z](\\d+([A-Z]{1,2}(\\d+)?)?)?$"^^ . + . + "^\\d+$"^^ . + . + . + _:Nc61e1ba3fdf94e6781d9d9a9ab3cfda2 . + "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."^^ . + . + "ChemSpider" . + "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol="^^ . + . + "genomics" . + "agrkb" . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + "pathway" . + "plant anatomy" . + . + . + "https://www.metanetx.org/equa_info/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MICRO_$1"^^ . + . + . + . + "false"^^ . + . + . + "ontology" . + . + . + . + . + "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#"^^ . + . + . + "false"^^ . + . + . + . + "https://bacteria.ensembl.org/id/$1"^^ . + . + . + "false"^^ . + . + . + . + "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."^^ . + . + . + . + "life science" . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . + . + . + . + . + . + . + . + . + "http://tuberculist.epfl.ch/quicksearch.php?gene+name=$1"^^ . + . + "NLXBR" . + "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."^^ . + "PSI-MOD" . + . + . + "https://modeldb.science/$1"^^ . + "PhosphoSite Protein" . + "^\\d{7}$"^^ . + . + "life science" . + . + . + "ecology" . + . + . + . + "michel.dumontier@gmail.com" . + . + "life science" . + "Michael Riffle" . + . + . + . + "false"^^ . + . + . + "Nucleic Acids Phylogenetic Profiling" . + . + . + . + . + "Gene Ontology Causal Assembly Model" . + . + "http://bacmap.wishartlab.com/maps/$1/index.html"^^ . + . + . + . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references experiments."^^ . + . + "data integration" . + "^\\w+$"^^ . + . + . + . + . + . + . + . + "botany" . + "0002502"^^ . + . + . + "An ontology designed to support the semantic annotation of epidemiology resources"^^ . + . + "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . + "false"^^ . + . + "pdumdv" . + . + . + "genomics" . + "false"^^ . + . + . + "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."^^ . + . + . + . + . + "https://semanticscience.org/resource/CHEMINF_$1" . + "phylogeny" . + . + . + . + . + . + . + . + . + "Laboratory of Systems Pharmacology Compound" . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "ontology" . + . + "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-$1"^^ . + . + . + "life science" . + . + . + "life science" . + "false"^^ . + . + "1a05"^^ . + . + "life science" . + "The Mouse Genome Database (MGD) project includes data on gene characterization, nomenclature, mapping, gene homologies among mammals, sequence links, phenotypes, allelic variants and mutants, and strain data."^^ . + . + "^\\d+$"^^ . +_:N65b33571236b47dba37254906e5e488b "agrovoc@fao.org" . + . + "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"^^ . + . + . + . + "The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome. The database is dedicated to rat gene nomenclature and should be consulted for queries in such matters"^^ . + "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."^^ . + . + . + "false"^^ . + "imdrf" . + "http://www.onto-med.de/ontologies/gfo.owl#$1"^^ . + . + . + "Cambridge Structural Database" . + "ontology" . + . + . + . + "geo" . + "The LifeWatch ERIC repository of semantic resources for the ecological domain." . + "false"^^ . + . + . + "DSSTox_CID" . + . + . + "DRUGBANK_ID" . + "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure."^^ . + . + . + . + "^[A-Za-z0-9\\-\\/]+$"^^ . + "peptideatlas" . + "cell biology" . + . + . + . . - . - . - . - "biology" . - . - . - "chebi" . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "regulation" . - . - . - "metaregistry" . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "^\\d+$"^^ . - . - "Yasset Perez-Riverol" . - . - . - . - . - . - "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-"^^ . - "gard" . - "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . - . - . - . - . - "bactibase" . - . - "0000004"^^ . - "biology" . - . - . - . - . - "measurement" . - "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=$1"^^ . - . - . - . - "cells" . - . - "false"^^ . - . - . - "owl" . - "^\\d{7}$"^^ . - "obo" . - "http://purl.obolibrary.org/obo/FYPO_"^^ . - . - . - "obib" . - "https://flybase.org/reports/$1"^^ . - "ND50028"^^ . - "genotype" . - . - . - . - "http://purl.obolibrary.org/obo/OMIT_"^^ . - . - . - . - "^casent\\d+(\\-D\\d+)?$"^^ . - . - . - . - "false"^^ . - . - "pancreas" . - "^GN_[A-Za-z0-9_:]+$"^^ . - "https://web.expasy.org/abcd/ABCD_"^^ . - "false"^^ . - . - . - "obo" . - . - "false"^^ . - "H00076"^^ . - "ontology" . - . - . - . - "nutritional science" . - "life science" . - . - "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . - . - "http://purl.obolibrary.org/obo/PCL_"^^ . - . - . - . - "0000027"^^ . - "mbrochhausen@gmail.com" . - "Experimental Factor Ontology" . - . - . - . - . - "HOMD Sequence Metainformation" . - . - . - . - . + . + "Infectious Disease Ontology holds entities relevant to both biomedical and clinical aspects of most infectious diseases."^^ . + "1000560"^^ . + "genome" . + "neuroscience" . + "Gene Location" . + . + "http://www.bindingdb.org/compact/"^^ . + . + . + "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."^^ . + "GLAndersen@lbl.gov" . + . + . + "http://cgsc.biology.yale.edu/Site.php?ID="^^ . + . + "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref$1"^^ . + . + . + . + . + . + . + "https://www.atcc.org/products/"^^ . + "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making."^^ . + "^[A-Za-z0-9]+$"^^ . + "5fde96bdc5f1aa9ff0cce18a"^^ . + . + "genome" . + . + . + . + "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"^^ . + . + . + . + "ontology" . + "Obstetric and Neonatal 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."^^ . + . + . + "FungiDB" . + "28"^^ . + . + "cohd" . + . + . + . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid="^^ . + . + "LOC_Os02g13300"^^ . + . + . + . + . + "nucleotide" . + "ehdaa" . + . + . + "image collection" . + "dcterms" . + . + "faseb list" . + "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form="^^ . + . + . + "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . + "UniProt journal" . + "HS000015122"^^ . + . + . + . + "IPP900099"^^ . + "S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix."^^ . + "The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms."^^ . + . + "pathway" . + . + . + . + "biomedical science" . + "NIFSTD" . + . + "^\\d{7}$"^^ . + . + . + "cells" . + "^[A-Za-z0-9]+$"^^ . + "https://pharmacome.github.io/conso/"^^ . + "^FB\\d{8}$"^^ . + . + . + . + . + "cog.category" . + "Influenza Ontology" . "false"^^ . - . - . - . - . - "BRENDA Ligand" . - . - . - . - . - . - . - "life science" . - . - . - . - . - "life science" . - "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . - "protein" . - "MSBNK-IPB_Halle-PB000166"^^ . - . - . - "genomics" . - "disease" . - . - "genecards.genenote" . - . - . - "biomedical science" . + "0000001"^^ . + "https://www.uniprot.org/database/"^^ . + . + . + "strain" . + . + . + . + . + . + "gene" . + . + "http://purl.obolibrary.org/obo/FBdv_"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "Pfam Clans" . + . + "ontology" . + . + . + "go.rule" . + "10007835"^^ . + . + . + "pathway" . + . + . + . + . + . + . + "0000156"^^ . + "Ontology"^^ . + . + . + . + . + "microsporidia" . + . + . + . + . + "false"^^ . + "KEGG DRUG contains chemical structures of drugs and additional information such as therapeutic categories and target molecules."^^ . + "panther.family" . + . + . + "cls" . + . + . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . + . + . + . + . + "Datanator Metabolite" . + "GL50803_102438"^^ . + . + . + . + . + "The global library cooperative OCLC maintains WorldCat. WorldCat is the world's largest network of library content and services. WorldCat libraries are dedicated to providing access to their resources on the Web, where most people start their search for information."^^ . + "^\\d{7}$"^^ . + "^\\w+$"^^ . + . + . + . + "hgnc.genegroup" . + "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession="^^ . + . + . + "epidemiology" . + . + "http://www.ensembl.org/Multi/GeneTree/Image?db=core;gt=$1"^^ . + . + . + . + . + . + "consulting" . + . + . + . + . + "^.*?--%3E.*?$"^^ . + . + . + "HIT000195363"^^ . + . + . + . + "ontology" . + . + . + "uberon"^^ . + . . - . - . - . - . - . - . - . - "controlled term" . - . - . - . - "http://purl.obolibrary.org/obo/DC_CL_"^^ . - . - "obo" . - . - "protcom" . - . - . - . - "rna" . - . - . - . - "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "PF" . - "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."^^ . - "^\\d{8}$"^^ . - "false"^^ . - "CE28239"^^ . - . - "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://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . + "March 2017 version "^^ . + . + . + . + "genes" . + . + . + "Database of RNA Junctions and Kissing loop Structures" . + . + . + . + . + "Nanbyo Disease Ontology" . + "genome" . + "CIP - potato ontology - december 2018"^^ . + . + . + . + "https://w3id.org/mixs/$1"^^ . + " Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.\n\nRhea covers the reactions described by the IUBMB Enzyme Nomenclature as well as many additional reactions and can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analyses. Rhea is the standard for enzyme and transporter annotation in UniProtKB."^^ . + "zoology" . + . + "Langua aLimentaria Thesaurus" . + . + . + . + "http://qudt.org/schema/qudt#"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "unipathway.pathway" . + "biomedical science" . + . + . + . + . + . + . + "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . + . + "273"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DC_CL_$1"^^ . + "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . + . + "rapdb.transcript" . +_:N1902992fefc74b64a0200f6ba3d98584 "First DataBank Customer Support" . + . + "ontology" . + "Influenza Research Database (IRD) contains information related to influenza virus, including genomic sequence, strain, protein, epitope and bibliographic information. The Segment Details page contains descriptive information and annotation data about a particular genomic segment and its encoded product(s)."^^ . + . + "^\\d{7}$"^^ . + "Peroxibase" . + "sbo" . + . + "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . + . "chemistry" . - . - . - . + . + "alpha.tom.kodamullil@scai.fraunhofer.de" . + . + . + . + "Registry of Research Data Repositories" . + "Ensembl Gene" . + "^\\d+$"^^ . + "https://e-cyanobacterium.org/models/model/$1"^^ . + "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."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "125768"^^ . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + "http://purl.obolibrary.org/obo/VT_$1"^^ . + . + "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . + . + "^\\d{7}$"^^ . + . + . + "243002_at"^^ . + "^\\w+\\_\\d+(\\.\\d+)?$"^^ . + . + "ena" . + "biology" . + "CropMRepository" . + . + . + . + . + . + . + "anatomy" . + "http://purl.obolibrary.org/obo/BCO_$1"^^ . + . + . + . + "obo" . + . + "agriculture" . + "Oryzabase Stage" . + . + . + . + . + "ontology" . + "ontology and terminology" . + . + . + . + . + . + . + . + "Xenopus Phenotype Ontology" . + . + . + "jgraybeal@stanford.edu" . + "biomedical science" . + . + . + . + "^\\d{7}$"^^ . + . + "goldbook" . + . + . + "http://purl.obolibrary.org/obo/ONS_$1"^^ . + . + "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l="^^ . + "Linguist" . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "obo" . + . + . + . + . + . + . + . + . + "dna" . + . + "https://athena.ohdsi.org/search-terms/terms/$1"^^ . + . + . + . + . . - . - . - "true"^^ . - "david.sehnal@gmail.com" . - "Nathan Edwards" . - . - . - "subject agnostic" . - . - . - . - . - . - "Gary L Andersen" . - . - . - "life science" . - . - "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . - . - . - . - "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases"^^ . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - "NLXRES" . - . - . - "gene expression" . - . - "https://lotus.naturalproducts.net/compound/lotus_id/"^^ . - . - . - "^[0-9]{1,7}$"^^ . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/MICRO_$1"^^ . - "affy.probeset" . - . - . - . - . - "ontology" . - . - . - "Alex Bateman" . - "false"^^ . - "Ontology for computer aided process engineering" . - "^\\d{6}$"^^ . - . - "sh" . - . - "biology" . - . - . - "^\\d+$"^^ . - . - "hsa-let-7a"^^ . - . - . - . - . - "ontology" . - . - "foodex2" . - . - . - . - "http://www.ifomis.org/bfo/1.1/snap#"^^ . - . - "chemistry" . - "pancreatic development" . - . - "veterinary medicine" . - . - . - "Alejandra Gonzalez-Beltran" . - . - . - "ontology" . - . -_:N5411953aa3da420b83011b159fcbf568 "nospam@iandavis.com" . - . - "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . - . - "false"^^ . + . + . + . + . + . + . + . + . + "chemistry" . + "clb" . + . + . + . + . + . + "false"^^ . + "4349895"^^ . + . + . + "^[A-Z-_0-9]+$"^^ . + . + "http://edamontology.org/data_$1" . + . + "genome" . + . + . + "mod" . + . + "The S/MAR transaction DataBase" . + . + . + "^COG\\d+$"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "This is a relational database of information about hemoglobin variants and mutations that cause thalassemia."^^ . + "dna" . + "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."^^ . + . + . + . + . + . + . + . + "alan.bridge@isb-sib.ch" . + "metabolomics" . + "microbiology" . + . + . + . + "http://purl.obolibrary.org/obo/ONE_$1"^^ . + "CAS_RN" . + . + . + . + . + "regulation" . + "iuphar.family" . + . + . + "endocrinology" . + . + . + "Jeffrey Grethe" . + . + . + "faldo" . + "17:41223048"^^ . + . + . + . + "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."^^ . + "ontology" . + "nlx.oen" . + "Health Procedure Ontology" . + "eukaryota" . + . + . . - . - . - "oci" . - . - "obo" . - "false"^^ . - . - "cryopreserved" . - "true"^^ . - . - "Description of Plant Viruses" . - "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. "^^ . - . - . - "civic.did" . - "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."^^ . - "ontology" . - . - . - . - . + . + . + . + . + . + . + . + . + "false"^^ . + "TS-0285"^^ . + "genome" . + . + . + . + . + "ENSG00000136147"^^ . + . + . + "12dgr161"^^ . + . + "PMC" . + "http://purl.obolibrary.org/obo/CVDO_$1"^^ . + . + . + . + "hc.trial" . + "hsa-let-7a-2-3p"^^ . + . + "afo" . + "https://bioregistry.io/registry/$1"^^ . + . + "U49845"^^ . + . + "^\\d+(-\\d+)?$"^^ . + . + . + . + . + . + . + "pmc" . + . + "3075966"^^ . + . + . + "^MF_\\d+$"^^ . + "Documentation of the Phenoscape Curation Workflow"^^ . + . + . + . + . + "morpheus.lab/morpheus"^^ . + "https://dbpedia.org/ontology/$1"^^ . + . + "265"^^ . + . + . + "false"^^ . + . + "0007807"^^ . + . + . + "https://stemcells.nindsgenetics.org?line="^^ . + "genatlas" . + . + "000204"^^ . + . + . + . + . + "phenx" . + "info@hoelzel.de" . + "Jennifer R Smith" . + . + . + "false"^^ . + "Idan Gabdank" . + . + . + "^\\d+/.+$"^^ . + "Cell line databases/resources"^^ . + "http://www.w3.org/ns/adms#"^^ . + "co_365" . + . + . + . + . + "subject agnostic" . + "https://cropontology.org/rdf/CO_345:$1"^^ . + "genomics" . + "^[0-9a-z_-]+$"^^ . + . + . + . + . + "^L\\d+$"^^ . + . + . + "Molecular Process Ontology" . + "117145750"^^ . + . + . + . + "wgs84" . + . + . + . + . + . + "Yuki Yamagata" . + . + . + "https://www.ebi.ac.uk/cgi-bin/imgt/hla/get_allele.cgi?"^^ . + . + . + "NeuroLex Dysfunction" . + "MOL000160"^^ . + "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1"^^ . + "peco" . + . + . + . + . + . + "19"^^ . + . + "allele" . + "https://biopragmatics.github.io/providers/uniprot.ptm/$1"^^ . + "dna" . + . + . + . + "false"^^ . + . + "begdb" . + . + . + . + . + . + "structure" . + . + . + . + "Mycobrowser is a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. This collection references Mycobacteria leprae information."^^ . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + . + "anatomy" . + "ontology" . + . + . + . + . + . + . + . + "https://cropontology.org/rdf/CO_333:"^^ . + "biology" . + "https://gold.jgi.doe.gov/resolver?id=$1"^^ . + . + "http://purl.bioontology.org/ontology/HOIP/HOIP_"^^ . + . + . + "HL7 External Code Systems" . + "https://catalog.hathitrust.org/Record/$1"^^ . + "https://www.kegg.jp/entry/"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "disease" . + . + "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . + "http://phenol-explorer.eu/foods/"^^ . + . + . + "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature=$1"^^ . +_:N200f6d51d8c24db9957971f3242ad505 "Crop Ontology Helpdesk" . + "false"^^ . + "biodiversity" . +_:N1f59a2d28185438fb66eb0dc254d8402 "custserv@nlm.nih.gov" . + . + . + . + "Eschmeyer's Catalog of Fishes" . + . + . + . + "21692"^^ . + . + "https://www.ncbi.nlm.nih.gov/nucleotide/$1"^^ . + . + . + . + "http://genomics.senescence.info/diet/details.php?id="^^ . + . + _:Nc7f4b51b50d3443c910d77680c53fbc7 . + . + . + . + "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . + "false"^^ . + "^\\d+$"^^ . + "nbo" . + . + "The anatomy of the Tick, Families: Ixodidae, Argassidae"^^ . + . + . + "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."^^ . + . + . + "ontology" . + . + . + "http://purl.obolibrary.org/obo/HSO_$1"^^ . + . + . + . + "life science" . + . + "https://www.biorxiv.org/content/10.1101/$1"^^ . + "PomBase" . + . + . + "Yeast Deletion and the Mitochondrial Proteomics Project" . + "metascience" . + "NASC code" . + "life science" . + "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1"^^ . + . + . + . + "A formal represention for drug-drug interactions knowledge."^^ . + "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions"^^ . + . + "genome" . + "developmental biology" . + . + . + "ontology" . + . + "false"^^ . + . + . + "BRENDA Enzyme" . + . + "74"^^ . + . + "https://bioregistry.io/metaregistry/"^^ . + . + . + . + "HOSAPI0399"^^ . + . + "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . + . + . + . + "BioMagResBank" . + . + "false"^^ . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + . + . + "false"^^ . + . + "false"^^ . + "neuronames" . + . + . + "^MMAR\\_\\d+$"^^ . + . + . + . + . + "gmd.ref" . + . + . + "https://flybase.org/reports/FBrf"^^ . + "FHIR External Terminologies" . + . + "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."^^ . + . + . + "The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored."^^ . + "agilent.probe" . + "Property"^^ . + . + "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://emmo.info/emmo#EMMO_"^^ . + "http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=$1"^^ . + . + . + . + "https://www.hipsci.org/lines/#/lines/"^^ . + . + . + . + . + "hgnc" . + . + . + . + . + . + "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)."^^ . + "jakkbl@gmail.com" . + . + . + . + "http://tables.pseudogene.org/[?species_name]/"^^ . + . + "baseDimensionEnumeration"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/TXPO_$1"^^ . + . + . + . + . + . + . + . + . + . + "bacmap.map" . + . + "0000319"^^ . + . + . + . + "yoh@dartmouth.edu" . . - . - . - "false"^^ . - "hsa-mir-200a"^^ . - "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium."^^ . - . - . - "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . - "pharmgkb.pathways" . - . - . - "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."^^ . - . - . - . - . - . - "false"^^ . - . - "https://mediadive.dsmz.de/ingredients/"^^ . - . - . - "version control" . - "https://viperdb.org/Info_Page.php?VDB="^^ . - "ACTRN" . - "https://www.drugbank.ca/categories/$1"^^ . - . - . - "imr" . - . - . - "EC_CODE" . - . - . -_:N9a58aee7324d447d80a82ed73e348c46 "ncictcaehelp@mail.nih.gov" . - . - "https://bioregistry.io/matrixdb.association:"^^ . - . - . - . - . - "JCGG-STR008690"^^ . - . - . - "http://unite.ut.ee/bl_forw.php?nimi="^^ . - "http://purl.obolibrary.org/obo/COB_$1"^^ . - . - . - . - "pathway" . - . - . - "0000000"^^ . - "https://drks.de/search/en/trial/$1"^^ . - . - . - . - . - "ATC_code" . - "eco" . - "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."^^ . - . + "638309541"^^ . + . + . + "ontology" . + "false"^^ . + "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."^^ . +_:Na0c300fd6bd246fc84f22a3874137663 "Ian Davis" . + . + "oma.protein" . + "false"^^ . + . + "false"^^ . "has resolver formatter" . - . - . - . - "https://coconut.naturalproducts.net/compound/coconut_id/"^^ . - . - . - "0000598"^^ . - . - . - "ontology" . - . - . - "PMC3084216"^^ . - . - "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . - "ICD" . - . - . - . - "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation."^^ . - . - . - . - "matt@tislab.org" . - "A gazetteer constructed on ontological principles"^^ . - . - "biomedical science" . - . - "false"^^ . - . - "0004486"^^ . - . - . - . - . - "GitHub is an online host of Git source code repositories."^^ . - "http://autism.mindspec.org/GeneDetail/"^^ . - . - . - . - "https://mmp.sfb.uit.no/databases/mardb/#/records/"^^ . - . -_:N2049abb829ed4f9d86c5fbb00ea6b058 "sschurer@med.miami.edu" . - "true"^^ . - . - . - "https://knowledge.lonza.com/cell?id="^^ . - . - "^\\d{7}$"^^ . - . - . - . - "oncology" . - "CYP2A6"^^ . - . - "http://opm.phar.umich.edu/protein.php?pdbid="^^ . - . - . - . - "http://purl.obolibrary.org/obo/PSDO_$1"^^ . - "wikidata.property" . - "small molecule" . - "https://bioregistry.io/cnrs:"^^ . - "Colorectal Cancer Atlas" . - "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . - . - . - "Vertebrate Skeletal Anatomy Ontology" . + . + "oarcs" . + . + . + . + "Melanoma Molecular Map Project Biomaps" . +_:N65b33571236b47dba37254906e5e488b "AGROVOC Team" . + . + "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://cameochemicals.noaa.gov/chemical/$1"^^ . + . + . + "The Database for Bacterial Group II Introns provides a catalogue of full-length, non-redundant group II introns present in bacterial DNA sequences in GenBank."^^ . + . + "dragondb.locus" . + "https://smid-db.org/smid/"^^ . + . + . + "^\\d{7}$"^^ . + "botany" . + . + . + . + . + . + "nemo" . + "^\\d+$"^^ . + "true"^^ . + . + "General Formal Ontology" . + "The Enzyme Classification contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzyme-catalysed reactions."^^ . + "false"^^ . + "img.gene" . + "arxiv" . + "ASKEM Epidemiology Prefixes" . + . + . + . + . + . + "F-SNP" . + . + "https://dos-gdc.ucsc-cgp-dev.org/ga4gh/dos/v1/dataobjects/"^^ . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + "Medical Subject Headings Vocabulary" . + . + "genomics" . + . + . + "A person" . + "occupational medicine" . + "interaction" . + "^\\d{6}$"^^ . + "https://amoebadb.org/amoeba/app/record/gene/"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "aspgd.protein" . + . + . + . + "RNA Virus Database" . + . + "UniProt Variants" . + "institution" . + . + "ontology" . + "Pocketome" . + "http://purl.obolibrary.org/obo/ARO_"^^ . + "edam.operation" . + . + . + "aro" . + "false"^^ . + . + . + "ontology" . + "https://chemapps.stolaf.edu/jmol/jmol.php?model=$1"^^ . + "GR_PROTEIN" . + . + . + . + . + . + "https://hdl.handle.net/hdl:20.500.12582/$1"^^ . + "http://purl.obolibrary.org/obo/XLMOD_"^^ . + "A download link for the given resource" . + . + . + . + "https://civicdb.org/links/assertions/$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 models."^^ . + . + . + . + "basic science" . + "false"^^ . + . + . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id=$1"^^ . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code="^^ . + . + . + "LIPID_MAPS_class" . + . + "ChEMBL" . + "life science" . + . + . + . + . + . + "^\\w+\\d+$"^^ . + . + "ontology" . + . + . + "^\\d+$"^^ . + "david.sehnal@gmail.com" . + . + "Chickpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + . + . + . + . + . + . + . + . + . + . + "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . + . + . + . + "European Genome-phenome Archive Dataset" . + . + . + . + "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . + "metabolite" . + . + "M77F7JM"^^ . + "^\\d{7}$"^^ . + . + "false"^^ . + "classification" . + "0000111"^^ . + "life science" . + . + . + "The COVID-19 Infectious Disease Ontology" . + . + . + . + . + "Vertebrate trait ontology" . + . + . + "http://purl.obolibrary.org/obo/DDANAT_$1"^^ . + . + . + "Database of Aligned Ribosomal Complexes" . + . + . + "NONCODE v3" . + . + . + . + . + . + "^(ev\\:)?E\\d+$"^^ . + . + "Extensible Markup Language" . + . + "obo" . + . + . + . + . + "14"^^ . + . + . + . + "life science" . + . + . + "ontology" . +_:Nc6e5fcb883644175825da682379a1cd8 "psidev-gps-dev@lists.sourceforge.net" . + "botany" . + . + . + "http://purl.obolibrary.org/obo/HP_$1"^^ . + "Minimum PDDI Information Ontology" . + "RNA Modification Database" . + . + . + "intact.molecule" . + . + . + "bioinformatics" . + . + . + . + "0000010"^^ . + . + . + "http://purl.obolibrary.org/obo/AEO_$1"^^ . + . + "https://bioregistry.io/cellbank.australia:"^^ . + . + "life science" . + . + . + "false"^^ . + . + "https://thebiogrid.org/interaction/"^^ . + . + . + "biodiversity" . + . + . + "https://www.addexbio.com/productdetail?pid="^^ . + . + . + . + . + . + "UMLS_CUI" . + "obo" . + . + "icd11" . + . + . + "https://bioregistry.io/fbol:"^^ . + . + "http://www.antweb.org/specimen.do?name=$1"^^ . + "true"^^ . + "ICEberg integrative and mobilizable element" . + . + "genome" . + "obo" . + . + "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id="^^ . + . + . + . + . + "Glycosciences.DB" . + "The Molecular Movements Database lists motions in proteins and other macromolecules. It is arranged around a multi-level classification scheme and includes motions of loops, domains, and subunits."^^ . + "http://purl.obolibrary.org/obo/VSMO_"^^ . + "true"^^ . + "0000630"^^ . + "ontology" . + "metabolomics" . + . + . + . + . + . + . + "false"^^ . + "http://opendata.inra.fr/ATOL/ATOL_"^^ . + "biology" . + . + . + . + "false"^^ . + . + . + "Ontology of Arthropod Circulatory Systems" . + "0000008"^^ . + . + . + "ECOCYC"^^ . + . + "http://www.cathdb.info/domain/"^^ . + "MolBase" . + . + . + "preclinical studies" . + . + "text mining" . + . + . + "Wheat ontology" . + . + "false"^^ . + . + . + . + "^\\d{4}-\\d{4}-\\d{4}-\\d{3}(\\d|X)$"^^ . + "^\\d+$"^^ . + . + "transcriptomics" . + "CC-BY-1.0"^^ . + "obo" . + "false"^^ . + . + . + . + "prediction" . + . + . + . + "recombinant inbred rat" . + . + "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID=$1"^^ . + . + . + . + . + "true"^^ . + "transcriptomics" . + . + . + . + . + . + . + "Nicolas Le Novere" . + . + "gaz" . "false"^^ . - "interaction" . - . - . - "genome" . - "cell" . - "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^ . - . - . - "JWS Online" . - . - . - . - . - "enzyme" . - "ontology" . - "^\\w+$"^^ . - . - . - . - . - . - . - "3851"^^ . - "RCSB_PDB" . - . - . - . - "A controlled vocabulary to support the study of transcription in the human brain"^^ . - . - . - "UniProt Proteomes" . - . - . - . - . - "Ramona Walls" . - . - "GO Evidence Code" . - . - "https://www.ebi.ac.uk/chembl/cell_line_report_card/"^^ . - . - "true"^^ . - . - . - . - . - "false"^^ . - . - . - "Adrien Coulet" . - "NLXCELL" . - "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The compound data set provides information regarding the reactions in which a compound participates as substrate, product or modifier (e.g. inhibitor, cofactor), and links to further information."^^ . - "selventa" . - "^cpd\\d+$"^^ . - . - . - . - "false"^^ . - . - . - "http://purl.obolibrary.org/obo/T4FS_$1"^^ . - "kupo" . - . - . - . - "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object="^^ . - . - . - . - "http://purl.obolibrary.org/obo/VSMO_$1"^^ . - . - . - . - . - . - "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . - "ontology" . - . - . - . - "http://purl.obolibrary.org/obo/ExO_$1"^^ . - . - "http://purl.org/spar/biro/$1"^^ . - . - . - . - . - . - . - "obo" . - . - . - . - . - . - . - "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."^^ . - "MESH_SUPPLEMENTAL_RECORD_UI" . - . - . - "https://www.sigmaaldrich.com/US/en/product/sigma/"^^ . - . - . - . - . - . - . - "1017"^^ . - "clinvar.submission" . - . - "http://purl.obolibrary.org/obo/PORO_$1"^^ . - . - "Tanja Bekhuis" . - . - "1000160"^^ . - "Anatomical Therapeutic Chemical Vetinary" . - . - "NONCODE is a database of expression and functional lncRNA (long noncoding RNA) data obtained from microarray studies. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. The collection references NONCODE version 4 and relates to gene regions."^^ . - . - "The Chemistry Dashboard is a part of a suite of databases and web applications developed by the US Environmental Protection Agency's Chemical Safety for Sustainability Research Program. These databases and apps support EPA's computational toxicology research efforts to develop innovative methods to change how chemicals are currently evaluated for potential health risks."^^ . - . - . - "genome" . - . - . - . - "data sharing" . - "https://www.wwpdb.org/pdb?id="^^ . - . - . - . - "Gianni Cesareni" . - . - "0000081"^^ . - . - "unique academic work identifier assigned in Web of Science bibliographic database (Web of Science Core Collection only and do not include WOS: prefix)"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "botany" . - "computational biology" . - . - . - . - "oboformat" . - "https://bioregistry.io/go.rule:"^^ . - . - "genome" . - . - . - . - . - . - . + . + . + . + "E-cyanobacterium model" . + "swo" . + "^\\d+$"^^ . + "OMIT" . + . + . + . + . + "glygen" . + . + "Simplified molecular-input line-entry system" . + "Plant Phenology Ontology" . + "flymine.chromosome" . + "^([A-Za-z]+)?(\\_)?([A-Za-z-]+)\\:([A-Za-z0-9 ]+)$"^^ . + . + "BAMSC981"^^ . + . + . + "http://www.gabipd.org/database/cgi-bin/GreenCards.pl.cgi?BioObjectId=$1&Mode=ShowBioObject"^^ . + . + . + "http://purl.org/phylo/treebase/phylows/study/$1?format=html"^^ . + . + "December 2019"^^ . + "false"^^ . + . + "^\\w{14}$"^^ . + . + "G02681"^^ . + . + "false"^^ . + . + "http://linkedlifedata.com/resource/umls/id/"^^ . + . + "false"^^ . + "co_337" . + . + . + . + . + . + . + "46"^^ . + "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."^^ . + "^\\w+(\\.)?\\w+(\\.)?\\w+$"^^ . + "http://www.w3.org/ns/dcat#$1"^^ . + "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . + "https://www.dsmz.de/collection/catalogue/details/culture/$1"^^ . + . + . + _:Nc576373e3ad5403485c64e5f575d52d2 . + . + . + . + . + "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science."^^ . + "Ddinter is a comprehensive, professional, and open-access database specific to drug-drug interactions. it provides abundant annotations for each ddi association including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety."^^ . + . + "informatics" . + . + . + . + "Academic Event Ontology" . + "life science" . + . + . + . + . + . + . + . + . + . + "health science" . + . + . + "false"^^ . + "pharmacogenomics" . + "^\\d{7}$"^^ . + . + "http://purl.org/ontology/bibo/$1"^^ . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + . + . + "rna" . +_:N1f3b094ee6cb47f5989b2a702e1e10e8 "custserv@nlm.nih.gov" . + . + . + . + . + . + . + . + . + . + "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."^^ . + "https://w3id.org/babelon/"^^ . + "DragonDB Protein" . + . + "http://purl.obolibrary.org/obo/GNO_"^^ . + "^[A-Za-z0-9]+$"^^ . + . + . + . + "31"^^ . + . + . + "^\\d{7,8}$"^^ . + . + . + "ontology" . + "Nikolaos Moustakas" . + "obo" . + . + . + . + . + . + . + . + "funcbase.human" . + "PASS01237"^^ . + "Curation of Neurodegeneration Supporting Ontology" . + "life science" . + "http://www.crop2ml.org/cropmdb/"^^ . + . + . + . + . + "population genetics" . + . + . + "genomics" . + "comparative genomics" . + . + "https://cropontology.org/rdf/CO_337:"^^ . + "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . + . + "computational chemistry" . + "PSEEN0001"^^ . + "life science" . + . + "Anatomical Therapeutic Chemical Classification System" . + . + . + "ietf.language" . + . + "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."^^ . + "false"^^ . + . + . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=$1"^^ . + . + "^\\d+$"^^ . + . + . + "protein" . + . + "Janna Hastings" . + . + "has canonical" . + . + . + . + . + . + "bitterdb.cpd" . + . + . + "false"^^ . + "SPU_000001"^^ . + . + "40592-R001-100"^^ . + . + . + "doi"^^ . + "false"^^ . + . + . + "http://pax-db.org/#!species/$1"^^ . + . + . + "medical informatics" . + "Gender, Sex, and Sexual Orientation Ontology" . + "ecology" . + "http://oryzatagline.cirad.fr/cgi-bin/general_mutant.pl?line="^^ . + "mmp.db" . + . + . + . + . + . + . + "https://www.uniprot.org/unirule/"^^ . + . + . + . + "http://darcsite.genzentrum.lmu.de/darc/view.php?id="^^ . + "GENO is an OWL model of genotypes, their more fundamental sequence components, and links to related biological and experimental entities. At present many parts of the model are exploratory and set to undergo refactoring. In addition, many classes and properties have GENO URIs but are place holders for classes that will be imported from an external ontology (e.g. SO, ChEBI, OBI, etc). Furthermore, ongoing work will implement a model of genotype-to-phenotype associations. This will support description of asserted and inferred relationships between a genotypes, phenotypes, and environments, and the evidence/provenance behind these associations. \n\nDocumentation is under development as well, and for now a slidedeck is available at http://www.slideshare.net/mhb120/brush-icbo-2013"^^ . + . + . + "Pearl millet ontology" . + "OHPI is a biomedical ontology in the area of host-pathogen interactions. OHPI is developed by following the OBO Foundry Principles (e.g., openness and collaboration)."^^ . + "ali.syed@kaust.edu.sa" . + "botany" . + "http://purl.obolibrary.org/obo/LOGGERHEAD_"^^ . + . + . + . + . + . + "^TA\\d+$"^^ . + "^\\d{7}$"^^ . + . + . + . + "ontology" . + . + "PK-DB" . + . + . + "ICD" . + "achcar11"^^ . + . + . + . + . + "The Epilepsy and Seizure Ontology (EpSO) is an application ontology developed to support epilepsy focused informatics tools for patient care and clinical research. "^^ . + "ontology" . + . + . + . + "true"^^ . + "https://bioregistry.io/ipi:"^^ . + "molecule" . + "http://purl.obolibrary.org/obo/TXPO_"^^ . + . + . + . + . + "The EcoGene database contains updated information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites."^^ . + . + . + . + "^\\w{1,2}\\d{8,10}$"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/HAO_"^^ . + "Bgee is a database to retrieve and compare gene expression patterns in multiple species, produced from multiple data types (bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data). This collection references genes in Bgee."^^ . + . + . + . + . + "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule=$1"^^ . + "0000072"^^ . + . + . + "^\\w+$"^^ . + . + . + "false"^^ . + "mlc" . + "Plant Anatomy Ontology" . + "https://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=$1"^^ . + . + . . - . - "^[A-Za-z0-9]+$"^^ . - "t3db" . - "false"^^ . - . - "isDocumentRelatedTo"^^ . - . - "false"^^ . - . - "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . - "BioProject" . - . - . - . - . - . -_:N5b864b9d0d9e47e2b9877a5fcffa278f "custserv@nlm.nih.gov" . - "^([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,})$"^^ . - . - . - . - . - "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name="^^ . - . - "gmd.profile" . - . - "https://w3id.org/biolink/vocab/"^^ . - "ontology" . - "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . - . - . - . - . - . - . - . - "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . - "anatomy" . - . - . - . - . - . - . - . - . - "smpdb" . - "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."^^ . - "AmoebaDB" . - . - "swisslipid" . - . - . - . - "PharmacoDB Datasets" . - "DataONE" . - . - . - . - . - . - . - "Consensus CDS" . - . - . - . - . - "dg.4dfc" . - . - . - . - . - "vuid" . - . - . -_:Nfd951b17478f477895aef1fdeccce346 "Crop Ontology Helpdesk" . - . - "biokc" . - . - . - "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . - . - . - . - "Ontology of Host Pathogen Interactions" . - "bioRxiv" . - . - . - . - "SNOWMEDCT_US" . - "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"^^ . - . - "hc.npn" . - . - . - . - . - . - "Q9P0K8"^^ . - . - . - . - . - . - . - . - . - . - "1257009"^^ . - . - "0001157"^^ . - "TF101014"^^ . - "false"^^ . - "paul.fabry@usherbrooke.ca" . - . - . - . - "https://cropontology.org/rdf/CO_320:$1"^^ . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . - . - . - . - . - "16793"^^ . - . - . - . - . - . - . - "http://stormo.wustl.edu/ScerTF/details/$1"^^ . - "ontology" . - . - "chemrof" . - . - . - . - "splash10-0zq2000000-77302b0326a418630a84"^^ . - "false"^^ . - . - "34"^^ . - "genetics" . - . - . - "^\\d{4,}((_[asx])?_at)$"^^ . - . - "Ada Hamosh" . - . - . - . - . - . - . - "CTCAE" . - . - "stato" . - "Intrinsically Disordered proteins with Extensive Annotations and Literature" . - "http://geneontology.org/docs/gene-product-information-gpi-format/#"^^ . - . - . - "false"^^ . - "http://www.genome.jp/kegg-bin/get_htext?-p+/kegg/brite/br+br"^^ . - . - . - . - "ontology" . - "Richard Scheuermann" . - "false"^^ . - . - . - . - . - . - "https://www.cbioportal.org/study/summary?id="^^ . - . - "Amphibian gross anatomy" . - . - . - "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - . - . - . - "life science" . - . - "^(MNXR\\d+|EMPTY)$"^^ . - . - "embryonic stem cell line" . - . - "https://cameochemicals.noaa.gov/chemical/$1"^^ . - "https://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"^^ . - "false"^^ . - "https://w3id.org/aio/"^^ . - "cmpo" . - "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem="^^ . - "transcriptomics" . - "https://transyt.bio.di.uminho.pt/reactions/$1"^^ . - . - "gold" . - "http://www.ebi.ac.uk/cmpo/CMPO_"^^ . - . - . - "dna" . - "^[A-Z]{1,2}\\d{5}$"^^ . - . - . - . - . - . - . - "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."^^ . - . - . - "taxonomy" . - . - "phenotype" . - . - . - . - "http://en.wikipedia.org/wiki/$1"^^ . - . - . - . - "^P(X|R)D\\d{6}$"^^ . - . - . - . - . - . - "IUPHARobj" . - . - . - "false"^^ . - "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic."^^ . - "false"^^ . - _:N5e5ef5c07ce54a41b7b91c5aada03718 . - . - "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID="^^ . - "genetics" . - . - . - "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."^^ . - "GLIDA Ligand" . - . - "P00266"^^ . - . - . - . - . - . - "gramene.reference" . - "^[AEP]-\\w{4}-\\d+$"^^ . - . - "The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc."^^ . - . - . - . - "https://vcell.org/biomodel-"^^ . - "Workspace (Git repository) for modeling projects managed by the Physiome Model Repository"^^ . - . - . - "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . - . - "opm" . - . - "^(ENSFM|ENSGTV:)\\d+$"^^ . - . - . - "false"^^ . - . - "genome" . - . - "false"^^ . - . - . - "An ontology to describe entities related to cardiovascular diseases"^^ . + "JGI Phytozome" . + . + . + "https://www.wormbase.org/db/seq/protein?name=$1"^^ . + "life science" . + _:N81fe899ae37e4bc6870b3fdde5669e37 . + "NIH HIV Reagent Program" . + . + "^[0-9]{1,7}$"^^ . + . + . + . + . + . + . + . + "http://terminology.hl7.org/CodeSystem/v2-"^^ . + . + . + . + . + . + . + "false"^^ . + . + "ACH-000001"^^ . + . + . + "http://purl.obolibrary.org/obo/OGI_$1"^^ . + . + . + . + . + . + "scpd" . + "^rs\\d+$"^^ . + . + "P0DP23"^^ . + . + "pigqtldb" . + . + . + . + . + . + . + "false"^^ . + . + . + . + "disprot" . + . + "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist="^^ . + . + . + . + . + "Exposure ontology" . + "A language for validating RDF graphs against a set of conditions"^^ . + . + "ontology" . + . + . + . + . + . + . . - . - "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GECKO_$1"^^ . - . - "conoserver" . - "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"^^ . - . - . - . - . - . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code="^^ . - "ctgov" . - . - . - . - "https://odc-sci.org/data/"^^ . - . - . - . - . - "Identifier of an entry from the AAindex database."^^ . - . - "ConoServer is a database specialized in the sequence and structures of conopeptides, which are peptides expressed by carnivorous marine cone snails."^^ . - "PF11_0344"^^ . - . - . - . - "false"^^ . - . - "005012"^^ . - . - . - "0000011"^^ . - . - . - . - "false"^^ . - . - "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form="^^ . - "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . - "^C\\d{4}$"^^ . - . - . - . - "http://purl.org/dc/terms/"^^ . - "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname="^^ . - "^\\d+$"^^ . - . - . - "smp-m3w9hbe"^^ . - . - . - . - . - . - . - "http://string.embl.de/interactions/"^^ . - . + "ENCSR163RYW"^^ . + . + "L000001"^^ . + . + "ArrayExpress Platform" . + . + "0000435"^^ . + "duo" . + "false"^^ . + . + "NCBI_GeneID" . + . + "^\\d+$"^^ . + . + . + . + . + . + "4201PAT-CCTCC00348"^^ . + "^\\d+$"^^ . + "SNOMED CT (Systematized Nomenclature of Medicine -- Clinical Terms), is a systematically organized computer processable collection of medical terminology covering most areas of clinical information such as diseases, findings, procedures, microorganisms, pharmaceuticals, etc."^^ . + . + . + . + . + . + . + . + "FuncBase Mouse" . + . + . + . + . + "image" . + . + . + . + . + "codelink" . + . + "imr" . + "^\\d+$"^^ . + . + "NanoParticle Ontology" . + . + . + . + . + . + . + . + "NCBITaxonomyID" . + . + . + . + . + "http://www.ecogene.org/gene/"^^ . + . + . + . + . + . + . + . + "aao" . + . + . + "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id=$1"^^ . + "^\\S+$"^^ . + . + "0007114"^^ . + "biology" . + . + . + . + . + . + "0000449"^^ . + . + "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id="^^ . + "false"^^ . + . + . + . + "https://biopragmatics.github.io/debio/$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."^^ . + . + . + . + . + "https://licebase.org/?q=$1"^^ . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references pig QTLs."^^ . + "false"^^ . + . + "SASDAX8"^^ . + "iceo" . + "systemic neuroscience" . + . + . + "http://uri.neuinfo.org/nif/nifstd/nifext_"^^ . + . + . + . + "false"^^ . + . + . + . + . + "http://mycobrowser.epfl.ch/marinosearch.php?gene+name="^^ . + "MIPF0000002"^^ . + . + "false"^^ . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + . + "Urmas Kõljalg" . + . + . + "Measurement method ontology" . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + "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)."^^ . + "microbial" . + . + "http://ctdbase.org/detail.go?type=disease&db=MESH&acc="^^ . . - . - . - . - "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . - . - "Cell line collections (Providers)"^^ . - "viroligo" . - "false"^^ . - . - "http://purl.obolibrary.org/obo/FOODON_"^^ . + . + . + "enzyme" . + . + . + . + . + . + . + "bionumbers" . + . + "false"^^ . + "jaiswalp@science.oregonstate.edu" . + . + . + . + . + . + "Daniel C. Berrios" . + . + . + . + . + "false"^^ . + "biology" . + . + . + . + "mutant strain" . + . + "true"^^ . + . + . + "life science" . + "false"^^ . + . + "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID="^^ . + . + "mw.project" . + . + . + "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id=$1"^^ . + . + "co_330" . + . + . + "DDB0016567"^^ . + . + "nlx.qual" . + . + . + . + . + "http://purl.obolibrary.org/obo/VT_"^^ . + "Ensembl Protists" . + . + . + . + . + "DBCAT000600"^^ . + "00100037"^^ . + "biology" . + . + "interaction" . + . + . + . + . + . + . + . + . + . + "Database of protein-protein complexes" . + . + . + . + "Kristian Axelsen" . + . + "^\\d+$"^^ . + . + "classification" . + "1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "rna" . + "PDC000351"^^ . + . + "Beta Cell Biology Consortium" . + . + . + . + . + . + "AT1G73965"^^ . + . + "A repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids."^^ . + "http://purl.obolibrary.org/obo/MSIO_$1"^^ . + . + . + . + . + . + . + . + . + "https://world-2dpage.expasy.org/repository/"^^ . + . + "botany" . + "https://www.rebuildingakidney.org/id/$1"^^ . + "ontology" . + . + . + . + . + . + . + . + "hoip" . + . + . + "false"^^ . + . + "_space_group_symop.operation_xyz"^^ . + "https://assets.nemoarchive.org/$1"^^ . + "obo" . + "traumatology" . + "false"^^ . + . + . + . + "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id="^^ . + . + "K"^^ . + . + . + . + "MeSH 2012" . + . + . + . + "https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/MACiE/entry/getPage.pl?id=$1"^^ . + . + . + . + . + "gear" . + "salamander" . + . + . + . + . + "https://pharmacodb.ca/cell_lines/"^^ . + . + . + . + . + . + "comptox" . + "gene" . + . + . + . + "pride.project" . + . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"^^ . + "pancreatic development" . + "^\\d{7}$"^^ . + "The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry" . + "false"^^ . + . + "Lipid"^^ . + . + . + . + "https://www.kew.org/data/grasses-db/www/"^^ . + . + . + "gene" . + . + "TubercuList" . + . + "obo" . + "sequence" . + "^MCDS_C_[a-zA-Z0-9]{1,10}$"^^ . + . + "protein" . + "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . + . + . + "^EBI\\-[0-9]+$"^^ . + . + . + "http://purl.obolibrary.org/obo/CEPH_"^^ . + . + "ontology" . + "102l"^^ . + "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards."^^ . + . + . + . + . + . + . + "https://pathbank.org/view/"^^ . + "false"^^ . + "http://bioinfo.lifl.fr/norine/result.jsp?ID=$1"^^ . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + "false"^^ . + "wbbt" . + . + . + . + "https://cells.ebisc.org/"^^ . + . + . + "empiar" . + "ChecklistBank" . + "Organization" . + "proteomics" . + "stock" . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection is species-independent."^^ . + "PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem Substance archives chemical substance records."^^ . + . + . + . + . + "catalog" . + . + . + "allergen" . + "Database of the dielectric properties of biological tissues."^^ . + . + . + "^\\d+$"^^ . + "ratmap" . + "http://www.onto-med.de/ontologies/gfo.owl#"^^ . + . + . + . + "JCGG-STR008690"^^ . + . +_:Nd0e161fdfff74c018182a797e85a4917 "Frédérick Giasson" . + . + . + "^\\d{5}$"^^ . + . + "Development Data Object Service" . + . + . + . + "^PRI\\d*$"^^ . + . + . + . + . + "physics" . + . + . + "ontology" . + . + . + . + "ATC_code" . + "https://grch38.togovar.org/variant/"^^ . + "MAO:0000061"^^ . + "101"^^ . + . + "Research Resource Identifiers" . + . + . + "^\\d{7}$"^^ . + "protein" . + "http://purl.obolibrary.org/obo/MCRO_"^^ . + . + "uminctr" . + "https://bioregistry.io/treebase:"^^ . + "0001079"^^ . + . + . + . + . + . + "nucleotide" . + "pkdb" . + . + . + . + "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . + . + "life science" . + . + "^\\d{9}$"^^ . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + . + "^NPC\\d+$"^^ . + . + "rateRule"^^ . + . + . + . + . + . + . + . + . + "tred" . + . + "DSSTox substance" . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cog/"^^ . + "false"^^ . + . +_:N799549267e7545d0961160c005e4ec68 "vlee@ebi.ac.uk" . + "DrugBank Salts" . + "CPD-10330"^^ . + . + "false"^^ . + . + . + . + . + . + "life science" . + "ontology" . + . + "life science" . + "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . + "10142"^^ . + . + "basic research" . + "Units of measurement ontology" . + . + . + "physiology" . + "http://purl.obolibrary.org/obo/REX_$1"^^ . + . + . + . + "Feature Type Thesaurus" . + . + . + "Registry" . + . + . + . + . + . + "Cellosaurus Publication" . + "ontology" . + . + "^UniRef(100|90|50)_([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}|UPI[A-F0-9]{10})$"^^ . + . + "http://www.bind.ca/Action?identifier=bindid&idsearch="^^ . + "http://purl.obolibrary.org/obo/ERO_"^^ . + . + . + . + "life science" . + "CYP2A6"^^ . + . + . + "http://www.ncbi.nlm.nih.gov/clinvar?term="^^ . + . + _:N1f3b094ee6cb47f5989b2a702e1e10e8 . + . + "http://purl.obolibrary.org/obo/OAE_"^^ . + "SRS086444"^^ . + "false"^^ . + . + "civic.mpid" . + "^RCV\\d+(\\.\\d+)?$"^^ . + "NKOS is devoted to the discussion of the functional and data model for enabling knowledge organization systems/services (KOS), such as classification systems, thesauri, gazetteers, and ontologies, as networked interactive information services to support the description and retrieval of diverse information resources through the Internet.\n\nKnowledge Organization Systems/Services (KOS) model the underlying semantic structure of a domain. Embodied as Web-based services, they can facilitate resource discovery and retrieval. They act as semantic road maps and make possible a common orientation by indexers and future users (whether human or machine). -- Douglas Tudhope, Traugott Koch (2004)."^^ . + "false"^^ . + . + "pubmed"^^ . + "false"^^ . + "dna" . + . + . + . + . + . + . + . + . + . + "HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes."^^ . + "https://www.ebi.ac.uk/ols4/ontologies/$1" . + . + . + . +_:N613e35d4094d47e4af9d8a0547acbfbf "World Health Organization" . + . + . + . + . + . + . + "http://www.w3.org/1999/02/22-rdf-syntax-ns#$1"^^ . + "health science" . + "A-GEOD-50"^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id="^^ . + . + "^\\d{7}$"^^ . + . + . + "^\\d{6}$"^^ . + . + . + . + . + . + . + . + "hölzel" . + . + . + . + _:Nb738ec851a6748268b17445305a9946c . + . + "epidemiology" . + "UniProt Archive" . + "https://bioregistry.io/panorama:"^^ . + . + . + "norine" . + "http://purl.obolibrary.org/obo/GECKO_"^^ . + "slkbase" . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID=$1"^^ . + "http://purl.jp/bio/4/id/$1"^^ . + . + "European Paediatric Cardiac Codes" . + . + "medicine" . + . + . + "^\\d+$"^^ . + . + "biomedical science" . + . + . + . + "Doug Howe" . + . + . + . + . + . + "small molecules" . + . + . + "^[a-zA-Z]+.+$"^^ . + "Drug Target Ontology" . + "http://data.europa.eu/89h/"^^ . + "swisslipid" . + "Computational Chemistry Ontology" . + . + "systems biology" . + . + . + . + "anatomy" . + . + "efo" . + . + . + . + . + "http://purl.obolibrary.org/obo/PATO_"^^ . + "genomics" . + . + "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key=$1"^^ . + . + "feature"^^ . + "0000423"^^ . + "false"^^ . + "https://bioregistry.io/mesh.2013:"^^ . + . + "false"^^ . + . + "37af84f2-bfd7-4653-b608-eaff44febba6"^^ . + . + . + "SNOMEDCT_US_2022_07_31" . + "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID="^^ . + "obo" . + . + . + . + "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://www.arraymap.org/pgx:$1"^^ . + "structure" . + . + "Food-Drug interactions automatically extracted from scientific literature"^^ . + "Database of biopesticides maintained by the University of Hertfordshire "^^ . + . + "https://lobid.org/gnd/$1"^^ . + . + "https://repo.napdi.org/study/"^^ . + . + . + . + . + . + "biochemistry" . + . + . + "http://www.ontology-of-units-of-measure.org/resource/om-2/$1"^^ . + "edam" . + "iedb" . + "http://purl.obolibrary.org/obo/LIPRO_"^^ . + . + . + . + "ontology" . + . + . + "wormbase" . + "300108/p3934_A-172"^^ . + . + . + . + . + "This is the element set of native RDF classes and properties described in the current text (Feb 2009) of the Functional Requirements for Bibliographic Records (FRBR) entity-relationship model. (from https://www.iflastandards.info/fr/frbr/frbrer.html)"^^ . + . + "pathogen" . + . + . + "PTHR12345"^^ . + . + . + . + . + "UPC04349"^^ . + . + . + . + . + "life science" . + "Integrated Microbial Genomes Gene" . + "cio" . + . + "SNOMED" . + "false"^^ . + "http://crdd.osdd.net/servers/virsirnadb/record.php?details=$1"^^ . + "Meng LIU" . + "isanchez@cnb.csic.es" . + . + . + "subject" . + "false"^^ . + "false"^^ . + . +_:N3b2786467c704005b88c4abc40a2e8e2 "po-discuss@plantontology.org" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . + "614"^^ . + . + "0000072"^^ . + . + . + . + . + . + "life sciences" . + . + . + . + "^N[0-9]{10}$"^^ . + . + . + "protein" . + "false"^^ . + . + . + "^PR\\d{5}$"^^ . + "true"^^ . + . + . + . + "ontology" . + "developmental biology" . + . + . + . + . + . + . + "reaction" . + "dna" . + "n.queralt_rosinach@lumc.nl" . +_:Nec5a327b3e5848b4b67c4f1df2c7dada "Allotrope Foundation" . + . + "swisslipids@isb-sib.ch" . + . + . + . + . + . + . + . + . + "false"^^ . + "Andrew G. McArthur" . + . + . + . + "preclinical studies" . + . + . + . + . + . + "sequence" . + . + . + "genome" . + . + "Stemcell Knowledge and Information Portal" . + . + "Maxwell L. Neal" . . - . - . - . - . - . - . - "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . - . - "^\\d{1,5}$"^^ . - "http://www.informatics.jax.org/accession/MGI:"^^ . - "http://www.orpha.net/ORDO/Orphanet_$1"^^ . - . - . - "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . - . - . - . - "^\\d+$"^^ . - "AB016785"^^ . - "http://purl.obolibrary.org/obo/AGRO_"^^ . - . - "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . - . - . - . + . + "^\\d{7}$"^^ . + . + . + "phylogenetics" . + "genetics" . + "https://biokb.lcsb.uni.lu/fact/"^^ . + . + . + . + . + "anatomy" . + _:N8250527cbee1453c9f2a02a7ba72613f . + . + . + "http://isbndb.com/search-all.html?kw="^^ . + . + . + . + . + . + . + . + . + . + "^(STUDY|FILE|DATASET)\\d+$"^^ . + "oridb.sacch" . + "matrixdb" . + . + . + "SysBioCancer2022"^^ . + "Zoë May Pendlington" . + . + . + . + . + . + "Potato ontology" . + "http://purl.org/sig/ont/fma/fma$1"^^ . + . + "ontology" . + . + . + "genetree" . + . + . + "Common Terminology Criteria for Adverse Events" . + . + "Don Gilbert" . + "false"^^ . + . + . + "ontology" . + "false"^^ . + "Cancer Data Standards Registry and Repository" . + "Metabolic Atlas Metabolite" . + "https://disprot.org/"^^ . + . + . + . + "false"^^ . + "Library of Congress Subject Headings" . + . + . + "biology" . + "bpeters@lji.org" . + "pmp" . + . + . + . + . + "Interlinking Ontology for Biological Concepts (IOBC) contains approximately 80,000 biological concepts such as biological phenomena, diseases, molecular functions, gene products, chemicals, and medical cares, and approximately 20,000 related concepts such as earth science and environmental science. The concepts are structured by thirty-five relations such as has function, has role, has quality, and precedes. Each concept has both of English and Japanese labels. For further information including the developmental method, see papers in the PUBLICATIONS PAGE. The license for this ontology is specified in the Creative Commons Attribution-NonCommercial 4.0 International. If you use data from this ontology, please be sure attribute this ontology as follows: \"Interlinking Ontology for Biological Concepts © National Bioscience Database Center licensed under CC Attribution-NonCommercial 4.0 International\"."^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "life science" . + . + "0032571"^^ . + . + . + . + "http://scop.berkeley.edu/sunid=$1"^^ . + . + "0000890"^^ . + "GlycoPOST" . + . + . + "Ontology of Adverse Events" . + . + . + "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . + . + . + . + . + . + "false"^^ . + . + "uniprot.proteome" . + "^\\d{7}$"^^ . + "^\\d+$"^^ . + . + . + "HomoloGene" . + . + . + "^C\\d{4}$"^^ . + . + . + "Nematode Expression Pattern DataBase" . + "Loggerhead nesting" . + . + "Livestock Product Trait Ontology" . + . + . + "http://purl.obolibrary.org/obo/MOP_"^^ . + . + . + . + . + "life science" . + "false"^^ . + . + "100000"^^ . + . + _:N5331d9cae68249828b269d4d462c8f93 . + . + . + . + "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . + . + . + . + . + "Environment Ontology" . + "blast" . + . + . + "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."^^ . + . + "http://purl.obolibrary.org/obo/MICRO_"^^ . + . + . + . + . + . + "Cellosaurus Registry" . + "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."^^ . + "https://www.probes-drugs.org/compound/"^^ . + . + . + . + . + . + "TarBase" . + . + "1000"^^ . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID="^^ . + . + "identifiers.namespace" . + . + . + "life science" . + . + . + . + . + "oba" . + . + "E-cyanobacterium rule" . + "amoebadb" . + . + . + "agriculture" . + "The set of prefixes used in the Cellosaurus resource"^^ . + "rgap" . + "false"^^ . + "false"^^ . + "^DBSALT\\d{6}$"^^ . + . + "dna" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + . + . + "2701"^^ . + "0000049"^^ . + "comparative genomics" . + . + . + "BacMap is an electronic, interactive atlas of fully sequenced bacterial genomes. It contains labeled, zoomable and searchable chromosome maps for sequenced prokaryotic (archaebacterial and eubacterial) species. Each map can be zoomed to the level of individual genes and each gene is hyperlinked to a richly annotated gene card. All bacterial genome maps are supplemented with separate prophage genome maps as well as separate tRNA and rRNA maps. Each bacterial chromosome entry in BacMap contains graphs and tables on a variety of gene and protein statistics. Likewise, every bacterial species entry contains a bacterial 'biography' card, with taxonomic details, phenotypic details, textual descriptions and images. This collection references genome map information."^^ . + . + . + . + . + "nmr" . + . + . + "Drosophila development" . + . + . + . + . + . + "7207"^^ . + . + "http://xmlns.com/foaf/0.1/"^^ . + "dbest" . + . + . + "Pathguide" . + . + . + . + "Information system with taxonomic data on plants, animals, fungi, and microbes of North America and the world."^^ . + "Transporter Classification Database" . + . +_:N5331d9cae68249828b269d4d462c8f93 "julie@igbmc.u-strasbg.fr" . + . + . + . + . + "http://purl.obolibrary.org/obo/GAZ_"^^ . + "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$"^^ . + . + . + . + "obo" . + . + "trichdb" . + "C0001"^^ . + . + . + . + . + . + . + . + "genetic material" . + . + "virus" . + "https://zenodo.org/record/"^^ . + . + . + "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=$1"^^ . + . + . + . + "ppdb@gifu-u.ac.jp" . + . + . + . + . + . + . + . + "https://bioregistry.io" . + . + . + "https://cropontology.org/rdf/CO_338:"^^ . + . + . + . + . + "chembl.target" . + . + . + . + . + . + "^(5?)\\d{7}$"^^ . + . + . + . + . + "lindsey.anderson@pnnl.gov" . + . + . + . + . + . + "BioPortal" . + "BioAssay Ontology" . + . + "obo" . + "INSDC CDS" . + "lectins/172"^^ . + . + . + . + . + . + "https://cropontology.org/rdf/CO_335:$1"^^ . + . + . + "Transcriptional Regulatory Element Database (TRED) has been built in response to increasing needs of an integrated repository for both cis- and trans- regulatory elements in mammals, and the lack of such resources at present."^^ . + "false"^^ . + . + . + . + . + . + "osa-miR446"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/XCO_"^^ . + "^\\d+$"^^ . + "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."^^ . + . + . + . + . + . +_:N1d6d2989305b482cad5c4f3d8442073c "Julian Seidenberg" . + . + "AGRO" . + . + . + "genome" . + . + "^\\d+$"^^ . + "classification" . + "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?"^^ . + "false"^^ . + . + "A type for entries in the Bioregistry's collections" . + . + . + "PjrpzUIAAAAJ"^^ . + "https://identifiers.org/$1:$2" . + . + "A set of guides on implementing various processes within hospitals or healthcare systems."^^ . + . + . + . + . + "434"^^ . + "http://isbndb.com/search-all.html?kw=$1"^^ . + . + "http://purl.obolibrary.org/obo/PSDO_$1"^^ . + "obo" . + . + . + . + . + "German Clinical Trials Register" . + . + . + . + . + "Unified Code for Units of Measure (UCUM) is a code system intended to include all units of measures being contemporarily used in international science, engineering, and business."^^ . + "Cellular Microscopy Phenotype Ontology" . + "dna" . + . + . + . + . + . + . + . + "false"^^ . + "Ontology of Biological Attributes" . + . + . + "life science" . + . + . + . + . + . + . + . + . + "https://biopragmatics.github.io/providers/dmba/$1"^^ . + . + . + . + . + "^[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}$"^^ . + . + . + " http://edamontology.org" . + . + . + "genome" . + "An ontology to represent genomics cohort attributes."^^ . + . + . + . + . + . + . + "^AT\\d+$"^^ . + . + "bgee@sib.swiss" . + . + . + "C6155"^^ . + . + "comparative genomics" . + . + "ybradford@zfin.org" . + . + "0000-0002-5355-2576"^^ . + "false"^^ . + . + "^RCB\\d+$"^^ . + . + "pathobiochemistry" . + . + "sio" . + . + "00000099"^^ . + "false"^^ . + "false"^^ . + . + . + . + "^Os\\S+g\\d{7}$"^^ . + . + . + . + "propreo" . + . + . + . + . + . + . + . + . + . + . + "jaxmice" . + . + . + . + "2673500"^^ . + "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId="^^ . + . + . + . + "Prefixes exported for the epidemiology domain knowledge graph in the ASKEM project." . + . + . + . + . + . + "IUPHAR_GPCR" . + . + "http://w3id.org/nkos/$1"^^ . + . + . + "HGNC Gene Group" . + "5UTR_107_ENST00000517291.2"^^ . + "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_"^^ . + . + "https://covid19.sfb.uit.no/api/records/$1"^^ . + "ontology" . + . + . + "proteomics" . + _:Nad42f8f18c534f0cb3d3fdabcabf743f . + . + . + . + "worm" . + "Tudor Oprea" . + . + . + . + "lagonzalezmo@unal.edu.co" . + . + . + "obo" . + . + "402558626"^^ . + "animal husbandry" . + "Drug_Central" . + "^\\w+$"^^ . + . + . + . + _:N890c5c3e89754d0e974e862d58120df2 . + . + "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."^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + "Oryzabase Mutant" . + "http://www.imgt.org/ligmdb/view?id=$1"^^ . + . + . + . + . + . + "greengenes" . + . + . + . + "pathway" . + "^[A-Z\\-]+$"^^ . + . + _:Nb5a54a1ea36043279d2fbde29f909ebc . + . + "confident.series" . + . + . + "false"^^ . + "colonatlas" . + "ssbd.project" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OHPI_"^^ . + . "G00123"^^ . - "genomics" . - . - "0040379"^^ . - "life science" . - . - . - . - . - . - . - "classification" . - "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query="^^ . - . - "http://purl.obolibrary.org/obo/XAO_$1"^^ . - . - "Transcriptional Regulatory Element Database" . - . - "EDDA Study Designs Taxonomy" . - . - . - . - . - . - . - . - "false"^^ . - . - "true"^^ . - . - . - . - . - . - . - "biology" . - . - "https://github.com/$1"^^ . - "^\\d{7}$"^^ . - "biomedical science" . - . - . - . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - "biomedical science" . - . - "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie="^^ . - . - . - . - . - . - . - . - . - "JGI Phytozome" . - . - . - "lncipedia" . - "health science" . - "DepMap Cell Lines" . - . - "^(G|P|U|C|S)\\d{5}$"^^ . - "http://bactibase.hammamilab.org/$1"^^ . - . - "https://scicrunch.org/resolver/RRID:AGSC_$1"^^ . - "false"^^ . - . - . - . - . - . - . - "^\\d+(-\\d+)?$"^^ . - . -_:N640b18da69e24f0fb18c32598a428ad3 "Bert Van Nuffelen" . - . - . - "false"^^ . - . - . - . - . - "false"^^ . - . - . - . - . - . - "https://biosimulations.org/projects/$1"^^ . - "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."^^ . - . - . - . - "protein" . - . - "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]."^^ . - . - . - "https://www.ncbi.nlm.nih.gov/bioproject/?term="^^ . - "reagents" . - "https://licebase.org/?q=$1"^^ . - . - "biology" . - "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."^^ . - "false"^^ . - "population genetics" . - "dna" . - "disorder" . - . - . - . - "LNCRNADB" . - "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://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . - "schema" . - "comparative genomics" . - . - . - . - . - . - . - . - . - "16129"^^ . - . - . - "false"^^ . - "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . - . - . - . - "Gramene Reference" . - . - . - . - . - "agriculture" . - "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma."^^ . - "pirsf" . - . - . - . - . - . - "batchelorc@rsc.org" . - . - . - . - . - . - . - "^\\d+$"^^ . - "traumatology" . - . - . - . - . - "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)."^^ . - . - . - "false"^^ . - . - . - "SM00015"^^ . - . - . - . - . - . - . - . - "https://smid-db.org/smid/"^^ . - . - "File inside StoreDB"^^ . - . - . + . + "Iranian Registry of Clinical Trials. This is a Primary Registry in the WHO Registry Network set up with the help from the Ministry of Health and Medical Education (MOHME) and hosted by Iran University of Medical Sciences (IUMS). (from homepage)\nNote that the website uses a different identifier then the one reported in this semantic space."^^ . + . + "false"^^ . + "subject agnostic" . + "GnpIS" . + . + . + . + "pancreatic islet function" . + "Erik van Nimwegen" . + "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . + . + . + "false"^^ . + . + "1455"^^ . + . + . + "http://pombe.oridb.org/details.php?id=$1"^^ . + . + . + . + . + . + "wdduncan@gmail.com" . + . + . + . + . + . + . + "- 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."^^ . + "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."^^ . + . + "BloodPAC" . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_$1"^^ . + . + "^XB\\-\\w+\\-\\d+$"^^ . + "ontology" . + "http://doqcs.ncbs.res.in/template.php?&y=accessiondetails&an="^^ . + . + "0002927"^^ . + "https://registry.identifiers.org/registry/$1"^^ . + . + . + "^\\d{7}$"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_inv_$1"^^ . + . + . + "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://purl.org/vocab/frbr/core#"^^ . + "P00747__P07355"^^ . + . + . + . + . + . + . + . + . + . + . + "Multum MediSource Lexicon" . + . + . + . + . + . + . + . + "ECU03_0820i"^^ . + "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"^^ . + . + "0000000"^^ . + . + . + "dna" . + "Assembly" . + "subtilist" . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/LBO_"^^ . + "http://purl.enanomapper.org/onto/ENM_$1"^^ . + . + "genomics" . + . + "Chemistry resources"^^ . + . + "obo" . + "ChEBI Integrated Role Ontology" . + "gene expression" . + . + . + "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . + "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."^^ . + "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_$1"^^ . + . + "Marc_Ciriello@hms.harvard.edu" . + . + . + . + "617102"^^ . . - . - "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . - . - . - . - . - . - . - . - "Bgee stage" . - . - . - "ebisc" . - . - . - "Genetic and Rare Diseases Information Center" . - . - "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name="^^ . - . - . - "genomics" . - . - "1010"^^ . - . - . - "^DAP\\d+$"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "cell lines" . - "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . - "^.*?--%3E.*?$"^^ . - . - . - . - . - . - "life science" . - . - "protein" . - . - "0290"^^ . - "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . - . - . - . - "co_358" . - . - . - . - "ontology" . - . - . - . - . - "MIMIC III Database" . - "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"^^ . - . - "pathway" . - "http://purl.obolibrary.org/obo/MICRO_"^^ . - . - "agriculture" . - "The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions."^^ . - "^[a-z]+(\\-[a-z]+)*$"^^ . - "^\\d+$"^^ . - "https://www.clinicaltrials.gov/study/"^^ . - . - . - "172"^^ . - . - . - . - . - . - "Minimal set of terms for anatomy"^^ . - "Homologous Vertebrate Genes Database" . - . - "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession="^^ . - "fish" . - . - "hl7.v2codesystem" . - . - . - "ECCODE" . - . - "Insect Cell Line Database" . - . - "0000066"^^ . - "life science" . - "OMA Group" . - "genome" . - . - . - "https://www.scopus.com/sourceid/$1"^^ . - . - . - "interaction" . - "false"^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - "Contains entries for various database identifiers" . - . - . - "Vertebrate Breed Ontology" . - "phylogenomics" . - . - "http://lincsportal.ccs.miami.edu/datasets/#/view/"^^ . - . + . + . + . + "idr" . + . + . + . + . + . + . + . + . + . + . + . + "knowledge and information systems" . + "PDBsum; at-a-glance overview of macromolecular structures" . + "swissregulon" . + "UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions. It provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB. UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc. This collection references compounds."^^ . + . + . + . + "CIViC Disease" . + . + . + . + . + . + "false"^^ . + . + . + "ontology" . + . + . "life science" . - "ILMN_129894"^^ . - . - . - . - . - . - "COG_Cluster" . - . -_:N5d69a50234384603b72e609a9e54e2b4 "Crop Ontology Helpdesk" . - . - . - "^\\w+$"^^ . - . - . - . - . - "https://envipath.org/package/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/HsapDv_$1"^^ . - . - . - . - . - "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"^^ . - "https://cropontology.org/rdf/CO_366:$1"^^ . - . - "Werner Müller" . - . - . - . - "false"^^ . - . - "^([hm]\\_)?\\w+Pathway$"^^ . - "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels."^^ . - "http://purl.obolibrary.org/obo/LOGGERHEAD_$1"^^ . - "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . - "cattleqtldb" . - . - "https://bioregistry.io/registry/$1" . - . - "BacDive" . - . - . - "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . - . - "gold standard" . - . - . - . - . - "Drosophila development" . - . - . - "false"^^ . - "environmental science" . - . - "NIA Mouse cDNA Project" . - "https://archive.softwareheritage.org/browse/swh:$1"^^ . - "false"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_cell_"^^ . - . - . - . - . - "decimal"^^ . - . - . - . - . - . - . - . - . - "ecology" . - "proteomics" . - "skosxl" . - . - . - . - "dbgap" . - . - . - . - "Basic Register of Thesauri, Ontologies & Classifications" . - . - . - "life science" . - "ICEberg integrative and conjugative element" . - "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide"^^ . - . - "false"^^ . - . - . - . - . - . - "obo" . - "Spider Ontology" . - . - . - "KEGG BRITE" . - "Peter Midford" . - "nlx.dys" . - . - . - . - . - "worm" . - "glycopost" . - "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"^^ . - . - "ontology" . - . - . - "^1\\d{4}-\\d{3}$"^^ . - . - . - "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."^^ . - . - . - . - . - . - . - . - "ontology" . - . - . - . - "pdumdv" . - "biomedical" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - "jaiswalp@science.oregonstate.edu" . - "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - "Mouse pathology ontology" . - "https://prefix.cc/" . - . - "life science" . - . - . - "false"^^ . - "Polymorphism and mutation databases"^^ . - . - . - . + "false"^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/clansum?clan="^^ . + . + "^[A-Z0-9]+$"^^ . + "FBgn0011293"^^ . + . + "bioportal" . + . + . + . + "F45.21"^^ . + . + . + . + . + . + "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession="^^ . + "00000101"^^ . + . + . + . + . + "odam" . + "vertebrate" . + "gene" . + "https://ssbd.riken.jp/database/project/"^^ . + "false"^^ . + "molecular biology" . + . + . + "Luis A. Gonzalez-Montana" . + . + . + "https://www.storedb.org/?"^^ . + . + . + "MMP02954345.1"^^ . +_:Nd0e161fdfff74c018182a797e85a4917 "fred@fgiasson.com" . + . + . + "bugbase.protocol" . + . + . + "Selventa legacy chemical namespace used with the Biological Expression Language"^^ . + . + . + . + . + "biomedical science" . + . + . + . + . + . + "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."^^ . + . + "sdgio" . + "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."^^ . + . + "Human Unidentified Gene-Encoded" . + "https://cropontology.org/rdf/CO_343:$1"^^ . + "DragonDB DNA" . + . + . + . + "Food Interactions with Drugs Evidence Ontology" . + . + . + . + . + "publishing" . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "ontology" . + . + . + . + . + . + "false"^^ . + . + "O08709"^^ . + . + "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . + "FBbi" . + "https://mediadive.dsmz.de/solutions/"^^ . + . + . + . + . + . + . + . + "iceberg.cime" . + "gene expression" . + "http://cellimagelibrary.org/images/"^^ . + "bioinformatics" . + . + . + "http://www.iclc.it/details/det_list.php?line_id=$1"^^ . + "thermofisher" . + "inbred rat strain" . + "gabdank@stanford.edu" . + . + "http://gmd.mpimp-golm.mpg.de/ReferenceSubstances/"^^ . + "hydrogeology" . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + "obo" . + . + "nextdb" . + . + "Bill Hogan" . + . + . + "CCDC Number" . + "gwascentral.study" . + . + "Reference Sequence Collection" . + . + . + "http://www.whocc.no/atc_ddd_index/?code="^^ . + . + . + . + . + . + "coriell" . + "oral surgery" . + . + "http://www.geneontology.org/formats/oboInOwl#$1"^^ . + . + . + "KEGG Disease" . + . + "medicine" . + "COG0001"^^ . + . + . + . + "glycosciencesdb" . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + . + "^\\d+$"^^ . + "http://phylomedb.org/?seqid="^^ . + . + "patrice.buche@inrae.fr" . + . + "ontology" . + . + . + "obo" . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID="^^ . + "WormBase RNAi" . + . + "apid.interactions" . + "http://ligand-depot.rutgers.edu/pyapps/ldHandler.py?formid=cc-index-search&target=$1&operation=ccid"^^ . + "T06648"^^ . + "false"^^ . + "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."^^ . + "Scientific Event Ontology" . + . + . + "false"^^ . + "false"^^ . + . + "Ontologized MIABIS" . + . + . + . + . + "https://datacommons.org/browser/$1"^^ . + "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 primary purpose of ISO 15926 is to provide a foundation ontology to support the integration and sharing of data related to the lifecycle of a process plant in such a way that it is consistent, unambiguous, and minimizing the number of ways something could be expressed. Further purpose of ISO 15926-14 is to meet needs for OWL 2 ontologies that are based on ISO 15926-2, that enable efficient reasoning and that capture lifecycle information. A specific purpose is to demonstrate lifecycle modelling through a representation of the lifecycle model of ISO/IEC 81346-1. Another specific purpose is to exemplify how this standard can be used to develop industrial ontologies through various real-world use cases from industry. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . + "The Ageing Gene Database" . + "Ontological Interpretations for Web Property Graphs" . + . + . + "ontology" . + . + . + "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."^^ . + "DASHR expression" . + . + "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="^^ . + . + . + . + "false"^^ . + . . - . - "research" . - . - "hms.lincs.dataset" . - . - . - "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term="^^ . - "ontology" . - "iNaturalist Place" . - . - "lagonzalezmo@unal.edu.co" . - . - "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."^^ . - . - "protein" . - "Expression"^^ . - "http://www.treefam.org/family/"^^ . - . - "TTD Drug" . - . - "0002350"^^ . - . - "Neural ElectroMagnetic Ontology" . - . - . - . - . - . - . - . - "Zebrafish Experimental Conditions Ontology" . - . - . - . - . - . - . - "ontology" . - . - . - "RISM Online" . - . - . - . - . - . - . - . - "scretf" . - "General Multilingual Environmental Thesaurus" . - . - . - . - "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)"^^ . - "https://civicdb.org/links/evidence/"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "dna" . - . - . - . - . - "0001410"^^ . + . + . + . + "false"^^ . + . + . + "zinc" . + "Sunflower ontology" . + "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."^^ . + "http://purl.unep.org/sdg/SDGIO_"^^ . + . + "4DN"^^ . + "tissue" . + . + . + "300165/p13898_2106T"^^ . + "Discourse Elements Ontology" . + "false"^^ . + . + "life science" . + . + . + . + "tarbase" . + . + "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."^^ . + . + "^ENSG\\d{11}$"^^ . + . + "https://www.kegg.jp/entry/$1"^^ . + . + . + . + . + . + . + . + "Damion Dooley" . + "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."^^ . + . + . + . + "tgbugs@gmail.com" . + "mirbase" . + "https://chem.nlm.nih.gov/chemidplus/rn/$1"^^ . + . + "NIF Standard Ontology: Digital Resources" . + "ontology" . + . + . + "Mouse Tumor Biology Database" . + . + . + "https://hamap.expasy.org/unirule/$1"^^ . + "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."^^ . + "https://glycopost.glycosmos.org/entry/$1"^^ . + . + . + "http://www.fairsharing.org/ontology/subject/SRAO_$1"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "^AS\\d{6}$"^^ . + "false"^^ . + "UCSC Genome Browser" . + . + "Philip Strömert" . + . + . + . + . + "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."^^ . + . + "https://www.wikidata.org/wiki/Property:"^^ . + . + . + "https://sitem.herts.ac.uk/aeru/vsdb/Reports/$1.htm"^^ . + . + . + . + . . - . - . - "yongqunh@med.umich.edu" . - . - "asfis" . - . - . - . - . - "^PDC\\d+$"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "MIPF0000002"^^ . - . - . - "cellular" . - . - "128011350"^^ . - . - . - "C2584994"^^ . - "http://purl.obolibrary.org/obo/BTO_$1"^^ . - "tfclass" . - . - "botany" . - . - "life science" . - . - "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . - "false"^^ . - . - "0000564"^^ . - "http://www.bind.ca/Action?identifier=bindid&idsearch=$1"^^ . - "https://scicrunch.org/resolver/RRID:BCBC_"^^ . - . - . - "ontology" . - . - "CHEBI" . - . + . + . + . + "FooDB compound" . + "http://purl.obolibrary.org/obo/MI_$1"^^ . + . + . + . + "https://civicdb.org/links/drugs/"^^ . + "MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation."^^ . + . + . + "Heidi L. Rehm" . + . + "28789"^^ . + "20003"^^ . + . + . + . + . + "false"^^ . + . + "http://www.nmpdr.org/FIG/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Annotation;feature="^^ . + "RETIRED_EHDAA2" . + "Abdomen"^^ . + "OHMI is a biomedical ontology that represents the entities and relations in the domain of host-microbiome interactions."^^ . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/MA_"^^ . + "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + "BIND accession number" . + . + . + "ontology" . + . + . + "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=$1"^^ . + . + . + . + . + "European Food Information Resource Network" . + . + . + . + . + "genome" . + "cog.pathway" . + "life science" . + . + . + . + . + . + . + . + . + . + "MI0026471"^^ . + . + "MPATH" . + . + . + "interaction" . + "ontology" . + . + . + . + . + . + . + "MMP3312982.2"^^ . + "glycomics" . + . + "false"^^ . + "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#"^^ . + . + "http://purl.obolibrary.org/obo/CHEMINF_$1"^^ . + . . - . - . - "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://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . - . - . - . - "false"^^ . - "Jingshan Huang" . - . - "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)."^^ . - "German Clinical Trials Register" . - . - . - . - "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . - . - "http://bigg.ucsd.edu/compartments/$1"^^ . - . - "true"^^ . - . - . - . - "Ontology for genetic interval" . - "https://dataguids.org/ga4gh/dos/v1/dataobjects/"^^ . - . - . - . - . - . - . - . - . - . - "mdm" . - "biology" . - . - . - . - . - "MNXC15"^^ . - "https://repeatsdb.org/protein/$1"^^ . - "institution" . - . - "vendor" . - . - . - "Germplasm Resources Information Network" . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - "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."^^ . - . - "^K[0-9]+$"^^ . - "The cell line vocabulary inside FlyBase"^^ . - . - "life science" . - . - "false"^^ . - "vmhmetabolite" . - . - . - . - . - . - . - . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references phosphorylation sites in proteins."^^ . - . - . - . - . - . - . - . - . - "A*01:01:01:01"^^ . - "^P\\d{5}$"^^ . - "activityBoundOf"^^ . - . - . - . - . - . - . - . - . - "31253.11.sciencedb.j00001.00123"^^ . - . - . - . - "^\\d{7}$"^^ . - . - "agriculture" . - . - . - . - . - . - . - "cbioportal" . - . - "false"^^ . - . - "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."^^ . - . - . - "true"^^ . - . - "genomics" . - "genome" . - . - . - . + . + . + . + . + . + "http://www.treefam.org/family/"^^ . + . + "biopragmatics/bioregistry/416"^^ . + "Steven G. E. Marsh" . + "false"^^ . + . + . + "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."^^ . + . + . + . + . + . + . + "Apple (Malus domestica) defines crop traits and variables to support the standardisation of apple breeding databases providing description of agronomic, morphological, physiological, quality traits, its methods and scales."^^ . + . + "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id="^^ . + "http://purl.obolibrary.org/obo/ATO_"^^ . + "Rafael Richards" . + . + "http://www.jcvi.org/charprotdb/index.cgi/view/"^^ . + . + . + . + . + . + . + "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . + . + "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."^^ . + . + "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID="^^ . + . + . + . + "yongqunh@med.umich.edu" . + "anatomy" . + . + "anatomy" . + . + "pharmacogenomics" . + . + . + "https://rapdb.dna.affrc.go.jp/viewer/gbrowse_details/irgsp1?name=$1"^^ . + "https://www.ribocentre.org/docs/$1"^^ . + . + "0459895"^^ . + "false"^^ . + "classification" . + . + . + . + . + . + . + "small molecule" . + . + . + . + . + "false"^^ . + "panther.pathway" . + . + . + "disease" . + . + "oridb.schizo" . + "^(\\w+\\d+(\\.\\d+)?)|(NP_\\d+)$"^^ . + . + . + "false"^^ . + "https://vac.niaid.nih.gov/view?id=$1"^^ . + . + "false"^^ . + . + . + "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The timed version of the human developmental anatomy ontology gives all the tissues present at each Carnegie Stage (CS) of human development (1-20) linked by a part-of rule. Each term is mentioned only once so that the embryo at each stage can be seen as the simple sum of its parts. Users should note that tissues that are symmetric (e.g. eyes, ears, limbs) are only mentioned once."^^ . + "false"^^ . + . + "GN_G03681DA"^^ . + . + . + . + . + "mex" . + "MIRIAM Registry collection" . + "false"^^ . + . + "translation_language"^^ . + . + "runBioSimulations" . + "drug" . + . + "true"^^ . + . + . + . . - . - "eukaryotic" . - . - "biologics" . - . - "horizon_discovery" . - "chromosome" . + . + "false"^^ . + "Alzforum mutations is a repository of genes and rare variants associated with Alzheimer's disease."^^ . + "plant breeding" . + "nucleotide" . + "^\\d+$"^^ . + . + "protein" . + . + "LINCS_LDP" . + . + . + "http://purl.obolibrary.org/obo/RNAO_"^^ . + . + . + . + "ontology" . + . +_:Na1ba3c668f924c12b186e383d49eb9a2 "patricia.brooks2@cms.hhs.gov" . + . + . + . + . + . + "recombinase" . + "metascience" . + . + . + . + . + "false"^^ . + . + "prodom" . + "regulation" . + "protein" . + "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid="^^ . + . + . + "David Sehnal" . + "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]"^^ . + "cteno" . + . + . + . +_:N08c690e074974bdfb9dbf805d1627267 "evoc@sanbi.ac.za" . + "health science" . + "cdd" . + . + "fplx" . + . + . + _:Na0c300fd6bd246fc84f22a3874137663 . + "zfs" . + "Infectious Disease Ontology" . + . + . + . + . + . + . + "samuel.friedman@cammlab.org" . + "SBGN Bricks data and ontology" . + . + "chemistry" . + . + . + . + . + "applied microbiology" . + "rfc" . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID="^^ . + . + "ontology" . + "genome" . + . + . + "https://www.ebi.ac.uk/biosamples/sample/"^^ . + . + . + . + "true"^^ . + . + . + "drugbank.reaction" . + . + . + . + . + . + "^NX_\\w+$"^^ . + . + . + . + "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + . + . + . + . + . + . + . + . + . + . + . + "miriam.collection" . + "http://purl.obolibrary.org/obo/SO_$1"^^ . + "false"^^ . + "https://www.google.com/patents/"^^ . + . + . + "false"^^ . + "Microarray experimental conditions" . + "gene expression" . + "true"^^ . + "co_366" . + . + . + "European Mouse Mutant Archive" . + . + . + . + . + . + . + . + "NIF Standard Ontology: Organisms" . + . + "small molecule" . + . + "https://biopragmatics.github.io/providers/bs/$1"^^ . + . + "https://w3id.org/babelon/$1"^^ . + . + . + . + . + . + "genome" . + . + . + . + . + . + . + "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."^^ . + "structural bioinformatcs" . + "relationships" . + "CHEBI" . + "yeastintron" . + . + "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . + . + . + . + "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."^^ . + . + "ecocyc" . + . + . + . + . + . + . + "Every entity in OpenCitations Meta (https://opencitations.net/meta) is assigned persistent internal identifier called OpenCitations Meta Identifier (OMID). The OMID has structure [[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]. For example, the first journal article ever processed has OMID br/0601 (the full URI is https://w3id.org/oc/meta/br/0601), where br is the abbreviation of bibliographic resource, and 060 corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., OpenCitations Meta). Finally, 1 indicates that this is the index's first bibliographic resource ever minted."^^ . + . + . + "SNOMECT" . + . + "https://www.pharmvar.org/gene/"^^ . + . +_:N1f59a2d28185438fb66eb0dc254d8402 "NLM Customer Service" . + . + . + . + . + . + . + . + "http://www.kegg.jp/entry/"^^ . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/arba/"^^ . + . + . + . + . + . + . + . + "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln="^^ . + "quality" . + "Sorghum ontology" . + . + . + . + . + . + . + . + . + . + . + . + "genomics" . + . + . + . + . + . + "nasc" . + "http://purl.obolibrary.org/obo/OMIT_$1"^^ . + "XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis."^^ . + "regulation" . + . + "^M\\d+$"^^ . + . + . + . + . + . + . + . + "false"^^ . + "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr=$1"^^ . + . + . + "anatomy" . + . + "http://data.food.gov.uk/codes/foodtype/id/$1"^^ . + "http://purl.obolibrary.org/obo/TAHH_$1"^^ . + "clinical studies" . + . + "false"^^ . + . + "19210-3"^^ . + . + "Colorectal Cancer Atlas" . + "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."^^ . + . + . + . + . + "false"^^ . + . + . + . + "geoinformatics" . + "NIF Cell" . + . + "supply" . + "http://purl.obolibrary.org/obo/DDPHENO_$1"^^ . + . + . + . + . + . + . + . + "GrainGenes" . + . + . + "cell replacement" . + . + "false"^^ . + "false"^^ . + "false"^^ . + "gene" . + . + "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."^^ . + "PRINTS compendium of protein fingerprints" . + . + "chictr" . + "datasubs@ebi.ac.uk" . + "false"^^ . + . + . + . + . + . + . + "leafsnap" . + "Leszek@missouri.edu" . + . + "foodb.food" . + . + "LNCipedia" . + "Sigma Aldrich is a life sciences supply vendor."^^ . + . + . + "ontology" . + "phylogeny" . + "0000060"^^ . + "Open Digital Rights Language Ontology" . + "SP_KW" . + . + . + . + . + "NCBI Bookshelf" . + "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."^^ . + . + . + . + . + . + . + "The ISRCTN registry is a primary clinical trial registry recognised by WHO and ICMJE that accepts all clinical research studies (whether proposed, ongoing or completed), providing content validation and curation and the unique identification number necessary for publication. All study records in the database are freely accessible and searchable. (from homepage)"^^ . + . + . + "KEGG BRITE" . + . + . + . + . + "Jeffrey A. Detras" . + "gene" . + . + . + . + "0005147"^^ . + "https://www.biolegend.com/Default.aspx?ID=6664&productid="^^ . + "^([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_.*)$"^^ . + "1"^^ . + "gene" . + "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . + . + . + . + . + . + . + . + "http://addgene.org/$1"^^ . + . + . + . + . + . + . + "https://panoramaweb.org/$1.url"^^ . + "http://virtualflybrain.org/reports/"^^ . + "protein" . + "http://www.cellsignal.com/products/$1.html"^^ . + . + "Identifier for a place in iNaturalist"^^ . + "MIRBASEM" . + . + "RNAloops" . + . + . + "https://www.rhea-db.org/rhea/"^^ . + . + . + "false"^^ . + "haiiu@dtu.dk" . + . + . + "https://www.ebi.ac.uk/chembl/entity/$1"^^ . + . + "genomics" . + "RGD Disease Ontology" . + . + . + . + . + . + . + . + . + . + . + "tsc" . + "^\\d{7}$"^^ . + "biomedical science" . + "Hepatitis C Virus Database Project" . + "https://umgear.org/p?id=$1"^^ . + "Continuous Automated Model Evaluation" . + . + . + "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."^^ . + . + . + . + . + . + . + . + "https://civicdb.org/links/molecular_profile/$1"^^ . + "structure" . + . + . + "74"^^ . + . + "pathway" . + "life science" . + "protein" . + "^PD\\d+$"^^ . + . + . + "dsm5" . + . + "false"^^ . + . + "^M\\d+$"^^ . + . . - . - "http://dicom.nema.org/resources/ontology/DCM/$1"^^ . - "biology" . - . - . - . - . - . - "iceberg.element" . - . -_:N9e98fa15e62c48f48e2f6b6195f1ae63 "curator@inoh.org" . + . + "Shape Expression Vocabulary" . + "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=$1"^^ . + . + . + . + . + . + "^[A-Za-z0-9\\/]+$"^^ . + . + "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo="^^ . + "https://pathbank.org/view/$1"^^ . + "true"^^ . + "gxa.gene" . + . + "daniel.c.berrios@nasa.gov" . + "life science" . + . + "The Gene Expression Omnibus (GEO) is a gene expression repository providing a curated, online resource for gene expression data browsing, query and retrieval."^^ . + "The BDGP EST database collects the expressed sequence tags (ESTs) derived from a variety of tissues and developmental stages for Drosophila melanogaster. All BDGP ESTs are available at dbEST (NCBI)."^^ . + . + "ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also rovide effective annotations, including human miRNA expression, virus infected tissues, annotation of virus and comparisons."^^ . + . + "cell types" . + "false"^^ . + . + . + . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + . + . + . + . + . + . + "^\\w{2,3}(-\\w+)?$"^^ . + . + "true"^^ . + "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene="^^ . + "gerhard.mayer@rub.de" . + "botany" . + . + . + . + . + . + "^\\w+$"^^ . + . + . + "development" . + "faseb list" . + . + . + . + "false"^^ . + "life science" . + . + . + "We have developed an online database describing the known cell lines from Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera that originated from crop pest insects. Cell line information has been primarily obtained from previous compilations of insect cell lines. (from homepage)"^^ . + . + . + . + "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid="^^ . + "International Classification of Diseases, 9th Revision, Clinical Modification" . + "^MMP\\d+.\\d+$"^^ . +_:Nc576373e3ad5403485c64e5f575d52d2 "albertgoldfain@gmail.com" . + "false"^^ . + "false"^^ . + . + "vsao" . + "ontology" . + "post-transcriptional modification" . + "DDInter20"^^ . + . + "https://www.vmh.life/#reaction/"^^ . + . + . + "^\\d+$"^^ . + . + . + "PiroplasmaDB" . + . + "91005"^^ . + "http://uri.neuinfo.org/nif/nifstd/sao"^^ . + "https://pb.apf.edu.au/phenbank/strain.html?id=$1"^^ . + . + . + "mutant mouse repository" . + "neurobiology" . + . + "Genetic Code" . + . + . + "obo" . + "funcbase.fly" . + "OBO Foundry" . + . + "Geonamaes" . + . + "obo" . + "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." . + "0221"^^ . + . + "false"^^ . + . + "geno" . + . + "EMD-1001"^^ . + "PF00004"^^ . + . + "http://www.imgt.org/ligmdb/view?id="^^ . + . + . + . + . + "paleodb" . + . + . + . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + . + . + "aa78a43f-9c4d-11eb-9e72-0ac135e8bacf"^^ . + . + . + . + "has reviewer" . + "Dataset"^^ . + . + "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . + . + . + "biology" . + "false"^^ . + . + . + . + . + . + "umls.cui" . + "ArrayExpress" . + "xsd" . + "Gene Ontology Registry" . + "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."^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ICEO_"^^ . + "obo" . + . + "Laurel Cooper" . + . + "502930"^^ . + . +_:Ndc164aac22f2496d8fe1558616e1d7dd "vlee@ebi.ac.uk" . + "structure" . + . + . + . + . + . + . + . + . + . + "https://ecocyc.org/gene?id=$1"^^ . + . + "cell_model_passport" . + . + . + . + . + "DRKS00031815"^^ . + "https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task="^^ . + . + . + "https://omim.org/MIM:PS"^^ . + . + . + "ontology" . + "KEGG compound contains our knowledge on the universe of chemical substances that are relevant to life."^^ . + . + . + . + . + "biomedical science" . + . + "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."^^ . + . + . + "GlyTouCan" . + . + . + . + "false"^^ . + . + "http://sweetontology.net/matrMineral/$1"^^ . + . + . + . + . + . + . + "Jie Zheng" . + "UniProt Resource" . + . + . + . + "disease" . + . + . + . + . + . + "^\\d{7}$"^^ . + "protein" . + . + "HMS LINCS Cell" . + "collagenmutdb" . + . + "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)"^^ . + "minid.test" . + "support@bel.bio" . + . + "john.garavelli@ebi.ac.uk" . + "http://kinase.bioinformatics.tw/showall.jsp?type=PhosphoProtein&info=Gene&name=$1&drawing=0&sorting=0&kinome=0"^^ . + "genomics" . + . + . + "T01B6.1"^^ . + "authorList"^^ . + "egon.willighagen@maastrichtuniversity.nl" . + "false"^^ . + . + . + . + . + . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/Spectrums/$1"^^ . + "HPSI0114i-bezi_1"^^ . + . + "metabolites" . + . + . + . + . + . + "Chlamydia"^^ . + . + "Manually curated collections of resources stored in the bioregistry"^^ . + . + "CNV syndromes in the DECIPHER genomics database that are linked to Human Phenotype Ontology terms"^^ . + "ICDCM_2005" . + "life science" . + . + . + "David Wishart" . + . + . + . + "false"^^ . + . + . + . + . + "^[EL]D[SG]-\\d+$"^^ . + . + "false"^^ . + . + "https://prosite.expasy.org/"^^ . + . + . + . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?db=HOGENOM5&query=$1"^^ . + . + "chenyangnutrition@gmail.com" . + . + . + "Martin Kuiper" . + . + . + . + . + "The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community."^^ . + "Histopathology Ontology" . + "https://www.thaiclinicaltrials.org/show/"^^ . + "https://biokb.lcsb.uni.lu/fact/$1"^^ . + . + . + . + "false"^^ . + . + . + . + . + "support@ccdc.cam.ac.uk" . + "http://viroligo.okstate.edu/main.php?vid=$1"^^ . + "cgd" . + "false"^^ . + . + . + "false"^^ . + . + "pathway" . + _:Ncacac89b73af4494b2963250287dad6c . + "artificial intelligence" . + . + "genomics" . + . + "^[\\w\\d\\.-]*$"^^ . + . + . + "mgnify.proj" . + "glycoepitope" . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + "^ARBA\\d+$"^^ . + . + . + . + . + . + "scr" . + . + . + . + . + "Coleoptera Anatomy Ontology" . + "http://hawaii.eagle-i.net/i/$1"^^ . + . + . + . + . + "biomedical science" . + "rna" . + . + . + . + . + . + . + . + "Human Ancestry Ontology" . + . + "https://www.kegg.jp/entry/"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "A comprehensive proteomics data and process provenance ontology."^^ . + "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . + "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."^^ . + _:Ne50f13c462df4890baab17f28398c834 . + "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value="^^ . + "http://purl.obolibrary.org/obo/ZP_$1"^^ . + "http://purl.obolibrary.org/obo/NBO_$1"^^ . + "gfrishkoff@gsu.edu" . + . + . + . + "BRENDA Ligand" . + "https://www.genome.jp/virushostdb/"^^ . + "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds."^^ . + . + . + . + "pathway" . + . + . + . + "obo" . + "^\\d{7}$"^^ . + . + . + "Pan African Clinical Trials Registry" . + "false"^^ . + . + . + . + . + "https://www.ebi.ac.uk/chembl/cell_line_report_card/"^^ . + . + . + . + . + "UMLS CUI" . + . + . + . + . + . + . + _:N3b2786467c704005b88c4abc40a2e8e2 . + . + . + . + . + . + . + "karr@mssm.edu" . + . + "Identifiers.org Ontology"^^ . + . + "^CAL\\d{7}$"^^ . + . + . + . + "false"^^ . + . + "000177759000002"^^ . + . + "13GS"^^ . + . + . + . + . "protein" . - . - . - . - . - "Henning Hermjakob" . - "0000091"^^ . - . - "protein" . - . - . - . - . - "life science" . - . - . - "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."^^ . + "false"^^ . + . + "pathway" . + "http://purl.org/spar/deo/"^^ . +_:Na1ba3c668f924c12b186e383d49eb9a2 "Pat Brooks" . + . + "http://edamontology.org/operation_$1"^^ . +_:N890c5c3e89754d0e974e862d58120df2 "bgee@isb-sib.ch" . + . + . + . + . + "Allotrope Merged Ontology Suite" . + . + . + . + "Database of Complete Genome Homologous Genes Families" . + "false"^^ . + . + "cell" . + . + "0001011"^^ . + . + . + . + . + . + "https://bioregistry.io/dbd:"^^ . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/SEPIO_"^^ . + . + "N:package:e3243db3-7986-488e-9a10-c7a0bfdcfe8a"^^ . + "caloha" . + . + . + . + . + . + "PicTar" . + "false"^^ . + "http://sideeffects.embl.de/se/"^^ . + . + . + . + . + "Charles Tapley Hoyt" . + . + . + . + . + . + . + . + . + "ebisc" . + . + "fbsp" . + "biology" . + . + "familyName"^^ . + "00100005"^^ . + "agriculture" . + . + . + . . - . - . - "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"^^ . - "http://www.ontologyrepository.com/CommonCoreOntologies/$1"^^ . - . - "^\\d+$"^^ . - . - . - . - "https://www.e-cyanobacterium.org/bcs/entity/$1"^^ . - . - "Store DB" . - . - . - . - "protein" . - . - . - . - "https://w3id.org/linkml/"^^ . - . - "The Universal Spectrum Identifier (USI) is a compound identifier that provides an abstract path to refer to a single spectrum generated by a mass spectrometer, and potentially the ion that is thought to have produced it."^^ . - "^\\d+$"^^ . - "PaxDb Protein" . - "^\\d{7}$"^^ . - "Pantelis Topalis" . - . - . - . - "^UPC\\d{5}$"^^ . - "http://purl.obolibrary.org/obo/EHDA_$1"^^ . - . - . - . - "miriam.collection" . - . - . - . - "https://zenodo.org/record/$1"^^ . - . - "00023232"^^ . - "http://purl.org/dc/dcmitype/$1"^^ . - . - . - "EC number" . - "CRISP Thesaurus, 2006" . - . - . - "https://www.ncbi.nlm.nih.gov/gene/"^^ . - . - . - . - . - . - . - . - . - "pd_st" . - . - . - . - . - "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database."^^ . - . - . - . - "biomedical science" . - . - . - . - . - . - "botany" . - "biomedical science" . - "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . - . - . - . - "NCBI_taxid" . - . - . - . - . - "0000123"^^ . - . - . - "clinical data" . - . - "false"^^ . - "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."^^ . - . - "true"^^ . - "drugbankv4.target" . - . - . - . - . - . - "Friend of a Friend" . - "0000000"^^ . - . - . - "life science" . - . - . - . - . - "biology" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/HTN_$1"^^ . - . - . - . - . - . - "^[1-9]\\d*$"^^ . - "obo" . - . - . - . - . - "false"^^ . - "obo" . - . - "http://aims.fao.org/aos/agrovoc/c_$1"^^ . - . - . - . - . - "^[A-Z0-9]+$"^^ . - "false"^^ . - "biomedical science" . - . - . - . - . - . - "243002_at"^^ . - . - "aism" . - . - "sheriff@ebi.ac.uk" . - . - . - . - "Identifier for a species on the noaa fisheries website"^^ . - "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . - . - . - . - . - . - . - . - . - "transgenic" . - . - . - "Ribocentre" . - "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."^^ . - . - . - "false"^^ . - "VIPERdb" . - "developmental biology" . - "http://www.chemspider.com/$1"^^ . - . - . - . - . - . - . - . - "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . - . - "chemistry" . - "whimar@ohsu.edu" . - . - . - . + . + . + . + . + . + . + "protein" . + . + . + . + "mbaudis@me.com" . + . + . + . + . + "Jean-Luc Jannink" . + . + . + . + . + . + . + . + . + . + . + . + "biology" . + "life science" . + . + . + . + . + "https://amzn.com/"^^ . + "https://flybase.org/reports/$1"^^ . + . + "google.book" . + . + . + "obo" . + "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein="^^ . + . + . + . + . + "JCGGDB (Japan Consortium for Glycobiology and Glycotechnology DataBase) is a database that aims to integrate all glycan-related data held in various repositories in Japan. This includes databases for large-quantity synthesis of glycogenes and glycans, analysis and detection of glycan structure and glycoprotein, glycan-related differentiation markers, glycan functions, glycan-related diseases and transgenic and knockout animals, etc."^^ . + . + . + . + "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id="^^ . + "^\\w+$"^^ . + . + "http://purl.obolibrary.org/obo/NCIT_$1"^^ . + . + . + . + . + . + "DRSC05221"^^ . + . + . + . + "Evidence Items are the central building block of the Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. The clinical Evidence Item is a piece of information that has been manually curated from trustable medical literature about a Variant or genomic ‘event’ that has implications in cancer Predisposition, Diagnosis (aka molecular classification), Prognosis, Predictive response to therapy, Oncogenicity or protein Function. For example, an Evidence Item might describe a line of evidence supporting the notion that tumors with a somatic BRAF V600 mutation generally respond well to the drug dabrafenib. A Variant may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical Evidence statement corresponds to a single citable Source (a publication or conference abstract)."^^ . + . + "protein" . + . + . + "SP_DI" . + "faseb list" . + . + "^\\w+$"^^ . + . + . + . + . + . + "Prefix Commons" . + "240-17-488-3-4-12"^^ . + "SIGNOR" . + "^(T0\\d+|\\w{3,5})$"^^ . + . + . + "metabolomics" . +_:Ne50f13c462df4890baab17f28398c834 "Cynthia Hake" . + . + . + . + . + "aop.stressor" . + . + . + "biologics" . + . + . + "life science" . + . + . + . + "metascience" . + "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."^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . + "InChIKey" . + . + . + "88"^^ . + . + . + "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . + "http://purl.obolibrary.org/obo/CMO_"^^ . + . + . + "HIP000030660"^^ . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org"^^ . + "emdb" . + . + . + "epidemiology" . + . + "DAP000773"^^ . + . + . + . + . + . + . + . + "epidemiology" . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "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."^^ . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "r3d100014165" . + "protein" . + . + "0000001"^^ . + "0000512"^^ . + "rmrich5@gmail.com" . + . + . + "5277619"^^ . + "tao" . + . + . + . + "protein" . + "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)."^^ . + "biomedical science" . + "An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum)."^^ . + . + . + . + "10004892"^^ . + . + . + . + "te" . + . + "http://purl.org/vocab/frbr/core#$1"^^ . + . + "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."^^ . + "social media" . + . + . + . + . + . + . + . + . + . + . + "0000038"^^ . + . + . + . + . + . + . + . + "http://aber-owl.net/ontology/$1" . + "functional genomics" . + . + . + . + "ecyano.rule" . + . + . + "Sri Lanka Clinical Trials Registry" . + . + "computational biology" . + . + . + "interactive portal" . + . + "0000052"^^ . + . + "CIViC Assertion" . + . + . + . + . + "life science" . + . + "http://dictybase.org/gene/$1"^^ . + . + . + "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . + "life science" . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . + "https://cls.shop/$1"^^ . + "DICOM Controlled Terminology"^^ . + "mpidb" . + "kegg.metagenome" . + . + . + . + . + . + . + "CTD Chemical" . + "Biomedical Informatics Research Network Lexicon" . + . + "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id="^^ . + . + . + "A structured, controlled vocabulary which describes the treatments, growing conditions, and/or study types used in plant biology experiments."^^ . + . + "4b848c342a4f4abc871bdf8a09a60807"^^ . + "MetaboLights Compound" . + . + . + . + . + . + . + . + . + "DG00301"^^ . + . + "^\\d{6}$"^^ . + . + . + . + . + . + "neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases."^^ . + . + "NLXDYS covers dysfunction, diseases, and disorders. Most classes are also in Disease Ontology (DOID), Monarch Disease Ontology (MONDO), Human Phenotype Ontology (HPO), etc."^^ . + . + "false"^^ . + . + . + "lipidmaps" . + "190000021540"^^ . + . + "https://bioregistry.io/metaregistry/scholia/"^^ . + "ontology" . + "false"^^ . + . + "brain regions" . + . + . + "icd9cm" . + "GPIb_IX_V"^^ . + . + . + . + . + . + . + . + . + "saddan"^^ . + . + . + . + . + . + . + . + . + "genetics" . + "19757"^^ . + "http://purl.obolibrary.org/obo/LBO_$1"^^ . + . + "https://bioregistry.io/metaregistry/ncbi/"^^ . + "http://www.co-ode.org/ontologies/galen#$1"^^ . + "false"^^ . + . + . + "life science" . + "Pathogen Transmission Ontology" . + "AberOWL" . + "ega.dataset" . + . + . + . + . + . + "gnpis" . + . + "MIRBASE_FAMILY" . + . + "ontology" . + . + . + . + . + . + "false"^^ . + . + "https://biopragmatics.github.io/providers/hba/"^^ . + "embryo" . + "BRENDA Ligand Group" . + "true"^^ . + . + "life science" . + "An ontology specifies terms that are used to annotate ontology terms for all OBO ontologies. The ontology was developed as part of Information Artifact Ontology (IAO)."^^ . + "https://odc-tbi.org/data/"^^ . + . + . + . + "^LGCEDe-S-\\d{9}$"^^ . + "ontology" . + "http://purl.obolibrary.org/obo/NCBITaxon_$1"^^ . + "true"^^ . + . + . + "controlled term" . + . + "atc" . + "https://www.metanetx.org/comp_info/$1"^^ . + "obo" . + "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."^^ . + . + "ontology" . + "0001056"^^ . + . + . + "http://purl.obolibrary.org/obo/MMO_$1"^^ . + . + "https://www.swisslipids.org/#/entity/SLM:"^^ . + . "^[0-9A-Za-z-_\\.]+/[0-9A-Za-z-_\\.]+$"^^ . - "biomedical science" . - . - . - . - "CAE46076"^^ . - . - "https://www.kew.org/data/grasses-db/www/"^^ . - "molecular medicine" . - . - . - . - . - . - . - . - . - . - . - "https://www.picb.ac.cn/limore/cellLines/single?para=$1"^^ . - "physiology" . - . - . - . - . - . - . - . - . - "https://amzn.com/$1"^^ . - . - "https://www.fishbase.ca/summary/$1"^^ . - . - "An application ontology built for beta cell genomics studies."^^ . - "PWY3O-214"^^ . - . - . - . - "NASC code" . + "https://github.com/prefixcommons/biocontext" . + . + . + . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/$1" . + . + . + "skos" . + . +_:Nda1f307f111446f48481d11b881079b1 "usha@molecularconnections.com" . + . + "An identifier for a country in numeric format per ISO 3166-1"^^ . + . + . + . + . + "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc="^^ . + . + . + . + . + . + "0003463"^^ . + "rpillich@ucsd.edu" . + "CHEBIID" . + "Medaka Developmental Stages" . + . + "jimhu@tamu.edu" . + "ontology" . + . + "ontology" . + "Carbohydrate Active EnZYmes" . + . + . + "hl7.v3codesystem" . + . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + . + . + . + . + . + "^[0-9]+\\.[0-9]+$"^^ . + . + . + . + . + "life science" . + "ardb" . + . + . + . + . + "doqcs.pathway" . + "obo" . + . + . + . + "^\\d+$"^^ . + "UR000124451"^^ . +_:N9e7c97749a6f4045a68fcff83d0fafd5 "Edd Wilder-James" . + . + . + "cath.superfamily" . + "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://oid-info.com/get/"^^ . + . + "An organization in FAIRsharing, including universities, labs, etc."^^ . + "salk" . + . + . + "biomedical science" . + "false"^^ . + . + . + . + . + . + "AB1925000"^^ . + "Conferences in EasyChair"^^ . + "embryology" . + "eukaryotic" . + "rna" . + . + . + "false"^^ . + "MRA-253"^^ . + "https://ensaiosclinicos.gov.br/rg/"^^ . + "http://vocab.getty.edu/page/tgn/$1"^^ . + "^HIT\\d{9}(\\.\\d+)?$"^^ . + "^PAp[0-9]{8}$"^^ . + "http://exac.broadinstitute.org/variant/$1"^^ . + "Open Researcher and Contributor" . + . + . + . + . + "biomedical science" . + . + . + "false"^^ . + . + . + "false"^^ . + . + . + "gainesville.core" . + "data science" . + "https://cropontology.org/rdf/CO_359:"^^ . + "Babelon" . + . + "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . + "disorders" . + "https://cropontology.org/ontology/$1" . + . + . + "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115="^^ . + . + . + . + . + "Rice Annotation Project Database (RAP-DB) is a primary rice (Oryza sativa) annotation database established in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project. RAP-DB provides comprehensive resources (e.g. genome annotation, gene expression, DNA markers, genetic diversity, etc.) for biological and agricultural research communities. This collection provides transcript information in RAP-DB."^^ . + . + . + "nuclearbd" . + . + "reagents" . + "true"^^ . + . + . + . . - . - . - "ViralZone is a resource bridging textbook knowledge with genomic and proteomic sequences. It provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures."^^ . - "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_"^^ . -_:N19ba2f4b49e149989c007cb1324ae430 "sschurer@med.miami.edu" . - . - "http://purl.obolibrary.org/obo/T4FS_"^^ . - . - "small molecule" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - "Gene Ontology Database references" . - "false"^^ . - . - . - . - . - . - . - . - . - . - "The EU Clinical Trials Register contains information on clinical trials conducted in the European Union (EU), or the European Economic Area (EEA) which started after 1 May 2004.\r\nIt also includes trials conducted outside these areas if they form part of a paediatric investigation plan (PIP), or are sponsored by a marketing authorisation holder, and involve the use of a medicine in the paediatric population."^^ . - "false"^^ . - "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . - . - . - . - "UPVAR" . - . - . - "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId="^^ . - "dna" . - . - . - . - . - . - . - "google.scholar" . - . - . - "https://www.ebi.ac.uk/pdbsum/$1"^^ . - . - "0000047"^^ . - . - "genatlas" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/SO_$1"^^ . - "elisa-kits" . - . - . - . - . - "model organism" . - . - "false"^^ . - . - . - . - "ontology" . - . - . - . - . - . - . - "wes_schafer@merck.com" . - . - "false"^^ . - . - . - . - "https://reactome.org/content/detail/$1"^^ . - . - "bugbase.expt" . - . - . - . - . - . - . - "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"^^ . - "http://uri.neuinfo.org/nif/nifstd/birnlex_"^^ . - . - . - . - . - . - "^TTHERM\\_\\d+$"^^ . - "Gramene Growth Stage Ontology" . - "embryo" . - "false"^^ . - "0471491039"^^ . - . - "^[a-z_A-Z0-9]+$"^^ . - "radiomics" . + . + . + "taxonomy" . + . + . + . + . + . + . + "metabolomics" . + . + . + . + . + . + . + "4.2.78"^^ . + "CAS Registry Number" . + "https://www.ebi.ac.uk/biostudies/studies/$1"^^ . + "BioProject" . + . + "UMR7315"^^ . + . + . + "6472"^^ . + "false"^^ . + "false"^^ . + . + "^EBI\\-[0-9]+$"^^ . + "Cell line collections (Providers)"^^ . + . + . + . + "^\\w+$"^^ . + . + . + "https://biopragmatics.github.io/providers/cvx/$1"^^ . + "^A\\d{6}$"^^ . + . + . + . + . + . + . + "AMDEFA"^^ . + . + "gene expression" . + "Q-2958"^^ . + . + . + . + "VSAO_RETIRED" . + . + . + "https://easychair.org/cfp/"^^ . + "dawood@helix.nih.gov" . + . + "37"^^ . + "^MNEST\\d+$"^^ . + "virology" . + . + . + "A database containing predicted viral miRNA candidate hairpins."^^ . + "swisslipids" . + "http://www.ebi.ac.uk/efo/EFO_"^^ . + . + . + . + . + . + "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . + "https://www.mlcommons.org/mlc-id/$1"^^ . + . + "false"^^ . + . + . + "CHEMBL3467"^^ . + . + . + "The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments and contains translated genome sequences for all species."^^ . + . + . +_:N12491eabd3e44c84bef06eb91f048151 "chebi-help@ebi.ac.uk" . + "ontology" . + "https://www.ebi.ac.uk/ols4/ontologies/cco/terms?obo_id=CCO:$1"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + . + "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."^^ . + . + "anatomy" . + . + . + . + "protein" . + . + . + "dna" . + "version control" . + . + "Clinical Trials Information System" . + . + . + . + "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . + "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."^^ . + . + . + "Gemeinsame Normdatei" . + . + "genomics" . + . + "MediaDive Solution" . + . + . + "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster=$1"^^ . + . + . + . + . + . + "epidemiology" . + . + "BiGG Compartment" . + . + . + . + . + . + . + "ontology" . + . + . + . + . +_:N818b7e54347f4b79b69a5d8c44ba1463 "J.Bard@ed.ac.uk" . + "Marie-Angélique Laporte" . + "https://bioregistry.io/medlineplus:"^^ . + "false"^^ . + "hms.lincs.antibody" . + . + . + "http://purl.obolibrary.org/obo/YPO_"^^ . + . + . + . + . + . + . + . + . + . + "csd" . + "kinetics" . + . + "ontology" . + . + . + . + . + "appears in" . + "200-003-9"^^ . + . + "Peroxibase provides access to peroxidase sequences from all kingdoms of life, and provides a series of bioinformatics tools and facilities suitable for analysing these sequences."^^ . + . + . + "ChEBI"^^ . + . + . + . + . + "Candida Genome Database" . + . + . + . + . + . + "ydpm" . + "false"^^ . + . + . + . + . + "RXN-14904"^^ . + . + "PhosphoSite Residue" . + "idot" . + "transposon" . + . + . + "huge" . + "^\\d{7}$"^^ . + . + "https://hdl.handle.net/hdl:20.500.12633/"^^ . + . + . + "edda" . + "obo" . + . + . +_:Nf15094c178294dd0b15e5d36b3dbb2d6 "curator@inoh.org" . + . + "sdis" . + . + "datanator.metabolite" . + . + "protein" . + . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + "plant breeding" . + . + . + . + "ftp://ftp.embl-heidelberg.de/pub/databases/protein_extras/hssp/$1.hssp.bz2"^^ . + . + "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines."^^ . + "^\\d{7}$"^^ . + "intenz" . + . + . + . + . + . + "biomedical science" . + "G protein-coupled receptor database" . + . + . + . + "http://purl.obolibrary.org/obo/ORNASEQ_"^^ . + "^AT[1-5]G\\d{5}(\\.\\d+)?$"^^ . + . + . + . + . + "scicrunch" . + . + "biomedical science" . + . + "csa" . + . + . + . + . + . + . + . + "Clinical measurement ontology" . + . + "false"^^ . + . + "ProteomicsDB Peptide" . + "6978836"^^ . + "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid="^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "physical geography" . + "^\\w+$"^^ . + . + . + . + . + "anatomy" . + . + . + "^[A-Z-_0-9]+$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MAT_$1"^^ . + "^\\w+$"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "(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."^^ . + . + . + . + "Gerhard Mayer" . + "SNOWMEDCT_US_2018_03_01" . + . + . + "EC_CODE" . + . + . + "Gene Ontology Registry" . + "zenodo.record" . + . + "ontology" . + "genetic" . + "3517823"^^ . + . + "RPCEC00000423"^^ . + . + . + "0000001"^^ . + . + . + "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . + . + "life science" . + . + . + . + . + . + "life science" . + "http://purl.obolibrary.org/obo/MONDO_$1"^^ . + . + "^\\d{8}$"^^ . + . + . + . + "icd10pcs" . + . + "Castor bean ontology" . + . + . + . + "expression" . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/HABRONATTUS_$1"^^ . + . + . + . +_:N818b7e54347f4b79b69a5d8c44ba1463 "Jonathan Bard" . + . + . + . + "^MMP\\d+.\\d+$"^^ . + _:Ne90637670289458180b3f4b6ec45ab94 . + . + "phs000768.v2.p1"^^ . + . + "proteomics" . + "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID="^^ . + "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term=$1"^^ . + . + . + . + . + "false"^^ . + "envo" . + . + . + "knowledge and information systems" . + "https://lincs.hms.harvard.edu/db/datasets/$1"^^ . + . + . + "https://www.gwascentral.org/marker/$1"^^ . + "^BG\\d+$"^^ . + . + "^DBCAT\\d+$"^^ . + . + . + "genomics" . + . + "mcarthua@mcmaster.ca" . + "zmp@ebi.ac.uk" . + . + . + . + "bioinformatics" . + "xenopus" . + . + "https://bioregistry.io/schema/#"^^ . + "A vocabulary and ontology repository for agronomy and related domains." . + "http://purl.obolibrary.org/obo/OVAE_"^^ . + . + . + . + "PaxDb Protein" . + "clinvar.submitter" . + . + "wikidata.property" . + "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=$1"^^ . + "false"^^ . + . + . + . + . + . + . + "Google Patents covers the entire collection of granted patents and published patent applications from the USPTO, EPO, and WIPO. US patent documents date back to 1790, EPO and WIPO to 1978. Google Patents can be searched using patent number, inventor, classification, and filing date."^^ . + . + . + "A web-based catalog of recommended measurement protocols selected by experts to include in studies with human participants."^^ . "taxonomy" . - "^MMP\\d+.\\d+$"^^ . - "life science" . - "enzyme" . - . - . - . - . - "PRJDB3"^^ . - . - . - . -_:N137416fe0fe14465a245cb8a86726e9d "info@who.int" . - "3355"^^ . - . - . - "shareloc" . - . - . - "^NPC\\d+$"^^ . - . - . - . - "Wormbase Gene" . - . - . - . - "The International Standard Book Number (ISBN) is for identifying printed books."^^ . - . - . - . - "http://www.genomesize.com/result_species.php?id="^^ . + . + . + "aquaculture" . + . + "pathway" . + . + "dermatology" . + "^S\\d+$"^^ . + . + "http://terminology.hl7.org/CodeSystem/v2-$1"^^ . + "human" . + "090803"^^ . + . + "uniprot.keyword" . + . + . + . + . + . + . + . + "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"^^ . + . + "wikidata" . + "false"^^ . + . + "Europe PMC Preprints" . + . + . + "http://purl.obolibrary.org/obo/DRON_$1"^^ . + "351"^^ . + . + . + . + . + . + "narcis" . + "pathway" . + . + "bioinformatics" . + . + "^\\d+$"^^ . + . + "TAX" . + "https://biosimulators.org/simulators/$1"^^ . + . + . + . + . + . + . + . + "small molecule" . + . + . + . + "false"^^ . + "Cowpea ontology" . + "M0001"^^ . + . + . + . + "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."^^ . + "genetics" . + "Terms from the source appear in the target resource" . + . + . + . + "Established in 2005 by professor Wu Taixiang and Li Youping team, West China Hospital, Sichuan University, and the Ministry of Health of China assigned it to be the representative of China to join WHO ICTRP in 2007. The Chinese Clinical Trial Registry provides the services include register for trials, consultation for trial design, central randomization for an allocation sequence, peer review for draft articles and training for peer reviewers. (from website)"^^ . + "drugbank.bioentity" . + "go" . + . + . + . + "false"^^ . + . + "transcriptomics" . + . + . + . + "David.Linke@catalysis.de" . + "hpa" . + . + . + "http://purl.obolibrary.org/obo/MIAPA_$1"^^ . + "false"^^ . + "AHR"^^ . + "ontology" . + . + . + . + . + . + . + . + . + . + . + . + "https://eol.org/pages/"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/sra/"^^ . + "F11903"^^ . + "117"^^ . + . + . + . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + . + . + "edam.data" . + . + . + "http://purl.obolibrary.org/obo/ADO_$1"^^ . + . + "^\\d{7}$"^^ . + "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . + . + . + "http://purl.obolibrary.org/obo/VIDO_$1"^^ . + . + "false"^^ . + . + "Fungal gross anatomy" . + "QJ51RV02"^^ . + . + "false"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/oen_$1"^^ . + . + "deepak.unni3@gmail.com" . + . + . + . + . + "health science" . + "biodiversity" . + . + . + " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1."^^ . + "^\\d{7}$"^^ . + . + "nmrshiftdb2" . + . + "BugBase Expt" . + . + . + . + . + "https://www.gleif.org/lei/"^^ . + . + "structure" . + "^\\w{3}\\d{5}(\\.\\d+)?$"^^ . + _:N799549267e7545d0961160c005e4ec68 . + . + "global health" . + "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . +_:N200f6d51d8c24db9957971f3242ad505 "helpdesk@cropontology-curationtool.org" . + "ontology" . + . + "false"^^ . + "mesh.2012" . + "Polymorphism and mutation databases"^^ . + . + . + . + "life science" . + . + . + . + . + "genome" . + . + . + . + "false"^^ . + . + "0000048"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_cell_$1"^^ . + "^RF\\d{5}$"^^ . + . + . + . + "gene" . + "genomics" . + "biozil" . + . + . + "https://loinc.org/$1"^^ . + . + . + "false"^^ . + . + . + . + "epidemiology" . + "^((BIOMD|MODEL)\\d{10})|(BMID\\d{12})$"^^ . + "http://purl.obolibrary.org/obo/NIF_CELL_$1"^^ . + . + "http://purl.obolibrary.org/obo/GAZ_$1"^^ . + . + . + "mass spectrometry" . + . + "biomodels.db" . + . + . + . + . + . + . + . + . + . + . + "sebastien.moretti@sib.swiss" . + "model organism" . + . + . + "PDBsum provides an overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them."^^ . + . + . + . + . + . + . + "aging" . + "DB14938"^^ . + "satyasahoo@ieee.org" . + . + . + . + "false"^^ . + . + . + . + . + . + "COSMIC is a comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. This collection references genes."^^ . + "These resources were listed in [Sharing biological data: why, when, and how](https://doi.org/10.1002/1873-3468.14067), which prompted further novel curation of the Bioregistry which included the addition of GenBank, Panorama Public, EMPIAR, and SSBD. It also prompted the curation of mappings to FAIRSharing when possible." . + . + "The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The UM-BBD Pathway Prediction System (PPS) predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The PPS recognizes organic functional groups found in a compound and predicts transformations based on biotransformation rules. These rules are based on reactions found in the UM-BBD database. This collection references those rules."^^ . + . + . + . + "http://purl.obolibrary.org/obo/NCIT_"^^ . + . + . + "http://www.gramene.org/db/genes/search_gene?acc="^^ . + "AC00963334"^^ . + "csv"^^ . + . + . + . + . + "gene" . + "OSC1416"^^ . + "ontology" . + "^\\d{7}$"^^ . + . + . + . + "database management" . + "^[0-9]+(LR)?$"^^ . + . + . + . + . + . + "vuid" . + . + . + . + . + . + "tcdb" . + . + . + "40000617"^^ . + . + . + "http://purl.obolibrary.org/obo/EMAP_"^^ . + "molecular biology" . + "epcc" . +_:Nba7394e70eed46019c593a60ce48ec28 "chinhda@alleninstitute.org" . + "3771992"^^ . + . + . + "AOPWiki" . + . + . + . . - . - . - "false"^^ . - . - . - . - . - "Jennifer R Smith" . - . - "https://covid19.sfb.uit.no/api/records/$1"^^ . - . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - . - . - . -_:Ne79eba7c8d2944bba4b664305e5179ca "Maria Herrero" . - . - "ontology" . - . - "regulation" . - . - . - . - "BioSimulators" . - . - . - "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . - . - "http://cerevisiae.oridb.org/details.php?id="^^ . - "67035"^^ . - . - "proteomics" . - . - . - . - . - . - "ATCC(in host)" . - . - . + . + . + . + "The bacterial tyrosine kinase database (BYKdb) that collects sequences of putative and authentic bacterial tyrosine kinases, providing structural and functional information."^^ . + . + "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID=$1"^^ . + . + . + "proteomics" . + "The Essential FRBR in OWL2 DL Ontology (FRBR) is an expression in OWL 2 DL of the basic concepts and relations described in the IFLA report on the Functional Requirements for Bibliographic Records (FRBR), also described in Ian Davis's RDF vocabulary. It is imported by FaBiO and BiRO."^^ . + . + . + . + "life science" . + "0040379"^^ . + . + . + "false"^^ . + "Rat Strain Ontology" . + . + "virology" . + . + "http://purl.obolibrary.org/obo/PO_"^^ . + . + . + . + . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + "Structural Database of Allergenic Proteins" . + . + . + . + "careerPrizeMoney"^^ . + . + . + . + "ontology" . + . + "recombinant host" . + . + . + . + . + "Ontology of Biological and Clinical Statistics" . + . + "reproduction" . + "false"^^ . + . + "http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$1]"^^ . + . + . + "ccle" . + . + "http://purl.obolibrary.org/obo/TAHH_"^^ . + . + . + . + . + "cst.ab" . + . + . . - . - "false"^^ . - . - "subject agnostic" . - . - "false"^^ . - . - . - . - . - . - "^[0-9]+$"^^ . - . - . - . - . - . - . - . - "PSEEN0001"^^ . - "http://www.onto-med.de/ontologies/gfo.owl#$1"^^ . - . - . - "Michael Baudis" . - "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . - "ontology" . - . - "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."^^ . - "version 2019 - pvs"^^ . - "false"^^ . - . - . - . - . - . - . - . - "prgr_human"^^ . - . - . - "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."^^ . - "false"^^ . - "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp="^^ . - . - "botany" . - . - . - . - "licebase" . - . - "Edison Ong" . - "medicine" . - . - "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response."^^ . - "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"^^ . - "gramene.taxonomy" . - "storedb" . - . - "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces."^^ . - "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."^^ . - "(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."^^ . - "Molecular database for the identification of fungi" . - "immunology" . - . - "ontology" . - . - . - . - "pathway" . - . - . - . - . - "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "^[A-Za-z]+\\/[0-9]+$"^^ . - . - . - . - "^\\d+$"^^ . - "false"^^ . - "namerxn" . - . - "^M\\d+$"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "^[1-9]\\d{0,5}$"^^ . - . - . - . - . - "limore" . - . - "classification" . - "http://purl.org/spar/pwo/$1"^^ . - "protein" . - . - . - "ZFA_RETIRED" . - "Harry Caufield" . - . - "https://go.drugbank.com/reactions/$1"^^ . - . - . - " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)"^^ . - "EDAM Topic" . - . - . - . - . - . - "gene" . - "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . - . - . - . - "lincs.protein" . - . - . - . - . - . - . - . - "6000122"^^ . - . - "The Ecosystem Ontology" . - . - "Name-to-Thing" . - . - "biology" . - . - . - . - . - "^\\d+$"^^ . - "^\\w+(\\-|\\.|\\w)*$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "genome" . - . - "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . - . - "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."^^ . - . - "Core Ontology for Biology and Biomedicine" . - . - . - . - . - . - . - . - . - "https://nanbyodata.jp/disease/NANDO:$1"^^ . - "molecular genetics" . - "https://gen3.theanvil.io/ga4gh/drs/v1/objects/"^^ . - . - "fbbt" . - . - . - . - "ontology" . - . - . - . - "^\\d+$"^^ . - "database" . - . - "JRC Data Catalogue" . - "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)."^^ . - "Collection" . - "false"^^ . - . - "phs000768.v2.p1"^^ . -_:N61f371b1d2fa4381a3fcd51f3dd48a97 "Jim Amsden" . - "vcell" . - "288"^^ . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/"^^ . - . - . - "http://purl.obolibrary.org/obo/RS_"^^ . - . - "false"^^ . - . - . - "http://edamontology.org/topic_$1"^^ . - . - . - . - "false"^^ . - . - . - "CIViC Assertion" . - . - "bioinformatics" . - . - . - . - . - . - . - . - . - . - "UniChem compound" . - . - "false"^^ . - . - "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . - "https://orcid.org/"^^ . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - "0745-4570"^^ . - . - . - "nhcdr" . - "GLAndersen@lbl.gov" . - . - "false"^^ . - . - . - . - "Saccharomyces cerevisiae promoter database" . - . - "chebi" . - "ogsf" . - . - . - . - . - "https://cropontology.org/term/$1:$2" . - . - . - . - . - . - . - "protein" . - . - . - "http://purl.obolibrary.org/obo/PAO_"^^ . - . - "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:"^^ . - . - "http://xmlns.com/foaf/0.1/"^^ . - . - . - "biology" . - . - "Cancer Data Standards Registry and Repository" . - . - . - "Ontology of units of Measure" . - . - . - . - "http://foodb.ca/compounds/"^^ . - "false"^^ . - . - . - "molecular biology" . - "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . - . - . - "Fossilworks Taxon" . - "^RCV\\d+(\\.\\d+)?$"^^ . - "NIF Standard Ontology" . - "protein families" . - "DIP-743N"^^ . - . - . - "MCDS_L_0000000001"^^ . - . - "addexbio" . - . - "http://www.bootstrep.eu/ontology/GRO#"^^ . - "^\\d{8}$"^^ . - "developmental biology" . - "anatomy" . - "https://neurovault.org/images/$1"^^ . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "0000005"^^ . - . - . - . - . - . - . - . - . - . - "http://ctdbase.org/detail.go?type=disease&db=MESH&acc="^^ . - . - . - . - "GWAS Central Marker" . - . - . - . - . - . - . - . - "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . - "https://cropontology.org/rdf/CO_360:"^^ . + "OMA Group" . + "http://rebase.neb.com/rebase/enz/$1.html"^^ . + . + "bibliometrics" . + . + "Metabolomics Workbench Project" . + . + . + "BEI_Resources" . + . + . + "UK Provider Reference Number" . + . + . + "obo" . + . + . + "http://cutdb.burnham.org/relation/show/"^^ . + . + . + "stefan.kuhn@dmu.ac.uk" . + "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . + . + . + . + "life science" . + . + . + . + "immunology" . + "emmo.cif" . +_:N2c2c85a20d454e07a2737aeb48617251 "Crop Ontology Helpdesk" . + "true"^^ . + "Cell line collections (Providers)"^^ . + . + "0000108"^^ . + . + . + "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23$1"^^ . + "en-GB"^^ . + . + "http://purl.uniprot.org/isoforms/"^^ . + "true"^^ . + . + "false"^^ . + . + "obo" . + . + . + . + . + . + "false"^^ . + "Web Annotation Ontology" . + "^\\d+\\w?$"^^ . + . + . + . + . + "genomics" . + "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id="^^ . + . + . + "BOLD Systems taxon" . + . + . + . + "dbprobe" . + . + . + "psdo" . + . + "^\\d+$"^^ . + "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."^^ . + . + "https://nanbyodata.jp/disease/NANDO:"^^ . + . + . + . + . + . + "EDDA Study Designs Taxonomy" . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://sorgerlab.github.io/famplex/"^^ . + . + . + "1178"^^ . + "Bio-Pesticides DataBase" . + . + "ontology" . + . + . + "rdo" . + . + . + "ontology" . + "plant anatomy" . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/UBERON_"^^ . + . + "0000004"^^ . + . + . + . + "https://mmp.sfb.uit.no/databases/marcat/#/records/$1"^^ . + "NPC139585"^^ . + "false"^^ . + "FxnI151FMs"^^ . + . + . + "00000098"^^ . + . + . + . + "http://www.gramene.org/db/literature/pub_search?ref_id="^^ . + . + . + . + "protein" . + . + . + . + . + . + "structure" . + . + "EDAM Topic" . + . + . + "SNOMEDCT_US_2023_02_28" . + . + . + . + "MarDB" . + "genomics" . + "false"^^ . + . + . + . + "https://scicrunch.org/resolver/RRID:BCBC_"^^ . + . + . + . + "Anatomical Therapeutic Chemical Vetinary" . + . + "ontology" . + . + "latitude"^^ . + . + . + "biomedical science" . + . + "uniprot.arba" . + . + . + "NCI Pathway Interaction Database: Pathway" . + "reactions" . + "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId="^^ . + . + "cell" . + . + . + . + . + . + "life science" . + . + . + . + . + . + . + . + "vsmo" . + "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]"^^ . + . + . + "ontology" . + . + "The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products."^^ . + . + "mirbase.mature" . + . + "agriculture" . + . "2h6o"^^ . - "false"^^ . - . - "obo" . - . - "phenomics" . - . - . - "false"^^ . - . - "^\\d+$"^^ . - "classification" . - . - . - . - "REACT" . - "A0A009E7X8"^^ . - "ontology" . - "phenotype" . - . - . - . - "^\\d{7}$"^^ . - . - . - "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."^^ . - . - . - "https://bioregistry.io/mesh.2012:"^^ . - . - . - . - "chemical" . - "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . - . - . - . - "WikiGenes is a collaborative knowledge resource for the life sciences, which is based on the general wiki idea but employs specifically developed technology to serve as a rigorous scientific tool. The rationale behind WikiGenes is to provide a platform for the scientific community to collect, communicate and evaluate knowledge about genes, chemicals, diseases and other biomedical concepts in a bottom-up process."^^ . - "ohpi" . - "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . - "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."^^ . - . - "gene expression" . - "Hathi Trust Digital Library" . - "431472"^^ . - . - . - . - . - . - . - . - . - "OpenCitations Corpus" . - "chemistry" . - . - . - . - . - "Korean Cell Line Bank" . - . - . - . + "^[a-z]+(\\-[a-z]+)*$"^^ . + . + . + "cmo" . + . + "LTS0004651"^^ . + "sequence" . + . + . + . + . + . + "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec="^^ . + . + . + "https://bioregistry.io/ecoliwiki:"^^ . + "obo" . + . + . + "kegg.ligand" . + . + . + . + . + . + "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OMP_$1"^^ . + . + "ontology" . + "uniprot.db" . + . + "oostt" . + "ontology" . + . + . + . + . + "go.chebi" . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + "International Classification of Diseases, 10th Revision" . + "FBbt_root" . + . + . + . + "0000000"^^ . + "http://purl.obolibrary.org/obo/TRANS_"^^ . + "^[A-Z0-9]+$"^^ . + . + . + . + . + . + "preclinical studies" . + "kegg.disease" . + "splicenest" . + . + "EDAM Ontology" . + . + "http://purl.bioontology.org/ontology/IDODEN_$1"^^ . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "asrp" . + "identifier for an academic research group issued by the CNRS"^^ . + "^\\w+(\\.)?(\\d+)?$"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "peff" . + . + "Surjeet Kumar Arya" . + . + . + "Akt_PKB"^^ . + "activityBoundOf"^^ . + "Circular double stranded DNA sequences composed" . + . + . + . + . + . + "computer science" . + "https://web.www.healthdatagateway.org/dataset/"^^ . + . + . + _:N1f59a2d28185438fb66eb0dc254d8402 . + . + . + . + . + . + . + . + . + . + . + "vendor" . + "false"^^ . + "KEGG Compound" . + "DataCite Ontology" . + . + . + . + "glyconavi" . + "https://knowledge.lonza.com/cell?id=$1"^^ . + "cco" . + . + "^(FBvd|XtroDO|HsapDO|MmusDO)\\:\\d+$"^^ . + . + . + "^\\d+$"^^ . + "https://ngdc.cncb.ac.cn/idog/breed/getBreedDetail.action?breedId=$1"^^ . + . + . + . + "Developing Mouse Brain Atlas" . + . + . + . + . + . + "ontology" . + . + . + . + . + . + . + "ero" . + . + . + . + . + . + . + "biomedical science" . + . + "metagenomics" . + . + . + . + . + . + . + . + "false"^^ . + . + "scomp" . + "pathbank" . + "false"^^ . + . + . + "^\\d+$"^^ . + . + "life science" . + . + . + "transcriptomics" . + . + . + . + . + . + "nlx.mol" . + . + . + . + . + "0005"^^ . + . + . + . + "TP53"^^ . + . + . + . + . + . + . + "^((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])?))$"^^ . + . + "https://www.phenxtoolkit.org/protocols/view/$1"^^ . + . + . + "The Simple Knowledge Organization System (SKOS) is a common data model for sharing and linking knowledge organization systems via the Semantic Web. SKOS-XL defines an extension for the Simple Knowledge Organization System, providing additional support for describing and linking lexical entities.This document provides a brief description of the SKOS-XL vocabulary."^^ . + . + "false"^^ . + "foodb.compound" . + "^\\d+$"^^ . + "The International Classification of Functioning, Disability and Health, known more commonly as ICF, is a classification of health and health-related domains. As the functioning and disability of an individual occurs in a context, ICF also includes a list of environmental factors. ICF is the WHO framework for measuring health and disability at both individual and population levels."^^ . + "The Vaccine Ontology (VO) is a community-based biomedical ontology in the domain of vaccine and vaccination. VO aims to standardize vaccine types and annotations, integrate various vaccine data, and support computer-assisted reasoning. The 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."^^ . + . + . + . + "obo" . + . + . + . + . + "taxonomy" . + . + . + . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources"^^ . + "http://www.pharmgkb.org/gene/$1"^^ . + . + "https://www.ebi.ac.uk/arrayexpress/experiments/"^^ . + "^\\d+$"^^ . + . + . + . + . + "Alberto Traverso" . + . + "The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2)."^^ . + . + "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]"^^ . + . + . + "http://www.w3.org/XML/1998/namespace#$1"^^ . + . + "ChEBI" . + "https://www.eionet.europa.eu/gemet/en/concept/"^^ . + . + . + . + . + . + "Vocabulary of Interlinked Datasets" . + . + "SNOMEDCT_US_2020_09_01" . + "https://www.ebi.ac.uk/ega/studies/$1"^^ . + . + "http://www.peptideatlas.org/PASS/"^^ . + . + . + . + . + "Data Catalog" . + . + . + . + . + . + "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."^^ . + . + . + "19803"^^ . + . + . + "false"^^ . + "TTD Drug" . + . + . + . + "IUPHAR family" . + . + . + . + . + "protein" . + "Epidemiology Ontology" . + . + . + "https://sorgerlab.github.io/famplex/$1"^^ . + . + "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://www.kegg.jp/entry/$1"^^ . + . + "oid" . + . + . + "ontology" . + . + . + "Genitourinary Development Molecular Anatomy Project" . + . + "MGYA00002270"^^ . + . + . + "Protein modification" . + "subject agnostic" . + "BacMap Map" . + "cabri" . + . +_:Nf61f2d7c1ff54380bf84884a9c9d8f51 "Anita Ghebeles" . + "MNXC15"^^ . + . + . + . + . + "stefanie.seltmann@ibmt.fraunhofer.de" . + "http://purl.obolibrary.org/obo/FLOPO_$1"^^ . + . + "SNOMEDCT_US_2016_03_01" . + . + . + . + "An ontology to support disciplinary annotation of Arctic Data Center datasets."^^ . + "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . + . + "https://cropontology.org/rdf/CO_322:$1"^^ . + . + . + "true"^^ . + . + "false"^^ . + . + "life science" . + . + . + "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name=$1"^^ . + . + . + . + "^\\d{7}$"^^ . + "^r3d\\d{9,9}$"^^ . + . + . + . + . + . + . + . + "function" . + "co_326" . + . + . + . +_:Nce56519a74584e27bab9646e3c0efa5e "vladimir.n.mironov@gmail.com" . + . + . + "obo" . + . + "Mammalian Feeding Muscle Ontology" . + . + "Developmental stages of the Zebrafish"^^ . + . + "nxr" . + . + . + . + "ontology" . + . + . + "anatomy" . + "Deepak Unni" . + . + . + . + "pancreatic islet development" . + . + "90801"^^ . + . + "false"^^ . + . + "population genetics" . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_"^^ . + . + . + "https://bioregistry.io/$1:$2" . + . + . + "https://viralzone.expasy.org/$1"^^ . + "Michael Baudis" . + . + . + . + "chemical" . + "0000066"^^ . + . + . + "00056"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "https://github.com/semanticchemistry/semanticchemistry" . + . + . + . + "Oryzabase Reference" . + . + . + "https://units-of-measurement.org/"^^ . + . + . + "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0=$1"^^ . + "molecule" . + "^\\w+$"^^ . + . + "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/$1"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/nuccore/$1"^^ . + "kegg.enzyme" . + . + . + . + "false"^^ . + . + . + . + . + "A vocabulary for annotating vocabulary descriptions" . + . + "chemdb" . + "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . + . + . + . + "false"^^ . + . + "support@bioontology.org" . + . + "90801"^^ . + "^[A-Z]+[A-Z-0-9]{2,}$"^^ . + . . - . - . - . - . - . - . - "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR)."^^ . - . - . - . - "pubchem.classification" . - . - . - . - "ontology" . - . - . - . - . - "^\\d{7}$"^^ . - . - . - . - "gene" . - . - . - "10.1038/s41597-022-01807-3"^^ . - . - "mihail.anton@chalmers.se" . - . - "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . - . - "false"^^ . - . - . - "false"^^ . - "orphanet.ordo" . - . - . - . - . - . - . - "experiment" . - . - "knowledge and information systems" . - "An ontology for mouse anatomy covering embryonic development and postnatal stages."^^ . - . - . - . - . - "^\\w+$"^^ . - . - "PNS12@cam.ac.uk" . - . - . - . - . - . - "NMRShiftDB structure" . - "Computational Chemistry Ontology" . - "Draft version"^^ . - "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."^^ . - "authoredBy"^^ . - "skos" . - . - "obo" . - . - . - . - . - "http://scop.berkeley.edu/sccs=$1"^^ . - "dc" . - . - "arrayMap is a collection of pre-processed oncogenomic array data sets and CNA (somatic copy number aberrations) profiles. CNA are a type of mutation commonly found in cancer genomes. arrayMap data is assembled from public repositories and supplemented with additional sources, using custom curation pipelines. This information has been mapped to multiple editions of the reference human genome."^^ . - "^\\d+$"^^ . - . - . - "inaturalist.observation" . - "NIF Standard Ontology: Organisms" . - . - "bel" . - . - . - "gene" . - . - "Carbohydrate Active EnZYmes" . - "chebi" . - . - . - "edam.topic" . - "assetConcepts"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - "46946"^^ . - . - . - "metabolite" . -_:N824a8517c4d74a26874edd72d326307f "Michelle Futornick" . - "tRNA Gene Database" . - . - "cell_biolabs" . - "false"^^ . - "biodiversity" . - "NLXCHEM covers chemicals. Most classes are also in ChEBI."^^ . - "false"^^ . - . - . - . - "intact.molecule" . - . - "Rat Genome Database strain" . - . - "biochemistry" . - . - . - . - . - . - "omp" . - "VMH Gene" . - "728"^^ . - "medicinal chemistry" . - . - . - . - . - . - . - . - . - . - . - "http://lipidbank.jp/cgi-bin/detail.cgi?id="^^ . - . - "biomedical science" . - . - "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."^^ . - . - . - "false"^^ . - "http://www.oid-info.com/get/2.16.840.1.113883.6" . - . - . - "SCTID_2010_1_31" . - "http://www.crop2ml.org/cropmdb/"^^ . - "false"^^ . - . - . - . - . - . - "genomics" . - . - "^PASS\\d{5}$"^^ . - . - . - . - "isfinder" . - "50885"^^ . - . - "http://www.bootstrep.eu/ontology/GRO#$1"^^ . - . - "https://www.fao.org/fishery/en/species/"^^ . - . - . - "model organism database" . - "UniProt Protein" . - . - . - "CALM1"^^ . - . - "sheeba.samuel@uni-jena.de" . - . - . - "http://purl.obolibrary.org/obo/YPO_"^^ . - "terms4FAIRskills" . - . + . + "EOL Secretariat" . +_:N8250527cbee1453c9f2a02a7ba72613f "maria.herrero@kcl.ac.uk" . + . + . + . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "sheriff@ebi.ac.uk" . + . + "virology" . + . + . + "https://www.aapc.com/codes/cpt-codes/"^^ . + "ontology" . + . + . + . + . + "A repository for high-quality gene models produced by the manual annotation of vertebrate genomes."^^ . + . + "k-12 teacher" . + . + "classyfire" . + . + . +_:N4fc383ac4b554144bf3019945d5dcd7d "adw_geeks@umich.edu" . + . + . + . + "Agronomy Ontology" . + . + "genetics" . + . + "^\\d+$"^^ . + "Mammalian Phenotype Ontology" . + "structure" . + "natural science" . + . + . + "jwest@rcsb.rutgers.edu" . + "100810"^^ . + "The VirOligo database (1) is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place."^^ . + . + "obo" . + "^PD\\d{6}$"^^ . + "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."^^ . + "98346"^^ . + "https://cropontology.org/rdf/CO_341:"^^ . + . + "dicom" . + . + "mdm" . + . + "Human Pluripotent Stem Cell Registry" . + "repository" . + . + . + "teddy" . + . + . + . + "Adrien Rougny" . + . + "^\\d+$"^^ . + "semapv" . + . + . + . + . + . + "265912"^^ . + "inchi" . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . . - . - . - "gene" . - "01027931310-01022252312"^^ . - "^\\d{7}$"^^ . - . - . - "207LH0002X"^^ . - . - . + . + . + "wasila.dahdul@usd.edu" . + . + . + . + "rexo" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + "structure" . + "http://purl.obolibrary.org/obo/CRO_$1"^^ . + . + . + . + "https://scicrunch.org/resolver/RRID:NXR_$1"^^ . + "WOrfDB (Worm ORFeome DataBase) contains data from the cloning of complete set of predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans. This collection describes experimentally defined transcript structures of unverified genes through RACE (Rapid Amplification of cDNA Ends)."^^ . + "^PTN\\d{9}$"^^ . + . + "false"^^ . + . + . + . + . + . + "A controlled vocabulary to support the study of transcription in the developing human brain"^^ . + . + . + . + . + "http://www.fungalbarcoding.org/BioloMICS.aspx?Table=Fungal barcodes&Rec=$1&Fields=All&ExactMatch=T"^^ . + . + . + . + "^GCST\\d{6}\\d*$"^^ . + . + . + "ontology" . + "ATCC number" . + . + . + . + . + . + . + "false"^^ . + . + "px" . + "wormpep" . + "has responsible" . + . + . + . + . + "MGgn0008978"^^ . + "1001"^^ . + "^LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4,6})?$"^^ . + "ordo" . + "^\\d+$"^^ . + . + "Website with general information about Arabidopsis and functionalities such as a genomic viewer"^^ . + "Mike Tyers" . + . + "http://www.informatics.jax.org/accession/MGI:$1"^^ . + . + "life science" . + "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."^^ . + . + "false"^^ . + . + "rnacentral" . + . + . + . + . + . + . + "The allele registry provides and maintains identifiers for genetic variants"^^ . + "The Clinical Research Information Service (CRIS) is a non-profit online registration system for clinical trials (researches) to be conducted in Korea. It has been established at the Korea Disease Control and Prevention Agency (KDCA) with support from the Ministry of Health and Welfare (MOHW). It joined the WHO International Clinical Trials Registry Platform (ICTRP) as 11th member of Primary Registry. (from about page)\nNote that the web page that resolves this trial does not correspond to the semantic space"^^ . + . + "http://ctdbase.org/detail.go?type=chem&acc=$1"^^ . + . + "silvio.tosatto@unipd.it" . + . + . + . + . + . + . + . + "^ACTRN\\d+$"^^ . + . + "cjmungall@lbl.gov" . + "schema" . + "^\\d+$"^^ . + . + "biology" . +_:Naf53a37095d24e73886a30c68eaa336f "hajo.rijgersberg@wur.nl" . + . + "Zebrafish developmental stages ontology" . + . + . + . + . + . + "Encyclopedia of DNA Elements" . + "http://purl.obolibrary.org/obo/VariO_"^^ . + . + . + . + "ontology" . + "genomics" . + "Metadata terms maintained by the Dublin Core Metadata Initiative, including properties, vocabulary encoding schemes, syntax encoding schemes, and classes.\n\n**Deprecation Notice**: While the `/elements/1.1/` namespace will be supported indefinitely, DCMI gently encourages use of the `/terms/` namespace (i.e., `dcterms`) ([source](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3))."^^ . + "GLDS-141"^^ . + . + . + . + "false"^^ . + . + . + "life science" . + . + . + . + "chemical" . + . + . + . + . + . + . + . + "pencehe@oneonta.edu" . + "false"^^ . + "icldb" . + "pazar" . + . + . + . + . + . + "ogi" . + "small molecule" . + . + . + . + . + "biomedical science" . + . "https://bioregistry.io/hssp:"^^ . - . - . - "Ctibor Škuta" . - . - . - . - "pharmgkb.gene" . - "http://www.arachnoserver.org/toxincard.html?id="^^ . - . - "KEGG Reaction" . - . - . - . - . - . - . - . - . - . - . - . - "RSC3"^^ . - . - "spider" . - "iceberg.ice" . - . - . - . - "2GC4"^^ . - . - . - . - . - "false"^^ . - "ontology" . - . - . - "tumor" . - . - . - . - . - . - "The COVID-19 epidemiology and monitoring ontology" . - . - . - "obo" . - . - . - "http://purl.obolibrary.org/obo/MAT_$1"^^ . - "endocrinology" . - "CryptoDB" . - "https://cropontology.org/rdf/CO_343:"^^ . - . - . - . - . - "doco" . - "ricenetdb.compound" . - . - "medgen" . - "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . - . - "pharmacology" . - . - . - . - . - . - "apd" . - . - . - "genetics" . - . - "reactions" . - . - . - "https://bioregistry.io/resolve/github/pull/$1"^^ . - "false"^^ . - "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."^^ . - . - . - . - "https://www.atcc.org/products/"^^ . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id="^^ . - "https://www.ebi.ac.uk/gwas/studies/$1"^^ . - . - . - "MeSH 2013" . - "omo" . - "hathitrust" . - . - "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources."^^ . - "computational biology" . - "false"^^ . - "genes" . - . - . - "gene" . - "551115"^^ . - . - . - . - . - . - . - "2A"^^ . - . - "The purpose of the OMIT ontology is to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists (cell biologists in particular) and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of important roles performed by miRs in humans' various diseases and biological processes (usually through miRs' respective target genes)."^^ . - . - . - "TubercuList knowledge base" . - . - "false"^^ . - . - . - "^\\d{7}$"^^ . - "Molecule role (INOH Protein name/family name ontology)" . - . - . - . - . - . - . - "SNOMEDCT_2020_03_01" . - . - "http://purl.obolibrary.org/obo/MA_$1"^^ . - . + "^\\w+$"^^ . + . + "ClinVar Submitter" . + "http://purl.obolibrary.org/obo/TAXRANK_"^^ . + "false"^^ . + . + . + "Yongqun Oliver He" . + . + "false"^^ . + "Maize gross anatomy"^^ . + . + . + "^IS\\w+(\\-\\d)?$"^^ . + . + . + . + "Molecular Modeling Database" . + . + . + "E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations.It provides concise mappings of mathematical models to a formalised consortium-agreed biochemical description, with the aim of connecting the world of biological knowledge with benefits of mathematical description of dynamic processes. This collection references entities."^^ . + . + . + "https://w3id.org/oc/oci/"^^ . + . + . + . + "true"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + . + "cob" . + . + "Compluyeast-2D-DB is a two-dimensional polyacrylamide gel electrophoresis federated database. This collection references a subset of Uniprot, and contains general information about the protein record."^^ . + . + "Vital Sign Ontology" . + . + "false"^^ . + . + "Health Canada Natural Product Number" . + "structure" . + . + . + . + . + "http://purl.obolibrary.org/obo/HsapDv_"^^ . + . + "^[0-9]+$"^^ . + . + "cpga" . + . + . + "life science" . + . + "0107180"^^ . + "https://vectorbase.org/gene/$1"^^ . + "Yeast Genome Order Browser" . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "Reaxys eMolecules" . + . + . + "preclinical studies" . + "epidemiology" . + . + . + . + . + . + "^\\d+$"^^ . + "insdc.cds" . + "autdb" . + . + . + . + "microbiology" . + "false"^^ . + "false"^^ . + "https://purl.dataone.org/odo/MOSAIC_"^^ . + "http://purl.obolibrary.org/obo/MAXO_"^^ . + "biomedical science" . + "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . + "https://www.datanator.info/gene/$1"^^ . + . + "cultured cell" . + . + . + "environmental science" . + . + . + "ECTO describes exposures to experimental treatments of plants and model organisms (e.g. exposures to modification of diet, lighting levels, temperature); exposures of humans or any other organisms to stressors through a variety of routes, for purposes of public health, environmental monitoring etc, stimuli, natural and experimental, any kind of environmental condition or change in condition that can be experienced by an organism or population of organisms on earth. The scope is very general and can include for example plant treatment regimens, as well as human clinical exposures (although these may better be handled by a more specialized ontology)."^^ . + . + "knowledge and information systems" . + . + . + . + _:N4fc383ac4b554144bf3019945d5dcd7d . + "Sergio José Rodríguez Méndez" . + . + "09200010"^^ . + "https://aopwiki.org/relationships/"^^ . "Protein Interaction Network Analysis" . - . - "^PM\\d{7}$"^^ . - . - "Gene Wiki" . - "smtifahim@gmail.com" . - "false"^^ . - . - . - "^\\d{6}$"^^ . - "true"^^ . - . - "FlyBase" . - . - . - . - . - . - "Environment Ontology for Livestock" . - . + . + . + . + . + . + . + . + "has resource example" . + "http://exac.broadinstitute.org/gene/"^^ . + . + "c"^^ . + . + "E-cyanobacterium Experimental Data" . + . + "https://www.storedb.org/?STOREDB:DATASET"^^ . + . + . + . + . + . + "life science" . + "genomics" . + . + . + "protein" . + . + "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system."^^ . + "^tgv[0-9]+$"^^ . + "Nicole Vasilevsky" . + "matthias.samwald@meduniwien.ac.at" . + . + . + . + "An initiative to empower the research community to harness microbiome data exploration and discovery through a collaborative integrative data science ecosystem."^^ . + . + . + "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + . + "https://civicdb.org/links/gene/"^^ . + . + "odc.tbi" . + "false"^^ . + . + . + . + . + . + "https://www.animalgenome.org/CorrDB/q/?id=CorrID:"^^ . + . + . + "https://pb.apf.edu.au/phenbank/strain.html?id="^^ . + . + . + . + . + . + . + "false"^^ . + . + . + "SNR17A"^^ . +_:N7ddd4d39a93142dfb150e76ca0925d12 "pbrooks@hcfa.gov" . + . + "GFAM" . + . + . + "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."^^ . + . + . + "Illumina probe identifiers for microarrays, such as those in Illumina HumanRef-6 v2.0 expression beadchip."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "ndfrt" . + . + . + "false"^^ . + . + "structure" . + . + . + . + . + . + . + "Tobias Schulze" . + . + . + . + . + "https://pypi.org/project/"^^ . + "innatedb" . + . + "small molecule" . + . + . + . + . + . + "http://ardb.cbcb.umd.edu/cgi/search.cgi?db=L&field=ni&term=$1"^^ . + . + . + "environmental science" . + "fungorum" . + "false"^^ . + . + . + . + . + "ribocenter" . + . + "isrctn" . + . + . + . + . + . + . + "Geographical Entity Ontology" . + . + "Leigh.Carmody@jax.org" . + . + . + . + . + _:N200f6d51d8c24db9957971f3242ad505 . + . + . + . + . + "Cell line collections (Providers)"^^ . + . + . + "^rxn\\d+$"^^ . + . + "dna" . + "https://repeatsdb.org/protein/"^^ . + . + . + . + . + . . - "ttd.drug" . - . - . - "fcb" . - . - . - . - . - . - "http://purl.bioontology.org/ontology/IDODEN_$1"^^ . - "http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2" . - . - . - . - "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . - . - . - . - "ICD9_2005" . - . - "http://tolweb.org/"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "aspgd.protein" . - . - . - . - . - "false"^^ . - "https://mged.sourceforge.net/ontologies/MGEDontology.php#"^^ . - . - . - . - . - "stock" . - . - . - . - "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."^^ . - . - . - . - "merops.family" . - . - "http://www.cellsignal.com/reference/pathway/$1.html"^^ . - . - "http://purl.org/spar/bido/$1"^^ . - "International Protein Index" . - . - . - "williams.antony@epa.gov" . - . - . - "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/$1"^^ . - . - . - . - "Assists in resolving data across cloud resources."^^ . - "PS00001"^^ . - "022586"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/FIX_$1"^^ . - . - "anne.morgat@sib.swiss" . - . - . - . - . - "immunology" . - . - . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "bcbc" . - . - . - "false"^^ . - . - . - "false"^^ . - . - "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . - "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."^^ . - . - "subject agnostic" . - "scdo" . - "https://bioregistry.io/cmecs:"^^ . - "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . - "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."^^ . - . + . + "omics" . + . + . + . + . + "http://purl.obolibrary.org/obo/ZECO_"^^ . + . + . + "ohpi" . + . + "Christine.Pourcel@u-psud.fr" . + . + . + "Arabidopsis Small RNA Project" . + . + . + . + "https://cordis.europa.eu/article/id/"^^ . + . + . + . + "LL379-9"^^ . + . + . + "unii" . + "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . + . + . + . + . + . + . + "bioinformatics" . + . + . + "Rat Resource and Research Center" . + . + "http://vocabularies.bridgedb.org/ops#"^^ . + "long-finned-pilot-whale"^^ . + "Identifier for an entity in open tree of life"^^ . + . + "liumeng94@sjtu.edu.cn" . + "http://purl.obolibrary.org/obo/BFO_$1"^^ . + "false"^^ . + . + "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . + . + "ontology" . + "Database of structurally defined protein interfaces" . + . + "gene" . + "http://purl.obolibrary.org/obo/MS_"^^ . + . + "nucleotide" . + . + . + . + . + . + . + . + . + . + "gtr" . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + . + . + . + "4544"^^ . + "chemistry" . + "ontology" . + . + "obo" . + . + . + . + "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." . + "ModelDB" . + . + "^\\d{7}$"^^ . + . + . + "HBG004341"^^ . + . + . + . + "PD10000"^^ . + "http://www.xmetdb.org/xmetdb/protocol/"^^ . + "dictybase" . + . + "false"^^ . + . + . + "molbase.sheffield" . + "BioSample" . + . + "fossilworks.journal" . + . + . + "^PRO_[0-9]{10}$"^^ . + . + "false"^^ . + . + . + . + . + "ZINC is not Commercial" . + "protein" . + . + . + . + "UPLOC" . + . + . + . + . + . + "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."^^ . + . + . + . + . + "protocol" . + "mutations" . + "biology" . + . + . + . + "Collection" . + "Erik Segerdell" . + . + . + . + . + "FundRef" . + . + "Martin Ramirez" . + . + . + "false"^^ . + "hoganwr@gmail.com" . + . + "true"^^ . + "true"^^ . + . + "false"^^ . + . + "^\\d+$"^^ . + "A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources" . + . + . "http://purl.obolibrary.org/obo/MP_$1"^^ . - . - "ontology" . - . - "^\\d{7}$"^^ . - . - . - "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog."^^ . - . - . - . - . - "bakerc@unb.ca" . - . - . - "https://ensaiosclinicos.gov.br/rg/$1"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "https://purl.dataone.org/odo/ADCAD_"^^ . - . - . - . - "sed-ml.level-1.version-1"^^ . - "Online Mendelian Inheritance in Animals" . - . - "biomedical science" . - . - "https://morpheus.gitlab.io/models/$1"^^ . - "http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1"^^ . - . - . - . - "data analysis" . - . - . - . - . - . - . - "false"^^ . - "protein" . - "2842"^^ . - "life science" . - "^([CHDEGTMKR]\\d+)|(\\w+:[\\w\\d\\.-]*)|([a-z]{3,5})|(\\w{2,4}\\d{5})$"^^ . - . - . - "GR:0080039"^^ . - . - . - "https://neurovault.org/collections/"^^ . - "model" . - . - . - . - . - "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."^^ . - "obo" . - . - "genome" . + . + . + . + . + "itmctr" . + . + "00000008"^^ . + . + . + . + . + . + . + . + "https://www.discoverx.com/searchproduct?searchtext=$1&searchmode=exact"^^ . + "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid="^^ . + . + . + "agriculture" . + . + "1915"^^ . + "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."^^ . + "http://w3id.org/owlstar/$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.."^^ . + . + . + "http://www.ontobee.org/ontology/$1" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "research" . + . + "Malaria Ontology" . + . + . + "protein" . + . + . + . + "008893080"^^ . + "co_324" . + "data set" . + "FlyBase Qualifiers" . + . + . + . + "plant genetics" . + . + . + "genome" . + "co_322" . + . + . + "GlyTouCan is the single worldwide registry of glycan (carbohydrate sugar chain) data."^^ . + . + . + . + . + "false"^^ . + "JMChandonia@lbl.gov" . + . + "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"^^ . + . + . + "genetics" . + . + "co_370" . + "pfam.clan" . + "https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#"^^ . + . + "cog" . + . + "obo" . + . + "https://bioregistry.io/vsdb:"^^ . + "ontology" . + . + . + . + . + . + . + . + "false"^^ . + . + "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."^^ . + . + . + . + . + . + . + . + "ontology" . + . + . + "^\\w+$"^^ . + . + . + "SCTID" . + . + . + . + "00005254"^^ . + "Josh Moore" . + . + . + "ontology" . + . + . + . + . + "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."^^ . + "false"^^ . + . + . + "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . + . + . + . + . + "dc" . + "false"^^ . + "1.10.10.200"^^ . + "^\\d{4,6}$"^^ . + . + . + . + . + . + "https://biopragmatics.github.io/providers/sdis/"^^ . + . + "EcoCyc" . + . + "l.andres.hernandez.18@student.scu.edu.au" . + . + . + . + . + "false"^^ . + "ontology" . + . + _:N1d66b6d5b1894f27847d3a13cf9a0222 . + "TP53-47"^^ . + . + . + . + . + . + "KEGG GENES is a collection of gene catalogs for all complete genomes and some partial genomes, generated from publicly available resources."^^ . + "raymond@caltech.edu" . + . + "RXCUI" . + . + . + . + . + "http://purl.obolibrary.org/obo/AISM_$1"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_dys_$1"^^ . + . + . + . + "life science" . + "computational biology" . + . + . + "171"^^ . + "false"^^ . + . + "transposon family" . + . + "^\\d+$"^^ . + "enrique.blanco@crg.eu" . + . + . + . + . + "drug" . + "NMR-instrument specific component of metabolomics investigations" . + . + . + . +_:N406478f8588d430e9efe5acde38344ea "Crop Ontology Helpdesk" . + "Mingxun Wang" . + . + . + . + . + "false"^^ . + . +_:Nec73fc3f397b45e4aa2ecdf3bfe3be4c "bioportal" . + . + . + "structure" . + "false"^^ . + "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."^^ . + "^MGYA\\d+$"^^ . + . + . + . + "PubMed" . + "Minimal Information about any Sequence" . + . + . + . + . + . + "anatomy" . + . + "S7000002168151102"^^ . + "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."^^ . + . + . + "ontology" . + . + . + . + "protein" . + "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."^^ . + . + "http://oncotree.mskcc.org/api/tumorTypes/search/code/$1"^^ . + _:Nd0865bd54b1d4b1f9895b1f6281f1800 . . - "false"^^ . - "agriculture" . - . - . - "https://www.ebi.ac.uk/chembl/cell_line_report_card/$1"^^ . - "http://purl.obolibrary.org/obo/LEPAO_"^^ . - . - "http://func.mshri.on.ca/human/genes/list_functional_scores/"^^ . - "^\\d+$"^^ . - . - "false"^^ . - "image" . - "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID="^^ . - "^(Gi|Gc)\\d+$"^^ . - . - . - "ncit" . - . - "ontology" . - "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . - "false"^^ . - . - "duplication" . - . - . - . - "Medical Dictionary for Regulatory Activities Terminology" . - . - . - . - . - "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)."^^ . - . - . - . - "salk" . - . - "chromium"^^ . - . - . - . - . - . - . - . - . - . - . - . - _:N848769ba5c1f4a738b2435e71207d3ee . - . - "false"^^ . - "false"^^ . - . - "https://biopragmatics.github.io/providers/cemo/$1"^^ . - "true"^^ . - . - "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."^^ . - . - . - . - "obo" . - . - . - . - . - _:N930481746a634af6b35ac1a972a4d6a1 . - "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."^^ . - . - "mpio" . - . + . + "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. "^^ . + "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . + . + "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?"^^ . + "Benjamin M. Gyori" . + "enzyme" . + . + "Prefixes useful in annotating documentation provenance." . + "Brassica ontology" . + . + "false"^^ . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=$1"^^ . + "EcoPortal" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CL_$1"^^ . + . + . + . + . + "1784"^^ . + "John Beverly" . + . + "http://www.isni.org/isni/"^^ . + . + "The Diseases Database is a cross-referenced index of human disease, medications, symptoms, signs, abnormal investigation findings etc. This site provides a medical textbook-like index and search portal covering areas including: internal medical disorders, symptoms and signs, congenital and inherited disorders, infectious diseases and organisms, drugs and medications, common haematology and biochemistry investigation abnormalities."^^ . + "Online Mendelian Inheritance in Man" . + "vaccine" . + "^\\d(\\d|\\w)$"^^ . + . + . + . + . + "zp" . + . + "10153"^^ . + "false"^^ . + . + . + . + . + . + "false"^^ . + "regulation" . + "The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes."^^ . + . + "cell regeneration" . + . + . + . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ega/studies/"^^ . + . + "0003"^^ . + . + "lter" . + "http://autism.mindspec.org/GeneDetail/"^^ . + "https://genelab-data.ndc.nasa.gov/genelab/accession/"^^ . + . + . + "botany" . + "agriculture" . + . + . + . + . + "ENVO" . + . + . + "3"^^ . + . + "subject agnostic" . + . + . + "^([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])$"^^ . + . + . + . + . + . + . + "gene" . + "false"^^ . + . + . + "UniRef" . + "^DRKS\\d+$"^^ . + "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . + "knockout" . + . + "An organization" . + . + . + . + . + . + . + "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://purl.bioontology.org/ontology/npo#NPO_$1"^^ . + "false"^^ . + . + "^[A-Z0-9]+$"^^ . + "Samuel Friedman" . + "rscheuermann@jcvi.org" . + . + "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."^^ . + "http://www.weizmann.ac.il/molgen/loqate/gene/view/"^^ . + . + . + . + . + . + . + . + . + . + . + "^ACH-\\d+$"^^ . + "Information Artifact Ontology" . + "ontology" . + . + "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"^^ . + "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://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId=$1"^^ . + "Life cycle stages for Medaka"^^ . + . + . + "^\\w+$"^^ . + . + . + "^\\w{2,4}\\d{5}$"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "Jason E. Stajich" . + . + . + . + "Ontology of Precision Medicine and Investigation" . + . + "small molecule" . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "SABIO-RK Compound" . + . + . + "expression" . + . + . + . + . + . + . + . + . + . + . + "Elspeth Bruford" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "safisher@upenn.edu" . + "orth" . + . + "ontology" . + "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=$1"^^ . + "http://xmlns.com/foaf/0.1/$1"^^ . + . + . + "https://mednet-communities.net/inn/db/ViewINN.aspx?i="^^ . + "http://purl.obolibrary.org/obo/FIDEO_"^^ . + . + . + "A high level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc) and their associations."^^ . + "false"^^ . + . + . + "dailymed" . + . + . + . + . + "linkml" . + . + "https://www.uniprot.org/tissues/$1"^^ . + . + . + . + "false"^^ . + . + "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp=$1"^^ . + . + . + . + . + . + "^\\w+$"^^ . + "^[a-zA-Z0-9_\\.]+$"^^ . + "Metabolome Express" . + . + "obo" . + . + . + . + "^[a-zA-Z0-9 +#'*]+$"^^ . + . + "false"^^ . + . + . + "neuroscience" . + . + "Genomic Data Commons Data Portal" . + . + . + . + . + . + "BioModels Database" . + "ruili.huang@nih.gov" . + . + . + . + "true"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://www.crop2ml.org/cropmdb/$1"^^ . + . + . + . + . + . + . + . + "nutritional science" . + . + "sider.effect" . + "SIDM01262"^^ . + . + . + "dna" . + . + . + . + . + . + . + . + "bioactivities" . + . + "^\\d{7}$"^^ . + "NXP" . + . + . + . + . + . + . + . + "rrid" . + "Philippe.Lemercier@sib.swiss" . + . + "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."^^ . + . + "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name="^^ . + . + . + "structure" . + . + "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."^^ . + "atcvet" . + . + . + . + . + . + . + . + . + "enzyme" . + . + . + . + . + "ontology" . + "pco" . + "classification" . + "ontology" . + "https://bioregistry.io/metaregistry/go/"^^ . + "NOR00681"^^ . + "false"^^ . + . + . + . + "ALA"^^ . + . + . + . + . + . + "ontology" . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to protein sequence information."^^ . + "cell" . + . + . + . + . + . + "4DN" . + . + . + "false"^^ . + . + "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . + . + "cosmic" . + "InterPro" . + "rbrinkman@bccrc.ca" . + . + . + . + "The data presented here is a result of systematically tracking the localization and abundance of 5330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2 and nitrogen starvation) using the GFP-tagged yeast library"^^ . + "https://www.nsf.gov/awardsearch/showAward?AWD_ID="^^ . + "false"^^ . + "DOULIX lab-tested standard biological parts, in this case linear double stranded DNA sequences."^^ . + . + "Dr Paul Schofield" . + "http://arabidopsis.org/servlets/TairObject?accession=AASequence:"^^ . + "genome" . + . + "Adriano Rutz" . + . + . + "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."^^ . + . + . + . + . + . + . + . + "http://www.gramene.org/db/literature/pub_search?ref_id=$1"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "Gwen Frishkoff" . + . + "uniref" . + . + "ontology" . + . + "dna" . + "chembank" . + "ontology" . + "https://www.hivreagentprogram.org/Catalog/HRPCellLines/$1.aspx"^^ . + "epio" . + "1433C_TOBAC_1_252"^^ . + "false"^^ . + . + . + "http://tuberculist.epfl.ch/quicksearch.php?gene+name="^^ . + . + . + . + "biomedical science" . + . + . + . + "false"^^ . + "xpo" . + "jRCTs041220087"^^ . + . + . + . + "http://purl.obolibrary.org/obo/LPT_"^^ . + "0000011"^^ . + "pathway" . + "ontology" . + . + "MoleculeRole Ontology is an ontology for proteins/chemicals. It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data."^^ . + . + . + "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/KISAO_$1"^^ . + "Genomic Epidemiology Ontology" . + "The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data."^^ . + "ecogene" . + . + . + . + . + "1398574"^^ . + . + "http://purl.obolibrary.org/obo/CLAO_"^^ . + "https://rrid.site" . + . + "^\\d+$"^^ . + "Protein Affinity Reagents" . + . + "has responsible" . + "false"^^ . + "pharmacology" . + . + . + . + "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)"^^ . + . + . + . + "ontology" . + . + "Drug Central" . + . + . + "^\\d+$"^^ . + "false"^^ . + "Legacy site for IETF RFC proposals"^^ . + . + . + "Stian Soiland-Reyes" . + "Draft version"^^ . + . + "fma" . + "fish" . + "^\\d+$"^^ . + . + . + . + "Michael Y Galperin" . + . + . + . + . + . + "cell biology" . + . + . + "metabolomics" . + . + "pathway" . + "ILMN_129894"^^ . + "https://purl.dataone.org/odo/SASAP_$1"^^ . + "OMA Protein" . + . + "MIMIC III Database" . + "enzyme" . + "Banco de Celulas do Rio de Janeiro" . + "identifier for a source/publication venue (journal, conference, etc) in Scopus"^^ . + . + . + . + . + . + . + "^\\w\\d+$"^^ . + "obo" . + . + "cryptodb" . + "false"^^ . +_:N1902992fefc74b64a0200f6ba3d98584 "cs@firstdatabank.com" . + . + . + . + . + . + "https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN="^^ . + . + . + . + . + "protein" . + . + "anatomy" . + . + . + . + "BAO" . + "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."^^ . + . + . + "Performance Summary Display Ontology" . + "false"^^ . + "6819"^^ . + . + . + . + . + "ontology" . + "http://purl.obolibrary.org/obo/EHDAA_"^^ . + "metacyc.reaction" . + "https://www.cancerrxgene.org/translation/Drug/$1"^^ . + . + "http://pepbank.mgh.harvard.edu/interactions/details/$1"^^ . + "Organism supplier which collects Drosophila stocks from laboratories all over the world, maintains them, and provides them to researchers upon request. [from RRID]"^^ . + . + . + . + . + "md.tyers@umontreal.ca" . + . + . + . + "discoverx" . + "^[a-zA-Z0-9-_]+$"^^ . + . + . + "ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "Fyler" . + "https://www.ncbi.nlm.nih.gov/books/"^^ . + "OSR0818"^^ . + "ucum" . + "do" . + . + . + "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."^^ . + . + . + . + . + "^NCT\\d{8}$"^^ . + "The EOL ontology describes environmental conditions of livestock farms. More specifically, it describes the feeding modalities, the environment, the structure of livestock farms and rearing systems."^^ . . - . - . - . - . - "14362"^^ . - . - . - . - . - "life science" . - . - . - "^[a-zA-Z0-9 +#'*]+$"^^ . - . - . - "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr="^^ . - . - . - . - . - "nemo2" . - . - . - . - . - "void" . - . - . - . - . - . - . - "http://www.drugbank.ca/drugs/$1"^^ . - . - "^(ZINC)?\\d+$"^^ . - . - . - . - . - . - . - "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . - . - "subject agnostic" . - . - "plant breeding" . - "bioregistry.registry" . - "ontology" . - . - "life science" . - . - . - "embryonic stem cell line" . - . - . - . - . - . - . - "Bitbucket" . - . - . - "hpiwowar@gmail.com" . - . - . - . - "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName="^^ . - "false"^^ . - . - . - "http://www.probonto.org/ontology#PROB_$1"^^ . - . - . -_:N930481746a634af6b35ac1a972a4d6a1 "radlex-feedback@lists.rsna.org" . - . - . - "C063233"^^ . - . - . - . - "glycomics" . - "0000204"^^ . - . - . - . - "Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. This collection is concerned with protist genomes."^^ . - "false"^^ . - . - "ontology" . - . - . - . - . - . - . - "The Plant Environment Ontology is a set of standardized controlled vocabularies to describe various types of treatments given to an individual plant / a population or a cultured tissue and/or cell type sample to evaluate the response on its exposure. It also includes the study types, where the terms can be used to identify the growth study facility. Each growth facility such as field study, growth chamber, green house etc is a environment on its own it may also involve instances of biotic and abiotic environments as supplemental treatments used in these studies."^^ . - "fbtc" . - . - "ontology" . - . - . - "ontology" . - "ICD-O" . - "^\\d{7}$"^^ . + . + . + "gorel" . + . + . + . + . + "Maize gross anatomy" . + "http://www.pharmgkb.org/pathway/$1"^^ . + . + "biology" . + . + "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=$1"^^ . + . + . + . + . . - . - . - . - . - . - "Thermo Fisher Scientific" . - . - . - . - "https://www.confident-conference.org/index.php/Event_Series:"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/MPIO_"^^ . + . + "github.issue" . + . + . + "Model Card Report Ontology" . + . + "life science" . + . + . + . + "worms" . + . + "false"^^ . + . + . + "Higher order grouping of Pfam families"^^ . + . + . + "A comprehensive database of\n\nhuman H/ACA and C/D box snoRNAs."^^ . + "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)."^^ . + "C. elegans development ontology" . + . + "agsc" . + . + "Identifier for a journal article in the fossilworks website"^^ . + . + . + . + . + "http://agroportal.lirmm.fr" . + . + "phenomics" . + "PF" . + "A database for Triticeae and Avena gene symbols."^^ . + . + "http://purl.bioontology.org/ontology/npo#NPO_"^^ . + . + . + . + "http://purl.obolibrary.org/obo/FAO_"^^ . + "cryopreservation" . + . + "gene" . + . + . + . + "pspub" . + . + "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."^^ . + . + "mbrochhausen@uams.edu" . + . + . + . + . + . + . + . + . + . + . + "ontology" . + . + . + "ctis" . + . + "A GI number (for GenInfo Identifier, sometimes written in lower case, _gi_) is a simple series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Version number of the sequence record. Each time a sequence record is changed, it is assigned a new GI number."^^ . + . + "metascience" . + . +_:N3b02556718da42d990354f82b5791ec2 "Heinrich Herre" . + "hPSCreg is a freely accessible global registry for human pluripotent stem cell lines (hPSC-lines)."^^ . + . + . + . + . + . + "Cell Image Library" . + "http://ctdbase.org/detail.go?type=gene&acc="^^ . + . + . + . + . + "^\\w+$"^^ . + "protein" . + "utrdb" . + . + . + "gomfid" . + . + . + . + "https://glygen.org/glycan/"^^ . + . + "false"^^ . + . + "chembl.compound" . + "A modeling paradigm-specific registry of prefixes and their URL expansions" . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFOMD_"^^ . + . + "http://ctdbase.org/detail.go?type=disease&db=MESH&acc=$1"^^ . + "ontology" . + . + "systems biology" . + . + "Rnaloops stores the information about n-way junctions (where n≥3) found in experimentally determined rna 3d structures deposited in the protein data bank."^^ . + . + . + . + "cldb" . + "dna" . + "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."^^ . + . + "transport and kinetic data" . + . + . + "transcriptomics" . + "http://www.kegg.jp/entry/$1"^^ . + "ChemIDplus" . + . + . + . + . + "SSSOM is a Simple Standard for Sharing Ontological Mappings, providing - a TSV-based representation for ontology term mappings - a comprehensive set of standard metadata elements to describe mappings and - a standard translation between the TSV and the Web Ontology Language (OWL). Most metadata elements, such as \"sssom:mapping_justification\" are defined in the sssom namespace."^^ . + . + . + . + "10001-101"^^ . + "https://nsrrc.missouri.edu/nsrrc$1info/"^^ . + "false"^^ . + "true"^^ . + . + . + "CASRAI Contributor Roles Taxonomy" . + . + . + "A nomenclatural ontology for biological names" . + "An ontology covering the taxonomy of teleosts (bony fish)"^^ . + . + "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . + . + . + "Rice ontology" . + "genome" . + "pocketome" . + . + . + "Minid are identifiers used to provide robust reference to intermediate data generated during the course of a research investigation."^^ . + . + "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)"^^ . + . + "medical biotechnology" . + "Colin Batchelor" . + . + . + "^CL\\d+$"^^ . + . + "life science" . + "KEGG_RCLASS" . + "485991"^^ . + "pierre.grenon@ifomis.uni-saarland.de" . + . + "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."^^ . + "http://purl.obolibrary.org/obo/RS_"^^ . + . + . + . + "http://tables.pseudogene.org/[?species_name]/$1"^^ . + . + . + . + "https://easychair.org/cfp/topic.cgi?tid="^^ . + . + . + . + "inaturalist.place" . + "depod@embl.de" . + . + . + . + "amphx" . + "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . + "Metabolomics Standards Initiative Ontology" . + . + "mim" . + . + . + . + . + _:Neb08671d822d4644a29d853b4a66d025 . + . + "http://purl.org/spar/c4o/"^^ . + . + "ontology" . + . + . + . + . + . + . + . + . + . + "X58356"^^ . + . + . +_:Nfa7ed40a90074ec19376c04d4c9a1c78 "Matt Berriman" . + . + . + "Identifier (name code) for a taxon in the catalogue of life in taiwan"^^ . + . + . + "mirex" . + . + "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . + "false"^^ . + "S000002493"^^ . + . + "A vocabulary for the catalysis disciplines" . + . + "^\\d{7}$"^^ . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/TTO_$1"^^ . + . + . + "frbr" . + . + . + . + "biology" . + . + . + . + . + . + . + . + "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . + . + "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . + "small molecule" . + . + . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information."^^ . + . + "anatomy" . + . + "false"^^ . + . + . + . + . + "cell line" . + "life science" . + . + . + . + . + . + . + . + . + . + "https://www.uniprot.org/proteomes/"^^ . + . + "^\\d+$"^^ . + "NLXCHEM" . + "ontology" . + "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."^^ . + . + . . - . - . - . - "International Nucleotide Sequence Database Collaboration (INSDC) Run" . - "owl" . - . - "wbphenotype" . - . - . - . - "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . - "SP_KW" . - . - "obo" . - . - . - . - . - . - "oban" . - "false"^^ . - "Bioregistry Schema" . - . - "obo" . - "https://www.probes-drugs.org/compound/"^^ . - . - "^IRCT\\d+N\\d+$"^^ . - "Beet Ontology ontology" . - "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . - . - . - . - . - . - . - "neurophysiology" . - "proteomics" . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "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."^^ . - . - "https://bioregistry.io/schema/#"^^ . - . - . - "BioLegend is a life sciences supply vendor."^^ . - "Asset"^^ . - "http://fossilworks.org/?a=taxonInfo&taxon_no=$1"^^ . - "false"^^ . - "000004"^^ . - . - "raymond@caltech.edu" . - . - "^EB\\d+$"^^ . - . - . - . - "Drug Central" . - . - . - . - "napdi" . - _:Nef1e0f2fdfb6453f867b6dc3d6aad05d . - . - . - . - . - . - . - . - . - . - "https://bioregistry.io/registry/$1"^^ . - . - "SNOMEDCT_US_2021_09_01" . - . - . - . - . - . - . - "oryzabase.gene" . - "imex" . - . - "3"^^ . - "rdf" . - "mmp.ref" . - . - . - "https://data.4dnucleome.org/experiment-set-replicates/"^^ . - . - "false"^^ . - "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."^^ . - . - "health science" . - . - . - . - . - "hgnc.family" . - "chemistry" . - "Chris Mungall" . - . - "https://smid-db.org/smid/$1"^^ . - . - "obo" . - "https://biomodels.net/vocab/idot.rdf#"^^ . - "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . - "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . - . - . - . - "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc."^^ . - . - "http://purl.obolibrary.org/obo/EPO_"^^ . - "subject agnostic" . - "Integrated Genomic Resources of human Cell Lines for Identification" . - "https://www.iedb.org/reference/$1"^^ . - . - . - . - "PhosphoPoint Phosphoprotein" . - "Jade Hotchkiss" . - . - . - . - . - . - "The National Drug Code (NDC) is a unique, three-segment number used by the Food and Drug Administration (FDA) to identify drug products for commercial use. This is required by the Drug Listing Act of 1972. The FDA publishes and updates the listed NDC numbers daily."^^ . - . - . - . - . - . - "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id="^^ . - . - "cp" . - . - . + . + "^B\\d{5}$"^^ . + . + "iuphar.receptor" . + "http://scop.berkeley.edu/sid=$1"^^ . + "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."^^ . + . + . +_:Nc729bd6327734c5b8747f5b552404699 "Michael Lincoln" . + . + . + . + "EDAM Data" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "co_331" . + . + . + "https://www.ukrlp.co.uk/ukrlp/ukrlp_provider.page_pls_provDetails?x=&pn_p_id=$1&pv_status=VERIFIED&pv_vis_code=L"^^ . + "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."^^ . + . + _:Ne99dc73b20714efa88f5c99a1754101f . + . + . + . + "gro" . + . + . + . + . + "obo" . + . + . + "bioinformatics" . + "ambystoma" . + "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)."^^ . + . + . + . + . + . + "true"^^ . + . +_:N3b02556718da42d990354f82b5791ec2 "heinrich.herre@imise.uni-leipzig.de" . + . + . + . + . + "Terry.Hayamizu@jax.org" . + . + "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."^^ . + "http://purl.obolibrary.org/obo/ZFA_$1"^^ . + . + . + . + . + . + . + . + "bioschema" . + . + "dashr@lisanwanglab.org" . + "iceberg.family" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "https://biopragmatics.github.io/providers/mba/$1"^^ . + . + . + . + . + . + "false"^^ . + "protein" . + "https://www.ncbi.nlm.nih.gov/protein/"^^ . + "bacdive" . + "agriculture" . + . + . + "tto" . + "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid="^^ . + "fbcv" . + "https://registry.identifiers.org/registry/$1" . + . + "EMAPA_RETIRED" . + . + "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . + "false"^^ . + . + "botany" . + "https://assets.nemoarchive.org/"^^ . + "false"^^ . + . + . + . + . + . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + "SED-ML data format" . + . + "human" . + . + . + . + "virology" . + "PS00001"^^ . + . + "systems biology" . + "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG"^^ . + "false"^^ . + . + "protein" . + . + "Activity"^^ . + "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."^^ . + . + . + . + . + "http://www.w3.org/2004/02/skos/core#$1"^^ . + . + "C138986"^^ . + "Brazilian Registry of Clinical Trials" . + "http://purl.obolibrary.org/obo/DIDEO_"^^ . + "false"^^ . + . + . + "http://bigg.ucsd.edu/models/universal/reactions/"^^ . + "neuroscience" . + "https://chemkg.github.io/chemrof/$1"^^ . + "1829126"^^ . + . + . + . + . + . + "https://commonchemistry.cas.org/detail?cas_rn="^^ . + "anatomy" . + . + . + . + . + . + . + . + "ontology" . + . + . + . + . + . + . + . + "0005067"^^ . + . + "http://bigg.ucsd.edu/models/$1"^^ . + "small molecule" . + "^GR\\:\\d+$"^^ . + . + "life science" . + . + "vendor" . + "PhosphoPoint Kinase" . + . + . + . + "obo" . + "^MMP\\d+.\\d+$"^^ . + . + . + "Kyoto Encyclopedia of Genes and Genomes" . + . + "NIFEXT" . + "^[0-9]{15}[0-9X]{1}$"^^ . + . + . + "https://www.thaiclinicaltrials.org/show/$1"^^ . + . + "health science" . + . + . + . + "http://www.sasbdb.org/data/"^^ . + "Matt Yoder" . + . + . + . + . + "civic.eid" . + "Antibiotic Resistance Genes Database" . + . + . + "http://purl.org/obo/owlEOL_$1"^^ . + . + "https://w3id.org/biolink/vocab/$1"^^ . + "https://www.uniprot.org/database/$1"^^ . + . + . + . + "protein" . + . + . + . + . + . + . + "drugbankv4.target" . + . + "https://www.ndexbio.org/viewer/networks/"^^ . + . + . + "protein" . + "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert="^^ . + . + . + . + "ClassyFire" . + "http://nava.liacs.nl/cgi-bin/nava.py?id=$1"^^ . + . + "isbn" . + . + . + . +_:N820b1b954de9446f91f3dc21bc674d09 "Jonathan Bard" . + . + . + . + "false"^^ . + "obo" . + "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . + "false"^^ . + . + . + . + "4776"^^ . + . + . + "^virsi\\d+$"^^ . + "Heather Piwowar" . + "psipar" . + . + . + "https://www.fisheries.noaa.gov/species/"^^ . + "go.chemicals" . + . + "ev:E00032"^^ . + . + . + . + . + "mmsl" . + . + . + . + "false"^^ . + . + "false"^^ . + . + "An ontology of physico-chemical methods and properties."^^ . + "https://medical-data-models.org/forms/$1"^^ . + . + . + . + "voc4cat" . + . + "dna" . + "https://www.uniprot.org/diseases/"^^ . + "chemical" . + . + . + . + "An ontology developed by the American Psychological Association (APA). Note that URIs in this ontology appear to have been generated with erroneous settings in Protege."^^ . + . + "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools" . + . + . + . + "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." . + . + . + "false"^^ . + "Plant Experimental Conditions Ontology" . + . + "Cell line collections (Providers)"^^ . + "https://e-cyanobacterium.org/bcs/rule/"^^ . + . + . + "An ontology for harmonizing and extending severeral existing resources in the vaccine and immunology domains"^^ . + . + . + . + . + "life sciences" . + . + "SDY2614"^^ . + "https://cropontology.org/rdf/CO_330:$1"^^ . + "nsv3875336"^^ . + "SM0000020"^^ . + . + . + . + . + . + "IPI"^^ . + "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."^^ . + . + "protein" . "false"^^ . - "pns12@hermes.cam.ac.uk" . - . - "genes" . - . - "subject agnostic" . - "cryopreservation" . - "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query="^^ . - "life science" . - "protein" . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . - "COVID-19 Surveillance Ontology" . - . - . - . - "^EBI\\-[0-9]+$"^^ . - "https://aopwiki.org/events/$1"^^ . - "Merck Millipore (EMD Millipore)" . - "https://pathbank.org/view/$1"^^ . - . - . - "AGR" . - "http://cgsc.biology.yale.edu/Site.php?ID=$1"^^ . - . - "Dublin Core Elements (1.1)" . - "NINDS Human Cell and Data Repository" . - . - "false"^^ . - "^\\d{7}$"^^ . - "eVOC mouse development stage" . - "^\\d+$"^^ . - . - . - . - "https://biopragmatics.github.io/providers/pba/$1"^^ . - . - . - "gene" . - "^\\d+$"^^ . - . - . - . - . - "pharmacology" . - . - . - "small molecule" . - "http://standards.iso.org/iso/15926/part14/$1"^^ . - . - . - . - "gene" . - "https://innopedia.kyinno.com/DataBase/CellLine.aspx?file=$1.pdf"^^ . - "^\\d{7}$"^^ . - "topics" . - . - . - . - "Identifier used by the Cancer Chemotherapy National Service Center."^^ . - . - . - . - "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . - "http://www.nlm.nih.gov/cgi/mesh/2013/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . - . - . - "http://lisanwanglab.org/DASHR/entry/"^^ . - . - . - . - . - . - "^\\d+$"^^ . - . - "phenotype" . - "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."^^ . - . - . + . + . + . + "metagenomics" . + . + . + . + . + "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."^^ . + . + . + "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo=$1"^^ . + "^[1-9]\\d{0,6}$"^^ . + . + . + . + "551115"^^ . + "^\\d{7}$"^^ . + "immds"^^ . + . + "https://horizondiscovery.com/en/search?searchterm="^^ . + . + . + "http://purl.obolibrary.org/obo/DISDRIV_$1"^^ . + . + "https://medlineplus.gov/genetics/condition/$1"^^ . + . + . + "We built this ontology primarily to support comparative effectiveness researchers studying claims data. They need to be able to query U.S. National Drug Codes (NDCs) by ingredient, mechanism of action (beta-adrenergic blockade), physiological effect (diuresis), and therapeutic intent (anti-hypertensive)."^^ . + "structure" . + . + "shareloc" . + "hpm.protein" . + . + "^[A-Z-0-9]+(\\:)?[A-Za-z0-9+_.%-:]+$"^^ . + "https://cropontology.org/term/$1:$2" . + . + "https://spdx.org/licenses/$1"^^ . + . + . + . + "life science" . + "^\\d+(\\w+)?$"^^ . + . + . + "medgen.gtr" . + "PubChem Substance ID (SID)" . + "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)."^^ . + "false"^^ . + . + "pictar" . + . + "ID in NIAID ChemDB"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "8000221"^^ . + "CUT"^^ . + "NOMEN is a nomenclatural ontology for biological names (not concepts). It encodes the goverened rules of nomenclature."^^ . + "hsa-mir-200a"^^ . + . + . + . + . + . + "Mathias Uhlen" . + . + "eNanoMapper ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "life science" . + . + "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . + "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://www.e-cyanobacterium.org/bcs/entity/$1"^^ . + "false"^^ . + . + . + "ogms/OMRE" . + "http://purl.obolibrary.org/obo/SBO_$1"^^ . + . + "http://purl.obolibrary.org/obo/CVDO_"^^ . + . + . + . + "1"^^ . + . + "http://purl.obolibrary.org/obo/PATO_$1"^^ . + "pharmacogenomics" . + . + . + . + . + . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . + . + . + "http://multicellds.org/MultiCellDB/"^^ . + "obo" . + . + . + . + . + . + . + . + "http://www2.idac.tohoku.ac.jp/dep/ccr/TKGdate/TKGvol08/$1.html"^^ . + "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."^^ . + "botany" . + "Daniel Gautheret" . + . + . + "life science" . + . + "Amphibian Taxonomy Ontology is an ontology of Amphibian species and genres. It is being integrated into UBERON resource"^^ . + "nasa/kepler-exoplanet-search-results"^^ . + . + "life science" . + "http://purl.obolibrary.org/obo/PPO_$1"^^ . + . + . + . + . + . + "R00100"^^ . + "https://www.ebi.ac.uk/ena/data/view/$1"^^ . + "^rs\\d+$"^^ . + . + "https://pdc.cancer.gov/pdc/study/$1"^^ . + . + "fsnp" . + "Philippe Le Mercier" . + . + . + . + "rism" . + . + "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=$1"^^ . + . + . + . + . + . + . + . + . + "PiroplasmaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera."^^ . + "^SL-\\d+$"^^ . + . + . + . + "transcriptomics" . + . + "HWUPKR0MPOU8FGXBT394"^^ . + . + . + . + "https://bioregistry.io/d1id:"^^ . + "esldb" . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/"^^ . + "https://bioregistry.io/beiresources:"^^ . + . + "^\\d+$"^^ . + . + "https://bioportal.bioontology.org/" . + . + . + . + . + . + . + "35742"^^ . + "PharmGKB Drug" . + "hcao" . + . + . + "coconut" . + "OASIS Open Services for Lifecycle Collaboration Core Vocabulary" . + . + . + . + . + "entrez" . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + "CC2(C)C\\1CCC(C)/C=C/12"^^ . + . + "oct 2016"^^ . + . + . + . + . + "Abcam" . + . + . + . +_:N2079c6c1c21d4ad782eb69b0c991d0ee "Jonathan Bard" . + "https://www.vmh.life/#gene/"^^ . + . + "false"^^ . + . + . + . + . + . + "life science" . + "BP100000"^^ . + "uBio NameBank" . + "genome" . + . + . + . + . + "http://purl.obolibrary.org/obo/ONTONEO_"^^ . + "MF_01400"^^ . + . + . + . + . + "FOBI (Food-Biomarker Ontology) is an ontology to represent food intake data and associate it with metabolomic data"^^ . + "phylogenetics" . + "b97957"^^ . + "Research Organization Registry" . + . + "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."^^ . + . + . + "structural biology" . + . + . + "http://purl.obolibrary.org/obo/BFO_"^^ . + . + . + . + . + . + . + . + "Glyma0021s00410"^^ . + . + . + . + . + . + "Wes Schafer" . + . + . + . + "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."^^ . + . + "^C\\d+$"^^ . + "The Mental Functioning Ontology is an overarching ontology for all aspects of mental functioning."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + . + "false"^^ . + . + . + "0000728"^^ . + . + "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."^^ . + "IntellectualContribution"^^ . + . + "false"^^ . + . + . + "ligandbox" . + . + . + . + . + . + . + . + "obo" . + . + . + "^(SMP|PW)\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "ChEMBL_ID" . + "false"^^ . + . + . + "http://www.narcis.nl/publication/RecordID/$1"^^ . + "The Food Ontology" . + . + "Human ancestry ontology for the NHGRI GWAS Catalog"^^ . + "obo" . + . + . + "biopixie" . + . + "obo" . + "chemical biology" . + . + "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references the Variant identifier."^^ . + . + . + . + . + . + "chemical" . + . + "SCTID_2010_1_31" . + . + . + "genomics" . + . + . + "Distributed Archives for Neurophysiology Data Integration" . + . + "^\\d+$"^^ . + . + "anatomy" . + "Identifiers for proposals/projects at the Joint Genome Institute"^^ . + . + . + "false"^^ . . - " A 7-character sid consists of \"d\" followed by the 4-character PDB ID of the file of origin, the PDB chain ID ('_' if none, '.' if multiple as is the case in genetic domains), and a single character (usually an integer) if needed to specify the domain uniquely ('_' if not). Sids are currently all lower case, even when the chain letter is upper case. Example sids include d4akea1, d9hvpa_, and d1cph.1."^^ . - . - "2639"^^ . - . - "Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. [from RRID]"^^ . - "true"^^ . - "obo" . - . - . - . - "https://rpcec.sld.cu/en/trials/"^^ . - . - "biology" . - . - "http://sugarbind.expasy.org/$1"^^ . - . - "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . - . - "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID="^^ . - . - . - "galen" . - "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . - . - "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . - . - . - "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."^^ . - "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . - "medicine" . - . - . - . - . - . - "265912"^^ . - . - . - "gene expression" . - "fungi" . - . - "The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites)."^^ . - "The Human Oral Microbiome Database (HOMD) provides a site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity. It contains genomic information based on a curated 16S rRNA gene-based provisional naming scheme, and taxonomic information. This datatype contains taxonomic information."^^ . - "pubchem.compound" . - "false"^^ . - . - . - . - . - "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . - . - "2673500"^^ . - . - . - "life science" . - . - "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."^^ . - . - . - . - . - "0000780"^^ . - . - . - . - "biominder" . - "Integrated Microbial Genomes Gene" . - . - . - . - . - . - . - . - . - . -_:N10720e6ba83e4d6c8be7c875b1455193 "michael.lincoln@med.va.gov" . - . - . - . - "ontology" . - . - . - . - . - . - "https://www.genenames.org/cgi-bin/genefamilies/set/"^^ . - . - "lepao" . - "https://cameochemicals.noaa.gov/chemical/"^^ . - _:N0402b08463784fa0bcdbaac63beec045 . - . - "DSSTox_CID" . - . - . - . - "https://www.ebi.ac.uk/QuickGO/GProtein?ac=$1"^^ . - . - . - . - . - . - "false"^^ . - "AKR-270"^^ . - . - . - "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."^^ . - . - . - . - . - . - . - . - "Akt_PKB"^^ . - . - "identifier of an entry in the NCI Drug Dictionary"^^ . - "false"^^ . - . - . - "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . - "icd10cm" . - . - "http://purl.obolibrary.org/obo/OBI_"^^ . - . - "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid="^^ . - . - "http://purl.obolibrary.org/obo/FBbt_"^^ . - "http://www.phosphosite.org/siteAction.do?id=$1"^^ . - . - "Schema for the export of the Bioregistry as RDF"^^ . - . - . - "alan.bridge@isb-sib.ch" . - . - . - "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid=$1"^^ . - . - "Addgene is a non-profit plasmid repository. Addgene facilitates the exchange of genetic material between laboratories by offering plasmids and their associated cloning data to not-for-profit laboratories around the world."^^ . - . - . - "^[0-9]+$"^^ . - "Scientific Evidence and Provenance Information Ontology" . - . - "anatomy" . - "anatomy" . - "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."^^ . - . - . - "Browser for the periodic table of the elements"^^ . - . - "bioregistry"^^ . - . - . - . - . - . - . - . - . - "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."^^ . - . - . - "medical microbiology" . - . - . - . - "aaeA"^^ . - . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "obo" . - "http://isbndb.com/search-all.html?kw="^^ . - "EntrezGene" . - . - "classification" . - "k-12 teacher" . - . - . - . - . - . - . -_:Nf284f4107996471c8eac6209f8069992 "julie@igbmc.u-strasbg.fr" . - . - "^[0-9]+$"^^ . - . - "mediadive.solution" . - . - "The pattern for expanded URIs in the given resource" . - . - . - "Suzi Aleksander" . - . - . - . - . - "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."^^ . - . - . - "dictybase" . - . - . - . - "sequence alignment" . - . - . - . - . - . - . - "cultured cell line" . - "false"^^ . - . - . - . - . - . - . - . - "life science" . - . - . - . - . - . - "https://rnacentral.org/rna/$1"^^ . - . - "ontology" . - . - . - . - "^\\d+$"^^ . - . - . + "uniprot.var" . + . + . + "false"^^ . + "^\\d+$"^^ . + . + . + . + . + "protein" . + . + . + "^WBRNAi\\d{8}$"^^ . + . + . + "BioCyc is a collection of Pathway/Genome Databases (PGDBs) which provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms."^^ . + . + . + . + "life science" . + . + "1023371"^^ . + . + . + "https://viperdb.org/Info_Page.php?VDB="^^ . + "WGS84 Geo Positioning" . + "^phs[0-9]{6}(.v\\d+.p\\d+)?$"^^ . + . + "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC="^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/GO_$1"^^ . + "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . + . + . + "lspci" . + . + . + . + "13"^^ . + "ontology" . + . + "genomics" . + "^\\d+$"^^ . +_:Nac74b2e569134e4aa3278a0ee126d26d "J.Bard@ed.ac.uk" . + "https://aopwiki.org/stressors/"^^ . + . + . + . + "Dalia Alghamdi" . + . + . + "PMID" . + . + "Stefanie Seltmann" . + . + . + "zhu@iastate.edu" . + . + "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_$1"^^ . + . + . + "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/"^^ . + "zebrafish" . + . + "Francesco Vitali" . + . + . + . + . + "pdbechem" . + . + . + . + . + . + "A web-developer centric archive of prefixes and URI prefixes" . + "chemistry" . + . + . + . + "cpt" . + "https://lincs.hms.harvard.edu/db/datasets/"^^ . + . + . + . + "nuclear" . + . + . + . + "http://emmo.info/emmo/cif-core#$1"^^ . + . + "medicine" . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "false"^^ . + "life science" . + "S1"^^ . + . + "rgd.strain" . + "Cell line databases/resources"^^ . + "ATCC(in host)" . + . + . + "^SCV\\d+(\\.\\d+)?$"^^ . + . + . + . + . + . + "Insect Resistance Ontology" . + . + . + "https://purl.dataone.org/odo/SALMON_"^^ . + . + . + "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."^^ . + . + . + . + . + . + . + "pandit" . + . + . + "lincs.data" . + "obo" . + . + . + . + . + . + . + . + . + . + . + . + . + "http://www.iclc.it/details/det_list.php?line_id="^^ . + . + . + . + . + . + "Spectra Hash Code" . + . + . + . + "https://metacyc.org/compound?orgid=META&id=$1"^^ . + . + "Human Gene Mutation Database" . + . + "obo" . + "https://www.ebi.ac.uk/biomodels/$1"^^ . + "^PMC\\d+$"^^ . + . + . + . + . + . + . + "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/$1"^^ . + "0002959"^^ . + . + . + "false"^^ . + "http://tolweb.org/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + _:N9753b3307f82484cbd3fe4a409beaccf . + . + . + . + . + . + . + . + "phylogeny" . + "SP_VAR" . + . + . + "data management" . + . + . + . + . + "01467"^^ . + "http://purl.obolibrary.org/obo/CIDO_"^^ . + "http://purl.dataone.org/odo/ECSO_"^^ . + . + "cdao" . + . + . + . + "MAM01234c"^^ . + . + . + . + . + "BioGRID" . + . + "Tanja Bekhuis" . + "false"^^ . + . + . + . + . + . + . + . + "^[1-9]\\d*$"^^ . + . + "^DDB\\d+$"^^ . + "vbrc" . + . + . + "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."^^ . + "A formal ontology of phenotypes observed in fission yeast."^^ . + . + . + . + "http://classyfire.wishartlab.com/tax_nodes/C"^^ . + . + "http://purl.obolibrary.org/obo/ECOCORE_"^^ . + . + . + "mcro" . + . + "http://purl.obolibrary.org/obo/FBdv_$1"^^ . + . + . + . + . + . + . + . + "MESH_SUPPLEMENTAL_RECORD_UI" . + . + "dc.elements" . + . + . + "This ontology covers the domain of social entities that are related to health care, such as demographic information and the roles of various individuals and organizations."^^ . + . + "002804"^^ . + . + "hms.lincs.compound" . + . + . + "ontology" . + . + "Unimod protein modification database for mass spectrometry" . + "false"^^ . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + "edeutsch@systemsbiology.org" . + "arrayexpress.platform" . + . + "FR-FCM-ZYGW"^^ . + . + "BiGG Metabolite" . + "Identifiers.org Ontology" . + "0001655"^^ . + . + . + . + . + "false"^^ . + "ontology" . + . + . + "clinvar.submission" . + . + . + "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . + . + "https://pdc.cancer.gov/pdc/study/"^^ . + "biology" . + "81944ba1-81d0-436e-8552-33d77a27834b"^^ . + . + . + . + "false"^^ . + . + "307"^^ . + . + . + "oryzabase.reference" . + . + . + "^\\d+$"^^ . + "July 2018"^^ . + . + . + . + . + . + "44259"^^ . + . + "https://www.iedb.org/reference/$1"^^ . + . + . + . + . + "100E"^^ . + "http://www.fairsharing.org/ontology/subject/SRAO_"^^ . + . + . + . + . + "MatrixDB" . + . + . + . + "false"^^ . + "hasPrimaryUriPattern"^^ . + . + . + "regulation" . + . + . + "https://www.gwascentral.org/study/$1"^^ . + . + . + . + . + . + . + . + . + . "http://purl.obolibrary.org/obo/ONTOAVIDA_$1"^^ . - . - "ontology" . - "false"^^ . - "http://www.cathdb.info/cathnode/$1"^^ . - . - . - . - . - "Georgeta Bordea" . - . - . - . - . - . - "http://edamontology.org/topic_"^^ . - . - . - "https://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/GeneDetails.html?sp="^^ . - "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."^^ . - . - "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."^^ . - . - . - . - "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . - "genomics" . - "http://bcrj.org.br/celula/$1"^^ . - . - "false"^^ . - "DBG2 Introns" . - "Tim Robertson" . - . - . - . - . - "biomodels.vocabulary" . - . - . - "0000026"^^ . - . - "life science" . - . - . - . - . - "biomedical science" . - "https://cordis.europa.eu/article/id/$1"^^ . - "organic chemistry" . - . - "cell lines" . - "gramene.qtl" . - "protein" . - . + . + . + . + "https://publons.com/researcher/"^^ . + . + . + "umbbd.rule" . + . + "institution" . + "smid" . + "Decentralized Identifier" . + . + "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."^^ . + "10.1621/vwN2g2HaX3"^^ . + . + . + . + . + . + "UniPathway Compound" . + . + . + . + . + . + . + . + "0000208"^^ . + . + "https://www.kew.org/data/grasses-db/www/$1"^^ . + "http://www.aspergillusgenome.org/cgi-bin/protein/proteinPage.pl?dbid=$1"^^ . + "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."^^ . + "loggerhead" . + "false"^^ . + . + "bs" . + . + . + "cell biology" . + "Selventa legacy disease namespace used with the Biological Expression Language"^^ . + . + . + . + "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . + . + . + . + "addgene" . + "agriculture" . + . + . + . + "clinical veterinary medicine" . + "false"^^ . + . + . + . + . + "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them."^^ . + . + . + . + . + "Nicholas Furnham" . + "https://www.webelements.com/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/MF_$1"^^ . + . + "Drosophila RNAi Screening Center" . + . + . + . + . + "Oryzabase Gene" . + "ttd.target" . + "bioregistry.schema" . + . + . + . + "life science" . + . + . +_:Nf15094c178294dd0b15e5d36b3dbb2d6 "INOH curators" . + "145"^^ . + . + . + . + . + "eurofir" . + "Fungal Nomenclature and Species Bank" . + . + "environmental science" . + "false"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "Google Patents" . + . + "Sue Bello" . + . + . + "It is an ontology model used to describe associations between biomedical entities in triple format based on W3C specification. OBAN is a generic association representation model that loosely couples a subject and object (e.g. disease and its associated phenotypes supported by the source of evidence for that association) via a construction of class OBAN:association. [from GitHub]"^^ . + "^[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}\\/[\\w-]+\\/[\\w^_]{8}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{4}-[\\w^_]{12}$"^^ . + . + . + . + . + . + . + . + "UDB000691"^^ . + "richard@cyganiak.de" . + "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO="^^ . + . + "Intelligence Task Ontology" . + "computational biology" . + . + . + . + . + . + "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . + . + "https://go.drugbank.com/reactions/"^^ . + . + . + "Biological Magnetic Resonance Data Bank" . + . . - . - "anatomy" . - . - . - . - . - . - "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."^^ . - "classification" . - "KEGG" . - "https://mediadive.dsmz.de/ingredients/$1"^^ . - . - . - "planp" . - "^\\d{7}$"^^ . - . - . - "" . - . - . - . - "biology" . - "ontology" . - "genome" . - "GSTA1"^^ . - . - . - "false"^^ . - "false"^^ . - . - . - "An ontology that enables characterization of the nature or type of citations, both factually and rhetorically."^^ . - "Animal Genome QTL" . - . - . - . - . - "The Cell Line Ontology 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."^^ . - . - . - . - . - "https://www.ebi.ac.uk/gxa/genes/"^^ . - . - . - . - . - "0001011"^^ . - . - "Daniel Gautheret" . - . - "7207"^^ . - . - . - . - . - . - "false"^^ . - "mediadive.ingredient" . - . - . - "BRENDA Enzyme" . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "gfo" . - . - . - . - . - . - "ncbi.assembly" . - "obo" . - . - . - . - . - . - . - . - . - . - . - "610"^^ . - . - . - "cheminformatics" . - . - . - "Health Procedure Ontology" . - . -_:Necdcf0cef45e47968707a7dee8f4a0d2 "J.Bard@ed.ac.uk" . - . - . - . - "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1"^^ . - "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."^^ . - "chickenqtldb" . - . - . - "Toxic Process Ontology" . - . - . - . - . - "SABIO-RK Reaction" . - "false"^^ . - "cl3603"^^ . + "A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just heart really means heart (CS 9-20). Timing details will be added to the abstract version of the ontology in a future release."^^ . + . + . + . + . + . + . + . + . + "nembase" . + "dna" . + . + "opmi" . + "GrainGenes" . + . + . + "0000001"^^ . + . + . + "anatomy" . + "The Amphioxus Development and Anatomy Ontology" . + . + . + . + . + . + . + . + . + . + "nlx.chem" . + "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."^^ . + . + . + . + . + . + "Jackson Laboratories Strain" . + . + "0002058"^^ . + "6038"^^ . + . + . + . + "blast" . + "http://www.obofoundry.org/" . + . + "https://www.ncbi.nlm.nih.gov/homologene/"^^ . + . + . + . + . + . + . + . + . + "sequence" . + . + . + . + "100000001"^^ . + . + . + . + . + . + "bio.tools" . + . + . + "https://hpscreg.eu/cell-line/$1"^^ . + "alistair.miles@linacre.ox.ac.uk" . + "ZFA description."^^ . + . + "David Blackburn" . + . + "Genetic and Rare Diseases Information Center" . + . + . + . + . + "17165"^^ . + . + . + . + "false"^^ . + "taxonomy" . + _:N93953f5709f34a838912b45663c37bb8 . + "lgai.cede" . + . + . + "mfo" . + "Role Ontology" . + . + . + . + . + . + . + . + . + "ontology" . + . + . + "protein" . + . + "https://scicrunch.org/resolver/RRID:$1_$2" . + "^(UCR|UCY|UER|ULS|UPA|UPC|UPX)\\d{5}$"^^ . + "protein" . + "^[A-Z_]{3}[0-9]{4,}$"^^ . + "protein" . + "false"^^ . + . + "Wikidata Property" . + . + . + . + "kronkcj@mail.uc.edu" . + . + "MMSsINC is a database of commercially-available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D formats."^^ . + "j.harry.caufield@gmail.com" . + . + "lipro" . + . + "1199"^^ . + . + "^\\d+$"^^ . + . + . + . + . + "organic chemistry" . + . + . + "false"^^ . + "false"^^ . + "491187"^^ . + . + . + . + "^PGS[0-9]{6}$"^^ . + "0000046"^^ . + "ontology" . + . + . + "Life cycle stages for Human"^^ . + "botany" . + "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."^^ . + "antibody" . + . + . + . + . + . + . + . + . + "http://purl.org/linked-data/cube#$1"^^ . + . + "ontology" . + . + "ontology" . + . + . + "cemo" . + "protein" . + "http://purl.obolibrary.org/obo/EO_$1"^^ . + "false"^^ . + . + "https://pubchem.ncbi.nlm.nih.gov/cell/$1"^^ . + . + "https://www.storedb.org/store_v3/download.jsp?fileId="^^ . + . + . + . + . + . + . + . + . + . + "true"^^ . + "The upper level ontology upon which OBO Foundry ontologies are built."^^ . + . + . + "174"^^ . + . + . + . + "structure" . + . + . + . + "International Traditional Medicine Clinical Trial Registry" . + "ontology" . + . + . + . + . + "EGAD00000000001"^^ . + "https://www.biorxiv.org/content/10.1101/"^^ . + "5fce9b7300001250"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + "life science" . + . + . + "https://viperdb.org/Info_Page.php?VDB=$1"^^ . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "http://www.phosphosite.org/proteinAction.do?id=$1"^^ . + "genepio" . + . + . + . + . + "protein" . + . + "ccds" . + . + . + "chemistry" . + "Vertebrate Homologous Organ Group Ontology" . + . + "http://purl.obolibrary.org/obo/FOODON_"^^ . + . + . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl="^^ . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "090701"^^ . + . + . + . + . + "false"^^ . + . +_:Neadaa30113554d4c98ff0c2fc706641b "sschurer@med.miami.edu" . + "^EDI_\\d+$"^^ . + "^\\d{7}$"^^ . + "registry" . + . + . + "doid" . + . + "^\\d+$"^^ . + . . - "https://www.uniprot.org/database/$1"^^ . - "AEO_RETIRED" . - "1100107"^^ . - . - "0000773"^^ . - "Amelanchier laevis"^^ . - . - . - . - . - . - "harukin@protein.osaka-u.ac.jp" . - . - . + . + "10194"^^ . + . + . + . + "niaest" . + . + "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."^^ . + . + . + . + "Christophe Dunand" . + . + "Paolo Romano" . + . + . + "ontology" . + "https://phytochem.nal.usda.gov/phytochem/chemicals/show/$1"^^ . + . + "false"^^ . + . + . + . + "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."^^ . + "PR00001"^^ . + "false"^^ . + . + . + "false"^^ . + . + "Cell line collections (Providers)"^^ . + . + "obo" . + . + "http://www.ontobee.org/ontology/BCGO?iri=http://purl.obolibrary.org/obo/$1"^^ . + "false"^^ . + "^([A-Z]\\d{5}|[A-Z]{2}\\d{6}|[A-Z]{4,6}\\d{8,10}|[A-J][A-Z]{2}\\d{5})(\\.\\d+)?$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/VO_"^^ . + . + . + "^\\d{7}$"^^ . + "Yeast Intron Database v3" . + "https://ximbio.com/reagent/$1"^^ . + "clo" . + "JCOIN" . + . + . + . + . + . + "RNA STRAND contains known RNA secondary structures of any type and organism. The ultimate goal of this database is to incorporate a comprehensive collection of known RNA secondary structures, and to provide the scientific community with simple yet powerful ways of analysing, searching and updating the proposed database."^^ . + . + . + . + . + "kaggle" . + "life science" . + "AKR-270"^^ . + . + . + . + . + "Computational gene function prediction can serve to focus experimental resources on high-priority experimental tasks. FuncBase is a web resource for viewing quantitative machine learning-based gene function annotations. Quantitative annotations of genes, including fungal and mammalian genes, with Gene Ontology terms are accompanied by a community feedback system. Evidence underlying function annotations is shown. FuncBase provides links to external resources, and may be accessed directly or via links from species-specific databases. This collection references human data."^^ . + . + . + "false"^^ . + "kerafast" . + . + . + . + . + "Vertebrate Taxonomy Ontology" . + . + . + "obo" . + . + . + "Cell line collections (Providers)"^^ . + "false"^^ . + . + "false"^^ . "mge" . - . - . - . - . - . - . - . - . - . - . - "RID1"^^ . - . - . - . - . - . - . - "https://reporter.nih.gov/project-details/"^^ . - . - . - . - . - "life science" . - . - . - . - . - "Gwen Frishkoff" . - "Rat Genome Database" . - . - . - . - "^(ACC|DSM|NC|PC|RT|AS|PV)-\\d+$"^^ . - . - . - . - "development" . - "AURKA"^^ . - . - "nbrc" . - "rgd.qtl" . - "false"^^ . - . - "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . - . + . + . + . + . + . + . + . + . + . + . + "YOR172W_571.0"^^ . + "^C\\d{8}$"^^ . + "false"^^ . + . + "https://schema.org/"^^ . + "^[0-9]+$"^^ . + "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . + "false"^^ . + "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.geonames.org/"^^ . + . + . + . + . + "pathway" . + . + . + . + "epigenetics" . + . + . + "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . + "^GPST[0-9]{6}$"^^ . + "^\\d{5}$"^^ . + . + "http://zfin.org/"^^ . + "beta-carotene"^^ . + "AddexBio cell line products" . + "DataONE" . + . + . + "publons.publication" . + . + "http://viaf.org/viaf/"^^ . + "COSMIC Gene" . + "TTDS00056"^^ . + . + "IPI00000001"^^ . + . + . + "http://aims.fao.org/aos/agrovoc/c_"^^ . + . + . + . + . + . + . + . + "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "http://www.informatics.jax.org/accession/MGI:"^^ . + . + . + . + . + . + . + . + "http://www.knapsackfamily.com/knapsack_core/information.php?word=$1"^^ . + "xl" . + . + . + . + "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources"^^ . + . + . + . + "phylogenetics" . + "chemistry" . + . + . + "obo" . + "dna" . + . + . + . + "SMID-DB" . + . + . + "Liz Allen" . + . + "Jianmin Wu" . + . + . + "false"^^ . + . + . + "The National Bibliography Number (NBN), is a URN-based publication identifier system employed by a variety of national libraries such as those of Germany, the Netherlands and Switzerland. They are used to identify documents archived in national libraries, in their native format or language, and are typically used for documents which do not have a publisher-assigned identifier."^^ . + "true"^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/nucest/"^^ . + . + "jax" . + . + . + . + . + . + . + . + . + . + "^[0-9a-zA-Z]{8}$"^^ . + "Veterinary Substances DataBase" . + "false"^^ . + . + "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"^^ . + . + . + . . - . - "computer science" . - . - . - . - . - . - "genome" . - "ontology" . - . - "^rs\\d+$"^^ . - "^[A-Z]+[0-9]+$"^^ . - "Dawood B. Dudekula" . - "small molecule" . - . - . - "goche" . - . - . - . - . - . - . - . - . - . + "facebase" . + . + . + . + "obo" . + "obo" . + "gene" . + . + . + "Satya S. Sahoo" . + . + "vcell"^^ . + . + "false"^^ . + . + . + . + "^A\\d{4}$"^^ . + . + . + "http://www.tcdb.org/search/result.php?tc="^^ . + "ontology" . + . + . + . + . + . + . + . + "scop.sccs" . + . . - . - "false"^^ . - . - . - . - "FungiDB" . - . - . - . - . - "RNA Modification Database" . - . - "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/"^^ . - "false"^^ . - . - . - . - . - . - . - . - "3G6A5W338E"^^ . - "nuclearbd" . - "Yeast Phenotype Ontology" . - "semantic web" . - "supply" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "Bactibase" . - "bugbase.protocol" . - "http://purl.obolibrary.org/obo/EO_$1"^^ . - _:Ncbaba8be38314faa87e015c819d05226 . - . - . - "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . - "http://purl.obolibrary.org/obo/MIRO_$1"^^ . - . - . - . - . - . - . - "https://www.rebuildingakidney.org/id/$1"^^ . - "Assembly" . - . - "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . - "http://purl.obolibrary.org/obo/MAO_"^^ . - . - . - . - . - . - . - . - "bsweeney@ebi.ac.uk" . - . - "^\\d+$"^^ . - . - . - . - . - . - "^AC[0-9]{8}$"^^ . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . - "000912"^^ . - . - . - "http://purl.obolibrary.org/obo/CMF_"^^ . - "^ARBA\\d+$"^^ . - . - . - "ontology" . - . - "^\\d{7}$"^^ . - "life science" . - . - . - . - "invertebrate" . - . - "Planarian Phenotype Ontology" . - "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."^^ . - . -_:N805816e4756c44619cdb57e0f012fd3c "rafael.goncalves@stanford.edu" . - "Ontology of Host-Microbiome Interactions" . - . - . - . - . - . - . - . - . - . - . - . - . - "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=$1"^^ . - . - . - . - . - . - . - . - "nucleotide" . - "A formal ontology of phenotypes observed in fission yeast."^^ . - . - . - . - . - . - "Psychology Ontology" . - "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession="^^ . - "tred" . -_:N698447d4b6454989b84712a255c0e38c "michael.lincoln@va.gov" . - "citexplore" . + . + . + . + . + . + . + "https://www.inaturalist.org/observations/"^^ . + . . - . - . - . - . - . - . - . - . - "^(([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9]))|(URS[0-9A-F]{10}(_[0-9]+){0,1})|(EBI-[0-9]+)$"^^ . - "A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org." . - . - . - . - . - . - . - "0000005"^^ . - "^\\d{7,8}$"^^ . - "sssom" . - . - "genome" . - "drug metabolism" . - . - . - . - . - . - . - . - . - . - . - . - . - "medicinal chemistry" . - . - "surjeet.arya@uky.edu" . - "^MSV\\d+$"^^ . - . - . - . - . - "FlyBrain Neuron Database" . - . - . - . - "ontology" . - . - . - "https://www.confident-conference.org/index.php/Event:"^^ . - "CH_001923"^^ . - . - . -_:Ndd49303c904448229b8b238eb16b593d "biomodels-net-support@lists.sf.net" . - . - "https://jrct.niph.go.jp/en-latest-detail/$1"^^ . - . - "bioinformatics" . - . - "datacite" . - . - . - . - . - "ontology" . - "germplasma" . - . - "BioKC" . - . - . - "subject agnostic" . - . - "false"^^ . - "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . - . - . - "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . - "http://purl.obolibrary.org/obo/APO_$1"^^ . - . - . - . - . - "SNOMEDCT_US_2016_03_01" . - . - . - "78"^^ . - "human" . - "http://genomics.senescence.info/diet/details.php?id="^^ . - "0000001"^^ . - "plant" . - "false"^^ . - . - . - . - "false"^^ . - . - . - . - . - "anatomy" . - "Workflow"^^ . - . - . - . - . - . - . - "false"^^ . - . - "eukaryotic" . - "true"^^ . - . - . - . - . - "Sickle Cell Disease Ontology" . - "Ontology for Parasite LifeCycle" . - . - . - "SIDER Side Effect" . - . - . - . - "cell lines" . - . - . - "UBERON" . - . -_:N29700f95c1bf4501949b0ce8eb8684aa "po-discuss@plantontology.org" . - . - "false"^^ . - . - . - . - . - . - "^IS\\w+(\\-\\d)?$"^^ . - . - "ORCiD" . - . - . - . - "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."^^ . - "cheminformatics" . - . - "false"^^ . - . - "Life cycle stages for Mus Musculus"^^ . - . - "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . - . - . - . - "protein" . - "^\\w{3}\\d+$"^^ . - . - "http://stormo.wustl.edu/ScerTF/details/"^^ . - . - . - . - "anatomy" . - . - "false"^^ . - "Ontology for General Medical Science" . - "toprea@salud.unm.edu" . - "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates."^^ . - . - . - . - . - "Regulation of Transcription"^^ . - "Lebanon Clinical Trials Registry" . - . - "false"^^ . - . - "gene expression" . - "This system submits an implementation plan to the Minister of Health, Labor and Welfare for clinical research conducted at medical institutions, etc. based on the provisions of the 'Clinical Research Act' and the 'Act on Ensuring Safety of Regenerative Medicine, etc.' It is a system for performing notification procedures such as In addition, based on the clinical research practice standards stipulated in the same law, we disclose information that the World Health Organization (WHO) requires to be disclosed, information that ensures the transparency of the research process, and information that contributes to the selection of participation in clinical research by the public. (translated from website)"^^ . - . - "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://biopragmatics.github.io/providers/sfam/$1"^^ . - "tokue" . - "Complex Portal" . - . - . - "http://purl.obolibrary.org/obo/HsapDv_"^^ . - . - . - . - . - . - "http://www.ebi.ac.uk/efo/EFO_"^^ . - . - "ChEMBL-Cells" . - "life science" . - . - "false"^^ . - . - "^[A-Za-z-0-9]+$"^^ . - "Publishing Workflow Ontology" . - "ontology" . - . - "genome" . - "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo="^^ . - "ideal" . - . - . - . - . - . - . - . - "^\\d{8}$"^^ . - . - "chemistry" . - . - "http://cellimagelibrary.org/images/$1"^^ . - "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . - "http://rdfs.org/ns/void#"^^ . - . - "chembl.compound" . - . - . - "false"^^ . - . - . - . - . - "life science" . - . - . - "mfmo" . - . - . - "computational biology" . - "https://fairsharing.org/organisations/"^^ . - "HomoloGene" . - "^\\d{7}$"^^ . - . - "12dgr161"^^ . - "eu89h" . - . - "http://purl.obolibrary.org/obo/RoleO_"^^ . - . - "epidemiology" . - "institution" . - . - . - . - . - "http://crdd.osdd.net/servers/virsirnadb/record.php?details="^^ . - . - . - . - . - . - "ontology" . - . - "^(bmr|bmse|bmst)?[0-9]{1,6}$"^^ . - . - "https://www.ebi.ac.uk/pdbe/entry/emdb/$1"^^ . - "cancer" . - . - . - . - . - "SNOMEDCT" . - "phylogenetics" . - . - "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id="^^ . - . - . - "false"^^ . - "0001350"^^ . - . - . - "http://purl.bioontology.org/ontology/npo#NPO_$1"^^ . - . - . - . - . - . - . - . - . - . - "5688061"^^ . - "https://bioregistry.io/dragondb.protein:"^^ . - . - "false"^^ . - . - . - . - . - "pencehe@oneonta.edu" . - . - . - . - . - . - "db-object-id"^^ . - . - . - . - . - . - . - "funcbase.yeast" . - "embryology" . - . - "life science" . - . - "Causal_Graphical_Model"^^ . - "meteorology" . - . - . - . - . - "false"^^ . - . - "false"^^ . - "ontology" . - "https://biopragmatics.github.io/providers/cemo/"^^ . - . - . - . - "protein" . - "paolo.romano@hsanmartino.it" . - "https://bioregistry.io/cghdb:"^^ . - "http://csbl.bmb.uga.edu/DOOR/operon.php?id=$1"^^ . - "http://purl.obolibrary.org/obo/DERMO_"^^ . - . - "ratmap" . - "false"^^ . - . - . - . - "http://data.food.gov.uk/codes/foodtype/id/$1"^^ . - "regulation" . - . - "bioregistry" . - . - "https://www-is.biotoul.fr/scripts/ficheIS.php?name="^^ . - . - . - "DB14938"^^ . + "Healthcare Common Procedure Coding System" . + "https://pypi.org/project/$1"^^ . + "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F$1"^^ . + . + . + "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . + "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species="^^ . + "Maize ontology" . + . + . + "ICEberg cis-integrative and mobilizable element" . + "Raymond Lee" . + "agriculture" . + . + "Unified Medical Language System Concept Unique Identifier" . + . + . + . + . + . + . + . + . + "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . + . + . + . + . + "medgen" . + "The ProteomeXchange provides a single point of submission of Mass Spectrometry (MS) proteomics data for the main existing proteomics repositories, and encourages the data exchange between them for optimal data dissemination."^^ . + . + "SIGNOR Relation" . + . + . + . + "co_358" . + . + . + "^[a-z0-9\\_]+$"^^ . + . + "An application ontology to represent genetic susceptibility to a specific disease, adverse event, or a pathological process."^^ . + . + "AphidBase Transcript" . + . + . + "Chemspider" . + "life science" . + "false"^^ . + "ovarian" . + . + "Guide to Pharmacology Target" . + . + "PXD000440"^^ . + "false"^^ . + "^\\d+$"^^ . + . + "panther.node" . + "Minimal set of terms for anatomy"^^ . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + "Documentation of HOGS (Homologous Organs Groups). Contains links to HOGs download, HOGs onthology, HOGs creation, composition, etc."^^ . + . + "movie" . + "^[A-Za-z_0-9]+$"^^ . + "http://purl.obolibrary.org/obo/ECTO_"^^ . + . + "dbmhc" . + . + . + "obo" . + . + . + "phenomics" . + "An ontology of processes triggered by homeostatic imbalance, with a focus on COVID-19 infectious processes."^^ . + . + . + "false"^^ . + "https://www.storedb.org/store_v3/study.jsp?studyId="^^ . + "conoserver" . + . + . + . + "ontology" . + "https://hl7.org/fhir/us/"^^ . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + "term"^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . +_:Nffebff26bbc4479fa3f91e9a82d84254 "Crop Ontology Helpdesk" . + "ontology" . + . + . + "protonet.proteincard" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "life science" . + "European Collection of Authenticated Cell Culture" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "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."^^ . + "^\\d+$"^^ . + . + . + "sabiork.compound" . + . + . + . + . + "Sirarat Sarntivijai" . + . + . + "https://www.pesticideinfo.org/chemical/$1"^^ . + . + "PathoPlant® is a database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. PathoPlant® also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment."^^ . + "false"^^ . + . + . + "kegg.drug" . + . + . + . + "biomedical science" . + . + "mcourtot@gmail.com" . + . + "life science" . + . + . + . + "ontology" . + "false"^^ . + . + . +_:Ne99dc73b20714efa88f5c99a1754101f "Crop Ontology Helpdesk" . + "This site contains a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase."^^ . + . + "co_345" . + "https://metazoa.ensembl.org/id/"^^ . + . + "vmhgene" . + "EAWAG Biocatalysis/Biodegradation Database" . + . + "^\\d{7}$"^^ . + . + . + "Gene Expression Ontology"^^ . + . + . + "^\\d{8}$"^^ . + . + "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."^^ . + "biomedical science" . + "miRNEST is a database of animal, plant and virus microRNAs, containing miRNA predictions conducted on Expressed Sequence Tags of animal and plant species."^^ . + "false"^^ . + "true"^^ . + . + . + . + "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + . + "ontology" . + . + "^\\d{7}$"^^ . + . + . + "ontology" . + . + "NONHSAT000001"^^ . + . + . + . + . + . + . + "umls" . + . + . + . + "nif.std" . + "false"^^ . + "jgrethe@ucsd.edu" . + . + . + . + "http://purl.org/dc/elements/1.1/$1"^^ . + "ontology" . + "false"^^ . + . + "M58335"^^ . + "^\\d{5}$"^^ . + . + "Human Induced Pluripotent Stem Cells Initiative" . + . + . + "ontology" . + "https://id.loc.gov/authorities/"^^ . + . + "00000003"^^ . + . + "mi" . + . + "00077f1c-c45a-47ba-8e6c-1bf6b6b43fce"^^ . + . + . + . + "^[0-9]+$"^^ . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to Locus information."^^ . + "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/"^^ . + . + . + "https://depmap.org/portal/cell_line/"^^ . + . + . + "regulation" . + . + "2842"^^ . + . + "ISCW007415"^^ . + . + "VIRsiRNA" . + . + "0002-1975-61"^^ . + . + . + "life science" . + . + . + . + "ICD9" . + . + "21723"^^ . + . + "^\\d{7}$"^^ . + . + . + . + "Locus Reference Genomic" . + . + "Ontology of Organizational Structures of Trauma centers and Trauma systems" . + "XAO represents the anatomy and development of the African frogs Xenopus laevis and tropicalis."^^ . + . + . + . + . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "obo" . + . + . + "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . + . + "Dan Brickley" . + "epso" . + . + . + . + . + "https://www.wwpdb.org/pdb?id=$1"^^ . + . + . + "false"^^ . + "business administration" . + . + . + . + . + . + "PIBASE is a collection of all protein structural interfaces extracted from the Protein Data Bank and PQS structure databases. Both chain-chain and domain-domain (SCOP and CATH definitions) interfaces are detected."^^ . + . + . + "^NONHSAT\\d{6}$"^^ . + "http://purl.uniprot.org/annotation/$1"^^ . + "https://www.genome.jp/virushostdb/$1"^^ . + "http://www.t3db.org/toxins/$1"^^ . + . + "^\\d{7}$"^^ . + "Mouse Developmental Anatomy Ontology with Theiler Stage" . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + "98"^^ . + . + . + . + "3dmet" . + . + . + . + . + . + . + "315.1"^^ . + . + "https://bioregistry.io/metaregistry/go/$1"^^ . + . + . + "0000001"^^ . +_:Nad42f8f18c534f0cb3d3fdabcabf743f "whocc@fhi.no" . + . + . + . + . + "experimental animal" . + . + . + . + . + . + "umbbd.compound" . + "1968"^^ . + "http://www.bootstrep.eu/ontology/GRO#$1"^^ . + . + . + "Publishing Roles Ontology" . + "RxNorm" . + . + "Peruvian Clinical Trial Registry" . + . + . + . + "100000000000001"^^ . + . + . + "1242"^^ . + . + . + "neurology" . + . + . + . + "Cell Signaling Technology Pathways" . + . + "^oai\\:cwi\\.nl\\:\\d+$"^^ . + . + . + . + "SECONDARY_CAS_RN" . + . + . + . + "toxoplasma" . + . + . + . + "mapping_justification"^^ . + "Common Anatomy Reference Ontology" . + . + "van_slyke@zfin.org" . + . + . + "obo" . + . + "ontology" . + "bigg.reaction" . + "co_320" . + "^M[0-9]{4,}$"^^ . + . + "obo" . + . + . + . + . + . + . + . + . + "http://www.ontology-of-units-of-measure.org/resource/om-2/"^^ . + "https://n2t.net" . + "CropMRespository is a database of soil and crop biophysical process models."^^ . + . + "https://caninecommons.cancer.gov/#/study/$1"^^ . + . + . + "MatrixDB is a freely available database focused on interactions established by extracellular matrix proteins, proteoglycans and polysaccharides"^^ . + . + . + . + . + . + . + "fypo" . + "Biolink Model Registry" . + . + . + "10343835"^^ . + . + . + . + . + . + . + "Erik.Segerdell@cchmc.org" . + "http://rulai.cshl.edu/cgi-bin/SCPD/getgene2?$1"^^ . + "SRX000007"^^ . + . + . + . + "Gerald Guala" . + "PyPI" . + "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."^^ . + . + . + . + . + "TF0001053"^^ . + . + . + "http://purl.obolibrary.org/obo/AGRO_$1"^^ . + . + . + . + "https://www.confident-conference.org/index.php/Event:$1"^^ . + "RDF Schema" . + . + . + . + "http://purl.obolibrary.org/obo/EMAPA_"^^ . + . + "^\\d{5}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^PR[0-9]{6}$"^^ . + . + . + . + "chemistry" . + "URS0000759CF4"^^ . + "small molecule" . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . + . + . + "life science" . + "http://www.proteinatlas.org/"^^ . + . + "obo" . + . + . + "EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)"^^ . + "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."^^ . + "SFB_COVID19_MW286762"^^ . + . + . + "https://w3id.org/oc/corpus/"^^ . + . + . + . + "arachnoserver" . + "true"^^ . + . + "false"^^ . + . + . + . + "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac=$1"^^ . + "https://run.biosimulations.org/simulations/$1"^^ . + . + . + "Mouse Developmental Anatomy Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "obo" . + "Supplier of mice for research purposes. [from RRID]"^^ . + . + "SNOMEDCT_US_2021_07_31" . + "false"^^ . + "an application ontology for supporting description and annotation of mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies."^^ . + . + "Drivers of human diseases including environmental, maternal and social exposures."^^ . + "false"^^ . + "17186"^^ . + "gene" . + "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id="^^ . + . + . + . + . + . + "agronomy" . + "life science" . + . + . + . + "https://medlineplus.gov/genetics/condition/"^^ . + . + . + . + "preclinical studies" . + . + . + . + . + "rxnorm" . + . + "BioPortal Prefixes" . + . + "vaccines" . + . + . + . + . + "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=$1"^^ . + . + . + "Identifier of a taxon or synonym in the Catalogue of Life"^^ . + . + "obo" . + "https://doulix.com/biomodules/$1"^^ . + "structure" . + . + "false"^^ . + "4685"^^ . + . + . + . + "http://fossilworks.org/?a=taxonInfo&taxon_no="^^ . + . + . + . + . + . + . + . + . + "IntAct Molecule" . + . + "spider" . + . + . + "prefixcommons" . + . + "pmap.substratedb" . + "0000012b-5661-2f63-2f73-b43980000000"^^ . + "database management" . + _:N6336578d53d547a592544f1d65a18759 . + . + . + . + "CHEMBL3307800"^^ . + . + . + "https://www.uniprot.org/keywords/$1"^^ . + . + . + . + . + "napdi" . + . + "false"^^ . + . + . + "HD+118-001"^^ . + . "^[A-Za-z0-9-]+$"^^ . - "kaggle" . - "ontology" . - "true"^^ . - "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1"^^ . - . - "http://www.w3.org/2003/11/swrl#"^^ . - . - . - . - "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . - . - . - "https://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id=$1"^^ . - "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."^^ . - . - . - . - . - "https://units-of-measurement.org/"^^ . - . - . - "rna" . - . - . - . - . - . - "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . - "http://mycobrowser.epfl.ch/marinosearch.php?gene+name="^^ . - "false"^^ . - . - "159787"^^ . - "^(C|D)\\d{6,9}$"^^ . - . - . - "Biolink Model" . - . - . - . - "cardiology" . - "^\\d{7}$"^^ . - . - . - "ontology" . - . - . - "ClassyFire" . - "life science" . - . - . - . - . - "ontology" . - . - . - . - "false"^^ . - "^DDInter\\d+$"^^ . - . - . - . - . - . - . - "Zebrafish Information Network Gene" . - . - . + "Vienna Drosophila Resource Center" . + . + "2d-page" . + "comparative genomics" . + . + . + "ontology" . + . + . + . + "cellosaurus" . + . + . + "Database of experimentally verified IRES structures" . + "false"^^ . + "biomedical science" . + "door" . + . + . + . + "https://www.ebi.ac.uk/gxa/genes/"^^ . + . + . + "http://www.jstor.org/stable/$1"^^ . + . + . + . + "false"^^ . + "knowledge and information systems" . + "goche" . + "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . + . + "http://edamontology.org/topic_"^^ . + . + . + . + "ECCODE" . + "^(\\w){3}$"^^ . + . + . + . + . + . + . + "Cube db" . + "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . + . + . + "http://purl.obolibrary.org/obo/COVOC_"^^ . + . + . + . + "AT1G01030.1"^^ . + . + . + . + "UniProtKB-SubCell" . + . + "48439"^^ . + "ised" . + "RSNA Informatics RadLex" . + . + "synthetic biology" . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "^\\d{7}$"^^ . + . + _:N18d11baf84d04ccaa32fc6ed3f139ddd . + "S-EPMC6266652"^^ . + . + . + . + . + "gene expression" . + . + . + . + . + . + "http://aber-owl.net" . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + . + "^\\d+$"^^ . + "Ontology for Chemical Kinetic Reaction Mechanisms" . + "http://www.transcriptionfactor.org/index.cgi?Search/Domain+domain:$1+cat:DBD"^^ . + . + "structure" . + "true"^^ . + . + . + . + . + "Vertebrate Skeletal Anatomy Ontology" . + "22-46615880-T-C"^^ . + . + "https://www.confident-conference.org/index.php/Event:"^^ . + "invertebrate" . + . + "schem" . + "ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases."^^ . + "protein" . + "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . + . + "https://www.ebi.ac.uk/metagenomics/projects/$1"^^ . + . + . + "^[0-9a-zA-Z\\.\\-\\_]+$"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/pubmed/"^^ . + "false"^^ . + _:N7474ab215e6849ba97c110a221df4162 . + . + . + "27106865"^^ . + . + "erm" . + . + . + . + "http://purl.obolibrary.org/obo/RO_$1"^^ . + . + . + "data sharing" . + . + "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."^^ . + . + "true"^^ . + "thomas@luetteke-online.de" . + . + . + . + . + . + . + . + "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession=$1"^^ . + "TrichDB" . + . + . + . + . + . + . + . + "Allyson Lister" . + . + . + . + . + "Sharkipedia Species" . + "https://run.biosimulations.org/simulations/"^^ . + . + "germplasma" . + . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + "life science" . + "0000000"^^ . + . + "bioinformatics" . + "0001"^^ . + "interaction" . + "sprint" . + . + . + . + . + . +_:Ndc164aac22f2496d8fe1558616e1d7dd "Vivian Lee" . + . + . + . + . + . + . + "false"^^ . + "An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)"^^ . + . + "Antibiotic Resistance Ontology" . + "bibliography" . + . + . + . + "false"^^ . + "life science" . + . + "clement.jonquet@inrae.fr" . + "helpdesk@cropontology-curationtool.org" . + "false"^^ . + . + "proglyc" . + . + "http://purl.obolibrary.org/obo/COLAO_$1"^^ . + "http://purl.obolibrary.org/obo/VHOG_$1"^^ . + "eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions."^^ . +_:Nd0865bd54b1d4b1f9895b1f6281f1800 "Crop Ontology Helpdesk" . + . + "http://purl.obolibrary.org/obo/CIO_$1"^^ . + . + . + "fao" . + . + "MarFun is manually curated database for marine fungi which is a part of the MAR databases."^^ . + . + . + . + . + "Endogenous retroviruses (ERVs) are common in vertebrate genomes; a typical mammalian genome contains tens to hundreds of thousands of ERV elements. Most ERVs are evolutionarily old and have accumulated multiple mutations, playing important roles in physiology and disease processes. The Human Endogenous Retrovirus Database (hERV) is compiled from the human genome nucleotide sequences obtained from Human Genome Projects, and screens those sequences for hERVs, whilst continuously improving classification and characterization of retroviral families. It provides access to individual reconstructed HERV elements, their sequence, structure and features."^^ . + . + . + . + "Fission Yeast Experimental Conditions Ontology" . + "dlxb" . + . + "Proteomics data and process provenance" . + . + "true"^^ . + . + . + . + "bioinformatics" . + . + "pubchem.classification" . + . + . + "ceph" . + . + "^\\d+$"^^ . + . + "A controlled vocabulary to describe phenotypic traits in plants."^^ . + "https://bioregistry.io/iceberg.ime:"^^ . + . + . + . + . + . + . + "https://biopragmatics.github.io/providers/hba/$1"^^ . + "https://schema.org/$1"^^ . + . + . + . + . + "NCBI Taxonomy" . + . + . + . + "false"^^ . + . + . + . + . + . + . + "00000000"^^ . + . + . + "false"^^ . + "ontology" . + "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac="^^ . + . + . + "viaf" . + . + . + . + "modeldb" . + . + . + "Selventa Diseases" . + "xlmod" . + . + "Michael K. Gilson" . + "http://biobanknetwork.telethon.it/Sample/View?sampleId="^^ . + "https://w3id.org/BCI-ontology#$1"^^ . + . + . + . + "model" . + . + "http://purl.obolibrary.org/obo/CTO_$1"^^ . + . + "Open Biological and Biomedical Ontologies" . + "rebase" . + . + . + "oslc" . + . + . + . + . + . + . + . + . + "protonet.cluster" . + . + "Hs635"^^ . + "^\\d+$"^^ . + . + "MEROPS Family" . + . + "Compluyeast-2D-DB" . + . + "medicine" . + . + . + . + . + . + "relations" . + . + . + . + . + "oryzabase.stage" . + . + . + . + . + . + "00000d53-99bc-4d3e-8ed7-6dc358baccb7"^^ . + . + "https://omabrowser.org/oma/hog/HOG:"^^ . + . + . + "http://www.bioinfo.org/NONCODEv4/show_gene.php?id=$1"^^ . . - "regulation" . - "archdb" . - . - . - "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains."^^ . - . - . - . - . - "fishbase" . - . - . - "has canonical" . - . - . - . - "https://bioregistry.io/prints:"^^ . - "http://biohackathon.org/resource/faldo#$1"^^ . - "cp390@cam.ac.uk" . - . - . - "DRKS00031815"^^ . - . - . - "NeuroLex Dysfunction" . - . - . - "Philippe.Lemercier@sib.swiss" . - "atc" . - . - "false"^^ . - . - . - "Jean-Luc Jannink" . - "PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry."^^ . - . - . - "false"^^ . - . - "obo" . - "biochemistry" . - . - . - . - "Mark Gerstein" . - . - "^\\d{7}$"^^ . - "gainesville.core" . - "false"^^ . - "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/browse_result.php?type=fam&fam_id=$1"^^ . - "^G(PL|SM|SE|DS)\\d+$"^^ . - . - . - "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . - . - . - . - . - "^ChiCTR\\d+$"^^ . - . - "ACH-000001"^^ . - . - "anatomy" . - . - . - "https://bioregistry.io/imgt.primerdb:"^^ . - . - . - . - . - "https://mmp.sfb.uit.no/databases/marfun/#/records/$1"^^ . - . - . - . - . - "flu" . - . - "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_$1"^^ . - . - "David Craik" . - . - "false"^^ . - "cell_model_passport" . - . - . - . - . - "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . - "UM-BBD compound" . - . - . - . - . - "obo" . - "https://www.ebi.ac.uk/miriam/main/"^^ . - "An ontology of human and animal behaviours and behavioural phenotypes"^^ . - . - . - . - "probesanddrugs" . - "neurobiology" . - . - "70"^^ . - . - "human" . - . - "datacommons" . - . - "https://biopragmatics.github.io/providers/hba/"^^ . - . - "false"^^ . - . - . - "iuphar.ligand" . - . - . - . - . - . - . - "satyasahoo@ieee.org" . - . - . - . - . - . - . - . - "fisheries science" . - . - . - "computational neuroscience" . - . - "Cell line databases/resources"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - "Andreas Ledl" . - "^\\d{7}$"^^ . - . - . - "^AS\\d{6}$"^^ . - . - . - "https://rpcec.sld.cu/en/trials/$1"^^ . - . - . - . - . - . - "protein-protein interactions" . - . - "Extensible Markup Language" . - . - "reo" . - . - . - "genomics" . - . - . - _:N612ccc06c1964e1ab2ea595e41a70881 . - . - "soybase" . - "botany" . - . - . - "Sharkipedia Trait" . - . - . - . - . - . - "life science" . - "Assists in resolving data across cloud resources."^^ . - . - . - . - . - "UMLS" . - "grin" . - . - . - . - "MAM01234c"^^ . - "1"^^ . - . - . - . - "^PIRSF\\d{6}$"^^ . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . - . - "pancreatic islet development" . - . - "ftt" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "life science" . - . - "fovt" . - . - "Shape Expression Vocabulary" . - . - "http://planttfdb.cbi.pku.edu.cn/tf.php?uid="^^ . - . - "http://string.embl.de/interactions/$1"^^ . - "nembase" . - . - . - . - . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . - . - . - . - "Mihail Anton" . - "https://www.gleif.org/lei/$1"^^ . - . - . - . - . - . - "edam.operation" . - "^\\d{8}$"^^ . - . - . - "D001151"^^ . - "ecology" . - "imsr_em" . - "ccdc" . - "transcriptomics" . - "GFAM" . - . - . - "datanator.reaction" . - . - . - . - . - . - "https://cropontology.org/rdf/CO_331:$1"^^ . - "true"^^ . - . - . - . - "life science" . - "biomedical science" . - . - "http://www.w3.org/XML/1998/namespace#$1"^^ . - . - "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code="^^ . - . - . - "pubmed"^^ . - . - . - "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA."^^ . - "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs)."^^ . - "frbr" . - . - "http://purl.obolibrary.org/obo/SEP_"^^ . - . - "The Bioinorganic Motif Database" . - . - . - . - . - "^MMP\\d+.\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "https://ecocyc.org/gene?id="^^ . - "ecology" . - "VMH reaction" . - . - "Units of measurement ontology" . - . - . + . + "computer science" . + . + . + "https://www.datanator.info/metabolite/$1"^^ . + . + "rna" . + . + . + "^\\d{8}$"^^ . + "http://purl.obolibrary.org/obo/OPL_$1"^^ . + "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks."^^ . + . + "^\\d+$"^^ . + . + . + . + . + "arXiv" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PCL_$1"^^ . + "perkinelmer" . + "validatordb" . + . + . + . + "false"^^ . + "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT="^^ . + . + . + "Signaling Gateway" . + . + "hybrid" . + . + . + "KEGG LIGAND" . + "false"^^ . + "BioCatalogue Service" . + . + . + . + "Tiffany J. Callahan" . + . + "biominder" . + . + . + "false"^^ . + . + "Unified Phenotype Ontology" . + "MNEST029358"^^ . + . + . + . + . + . + "data model" . + . + . + . + "14362"^^ . + "BRIP1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "The Statistical Methods Ontology" . + . + "^\\d+$"^^ . + "false"^^ . + . + . + . +_:Nb738ec851a6748268b17445305a9946c "William Bug" . + . + "dispositions" . + . + . + . + . + . + "http://www.bioguo.org/AnimalTFDB/family.php?fam=$1"^^ . + "false"^^ . + "https://fairsharing.org/"^^ . + . + . + "https://data.4dnucleome.org/experiment-set-replicates/"^^ . + . + . + "1a24"^^ . + . + . + . + . + . + . + . + . + "000912"^^ . + . + . + . + "Vitis ontology" . + "enzyme" . + . + "false"^^ . + . + . + . + . + . + "Porifera Ontology" . + . + "https://fairsharing.org/$1" . + "https://datalab.rwth-aachen.de/MINDER/resource/$1"^^ . + "structure" . + "CO_325" . + . + . + . + . + . + . + "engelsta@ohsu.edu" . + "food chemistry" . + . + "https://www.disprot.org/$1"^^ . + . + "Online Mendelian Inheritance in Animals" . + "https://civicdb.org/links/variant/$1"^^ . + . + . + "^\\d+(\\.\\d+(\\.\\d+(\\.\\d+)?)?)?$"^^ . + "anatomy" . + . + "Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and associated genes and variants in 363 animal species (other than human and mouse and rats and zebrafish, which have their own resources)."^^ . + "0000086"^^ . + "genome" . + "The SEED;" . + . + "seinet" . + "0000639"^^ . + . + "WikiPathways is a database of biological pathways maintained by and for the scientific community."^^ . + "https://www.ebi.ac.uk/interpro/genomeproperties/#"^^ . + "false"^^ . + "https://www.ebi.ac.uk/pdbsum/"^^ . + . + . + . + . + "ubprop" . + "http://purl.obolibrary.org/obo/PLO_"^^ . + . + . + "3905431"^^ . + . + "Animal Diversity Web (ADW) is an online database of animal natural history, distribution, classification, and conservation biology."^^ . + . + . + . + . + "Reactome" . + "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac=$1"^^ . + . + "ontology" . + . + "repository" . + . + . + . + "1001"^^ . + "Luis González-Montaña" . + "https://www.uniprot.org/database/" . + . + . + . + . + . + "https://ssbd.riken.jp/database/project/$1"^^ . + "http://sugarbind.expasy.org/"^^ . + "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . + . + "The Austrian Library Network (OBV) is the largest network of scientific and administrative libraries in Austria with 70 participants, representing more than 90 individual institutions - including the Austrian National Library, university libraries, the colleges of education, individual ministries, numerous technical colleges and other important collections."^^ . + . + . + . + "cell lines" . + "false"^^ . + . + . "rna" . - . - . - . - "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . - . - . - "lynn.schriml@gmail.com" . - . - "Microbial Conditions Ontology is an ontology..."^^ . - . - . - . - . - "141"^^ . - . - . - . - . - "obo" . - . - . - . - . - "immunology" . - . - "SIGNOR-C41"^^ . - "false"^^ . - . - . - "^[a-z]+(\\..*?)?$"^^ . - . - "https://lincs.hms.harvard.edu/db/sm/$1"^^ . - . - . - . - "anatomy" . - . - . - . - "88"^^ . - . - . - . - . - "InterPro" . - "agriculture" . - . - . - "false"^^ . - . - . - . - "1000001"^^ . - . - . - . - . - "0000032"^^ . - . - "biology" . - . - "rnacentral" . - "^[1-9][0-9]*$"^^ . - . - . - . - "^\\d+$"^^ . - . - . - . - . - "neurovault.image" . - . - . - . - "Sandra Orchard" . - . - . - . - "frederique.lisacek@isb-sib.ch" . - "https://cells.ebisc.org/$1"^^ . - . - "https://prosite.expasy.org/$1"^^ . - . - "WikiPathways Ontology" . - "hsapdv" . - . - "ontology" . - . - . - . - . - . - "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . - . - . - . - . - . - "hsa-let-7a-2-3p"^^ . - "http://purl.org/spar/biro/"^^ . - "ontology" . - "ontology and terminology" . - . - . - . - . - . - "0000125"^^ . - "obo" . - "ontology" . - . - "1001"^^ . - "Cell Biolabs cell line products" . - "BRENDA Ligand Group" . - . - . - "obo" . - . - "^\\d+$"^^ . - . - . - . - "false"^^ . - "http://purl.obolibrary.org/obo/ONTONEO_$1"^^ . - . - "^\\d+$"^^ . - . - "^\\d(\\d|\\w)$"^^ . - "patrice.buche@inrae.fr" . - . - . - "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies."^^ . - "https://www.genedb.org/gene/$1"^^ . - . - . - "bioportal" . - . - . - "0000423"^^ . - . - . - . - . - "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . - . - "Habronattus courtship" . - . - "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . - "genome" . - . - . - . - "commoncoreontology" . - . - "false"^^ . - "ontology" . - . - "pharmacy" . - . - . - . - . - . - . - . - . - . - . - "CATH domain" . - "false"^^ . - "JAX Mice" . - "cba" . - "http://purl.obolibrary.org/obo/COLAO_"^^ . - . - "SPIKE Map" . - "PubChem Classification" . - . - . - . - . - . - "safisher@upenn.edu" . - . - . - "C34"^^ . - . - "This collection contains various brain atlases from the Allen Institute." . - "http://purl.obolibrary.org/obo/MAXO_$1"^^ . - "SCTID" . - . - . - . - . - . - . - . - . - "MetaboLights Compound" . - "false"^^ . - "PXD000500"^^ . - . - . - "^\\d+$"^^ . - "https://hpscreg.eu/cell-line/$1"^^ . - . - "E-MTAB-2037"^^ . - . - "proteins" . - . - . - . - "false"^^ . - . - . - "F-SNP" . - . - . - . - "https://w3id.org/mixs/$1"^^ . - . - . - . - . - "structural biochemistry" . - . - . - "MMP0523"^^ . - "SABIO-RK Compound" . - . - . - . - . - . - . -_:N1ee708fba9894af0bfe9c04bade98c46 "helpdesk@cropontology-curationtool.org" . - . - . - . - . - "Ontology of standardized units"^^ . - . - . - . - . - . - _:Nb01e8f454a334f6aa890c77212852321 . - . - "https://cropontology.org/rdf/CO_335:$1"^^ . + "kegg.genes" . + "estdab" . + "mmusdv" . + . + . + "Allergy"^^ . + "http://www.ebi.ac.uk/astd/geneview.html?acc="^^ . + . + . + . + . + "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . + "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid=$1"^^ . + "http://www.arachnoserver.org/toxincard.html?id="^^ . + . + . + "https://www.ebi.ac.uk/metagenomics/samples/$1"^^ . + "https://terminology.hl7.org/CodeSystem-v3-"^^ . + . + . + . + . + . + . + . + . + "dictyBase" . + "false"^^ . + . + . + . + . + . + "A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, and ants)"^^ . + . + "false"^^ . + . + "67035"^^ . + . + "http://www.w3.org/ns/shacl#"^^ . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "gene" . + . + . + . + . + . + . + . + . + . + "viroligo" . + "life science" . + "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . + "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:"^^ . + "EGID" . + . + "https://gudmap.org/id/"^^ . + "http://lincsportal.ccs.miami.edu/cells/#/view/$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."^^ . + . + . + "Disease Drivers Ontology" . + "developmental biology" . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_func_$1"^^ . + . + . + "ido" . + . + . + . + . + "NIH Human Embryonic Stem Cell Registry" . + "^\\d{7}$"^^ . + "2.1.1"^^ . + . + . + . + "obo" . + "rat" . + "^[1-9][0-9]*$"^^ . + . "^\\d{7}$"^^ . - "mro" . - "40565"^^ . - . - . - "A10BA02"^^ . - . - "7123"^^ . - . - "The reviewer of a prefix" . - . - . - . - . - . - . - . + . + . + . + "^\\d+$"^^ . + . + . + . + "^ChiCTR\\d+$"^^ . + . + "irct" . + "sopharm" . + "https://cropontology.org/rdf/CO_320:"^^ . + . + . + "genomics" . + . + "false"^^ . + . + . + . + . + "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."^^ . + . + "nutritional science" . + . + "Gainesville Core Ontology" . + . + . + . + . + . + . + "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project."^^ . + "Welcome to the web site of the Handle.Net Registry (HNR), run by Corporation for National Research Initiatives (CNRI). CNRI is a Multi-Primary Administrator (MPA) of the Global Handle Registry (GHR), authorized by the DONA Foundation to allot prefixes to users of the Handle System. The DONA Foundation is a non-profit organization based in Geneva that has taken over responsibility for the evolution of CNRI's Digital Object (DO) Architecture including outreach around the world. One of the Foundation's responsibilities is to administer and maintain the overall operation of the GHR, a task that was previously performed by CNRI. (from website)"^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/probe/?term="^^ . + "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."^^ . + . + . + . + . + . + . + . + . + "00050"^^ . + "MINID Test" . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PLANA_$1"^^ . + . + . + "ecology" . + "https://pir.georgetown.edu/cgi-bin/ipcSF?id=$1"^^ . + . + "http://swissregulon.unibas.ch/query/$1"^^ . + "true"^^ . + "^PA\\d+$"^^ . + . + "demographics" . + "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."^^ . + . + . + "anatomy" . + . + . + . + . + "nemo2" . + . + . + . + . + "http://www.icd9data.com/getICD9Code.ashx?icd9=$1"^^ . + . + . + . + "ontology" . + "zachll@umich.edu" . + "ArrayMap" . + "This is a record of the Bilateria anatomy terminology and ontology. We have been unable to find any further information about this resource."^^ . + "mmsinc" . + . + . + . + . + . + "^(ISBN)?(-13|-10)?[:]?[ ]?(\\d{2,3}[ -]?)?\\d{1,5}[ -]?\\d{1,7}[ -]?\\d{1,6}[ -]?(\\d|X)$"^^ . + . + . + . + "0000001"^^ . + . + . + . + "http://purl.obolibrary.org/obo/BSPO_$1"^^ . + "SIGNOR-C41"^^ . + . + "Controlled vocabulary pertaining to RNA function and based on RNA sequences, secondary and three-dimensional structures."^^ . + . + . + . + . + "ArachnoServer" . + . + "CIViC variant" . + . + . + "micro" . + "rna" . + "http://purl.obolibrary.org/obo/AGRO_"^^ . + . + "16129"^^ . + "cstr" . + . + "EGAS00000000001"^^ . + . + . + . + . + "ShiBASE" . + . + "http://purl.obolibrary.org/obo/ZP_"^^ . + "John Graybeal" . + . + . + . + "http://genomics.senescence.info/genes/details.php?id="^^ . + . + . + "An ontology describing the anatomical structures and characteristics of Porifera (sponges)"^^ . + . + . + . + "nje5@georgetown.edu" . + . + . + "obo" . + . + . + "false"^^ . + "Provenance, Authoring, and Versioning Vocabulary" . + "umls.aui" . + "UBERON" . + "The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format."^^ . + . + "ontology" . + "Gene Normal Tissue Expression" . + . + "bco" . + . + . + . + . + "^CPX-[0-9]+$"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "health science" . + . + . + . + "false"^^ . + . + "Federica Quaglia" . + . + . + . + "56305849200"^^ . + "^\\d{7}$"^^ . + . + "Simple Standard for Sharing Ontological Mappings" . + _:Neadaa30113554d4c98ff0c2fc706641b . + . . - . - . - "http://purl.obolibrary.org/obo/FBcv_"^^ . - . - "phenxtoolkit" . - "csv"^^ . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/GAZ_$1"^^ . - . - "Cluster of orthologous genes" . - . - . - . - . - . - . - . - . - . - . - "ontology" . - . - "life science" . - "sequence" . - "SIDER (Side Effect Resource) is a public, computer-readable side effect resource that connects drugs to side effect terms. It aggregates dispersed public information on side effects. This collection references side effects of drugs as referenced in SIDER."^^ . - "false"^^ . - . - . - "phylogenetics" . - "human" . - . - . - . - . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/DRON_"^^ . - "metaproteomics" . - "PhosphoPoint Kinase" . - . - . - . - . - "https://cropontology.org/rdf/CO_348:"^^ . - . - "ontology" . - . - . - "JMChandonia@lbl.gov" . - . - . - "Matthew Brush" . - "^\\w+$"^^ . - . - . - "Project"^^ . - . - "false"^^ . - . - "c elegans" . - . - . - "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code="^^ . - . - . - . - "Scholarly Contributions and Roles Ontology" . - "has download URL" . - "obo" . - . - "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."^^ . - "https://bioregistry.io/vsdb:"^^ . - . - . - . - . - "false"^^ . - . - "ENVO" . - . - "http://purl.org/spar/cito/$1"^^ . - . - . - . - . - . - . - . - "^(?:\\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\\d+)?)$"^^ . - . - . - . - . - . - . - . - . - . - "classification" . - . - . - "botany" . - "http://www.cellsignal.com/products/$1.html"^^ . - . - "^\\d{7}$"^^ . - . - . - "protein" . - . - "preclinical studies" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/AERO_$1"^^ . - . - "false"^^ . - "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . - . - . - . - . - . - "http://zfin.org/"^^ . - . - . - "dbsnp" . - . - "false"^^ . - "^\\d+$"^^ . - . - . - "Taconic Biosciences" . - . - . - . - . - . - . - "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."^^ . - . - "BioCatalogue Service" . - . - . - . - . - "ChEMBL target" . - . - . - "bitbucket" . - . - . - . - . - . - . - "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."^^ . - . - . - . - . - "hasDbXref"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - "morpheus" . - "false"^^ . - . - "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."^^ . - "false"^^ . - . - "mco" . - . - "https://loinc.org/"^^ . - . - . - . - "synthetic biology" . - . - . - "vsmo" . - "gold.genome" . - . - "B00162"^^ . - . - . - . - "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)."^^ . - . - . - "http://www.nlm.nih.gov/cgi/mesh/2012/MB_cgi?mode=&index=$1&view=expanded"^^ . - . - . - . + . + "TripleExpression"^^ . + . + "http://purl.obolibrary.org/obo/GNO_$1"^^ . + . + . + . + "parasitology" . + "Pearl millet Trait Dictionary in template 5 - ICRISAT/INERA - April 2016"^^ . + "wikipedia.en" . + "mcc" . + "The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, and information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors."^^ . + . + "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."^^ . + "ISO Object Identifier" . + "Rebecca Jackson" . + . + . + "C12345"^^ . + . + . + . + . + . + . + . + "Biofactoid" . + . + _:Ncff35745bc0b4cb4882876319048a670 . + . + . + . + . + . + "KC-0979"^^ . + . + "merops.entry" . + . + . + "http://purl.obolibrary.org/obo/FIDEO_$1"^^ . + "medicine" . + "http://www.proglycprot.org/detail.aspx?ProId=$1"^^ . + . + "EC number" . + "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id="^^ . + . + . + "https://biopragmatics.github.io/providers/pba/$1"^^ . + "phenomics" . + "^\\d+$"^^ . + . + "https://www.wicell.org/home/stem-cells/catalog-of-stem-cell-lines/$1.cmsx?closable=true"^^ . + . + . + . + . + . + "small molecule" . + "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."^^ . + . + . + . + "Terminologia Embryologica" . + . + . + . + . + . + . + "HMDB00001"^^ . + "ZINC1084"^^ . + . + . + . + "Store DB" . + "awalker@apa.org" . + . + "http://sideeffects.embl.de/drugs/$1"^^ . + . + "Small Angle Scattering Biological Data Bank" . + . + "ontology" . + "The GeoNames geographical database covers all countries and contains over eleven million placenames that are available for download free of charge."^^ . + . + "false"^^ . + "cellbank.australia" . + . + "phenotypes" . + "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."^^ . + . + "myco.marinum" . + . + "celia.michotey@inrae.fr" . + . + . + . + "abm" . + "https://bioregistry.io/ppdb:"^^ . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + . + . + "genome" . + . + "164750"^^ . + . + "DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action."^^ . + . + . + . + . + . + "false"^^ . + "systems biology" . + "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . + . + "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1"^^ . + . + . + "ChemBank is a public, web-based informatics environment created by the Broad Institute's Chemical Biology Program and funded in large part by the National Cancer Institute's Initiative for Chemical Genetics (ICG)."^^ . + . + . + . + "yrcpdr" . + . + . + . + "https://www.pirbright.ac.uk/node/"^^ . + . + . + . + . + "paxdb.organism" . + . + . + . + . + . + "life-cycle" . + "p.buttigieg@gmail.com" . + "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie="^^ . + "hbvar" . + "SNOMEDCT_2005_07_31" . + . + "The purpose of the UniProtKB/Swiss-Prot variant pages is: to display the variant related information extracted from UniProtKB/Swiss-Prot, and to provide useful additional information such as the conservation of the modified residues across orthologous species."^^ . + . + . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by dataset."^^ . + "false"^^ . + . + "A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis."^^ . + . + . + . + . + "OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across vertebrates, arthropods, and fungi. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database of orthologs presents available protein descriptors, together with Gene Ontology and InterPro attributes, which serve to provide general descriptive annotations of the orthologous groups"^^ . + . + . + . + . + . + . + . + . + . + "1868"^^ . + "true"^^ . + "^\\d{7}$"^^ . + . + "The Arabidopsis Information Resource" . + "http://purl.obolibrary.org/obo/XCO_$1"^^ . + "https://www.biozol.de/en/product/"^^ . + "G00054MO"^^ . + . + . + "SNOMEDCT_2010_1_31" . + . + . + . + . + . + . + . + . + . + . "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . - "nxr" . - "http://edamontology.org/operation_$1"^^ . - . - "^\\d+$"^^ . - . - . - . - "https://biopragmatics.github.io/providers/dmba/"^^ . - . - "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."^^ . - _:N17cb05833e8648b0b00adfc7b9e48962 . - "1000003"^^ . - . - . - "0019171"^^ . - . - . - "Q-2958"^^ . - . - . - . - . - . - "http://scop.berkeley.edu/sunid="^^ . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Locus"^^ . - . - "ontology and terminology" . - . - _:N107b1aebb90649278084a97fd9727b0c . - "GPM32310002988"^^ . - . + . + . + "false"^^ . + . + . + "Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols."^^ . + "DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders"^^ . + . + . + "AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology"^^ . + . + . + . + . + . + . + "0000071"^^ . + "false"^^ . + "^[1-9]\\d*$"^^ . + "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"^^ . + "PharmGKB Gene" . + . + . + "968"^^ . + "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:"^^ . + "glycomics" . + . + . + . + . + "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid=$1"^^ . + "genomics" . + . + . + "genome" . + "erik.vannimwegen@unibas.ch" . + . + . + . + . + . + . + . + "https://bioregistry.io/bacmap.map:"^^ . + . + "swh" . + "http://www.cathdb.info/cathnode/"^^ . + "ontology" . + "UMLSSG" . + . + . + . + . + . + . + "ribocentre" . + . + "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id="^^ . + "systems biology" . + . + . + . + . + "Ribocentre" . + . + . + . + . + "drug" . + . + "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."^^ . + . + "cheminformatics" . + . + . + . + "HsapDv" . + . + "zea" . + . + . + "http://purl.obolibrary.org/obo/DINTO_$1"^^ . + . + . + "life science" . + . + . + "false"^^ . + "life science" . + . + . + . + "false"^^ . + "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]."^^ . + "rnavdb" . + . + "dna" . + "https://www.yeastgenome.org/locus/$1"^^ . + "MESHA" . + . + . + . + . + . + "annethessen@gmail.com" . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + "http://purl.org/spar/bido/"^^ . + . + "metagenomics" . + "disease" . + . + "http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=$1"^^ . + "^\\d{7}$"^^ . + "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."^^ . + "12300"^^ . + . + "http://open-services.net/ns/core#$1"^^ . + "Catalogue of Life" . + . + . + "false"^^ . + . + "genecards.geneloc" . + . + . + "NLXSUB" . + . + . + "3355"^^ . + "meteorology" . + . + "PubChem Cell Line" . + . + . + "Google Books" . + "^\\d{7}$"^^ . + "false"^^ . + . + . + "mathematics" . + . + . + . + . + . + "false"^^ . + . + "gpcrdb" . + . + "Ontology of Zebrafish Experimental Conditions"^^ . + "http://purl.obolibrary.org/obo/OGI_"^^ . + _:Na829664083dd4fbeb40853897acda040 . + "^\\d+$"^^ . + "fovt" . + . + . + . + "statistics" . + . + "^\\d+$"^^ . + "obo" . + "fcb" . + "Arabidopsis Small RNA Project is a repository of data on Arabidopsis small RNA genes."^^ . + . + . + . + . + "genome" . + . + . + "Long Term Ecological Research Controlled Vocabulary" . + . + . + . + . + . + . + . + "http://ensembl.org/glossary/ENSGLOSSARY_$1"^^ . + . + "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."^^ . + . + . + "environmental science" . + "SM00015"^^ . + . + . + . + "false"^^ . + . + . + "mutant" . + "https://bioregistry.io/resolve/github/issue/$1"^^ . + "0000618"^^ . + "^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$"^^ . + "Workflow"^^ . + "oharb@pcbi.upenn.edu" . + . + . + . + . + . + . + . + . + "https://web.expasy.org/cellosaurus/cellopub/$1"^^ . + . + . + "orthodb" . + "https://bioregistry.io/vdrc:"^^ . + . + . + . + "ontology" . + "true"^^ . + "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key="^^ . + . + . + "https://cropontology.org/rdf/CO_366:"^^ . + . + "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."^^ . + . + "Rosemary Shrestha" . + . + . + . + "100"^^ . + . + "ontology" . + . + "false"^^ . + "false"^^ . + "N0000001662"^^ . + . + . + "LINCS Protein" . + "proteomicsdb.protein" . + "International Protein Index" . + . + "genomics" . + . + . + . + . + "CIViC Therapy" . + . + . + "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."^^ . + "alleles" . + . + "obo" . + "pathway" . + . + . + . + . + "hesa" . + "false"^^ . + "Ensembl Metazoa, the Ensembl database for accessing genome-scale data from non-vertebrate metazoa." . + . + . + "PANTHER Pathway" . + . + . + . + . + "0001885"^^ . + . + "http://purl.obolibrary.org/obo/DISDRIV_"^^ . + . + "3618"^^ . + "true"^^ . + . + "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . + "frederic.bastian@unil.ch" . + "aaindex" . + . + . + . + "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem=$1"^^ . + . + "false"^^ . + . + "http://www.pantherdb.org/pathway/pathCatDetail.do?clsAccession="^^ . + . + . + "PharmacoDB Datasets" . + "BindingDB is the first public database of protein-small molecule affinity data."^^ . + . + . + . + . + "vbase2" . + "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."^^ . + . + "Functional Requirements for Bibliographic Records Entity-Relationship Model" . + "upper-level ontology" . + . + "LINCS Small Molecule" . + . + "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."^^ . + "false"^^ . + "true"^^ . + "http://bioportal.bioontology.org/ontologies/"^^ . + . + . + . + . + . + "Carrine Blank" . + "ontology" . + . + . + . + . + "life science" . + . + . + . + "Structural Classification of Proteins - Unique Identifier" . + . + "epigenetics" . + "biomedical science" . + "inbred" . + . + . + . + . + "ontology" . + . + . + "http://cegg.unige.ch/orthodb/results?searchtext="^^ . + . + "obo" . + . + . + "131392"^^ . + "conference" . + . + . + "false"^^ . + . + "true"^^ . + "https://archive.softwareheritage.org/browse/swh:"^^ . + "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."^^ . + . + . + "bmrb.restraint" . + . + . + . + "Name-to-Thing" . + . + "Mark Engelstad" . + . + . + "mesh.vocab" . + . + "life science" . + "^[0-9]+$"^^ . + "developmental biology" . + . + . + "^(E|D|S)RR[0-9]{6,}$"^^ . + "drug discovery" . + "false"^^ . + "COlleCtion of Open Natural ProdUcTs" . + "A structured controlled vocabulary of phenotypes of the slime-mould Dictyostelium discoideum."^^ . + . + . + "An ontology describing phenomena encountered in the literature surrounding neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, tauopathies, and related protein aggregation diseases."^^ . + . + . + . + . + "false"^^ . + . + "BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. It more published genome-scale metabolic networks into a single database with a set of stardized identifiers called BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations, and metabolites are linked to many external databases (KEGG, PubChem, and many more). This collection references model compartments."^^ . + . + . + "medicine" . + "REFSEQ_PROT" . + . + . + "botany" . + "false"^^ . + . + "pseudogene.org" . + "KEGG.DRUG" . + . + . + "1-55516888-G-GA"^^ . + . + . + . + "Crop Ontology Curation Tool" . + . + . + "^\\d{7}$"^^ . + . + . + "NeuroVault Image" . + . + "gmelin" . + . + . + . + "oio" . + "ecyano.entity" . + . + . + "ontology" . + . + . + . + . + "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.subtiwiki.uni-goettingen.de/wiki/index.php/$1"^^ . + "https://bioregistry.io/p3db.site:"^^ . + "https://purl.dataone.org/odo/ADCAD_$1"^^ . + . + . + "mKIAA4200"^^ . + . + . + . + . + "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." . + . + _:N497517396e9a4f43959d71e6099fbdfd . + "co_338" . + . + . + "https://cropontology.org/rdf/CO_338:$1"^^ . + . + . + "https://bioregistry.io/cldb:"^^ . + . + . + "MAMpol005339"^^ . + . + . + . + . + . + "PWY3O-214"^^ . + "^\\d+$"^^ . + . + "sequenced strain" . + "SNOMEDCT_US_2021_03_01" . + . + "scop" . + "Jeffrey Wong" . + . + "urn:nbn:fi:tkk-004781"^^ . + . + "^[0-9]+$"^^ . + . + . + "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."^^ . + . + . + . + "false"^^ . + "DBSALT001211"^^ . + . + . + . + "virmirdb" . + . + . + . + "GenAtlas is a database containing information on human genes, markers and phenotypes."^^ . + . + . + . + . + "The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for UniProtKB protein sequences."^^ . + . + . + "https://scicrunch.org/scicrunch/interlex/view/ilx_$1"^^ . + . + "sharkipedia.species" . + . + . + . + "https://hamap.expasy.org/unirule/"^^ . + "http://h-invitational.jp/hinv/spsoup/locus_view?hix_id="^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/ONTOAVIDA_"^^ . + . + "gene" . + "subject agnostic" . + . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id="^^ . + . + . + . + "CIViC gene" . + . + . + "None"^^ . +_:N406478f8588d430e9efe5acde38344ea "helpdesk@cropontology-curationtool.org" . + "^\\d+$"^^ . + . + "crossref.funder" . + "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."^^ . + . + . + "pathway" . + "UK Higher Education Statistics Agency" . + . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + . + . + "echinobase" . + . + "false"^^ . + "https://bioregistry.io/elm:"^^ . + . + "Pathogen Host Interaction Phenotype Ontology" . + . + . + "obo" . + . + "http://bigg.ucsd.edu/models/universal/reactions/$1"^^ . + "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."^^ . + "veNOG12876"^^ . + "Call for paper topics in EasyChair"^^ . + . + . + . + . + . + "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus=$1"^^ . + . + . + . + "^\\d+$"^^ . + . + "obo" . + "genome" . + . + . + . + "A collection of ontologies relevant for chemistry.\n\nSkipped:\n- DOLCE (dead links)" . + . + "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."^^ . + "false"^^ . + . + . + . + "https://bioregistry.io/metaregistry/biocontext/$1" . + "http://www.jstor.org/stable/"^^ . + . + . + . + . + "false"^^ . + . + "gene" . + "https://depmap.org/portal/cell_line/$1"^^ . + . + . + . + "dna" . + . + . + . + . + "IGSN is a globally unique and persistent identifier for material samples and specimens. IGSNs are obtained from IGSN e.V. Agents."^^ . + . + . + . + "Blue Brain Project Topological sampling Knowledge Graph" . + . + "0000008"^^ . + . + . + "astrophysics and astronomy" . + . + . + "eVOC (Expressed Sequence Annotation for Humans)" . + . + "288"^^ . + . + "Studies in dbVar."^^ . + "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."^^ . + "false"^^ . + . + . + "MLCommons Association artifacts, including benchmark results, datasets, and saved models."^^ . + . + . + . + . + . + . + "ontology" . + . + . + . + . + . + "GeoNames Feature Code" . + . + . + . + . + "https://fungidb.org/fungidb/app/record/gene/$1"^^ . + "biomedical science" . + . + . + "India Clinical Trials Registry" . + "The SENSO ontology is designed to provide classification terms for labeling sensitive data for data archival and sharing."^^ . + . + . + "The Cell Version Control Repository is the single worldwide version control repository for engineered and natural cell lines"^^ . + . + "ontology" . + . + . + "https://cropontology.org/rdf/CO_341:$1"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "Harry Caufield" . + . + . + . + "^\\w{3}\\d+$"^^ . + . + . + . + . + . + . + . + "life science" . + . + "structure" . + . + "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E."^^ . + . + . + "Golm Metabolome Database Analyte" . + . + . + . + "Protein covalent bond" . + . + . + . + . + . + . + . + . + . + "isni" . + . + . + "francesco.vitali@ibba.cnr.it" . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + "chemistry" . + "An ontology that enables the description of reviews of scientific articles and other scholarly resources."^^ . + "false"^^ . + "http://purl.org/spar/c4o/$1"^^ . + . + "NIF Standard Ontology" . + "pathway" . + . + "http://www.cathdb.info/cathnode/$1"^^ . + . + . + . + "Search Tool for Retrieval of Interacting Genes/Proteins" . + . + . + . + . + . + . + "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id="^^ . + "Resource" . + . + . + . + . + . + . + "wicell" . + "narcis.fernandez@gmail.com" . + . + "https://pubchem.ncbi.nlm.nih.gov/bioassay/$1"^^ . + "dna" . + . + "https://biopragmatics.github.io/providers/cemo/$1"^^ . + . + . + "sisu" . + "biocuration" . + "syoid" . + "Protein Affinity Reagents (PSI-PAR) provides a structured controlled vocabulary for the annotation of experiments concerned with interactions, and interactor production methods. PAR is developed by the HUPO Proteomics Standards Initiative and contains the majority of the terms from the PSI-MI controlled vocabular, as well as additional terms."^^ . + . + . + "https://icd.who.int/browse11/l-m/en#/http://id.who.int/icd/entity/"^^ . + . + . + . + "http://pax-db.org/#!protein/"^^ . + . + "^\\d+$"^^ . + "genome" . + "Cell line collections (Providers)"^^ . + "proteomics" . + "^(cl|tum)\\d+$"^^ . + . + "The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies."^^ . + "http://purl.obolibrary.org/obo/WBls_$1"^^ . + . + "Pfam" . + . + "SNOMEDCT_US" . + "structure" . + . + . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Marker."^^ . + . + "LipidBank is an open, publicly free database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins."^^ . + "International repository of Adverse Outcome Pathways."^^ . + . + "life science" . + . + "^[A-Za-z0-9]+$"^^ . + . + . + "false"^^ . + . + . + "biology" . + . + . + "obo" . + . + . + "false"^^ . + "MedDRA" . + "2244"^^ . + "structure" . + . + "http://www.hmdb.ca/metabolites/"^^ . + . + . + "geography" . + "^((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + . + "^\\d+$"^^ . + . + . + . + "chemistry" . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + "HL7 V2 Code Systems" . + "http://senselab.med.yale.edu/ORDB/Data/$1"^^ . + . + . + . + . + . + "^[0-9]+$"^^ . + . + "http://purl.obolibrary.org/obo/OOSTT_"^^ . + "A modern method of records management and an automated cross-referenced subject index for accurate and comprehensive information retrieval developed by the US FDA's Bureau of Foods"^^ . + . + . + "ontology" . + "obo" . + . + . + "ESi007-A"^^ . + . + "The Intermediate Filament Database functions as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants."^^ . + "https://www.signalingpathways.org/datasets/dataset.jsf?doi=$1"^^ . + . + . + "Database for integrating species source of natural products & connecting natural products to biological targets via experimental-derived quantitative activity data.\n"^^ . + . + . + . + . + . + . + "https://vocab.org/vann/$1"^^ . + . + "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."^^ . + . + . + . + . + . + . + . + . + "1058367"^^ . + . + . + . + "bsg-000052"^^ . + . + . + . + . + "http://www.genome.jp/dbget-bin/www_bget?ec:$1"^^ . + . + . + "https://cropontology.org/rdf/CO_340:"^^ . + "obo" . + "false"^^ . + "life science" . + "dg.f82a1a" . + "Common Access to Biological Resources and Information Project" . + . + . + . + . + . + . + . + "Chemical Information Ontology" . + . + . + . + . + "Nematode & Neglected Genomics" . + . + . + "research" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CL_"^^ . + "The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities."^^ . + . + . + . + . + . + . + . + . + "biomedical science" . + "^\\d{8}$"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://biomodels.net/rdf/vocabulary.rdf#$1"^^ . + "MESH_DESCRIPTOR_UI" . + . + "dmba" . + "Nathan Edwards" . + . + "drug repositioning" . + . + "gene expression" . + "brendanx@uw.edu" . + . + . + . + "https://lincs.hms.harvard.edu/db/proteins/$1"^^ . + "life science" . + . + . + "YRC PDR" . + "experiment" . + "false"^^ . + . + . + . + "stem cell" . + "cell_biolabs" . + "biomedical science" . + . + . + . + "pdb" . + "SEO is a reference ontology for modelling data about scientific events such as conferences, symposioums and workshops."^^ . + "mirte" . + "small molecule" . + . + "dideo" . + . + . + . + . + . + . + "375364"^^ . + . + . + "hcvdb" . + . + . + . + "dg.6vts" . + . + "Polygenic Score Catalog" . + "BDGP gene disruption collection provides a public resource of gene disruptions of Drosophila genes using a single transposable element."^^ . + "bio.tools" . + "http://purl.obolibrary.org/obo/VSMO_$1"^^ . + . + . + . + . + "NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases."^^ . + . + "embryo" . + "^\\d+$"^^ . + . + "kclb" . + . + . + . + . + "^D\\d+$"^^ . + . + . + . + . + "kestrelo" . + "nlx.br" . + "49"^^ . + . + . + . + "Animal Trait Ontology for Livestock" . + "http://genecards.weizmann.ac.il/geneloc-bin/marker_cards.pl?id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + "The health Surveillance Ontology (HSO) focuses on \"surveillance system level data\", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. It aims to support One-Health surveillance, covering animal health, public health and food safety surveillance."^^ . + . + . + . + "health science" . + "life science" . + . + . + . + "Dawood B. Dudekula" . + . + . + . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . + . + "http://purl.obolibrary.org/obo/FLOPO_"^^ . + "^HGVPM\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "dbg2introns" . + . + . + . + . + "sugarbind" . + "Biomaterial supply resource which collects, maintains, and distributes independent transgenic fly lines. Most of the 38,000 fly lines are RNAi lines, but VDRC also maintains a collection of enhancer-GAL4 driver lines. Nearly all lines are in duplicate. Users can search for the stocks or DNA constructs for the gene of interest by entering CG number, synonym, or Transformant ID. [from RRID]"^^ . + . + . + "0000139"^^ . + . + . + . + "genome" . + . + . + . + . + . + . + "http://edamontology.org/data_$1"^^ . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/INO_$1"^^ . + "MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes."^^ . + "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references."^^ . + . + . + . + . + "Relation Ontology" . + "SchemaDefinition"^^ . + . + . + "https://civicdb.org/links/assertions/"^^ . + "humIGHV025"^^ . + . + "Interlab Cell Line Collection" . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_cell_"^^ . + . + "CLPUB00496"^^ . + . + . + "structure" . + . + "4195"^^ . + "SEED Compound" . + . + . + . + "https://www.obofoundry.org/ontology/$1" . + . + "gnomad" . + . + . + . + "monique.zahn@sib.swiss" . + . + . + . + . + . + "International Standard Book Number" . + . + "fetus" . + . + . + . + . + "oncology" . + . + . + . + . + "classification" . + . + . + . + . + . + . + . + . + "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id=$1"^^ . + "phenotype" . + "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."^^ . + "Jesualdo Tomás Fernández-Breis" . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID=$1"^^ . + . + "https://www.nextprot.org/term/FA-"^^ . + . . - . - . - "https://www.bgee.org/gene/$1"^^ . - "KEGG_DRUG_GROUP" . - "http://purl.obolibrary.org/obo/EUPATH_$1"^^ . - . - "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . - . - . - "biocyc" . - . - "0000400"^^ . - . - . - . - "uberon" . - "Pierre-Yves LeBail" . - "https://www.ebi.ac.uk/interpro/entry/pfam/"^^ . - "scop.sunid" . - . - . - . - . - . - "has URI prefix" . - . - "life science" . - "^PMC\\d+$"^^ . - . - . - . - "DAPK1"^^ . - "^\\d+$"^^ . - . - . - . - "https://dbpedia.org/ontology/$1"^^ . - . - "Maize Trait Dictionary in template 5 - CIMMYT- September 2016"^^ . - . - . - "Common Access to Biological Resources and Information Project" . - . - . - . - "false"^^ . - . - "https://www.jax.org/strain/"^^ . - . - . - . - . - "life science" . - . - . - "protein" . - . - "BloodPAC" . - . - . - "gomfid" . - . - . - . - "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code=$1"^^ . -_:N9a58aee7324d447d80a82ed73e348c46 "CTCAE Help" . - . - "Human Phenotype Ontology" . - . - . - "http://purl.obolibrary.org/obo/PECO_"^^ . - . - . - . - . - "ontology" . - . - "http://ensembl.org/glossary/ENSGLOSSARY_$1"^^ . - "GPST000024"^^ . - "marilyn.safran@weizmann.ac.il" . - "biomedical science" . - "ExAC Transcript" . -_:Nc5efd8506e27413980b3c557b7d6565f "Ramesh Verna" . - . - . - . - "DisProt is a database of intrinsically disordered proteins and protein disordered regions, manually curated from literature."^^ . - . - "BBA0001"^^ . - . - . - . - "metabolites" . - . - . - "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . - . - "http://purl.obolibrary.org/obo/OHD_"^^ . - "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . - . - . - . - . - . - . - . - . - . - "false"^^ . - . - . - "ICD9CM" . - . - . - . - . - "life science" . - "oral surgery" . - . - . - . - . - "0001000"^^ . - . - "Natural Product Activity and Species Source Database" . - "RGD Disease Ontology" . - . -_:N6d2a57bcd6da4511b6f2ea2a501201de "ted@tklein.com" . - "Applied Biological Materials cell line products" . - . - . - . - . - "false"^^ . - "4390079"^^ . - . - . - . - . - . - "1000000"^^ . - . - "false"^^ . - "developmental biology" . - "kisao" . - . - . - "grin.taxonomy" . - . - "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . - . - . - "^CL\\d+$"^^ . - . - "International Fungal Working Group Fungal Barcoding." . - . - "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . - . - "obi" . - . - . - "chenyangnutrition@gmail.com" . - . - . - "^\\d{7}$"^^ . - . - . - "100000001"^^ . - "false"^^ . - . - . - . - "http://purl.obolibrary.org/obo/EO_"^^ . - . - "false"^^ . - . - "dna" . - . - "classification-model"^^ . - "Ontology Concept Identifiers" . - . - . - . - . - . - . - . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "reaction" . + . + . + . + "^\\S+$"^^ . + . + "protein" . + . + "0000632"^^ . + . + . + "http://purl.org/dc/dcmitype/"^^ . + . + . + . + "tahe" . + . + . + . + "false"^^ . + . + "Collagen Mutation Database" . + . + "snctp" . + "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId="^^ . + "vectorbase" . + . + "false"^^ . + . + . + . + . + . + . + . + "http://www.alanwood.net/pesticides/$1.html"^^ . + "^cpd\\d+$"^^ . + . + . + "2"^^ . + "taxon" . + . + . + "^AC[0-9]{8}$"^^ . + . + . + . + "gene expression" . + "pubchem_id" . + "Tatsuya Kushida" . + "ontology" . + . + . + . + . + . + . + "688"^^ . + "omp" . + . + "UniProt Diseases" . + . + "MaizeGDB Locus" . + . + "RNACentral" . + . + "0001290"^^ . + . + "Val Wood" . + . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + . + . + . + "co_350" . + "0000046"^^ . + . + . + "biomedical science" . + . + . + . + "^IPR\\d{6}$"^^ . + . + . + . + "false"^^ . + "ontology" . + . + "gene" . + "Browser for the periodic table of the elements"^^ . + . + "pharmacology" . + . + "https://mednet-communities.net/inn/db/ViewINN.aspx?i=$1"^^ . + . + . + . + . + "0000013"^^ . + . + "knowledge and information systems" . + "Carissa Park" . + . + "https://flowrepository.org/id/"^^ . + "http://www.whocc.no/atcvet/atcvet_index/?code=$1"^^ . + . + "protein" . + . + "small molecule" . + "dsm4" . + "^\\d+$"^^ . + . + . + . + . + . + . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . + "biomaterial" . + . + . + "^\\d+$"^^ . + . + "botany" . + "openalex" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PGDSO_"^^ . + . + . + . + . + "LigandBox" . + "false"^^ . + . + "interaction" . + . + "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$"^^ . + . + "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."^^ . + "http://www.receptors.org/nucleardb/proteins/$1"^^ . + "http://mirbase.org/cgi-bin/mature.pl?mature_acc=$1"^^ . + "research" . + "obo" . + . + "http://ddinter.scbdd.com/ddinter/interact/$1"^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_func_"^^ . + . + "false"^^ . + . + . + . + "Barley ontology" . + "http://www.genome.jp/dbget-bin/www_bget?cpd:"^^ . + . + . + . + . + . + . + "controlled vocabularies" . + . + . + . + . + . + "false"^^ . + . + . + . + "life science" . + "PesticideInfo chemical ID" . + . + . + "wikipathways.vocab" . + "false"^^ . + . + . + "SKIP is aiming to promote the exchange of information and joint research between researchers by aggregating various information of stem cells (iPS cells, iPS cells derived from patients, etc.) to stimulate research on disease and regenerative medicine."^^ . + "comparative genomics" . + . + "https://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist="^^ . + "phismith@buffalo.edu" . + "000000001"^^ . + "rnaloops" . + . + "dna" . + . + "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation."^^ . + "^PA\\w+$"^^ . + . + "This collection contains the many prefixes for the different repackaging of the International Classification of Diseases (ICD) throughout its major revisions." . + "0000189"^^ . + "http://cellimagelibrary.org/images/$1"^^ . + "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid=$1"^^ . + "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . + "neXtProt family" . + . + "dinto" . + . + . + . + . + . + . + . + . + . + . + "http://ecmdb.ca/compounds/"^^ . + . + "botany" . + . + . + . + "000000341"^^ . + . + . + . + . + "eugenes" . + "/53355/cl010066723"^^ . + . + "mediadive.ingredient" . + "disease" . + . + . + "LINCS Cell" . + . + "FAIRsharing User" . + . + "PROSITE" . + . + "https://www.arabidopsis.org/servlets/TairObject?type=locus&name="^^ . + "ontology" . + . + "^[0-9]{5}(-[a-zA-Z0-9-]{0,7})?$|^[0-9]{10}$"^^ . + . + . + "false"^^ . + "MESH" . + "http://www.w3.org/2000/01/rdf-schema#"^^ . + . + . + "ontology" . + . + . + . + "CAA71118.1"^^ . + "HUMAN16963"^^ . + . + . + "systems biology" . + "false"^^ . + "botany" . + "life science" . + . + . + "http://comgen.pl/mirex1/?page=results/record&name=$1&exref=pp2a&limit=yes"^^ . + "protein" . + "^DDB_G\\d+$"^^ . + . + . + . + . + . + . + . + . + . +_:N368ac74c696846f0a3f1d215ab684b1f "GenBank Support" . + . + . + . + "eggNOG" . + "R. Burke Squires" . + . + "http://www.3dmet.dna.affrc.go.jp/cgi/show_data.php?acc=$1"^^ . + "Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combinations of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format."^^ . + "https://scicrunch.org/scicrunch/interlex/view/ilx_"^^ . + "false"^^ . + "life science" . + . + "ricenetdb.gene" . + . + "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."^^ . + . + . + . + . + . + "NRFC051"^^ . + "http://www.cathdb.info/cathnode/"^^ . + . + . + . + "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e="^^ . + . + "https://animaldiversity.org/accounts/$1"^^ . + . + . + . + . + "drugbank.target" . + "false"^^ . + "pdb-ccd" . + . + "PTPN1"^^ . + "Applied Biological Materials cell line products" . + . + . + "http://purl.obolibrary.org/obo/LEPAO_"^^ . + . + "PANTHER Node" . + . + . + . + . + "virus" . + "mir" . + . + "^[0-9]{10}$"^^ . + "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"^^ . + "uniprot.isoform" . + "venom" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MP_"^^ . + "http://purl.obolibrary.org/obo/GEO_$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."^^ . + . + . + "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . + "MOSAiC Ontology" . + . + . + . + . + . + "Collection"^^ . + "projects_to"^^ . + "An identifier for a resource or metaresource." . + "GPCR Natural Variants database" . + . + . + . + . + "slm" . "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. "^^ . - . - . - "proteomics" . - . - "https://nci-crdc.datacommons.io/ga4gh/drs/v1/objects/"^^ . - "AB1925000"^^ . - . - . - . - "false"^^ . - "false"^^ . - "false"^^ . - . - . - . - "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . - "CDC2"^^ . - . - . - "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . - "http://purl.obolibrary.org/obo/SCDO_$1"^^ . - . - "biomedical science" . - . - . - "http://edamontology.org/data_$1"^^ . - "European Nucleotide Archive" . - . - . - . - . - . - "false"^^ . - . - . - "https://covid19.sfb.uit.no/api/records/"^^ . - "http://id.nlm.nih.gov/mesh/vocab#$1"^^ . - "Open Digital Rights Language Ontology" . - . - . - . - . - . - . - "biochemistry" . - . - "EC number" . - . - . - . - "pmap.cutdb" . - . - . - . - . - "^[OPQopq][0-9][A-Za-z0-9]{3}[0-9]|[A-Na-nR-Zr-z][0-9]([A-Za-z][A-Za-z0-9]{2}[0-9]){1,2}$"^^ . - . - "http://purl.obolibrary.org/obo/ZEA_$1"^^ . - . - . - "Kaggle" . - "^\\d+$"^^ . - "intenz" . - . - . - . - . - "crisprdb" . - . - "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . - . - . - "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)."^^ . - "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . - . - "mbrochhausen@uams.edu" . - "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."^^ . - "http://www.w3.org/ns/adms#$1"^^ . - "pdc.study" . - . - "0000012b-5661-2f63-2f73-b43980000000"^^ . - . - . - . - . - . + . + "lutz.fischer@tu-berlin.de" . + . + . + "false"^^ . + "false"^^ . + "https://tools.ietf.org/rfc/rfc"^^ . + "ontology" . + . + "biomedical science" . + "genetics" . + . + "bioinformatics" . + "BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML)."^^ . + "nucc.taxonomy" . + . + "cell" . + . + . + . + "ArachnoServer (www.arachnoserver.org) is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. It include a molecular target ontology designed specifically for venom toxins, as well as current and historic taxonomic information."^^ . + "true"^^ . + . + . + . + . + "biology" . + . + . + . + "https://www.proteomicsdb.org/#human/proteinDetails/"^^ . "ekaterina.chuprikova@eurac.edu" . - "false"^^ . - . - "computer science" . - "ontology" . - . - "National Experimental Cell Resource Sharing Platform" . - . - . - . - . - "adw" . - "0000630"^^ . - . - . - . - . - "NPC139585"^^ . - . - . - "2"^^ . - . - . - . - "^\\d{7}$"^^ . - "0002066"^^ . - . - . - . - . - "Publons publication" . - "Australian New Zealand Clinical Trials Registry" . - "genome" . - . - . - . - . - "ISO 15926-14" . - . - . - "omia" . - . - . - . - "DBSALT001211"^^ . - "Lindsay Cowell" . - . - . - . - . - . - "functional genomics" . - . + . + . + "^ML\\w+$"^^ . + "^\\d+$"^^ . + . + . + . + "obo" . + "biomedical science" . + "NIAID ChemDB ID" . + . + "false"^^ . + . + . + . + "The database focuses on the comparative genomics of Shigella and provides a way to summarize large volumes of genomic and comparison data in a visually intuitive format."^^ . + "agriculture" . + . + . + . + . + . + "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."^^ . + . + . + "functional genomics" . + "Fababean ontology" . + "^\\d+$"^^ . + . + "false"^^ . + . + . + "ontology" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#$1"^^ . + . + . + . +_:N02158d1ce8ce424abc89d4bad17cc26b "custserv@nlm.nih.gov" . + "CALIPHO Group Ontology of Human Anatomy" . + "animal" . + . + "pmid" . + "ECMDB00005"^^ . + . + . + . + . + . + . + . + . + "ontology" . + "true"^^ . + . + . + . + "false"^^ . + "MultiCellDS" . + . + . + "subject agnostic" . + . + "^\\d+$"^^ . + . + . + . + . + "https://hdl.handle.net/hdl:20.500.12582/"^^ . + "henrich@embl.de" . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/nlmcatalog/"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/INO_"^^ . + "http://purl.uniprot.org/annotation/"^^ . + . + . + . + "trans" . + "false"^^ . + . + . + . + "https://www.ebi.ac.uk/chembl/compound/inspect/$1"^^ . + . + . + . + "https://bioregistry.io/ligandexpo:"^^ . + "906801"^^ . + "true"^^ . + "false"^^ . + "yperez@ebi.ac.uk" . + . + . + "datacommons" . + "http://www.pharmgkb.org/gene/"^^ . + "http://purl.obolibrary.org/obo/DERMO_"^^ . + . + . + "false"^^ . + "https://glytoucan.org/Structures/Glycans/$1"^^ . + . + . + "false"^^ . + . + . + "https://www.genenames.org/cgi-bin/gene_symbol_report?match=$1"^^ . + . + "false"^^ . + "A vocabulary for describing semantic assets, defined as highly reusable metadata (e.g. XML1 schemata, generic data models) and reference data (e.g. code lists, taxonomies, dictionaries, vocabularies)."^^ . + . + "deo" . + . + . + . + . + "0001157"^^ . + . + . + . + "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115=$1"^^ . + . + . + "false"^^ . + . + . + "The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. It provides information on the sequence and target of individual transcription factors."^^ . + . + . + "http://purl.obolibrary.org/obo/CTO_"^^ . + "CATH is a classification of protein structural domains. We group protein domains into superfamilies when there is sufficient evidence they have diverged from a common ancestor. CATH can be used to predict structural and functional information directly from protein sequence."^^ . + "DeBiO" . + "^PPR\\d+$"^^ . + "ncithesaurus" . + . + . + _:N406478f8588d430e9efe5acde38344ea . + . + . + . + "https://www.animalgenome.org/CorrDB/q/?id=CorrID:$1"^^ . + . + . + "lbo" . + "Human Phenotype Ontology" . + . + "Lindsay.Cowell@utsouthwestern.edu" . + "false"^^ . + . + "SNOMEDCT" . + . + . + . + . + . + . + "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/ols/ontologies/nmrcv/terms?short_form=NMR:"^^ . + . + . + "NIF Standard Ontology: Cognitive Function" . + "false"^^ . + . + . + . + . + . + . + . + . + . + "ev" . + . + . + . + "false"^^ . + . + "protein" . + . + "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid="^^ . + . + "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."^^ . + . + "Alejandra Gonzalez-Beltran" . + . + "false"^^ . + . + "SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt."^^ . + . + . + . + "http://usefulinc.com/ns/doap#$1"^^ . + . + . + "Database of rare diseases and related terms, including symptoms, healthcare resources, and organizations supporting research of the disease."^^ . + . + . + "http://purl.bioontology.org/NEMO/ontology/NEMO.owl#NEMO_"^^ . + . + . + "dsonensh@odu.edu" . + "CNP0171505"^^ . + . + . + "http://umbbd.ethz.ch/servlets/pageservlet?ptype=p&pathway_abbr="^^ . + "http://bigg.ucsd.edu/models/universal/metabolites/$1"^^ . + . + "http://purl.obolibrary.org/obo/PROPREO_$1"^^ . + . + . + "fairsharing.organization" . + . + . + "xmetdb" . + . + . + . + "false"^^ . + . + . + . + . + "Inge Jonassen" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/HABRONATTUS_"^^ . + . + . + "https://mediadive.dsmz.de/solutions/$1"^^ . + "life science" . + . + . + "http://purl.obolibrary.org/obo/OAE_$1"^^ . + . + "developmental biology" . + "pd_st" . + . + . +_:N4b239e856348428b86c8044d5a72bbff "European Food Safety Authority" . + . + . + . + "interfil" . + . + . + . + . + "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."^^ . + . + "pdb.ligand" . + . + "AllSomeInterpretation"^^ . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + "2526"^^ . + . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas=$1"^^ . + "preclinical studies" . + . + "false"^^ . + . + . + . + "0000000"^^ . + . + . + . + . + "false"^^ . + "biotools" . + . + . + . + "Jörg Overmann" . + . + "tgn" . + . + "ontology" . + . + "genome" . + "MultiCellDS Digital snapshot" . + . + . + . + "ORCiD" . + . + "NCIT_Thesaurus" . + . + . + . + . + . + "http://www.molmovdb.org/cgi-bin/morph.cgi?ID=$1"^^ . + "false"^^ . + "HL7 V2 Code Systems" . + "mf" . + "Karen Eilbeck" . + "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . + "http://eugenes.org:7072/.bin/fbidq.html?$1"^^ . + . + "Event (INOH pathway ontology)" . + . + "The Python Package Index (PyPI) is a repository for Python packages."^^ . + "This website provides access to our 2003 and 2005 miRNA-Target predictions for Drosophila miRNAs"^^ . + . + "https://www.metanetx.org/chem_info/$1"^^ . + "anatomy" . + . + . + . + . + "Genotype Ontology" . + . + . + . + . + "reaxys" . + . + "bioinformatics" . + . + . + . + . + "tair.gene" . + . + . + "trait" . + . . - . - . - "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . - . - . - . - . - . - . - . - "PRI10"^^ . - "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . - . - . - "Martin Kuiper" . - . - "dbmhc" . - "gene expression" . - "The GenPept database is a collection of sequences based on translations from annotated coding regions in GenBank."^^ . - . - . - "rdf" . - "^[0-9a-z_-]+$"^^ . - "LDS-1110"^^ . - . - "90801"^^ . - "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . - . - . - . - "jeffvin.wong@utoronto.ca" . - . - . - "ACTRN12623000498695"^^ . - "natural history" . - "obo" . - . - . - . - "Image Data Resource (IDR) is an online, public data repository that seeks to store, integrate and serve image datasets from published scientific studies. We have collected and are continuing to receive existing and newly created “reference image\" datasets that are valuable resources for a broad community of users, either because they will be frequently accessed and cited or because they can serve as a basis for re-analysis and the development of new computational tools."^^ . - "false"^^ . - . - . - . - . - . - . - . - . - . - "molecular chemistry" . - "YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references."^^ . - . - "publishing" . - "0000066"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_br_"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - "^rs\\d+$"^^ . - "pharmacogenomics" . - . - "vac" . - "confident.event" . - . - "^[A-Za-z0-9+_.%-:]+$"^^ . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . - . - . - . - "OBO Metadata Ontology" . - "http://degradome.uniovi.es/cgi-bin/protease/$1"^^ . - . - . - . - . - . - "miriam" . - . - . - . - . - . - . - . - "genetics" . - . - . - . - "The Data Science Ontology is a research project of IBM Research AI and Stanford University Statistics. Its long-term objective is to improve the efficiency and transparency of collaborative, data-driven science."^^ . - . - . - . - "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . - . - . - . - . - . - "hcao" . - . - . - . - . - . - . - . - . - "0000041"^^ . - "^[A-Za-z 0-9]+$"^^ . - . - "fcsfree" . - . - . - "ChemDB" . - . - "http://purl.obolibrary.org/obo/RNAO_$1"^^ . - . - "EDAM Ontology" . - "^\\d+$"^^ . - . - . - "medical informatics" . - . - . - . - . - . - . - . - . - . - . - . - . - "systemic neuroscience" . -_:N6d2a57bcd6da4511b6f2ea2a501201de "W. Ted Klein" . - "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . - "https://www.uniprot.org/journals/$1"^^ . - . - . - . - "http://purl.obolibrary.org/obo/XCO_$1"^^ . - "ChemIDplus is a web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. It also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest."^^ . - . - . - . - "^\\d{5}$"^^ . - "https://www.perkinelmer.com/searchresult?searchName=$1"^^ . - "false"^^ . + . + "dct" . + "Association-Rule-Based Annotator" . + "false"^^ . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . + "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac="^^ . + "23159291"^^ . + "^\\d+$"^^ . + . + . + "linikujp@gmail.com" . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid="^^ . + . + . + . + . + "Gramene Growth Stage Ontology" . + . + . + . + "SNOMEDCT_US_2022_12_31" . + . + "Cell Line Ontology [derivative]" . + "cmf" . + . + "chemistry" . + "CranioMaxilloFacial ontology" . + "Sciflection" . + . + . + "false"^^ . + "microarray" . + . + "ontology" . + . + "false"^^ . + . + . + . + "http://www.yeastract.com/view.php?existing=locus&orfname="^^ . + "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"^^ . + "https://bioregistry.io/csd:"^^ . + "false"^^ . + "http://www.lipidmaps.org/data/LMSDRecord.php?LMID="^^ . + "101775319"^^ . + "genetics" . + "Cell line collections (Providers)"^^ . + "medical microbiology" . + "hpscreg" . + . + . + "ontology" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "NCI Drug Dictionary ID" . + "0005452"^^ . + "taxonomy" . + "BioGRID is a database of physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe."^^ . + . + . + "The Gene Expression Atlas (GXA) is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. This collection references genes."^^ . + "false"^^ . + "An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the Drosophila melanogaster."^^ . + . + . + . + "http://purl.obolibrary.org/obo/MIRO_"^^ . + "knowledge and information systems" . + "The ALlele FREquency Database" . + "life science" . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/wildCore/detail/"^^ . + "3966782"^^ . + . + "pandey@jhmi.edu" . + . + . + . + . + . + . + . + . + . + . + "cmpo" . + _:N161c830f834442a4b8b33f16f6be7221 . + . + . + "^\\d+$"^^ . +_:N8250527cbee1453c9f2a02a7ba72613f "Maria Herrero" . + . + . + . + "false"^^ . + . + . + . + . + . + "ucas" . + . + "GCA_000155495.1"^^ . + "false"^^ . + "A representation of the variety of methods used to make clinical and phenotype measurements."^^ . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + "ForwardStrandPosition"^^ . + "NONHSAG00001"^^ . + "false"^^ . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id="^^ . + . + "^UMIN\\d+$"^^ . + . + "4"^^ . + . + . + "genomics" . + . + . + "biomedical science" . + . + . + . + "life science" . + . + "http://bactibase.hammamilab.org/$1"^^ . + . + . + . + . + . + "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . + "https://www.disprot.org/"^^ . + "Linear double stranded DNA sequences" . + . + . + . + . + . + . + . + . + . + "hmsl_id" . + . + . + . + . + . + . + . + . + "phenotype" . + "cas_id" . + "Variant Groups in CIViC provide user-defined grouping of Variants within and between genes based on unifying characteristics. CIViC curators are required to define a cohesive rationale for grouping these variants together, summarize their relevance to cancer diagnosis, prognosis or treatment and highlight any treatments or cancers of particular relevance"^^ . + . + . + "false"^^ . + . + . + . + "MSH" . + . + . + "UBREL" . + "false"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "^EGAD\\d{11}$"^^ . + . + "Cardiovascular Disease Ontology" . + "taxonomy" . + . + . + "dce" . + . + . + . + . + "Open Data for Access and Mining" . + . + "ontology" . + "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId=$1"^^ . + . + "Unipathway" . + "00000443"^^ . + . + . + . + . + . + "MSH2010_2010_02_22" . + "false"^^ . + "metabolite" . + . + . + "false"^^ . + . + . + . + . + . + "AT5G05330"^^ . + . + . + "drduke" . + . + . + "http://www.cathdb.info/cathnode/$1"^^ . + "https://cellmodelpassports.sanger.ac.uk/passports/"^^ . + "NIF Standard Ontology: OEN Terms in Neurolex" . + . + . + . + . + . + . + . + "cvx" . + "http://purl.obolibrary.org/obo/OBCS_"^^ . + . + . + . + . + . + "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . + . + . + "MGnify Project" . + . + "false"^^ . + . + . + . + . + . + . + "drosophilidae" . + . + "biomedical science" . + . + . + . + . + . + "A database of fly neurons and pathways with an associated 3D viewer."^^ . + . + "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession="^^ . + . + . + . + . + "00573"^^ . + . + . + . + "false"^^ . + . + "0002233"^^ . + . + . + "life science" . + . + . + . + . + . + . + "https://www.ebi.ac.uk/ega/datasets/$1"^^ . + . . - . - "model" . - . - . - . - "http://purl.obolibrary.org/obo/CEPH_$1"^^ . - . - "pathway" . - . - "0000205"^^ . - "BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity."^^ . - . - "1200031"^^ . - . - "FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge."^^ . - . - "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID="^^ . - . - . - . - . - . - . - . - . - "life science" . - "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . - . - . - . - "0000003"^^ . - "^5\\d{4}$"^^ . - . - . - . - . - "https://transyt.bio.di.uminho.pt/reactions/"^^ . - . - . - . - "bioinformatics" . - . - "^DP\\d{5}r\\d{3}$"^^ . - . - . - . - . - "^\\w{5}\\.\\d{2}\\..*$"^^ . - "rna" . - . - "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . - "1009107926"^^ . - . - . - . - . - "Human Plasma Membrane Receptome Families" . - . - . - "jwest@rcsb.rutgers.edu" . - "botany" . - . - "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . - "^\\d{7}$"^^ . - "https://cropontology.org/rdf/CO_347:$1"^^ . - . - . - . - "graingenes.symbol" . - "https://www.swisslipids.org/#/entity/SLM:$1"^^ . - . - . - . - . - "false"^^ . - . - "gamete" . - "fix" . - "Lucas Leclere" . - . - . - . - . - . - "Agronomy Ontology" . - "https://sorgerlab.github.io/famplex/$1"^^ . - "The MetNet database (MetNetDB) contains information on networks of metabolic and regulatory and interactions in Arabidopsis. Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another."^^ . - . - "pubchem.element" . - "https://cropontology.org/rdf/CO_347:"^^ . - . - . - . - "SD00043"^^ . + "biomedical science" . + . + "^\\d+$"^^ . + . + "Anne Thessen" . + . + "bakerc@unb.ca" . + . + . + . + . +_:Nf61f2d7c1ff54380bf84884a9c9d8f51 "af8d@nih.gov" . + . + . + "plant breeding" . + . + "true"^^ . + . + . + "Planarian Phenotype Ontology is an ontology of phenotypes observed in the planarian Schmidtea mediterranea."^^ . + . + . + "Panorama Public" . + . + "dmendez@ebi.ac.uk" . + "ERM00000044"^^ . + "lonza" . + . + . + . + "true"^^ . + . + . + . + "false"^^ . + . + "Stress Knowledge Map" . + "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."^^ . + . + "false"^^ . + . + "^\\w\\d{4}\\w\\d{2}(\\-[35])?$"^^ . + "clinical trials" . + "National Repository of Fish Cell Lines" . + "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."^^ . + . + "medicine" . + . + . + "gold" . + "http://champ-project.org/images/ontology/cao.owl#CAO_$1"^^ . + . + . + . + . + . + "chemistry" . . - . - "ydpm" . - "ontology" . - . - . - . - . - . - . - . - "obo" . - "ontology" . - "obo" . - "protein" . - . - . - "http://hawaii.eagle-i.net/i/$1"^^ . - . - . - . - "nomen" . - "false"^^ . - "FullySpecifiedAtom"^^ . - "dna" . - . - "false"^^ . - "CALIPHO Group Ontology of Human Anatomy" . - . - "eukaryotic" . - "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]"^^ . - "http://www.conoserver.org/?page=card&table=protein&id=$1"^^ . - . - . - "noaa" . - . - "http://purl.obolibrary.org/obo/LBO_"^^ . - . - "Jianmin Wu" . - . - . - . - "ontology" . - . - "https://schema.org/"^^ . - . - "genetic" . - "obo" . - . - . - "sequence" . - "dna" . - "GRSDB is a database of G-quadruplexes and contains information on composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in the eukaryotic pre-mRNA sequences, including those that are alternatively processed (alternatively spliced or alternatively polyadenylated). The data stored in the GRSDB is based on computational analysis of NCBI Entrez Gene entries and their corresponding annotated genomic nucleotide sequences of RefSeq/GenBank."^^ . - . - . - . - "life science" . - "botany" . - . - . - "India Clinical Trials Registry" . - . - . - . - "The Degradome Database contains information on the complete set of predicted proteases present in a a variety of mammalian species that have been subjected to whole genome sequencing. Each protease sequence is curated and, when necessary, cloned and sequenced."^^ . - . - _:N08e1f9097d1b4dae9796095cf1ebccef . - . - . - "SubstrateDB" . - . - . - . - "The Aspergillus Genome Database (AspGD) is a repository for information relating to fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. This collection references gene information."^^ . - . - "^\\d+$"^^ . - . - "roundworm" . - "molecular biology" . - "biomodels.kisao" . - . - "https://www.ebi.ac.uk/arrayexpress/experiments/"^^ . - "pesticides" . - . - . - . - . - . - . - . - . - . - . - "United States Patent and Trademark Office" . - . - "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . - . - "http://purl.obolibrary.org/obo/DDPHENO_"^^ . - "http://purl.obolibrary.org/obo/PD_ST_"^^ . + . + "ICD-10" . + . + . + . + . + . + . + . + . + . + "ontology" . + "http://purl.obolibrary.org/obo/ATO_$1"^^ . + . + "http://www.semanticweb.org/pallabi.d/ontologies/2014/2/untitled-ontology-11#"^^ . + "Database of human Major Histocompatibility Complex" . + "https://www.merckmillipore.com/catalogue/item/$1"^^ . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode=$1"^^ . + . + . + . + "00020007"^^ . + . + . + . + . + . + . + . + "rna" . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references individual images."^^ . + . + . + "cells" . + . + "^\\d+$"^^ . + . + . + "domain" . + . + . + . + . + "ontology" . + . + . + . + . . - "false"^^ . - . - "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + "false"^^ . + . + "Emotion Ontology" . + . + "^\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/DINTO_"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "MESHCS" . + . + . + "false"^^ . + . + "KIAA0001"^^ . + . + . + . + . + . + "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"^^ . + . + . + . + . + "Ryan Brinkman" . + . + "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_"^^ . + "infectious disease medicine" . + "cido" . + . + . + . + "botany" . + "obo" . + . + . + . + . + . + . + "treebase" . + . + "false"^^ . + . + "metabolite" . + . + "https://cropontology.org/rdf/CO_323:$1"^^ . + . + "false"^^ . + . + . + "3532759"^^ . + . + . + . + "genomics" . + "protein" . + . + . + . + . + . + . + . + "gene" . + . + "false"^^ . + "pathguide" . + . + "NIF Standard Ontology: Chemical" . + . + . + "^\\d+$"^^ . + . + "taxonomy" . + . + . + "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."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^8\\d{4}$"^^ . + "graingenes.reference" . + . + "true"^^ . + . + . + "mfomd" . + . + . + . + "false"^^ . + "false"^^ . + . + "protein" . + "false"^^ . + "neurobiology" . + . + "larvae" . + . + . + . + "true"^^ . + "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."^^ . + "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)."^^ . + . + . + "ogsf" . + "https://rism.online/$1"^^ . + . + "cheminformatics" . + . + . + . + . + . + . + . + "obo" . + . + . + . + . + "^\\w+$"^^ . + "^(R)?PXD\\d{6}$"^^ . + . + . + "NeuroLex Anatomy" . + . + . + . + . + . + "gramene.reference" . + . + . + . + "BibliographicRecord"^^ . + . + . + . + . + . + "^(ZINC)?\\d+$"^^ . + . + . + . + "EROP-Moscow is a curated oligopeptide (2-50 amino acid residues) sequence database which strives to provide a high level of annotations (such as descriptions of the structure of an oligopeptide, its source and function, post-translational modifications, etc.)."^^ . + "^\\d{9,9}$"^^ . + "come" . + "^[AMCST][0-9x][0-9]$"^^ . + . + . + "https://ssbd.riken.jp/database/dataset/$1"^^ . + . + "fly" . + . + . + "https://bartoc.org/en/node/$1" . + . + "Standards and Ontologies for Functional Genomics (SOFG) Anatomy Entry List" . + . + . + "vendor" . + . + "true"^^ . + . + "0011140"^^ . + . + . + . + . + "Drug-drug Interaction and Drug-drug Interaction Evidence Ontology" . + "The nomenclature used for named reactions in text mining software from NextMove. While it's proprietary, there are a few publications listing parts. 487/1,855 have mappings to the Reaction Ontology (RXNO)."^^ . + . + . + . + "ontology" . + "^N:package:[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . + "metabolomics" . + "wbphenotype" . + . + "gramene.ref" . + "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name="^^ . + . + "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id=$1"^^ . + . + . + . + . + "Identifier for a species in iNaturalist"^^ . + . + "^\\d+$"^^ . + . + . + "obo" . + . + . + . + . + "false"^^ . + . + . + "poro" . + "5ede4273-b26c-4ea4-adb7-3ce294ab3397"^^ . + "000017"^^ . + . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/FBbi_"^^ . + . + . + . + "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid="^^ . + . + "This namespace is used for GA4GH Data Repository Service (DRS) access to the USA National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI), Genomic Analysis, Visualization and Informatics Lab-space (AnVIL) program data. AnVIL is a cloud-based genomic data sharing and analysis platform which facilitates integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by the National Institutes of Health (NIH) or by other agencies that support human genomics research. "^^ . + . + . + . + . + "false"^^ . + "bibliometrics" . + "2966"^^ . + . + . + . + . + "^[0-9]{4}$"^^ . + "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId="^^ . + . + "true"^^ . + . + . + "ReviewVersion"^^ . + . + . + . + . + . + "gene" . + . + "chemistry" . + "KEGG Orthology (KO) consists of manually defined, generalised ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes in all organisms."^^ . + . + . + . + "RNA SSTRAND" . + . + "gene" . + "chemspider" . + . + "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . + "EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823"^^ . + . + . + "0000411"^^ . + . + . + "ncbigene" . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFO_$1"^^ . + "1000290"^^ . + . + "tads" . + "YAL001C"^^ . + . + "https://metabolicatlas.org/identifier/MetabolicAtlas/"^^ . + "nif.dysfunction" . + . + "https://europepmc.org/article/CTX/"^^ . + "^[A-Za-z0-9]+$"^^ . + "false"^^ . + "Agronomy Vocabulary" . + . + "false"^^ . + . + . + . + "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster="^^ . + . + "https://europepmc.org/article/ppr/$1"^^ . + . + . + . + . + "false"^^ . + . + . + "A structured controlled vocabulary for the annotation of sample processing and separation techniques in scientific experiments."^^ . + "0002989"^^ . + "03307879"^^ . + "^[0-9]{12}$"^^ . + . + . + . + . + . + . + . + . + . + . + "http://www.bmrb.wisc.edu/data_library/generate_summary.php?bmrbId=$1"^^ . + . + . + "Person" . + . + . + . + . + . + . + "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://www.vmh.life/#metabolite/$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."^^ . + "obo" . + . + . + . + "https://bioregistry.io/matrixdb.association:"^^ . + "https://www.atcc.org/products/$1"^^ . + . + . + . + "neuromorpho" . + . + "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid="^^ . + "https://bioregistry.io/metaregistry/ncbi/$1"^^ . + "Sweet Potato ontology" . + . + "false"^^ . + . + "rouge" . + . + . + . + "ICDO" . + . + "life science" . + . + "eol" . + "14"^^ . + "false"^^ . + . + . + . + "https://www.signalingpathways.org/datasets/dataset.jsf?doi="^^ . + . + . + "pepbank" . + . + "false"^^ . + "http://getentry.ddbj.nig.ac.jp/getentry/dad/"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code="^^ . + "scopus.publication" . + "medical informatics" . + . + "radiology" . + . + "A database for Triticeae and Avena references."^^ . + . + . + . + "Astrophysics Source Code Library" . + . + . + . + "http://purl.obolibrary.org/obo/MSIO_"^^ . + . + . + . + "Vertebrate Gene Nomenclature Committee" . + . + . + . + "http://neuromorpho.org/neuron_info.jsp?neuron_name=$1"^^ . + "SMP0000219"^^ . + "Variants in dbVar."^^ . + "https://sitem.herts.ac.uk/aeru/bpdb/Reports/$1.htm"^^ . + . + . + . + . + "uniprot.keyword" . + . + . + "http://purl.obolibrary.org/obo/GSSO_"^^ . + . + . + "timrobertson100@gmail.com" . + . + . + . + . + "A UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location."^^ . + . + . + . + . + . + "epidemiology" . + . + . + "false"^^ . + "orthology" . + . + . + "true"^^ . + "^PA\\d+$"^^ . + "false"^^ . + . + . + . + . + "34"^^ . + . + . + "General Enquiries" . + . + "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."^^ . + "http://purl.obolibrary.org/obo/FOVT_"^^ . + . + . + . + "murine" . + . + . + . + . + "ontology" . + . + "medicine" . + . + . + "An application ontology designed to annotate next-generation sequencing experiments performed on RNA."^^ . + . + "abs" . + . + . + . + . + . + . + "true"^^ . + . + "veterinary medicine" . + "fortuna@ebd.csic.es" . + . + . + "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."^^ . + "http://purl.obolibrary.org/obo/LPT_$1"^^ . + "^C\\d+$"^^ . + "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."^^ . + . + . + "dbvar.variants" . + . + . + . + "ontology" . + . + "life science" . + "genome" . + . + "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id=$1"^^ . + . + "An ontology of prokaryotic phenotypic and metabolic characters"^^ . + . + . + . + . + "P683" . + "iclc" . + "^\\d{7}$"^^ . + "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."^^ . + . + "CategorialBibliometricData"^^ . + "The human diseases in which proteins are involved are described in UniProtKB entries with a controlled vocabulary."^^ . + . + . + . + . + "biomedical science" . + . + . + . + "life science" . + "LBCTR2023015204"^^ . + "568815597"^^ . + . + "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . + . + . + "ontology" . + . + . + . + . + . + . + . + . + "Variation Ontology" . + . + "^\\d+$"^^ . + . + "Alan Wood's Pesticides" . + "tair.protein" . + "http://leafsnap.com/species/$1/"^^ . + . + . + "protein" . + . + . + "trait" . + . + . + "090924"^^ . + . + . + "preclinical studies" . + . + . + . + "Hymenoptera Anatomy Ontology" . + . + "biomedical science" . + . + "epidemiology" . + . + . + . + . + . + "true"^^ . + . + . + "http://plugins.biogps.org/cgi-bin/wp.cgi?id=$1"^^ . + "false"^^ . + "0000400"^^ . + . + . + . + "ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. Moreover, ClassyFire allows for text-based search via its web interface. It can be accessed via the web interface or via the ClassyFire API."^^ . + "^P\\d{5}$"^^ . + "https://bioregistry.io/schema/#$1"^^ . + . + "ERP004492"^^ . + . + . + "Cotton ontology" . + . + "sheeba.samuel@uni-jena.de" . + "taxonomy" . + . + "drug" . + . + "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp="^^ . + "Maria Gould" . + . + . + . + . + "^\\d+$"^^ . + . + "https://biopragmatics.github.io/providers/sfam/$1"^^ . + "life science" . + "STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature."^^ . + "Enzo Life Sciences" . + . + . + "true"^^ . + . + . + "worldavatar.compchem" . + . + "multicellds.snapshot" . + . + . + . + "cnrs" . + . + . + . + . + . + . + . + "false"^^ . + "c0000005"^^ . + "gabi" . + . + . + "false"^^ . + . + . + "birnlex" . + . + . + . + . + . + . + . + "AN0097748"^^ . + . + . + "http://purl.obolibrary.org/obo/PR_"^^ . + "sjwang@mcw.edu" . + "false"^^ . + "Apollo Structured Vocabulary" . + . + "false"^^ . + . + "subject agnostic" . + . + . + . + . + . + "ontology" . + . + "NucleaRDB" . + . + . + . + "The standard reference for nomenclature and diagnostic criteria in toxicologic pathology."^^ . + . + . + "Addgene Plasmid Repository" . + . + . + . + . + . + . + . + . + . + . + . + . + "ontology" . + . + . + "false"^^ . + . + . + . + . + . + . + . + "Cluster of orthologous genes" . + . + . + "A controlled vocabulary to support the study of transcription in the primate brain"^^ . + "developmental biology" . + "jkissing@uga.edu" . + . + . + . + . + "ontology" . + "false"^^ . + . + "false"^^ . + . . - "Deepak Unni" . - . - "0000156"^^ . - . - . - . + . + "molecular dynamics" . + . + "DataONE provides infrastructure facilitating long-term access to scientific research data of relevance to the earth sciences."^^ . + . + . + "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id="^^ . + "^\\d{8}$"^^ . + . + "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."^^ . + . + "glycomics" . + "http://matrixdb.univ-lyon1.fr/cgi-bin/current/newPort?type=biomolecule&value=$1"^^ . + "protein" . + "^(cd)?\\d{5}$"^^ . + . + . + . + "11002"^^ . + . + . + "subject agnostic" . + . + . + "4DNESWX1J3QU"^^ . + "^TS-\\d+$"^^ . + "icepo" . + . + . + "00000014"^^ . + . + . + . + "affy.probeset" . + "umls.sty" . + . + . + "Homeostasis imbalance process ontology" . + . + . + . + . + "sharkipedia.trend" . + . + . + "mfoem" . + . + . + . + . + "Ecocore is a community ontology for the concise and controlled description of ecological traits of organisms."^^ . + . + . + . + . + "false"^^ . + "https://cordis.europa.eu/project/id/"^^ . + "436605"^^ . + . + . + . + "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . + . + "http://n2t.net/ark:"^^ . + "false"^^ . + . + . + "GWAS Central Marker" . + "TIGR protein families" . + . + "nucc.characteristic" . + "r0001"^^ . + . + . + . + . + . + . + . + "http://purl.org/dc/terms/"^^ . + "false"^^ . + . + . + . + . + . + "https://www.emsl.pnnl.gov/project/"^^ . + . + . + "https://bioregistry.io/odor:"^^ . + . + . + "^\\d+$"^^ . + "structure" . + . + . + . + "protein" . + "false"^^ . + . + . + . + . + "977869"^^ . + "tctr" . + . + "Sharkipedia Trait" . + . + "dlxc" . + . + "NIF Standard Ontology: Cell Types" . + . + "comparative genomics" . + . + "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)."^^ . + "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."^^ . + "rna" . + . + . + "0745-4570"^^ . + . + "4dn.replicate" . + . + . + "VFG2154"^^ . + "structure" . + . + . . - . - "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."^^ . - . - . - . - "https://www.pesticideinfo.org/chemical/$1"^^ . - "KG09531"^^ . - "ontology" . - . - . - . - . - . - . - . - . - "genomics" . - . - . - "https://portal.gdc.cancer.gov/cases/"^^ . - "HPA000698"^^ . - . - "obo" . - "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1"^^ . - . - . - . - . - "IDPO is used to describe structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state. GO is used to describe functional aspects of an IDP/IDR."^^ . - . - "3639"^^ . - "google.book" . - "genomics" . - . - "WBGene00000001"^^ . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - "gene" . - "false"^^ . - "linguistics" . - . - . - . - . - . - . - . -_:Nde452a2f59d5417986ed5e9498c51a7e "Onard Mejino" . - . - "false"^^ . - "cell replacement" . - "Coriell Institute for Medical Research" . - . - . - "epidemiology" . - "gc" . - . - . - . - . - . - "^\\d{7}$"^^ . - "oslc" . + . + . + . + . + "drugs" . + . + . + . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/nuccore/"^^ . + . + "cherry@genome.stanford.edu" . + "wyeth@cmmt.ubc.ca" . + . + . + . + "ontology" . + . + . + . + "http://purl.bioontology.org/ontology/NDDF/"^^ . + . + . + "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."^^ . + . + "false"^^ . + "topics" . + . + . + "infectious" . + . + . + "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."^^ . + "ontology" . + . + . + "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://bioregistry.io/cmecs:"^^ . + . + "preclinical studies" . + . + . + . + . + . + "ecology" . + . + "http://foodb.ca/compounds/"^^ . + . + "has identifier space owner" . + . + . + . + . + . + "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"^^ . + . + . + . + . + . + . + "gsso" . + . + . + . + "gc_id" . + "https://www.alliancegenome.org/accession/"^^ . + . + . + "http://purl.obolibrary.org/obo/ExO_$1"^^ . + "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."^^ . + . + . + "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf="^^ . + "anatomy" . + . + . + "false"^^ . + . + "DepMap Cell Lines" . + . + "genomics" . + "http://purl.obolibrary.org/obo/SEP_$1"^^ . + . + "https://cmecscatalog.org/cmecs/classification/unit/$1.html"^^ . + . + "obo" . + "COG Categories" . + "NLX" . + . + "false"^^ . + . + . + "panorama" . + . + "false"^^ . + . + _:Nec73fc3f397b45e4aa2ecdf3bfe3be4c . + . + "^c\\d+$"^^ . + . + "obo" . + . + "https://bioregistry.io/dragondb.protein:"^^ . + . + "JAX Mice" . + "biology" . + . + . + "https://www.ebi.ac.uk/miriam/main/"^^ . + "PACTR202304525632216"^^ . + "http://purl.obolibrary.org/obo/XPO_"^^ . + "3305"^^ . + . + . + . + . + . + . + "https://go.drugbank.com/indications/$1"^^ . + "genetics" . + "knockout" . + . + . + "0000066"^^ . + "DP00086r013"^^ . + . + . + "obo" . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . + . + . +_:N161c830f834442a4b8b33f16f6be7221 "Pierre Sprumont" . + "neuroscience" . + "http://purl.obolibrary.org/obo/TTO_"^^ . + . + "bitbucket" . + . + . + . + "https://civicdb.org/links/drugs/$1"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + . + "earth science" . + "anatomy" . + "paolo.romano@hsanmartino.it" . + . + "0000001"^^ . + . + . + "false"^^ . + . . - . - . - . - "hba" . - . - . - . - . - . - . - "^\\w+:[\\w\\d\\.-]*$"^^ . - . - . - "structural biology" . - . - "daniel.c.berrios@nasa.gov" . - . - "17165"^^ . - . - . - . - . - "International Classification of Diseases, 11th Revision" . - . - "https://cordis.europa.eu/article/id/"^^ . + "https://datacommons.org/browser/"^^ . + "2.16.840"^^ . + "hivreagentprogram" . + "http://pax-db.org/#!species/"^^ . + . + . + . + "false"^^ . + . + "functional genomics" . + "Description of Plant Viruses" . + . + . + . + "Tb927.8.620"^^ . + . + . + "An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy."^^ . + . + . + "http://nava.liacs.nl/cgi-bin/nava.py?id="^^ . + "^\\d{7}$"^^ . + . + "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."^^ . + . + . + "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no="^^ . + . + . + . + "false"^^ . + . + . + "ontology" . + . + . + "DrugBank" . + . + . + . + "Georgeta Bordea" . + . + "life science" . + . + "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."^^ . + . + . + "Ontology for the Anatomy of the Insect SkeletoMuscular system" . + "http://purl.bioontology.org/ontology/HCPCS/$1"^^ . + . + . + "pmdb" . + . + . + . + . + "protein" . + "false"^^ . + . + "0000002"^^ . + . + "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."^^ . + "https://www.worldwildlife.org/ecoregions/"^^ . + "nb2018006591"^^ . + . + . + . + "structure" . + . + . + "false"^^ . + . + . + _:Ndf03f6d8403c435dbcd86c77420d1bf0 . + . + . + . + . + "Lentil ontology" . + . + "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."^^ . + "The Oral Health and Disease Ontology is used for representing the diagnosis and treatment of dental maladies."^^ . + . + . + "https://cropontology.org/rdf/CO_358:$1"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + " The Australian New Zealand Clinical Trials Registry (ANZCTR) is an online register of clinical trials being undertaken in Australia, New Zealand and elsewhere. The ANZCTR includes trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies.\n\nIn 2007 the ANZCTR was one of the first three trial registries to be recognised by the World Health Organization International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognises registries as Primary Registries if they fulfil certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch. (from website)"^^ . + . + "^\\d{7}$"^^ . + "MarCat is a gene (protein) catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples."^^ . + . + "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:"^^ . + . + . + . + . + "ontology" . + "Golm Metabolome Database" . + "^PKDB[0-9]{5}$"^^ . + . + . + "obo" . + . + . + . + . + . + "ontology" . + "A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes"^^ . + "CIViC Molecular Profile" . + . + "false"^^ . + . + . + "subject agnostic" . + . + "transyt" . + "Peter Midford" . + . + . + . + "echobase" . + "mim.ps" . + "life science" . + . + "NCIt" . + "false"^^ . + . + . + . + . + . + . + "A database that describes manually curated macromolecular complexes and provides links to details about these complexes in other databases."^^ . + . + "false"^^ . + . + . + "ClinVar Record" . + . + . + "The International Standard Book Number (ISBN) is for identifying printed books."^^ . + . + "^GLDS-\\d+$"^^ . + "life science" . + "FuncBase Yeast" . + . + "http://purl.obolibrary.org/obo/MC_$1"^^ . + . + . + . + "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . + . + . + "RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database. By providing links between these vocabularies, RxNorm can mediate messages between systems not using the same software and vocabulary."^^ . + . + "false"^^ . + "^\\d{7}$"^^ . + "co_343" . + . + "Ascomycete phenotype ontology" . + . + . + . + . + "1458400"^^ . + . + . + . + . + . + . + "01N50ZZ"^^ . + "21877"^^ . + . + . + "civic.did" . + . + "false"^^ . + "1755"^^ . + . + "^GPM\\d+$"^^ . + . + . + . + . + "pathology" . + . + "^\\d+$"^^ . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Study&StudyID=$1"^^ . + "false"^^ . + . + . + . + "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/MPIO_$1"^^ . + . + "false"^^ . + . + "spdx" . + . + "spp" . + . + "^\\d+$"^^ . + "cogs@ncbi.nlm.nih.gov" . + . + . + . + . + "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id="^^ . + . + . + . + . + . + . + "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot=$1"^^ . + . + . +_:N8f29cebc16e44d6c87f3a1f551121218 "Patricia Brooks" . + "Dengue Fever Ontology" . + "NLXCELL conatins cell types with a focus on neuron types."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "duplication" . + "Fahim Imam" . + . + . + "^[A-Za-z_]+$"^^ . + . + . + . + "false"^^ . + "allele" . + . + "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . + "Gs0000008"^^ . + "obo" . + "false"^^ . + . + . + "^[A-Za-z]{2,4}[A-Za-z0-9.-]{1,71}$"^^ . + "^\\d+$"^^ . + "3447"^^ . + . + . + . + . + "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. "^^ . + . + . + . + "crisprdb" . + "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."^^ . + . + . + "damion_dooley@sfu.ca" . + . + "Progenetix" . + . + . + . + . + "http://purl.obolibrary.org/obo/MIRNAO_$1"^^ . + . + "https://www.flymine.org/flymine/report/ChromosomeBand/"^^ . + . + . + "siiraa@umich.edu" . + . + . + . + . + "ontology" . + . + "https://www.checklistbank.org/dataset/"^^ . + . + "uniprot.chain" . + . + "co_348" . + . + . + . + "http://ciliate.org/index.php/feature/details/$1"^^ . + "ontology" . + . + . + "false"^^ . + . + . + "The [Global Biodata Coalition](https://globalbiodata.org) released a [curated list](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/) of 37 life sciences databases in December 2022 that they consider as having significant importance (see criteria [here](https://doi.org/10.5281/zenodo.5845116)). While it's not a primary goal of the Bioregistry to cover life science databases (other resources like Wikidata and [FAIRsharing](https://fairsharing.org) already do an excellent job of this), many notable databases induce one or more semantic spaces that are relevant for curation and prefix assignment in the Bioregistry. Therefore, a large number of the resources in this list correspond 1-to-1 with prefixes in the Bioregistry, a small number (e.g., Orphanet, CIViC, PharmGKB) correspond to multiple prefixes, some have a complicated relationship with many-to-1 relationships to prefixes (DNA Data Bank of Japan, European Nucleotide Archive), and some constitute databases that simply reuse other key vocabularies (e.g., STRING reuses UniProt, GWAS Catalog reuses dbSNP and EFO). Among the databases that don't induce semantic spaces or have simple relationships to prefixes are:\n\n- [Clinical Genome Resource](https://www.clinicalgenome.org/) (uses HGNC, MONDO, PharmGKB, etc.)\n- [DNA Data Bank of Japan](https://www.ddbj.nig.ac.jp/) (uses INSDC)\n- [GENCODE](https://www.gencodegenes.org/) (uses GenBank)\n- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) (uses dbSNP, EFO, etc)\n- [STRING](https://string-db.org/) (uses UniProt)" . + . + . + . + . + "The UniProt Tissue List is a controlled vocabulary of terms used to annotate biological tissues. It also contains cross-references to other ontologies where tissue types are specified."^^ . + . + "variation" . + "life science" . + . + . + . + . + "151022"^^ . + "^\\w+$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + "https://dandiarchive.org/dandiset/"^^ . + "John Westbrook" . + . + "Plant Transcription Factor Database" . + . + "https://www.wwpdb.org/pdb?id="^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + "Environmental Molecular Sciences Laboratory Project" . + . + . + . + . + . + "^MSV\\d+$"^^ . + . + . + . + . + . + . + "65"^^ . + . + . + "bioinformatics" . + . + . + . + "false"^^ . + "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . + "false"^^ . + . + "ontology" . + "life science" . + . + "ontology" . + . + "Alzheimer's Disease Ontology" . + "http://bitterdb.agri.huji.ac.il/Receptor.php?id=$1"^^ . + "1"^^ . + . + . + "https://www.ebi.ac.uk/arrayexpress/experiments/$1"^^ . + "https://www.checklistbank.org/dataset/3LR/taxon/$1"^^ . + . + "false"^^ . + "http://opm.phar.umich.edu/protein.php?pdbid=$1"^^ . + . + . + . + "EDAM Format" . + . + "https://pir.georgetown.edu/cgi-bin/ipcSF?id="^^ . + "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."^^ . + . + . + . + "Andreas Ledl" . + . + "918902"^^ . + "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."^^ . + "chemistry" . + . + "Name-to-Thing" . + "http://www.sbgnbricks.org/BKO/full/entry/all/BKO:$1"^^ . + "ontology" . + "life science" . + . + "https://reaxys.emolecules.com/cgi-bin/more?vid="^^ . + "The ODRL Vocabulary and Expression defines a set of concepts and terms (the vocabulary) and encoding mechanism (the expression) for permissions and obligations statements describing digital content usage based on the ODRL Information Model."^^ . + . + . + . + . + "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."^^ . + "Current Procedural Terminology" . + . + . + "0000947"^^ . + "https://www.encodeproject.org/$1"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + . + "taxonomy" . + "false"^^ . + "developmental biology" . + "false"^^ . + . + . + . + . + . + . + . + . + "comparative genomics" . + . + . + "Variation Modelling Collaboration" . + "0000609"^^ . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + "0000780"^^ . + "http://purl.obolibrary.org/obo/IDOMAL_$1"^^ . + . + . + . + . + . + "A vocabulary of taxonomic ranks (species, family, phylum, etc)"^^ . + "00000532"^^ . + . + "The Barcode of Life Data System (BOLD) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. The associated taxonomy browser shows the progress of DNA barcoding and provides sample collection site distribution, and taxon occurence information."^^ . + "biomedical science" . + . + "^\\d{5}$"^^ . + "microarray" . + "^\\d{7}$"^^ . + . + "false"^^ . + "CiteXplore" . + . + . + "Ontology about C. elegans and other nematode phenotypes"^^ . + . + . + "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch="^^ . + "Cell line collections (Providers)"^^ . + . + "obo" . + . + . + . + . + . + . + . + . + . + . + "igrhcellid" . + . + . + . + "https://scicrunch.org/resolver/RRID:NXR_"^^ . + . + . + "genetics" . + . + . + . + . + . + "false"^^ . + "Immune Epitope Database" . + . + . + . + . + "Alistair Miles" . + . + . + "215"^^ . + "obo" . + "Ontology for Nutritional Epidemiology" . + . + . + "The Virtual Metabolic Human (VMH) is a resource that combines human and gut microbiota metabolism with nutrition and disease."^^ . + "ontology" . + "BugBase is a MIAME-compliant microbial gene expression and comparative genomic database. It stores experimental annotation and multiple raw and analysed data formats, as well as protocols for bacterial microarray designs. This collection references design protocols."^^ . + . + . + . + . + . + "merops.family" . + . + . + . + "^\\d{4,}$"^^ . + . + . + "https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:"^^ . + . + . + . + "The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest.\n\nCCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). Accordingly, CCO classes and relations are heavily constrained by the BFO framework, from which it inherits much of its basic semantic relationships."^^ . + . + . + . + "functional genomics" . + "MAM01234c"^^ . + . + "https://www.checklistbank.org/dataset/$1"^^ . + . + "https://protists.ensembl.org/id/$1"^^ . + . + . + "tol" . + . + "experiment" . + "IUPHAR_LIGAND_ID" . + . + . + "The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort."^^ . + . + . + . + . + . + . + . + "0000712_1"^^ . + . + . + . + . + "false"^^ . + . + . + "A translation of the full Galen ontology (from the OpenGALEN project) into the OWL description logic."^^ . + "false"^^ . + "Cell line collections (Providers)"^^ . + . + . + . + "biochemistry" . + . + . + . + "pharmacogenomics" . + "^\\d+$"^^ . + "chemistry" . + . + . + "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id=$1"^^ . + "genome" . + "0000001"^^ . + "Datasets around different cancer cell lines generated by the Broad Institute and Novartis"^^ . + . + "jupp@ebi.ac.uk" . + . + . + . + . + "A hierarchical classification of congenital heart disease "^^ . + "http://purl.obolibrary.org/obo/CEPH_$1"^^ . + . + "The Sri Lanka Clinical Trials Registry (SLCTR) is a Registry for clinical trials involving human subjects, conducted in Sri Lanka or overseas. The SLCTR is a Primary Registry linked to the Registry Network of the International Clinical Trials Registry Platform of the WHO (WHO-ICTRP). It is a not-for-profit Registry, with free and open access to researchers, clinicians, and the general public. (from homepage)"^^ . + . + . + "epigenomics" . + "http://www.dpvweb.net/dpv/showdpv.php?dpvno="^^ . + . + . + . + "^\\d+$"^^ . + "http://www.soybase.org/sbt/search/search_results.php?category=SNP&search_term="^^ . + . + . + . + . + "biomedical science" . + . + . + . + . . - . - "0001114"^^ . - . - . - . - . - . - . - . - "0001707"^^ . - . - "co_322" . - . - . - . - "https://cropontology.org/rdf/CO_338:"^^ . - . - "protein" . - . - "PED00037"^^ . -_:N56d4e713323645afb58017bd33f565ae "Tim Vandermeersch" . - "hgnc" . - . - "uspto" . - . - . - . - "CAMEO Chemicals ID" . - . - . - . + . + "go.ref" . + . + . + "false"^^ . + . + . + . + . + . + . + "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=$1"^^ . + "^H\\d+$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/VIDO_"^^ . + "Curated Drug-Drug Interactions Database - Interaction" . + "^EMD-\\d{4,5}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . +_:Nd0865bd54b1d4b1f9895b1f6281f1800 "helpdesk@cropontology-curationtool.org" . + . + . + . + . + "https://precision.fda.gov/uniisearch/srs/unii/"^^ . + . + . + . + "1h68"^^ . + "GCST000035"^^ . + . + . + "prediction" . + . + . + "http://purl.obolibrary.org/obo/BSPO_"^^ . + "Ontology of Vaccine Adverse Events" . + "false"^^ . + . + . + . + "false"^^ . + . + "Bryce Mecum" . + . + . + . + . + "reproduceme" . + "http://biohackathon.org/resource/faldo#$1"^^ . + . + "Natural Product Activity and Species Source Database" . + . + . + "^\\d+$"^^ . + . + . + . + "Pathguide contains information about 325 biological related resources and molecular interaction related resources."^^ . + . + "false"^^ . + "1122888"^^ . + "http://purl.obolibrary.org/obo/ADO_"^^ . + "UniProt Chain" . + . + "https://metacyc.org/compound?orgid=META&id="^^ . + "ecocore" . + . + . + . + . + . + . + "false"^^ . + "community care" . + "http://www.drugtargetontology.org/dto/DTO_$1"^^ . + . + . + "chmo" . + . + "ssbd.dataset" . + . + . + . + . + . + . + "bioPIXIE is a novel system for biological data integration and visualization. It allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate."^^ . + "NCI_Thesaurus" . + . + "clinvar" . + "gamete" . + "MGD" . + . + . + "GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. It gathers datasets from public domain projects, and accepts direct data submission. It is based upon Marker information encompassing SNP and variant information from public databases, to which allele and genotype frequency data, and genetic association findings are additionally added. A Study (most generic level) contains one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. This collection references a GWAS Central Study."^^ . + "BioLegend is a life sciences supply vendor."^^ . + . + . + "BT20_BREAST"^^ . + "chemistry" . + "Theoretical explanation of a purely spatial ontology supporting snapshot views of the world at successive instants of time, as part of a modular ontology of the dynamic features of reality."^^ . + "^(XAO|ZFA|EHDAA|EMAPA|EV|MA)\\:\\d+$"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/EPO_$1"^^ . + . + "Joint Genome Institute Proposals" . + . + . + . + . + . + . + . + "95-0166C6"^^ . + . + . + . + . + . + "http://gmd.mpimp-golm.mpg.de/Metabolites/$1.aspx"^^ . + "false"^^ . + "The Saccharomyces Genome Database (SGD) project collects information and maintains a database of the molecular biology of the yeast Saccharomyces cerevisiae."^^ . + . + "dna" . + "ImMunoGeneTics database covering immunoglobulins and T-cell receptors" . + . + "^\\d{7}$"^^ . + . + . + . + "biosimulations" . + . + . + . + . + "subject agnostic" . + . + . + "00000"^^ . + . + "http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN="^^ . + . + "ISO 3166-1 Country Code" . + "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."^^ . + "Clinical Trial Registries" . + . + . + . + . + "druzinsk@uic.edu" . + . + "asin" . + . + "Stephen Fisher" . + . + . + . + . + . + "ppdb" . + . + . + . + "TA_H3"^^ . + "A structured controlled vocabulary of the adult anatomy of the mouse (Mus)"^^ . + "http://crdd.osdd.net/servers/virsirnadb/record.php?details="^^ . + "ontology" . + "Thermo Fisher Scientific" . + "biodiversity" . + "https://cropontology.org/rdf/CO_322:"^^ . + . + . + . + "Human Protein Reference Database" . + . + . + . + . + . + "^OSR\\d{4}$"^^ . + . + . + "obo" . + . + . + "http://exac.broadinstitute.org/variant/"^^ . + . + . + "false"^^ . + . + . + . + "odrl" . + . + . + . + . + . + "false"^^ . + . + "Jonathan Karr" . + . + "pylebail@rennes.inra.fr" . + . + . + . + . + . + . + "biomedical science" . + "ncbi.resource" . + "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . + "fairsharing" . + "RCSB_PDB" . + "2023-503698-40-00"^^ . + "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."^^ . + . + . + "proteomics" . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code=$1"^^ . + . + . + . + "bt0001"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + "false"^^ . + "genetic construct" . + "nlx.org" . + . + "0000171"^^ . + "co_359" . + "biology" . + . + . + "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."^^ . + "https://fungidb.org/fungidb/app/record/gene/"^^ . + . + . + . + . + "true"^^ . + . + . + . + "The Japan Collection of Microorganisms (JCM) collects, catalogues, and distributes cultured microbial strains, restricted to those classified in Risk Group 1 or 2."^^ . + . + "model organism" . + "SUM Breast Cancer Cell Line Knowledge Base" . + . + . + . + "false"^^ . + . + . + . + . + "8668"^^ . + "VMH Gene" . + . + . + . + . + . + "hescriva@obs-banyuls.fr" . + . + . + "preclinical studies" . + . + "http://www.w3.org/ns/oa#$1"^^ . + . + "Variable"^^ . + . + "PS" . + . + _:Nab17e8af5a024810b922e139a33dedf0 . + . + . + . + . + . + . + . + "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id=$1"^^ . + . + . + . + "subject agnostic" . + . + . + "The Gemeinsame Normdatei (Integrated Authority File) or GND is an international authority file for person names, subject headings and corporate bodies. It is used mainly for documentation in libraries and increasingly also by archives and museums. The GND is managed by the German National Library in cooperation with various regional library networks in German-speaking Europe and other partners."^^ . + . + "5"^^ . + . + . + . + . + . + . + . + . + . + "hsa00190"^^ . + . + "https://caninecommons.cancer.gov/#/study/"^^ . + "International Nucleotide Sequence Database Collaboration (INSDC) Run" . + . + . + . + . + . + "fairsharing.user" . + "geology" . + . + . + . + . + "marilyn.safran@weizmann.ac.il" . + . + . + . + "172"^^ . + . + "genome" . + . + "The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Accompanying data includes detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram."^^ . + "^FB\\w{2}\\d{7}$"^^ . + "classification" . + . + . + . + "https://www.findacode.com/code.php?set=ICD10PCS&c="^^ . + "https://www.genedb.org/gene/$1"^^ . + . + . + . + . + . + "^TTHERM\\_\\d+$"^^ . + . + "https://bioregistry.io/resolve/github/issue/"^^ . + . + "clustering" . + "https://gen3.theanvil.io/ga4gh/drs/v1/objects/"^^ . + . + . + . + "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"^^ . + . + "false"^^ . + "https://www.internationalgenome.org/data-portal/sample/$1"^^ . + "NLXOEN prefixed identifiers are from the version of the Ontology for Experimental Neurophysiology (OEN; https://github.com/G-Node/OEN) that were originally deposited in Neurolex (for examples, see https://scicrunch.org/scicrunch/interlex/search?q=NLXOEN results)."^^ . + . + "^\\d+$"^^ . + "https://models.physiomeproject.org/exposure/$1"^^ . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_dys_"^^ . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references antibody products."^^ . + "biology" . + . + . + "CorrDB" . + "The Network Data Exchange (NDEx) is an open-source framework where scientists and organizations can store, share, manipulate, and publish biological network knowledge."^^ . + "false"^^ . + "UniRef90_P00750"^^ . + . + "RNAJunction is a database of RNA junctions and kissing loop structures. It contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. It allows searching by PDB code, structural classification, sequence, keyword or inter-helix angles. RNAJunction is designed to aid analysis of RNA structures as well as design of novel RNA structures on a nanoscale. "^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "transcriptomics" . + . + "false"^^ . + . + . + . + . + "emolecules" . + "false"^^ . + "https://www.deciphergenomics.org/syndrome/$1"^^ . + . + . + . + "pathway" . + . + . + "https://biopragmatics.github.io/providers/bs/"^^ . + . + . + . + "Bloomington Drosophila Stock Center" . + . + "literalForm"^^ . + . + . + . + "ontology" . + "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs)."^^ . + . + . + . + . + . + "metascience" . + "transposon insertion" . + "http://purl.obolibrary.org/obo/DC_CL_"^^ . + . + . + . + . + "prgr_human"^^ . + "^(urn|URN):(nbn|NBN)(:[A-Za-z_0-9]+)*.+$"^^ . + . + "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/"^^ . + "regulation" . + "SABIO-RK" . + . + "classification" . + "life science" . + . + "genes" . + "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:$1"^^ . + "annika.jahnke-bornemann@uni-hamburg.de" . + . + . + "UniProt Isoform" . + "https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id="^^ . + . + . + . + . + . + . + "27223"^^ . + . + "tngb" . + "bila" . + "https://bioregistry.io/lgic:"^^ . + . + . + "ontology" . + "gecko" . + . + . + "false"^^ . + . + "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."^^ . + . + "http://topdb.enzim.hu/?m=show&id=$1"^^ . + . + "https://agricola.nal.usda.gov/vwebv/holdingsInfo?bibId=$1"^^ . + . + . + "0000001"^^ . + . + "statistics" . + . + "wes_schafer@merck.com" . + . + "viralzone" . + "ontology" . + "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID="^^ . + . + . + . + "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. "^^ . + . + . + . + . + "Tuan Amith" . + . + . + "http://purl.org/sig/ont/fma/fma"^^ . + "lepao" . + . + "development" . + "HMS-LINCS" . + . + "rex" . + "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . + . +_:N1d66b6d5b1894f27847d3a13cf9a0222 "Crop Ontology Helpdesk" . + . + . + . + . + . + "0000460"^^ . + . + "3000887619"^^ . + . + . + . + "https://bioregistry.io/combine.specifications:"^^ . + . + . + . + . + . + "The identifier for an observation in iNaturalist"^^ . + . + . +_:Na829664083dd4fbeb40853897acda040 "helpdesk@cropontology-curationtool.org" . + "Yeast Searching for Transcriptional Regulators and Consensus Tracking" . + "^\\d{7}$"^^ . + . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + "life science" . + . + "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object="^^ . + . + . + . + "67"^^ . + . + . + "storedb.file" . + . + . + . + . + "Cell line collections (Providers)"^^ . + . + "false"^^ . + . + . + "mbrochhausen@gmail.com" . + . + . + "https://github.com/biolink/biolink-model" . + . + "classification" . + . + . + . + . + "d4akea1"^^ . + . + . + "glycomics" . + "Antony Williams" . + . + . + . + . + . + . + . +_:N02158d1ce8ce424abc89d4bad17cc26b "NLM Customer Service" . + . + . + . + . + . + . + . + "pina" . + . + . + . + "obo" . + "^(\\d{1,7}\\-\\d{2}\\-\\d)|([A-Za-z0-9\\+\\-\\_]+)$"^^ . + "false"^^ . + . + "ORCID (Open Researcher and Contributor ID) is an open, non-profit, community-based effort to create and maintain a registry of unique identifiers for individual researchers. ORCID records hold non-sensitive information such as name, email, organization name, and research activities."^^ . + . +_:Nee4e59f3e724439c8721b03d893e8269 "mssohelp@meddra.org" . + . + . + . + . + . + "false"^^ . + . + . + . + . + "reactome" . + . + "biomedical science" . + . + "^[0-9]+$"^^ . + . + "storedb.dataset" . + . + "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^ . + . + . + "health sciences" . + "assays" . + "Ardan Patwardhan" . + . + . + . + . + "software engineering" . + . + "structural biology" . + . + "life science" . + . "http://senselab.med.yale.edu/ORDB/Data/"^^ . - "Health Surveillance Ontology" . - "Description of a Project" . - "img.gene" . - . - . - . - . - . - "false"^^ . - . - "http://purl.uniprot.org/annotation/VAR_"^^ . - "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."^^ . - . - . - . - "KEGG.DRUG" . - "phenolexplorer" . - . - "Open Biomedical Annotations" . - . - . - . - . - . - . - "microbial" . - . - . - . - . - . - "true"^^ . - . - "AddexBio cell line products" . - "https://w3id.org/faircookbook/$1"^^ . - . - . - "Willy Wong" . - . - . - . - . - "metacyc.reaction" . - "OriDB is a database of collated genome-wide mapping studies of confirmed and predicted replication origin sites in Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This collection references Saccharomyces cerevisiae."^^ . - "omics" . - . - . - . - "true"^^ . - "br/0601"^^ . - . - "obo" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "adenovirus" . + . + "JWS Online" . + "false"^^ . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "ontology" . + . + "maxneal@gmail.com" . + . + . + . + . + "pdbe" . + . + . + . + "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."^^ . + . + . + . + "NCT" . + "https://civicdb.org/links/sources/"^^ . + "otl" . + "https://epd.expasy.org/cgi-bin/epd/query_result.pl?out_format=NICE&Entry_0=$1"^^ . + . + . + "chemistry" . + . + "National Experimental Cell Resource Sharing Platform" . + "UCR00226"^^ . + "^\\w{1,2}\\d+$"^^ . + . + "false"^^ . + . + . + . + "Gene Ontology" . + . + . + "metabolite" . + . + . + "proteomics" . + "http://purl.obolibrary.org/obo/STATO_"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "dna" . + . + . + . + . + "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)." . + "1000001"^^ . + . + . + . + . + "Clare Pilgrim" . + "tfclass" . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . + . + . + "dbSNP Reference SNP number" . + . + . + . + . + . + "http://func.mshri.on.ca/human/genes/list_functional_scores/$1"^^ . + . + "National Drug Data File" . + . + "TGME49_053730"^^ . + . + . + "frapo" . + . + "^\\d{8}$"^^ . + "LGCEDe-S-000002244"^^ . + . + . + "http://unite.ut.ee/bl_forw.php?nimi="^^ . + "TC010103"^^ . + "ettensohn@cmu.edu" . + "ontology" . + "MIRT000002"^^ . + "0000022"^^ . + . + . + . + . +_:Na829664083dd4fbeb40853897acda040 "Crop Ontology Helpdesk" . + . + "https://cellrepo.ico2s.org/repositories/$1"^^ . + "database" . + "MM00040"^^ . + . + "omics" . + "^10.\\w{4}/\\w{10}$"^^ . + . + "https://cropontology.org/rdf/CO_360:$1"^^ . + . + "angiology" . + "http://purl.obolibrary.org/obo/MPATH_"^^ . + . + "life science" . + "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://purl.obolibrary.org/obo/FBcv_$1"^^ . + "An ontology which represents information about the State of Alaska's Salmon and People (SASAP) project, as well as knowledge about salmon, features of their habitats, salmon stakeholders, and related entities."^^ . + "https://w3id.org/sssom/"^^ . + . + . + . + . + . + . + "false"^^ . + "^10.\\d{2,9}/.*$"^^ . + . + . + . + . + . + . + . + . + . + "SNOMED CT (International Edition)" . + "false"^^ . + "f665230-5267"^^ . + . + . + . + . + . + . + "http://www.w3.org/ns/shacl#$1"^^ . + . + . + . + . + "phosphopoint.kinase" . + . + . + "google.scholar" . + . + . + . + "http://www.w3.org/ns/odrl/2/"^^ . + . + . + "0001191"^^ . + "National Science Foundation Award" . + . + "false"^^ . + . + . + "1"^^ . + . + . + . + "lincs.protein" . + . + . + "earth science" . + "http://purl.obolibrary.org/obo/EUPATH_"^^ . + "1"^^ . + . + "metlin" . + . + "true"^^ . + . + "subject agnostic" . + . + . + . + . + . + "https://www.cellosaurus.org/CVCL_"^^ . + . + "false"^^ . + "false"^^ . + . + "http://www.gramene.org/db/ontology/search?id=GRO:"^^ . + "http://www.radiomics.org/RO/"^^ . + . + "Identifiers.org Terms (idot) is an RDF vocabulary providing useful terms for describing datasets."^^ . + . + "^NONHSAG\\d{5}$"^^ . + "037727"^^ . + . + . + "false"^^ . + . + . + . + . + "SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature."^^ . + . + "miRBase mature miRNA" . + . + "laml_tcga_pub"^^ . + . + . + . + . + "SNOMEDCT_US_2015_03_01" . + . + "Frederique Lisacek" . + . + "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code="^^ . + "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."^^ . + . + . + . + . + . + . + "life science" . + . + "http://purl.obolibrary.org/obo/CHMO_$1"^^ . + "http://purl.obolibrary.org/obo/FBSP_"^^ . + . + . + . + . + . + "interaction" . + . + . + . + . + "marker" . + "GeneAnnot: Microarray Gene Annotation" . + "interaction" . + . + "pmap.cutdb" . + "dna" . + . + "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."^^ . + . + "UPVAR" . + . + . + "FB00000917"^^ . + "https://cordis.europa.eu/project/id/$1"^^ . + "^([A-Z][0-9][0-9AB]((-[A-Z][0-9][0-9AB])|(\\.[0-9A-KXZ]([0-9A-EXYZ]([0-9A-HX][0-59A-HJKMNP-S]?)?)?)?))$"^^ . + "https://bioregistry.io/pocketome:"^^ . + . + . + "2019-08-03_00000089_1"^^ . + . + . + "m.a.laporte@cgiar.org" . + "drsbello@gmail.com" . + . + "ontology" . + "ird.segment" . + . + . + "0000001"^^ . + . + . + . + . + . + . + . + . + "https://euclinicaltrials.eu/app/#/view/$1"^^ . + "cell line" . + . + . + "http://purl.obolibrary.org/obo/EPIO_$1"^^ . + "anatomy" . + . + . + . + "http://purl.obolibrary.org/obo/OMIABIS_"^^ . + . + . + . + . + . + . + "HMS Library of Integrated Network-based Cellular Signatures Antibodies" . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/gene/"^^ . + . + . + "nif.cell" . + "health science" . + . + "http://www.pantherdb.org/panther/family.do?clsAccession=$1"^^ . + . + . + "http://purl.obolibrary.org/obo/OMO_"^^ . + . + . + . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + . + . + "true"^^ . + . + . + "ModelDB concept" . + "eropmoscow" . + . + "PPR103739"^^ . + "MassBank" . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "http://opendata.inra.fr/ATOL/ATOL_$1"^^ . + . + . + . + . + . + . + . + . + . + "http://antibodyregistry.org/AB_$1"^^ . + . + . + "false"^^ . + "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."^^ . + . + "The Protein Model DataBase (PMDB), is a database that collects manually built three dimensional protein models, obtained by different structure prediction techniques."^^ . + "75"^^ . + . + "A collection of clinical trial registries appearing in the World Health Organization's [International Clinical Trials Registry Platform (ICTRP)](https://trialsearch.who.int/)" . + . + "http://purl.obolibrary.org/obo/RS_$1"^^ . + . + . + . + "Selventa Chemicals" . + . + . + . + "0001"^^ . + "obo" . + "false"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + "https://e-cyanobacterium.org/bcs/rule/$1"^^ . + . + . + . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + "registry" . + "^\\d+$"^^ . + "Gmelins Handbuch der anorganischen Chemie" . + "clinical studies" . + . + . + . + . + "0000025"^^ . + . + "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=$1"^^ . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "NCBI Protein" . + . + . + "^[0-9]+$"^^ . + . + "false"^^ . + . + "genome" . + "false"^^ . + . + . + "jcggdb" . + . + . + "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."^^ . + "zfa" . + . + "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn=$1"^^ . + . + "TF101014"^^ . + . + . + "LOTUS Initiative for Open Natural Products Research" . + . + "life science" . + "M00002"^^ . + . + "^2-s2\\.0-\\d+$"^^ . + "false"^^ . + . + . + . + . + "oai:cwi.nl:4725"^^ . + . + . + . + . + "Coronavirus Infectious Disease Ontology" . + . + . + . + . + . + "proteomics" . + . + . + "false"^^ . + "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."^^ . + . + . + "^grid\\.[0-9]+\\.[a-f0-9]{1,2}$"^^ . + . + . + "structural biology" . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_"^^ . + "112081"^^ . + . + . + . + "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"^^ . + . + . + "mice" . + "http://search.sisuproject.fi/#/variant/"^^ . + "EHDAA:2185"^^ . + "stitch" . + . + . + . + . + . + "lncipedia" . + "http://edamontology.org/format_"^^ . + . + "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."^^ . + . + "biosimulators" . + . + "ICEberg family" . + "mark@gersteinlab.org" . + . + . + . + . + . + . + . + . + . + . + . + "Cell Lines in PubChem"^^ . + . + "mouse" . + . + . + . + . + . + . + . + . + . + "MIMPS" . + "http://purl.org/dc/dcmitype/$1"^^ . + . + . + . + "Cell line collections (Providers)"^^ . + . + "http://dictybase.org/gene/"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://www.kegg.jp/entry/"^^ . + . + . + . + . + . + "Jesper Friis" . + . + . + . + . + "https://biopragmatics.github.io/providers/icepo/"^^ . + . + . + . + "https://mmp.sfb.uit.no/databases/marref/#/records/"^^ . + . + "137"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "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."^^ . + "nicole@tislab.org" . + . + . + . + "https://precision.fda.gov/uniisearch/srs/unii/$1"^^ . + "0000093"^^ . + "obo" . + . + "http://www.chemspider.com/inchikey=$1"^^ . + . + "https://cellrepo.ico2s.org/repositories/"^^ . + . + "false"^^ . + . + . + . + . + . + "nsc" . + . + . + "aop.relationships" . + . + "http://ecoportal.lifewatch.eu/ontologies/$1" . + "http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=$1"^^ . + . + . + . + "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + "F0001"^^ . + . + . + . + "RID1"^^ . + "Luana Licata" . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references drug information."^^ . + "obo" . + . + "Maria Taboada" . + "false"^^ . + . + "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . + . + . + . + "^[1-9]\\d*$"^^ . + . + "ontology" . + . + . + . + . + "false"^^ . + . + "nif_subcellular" . + . + "sedml.language" . + "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."^^ . + "^G\\d+$"^^ . + "ontology" . + . + "software and information systems" . + . + . + "ontology" . + "https://n2t.net/$1:" . + "ecology" . + "inaturalist.user" . + . + "true"^^ . + "orphanet" . + "https://www.infrafrontier.eu/emma/strain-search/straindetails/?q=$1"^^ . + "^\\d{7}$"^^ . + . + "developmental biology" . + "16941567"^^ . + . + "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://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=$1"^^ . + . + "Symptom Ontology" . + "DOMMINO is a database of macromolecular interactions that includes the interactions between protein domains, interdomain linkers, N- and C-terminal regions and protein peptides."^^ . + "Richard Cyganiak" . + . + . + . + "true"^^ . + . + "chemistry" . + . + . + . + "This website supports the undertaking and oversight of clinical trials in the European Union (EU) and European Economic Area (EEA). It is part of a broad initiative to transform the EU/EEA clinical trials environment in support of large clinical trials in multiple European countries, to the benefit of medical innovation and patients. (from homepage)"^^ . + . + "https://bioregistry.io/hivreagentprogram:"^^ . + . + . + "Signaling Pathways Project" . + . + . + . + . + "https://www.grid.ac/institutes/"^^ . + . + . + . + "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."^^ . + . + . + . + "The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)"^^ . + . + . + "https://www.sharkipedia.org/trends/"^^ . + . + . + "false"^^ . + . + . + "AOPWiki (Key Event)" . + "http://www.w3.org/2001/XMLSchema#"^^ . + . + . + "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q=$1"^^ . + "EY223054.1"^^ . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "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."^^ . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/OMRSE_$1"^^ . + . + . + . + . + . + . + . + . + . + "https://phytochem.nal.usda.gov/phytochem/chemicals/show/"^^ . + . + . + "Cell line databases/resources"^^ . + . + . + . + "computer science" . + . + "https://radlex.org/RID/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://sed-ml.org/urns.html#language:"^^ . + . + . + "PSI-MI" . + . + . + "ontology" . + "obo" . + . + . + "CID" . + "^\\d+$"^^ . + "drug discovery" . + "^([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})$"^^ . + "false"^^ . + . + . + . + . + "protclustdb" . + . + . +_:Naf53a37095d24e73886a30c68eaa336f "Hajo Rijgersberg" . + . + . + . + "protein" . + . + . + "https://www.uniprot.org/journals/$1"^^ . + "Evidence ontology" . + . + . + . + "http://thebiogrid.org/$1"^^ . + "https://www.fao.org/fishery/en/species/$1"^^ . + "https://bdsc.indiana.edu/stocks/"^^ . + . + "Fetal Calf Serum-Free Database" . + . + "ontology" . + "Biosapiens Protein Feature Ontology" . + "^\\d{8}$"^^ . + "dc11" . + . + . + . + "interaction" . + "^NBK\\d+$"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/homologene/$1"^^ . + "biology" . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\-\\d+)$"^^ . + . + "measurement" . + . + . + "Online Mendelian Inheritance in Man is a catalog of human genes and genetic disorders."^^ . + "Transport Systems Tracker" . + . + . + . + . + . + . . - . - "ontology" . - . - . - "http://www.t3db.org/toxins/"^^ . - . - "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . - . + "http://purl.obolibrary.org/obo/CHEMINF_"^^ . + . + . + "http://purl.bioontology.org/ontology/VANDF/"^^ . + "registry" . + . + . + . + "The Prescription of Drugs Ontology" . + . + . + "dna" . + . + . + "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."^^ . + "Wikipedia" . + . + "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."^^ . + . + . + "dna" . + . + . + "MGI" . + . + . + "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."^^ . + . + "life science" . + . + . + "agriculture" . + . + . + "Os01t0883800-02"^^ . + "biochemistry" . + "Fossilworks Journal" . + . + . + . + "^\\d+$"^^ . + . +_:Nc61e1ba3fdf94e6781d9d9a9ab3cfda2 "chEBI" . + . + "https://fairsharing.org/organisations/"^^ . + "knowledge and information systems" . + . + . + . + . + "embryonic stem cell" . + "disdriv" . + . + . + . + "LABO is an ontology of informational entities formalizing clinical laboratory tests prescriptions and reporting documents."^^ . + . + . + . + . + . + . + . + "https://pharmacome.github.io/conso/$1"^^ . + . + . + . + "dermo" . + . + . . - . - "ogg" . - . - . - . - "^[a-z][a-z0-9_]+[a-z0-9]$"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - "Montana Smith" . - "SNOMED_CT_US_2018_03_01" . - . - "KEGG reaction contains our knowledge on the universe of reactions that are relevant to life."^^ . - "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster="^^ . - . - . - . - "http://purl.obolibrary.org/obo/ZEA_"^^ . - . - . - "false"^^ . - . - . - . - . - . - . - "computer science" . - . - . - "ontology and terminology" . - . - . - . - . - "molecule" . - . - "UniProt Resource" . - . - . - "chemistry" . - . - "Integrated Taxonomic Information System" . - . - . - . - . - . - . - "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."^^ . - . - . - . - "developed by ICARDA - Dec 2018"^^ . - . - . - . - "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . - "https://bioregistry.io/bykdb:"^^ . - . - "ADH1"^^ . - . - "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . - "genome" . - "biopesticides" . - "GiardiaDB" . - "A manually curated resource for the representation and annotation of metabolic pathways"^^ . - . - . - "http://www.arabidopsis.org/servlets/TairObject?accession=Locus:"^^ . - . - . - "https://www.metanetx.org/equa_info/$1"^^ . - . - . - "https://registry.identifiers.org/registry/$1" . - "pubchem.substance" . - "oma.grp" . - "fossilworks.journal" . - . - "chemistry" . -_:N93c2c94de4ce46f29e17ab0a916cf895 "Jonathan Bard" . - "pathobiochemistry" . - . - "ontology" . - . - "The Compendium is popularly referred to as the \"Gold Book\", in recognition of the contribution of the late Victor Gold, who initiated work on the first edition. It is one of the series of IUPAC \"Colour Books\" on chemical nomenclature, terminology, symbols and units (see the list of source documents), and collects together terminology definitions from IUPAC recommendations already published in Pure and Applied Chemistry and in the other Colour Books.\n\nTerminology definitions published by IUPAC are drafted by international committees of experts in the appropriate chemistry sub-disciplines, and ratified by IUPAC's Interdivisional Committee on Terminology, Nomenclature and Symbols (ICTNS). In this edition of the Compendium these IUPAC-approved definitions are supplemented with some definitions from ISO and from the International Vocabulary of Basic and General Terms in Metrology; both these sources are recognised by IUPAC as authoritative. The result is a collection of nearly 7000 terms, with authoritative definitions, spanning the whole range of chemistry."^^ . - . - "bioschemas" . - . - . - "protein" . - . - "The Event Ontology is an ontology of pathways. It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure."^^ . - "Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, foundamentally structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelational entities that demonstrate the nextwork of the understanding on Alzheimer's disease and can be readily applied for text mining."^^ . - "false"^^ . - . - "false"^^ . - . - "ero" . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "b97957"^^ . - "http://purl.obolibrary.org/obo/CLYH_$1"^^ . - "interaction" . - . - . - . - "0000000"^^ . - . - . - "^[A-Za-z0-9]+$"^^ . - . - "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . - . - . - "genomics" . - . - . - . - "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."^^ . - . - . - . - "map" . - . - . - "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . - . - . - . - "http://id.who.int/icd/entity/"^^ . - . - "EHDAA2_RETIRED" . - . - "Diagnostic tool for epidemiology, health management and clinical purposes, maintained by the World Health Organization (WHO). It provides a system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease."^^ . - . - "- DEPRECATION NOTE -\nPlease, keep in mind that this namespace has been superseeded by ‘gold’ prefix at https://registry.identifiers.org/registry/gold, and this namespace is kept here for support to already existing citations, new ones would need to use the pointed ‘gold’ namespace.\n\nThe GOLD (Genomes OnLine Database)is a resource for centralised monitoring of genome and metagenome projects worldwide. It stores information on complete and ongoing projects, along with their associated metadata. This collection references the sequencing status of individual genomes."^^ . - . + . + . + "^[a-zA-Z0-9][A-Za-z0-9_]+$"^^ . + . + . + . + . + . + . + "endocrinology" . + "caps" . + "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."^^ . + . + . + . + "smtifahim@gmail.com" . + "interaction" . + . + . + "https://www.ebi.ac.uk/arrayexpress/arrays/"^^ . + . + "metabolites" . + . + . + . + . + . + . + . + "EUCTR" . + "https://www.ebi.ac.uk/interpro/entry/pfam/"^^ . + "subject agnostic" . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + "https://bioregistry.io/metaregistry/cellosaurus/"^^ . + "https://biopragmatics.github.io/providers/dmba/"^^ . + . + "1017"^^ . + "isDocumentRelatedTo"^^ . + "https://rapdb.dna.affrc.go.jp/viewer/gene_detail/irgsp1?name=$1"^^ . + "computational biology" . + . + "http://vocab.getty.edu/page/tgn/"^^ . + . + . + . + "vsdb" . + . + "^\\d{7}$"^^ . + . + "ontology" . + "http://purl.obolibrary.org/obo/MI_"^^ . + "013681"^^ . + . + "false"^^ . + . + "http://www.kegg.jp/entry/"^^ . + . + . + "microbial" . + "FBgn0000015"^^ . + . + . + "http://www.violinet.org/vaxquery/vaccine_detail.php?c_vaccine_id=$1"^^ . + . + . + . + . + . + . + . + . + "http://doqcs.ncbs.res.in/template.php?&y=pathwaydetails&pn="^^ . + . + "false"^^ . + "http://purl.obolibrary.org/obo/YPO_$1"^^ . + . + . + "^\\d+$"^^ . + "protein" . + . + "life science" . + "co_357" . + . + . + "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/"^^ . + . + "false"^^ . + . + . + "Small Molecule Pathway Database" . + "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)."^^ . + "protein" . + . + . + "sider.drug" . + "^[0-9]+$"^^ . + . + . + . + . + "rna_sstrand" . + . + "^E\\d+$"^^ . + "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."^^ . + . + . + . + . + . + "0101963"^^ . + . + "https://cropontology.org/rdf/CO_331:$1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/FBcv_"^^ . + "Biological Imaging Methods Ontology" . + "co_336" . + . + . + "Vir-Mir db" . + "funderregistry" . + . + "^[a-z0-9]+$"^^ . + . + . + . + "PathoPlant®" . + "false"^^ . + "http://uri.neuinfo.org/nif/nifstd/oen_"^^ . + . + . + . + "C00000001"^^ . + . + "Akhilesh Pandey" . + "tcb" . + "ontology" . + "qb" . + "https://dgrc.bio.indiana.edu/product/View?product="^^ . + . + "life science" . + . + "dna" . + "atmospheric science" . + "An additional Japanese clinical trial registry"^^ . + . + "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."^^ . + . + . + . + . + . + "database" . + . + . + . + "gene" . + . + "biomedical science" . + . + "https://openalex.org/$1"^^ . + . + . + . + . + . + . + "ontology" . + "data visualization" . + . + "^LBCTR\\d+$"^^ . + "Experiment details about PeptideAtlas entries. Each PASS entry provides direct access to the data files submitted to PeptideAtlas."^^ . + . + . + . + "https://cstr.cn/$1"^^ . + . + "http://purl.obolibrary.org/obo/TAO_"^^ . + . + . + . + . + "Registry of Toxic Effects of Chemical Substances" . + . + "^((\\d+)|(\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+)|(\\d+\\.\\d+\\.\\d+\\.\\d+))$"^^ . + . + "bioactivities" . + . + "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."^^ . + . + . + "ontology" . + . + . + "ClinicalTrials.gov" . + . + "sweetrealm" . + . + "https://ror.org/"^^ . + . + "a.39.1.1"^^ . + . + "Toxic Process 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"^^ . + "iNaturalist User" . + . + "K00001"^^ . + "^\\d\\w+$"^^ . + . + "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."^^ . + . + . + . + "computer science" . + . + "https://bioschemas.org/profiles/$1"^^ . + . + "SEED Reactions" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PCO_$1"^^ . + "RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project"^^ . + "Food Classification and Description System" . + . + . + . + "KEGG Genome" . + "G-Rich Sequences Database" . + "life science" . + "^jRCT\\w?\\d+$"^^ . + . + . + . + "false"^^ . + "biomedical science" . + . + "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . + . + "Sickle Cell Disease Ontology" . + . + "^\\d{5,}$"^^ . + . + "false"^^ . + "false"^^ . + "http://purl.obolibrary.org/obo/PAO_$1"^^ . + "http://pathway.gramene.org/RICE/NEW-IMAGE?type=PATHWAY&object=$1"^^ . + "botany" . + "https://cropontology.org/rdf/CO_345:"^^ . + . + . + . + . + "deepak.unni3@lbl.gov" . + "http://purl.obolibrary.org/obo/CDNO_"^^ . + . + . + . + . + . + "ddpheno" . + "3546"^^ . + . + . + . + "http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid=$1"^^ . + . + . + . + . + "nando" . + . + "OGI.owl" . + . + . + . + "This is the RDF Schema for the RDF vocabulary terms in the RDF Namespace, defined in RDF 1.1 Concepts"^^ . + . + . + "dna" . + . + "http://edamontology.org/format_$1"^^ . + . + . + . + "population dynamics" . + "278"^^ . + "Intrinsically Disordered Proteins Ontology" . + . + "PhosphoPoint Phosphoprotein" . + . + "https://reactome.org/content/detail/$1"^^ . + . + . + . + "aclame" . + . + . + "physiology" . + "nucleotide" . + . + . + . + . + "false"^^ . + . + . + . + . + "^\\D{4}\\d{6}(\\-\\D{2})?$"^^ . + . + . + "Global Research Identifier Database" . + "merops.inhibitor" . + . + "^\\d{7}$"^^ . + . + . + . + . + "bold.taxonomy" . + . + . + . + . + . + "hba" . + . + "The Informed Consent Ontology (ICO) is an ontology for the informed consent and informed consent process in the medical field."^^ . + . + . + . + . + "false"^^ . + . + . + . + "Semantic Web Context" . + "Sensitive Data Ontology" . + "sequence" . + . + . + . + "CLO" . + . + "col" . + . + . + "https://sed-ml.org/urns.html#language:$1"^^ . + . + "developmental biology" . + . + . + . + . + . + . + . + "https://www.rrrc.us/Strain/?x="^^ . + . + "0000690"^^ . + "mobidb" . + "false"^^ . + . + . + . + "https://web.www.healthdatagateway.org/dataset/$1"^^ . + "^E(S|D)i\\d+-\\w$"^^ . + "https://www.gleif.org/lei/$1"^^ . + . + "euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information."^^ . + . + "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name=$1"^^ . + "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."^^ . + . + "ENSG00000139618"^^ . + "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."^^ . + . + "This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations."^^ . + . + "false"^^ . + . + "https://www.ebi.ac.uk/biomodels/"^^ . + "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."^^ . + "PA447218"^^ . + . + . + . + . + . + . + . + "10046"^^ . + . + "small molecule" . + "yuki.yamagata@riken.jp" . + . + . + "life science" . + . + . + "interaction" . + . + "https://www.ribocentre.org/docs/"^^ . + . + . + . + . + . + . + . + . + . + "wwf.ecoregion" . + "Echinobase" . + "interaction" . + . + "Molecule role (INOH Protein name/family name ontology)" . + . + . + . + . + . + "CTCAE" . + "http://gmd.mpimp-golm.mpg.de/Spectrums/"^^ . + "https://civicdb.org/links/evidence/$1"^^ . + "Katy Börner" . + . + "The PASS2 database provides alignments of proteins related at the superfamily level and are characterized by low sequence identity."^^ . + "LinJ.20.0070"^^ . + . + "RL3R1_HUMAN"^^ . + . + . + . + . + . + . + "data governance" . + . + "^m\\w+$"^^ . + "Marilyn Safran" . + "^\\d+$"^^ . + . + "image" . + . + "protein" . + "0000003"^^ . + "img.taxon" . + . + . + . + "KEGG Module" . + . + . + . + "false"^^ . + . + "obo" . + . . - . - . - "http://jaxmice.jax.org/strain/$1.html"^^ . - "Cell line collections (Providers)"^^ . - . - . - . - "false"^^ . - . - "https://bioregistry.io/pocketome:"^^ . + . + "https://loinc.org/"^^ . + . + "sep" . + . . - "1433C_TOBAC_1_252"^^ . - "PD000596"^^ . - . - . - . - "^\\d+$"^^ . - "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."^^ . - "small molecule" . - "ricenetdb.reaction" . - "ontology" . - "jason.stajich@ucr.edu" . - . - "novus" . - . - . - "https://bitbucket.org/$1"^^ . - "OpenAlex" . - . - "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . - "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . - "63250"^^ . - . - . - "bioinformatics" . - . - . - . - "ATCC(dna)" . - "0000190"^^ . - "structural biology" . - . - . - . - . - . - . - . - . - "fabio" . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/$1"^^ . - "metabolites" . - . - "dna" . - "FBdv" . - "^\\d+$"^^ . - "structure" . - . - . - "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."^^ . - "http://purl.org/spar/pro/$1"^^ . - . - . - . - "^(\\w+)?\\d+$"^^ . - "structure" . - "sdbs" . - "SWRL enables Horn-like rules to be combined with an OWL knowledge base."^^ . - . - "obo" . - "false"^^ . - "plant anatomy" . - . - "Philipp Bucher" . - . - "false"^^ . - . - . - "Veterans Health Administration (VHA) unique identifier" . - "conferences" . - . - . - . - . - "obo" . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/clinvar/variation/"^^ . - . - . - . - . - "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments."^^ . - . - "https://portal.gdc.cancer.gov/cases/$1"^^ . - . - "genome" . - "^CHEMBL\\d+$"^^ . - . - "LO362836C"^^ . - "101"^^ . - . - "dbo" . - "ontology" . - "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://cropontology.org/rdf/CO_336:"^^ . + . + "Raimond Winslow" . + "infectious disease medicine" . + . + "https://bioregistry.io/cst:"^^ . + . + . + . + . + "http://eugenes.org:7072/.bin/fbidq.html?"^^ . + . + . + . + . + . + "Ontology for genetic interval" . + . + . + . + . + . + . + "https://glytoucan.org/Structures/Glycans/"^^ . + . + . + "0001927"^^ . + . + . + "http://lipidbank.jp/cgi-bin/detail.cgi?id="^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + "RCV000033555.3"^^ . + "false"^^ . + . + "obo" . + . + . + . + . + . + "false"^^ . + "cl" . + . + "^[A-Z]{1,2}\\d{5}$"^^ . + "unique academic work identifier assigned in Scopus bibliographic database"^^ . + . + . + "Process Chemistry Ontology" . + "EAWAG Biocatalysis/Biodegradation Database" . + . + "Catalog of purchasable reagents and building blocks"^^ . + "contributor"^^ . + "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://swbiodiversity.org/seinet/taxa/index.php?taxon=$1"^^ . + . + . + . + "phosphosite.sitegroup" . + . + . + . + . + "^[A-Za-z0-9\\-\\_]+$"^^ . + . + . + "ogg" . + . + . + "genomics" . + "0000255"^^ . + . + "asfis" . + "dbgap" . + "25011"^^ . + "commoncoreontology" . + . + . + . + "uniprot/swiss-prot" . + . + "false"^^ . + "Paragraph"^^ . + . + . + . + . + . + . + "sequence" . + . + "https://data.bloodpac.org/ga4gh/drs/v1/objects/$1"^^ . + "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."^^ . + "http://www.bioassayontology.org/bao#BAO_$1"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "structure" . + "^M\\d{4}$"^^ . + "ontology" . + "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 Schizosaccharomyces pombe."^^ . + . + "false"^^ . + . + . + . + "knowledge and information systems" . + "PED00037"^^ . + . + "Interaction Network Ontology" . + . + "https://amoebadb.org/amoeba/app/record/gene/$1"^^ . + . + "https://bioregistry.io/gabi:"^^ . + . + . + . + . + "000000012281955X"^^ . + . + "^[A-Z][a-z][0-9]+$"^^ . + . + "environmental science" . + "fisheries science" . + . + "^\\d+$"^^ . + . + . + . + . + "^BAMSC\\d+$"^^ . + "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."^^ . + . + "8497"^^ . + . + . + "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."^^ . + "GALEN" . + . + "TA14985"^^ . + "Anvil" . + . + "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."^^ . + . + . + . + . + . + . + . + . + "cell biology" . + "https://kyotofly.kit.jp/cgi-bin/stocks/search_res_det.cgi?DB_NUM=1&DG_NUM=$1"^^ . + "obo" . + . + . + "http://purl.obolibrary.org/obo/NOMEN_$1"^^ . + "https://biosimulations.org/projects/$1"^^ . + . + . + . + "MSBNK-IPB_Halle-PB000166"^^ . + . "ontology" . - . - . - . - "rna-seq" . - . - . - . - . - . - "HMDB00001"^^ . - "NLXINV" . - . - . - . - "cmecs" . - . - "^TS-\\d{4}$"^^ . - . - "http://tumor.informatics.jax.org/mtbwi/strainDetails.do?key="^^ . - "false"^^ . - . - . + . + . + . + . + . + . + "Aclame" . + . + . + . + . + . + . + . + . + . + . + "0000288"^^ . + . + "BindingDB" . + "16"^^ . + "Gazetteer" . + . + . + "https://www.cellbiolabs.com/search?keywords=$1"^^ . + "subject agnostic" . + "IRCT20080904001199N7"^^ . + . + . + . + . + "false"^^ . + . + "title"^^ . + "health science" . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/ExO_"^^ . + . + . + "medicine" . + . + "http://bigg.ucsd.edu/models/universal/metabolites/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "G. Thomas Hayman" . + . + . + "http://www-snorna.biotoul.fr/plus.php?id=$1"^^ . + "CAA71118.1"^^ . + . + . + . + . + "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . + . + "molecular biology" . + . + . + . + "drugbank.category" . + "http://www.w3.org/2008/05/skos-xl#"^^ . + . + "protein" . + . + "false"^^ . + . + . + "life science" . + "http://purl.obolibrary.org/obo/GENEPIO_$1"^^ . + "^\\d+$"^^ . + "casent0106247"^^ . + . + . + "0000001"^^ . + . + . + "ontology" . + "Quinoa Ontology ontology" . + "ATCC" . + . + . + "life science" . + "DrugBank Reaction" . + . + . + . + "http://purl.obolibrary.org/obo/NIF_DYSFUNCTION_"^^ . + . + . + . + . + "http://arabidopsis.org/servlets/TairObject?accession=Gene:"^^ . + "http://purl.obolibrary.org/obo/SOPHARM_$1"^^ . + . + "Reaxys" . + . + . + . + . + "Experimental Factor Ontology" . + . + . + . + "Daniel Sonenshine" . + "^\\d{7}$"^^ . + . + . + . + . + "peteremidford@yahoo.com" . + . + "functional genomics" . + . + "false"^^ . + "false"^^ . + "Mutant Mouse Resource and Research Centers" . + . + . + "false"^^ . + . + . + "1.1.1.1"^^ . + . + "false"^^ . + "0000027"^^ . + "Human developmental anatomy, timed version" . + . + . + "depends on" . + . + . + . + . + . + "0000002"^^ . + . + . + . + "http://snp500cancer.nci.nih.gov/snp.cfm?both_snp_id="^^ . + "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."^^ . + . + "ae8c77fe-e6c8-44d5-8265-4a38c637bbef"^^ . + . + "NCBI Gene Expression Omnibus" . + . + . + "microbiome" . + "87"^^ . + "lcnaf" . + . + . + . + . + . + "^CHEMBL\\d+$"^^ . + . + "exac.transcript" . + "galen" . + . + . + . + . + . + "1801.012"^^ . + . + . + . + . + "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID="^^ . + . + . + "ontology" . + . + "fao.asfis" . + . + . + . + . + "ontology" . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "http://en.wikipedia.org/wiki/$1"^^ . + . + "^SAM[NED](\\w)?\\d+$"^^ . + "LNCRNADB" . + . + "ontology" . + "h_aktPathway"^^ . + . + . + . + . + "pain medicine" . + . + "Metabolic Encyclopedia of metabolic and other pathways" . + "https://purl.dataone.org/odo/ADCAD_"^^ . + . + . + . + "International Nonproprietary Names" . + "obo" . + "ontology" . + "1"^^ . + . + . + . + "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."^^ . + "expression" . + . + . + "false"^^ . + . + . + . + "interaction" . + . + "UP000005640"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "antibodies" . + "Michel Dumontier" . + . + "1250"^^ . + "false"^^ . + . + "biology" . + "analytical chemistry" . + . + . + "https://www.brenda-enzymes.de/ligand.php?brenda_ligand_id=$1"^^ . + "life science" . + "InterLex" . + "structure" . + "Multiple alignment" . + "2004-2820"^^ . + . + "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"^^ . + . + . + . + . + . + . + "^\\w+$"^^ . + "ontology" . + "^\\d{7}$"^^ . + . + . + "An application ontology to cover all aspects of malaria as well as the intervention attempts to control it."^^ . + . + . + . + "Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science."^^ . + . + . + . + "BIOMD0000000048"^^ . + . + . + "https://covid19.sfb.uit.no/api/records/"^^ . + "biomaterial supply resource" . + "http://csbl.bmb.uga.edu/DOOR/operon.php?id="^^ . + . + . + "^\\d+$"^^ . + . + . + . + "environmental science" . + "life science" . + . + . + "ontology" . + . + "protein" . + "http://id.nlm.nih.gov/mesh/vocab#"^^ . + . + "rxno" . + "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."^^ . + "biomedical science" . + . + . + . + . + . + "nci.drug" . + "bartoc" . + "unirule" . + "http://www.ontologyrepository.com/CommonCoreOntologies/"^^ . + "cp390@cam.ac.uk" . + "ontology" . + . + . + "true"^^ . + . + . + "Virus Pathogen Resource" . + "https://vcell.org/biomodel-$1"^^ . + . + . + . + "ontology" . + . + . + . + . + "reagent" . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "neurobiology" . + . + "subject agnostic" . + . + . + . + "jws" . + . + "^\\d{7}$"^^ . + "Product number for the European Medicines Agency"^^ . + . + "c0001"^^ . + . + "degradome" . + . + . + "ontology" . + . + . + . + . + . + "molecule" . + "gene prediction" . + . + "ken.sd.hsu@gmail.com" . + . + . + . + "quantitative genetics" . + . + . + . + . + "phenomics" . + . + "Marc Ciriello" . + "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/"^^ . + "imsr_tac" . + "est" . + . + . + . + "https://www.disprot.org/idpo/IDPO:"^^ . + "hmdb" . + "^C\\d+$"^^ . + "biomedical science" . + . + . + . + . + . + "Coriell Institute for Medical Research" . + "ZFIN" . + . + _:Ndc164aac22f2496d8fe1558616e1d7dd . + "chemistry" . + "ontology" . + . + . + "^MIRT\\d{6}$"^^ . + . + . + . + "Natural Product-Drug Interaction Research Data Repository" . + "PANTHER Family" . + . + . + . + . + . + . + "001"^^ . + . + . + . + . + . + "world2dpage" . + . + . + "https://vocab.lternet.edu/vocab/vocab/index.php?tema="^^ . + "biomedical science" . + "false"^^ . + . + . + . + . + . + "LigandBook" . + . + "One of the precursors to the EuropePMC project. Now EuropePMC is able to resolve CiteXplore codes."^^ . + "https://bacdive.dsmz.de/strain/$1"^^ . + "drugbank" . + . + "https://www.cameo3d.org/sp/targets/target/$1"^^ . + . + . + . + "health" . + "life science" . + . + . + . + . + . + "http://ensembl.org/glossary/ENSGLOSSARY_"^^ . + . + . + "NIST" . + "https://www.uniprot.org/uniref/$1"^^ . + "false"^^ . + . + "http://purl.org/spar/scoro/$1"^^ . + . + . + "dc_cl" . + . + . + . + . + . + . + . + . + "life science" . + . + . + . + . + . + . + . + "gene" . + . + . + . + "^((EB\\w+)|([A-Z0-9]+\\_[A-Z0-9]+))$"^^ . + . + . + . + "biodiversity" . + "0000004"^^ . + . + "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=$1"^^ . + . + . + . + . + "ClinicalTrials.gov provides free access to information on clinical studies for a wide range of diseases and conditions. Studies listed in the database are conducted in 175 countries"^^ . + . + . + "Genatlas" . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "ontology" . + "MTBLS1"^^ . + "Cell line databases/resources"^^ . + . + "ClinVar Submission" . + "ontology" . + . + "bgee.family" . + "obo" . + "UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries."^^ . + "^DAP\\d+$"^^ . + "HIX0004394"^^ . + "life science" . + . + "Dimension"^^ . + "false"^^ . + "sequence" . + . + . + . + "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + "IC9CM" . + . + . + "ecoliwiki" . + . + . + . + . + "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."^^ . + "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . + . "^\\d+$"^^ . - "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . - "life science" . - . - . - "0000078"^^ . - . - . - . - "zfs" . - "https://pubchem.ncbi.nlm.nih.gov/classification/#hid=$1"^^ . - . - "https://metazoa.ensembl.org/id/$1"^^ . - . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . - . - . - . - "bibliography" . - . - "200-003-9"^^ . - . - "https://www.kegg.jp/entry/"^^ . - "3532759"^^ . - "genomics" . - . - . - . - . - . - . - "chemical biology" . - . - . - . - . - . - . - "false"^^ . - . - "DASHR reports the annotation, expression and evidence for specific RNA processing (cleavage specificity scores/entropy) of human sncRNA genes, precursor and mature sncRNA products across different human tissues and cell types. DASHR integrates information from multiple existing annotation resources for small non-coding RNAs, including microRNAs (miRNAs), Piwi-interacting (piRNAs), small nuclear (snRNAs), nucleolar (snoRNAs), cytoplasmic (scRNAs), transfer (tRNAs), tRNA fragments (tRFs), and ribosomal RNAs (rRNAs). These datasets were obtained from non-diseased human tissues and cell types and were generated for studying or profiling small non-coding RNAs. This collection references RNA records."^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "National Bibliography Number" . - . - "AOPWiki (Key Event)" . - . - "000000021"^^ . - "taxonomy" . - "genomics" . - "DisProt" . - "Internet Engineering Task Force Language Tag" . - "Sol Genomics Network" . - . - . - . - "ambystoma" . - "benjamin_gyori@hms.harvard.edu" . - "Identifier for a user in iNaturalist"^^ . - . - . - "GenInfo Identifier" . - "^[a-z0-9\\-_]+$"^^ . - . -_:N612ccc06c1964e1ab2ea595e41a70881 "mb4@sanger.ac.uk" . - "Lepidoptera Anatomy Ontology" . - "CTD Chemical" . - . - . - "The Pan African Clinical Trials Registry (PACTR) is a regional register of clinical trials conducted in Africa. The registry is an African initiative serving the needs of Africans. It provides an open-access platform where clinical trials can be registered free of charge. The PACTR aims to increase clinical trial registration in Africa by developing awareness of the need to register trials and supporting trialists during registration. (from homepage)"^^ . - "0000339"^^ . - . - . - . - "109082"^^ . - . - "https://www.thaiclinicaltrials.org/show/"^^ . - . - "https://www.nextprot.org/db/entry/"^^ . - "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."^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - . - . - . - . - . - "ontology" . - . - "false"^^ . - "jrct" . - . - . - "true"^^ . - . - "ArchDB" . - . - . - "53784"^^ . - "bibliography" . - "subject agnostic" . - . - "DRS server that follows the Gen3 implementation. Gen3 is a GA4GH compliant open source platform for developing framework services and data commons. Data commons accelerate and democratize the process of scientific discovery, especially over large or complex datasets. Gen3 is maintained by the Center for Translational Data Science at the University of Chicago. https://gen3.org"^^ . - . - . - . - . - . - . - . - . - . - . - "Pathway Commons" . - "^\\d{6}$"^^ . - "dna" . - "bioschema" . - . - . - . - . - . - . - . - . - . - . - . - "Mouse gross anatomy and development, timed" . - . - . - "Q2207226"^^ . - . - . - "CVCL" . - "Nematode & Neglected Genomics" . - "http://purl.dataone.org/odo/ECSO_$1"^^ . - "ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al."^^ . - . - "easychair.cfp" . - . - . - . - . - "^[a-z_A-Z0-9]+$"^^ . - "strain" . - "virology" . - _:N40de88241fe445dc8d11e9c9b635f056 . - "John Kunze" . - . - . - . - . - "https://vocab.org/vann/$1"^^ . - "http://purl.obolibrary.org/obo/NIF_GROSSANATOMY_"^^ . - . - . - "subject agnostic" . - . - . - "^PACTR\\d+$"^^ . - . - . - . - . - . - . - . - . - "Golm Metabolome Database Reference Substance" . - "alpha.tom.kodamullil@scai.fraunhofer.de" . - . - "^DTXSID\\d+$"^^ . - "https://fairsharing.org/users/$1"^^ . - . - "alleles" . - "^\\d{7}$"^^ . - . - . - "http://purl.org/spar/doco/"^^ . - "insdc.cds" . - . - . - . - . - "frbrer" . - . - . - "life science" . - . - . - . - "https://sumlineknowledgebase.com/?page_id=$1"^^ . - . - . - . - . - "radlex" . - . - "expression" . - . - "phenomics" . - . - "https://cropontology.org/rdf/CO_341:$1"^^ . - "taxonomy" . - . - . - . - . - . - "pathway" . - "C. elegans phenotype" . - "wb" . - . - . - _:Neb0864156da647c4b350d1c2d17e099a . - . - . - . - . - . - "true"^^ . - . - . - . - "true"^^ . - . - _:N80cd99ec595a4d0599dce7bf309e7f23 . - "http://www.w3.org/2008/05/skos-xl#$1"^^ . - "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . - . - "life science" . - "chemistry" . - . - "Antibiotic Resistance Ontology" . - . - . - . - . - . - . - . - . - . - . - "protein" . - . - "^\\d+$"^^ . - . - "NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins."^^ . - "pharmacology" . - . - . - . - "Observation"^^ . - . - . - "allele" . - "http://fossilworks.org/?a=referenceInfo&reference_no=$1"^^ . - . - . - . - . - "small molecule" . - "biomedical science" . - . - . - . - . - "true"^^ . - "HOSAPI0399"^^ . - . - . - "subject agnostic" . - . - . - . - "false"^^ . - . - . - . - "0010316"^^ . - . - "pfr" . - . - . - . - "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id="^^ . - . - . - . - "^PR[0-9]{6}$"^^ . - . - . - . - . - "A database for Triticeae and Avena gene symbols."^^ . - "Maxwell L. Neal" . - "TOKU-E Cell-culture Database" . - . - . - . - . - . - "gene" . - . - "FHIR United States Implementation Guides" . - "Addgene Plasmid Repository" . - "conferences" . - . - . - . - . - . + . + "drugs" . + . + . + "biology" . + . + . + "obo" . + . + . + "https://w3id.org/scholarlydata/ontology/conference-ontology.owl#$1"^^ . + . + "cro" . + . + . + . + . + "627"^^ . + . + "The Code on Dental Procedures and Nomenclature (the CDT Code) assures consistency in documenting dental treatment.\n\nNote that CDT codes should look like D2150 but for some reason the ontology conversion that is reused across OBO rewrites them as CPT_000 + the four numbers without the leading D."^^ . + . + . + . + "AP00378"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + "2gc4"^^ . + . + . + "ontology" . + . + . + . + "^\\d{7}$"^^ . + . + . + "Ambystoma Genetic Stock Center" . + "NM_006262"^^ . + "false"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . + "http://purl.obolibrary.org/obo/APOLLO_SV_"^^ . + . + . + . + . + "0000253"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_res_"^^ . + . + "true"^^ . + "medicine" . + . + . + "PROV Namespace" . + . + . + . + . + "^[A-Za-z-0-9_]+(\\@)?$"^^ . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OGSF_"^^ . + . + "metagenomics" . + . + . + . + . + . + . + . + "probonto" . + "https://biofactoid.org/document/"^^ . + "Database of Macromolecular Interactions" . + . + . + "structure" . + "E-cyanobacterium entity" . + "cell line" . + . + . + . + . + "false"^^ . + . + . + "false"^^ . + "A curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs. In the current update, the UTR entries are organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated. The integration of UTRdb with genomic data has allowed the implementation of an efficient annotation system and a powerful retrieval resource for the selection and extraction of specific UTR subsets. "^^ . + . + . + . + "software engineering" . + . + "https://aopwiki.org/aops/"^^ . + . + . + . + . + . + "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_"^^ . + . + . + "Metabolites in drugbank"^^ . + . + "http://scop.berkeley.edu/sunid="^^ . + . + "https://www.isrctn.com/$1"^^ . + . + . + . + . + . + "genomics" . + . + . + "fishbase" . + "0000685"^^ . + . + . + . + "A large RDF store built from American governmental data. This semantic space has a mixture of direct terms and subspaces."^^ . + . + . + . + "MeSH 2013" . + . + . + . + . + . + "string" . + "DEF"^^ . + . + "GeneFarm" . + "IID00001"^^ . + "Open Biomedical Annotations" . + "^\\d+$"^^ . + "NLXOEN" . + . + . + . + "scop.sid" . + "cto" . + . + "drugbank.condition" . + "false"^^ . + . + . + "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."^^ . + . + "hepro" . + "FamPlex is a collection of resources for grounding biological entities from text and describing their hierarchical relationships."^^ . + . + . + . + . + . + "https://web.expasy.org/abcd/ABCD_"^^ . + "somatic" . + "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'."^^ . + . + . + . + . . - "http://purl.obolibrary.org/obo/COVOC_$1"^^ . - . - . - . - "Mike Cherry" . - . - . - . - "CORDIS Project" . - . - . - "https://cropontology.org/rdf/CO_348:$1"^^ . - . - "agriculture" . - . - . - . - "https://uniresolver.io/#did:$1"^^ . - "http://purl.obolibrary.org/obo/CHMO_$1"^^ . - "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1"^^ . - "617102"^^ . - "https://www.glycoepitope.jp/epitopes/$1"^^ . - "The MMRRC database is a repository of available mouse stocks and embryonic stem cell line collections."^^ . - . - . - . - . - . - "damion_dooley@sfu.ca" . - "^\\d{7}$"^^ . - "false"^^ . - "0001191"^^ . - "https://www.sigmaaldrich.com/US/en/product/sigma/$1"^^ . - "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . - "^C\\d+$"^^ . - . - "URGI Contact" . - "https://omabrowser.org/oma/hog/HOG:$1"^^ . - . - . - . - . - "http://www.w3.org/2006/time#$1"^^ . - "false"^^ . - . - . - . - . - . - "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."^^ . - . - . - . + "false"^^ . + "Pubchem" . + . + . + "SNP2TFBS is aimed at studying variations (SNPs/indels) that affect transcription factor binding (TFB) in the Human genome."^^ . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID="^^ . + . + "glycopost" . + . + . + "eagle-i resource ontology" . + . + . + "https://biopragmatics.github.io/providers/schem/$1"^^ . + . + "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."^^ . + . + . + "false"^^ . + . + "ga4ghdos" . + . + "ontology" . + . + . + "go.gpi" . + . + . + . + . + . + . + "false"^^ . + "https://www.novusbio.com/products/"^^ . + . + . + "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)"^^ . + . + . + . + "Ensembl Glossary" . + . + "wikidata" . + . + "An ontology supporting data modeling in WikiPathways"^^ . + "Ximbio" . + . + . + "The Drug Ontology" . + "classification" . + . + . + "life science" . + "http://purl.obolibrary.org/obo/T4FS_"^^ . + "http://ftp.ebi.ac.uk/pub/databases/lrgex/$1.xml"^^ . + . + "false"^^ . + . + . + . + . + "The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources."^^ . + . + . + "genefarm" . + . + "nlx.sub" . + "classification-model"^^ . + . + "EMEA/H/C/000181"^^ . + . + "false"^^ . + "Nucleotide" . + . + . + "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . + . + "http://purl.obolibrary.org/obo/MRO_"^^ . + . + . + . + . + "^1\\d{4}-\\d{3}$"^^ . +_:Naa71f4b9d1a3472aafbbf8cea9abd883 "radlex-feedback@lists.rsna.org" . + . + "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName="^^ . + . + . + . + "cell biology" . + "HGNC gene family" . + "adrien.coulet@loria.fr" . + . + "classification" . + "^\\d+$"^^ . + . + . + . + "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Summarize_Peptide?query=QUERY&searchForThis="^^ . + . + . + . . - . - "Human Oral Microbiome Database" . - "ontology" . - "https://bioregistry.io/lrg:"^^ . - . - . - . - . - "false"^^ . - "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."^^ . - . - "The Statistical Methods Ontology" . - . - . - "false"^^ . - "protein" . - . - "preclinical studies" . - . - . - . - "maize" . - . -_:Ne9d7876377624aa795c29d593ee4a373 "edd@usefulinc.com" . - . - "Neuronal cell types"^^ . - "cell" . - "^[A-Z0-9]+$"^^ . - . - "phylogenetics" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/CLO_"^^ . - "https://cls.shop/$1"^^ . - . - "structural biology" . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - "neuroscience" . - . - . - . - . - "obo" . - "G77500AY"^^ . - . - . - . - . - . - "The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate quantum mechanics (QM) calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods."^^ . - . - . - . - "false"^^ . - "UniProt Variants" . - "idpo" . - . - "false"^^ . - "^[0-9][A-Za-z0-9]{3}$"^^ . - . - "genome" . - . - . - . - . - "STOREDB at University of Cambridge" . - "ontology" . - . - "kdurante@stanford.edu" . - . - "Marilyn Safran" . - . - "0000001"^^ . - "iceo" . - . - . - . - . + . + "EDAM Operation" . + "^\\d{4}$"^^ . + . + . + . + . + . + . + . + . + "https://www.cancerrxgene.org/translation/Drug/"^^ . + "ligea" . + . + "ExO" . + "Geomames" . + . + . + . + "An ontology of traits covering vertebrates"^^ . + . + . + "https://www.genecards.org/cgi-bin/carddisp.pl?gene="^^ . + "phenomics" . + "Grant"^^ . + . + . + "A pull request in any public repository on GitHub."^^ . + . + . + . + "http://data.food.gov.uk/codes/foodtype/id/"^^ . + "^IRCT\\d+N\\d+$"^^ . + "ncbibook" . + "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."^^ . + . + . + "http://multicellds.org/MultiCellDB/"^^ . + . + . + "^\\d+$"^^ . + "upper-level ontology" . + "D0001"^^ . + . + "Epilepsy Ontology" . + . + "opb" . + . + . + "https://www.ccdc.cam.ac.uk/services/structures?pid=csd:$1&sid=IDORG"^^ . + . + . + "^\\d{7}$"^^ . + . + "Soybean ontology" . + "0000006"^^ . + "ecyano.model" . + . + "Mosquito insecticide resistance" . + . + "mat" . + "kegg.glycan" . + . + "051"^^ . + . + "http://bioinfo.lifl.fr/norine/result.jsp?ID="^^ . + . + "protein" . + "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."^^ . + . + "http://icd9cm.chrisendres.com/index.php?action=search&srchtext=$1"^^ . + . + . + "^[a-z_A-Z0-9]+$"^^ . + "STOREDB at University of Cambridge" . + . + . + "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."^^ . + . + . + . + . + . + "http://modelseed.org/biochem/compounds/$1"^^ . + . + "http://exac.broadinstitute.org/transcript/"^^ . + "http://purl.obolibrary.org/obo/APO_$1"^^ . + . + . + "BugBase Protocol" . + "Gene Ontology Rules" . + "interaction" . + . + "http://www.w3.org/2000/01/rdf-schema#$1"^^ . + . + . + "http://worfdb.dfci.harvard.edu/index.php?search_type=name&page=showresultrc&race_query=$1"^^ . + . + . + . + . + "The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences."^^ . + . + "3771877"^^ . + . + "ontology" . + . + . + . + "Al Kikhney" . + . + . + "https://www.metabolome-express.org/datasetview.php?datasetid="^^ . + "inaturalist.taxon" . + . + . + "http://purl.obolibrary.org/obo/TGMA_$1"^^ . + . + "vmhmetabolite" . + _:Nba7394e70eed46019c593a60ce48ec28 . + . + . + "ECMDB" . + "Ontology of Microbial Phenotypes" . + . + "http://www.semanticweb.org/mca/ontologies/2018/8/untitled-ontology-47#$1"^^ . + "http://purl.obolibrary.org/obo/UPHENO_$1"^^ . + . + "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid="^^ . + "Xeni Kechagioglou" . + . + "matrixdb.association" . + . + "ontology" . + . + "modeldb.concept" . + . + "classification" . + . + . + "biopragmatics/bioregistry"^^ . + "robert.hoehndorf@kaust.edu.sa" . + "^[A-Z]{2,4}\\d+([A-Z])?([0-9])?$"^^ . + . + . + . + . + "^\\d+$"^^ . + "structural biology" . + . + . + "0000123"^^ . + . + . + . + "pgxbs-kftva5zv"^^ . + . + . + . + "ico" . + "http://bioinfo2.weizmann.ac.il/cgi-bin/genenote/GN_results.pl?keyword_type=2_gc_id&keyword=$1&data_type=norm2&results=yes"^^ . + "http://edamontology.org/operation_"^^ . + "false"^^ . + "ontology" . + "false"^^ . + . + "5HT3Arano"^^ . + "ontology" . + "^\\d+$"^^ . + "European Nucleotide Archive" . + "MetaNetX reaction" . + . + "Observational Medical Outcomes Partnership" . + . + "^UPI[A-F0-9]{10}$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://cn.dataone.org/cn/v2/resolve/{$1}"^^ . + "Gramene Gene" . + "gene" . + . + . + . + "http://www.dpvweb.net/dpv/showdpv.php?dpvno=$1"^^ . + "D053716"^^ . + "fhir.implementation" . + "piroplasma" . + . + "subject agnostic" . + . + . + "PELNAW"^^ . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "Drosophila gross anatomy" . + . + "Meghan Balk" . + . + _:N12268bc5728c47d7a4381e5d54096fd5 . + "https://www.ebi.ac.uk/thornton-srv/databases/CSA/SearchResults.php?PDBID=$1"^^ . + "bioinformatics" . + . + . + . + "http://classyfire.wishartlab.com/tax_nodes/C$1"^^ . + . + "Tick Cell Biobank" . + "Paul Schofield" . + "^(MNXM\\d+|BIOMASS|WATER)$"^^ . + . + . + . + "John Garavelli" . + "^\\d{3}\\.\\d{2}$"^^ . + . + "ontology" . + "obo" . + . + . + . + . + . + . + . + "orcid" . + . + . + . + . + . + _:N13bb372bbe454a47a953e75ba60f7f8d . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id=$1"^^ . + . + "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id="^^ . + . + "^\\d{4}\\-\\d{6}\\-\\d{2}$"^^ . + . + "http://purl.org/dc/terms/$1"^^ . + . + . + . + . + . + "Cell line collections (Providers)"^^ . + . + . + . + . + . + . + . + "rpcec" . + . + . + . + "Virus' miRNA target" . + . + . + "Japan Consortium for Glycobiology and Glycotechnology Database" . + "animal model" . + . + . + . + . + "ontology" . + "Traits and phenotypes of flowering plants occurring in digitized Floras"^^ . + "mco" . + . + "^\\d{7}$"^^ . + "^\\d{8}$"^^ . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno=$1"^^ . + . + . + . + "chemistry" . + . + "^[0-9]+$"^^ . + . + "Tohoku University cell line catalog" . + . + . + . + . + "PaxDb Organism" . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "molecular biology" . + "obo" . + "biochemistry" . + . + . + "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name="^^ . + . + "grin" . + . + . + . + "Rat Genome Database" . + "An ontology representing knowledge about salmon, features of their habitats, salmon stakeholders, and related entities. This ontology is considered to be in the early stages of development, though it is based upon considerable previous work. Contributions of all kinds are welcome and encouraged, including alignments, updates to existing terms, and new terms."^^ . + "Systems Biology Ontology" . + . + . + "DECIPHER CNV Syndromes" . + "ontology" . +_:N613e35d4094d47e4af9d8a0547acbfbf "info@who.int" . + "proteomics" . + . + . + "Anita Bandrowski" . + "Kidney and Urinary Pathway Ontology" . + . + . + . + . + . + . + . + "classification" . + "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . + . + . + "http://www.phosphosite.org/siteAction.do?id="^^ . + . + . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id=$1"^^ . + "true"^^ . + "obo" . + . + . + . + . + . + "genetics" . + . + . + . + . + . + . + . + . + "medicine" . + "http://purl.obolibrary.org/obo/PAO_"^^ . + . + . + "https://www.inaturalist.org/observations/$1"^^ . + "GO Relations" . + "human" . + . + "00000001"^^ . + . + . + "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID="^^ . + . + . + . + "false"^^ . + . + "pathways" . + . + . + "Ion Channel Electrophysiology Ontology" . + . + . + . + . + "0278"^^ . + "IntAct provides a freely available, open source database system and analysis tools for protein interaction data. This collection references interactor molecules."^^ . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The EC record provides for a given enzyme classification (EC) the associated list of enzyme-catalysed reactions and their corresponding kinetic data."^^ . + "The RNA modification database provides a comprehensive listing of post-transcriptionally modified nucleosides from RNA. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA."^^ . + . + . + . + . + . + . + "strain" . + . + . + "https://jrct.niph.go.jp/en-latest-detail/"^^ . + . + . + "^\\d+$"^^ . + "nikolaos.moustakas@catalysis.de" . + . + "Lin Huang" . + . + . + "false"^^ . + "KEGG Orthology" . + . + . + . + . + . + . + . + . + . + . + "rwinslow@jhu.edu" . + . + . + . + . + "ATCC(dna)" . + "ec-code" . + . + . + "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . + "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."^^ . + . + . + . + . + "^DP\\d{5}$"^^ . + "^\\d{7}$"^^ . + . + "^[A-Z_a-z]+$"^^ . + "http://h-invitational.jp/hinv/protein/protein_view.cgi?hip_id=$1"^^ . + "humanities" . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/GO_"^^ . + . + "Rice Genome Annotation Project" . + . + . + . + . + "https://w3id.org/reproduceme#"^^ . + . + . + . + . + . + "A structured controlled vocabulary of sample preparation, visualization and imaging methods used in biomedical research."^^ . + . + "AURKA"^^ . + "true"^^ . + . + "agriculture" . + "epidemiology" . + . + "ordb" . + "immunology" . + . + . + . . - . - "emapa" . - "GLDS-141"^^ . - . - . - "agsc" . - . - "false"^^ . - "ontology" . - "PSI-MOD" . - "lspci" . - . - . - "^\\d{7}$"^^ . - "te" . - . - . - . - "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="^^ . - . - . - "Identifier for an entity in open tree of life"^^ . - "BARC-013845-01256"^^ . - "http://purl.obolibrary.org/obo/MPATH_"^^ . - . - . - . - . - . - . - . - "Trushar Shah" . - . - . - . - "geno" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PLO_"^^ . - . - "embryo" . - . - "https://www.ebi.ac.uk/complexportal/complex/"^^ . - . - "^IHW\\d+$"^^ . - . - . - . - . - . - . - "Functional Requirements for Bibliographic Records" . - . - "planttfdb" . - "The Prescription of Drugs Ontology" . - . - "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice="^^ . - . - "data management" . - "Japan Registry of Clinical Trials" . - . - . - . + . + . + "^[a-z]{3}\\-(mir|let|lin)\\-\\w+(\\-\\w+\\-\\w+)$"^^ . + . + . + "agb@ebi.ac.uk" . + . + . + . + "CA981206459"^^ . + . + . + . + . + . + "http://www.ifomis.org/bfo/1.1/snap#$1"^^ . + . + . + "secretariat@eol.org" . + "bigg.compartment" . + "structure" . + . + . + . + . + "genomic sequence" . + . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "Social Insect Behavior Ontology" . + . + . + . + "http://dictybase.org/db/cgi-bin/feature_page.pl?primary_id="^^ . + . + . + . + . + "GO Chemicals" . + "ccf" . + . + . + . + . + "http://en.wikipedia.org/wiki/"^^ . + . + . + . + . + . + "Mathias Brochhausen" . + . + "dna" . + . + . + "000000159"^^ . + . + . + "Karel Berka" . +_:Nb738ec851a6748268b17445305a9946c "wbug@ncmir.ucsd.edu" . + . + "faseb list" . + . + . + "http://ecmdb.ca/compounds/$1"^^ . + "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id=$1"^^ . + "^[A-Z_0-9]+$"^^ . + "http://uri.neuinfo.org/nif/nifstd/nifext_$1"^^ . + . + "http://jglobal.jst.go.jp/en/redirect?Nikkaji_No="^^ . + "http://uri.neuinfo.org/nif/nifstd/nlx_organ_$1"^^ . + "dna" . + . + "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_$1"^^ . + . + "meghan.balk@gmail.com" . + . + . + . + . + "http://metnetonline.org/browse_pathway2.php?pthID=$1"^^ . + . + . + "enzo" . + . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "nanotechnology" . + . + "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code="^^ . + . + . + . + "WBPhenotype" . + . + . + "LOC_Os01g49190.1"^^ . + . + . + . + . + "idoo" . + "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line="^^ . + "tissue" . + . + "^\\d{6,8}$"^^ . + . + "neurophysiology" . + . + "603903"^^ . + . + . + . + . + . + "Biological Expression Language" . + "molbase" . + "349124"^^ . + . + "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."^^ . + "Xenbase" . + "Database of Quantitative Cellular Signaling: Model" . + "https://bioportal.bioontology.org/ontologies/OPB/?p=classes&conceptid=http%3A%2F%2Fbhi.washington.edu%2FOPB%23OPB_"^^ . + . + . + "1"^^ . + . + . + "Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis." . + "false"^^ . + "http://purl.obolibrary.org/obo/AEO_"^^ . + . + "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://web.expasy.org/abcd/ABCD_$1"^^ . + "psychology" . + . + . + . + . + . + "https://proteininformationresource.org/cgi-bin/resid?id=$1"^^ . + . + "REBASE Enzyme Number" . + . + . + . + "knowledge and information systems" . . - . - "Coconut ontology" . - "International Classification of Diseases, 10th Revision, Clinical Modification" . - . - . - . - . - . - "Curator name: Clara S. Stanschewski; Curator Affiliation: King Abdullah University of Science and Technology; Contributing Scientists or Crop expert group: The Salt Lab and the Quinoa Phenotyping Consortium Creation Date: 23.05.2021"^^ . - "protonet.cluster" . - "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e="^^ . - "^\\d{8}$"^^ . - "nihhesc" . - . - "RSNA Informatics RadLex" . - . - . - . - "0000041"^^ . - . - . - "obo" . - "System Science of Biological Dynamics project" . - . - . + . + "geodesy" . + . + "https://ocid.ontochem.com/prefname?ocid=$1"^^ . + . + . + . + "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"^^ . + . + . + . + . + "Intrinsically Disordered proteins with Extensive Annotations and Literature" . + . + . + "mpio" . + . + "A registry of commonly used prefixes in the life sciences and linked data. The source data for this registry is a spreadsheet on Google called the Life Science Registry. This registry was previously known as Prefix Commons and was available at https://prefixcommons.org." . + "Brachiaria ontology" . . - "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."^^ . - . - "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://www.phosphosite.org/siteAction.do?id="^^ . - . - . - "https://biopragmatics.github.io/providers/hog/$1"^^ . - . - . - "0000010"^^ . - "http://www.hmdb.ca/metabolites/"^^ . - . - "life science" . - "ontology" . - . - "false"^^ . - . - . - "protein" . - . + . + "zfin" . + "sepio" . + "http://wodaklab.org/iRefWeb/interaction/show/"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/VBO_$1"^^ . + "http://uri.neuinfo.org/nif/nifstd/birnlex_"^^ . + "deletion" . + . + . + . + . + . + . + . + "PA146123006"^^ . + . + "https://www.ncbi.nlm.nih.gov/gene/$1"^^ . + "pgx" . + . + . + . + "false"^^ . + "bibliometrics" . + "life science" . + . + "G24361QY"^^ . + . + . + . + . + . + "0000081"^^ . + . + . + . + "Genomic Distribution of structural Superfamilies" . + . + . + . + . + "pso" . + . + . + . + . + . + "TIGR00010"^^ . + . + "slime-mould" . + "kegg.rclass" . + . + . + "^\\w+$"^^ . + . + "iuphar.ligand" . + "obi" . + "Terminology of Anatomy of Human Embryology" . + . + "model" . + . + "Mechanism, Annotation and Classification in Enzymes" . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "1"^^ . + "The International Molecular Exchange (IMEx) is a consortium of molecular interaction databases which collaborate to share manual curation efforts and provide accessibility to multiple information sources."^^ . + "GeneFarm is a database whose purpose is to store traceable annotations for Arabidopsis nuclear genes and gene products."^^ . + "FunderRegistry" . + . + . + . + . + "European Genome-phenome Archive Study" . + . + . + "Signaling Network Open Resource" . + "http://www.proglycprot.org/detail.aspx?ProId="^^ . + . + "^[0-9][A-Za-z0-9]{3}$"^^ . + "ontology" . + . + "false"^^ . + "developmental biology" . + "molecular biology" . + . + . + . + . + "TriTrypDB" . + . + . + "IPR016380"^^ . + . + . + . + "Vendor for assays, cells, and antibodies"^^ . + . + "false"^^ . + "lincs.smallmolecule" . + . + "false"^^ . + . + . + "https://biosimulations.org/projects/"^^ . + "National Library of Medicine Catalog" . + . + . + "owl" . + "https://chem.nlm.nih.gov/chemidplus/rn/"^^ . + . + "http://purl.obolibrary.org/obo/PROCO_$1"^^ . + . + "false"^^ . + . + . + . + . + "KEGG_REACTION" . + . + . + "^2\\d{4}$"^^ . + . + . + "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . + "brenda" . + . + . + "biomedical science" . + "dto" . + "http://unite.ut.ee/bl_forw.php?nimi=$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "protein-protein interactions" . + . + . + . + . + . + "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). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line"^^ . + "mro" . + "0000198"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + "Lindsay Cowell" . + . + . + "Integrated Resource for Domestic Dog" . + "false"^^ . + . + "eVOC mouse development stage" . + . + "http://purl.obolibrary.org/obo/SEPIO_$1"^^ . + . + "medical informatics" . + . + . + "false"^^ . + . + "NCBI_gi" . + "false"^^ . + . + . + "Performance Summary Display Ontology (PSDO) is an application ontology about motivating information in performance summaries and the visual and textual entities that are used to communicate about performance. Motivating information includes performance comparisons and changes that motivate improvement or sustainment, such as improvement towards a goal, loss of high performer status, or the presence of a performance gap. Visual and textual entities include charts, tables, and graphs that display performance information. PSDO's domain focus is healthcare organizations that use clinical quality dashboards and feedback interventions for healthcare professionals and teams. Performance information is commonly about the quality of care and health outcomes that have 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 supported by the NIH, National Library of Medicine (1K01LM012528-01, 1R01LM013894-01).\n\nLandis-Lewis Z, Stansbury C, Rincón J, Gross C. Performance Summary Display Ontology: Feedback intervention content, delivery, and interpreted information. International Conference on Biomedical Ontology 2022 (ICBO 2022). https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_2172.pdf"^^ . + . + . + . + "hsa-mir-200a"^^ . + . + . + "pharmacology" . + "tigrfam" . + "false"^^ . + "gene" . + . + "biomedical science" . + . + "GXA Expt" . + . + "0000547"^^ . + "false"^^ . + "obo" . + . + "https://pharmacodb.ca/tissues/"^^ . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/bioassay/"^^ . + . + . + "284196006"^^ . + "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."^^ . + "antibodyregistry" . + . + . + . + . + . + . + . + "FaBiO, the FRBR-aligned Bibliographic Ontology" . + . + . + . + . + "bacmap.biog" . + . + . + . + "^CHEMBL\\d+$"^^ . + "Psychology Ontology" . + "ontology" . + "http://zfin.org/$1"^^ . + . + "chebi" . + . + . + . + . + "https://purl.dataone.org/odo/MOSAIC_$1"^^ . + . + "^\\d+$"^^ . + . + "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . + "High-quality Automated and Manual Annotation of microbial Proteomes" . + "aging" . + . + . + . + . + "https://www.ebi.ac.uk/metagenomics/analyses/"^^ . + "^\\d+$"^^ . + . + . + "false"^^ . + "false"^^ . + . + "ontology" . + . + "Search the world's most comprehensive index of full-text books."^^ . + "http://www.receptors.org/nucleardb/proteins/"^^ . + . + "false"^^ . + . + . + . + . + "PlasmoDB" . + "ymdb" . + "hprd" . + . + . + "Physico-chemical process" . + . + "Sofia Robb" . + "scholia.resource" . + . + . + . + . + "bspo" . + "false"^^ . + . + . + "LCL-2085"^^ . + "International Molecular Exchange" . + "scopus" . + "21393"^^ . + . + . + . + "ontology" . + "https://www.google.com/patents/$1"^^ . + . + . + . + "interaction" . + . + "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . + . + . + "life science" . + "phenotype" . + . + . + . + . + "https://e-cyanobacterium.org/models/model/"^^ . + . + "6VDC956"^^ . + "structure" . + "^[A-Z0-9]+$"^^ . + "protein" . + . + . + . + . + "organ" . + "^\\d{3}$"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "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."^^ . + . + . + . + "obo" . + "https://cropontology.org/rdf/CO_325:"^^ . + "^\\w+:[\\w\\d\\.-]*$"^^ . + "disorder" . + . + . + . + "Matthew Brush" . + . + . + "obo" . + . + "75"^^ . + . + . + . + . + . + . + "http://www.gramene.org/db/genes/search_gene?acc=$1"^^ . + . + . + . + "life science" . + "tol.webproj" . + "ConoServer" . + "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ="^^ . + . + "mycobank" . + . + . + . + . + . + . + . + "https://www.kaggle.com/"^^ . + . + . + . + . + . + . + "https://plants.ensembl.org/id/"^^ . + . + . + "1047874"^^ . + . + . + . + . + "MFO_0000001"^^ . + . + . + . + "YBR125c"^^ . + . + . + "http://purl.obolibrary.org/obo/MIRNAO_"^^ . + . + "http://www.hprd.org/protein/$1"^^ . + "bioregistry"^^ . + "rna" . + "^\\d+$"^^ . + "biodiversity" . + . + . + "DCAT is an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web"^^ . + . + . + . + . + "NCI Thesaurus" . + . + "h2o"^^ . + . + . + . + . + . + . + "PharmacoDB Cells" . + . + "label"^^ . + "Philippine Health Research Registry" . + "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym="^^ . +_:N897a2f3e7af8401db8644acbfa753ed9 "Josef Hardi" . + . + . + . + . + . + "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . + . + . + . + . + . + . + "ontology" . + . + . + . + . . - . - . - "M0001"^^ . - "scopus.work" . - "https://www.kew.org/data/grasses-db/www/$1"^^ . - . - . - "General Enquiries" . - "http://purl.obolibrary.org/obo/FIX_"^^ . - "t4fs" . - "http://substrate.burnham.org/protein/annotation/$1/html"^^ . - "https://ontology.iedb.org/ontology/ONTIE_$1"^^ . - . - . - . - "ons" . - . - "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . - "https://www.ncbi.nlm.nih.gov/nucest/"^^ . - . - "https://genelab-data.ndc.nasa.gov/genelab/accession/"^^ . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . - . - . - . - . - "false"^^ . - "false"^^ . - "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . - . - "prov" . - "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . - . - . - . - . - . - "Non-Coding RNA Ontology" . - . - . - "uBio NameBank" . - . - "^LSM-\\d+$"^^ . - . - . - "false"^^ . - . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/FLOPO_"^^ . - . - "01.01.005"^^ . - "ontology" . - . - . - . - "^[A-Za-z-0-9_]+(\\@)?$"^^ . - . - . - . - "true"^^ . - "life science" . - . - "development" . - . - . - . - . - . - . - . - . - . - . - . - "puro" . - . - . - . - "https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=worm&c=Gene&l="^^ . - . - "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . - . - . - . - . - . - "th" . - . - . - . - "Interaction Network Ontology" . - . - . - "ontology" . - . - . - . - . - . - . - . - . - "false"^^ . - "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . - . - "fortuna@ebd.csic.es" . - . - . - . - . - "https://github.com/biolink/biolink-model" . - . - "dc_cl" . - . - . - . + "ontology" . + "Yeast Intron Database v4.3" . + . + . + "COCONUT (COlleCtion of Open Natural ProdUcTs) Online is an open source project for Natural Products (NPs) storage, search and analysis. It gathers data from over 50 open NP resources and is available free of charge and without any restriction. Each entry corresponds to a \"flat\" NP structure, and is associated, when available, to their known stereochemical forms, literature, organisms that produce them, natural geographical presence and diverse pre-computed molecular properties."^^ . + "International Classifications of Diseases" . + . + . + . + "0000124"^^ . + . + . + "^T[A-Z]\\d{7}$"^^ . + . + "^\\d{7}$"^^ . + . + "http://purl.obolibrary.org/obo/SPD_$1"^^ . + "https://bbp.epfl.ch/nexus/web/studios/public/$1"^^ . + "ST000900"^^ . + . + . + "https://bioregistry.io/phosphopoint.protein:"^^ . + "ElementNumber"^^ . + . + . + "SUPERFAMILY" . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references protein entries in the database."^^ . + "false"^^ . + . + "fish" . + . + "http://www.kegg.jp/entry/$1"^^ . + . + . + "https://bioregistry.io/pesticides:"^^ . + "000004"^^ . + "konigmatt@googlemail.com" . + . + "Homology Ontology" . + "NCBIGene" . + . + . + . + . + . + "development" . + "Microbial Protein Interaction Database" . + . + . + "^\\d{7}$"^^ . + . + . + "https://www.inaturalist.org/places/$1"^^ . + . + "pathway" . + "http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=$1"^^ . + . + . + "false"^^ . + "NCI Metathesaurus" . + . + . + . + . + . + "Codon Usage Tabulated from GenBank" . + . + . + . + "molecular neuroscience" . + . + . + . + . + . + . + . + . + "diapriid@gmail.com" . + . + . + . + . + . + "software engineering" . + . + "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/"^^ . + . + "^\\d{6}$"^^ . + . + "flowrepository" . . - "pdro" . - "Global Biodiversity Information Facility" . - "http://lincsportal.ccs.miami.edu/cells/#/view/$1"^^ . - . - "http://bigg.ucsd.edu/models/"^^ . - "3"^^ . - . - . - . - . - . - . - "life science" . - "comparative neurobiology" . - "danbri@w3.org" . - "clinvar.submitter" . - "Sabine Oesterle" . - "The Simple Modular Architecture Research Tool (SMART) is an online tool for the identification and annotation of protein domains, and the analysis of domain architectures."^^ . - "Semantic Web Context" . - . - . - . - . - "ontology" . -_:N3abf7e22f0e74131a3b6b2ff255f1b2b "Crop Ontology Helpdesk" . - . - . - "conso" . - . - . - "biomedical science" . - . - . - . - . - . - . - . - "kegg.compound" . - . - "^\\w+$"^^ . - . - "anatomy" . - . - . - "false"^^ . - "OpenCitations Meta Identifier" . - "https://proteinensemble.org/"^^ . - "3618"^^ . - . - "^\\w+(\\.\\d+)?(\\.\\d+)?$"^^ . - . - . - . - . - "drug" . - . - . - "structure" . - "interaction" . - "ontology" . - . - . - "botany" . - . - . - . - . - . - "CO_325" . - "https://giardiadb.org/giardiadb/app/record/gene/"^^ . - . - . - "ncro" . - . - "https://vocab.lternet.edu/vocab/vocab/index.php?tema="^^ . - "https://restraintsgrid.bmrb.io/NRG/MRGridServlet?block_text_type=2-parsed&db_username=wattos1&file_detail=2-parsed&format=n%2Fa&program=STAR&request_type=block&subtype=full&type=entry&mrblock_id="^^ . - . - . - . - . - . - . - . - "PLANA, the PLANarian Anatomy Ontology, encompasses the anatomy of developmental stages and adult biotypes of Schmidtea mediterranea."^^ . - . - . - . - "snoRNABase" . - . - "^SEQF\\d+$"^^ . - . - . - "co_325" . - "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . - "53504"^^ . - . - . - "obo" . - "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."^^ . - . - . - . - . - . - "ConfIDent Event" . - . - . - . - "^[0-9]+$"^^ . - "https://cropontology.org/rdf/CO_356:"^^ . - "Medical Subject Headings" . - . - "Interlab Cell Line Collection" . - . - . - . - . - . - . + "Lynn Schriml" . + "signaling-gateway" . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "0001"^^ . + . + . + . + "^\\d{7}$"^^ . + "subject agnostic" . + "c4o" . + . + "false"^^ . + "protein" . + . + "128011350"^^ . + "SNOMEDCTCT_2018_03_01" . + . + . + "ms" . + . + . + "https://www.kegg.jp/entry/$1"^^ . + "Metabolic Atlas Reaction" . + "OdorDB stores information related to odorous compounds, specifically identifying those that have been shown to interact with olfactory receptors"^^ . + . + . + "Amos.Bairoch@sib.swiss" . + "CGNC" . + "ScerTF" . + "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . + . + . + . + "identifier for an educational organization issued by the UK Register of Learning Providers"^^ . + . + . + . + . + . + "ontology" . + "^\\d+$"^^ . + . + "false"^^ . + . + . + . + . + . + "glytoucan" . + . + . + "https://www.ncbi.nlm.nih.gov/genome/$1"^^ . + "NIF Standard Ontology: Subcellular Entities" . + "https://models.physiomeproject.org/exposure/"^^ . + . + . + . + . + "interaction" . + . + "stacia@stanford.edu" . + "Stacia R Engel" . + . + . + "^\\d{7}$"^^ . + . + . + . + "A public repository, standards compliant, for proteomics image data published in the literature. This repository currently contains data from 16 published articles, putting together 22 reference maps for 15 species, totalizing nearly 4'400 identified spots."^^ . + "ICD-11" . + "https://repeatsdb.org/protein/$1"^^ . + . + "https://gen3.theanvil.io/ga4gh/drs/v1/objects/$1"^^ . + "https://www.sharkipedia.org/traits/"^^ . + . + . + . + "structural biology" . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "agriculture" . + . + . + "genome" . + "http://bcrj.org.br/celula/$1"^^ . +_:Nc7f4b51b50d3443c910d77680c53fbc7 "helpdesk@cropontology-curationtool.org" . + . + . + . + "http://bgee.unil.ch/bgee/bgee?page=gene_family&action=family_details&gene_family_id=$1"^^ . + . + . + "https://bbp.epfl.ch/nexus/web/studios/public/"^^ . + . + "https://id.loc.gov/authorities/$1"^^ . + . + "false"^^ . + . + . + . + . + . + "ma" . + "Conserved Domain Database at NCBI" . + . + . + "Dictyostelium discoideum phenotype ontology" . + . + . + . + . + . + "false"^^ . + . + "PubChem Classification" . + . + . + . + "medicine" . + "817732"^^ . + "false"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "life science" . + "bgee.organ" . + "false"^^ . + . + . + . + "false"^^ . + "gene" . + "BioNumbers is a database of key numberical information that may be used in molecular biology. Along with the numbers, it contains references to the original literature, useful comments, and related numeric data."^^ . + "signor.relation" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "miro" . + . + "^\\d{8}$"^^ . + . + . + . + . + . + "http://www.w3.org/XML/1998/namespace#"^^ . + . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + _:N0f79c573c15a4405a1d8a67adb3a8e7a . + "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."^^ . + . + "https://bioregistry.io/p3db.protein:"^^ . + "omrse" . + "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."^^ . + . + . + "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."^^ . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "https://www.abcam.com/$1.html"^^ . + . + "https://commonchemistry.cas.org/detail?cas_rn=$1"^^ . + . + . + . + "ortholog" . + "https://labsyspharm.github.io/lspci/$1"^^ . + "obo" . + . + "keilbeck@genetics.utah.edu" . + . + "KEGG DRUG" . + "kisao" . + . + "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid="^^ . + "biomedical science" . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "90000018"^^ . + . + "protein" . + "organic chemistry" . + "IUPHAR_LIGAND" . + . + . + . + . + . + . + "HMS Library of Integrated Network-based Cellular Signatures Datasets" . + "Citation Typing Ontology" . + . + . + "Ensembl Plants" . + . + . + "NINDS Human Cell and Data Repository" . + "http://planttfdb.cbi.pku.edu.cn/tf.php?uid="^^ . + . + . + "false"^^ . + . + "eggnog" . + "2679240"^^ . + . + . + . + . + . + "obo" . + "https://www.kegg.jp/entry/"^^ . + . + . + "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . + "ontology" . + . + "relationships" . + "Indications and other conditions in drugbank"^^ . + . + . + . + "Bioregistry Collections" . + . + . + "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id="^^ . + . + . + . + "312.33"^^ . + . + . + . + . + . + . + . + . . - . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "https://w3id.org/oc/oci/"^^ . - "MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. This collection references individual metabolomics studies."^^ . - . - . - . - "http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d/2d.cgi?ac="^^ . - "false"^^ . - . - . - . - . - . - . - "ngl" . - . - "genetic analysis" . - . - . - . - . - "obo" . - . - "obo" . - . - . - . - . - . - . - . - "http://www.drugbank.ca/drugs/"^^ . - . - . - "^\\d+$"^^ . - . - "false"^^ . - "sdgio" . - "MULT_4_VAR1_bovine"^^ . + . + . + "ensembl.bacteria" . + . + "1"^^ . + . + . + . + . + . + . + "protein" . + . + "https://cropontology.org/rdf/CO_320:$1"^^ . + "https://jjj.bio.vu.nl/models/$1"^^ . + "false"^^ . + . + "mmdb" . + . + "CPX-263"^^ . + . + . + "AntiBodies Chemically Defined database" . + . + "https://fcs-free.org/fcs-database?"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "^[1-9]\\d{5}$"^^ . + "Sequencing Initiative Suomi" . + . + "false"^^ . + . + . + . + "tRNA Gene Database" . + "bioinformatics" . + "https://www.ncbi.nlm.nih.gov/medgen/$1"^^ . + . + "Open Tree of Life" . + . + "GRIN (Germplasm Resources Information Network) Taxonomy for Plants provides information on scientific and common names, classification, distribution, references, and economic impact."^^ . + "1000000"^^ . + . + . + "^[0-9X\\-]+$"^^ . + "false"^^ . + "true"^^ . + "ontology" . + "gene expression" . + . + "Rebuilding a Kidney" . + . + "Ontology of Prokaryotic Phenotypic and Metabolic Characters" . + . + "LIPID MAPS" . + . + "knowledge and information systems" . + "mzspec" . + . + "Animal Genome Size Database" . + . + "biology" . + . + "false"^^ . + . + . + . + . + "uniprot.resource" . + . + . + . + . + "4140"^^ . + . + "Veterans Health Administration (VHA) unique identifier" . + "vw253@cam.ac.uk" . + "http://purl.obolibrary.org/obo/CDNO_$1"^^ . + . + "http://vegbank.org/cite/"^^ . + . + "0000586"^^ . + . + . + . + "http://purl.obolibrary.org/obo/NCBITaxon_"^^ . + "^\\w+(\\-|\\.|\\w)*$"^^ . + . + . + . + "false"^^ . + "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."^^ . + . + . + . + . + . + "Neuroscience Multi-Omic BRAIN Initiative Data" . + . + . + "Gramene Taxonomy" . + "^\\d{7}$"^^ . + "SIDER Side Effect" . + . + . + . + . + . + . + . + . + . + . + . + "life science" . + "DiscoverX cell line products" . + . + . + . + . + . + . + "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query="^^ . + . + . + . + . + "https://morpheus.gitlab.io/models/$1"^^ . + . + . + . + "genomics" . + . + "dna" . + "neurovault.image" . + . + . + . + . + "Mauno Vihinen" . + . + "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . + "anatomy" . + . + . + . + . + . + "REACT" . + . + . + "protein" . + . + . + "Ontology of Physics for Biology" . + . + . + "^[0-9]+$"^^ . + . + "^ENSG\\d{11}$"^^ . + . + . + . + . + . + "https://pk-db.com/data/"^^ . + . + "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id=$1"^^ . + . + "https://www.inaturalist.org/taxa/$1"^^ . + . + . + "cell reprogramming" . + . + . + . + . + . + . + "Ontology that describes data types and image processing operations in Cryo Electron Microscopy of Single Particles"^^ . + . + "GenPept" . + . + "The IMGT/PRIMER-DB database provides standardized information on oligonucleotides or primers of the immunoglobulins (IG) and T cell receptors (TR)."^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/pdbe/entry/emdb/"^^ . + . + . + "urmas.koljalg@ut.ee" . + . + "http://www.co-ode.org/ontologies/galen#"^^ . + "false"^^ . + . + "0001017"^^ . + . + "https://swissmodel.expasy.org/repository/uniprot/"^^ . + . + "Sequence Read Archive" . + . + . + . + . + . + . + "genomics" . + "oriental-cds@163.com" . + . + . + . + . + "rna" . + . + . + "https://bitbucket.org/"^^ . + . + . + "false"^^ . + "blast" . + . + . + "0000091"^^ . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/compounddetails.php?ID="^^ . + . + . + "^[0-9]+$"^^ . + "sabiork.kineticrecord" . + . + "https://www.ebi.ac.uk/ols/ontologies/nmrcv/terms?short_form=NMR:$1"^^ . + . + "Edison Ong" . + "true"^^ . + . + "false"^^ . + "bioinformatics" . + . + "^[0-9]+$"^^ . + . + . + . + . + . +_:N9c645ce04f594b14a09661a17b0ccc23 "helpdesk@cropontology-curationtool.org" . + . + "chemistry" . + . + "msig" . + "life science" . + "subject agnostic" . + . + . + . + . + . + . + "PolBase" . + "An ontology for representing clinical data about hypertension, intended to support classification of patients according to various diagnostic guidelines"^^ . + . + . + "Assists in resolving data across cloud resources."^^ . + "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."^^ . + . + "roleo" . + . + "^([3-5][A-Z])\\w+[^A-Z][0-9]$"^^ . + . + . + . + . + . + . + . + . + "app-d678n-tottori"^^ . + . + . + . + "COL3A1"^^ . + . + "https://w3id.org/sssom/$1"^^ . + "^(\\d{1,2},?\\d{3},?\\d{3}|(PP|RE|AI|RX)\\d{2},?\\d{3}|(D|T|H|X)\\d{3},?\\d{3})$"^^ . + "438782"^^ . + "interpro" . + . + . + . + "pba" . + . + . + . + . + "Leafsnap" . + "http://cell-lines.toku-e.com/Cell-Lines_$1.html"^^ . + "^[a-z0-9\\-_]+$"^^ . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + . + . + "The World-2DPAGE database" . + "maria.taboada@usc.es" . + . + . + . + . + "social science" . + "A database of GlycoMaps containing 2585 conformational maps."^^ . + "millipore" . + "https://bioregistry.io/gard:"^^ . + . + . + "0000ffeb-36e0-4a29-b21d-84423bda979d"^^ . + "PRIDE Controlled Vocabulary" . + "false"^^ . + "Rv1908c"^^ . + . + . + . + . + "subject agnostic" . + "http://purl.obolibrary.org/obo/CARO_$1"^^ . + "false"^^ . + "false"^^ . + . + . + "vendor" . + . + . + . + . . - . + "oryzabase.strain" . + . + "mutation" . + "National Center for Advancing Translation Sciences BioPlanet" . + "false"^^ . + "false"^^ . + . + . + "NCITm" . + . + . + . + "false"^^ . + . + . + . + "Ali Syed" . + . + . + . + "0024"^^ . + "https://cropontology.org/rdf/CO_339:$1"^^ . + . + . + "bto" . + . + . + "false"^^ . + . + "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . + "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid=$1"^^ . + . + "https://bioregistry.io/tkg:"^^ . + "virology" . + . + "Mosquito gross anatomy ontology" . + . + "gnps.task" . + . + "CRISP is a terminology used for indexing biomedical information. CRISP contains over 8,000 preferred terms that are grouped hierarchically into 11 domains."^^ . + "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."^^ . + . + . + . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="^^ . + . + . + "false"^^ . + . + "crop2ml" . + . + "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."^^ . + "false"^^ . + "Identifiers for relationships between proteins and complexes, along with their type and provenance"^^ . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/IAO_$1"^^ . + . + . + . + . + . + "Metabolic Atlas" . + "schemaorg" . + . + "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#$1"^^ . + . + . + . + "mgnify.samp" . + "true"^^ . + . + "evolutionary biology" . + . + . + . + . + . + . + . + "https://www.nextprot.org/db/entry/$1"^^ . + . + "SNOMEDCT_US_2020_03_01" . + "biology" . + "A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources."^^ . + . + "dietary restriction" . "false"^^ . - "UM-BBD_enzymeID" . - . - . - . -_:Neb149b8fd9b444d5a596c99172b80614 "NLM Customer Service" . - . - . - . - . - . - "http://www.pharmgkb.org/pathway/"^^ . - . - "protein" . - . - "chembl.cell" . - "The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data."^^ . - . - "life science" . - . - . - . - . - "1755"^^ . - . - . - . - . - . - "CIViC Source" . - . - "https://web.expasy.org/abcd/ABCD_$1"^^ . - . - . - "rgd.strain" . - . - . - . - . - "ontology" . - . - "Networked Knowledge Organization Systems/Services/Structures" . - "xsd" . - . - . - "Pigeonpea Trait Dictionary in template v5 - ICRISAT - July 2015"^^ . - . - . - . - . - "Sorghum TDv5 - Oct 2019"^^ . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "fly lines" . - . - "Hölzel Diagnostika" . - . - . - . + "vmc" . + . + . + . + . + . + . + "PhylomeDB" . + . + "Mouse Genome Informatics" . + "virus" . + . + . + . + . + "STUDY1040"^^ . + . + . + . + . + . + "^HGVST\\d+$"^^ . + . + . + . + "comparative genomics" . + . + . + "VCell Published Models" . + "false"^^ . + "dna" . + "NCBI_Taxon_ID" . + "miapa" . + . + . + . + "botany" . + . + . + . + . + "Austrian Library Network" . + . + "FishBase" . + "^[A-Za-z0-9+_.%-:]+$"^^ . + . + "metatlas.reaction" . + "reaction" . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + "HEPRO is an ontology of informational entities and processes related to health procedures and health activities."^^ . + "0000080"^^ . + . + . + . + "ontology" . + "false"^^ . + . + . + . + "anatomy" . + "The Role Ontology (RoleO) is a ontology in the domain of role classification. RoleO aims to standardize role classification and support computer-assisted reasoning. RoleO is a community-based ontology, and its development follows the OBO Foundry principles."^^ . + . + "subject agnostic" . + "http://www.innatedb.ca/getGeneCard.do?id=$1"^^ . + . + . + . + "91792"^^ . + "https://cropontology.org/rdf/CO_327:$1"^^ . + "false"^^ . + . + . + "The Gmelin database is a large database of organometallic and inorganic compounds updated quarterly. It is based on the German publication Gmelins Handbuch der anorganischen Chemie which was originally published by Leopold Gmelin in 1817; the last print edition, the 8th, appeared in the 1990s."^^ . + "UBPROP" . + . + . + . + "splash10-0zq2000000-77302b0326a418630a84"^^ . + "https://www.iedb.org/reference/"^^ . + . + . + "true"^^ . + . + "obo" . + . + "obo" . + . + "Sebastian Koehler" . + "lipid" . + . + . + "International Medical Device Regulators Forum" . + "ND50028"^^ . + . + . + . + . + "population genetics" . + . + "imanis" . + . + . + . + . + "A catalog of mouse genes expressed in early embryos, embryonic and adult stem cells, including 250000 ESTs, was assembled by the NIA (National Institute on Aging) assembled.This collection represents the name and sequence from individual cDNA clones."^^ . + . + . + . + "I31.952"^^ . + . + "WWF ecoregions are large unit of land or water containing a geographically distinct assemblage of species, natural communities, and environmental conditions."^^ . + "project management" . + "CHEBI" . + "gaoj@mskcc.org" . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to DNA sequence information."^^ . + . + "evan@epatters.org" . + . + . + "functional genomics" . + . + "imsr.apb" . + . + . + . + . + "data management" . + . + . + . + . + . + "classification" . + "cognitive neuroscience" . + . + "Bob Thacker" . + . + . + . + . + . + "CL070"^^ . + . + "hathitrust" . + . + . + . + . + . + . + . + "ENSGT00550000074763"^^ . + "^[A-Z0-9]{5}\\d+$"^^ . + . + "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$"^^ . + "genetics" . + "agriculture" . + . + . + "false"^^ . + . + "TDR" . + . + . + "Oryzabase Strain" . + "false"^^ . + . + . + "statistics" . + . + . + . + "RNA ontology" . + . + "https://chemapps.stolaf.edu/jmol/jmol.php?model="^^ . + "IUPHARfam" . + . + "eukaryotic" . + . + . + . + . + . + "gene" . + "KEGG COMPOUND" . + . + . + . + "http://purl.obolibrary.org/obo/ZFA_"^^ . + . + . + . + "NCit" . + "RiceNetDB Compound" . + . + . + "life science" . + . + "natural producs" . + . + "ontology and terminology" . + . + . + . + . + . + . + "nif.ext" . + . + "http://purl.obolibrary.org/obo/TGMA_"^^ . + . + . + "SABIO-RK is a relational database system that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. The reaction data set provides information regarding the organism in which a reaction is observed, pathways in which it participates, and links to further information."^^ . + . + . + . + . + . + . + . + . + "true"^^ . + . + "^HMDB\\d+$"^^ . + . + . + . + "false"^^ . + . + "linguist" . + . + "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . + "Electrocardiogram Ontology" . + "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."^^ . + "David Brodbelt" . + . + . + . + . + "D001151"^^ . + . + "gene" . + "Saccharomyces Genome Database" . + . + . + . + "GXA Gene" . + . + "life science" . + . + "Fly taxonomy" . + "The Mammalia Polymorphism Database is a secondary database designed to provide a collection of all the existing polymorphic sequences in the MammaliaOnline query interfaces facilitate data interrogation by different polymorphism parameter values and keyword queries (based on SQL searches)."^^ . + "0000389"^^ . + . + "http://purl.obolibrary.org/obo/EHDA_$1"^^ . "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid="^^ . - . - . - . - "Enzo Life Sciences" . - . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID="^^ . - "Genome Aggregation Database" . - . - "https://scicrunch.org/resolver/RRID:"^^ . - "true"^^ . - "ontology" . - . - "http://uri.neuinfo.org/nif/nifstd/sao"^^ . - . - . - . - "fly" . - . - "https://thebiogrid.org/interaction/"^^ . - . - "^TF\\w+$"^^ . - . - "ontology" . - "Paul Schofield" . - . - "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line=$1"^^ . - . - . - . - . - "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . - "omop" . - "Bryce Mecum" . - "http://erop.inbi.ras.ru/result2.php?PepName="^^ . - . - "depod@embl.de" . - . - . - "miaa" . - . - "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas."^^ . - "genome" . - . - . - "dna" . - "mfomd" . - . - "1150"^^ . - "jak@ucop.edu" . - "glycomics" . - "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-"^^ . - "afo" . -_:N7462add7e86d4deea995dffb95f5cd6b "ICARDA Ethiopia" . - . - "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://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec="^^ . - . - "Five Stars of Online Research Articles Ontology" . - "transcriptomics" . - . - "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . + . + "Sample processing and separation techniques" . + "http://purl.obolibrary.org/obo/OPMI_"^^ . + . + . + "CIViC Variant Group" . + "bioRxiv" . + "1000000"^^ . + . + "SoyBase" . + . + . + "https://rnajunction.ncifcrf.gov/JunctionPage.php?jid="^^ . + . + . + . + "false"^^ . + "1cukA01"^^ . + . + "http://purl.obolibrary.org/obo/MCRO_$1"^^ . + . + . + . + "http://purl.obolibrary.org/obo/LEPAO_$1"^^ . + "Matthias Samwald" . + . + . + . + . + . + . + . + . + "obo" . + . +_:Ne90637670289458180b3f4b6ec45ab94 "helpdesk@cropontology-curationtool.org" . + "Archival Resource Keys (ARKs) serve as persistent identifiers, or stable, trusted references for information objects. Among other things, they aim to be web addresses (URLs) that don’t return 404 Page Not Found errors. The ARK Alliance is an open global community supporting the ARK infrastructure on behalf of research and scholarship. End users, especially researchers, rely on ARKs for long term access to the global scientific and cultural record. Since 2001 some 8.2 billion ARKs have been created by over 1000 organizations — libraries, data centers, archives, museums, publishers, government agencies, and vendors. They identify anything digital, physical, or abstract. ARKs are open, mainstream, non-paywalled, decentralized persistent identifiers that can be created by an organization as soon as it is registered with a NAAN (Name Assigning Authority Number). Once registered, an ARK organization can create unlimited numbers of ARKs and publicize them via the n2t.net global resolver or via their own local resolver."^^ . + "http://purl.obolibrary.org/obo/CHEBI_"^^ . + "interaction" . + "0000005"^^ . + . + . + "Mass spectrometry ontology" . + "eo" . + "http://purl.obolibrary.org/obo/PdumDv_$1"^^ . + "false"^^ . + "http://www.w3.org/ns/prov#"^^ . + "vmhreaction" . + "structrual bioinformatics" . + . + . + "isfinder" . + "OBO Metadata Ontology" . + . + . + "myco.tuber" . + "00000021"^^ . + "^\\d{7}$"^^ . + "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=$1"^^ . + . + . + "systems biology" . + . + "database" . + . + "Quality"^^ . + . + . + . + . + "botany" . + "pr" . + . + . + . + . + "slctr" . + . + . + . + . + . + "AKR"^^ . + . + "3D Metabolites" . + . + . + . + "https://sed-ml.org/urns.html#format:$1"^^ . + "Sabine.Oesterle@sib.swiss" . + . + . + . + "0000078"^^ . + . + "chembl.cell" . +_:N1d66b6d5b1894f27847d3a13cf9a0222 "helpdesk@cropontology-curationtool.org" . + . + . + . + . + "life science" . + . + . + . + "Gramene Reference" . + . + . + "genedb" . + . + "c.dudek@tu-braunschweig.de" . + . + "National Xenopus Resource" . + . + . + . + "http://purl.obolibrary.org/obo/FBSP_$1"^^ . + . + . + "Study inside StoreDB"^^ . + "http://repository.topdownproteomics.org/proteoforms/"^^ . + "^[A-Za-z0-9+_.%-:]+$"^^ . + . + . + . + . + . + . + "pathway" . + . + "false"^^ . + "biochemistry" . + . + "mirEX" . + _:N7ddd4d39a93142dfb150e76ca0925d12 . + "http://purl.obolibrary.org/obo/MOD_"^^ . + . + . + . + . + "rdb20@pitt.edu" . + . + . + . + . + . + . + . + . + . + "https://web.expasy.org/cellosaurus/cellopub/"^^ . + . + . + . + . + "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.icd9data.com/getICD9Code.ashx?icd9="^^ . + . + . + . + . + . + . + . + . + . + "http://usefulinc.com/ns/doap#"^^ . + "nickf@ebi.ac.uk" . + . + "http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1"^^ . + . + . + . + . + . + . + "NIF Standard Ontology: Qualities" . + . + . + "https://go.drugbank.com/bio_entities/"^^ . + "Catalytic Site Atlas" . + "Ontology of RNA Sequencing" . + . + "pato" . + . + . + "http://sabiork.h-its.org/newSearch?q="^^ . + "false"^^ . +_:N6336578d53d547a592544f1d65a18759 "info@who.int" . + . + . + "developmental biology" . + . + "https://repeatsdb.org/structure/$1"^^ . + "biomedical science" . + . + . + _:N897a2f3e7af8401db8644acbfa753ed9 . + "Medical Subject Headings" . + "NCBI Genome" . + "BRAF"^^ . + . + . + . + . + "0001114"^^ . + . + . + "true"^^ . + "sequence" . + . + "ontology" . + . + "http://purl.obolibrary.org/obo/PECO_"^^ . + "ontology" . + "http://purl.org/obo/owlEOL_"^^ . + "false"^^ . + . + . + "cryopreserved" . + "http://purl.org/spar/biro/$1"^^ . + . + . + "0002005"^^ . + . + "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."^^ . + . + . + "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."^^ . + . + . + . + . + . + "kegg.environ" . + . + "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/cell/"^^ . + "false"^^ . + "90062901"^^ . + . + "0000194"^^ . + "http://sabiork.h-its.org/reacdetails.jsp?reactid=$1"^^ . + . + "contact@bacdive.de" . + . + "^[A-Z0-9*:]+$"^^ . + . + . + . + . + . + "obo" . + . + "https://europepmc.org/article/CBA/$1"^^ . + "true"^^ . + "biology" . + . + . + . + "http://purl.obolibrary.org/obo/MFMO_$1"^^ . + "http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i="^^ . + "http://www.pharmgkb.org/drug/"^^ . + "^\\d+$"^^ . + "pactr" . + . + "1251"^^ . + "Suzi Aleksander" . + "false"^^ . + "InChI" . + "5.1"^^ . + "^CCDS\\d+\\.\\d+$"^^ . + "PRO_0000016681"^^ . + "habronattus" . + "The Shape Expressions (ShEx) language describes RDF nodes and graph structures. A node constraint describes an RDF node (IRI, blank node or literal) and a shape describes the triples involving nodes in an RDF graph. These descriptions identify predicates and their associated cardinalities and datatypes. ShEx shapes can be used to communicate data structures associated with some process or interface, generate or validate data, or drive user interfaces."^^ . + . + . + "National Microbial Pathogen Data Resource" . + "http://purl.obolibrary.org/obo/OBIB_$1"^^ . + "https://cropontology.org/rdf/CO_367:"^^ . + "^ILMN_\\d+$"^^ . + . + . + . + . + . + "^\\d{4}$"^^ . + "http://www.molmovdb.org/cgi-bin/morph.cgi?ID="^^ . + . + . + . + . + "ontology" . + . + . + "M94112"^^ . + . + "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1=$1"^^ . + . + . + "^\\d+$"^^ . + . + "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."^^ . + . + "obo" . + . + . + "gmd" . + . + . + . + . + "InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3"^^ . + "domain" . + . + "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . + . + . + . + . + "Veterinary pharmaceuticals are biologically active and potentially persistent substances which are recognised as a continuing threat to environmental quality. Whilst the environmental risk of agricultural pesticides has had considerable attention in recent decades, risks assessments for veterinary pharmaceuticals have only relatively recently began to be addressed. Risk assessments and risk modelling tend to be inherently data hungry processes and one of the main obstacles to consistent, accurate and efficient assessments is the need for a reliable, quality and comprehensive data source."^^ . + . + "^[A-Za-z0-9-]+$"^^ . + . + . + . + . + . + . + . + . + "organism supplier" . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "small molecule" . + "ontology and terminology" . + "The Virus Infectious Disease Ontology" . + . + . + "false"^^ . + . + "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . + . + . + . + . + . + "false"^^ . + . + "ontology" . + "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."^^ . + "Rat Genome Database strain" . + . + . + "false"^^ . + "false"^^ . + . + . + "drug development" . + . + . + "BG11523"^^ . + "Vertebrate skeletal anatomy ontology."^^ . + . + . + "gthayman@mcw.edu" . +_:Nce56519a74584e27bab9646e3c0efa5e "Vladimir Mironov" . + . + . + "r.court@ed.ac.uk" . + . + . + "Cell line collections (Providers)"^^ . + "lipid" . + . + . + . + . + . + "https://flybase.org/reports/FBtc"^^ . + . + . + . + "uniprot.journal" . + . + . + "chiro" . + . + . + "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."^^ . + . + . + . + "Biolink Model" . + . + "false"^^ . + . + . + . + . + . + . + "https://civicdb.org/links/sources/$1"^^ . + "Kaggle" . + . + . + "iresite" . + . + . + "false"^^ . + "Kinetic Simulation Algorithm Ontology" . + "false"^^ . + . + . + "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"^^ . + . + "rdf" . + . + . + . + . + . + . + . + . + . + . + . + . + "http://ddinter.scbdd.com/ddinter/drug-detail/"^^ . + . + "issn" . + "Basic Formal Ontology" . + . + "NASA GeneLab" . + "Ligand-Gated Ion Channel database" . + . + "NCBI_taxid" . + "genome" . + . + . + . + . + "https://datalab.rwth-aachen.de/MINDER/resource/"^^ . + "uniprot" . + . + . + . + . + "http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=$1"^^ . . - "ontology" . - "birnlex" . - . - "COG Categories" . - . - "https://units-of-measurement.org/$1"^^ . - "http://champ-project.org/images/ontology/cao.owl#CAO_"^^ . - . - . - . - "false"^^ . - . - . - . - . - "iso.3166" . - "^[A-Za-z0-9]+$"^^ . - . - . - "fao.asfis" . - . -_:N8b0188fd98fb4f68a9d1f2d2f5c39af7 "Crop Ontology Helpdesk" . - . - . - . - "info@casrai.org" . - . - . - . - "GeneFarm" . - "genome" . - . - . - "false"^^ . - . - . + . + "biomedical science" . + . + . + "drug-drug interactions" . + "272"^^ . + . + "https://scicrunch.org/resolver/RRID:AGSC_$1"^^ . + . + . + "983"^^ . + . + . + . + "https://bdsc.indiana.edu/stocks/$1"^^ . + . + . + . + "Coconut ontology" . + . + . + . + "Catalogue of Life in Taiwan" . + "false"^^ . + . + "0000858"^^ . + . + . + "http://www.evocontology.org/site/Main/BrowseEvoc?x_termid="^^ . + . + . + "https://arxiv.org/abs/$1"^^ . + . + . + . + . + . + . + . + "^[0-9]+$"^^ . + "ontology" . + . + . + "stock" . + . + "false"^^ . + "GitLab" . + . + . + . + . + . + . + . + "polysaccharide" . + . + "A Knowledge Resource for Innate Immunity Interactions and Pathways" . + "https://www.nextprot.org/term/FA-$1"^^ . + . + "false"^^ . + . + "Assists in resolving data across cloud resources."^^ . + "neuroname" . + "dna" . + . + . + "false"^^ . + . + "http://solgenomics.net/phenome/locus_display.pl?locus_id="^^ . + . + "ontology" . + "Datanator Reaction" . + "ontology" . + "medicine" . + "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id="^^ . + "false"^^ . + "https://www.webelements.com/$1"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"^^ . + . + . + . + "cellimage" . + . + . + . + . + . + . + "ontology" . + "psychiatry" . + . + . + . + . + "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."^^ . + "ko00071"^^ . + . + . + . + . + "Radiomics Ontology" . + . + . + "http://purl.obolibrary.org/obo/UO_$1"^^ . + . + "false"^^ . + . + _:N65b33571236b47dba37254906e5e488b . + . . - "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . - . - . - "ontology" . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "ecology" . - . - . - . - "A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes."^^ . - "CPX-263"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/WBls_"^^ . - "CiteXplore" . - "ENSGT00550000074763"^^ . - . - . - . - "An ontology of minimum information regarding potential drug-drug interaction information."^^ . - "genome" . - . - . - . - "https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1"^^ . - "cosmic" . - . - . - "agriculture" . - "0045310"^^ . - "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?$1"^^ . - . - . - . - . - . - _:Na592003593484832bee836301b205107 . - . - . - . - . - "false"^^ . + "obo" . + . + "000064"^^ . + . + "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."^^ . + . + . + "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"^^ . + "obo" . + "knowledge graph" . + . + . + "https://www.ebi.ac.uk/miriam/main/resources/"^^ . + . + "The Pharmacogene Variation (PharmVar) Consortium is the new home for PGx gene nomenclature serving as a centralized ‘Next-Generation’ Pharmacogene Variation data repository. The major focus of PharmVar is to catalogue allelic variation of genes impacting drug metabolism, disposition and response and provide a unifying designation system (nomenclature) for the global pharmacogenetic/genomic community. Efforts are synchronized between PharmVar, the Pharmacogenomic KnowledgeBase, and the Clinical Pharmacogenetic Implementation Consortium."^^ . + . + "false"^^ . + . + . + "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."^^ . + "ontology" . + "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."^^ . + "https://scicrunch.org/resolver/RRID:BCBC_$1"^^ . + "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . + "https://bioregistry.io/n2t:"^^ . + "Telethon Network of Genetic Biobanks" . + . + . + . + "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."^^ . + . + . + "A0A009E7X8"^^ . + . + "http://bitterdb.agri.huji.ac.il/bitterdb/compound.php?id="^^ . + . + . + . + "false"^^ . + "ontology" . + "false"^^ . + . + "Proteomic Data Commons" . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + "aspgd.locus" . + "bel" . + "biomedical science" . + . + . + . + . + . + "Germplasm Resources Information Network" . + . + . + . + "model organism database" . + . + . + "ecso" . + "^\\d{7}$"^^ . + . + "https://sparontologies.github.io/fabio/current/fabio.html#"^^ . + . + . + "false"^^ . + . + . + . + "Physiome Model Repository workspace" . + . + . + . + . + . + . + . + "https://umgear.org/p?id="^^ . + "An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time."^^ . + . + "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid="^^ . + . + "false"^^ . + . + . + "Publishing Workflow Ontology" . + . + "ISNI is the ISO certified global standard number for identifying the millions of contributors to creative works and those active in their distribution, including researchers, inventors, writers, artists, visual creators, performers, producers, publishers, aggregators, and more. It is part of a family of international standard identifiers that includes identifiers of works, recordings, products and right holders in all repertoires, e.g. DOI, ISAN, ISBN, ISRC, ISSN, ISTC, and ISWC.\r\n\r\nThe mission of the ISNI International Authority (ISNI-IA) is to assign to the public name(s) of a researcher, inventor, writer, artist, performer, publisher, etc. a persistent unique identifying number in order to resolve the problem of name ambiguity in search and discovery; and diffuse each assigned ISNI across all repertoires in the global supply chain so that every published work can be unambiguously attributed to its creator wherever that work is described."^^ . + . + . + "http://champ-project.org/images/ontology/cao.owl#CAO_"^^ . + "^\\d+$"^^ . + . + "obo" . + "George Gkoutos" . + "SNOWMEDCT" . + "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."^^ . + "https://bioregistry.io/cst.ab:"^^ . + . + "http://www.pathwaycommons.org/pc/record2.do?id=$1"^^ . + "http://ascl.net/"^^ . + "BUNA790102"^^ . + "false"^^ . + . + . + "Global Natural Products Social Molecular Networking Task" . + "https://github.com/$1"^^ . + "http://purl.obolibrary.org/obo/SIBO_$1"^^ . + . + "batchelorc@rsc.org" . + "so" . + "The Artificial Intelligence Ontology" . + . + . + . + "false"^^ . + . + "true"^^ . + "Cotton ontology from CottonGen database - June 2019"^^ . + . + . + . + "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID="^^ . + . + "tetrahymena thermophila" . + "chemistry" . + . + "Protein Ontology" . + . + . + . + "^\\d+$"^^ . + . + . + . + "bioinformatics" . + . + . + . + . + . + "LOC_Os01g49190"^^ . + . + . + "Taconic Biosciences" . + . + . + "false"^^ . . - . - . - . - "I31.952"^^ . - . - . - "Flora Phenotype Ontology" . - . - . - . - "ontology" . - "biology" . - . - . - . - . - "chemical" . - . - . - . + . + "NIST Chemistry WebBook" . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + "http://webprod.hc-sc.gc.ca/nhpid-bdipsn/ingredReq.do?id="^^ . + "drug repositioning" . + "false"^^ . + . + . + "bioinformatics" . + . + "https://reporter.nih.gov/project-details/$1"^^ . + "http://purl.org/oban/$1"^^ . + . + "pharmacodb.dataset" . + "false"^^ . + "Allergome" . + . + . + . + . + . + . + "https://proteinensemble.org/$1"^^ . + . + . . - . - . - . - "^\\d{7}$"^^ . - "http://purl.obolibrary.org/obo/CHEBI_"^^ . - . - . - "^10.\\d{2,9}/.*$"^^ . + . + "false"^^ . + . + "ontology" . + . + . + . + "TaxonomyID" . + . + . + . + "ontology" . + "false"^^ . + . + . + . + . + "statistics" . + . + . + "mpjensen@buffalo.edu" . + . + "https://bioregistry.io/leafsnap:"^^ . + . + . + "Expression"^^ . + . + . + . + . + . + "false"^^ . + "DI" . + . + "life science" . + . + . + . + . + "foaf" . + . + "bioinformatics" . + . + "medicine" . + "taxonomy" . + "obo" . + "resid" . + . + . + . + "0000598"^^ . + . + "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."^^ . + "ontology" . + . + . + . + "https://www.wormbase.org/get?name="^^ . + . + . + . + . + . + "nfdi4chem.osmo" . + "https://www.ebi.ac.uk/intact/imex/main.xhtml?query=IM-"^^ . + . + "surjeet.arya@uky.edu" . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . + . + "false"^^ . + "NIF Standard Ontology: Neurolex" . + "Disease Class" . + "false"^^ . + . + . + "https://pharmacodb.ca/cell_lines/$1"^^ . + . + . + . +_:N8a1cf018ca2c4c11bf7f165adebf9721 "po-discuss@plantontology.org" . + "obo" . + . + . + . + "false"^^ . + . + . + "ABL1"^^ . + "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."^^ . + "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object=$1"^^ . + . + "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.n\\d{1,3})?$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + "louis@imbb.forth.gr" . + . + . + "chemical in the database supplied by Pesticide Action Network North America"^^ . + "NCBI Registry" . + . + "https://www.uniprot.org/database/$1" . + . + . + "igsr" . + . + . + . + . + "https://www.kegg.jp/entry/$1"^^ . + . + "^\\d+$"^^ . + "Non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. Users may browse by strain, gene, phenotype, or human disease. Its primary objective is to establish and manage a unified repository for maintaining medically relevant mouse mutants and making them available to the scientific community. Therefore, EMMA archives mutant strains and distributes them to requesting researchers. EMMA also hosts courses in cryopreservation, to promote the use and dissemination of frozen embryos and spermatozoa. Dissemination of knowledge is further fostered by a dedicated resource database. Anybody who wants their mutant mouse strains cryopreserved may deposit strains with EMMA. However depositors must be aware that these strains become freely available to other researchers after being deposited.With more than 8400 mutant mouse strains and asmall but increasing number of rat mutant strains available, EMMA is the primary mouse repository in Europe and the third largest non-profit repository worldwide. [from RRID]"^^ . + "00000001"^^ . + . + . + . + "false"^^ . + . + "http://www.humanproteomemap.org/spectrum.php?pep_id=$1"^^ . + . + . + . + . + "fcsfree" . + . + . + . + . + . + "ontology" . + . + . + . + . + . + . + . + . + . + . + "nfdi4chem.cao" . + . + . + . + "genbank" . + . + "false"^^ . + "materials informatics" . + . + . + . + "natural history" . + . + . + "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."^^ . + . + "sean@arabidopsis.org.uk" . + . + . + . + "http://jaxmice.jax.org/strain/$1.html"^^ . + . + . + "Physical Medicine and Rehabilitation" . + "tissue" . + "ontology" . + . + . + "PdumDv" . + "proteomics" . + "http://www.genome.jp/dbget-bin/www_bget?aaindex:$1"^^ . + . + "false"^^ . + . +_:N098f5affb8dd45a592472db7bcd9e9e5 "helpdesk@eionet.europa.eu" . + . + "An ontology to capture confidence information about annotations."^^ . + "https://biopragmatics.github.io/providers/cvx/"^^ . + . + . + . + "146421"^^ . + "co_339" . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "http://purl.obolibrary.org/obo/CRO_"^^ . + . + "^\\w{1,3}$"^^ . + . + . + . + . + . + "biomedical science" . + . + "SwissProt" . + . + . + "false"^^ . + . + "kupo" . + "Represent chemical entities having particular CHEBI roles"^^ . + . + . + "^([hm]\\_)?\\w+Pathway$"^^ . + "https://www.bgee.org/gene/$1"^^ . + . + . + . + . . - "NLXMOL" . - "MU9_3181"^^ . - . - . - "^r\\d+$"^^ . - . - . - . - "http://purl.obolibrary.org/obo/OOSTT_"^^ . - . - . - . - . - . - . - . - . - "lgic" . - "IntAct Molecule" . - . - "http://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/IDO_$1"^^ . - "The Ontology for Biobanking (OBIB) is an ontology for the annotation and modeling of the activities, contents, and administration of a biobank. Biobanks are facilities that store specimens, such as bodily fluids and tissues, typically along with specimen annotation and clinical data. OBIB is based on a subset of the Ontology for Biomedical Investigation (OBI), has the Basic Formal Ontology (BFO) as its upper ontology, and is developed following OBO Foundry principles. The first version of OBIB resulted from the merging of two existing biobank-related ontologies, OMIABIS and biobank ontology."^^ . - . - "EY223054.1"^^ . - . - . - . - . - . - . - . - . - "ENSFM00500000270089"^^ . - "1178"^^ . - . - . - . - . - . - "subject agnostic" . - . - . - . - . - "validatordb" . - . - "ev:E00032"^^ . - "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT="^^ . - . - . - . - . - "^\\d+$"^^ . - . - "ontology" . - . - . - "https://fairsharing.org/"^^ . - "protein" . - . - "https://www.inaturalist.org/users/"^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/pathway/"^^ . - . - "botany" . - "^MAR\\d{5}$"^^ . - "PeptideAtlas" . - . - "sabiork.ec" . - . - . - . - "1426686"^^ . - . - "TS-0001"^^ . - . - . - "2701"^^ . - . - . - "http://purl.bioontology.org/ontology/CSP/$1"^^ . - "false"^^ . - . - "biopragmatics/bioregistry/424"^^ . - . - "http://leafsnap.com/species/$1/"^^ . - "https://sparontologies.github.io/fabio/current/fabio.html#"^^ . - "ontology" . - . - "UniProt Archive" . - . - "kegg.genome" . - . - . - . - "2008-005144-16"^^ . - . - . - "https://bioregistry.io/phosphopoint.protein:"^^ . - . - "http://purl.obolibrary.org/obo/CLAO_"^^ . - "false"^^ . - . - "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . - . - "https://www.gbif.org/species/$1"^^ . - "false"^^ . - . - "ECU03_0820i"^^ . - . - . - . - "false"^^ . - . - . - . - . - "caro" . - . - "ontology" . - "0000295"^^ . - . - "transcriptomics" . - . - . - . - . - . - . - . - . - "https://flybase.org/reports/FBtc"^^ . - "ontology" . - . - . - . - . - "false"^^ . - "Ontology of Genetic Susceptibility Factor" . - . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PRIDE_"^^ . - "http://ecoportal.lifewatch.eu/ontologies/$1" . - . - . - . - . - . -_:N4c3911b9ef174a30896482a25f2207f2 "NLM Customer Service" . - . - . - . - . - "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."^^ . - "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . - . - . - . - . - "vectorbase" . - "false"^^ . - "millipore" . - . - . - . - "^[A-Za-z_0-9]+$"^^ . - "eVOC (Expressed Sequence Annotation for Humans)" . - . - . + . + . + . + "obo" . + . + "^[a-z]{3}-[a-km-z0-9]{7}$"^^ . + "http://purl.uniprot.org/annotation/VAR_$1"^^ . + "canal"^^ . + "ontology" . + . + "^\\w+$"^^ . + . + "Daniel Himmelstein" . + . + . + . + "The Swiss Personalized Health Network is a national infrastructure initiative with the aim to develop, implement, and validate coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. The sphn RDF schema builds the foundation for all data exchanges within the sphn by integrating semantic information defined in the [sphn dataset](https://sphn.ch/document/sphn-dataset/)."^^ . + . + . + "2c6s"^^ . + . + . + _:Ndcd602300ff0433da46693e96d7101e7 . + . + . + . + . + "SUBSET_SIREN" . + "^[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/VariO_$1"^^ . + . + "reactions" . + . + "0002350"^^ . + . + "LG Chemical Entity Detection Dataset (LGCEDe)" . + "botany" . + . + "uniprot.database" . + . + "Data Use Ontology" . + "16333295"^^ . + . + "https://www.ebi.ac.uk/metabolights/"^^ . + . + . + "http://birdgenenames.org/cgnc/GeneReport?id="^^ . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "http://avis.princeton.edu/pixie/viewgraph.php?graphID="^^ . + "BioSystems" . + "false"^^ . + "https://flybase.org/reports/"^^ . + . + "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."^^ . + . + . + "selventa" . + "mmp.fun" . + "Pseudomonas Genome Database" . + "eccode" . + "http://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId="^^ . + . + . + "15567"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + "metacyc.compound" . + . + . + . + . + . + . + . + . + . + . + . + "Stefan Kuhn" . + "ontology" . + "dolce" . + . + "Arctic Data Center Academic Disciplines Ontology" . + "neurondb" . + "0000550"^^ . + . + . + . + "Nicolas Matentzoglu" . + . + . + . + "false"^^ . + . + . + . + . + "biomedical science" . + "https://smpdb.ca/view/$1"^^ . + . + "kdurante@stanford.edu" . + "molecule" . + . + "msio" . + . + . + . + . + "http://purl.obolibrary.org/obo/XPO_$1"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/GSSO_$1"^^ . + . + . + . + "0000024"^^ . + . + . + . + "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . + "drug discovery" . + . + . + . + . + . + . + . + "IMGT/PRIMER-DB" . + . + . + "immunogenetics" . + . + . + "Provisional Cell Ontology" . + . + . + . + . + . + "XML Schema Definition" . + . + . + "Jessica Kissinger" . + . + . + . + . + . + . + "protein" . + "false"^^ . + . + "http://purl.obolibrary.org/obo/ONS_"^^ . + . + . + "1000100"^^ . + "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."^^ . + . + . + . + . + . + "laia.subirats@gmail.com" . + . + . + "Alayne Cuzick" . + "https://www.fisheries.noaa.gov/species/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/CLO_"^^ . + . + . + "has provider formatter" . + . + . + "NLXINV" . + . + . + . + "dna" . + . + . + . + "^\\d{7}$"^^ . + "^(\\d\\d\\d|V\\d\\d|E[8-9]\\d\\d)(\\.\\d{1,2})?$"^^ . + . + . + . + . + . + . + "A vocabulary about species to support the environmental research community in Arizona and New Mexico"^^ . + . + . + . + "MGnify Analysis" . + "^\\d{7}$"^^ . + . + . + "Ontology for MicroRNA Target" . + . + "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 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."^^ . + . + "nextprot.family" . + . + . + . + "http://purl.obolibrary.org/obo/MFMO_"^^ . + "^\\d+$"^^ . + . + "Ana Rath" . + "SABIO Reaction Kinetics" . + . + "Human Developmental Stages" . + . + . + "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://purl.obolibrary.org/obo/FBbi_$1"^^ . + . + "http://aps.unmc.edu/AP/database/query_output.php?ID="^^ . + "National Swine Resource and Research Center" . + . + "seed" . + . + "epigenetics" . + "false"^^ . + . + "vendor" . + "semantic web" . + . + . + . + . + . + "nucleotide" . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "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."^^ . + "http://beetlebase.org/cgi-bin/gbrowse/BeetleBase3.gff3/?name="^^ . + . + "pubchem.cell" . + . + . + . + . + "biomedical science" . + . + "small molecule" . + "https://radlex.org/RID/$1"^^ . + . + "http://wheat.pw.usda.gov/report?class=gene;name=$1"^^ . + "biology" . + "false"^^ . + . + "false"^^ . + . + . + "animal breeding" . + . + "http://modbase.compbio.ucsf.edu/pibase-cgi/get_details.pl?object_type=complexes&bdp_id="^^ . + . + . + . + "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid="^^ . + . + . . - . - . - . - "gene" . - . - . - . - "eukaryotic" . - "http://www.kegg.jp/entry/"^^ . - "uc001rvw.5"^^ . - . - . - "https://www.phenxtoolkit.org/protocols/view/$1"^^ . - . - "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."^^ . - . - "wormpep" . - "protein" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - "TTDS00056"^^ . - . - . - . - "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof"^^ . - "false"^^ . - "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."^^ . - "FBbi" . - . - . - "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . - . - . - . - "https://www.kegg.jp/entry/"^^ . - . - "false"^^ . - . - "^([A-Z]+)?\\d+(\\.\\d+)?$"^^ . - "false"^^ . - "Maize gross anatomy"^^ . - . - "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." . - . - . - . - "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome."^^ . - . - "icd10pcs" . - "Wikipedia" . - . - "molecular biology" . - . - . - . - "geneotype" . - "false"^^ . - "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://datanator.info/reaction/$1"^^ . - . - . - . - . - . - "https://bioregistry.io/metaregistry/cellosaurus/"^^ . - . - . - . - . - . - "T30002"^^ . - . - . - . - . - . - . - "gerhard.mayer@rub.de" . - . - . - "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . - "life science" . - "hinv.protein" . - . - . - . - . - . - "AntiBodies Chemically Defined database" . - . - "^\\d{7}$"^^ . - . - . - . - "https://models.physiomeproject.org/workspace/$1"^^ . - . - . - "OMIT" . - . - . - . - . - . - . - . - "ProteomicsDB Protein" . - . - . - . - "bto" . - "edam.format" . - "CTD Gene" . - . - . - "small molecule" . - . - "gene" . - "false"^^ . - . - . - . - . - "NIFSTD" . - "^URS[0-9A-F]{10}(\\_\\d+)?$"^^ . - "ontology" . - . - "https://cropontology.org/rdf/CO_358:"^^ . - "GrassBase" . - "Clement Jonquet" . - . - "http://scop.berkeley.edu/sid=$1"^^ . - . - . - "https://www.disprot.org/"^^ . - "^[0-9]{9}$"^^ . - "medicine" . - . - "true"^^ . - . - . - "idocovid19" . - "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . - . - " 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."^^ . - "gc_id" . - . - . - . - . - "https://www.ebi.ac.uk/miriam/main/resources/$1"^^ . - "^HBG\\d+$"^^ . - "hp" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - "reto" . - . - "https://metacyc.org/compound?orgid=META&id="^^ . - . - . - . - "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."^^ . - . - . -_:Nc8087639f8dd4c109937179d880ccef7 "FALDO group" . - "http://purl.obolibrary.org/obo/ONS_$1"^^ . - . - "anatomy" . - . - . - "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."^^ . - "hovergen" . - . - "false"^^ . - . - "http://swissregulon.unibas.ch/query/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - "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://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?mode=output&display_format=page&i=$1"^^ . - "Simon Jupp" . - . - . - . - . - "massive" . - . - . - . - . - "WoRMS-ID for taxa" . - "http://purl.jp/bio/4/id/"^^ . - . - . - . - . - "https://www.genecards.org/cgi-bin/carddisp.pl?gene="^^ . - "pathways" . - "epidemiology" . - "drugbank.reaction" . - "European Mouse Mutant Archive" . - . - . - "PharmacoDB Tissues" . - . - . - "Frederique Lisacek" . - "true"^^ . - "encode" . - . - . - . - "life science" . - "obo" . - "https://www.thaiclinicaltrials.org/show/$1"^^ . - . - . - "false"^^ . - "dna" . - . - . - "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?"^^ . - "http://purl.obolibrary.org/obo/ICO_$1"^^ . - . - "issaku@noguchi.or.jp" . - "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"^^ . - "gwascentral.study" . - "nsf.award" . - . - "Mammalia Polymorphism Database" . - . - "https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-$1.md"^^ . - . - "false"^^ . - . - . - "http://fermi.utmb.edu/cgi-bin/SDAP/sdap_02?dB_Type=0&allid="^^ . - . - . - "https://bioportal.bioontology.org/ontologies/VSO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FVSO_$1"^^ . - . - . - . - "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . - . -_:Nfd951b17478f477895aef1fdeccce346 "helpdesk@cropontology-curationtool.org" . - . - "protein" . - "organism supplier" . - . -_:N4c3911b9ef174a30896482a25f2207f2 "custserv@nlm.nih.gov" . - . - . - "genome" . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - . - . - "obo" . - "gene" . - . - "Informed Consent Ontology" . - "090924"^^ . - . - . - . - . - "life science" . - . - "https://molmedb.upol.cz/mol/$1"^^ . - . - "NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties."^^ . - . - . - "ontology" . - "ontology" . - . - . - "pharmgkb.drug" . - . - "DP00086r013"^^ . - "Gerald Guala" . - "ctibor.skuta@img.cas.cz" . - "false"^^ . - . - . - . - . - "^\\d+$"^^ . - "Human Dermatological Disease Ontology" . - . - . - "ICD10CM" . - . - . - . - . - . - "Lonza" . - . - "^\\d+$"^^ . - . - "http://purl.obolibrary.org/obo/MFOEM_$1"^^ . - . - . - . - . - . - . - "Virus Pathogen Resource" . - . - "DUO is an ontology which represent data use conditions."^^ . - "COSMIC Cell Lines" . - "GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources"^^ . - "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id=$1"^^ . - "InChIKey" . - "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."^^ . - . - . - . - . - "0002927"^^ . - . - . - "metatlas" . - . - "false"^^ . - "false"^^ . - . - "https://www.xenbase.org/entry/$1"^^ . - "Chemical Information Ontology" . - . - . - . - "functional genomics" . - . - . - . - . + "^001\\d{5}$"^^ . + . + . + "W2741809807"^^ . + "biochemistry" . + . + "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."^^ . + . + . + "Homologous Vertebrate Genes Database" . + "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . + . + "true"^^ . + "sasap" . + "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."^^ . + "ctd.disease" . + "licebase" . + . + "^e\\d+$"^^ . + "Human Brain Atlas" . + . + . + . . - "REBASE Enzyme Number" . - . - . - "International Classification of Diseases, 9th Revision" . - "0003463"^^ . - "false"^^ . - . - . - . - . - . - "achcar11"^^ . - . - . - . - . - "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . - "small molecule" . - . - "https://www.scopus.com/affil/profile.uri?afid="^^ . - . - . - "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid="^^ . - . - . - . - . - . - "https://schema.org/$1"^^ . - . - . - . - . - . - . - "Open Data Commons for Spinal Cord Injury" . - . - . - "csa" . - . - . - . - . - "http://purl.obolibrary.org/obo/MPATH_$1"^^ . - "oridb.sacch" . - . - . - . - . - "entrez gene/locuslink" . - "http://viroligo.okstate.edu/main.php?vid=$1"^^ . - . - . - "lcnafid" . - "http://purl.obolibrary.org/obo/ECTO_$1"^^ . - . - "ISA1083-2"^^ . - "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."^^ . - "splash" . - . - . - "PathoPlant®" . - . - "00056"^^ . - . - "subject agnostic" . - "mipmod" . - "owl" . - . - . - "metabolomics" . - . - . - "false"^^ . - "experiment" . - . - "LK99"^^ . - . - . - "http://purl.obolibrary.org/obo/RXNO_$1"^^ . + . + "Gene"^^ . + "0187632"^^ . + . + . + . + . + . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "DailyMed provides information about marketed drugs. This information includes FDA labels (package inserts). The Web site provides a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts. Drug labeling is the most recent submitted to the Food and Drug Administration (FDA) and currently in use; it may include, for example, strengthened warnings undergoing FDA review or minor editorial changes. These labels have been reformatted to make them easier to read."^^ . + . + . + . + . + . + "MMSL_CODE" . + "The Canadian Drug Product Database (DPD) contains product specific information on drugs approved for use in Canada, and includes human pharmaceutical and biological drugs, veterinary drugs and disinfectant products. This information includes 'brand name', 'route of administration' and a Canadian 'Drug Identification Number' (DIN)."^^ . + . + "life science" . + . + . + "^\\d+$"^^ . + . + . + . +_:Nc6e5fcb883644175825da682379a1cd8 "SEP developers via the PSI and MSI mailing lists" . + . + . + . + "Vaccine Adjuvant Compendium" . + . + "ontology" . + . + . + . + . + . + "rna" . + . + "Global Biodata Coalition - Global Core Biodata Resources" . + "In CIViC, each Evidence Item must be associated with a Source Type and Source ID, which link the Evidence Item to the original source of information supporting clinical claims. Currently, CIViC accepts publications indexed on PubMed OR abstracts published through the American Society of Clinical Oncology (ASCO). Each such source entered into CIViC is assigned a unique identifier and expert curators can curate guidance that assists future curators in the interpretation of information from this source."^^ . + . + "ecyano.experiment" . + . + "genewiki" . + . + "false"^^ . + "C2584994"^^ . + . + . + "nihreporter.project" . + "false"^^ . + . + . + . + . + . + "http://www.tcdb.org/search/result.php?tc=$1"^^ . + . + "Information for ligand groups (chemical classes)."^^ . + . + . + "biomedical science" . + . + "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . + "^D\\d+$"^^ . + . + . + "ontology" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=$1"^^ . + "GCF_000005845.2"^^ . + . + "A frontend to Wikidata"^^ . + . + . + . + . + "metadata" . + "Alvin Walker" . + . + . + . + . + "https://molmedb.upol.cz/mol/$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 genes in Gramene."^^ . + "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data."^^ . + . + . + . + . + . + . + "https://ccg.epfl.ch/cgi-bin/snp2tfbs/snpviewer_form_parser.cgi?snpid=$1"^^ . + . + "false"^^ . + "https://www.ebi.ac.uk/complexportal/complex/"^^ . + . + "http://purl.obolibrary.org/obo/ICEO_$1"^^ . + "OMOP" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "A0TMC"^^ . + . + . + "CHEBI" . + "MeDRA" . + "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."^^ . + "ontology and terminology" . + . + . + . + "BBA0001"^^ . + . + . + . + . + "Fernanda Farinelli" . + . + . + "https://civicdb.org/links/variant/"^^ . + . + . + "protein" . + "http://purl.obolibrary.org/obo/AEON_$1"^^ . + . + . + "life sciences" . + "Cassava Trait Dictionary in template 5 - IITA - July 2015, updated in February 2016"^^ . + . + . + "^\\d{5,6}$"^^ . + "mba" . + . + . + . + "phosphosite.residue" . + . + "A database-specific registry supporting curation in the Gene Ontology"^^ . + . + . + "regulation" . + . + "false"^^ . + . + "http://dictybase.org/gene/$1"^^ . + "DSMZCellDive" . + "http://purl.obolibrary.org/obo/MCO_"^^ . + "Thai Clinical Trials Registry" . + . + "dhowe@zfin.org" . + . + . + "http://www.lipidmaps.org/data/LMSDRecord.php?LMID=$1"^^ . + . + "Norine is a database dedicated to nonribosomal peptides (NRPs). In bacteria and fungi, in addition to the traditional ribosomal proteic biosynthesis, an alternative ribosome-independent pathway called NRP synthesis allows peptide production. The molecules synthesized by NRPS contain a high proportion of nonproteogenic amino acids whose primary structure is not always linear, often being more complex and containing cycles and branchings."^^ . + "gene mapping" . + "559"^^ . + . + "Cephalopod Ontology" . + "functional genomics" . + . + . + . + "false"^^ . + . + "InTextReferencePointer"^^ . + . + "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . + . + . + . + . + . + "^[1-9][0-9]{14}$"^^ . + "^\\d{8}$"^^ . + . + . + . + . + "FDB002100"^^ . "false"^^ . - "http://www.scopus.com/record/display.url?origin=inward&eid="^^ . - "utrdb" . - _:Nf284f4107996471c8eac6209f8069992 . - "AutDB" . - . - "false"^^ . - "^\\d{7}$"^^ . - . - . - "Allen Institute Ontologies" . - . - "taxonomy" . - . - "adult" . - . - . - . - "http://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession="^^ . - "Kinetic Simulation Algorithm Ontology" . - "dsonensh@odu.edu" . - "Arabidopsis Small RNA Project" . - "experimental animal" . - "Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information."^^ . - . - . - "http://www.interfil.org/details.php?id="^^ . - "https://www.inaturalist.org/observations/"^^ . - "^NONHSAG\\d{5}$"^^ . - "^\\d{6}$"^^ . - . - . - . - "animal breeding" . - . - . - . - . - "false"^^ . - . - . - "pierre-alain.binz@chuv.ch" . - . - "^\\d+$"^^ . - "Oryzabase provides a view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information. It contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. This collection references gene information."^^ . - . - . - . - "Richard Cyganiak" . - . - . - "Haruki Nakamura" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "An ontology to support disciplinary annotation of Arctic Data Center datasets."^^ . - "^RID\\d+$"^^ . - "Lindsey N. Anderson" . - "ontology and terminology" . - "BioMagResBank" . - . - . - . - "cgnc" . - "n.queralt_rosinach@lumc.nl" . - . - "fish" . - "0000001"^^ . - "http://www.genome.jp/dbget-bin/www_bget?ec:"^^ . - . - . - "ascl" . - . - . - . - "pathway" . - . - "phenotype" . - . - "37af84f2-bfd7-4653-b608-eaff44febba6"^^ . + "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."^^ . + . + . + . + . + "^M\\d{5}$"^^ . + . + . + . + . + . + "EJH014"^^ . + . + "genetic engineering" . + _:N368ac74c696846f0a3f1d215ab684b1f . + . + . + . + "Annotated Regulatory Binding Sites" . + . + . + . + "Robert Hoehndorf" . + . + "https://bioregistry.io/discoverx:"^^ . + . + "NMRShiftDB structure" . + . + . + "Alan Bridge" . + . + "CCDS13573.1"^^ . + . + . + . + "imex" . + . + . + "^\\d+\\-\\d+\\-\\d+$"^^ . + . + . + . + "GR_QTL" . + . + . + . + . + . + "rna" . + . + . + . + . + . + . + . + "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . + . + "biomedical science" . + . + "00620027"^^ . + "https://www.hoelzel-biotech.com/de/catalogsearch/result/?q="^^ . + . + . + . + . + . + . + . + "has URI prefix" . + . + . + "biomodels.vocabulary" . + "C0026339"^^ . + . + "http://purl.obolibrary.org/obo/MOD_$1"^^ . + . + . + "biomedical science" . + . + "An ontology representation of the LIPIDMAPS nomenclature classification."^^ . + . + . + "ctcae" . + . + . + "complexportal" . + . + . + . + "https://abrc.osu.edu/stocks/number/SALK_$1"^^ . + . + . + "Amazon Standard Identification Number" . + "wos" . + "https://w3id.org/mixs/"^^ . + "Sabrina Toro" . + . + "false"^^ . + . + "http://oid-info.com/get/$1" . + . + . + . + . + . + "biomedical science" . + "false"^^ . + . + . + . + . + . + . + . + . + . + "social science" . + "https://www.ncbi.nlm.nih.gov/biosystems/"^^ . + "9606"^^ . + . + . + "Virtual Fly Brain" . + . + . + "^(data|topic|operation|format)\\_\\d{4}$"^^ . + . + "WP732"^^ . + . + . + . + . + "^Q[A-Z0-9]+$"^^ . + . + "^\\d+$"^^ . + . + . + "clustering" . + . + . + . + . + "NameRXN" . + . + "classification" . + "^\\d+$"^^ . + . + . + "http://mods.rna.albany.edu/mods/modifications/view/"^^ . + . + "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."^^ . + . + "molmovdb" . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . + . + "https://www.ccdc.cam.ac.uk/services/structures?pid=ccdc:$1&sid=IDORG"^^ . + . + . + . + . + . + "https://odc-sci.org/data/"^^ . + . + "Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models. [from RRID]"^^ . + "false"^^ . + "^\\d{6}$"^^ . + "51"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "85163"^^ . + "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."^^ . + . + . + . + . + "ProteomicsDB Protein" . + . + . + "https://www.sharkipedia.org/traits/$1"^^ . + . + . + "false"^^ . + . + "https://www.wormbase.org/species/c_elegans/rnai/$1"^^ . + "^\\d{7}$"^^ . + "ftt" . + . + "nextprot" . + . + . + . + . + . + . + . + "39421"^^ . + . + "http://purl.obolibrary.org/obo/UBERON_$1"^^ . + "cazy" . + "^\\d+$"^^ . + . + . + . + . + "ecolexicon" . + "false"^^ . + . + . + "SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome."^^ . + . + "http://purl.obolibrary.org/obo/MS_$1"^^ . + . + . + "vbo" . + . + "Identifiers.org" . + . + "https://portal.issn.org/resource/ISSN/$1"^^ . + . + . + . + . + "^\\d+$"^^ . + . + . + . + "ecacc" . + "ontology" . + . + "USA National Service Center Number" . + . + "drugbank.salt" . + . + . + "^\\w{1,2}\\.(\\w{1,2}\\.)?[A-Za-z0-9]+$"^^ . + . + "pfr" . + . + "false"^^ . + . + "ChEMBL database of bioactive drug-like small molecules - Cell lines section" . + . + "^[a-z0-9]+:[A-Za-z0-9.\\-:]+$"^^ . + . + "^\\d+$"^^ . + . + "Korean Clinical Research Information Service" . + . + . + . + "^\\d+$"^^ . + _:Ncfadbc34f17648fd84f1b3281ce5bb0d . + . + "earth science" . + . + "^\\d+$"^^ . + "3403"^^ . + . + "small molecule" . + . + . + "Orphanet" . + . + . + "false"^^ . + . + . + . + . + "https://reporter.nih.gov/project-details/"^^ . + "http://purl.org/spar/deo/$1"^^ . + "pombase" . + "https://www.metanetx.org/comp_info/"^^ . + . + . + . + . + "53d583d8-40c6-40e1-9296-23f821cd77a5"^^ . + . + "pgs" . + "https://cropontology.org/rdf/CO_357:"^^ . + . + "cognitive neuroscience" . + . + . + "fly lines" . + . + "12"^^ . + . + . + . + . + . + . + "The Bioregistry's meta-registry"^^ . + . + . + . + . + "Web Ontology Language" . + "http://edamontology.org/topic_$1"^^ . + "http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=$1"^^ . + "nmckenna@bcm.edu" . + . + "mhb120@gmail.com" . + "false"^^ . + . + "jfernand@um.es" . + . + . + . + "^\\d{8}$"^^ . + . + . + "genetics" . + "false"^^ . + . + "David Linke" . + "biomedical science" . + . + "tccd" . + "https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/$1"^^ . + . + . + . + "^\\d+$"^^ . + "exac.gene" . + "FAIRSharing" . + . + "rnamod" . + . + "Semanticscience Integrated Ontology" . + "life science" . + "^FDB\\d+$"^^ . + . + . + . + "false"^^ . + . + "ProDom" . + "false"^^ . + . + . + "obo" . + . + . + . + . + . + . + . + . + . + "development" . + "0001350"^^ . + . + "bandrow@gmail.com" . + . + . + "0000001"^^ . + . + . + "The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database." . + "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam="^^ . + . + "false"^^ . + "TS-0001"^^ . + . + "https://lincs.hms.harvard.edu/db/antibodies/$1"^^ . + . + . + "classification" . + . + . . - . - . - . - "DrugBank" . - "^GCST\\d{6}\\d*$"^^ . - . - . - "http://purl.obolibrary.org/obo/HP_$1"^^ . - . - . - . - . - . - . + . + "Physico-chemical methods and properties" . + "false"^^ . + "Data Commons" . + . + . + . + "^(\\w+)?\\d+$"^^ . + "https://www.ncbi.nlm.nih.gov/gtr/conditions/"^^ . + . + . + . + "genome" . + "umbbd.pathway" . + "The Licensed Natural Health Products Database contains information about natural health products that have been issued a product licence by Health Canada."^^ . + "smpdb" . + . + . + "prints" . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/MCO_$1"^^ . + "NCI Data Commons Framework Services" . + . + "IUPHARobj" . + "8"^^ . + . + "http://www.w3.org/2003/11/swrl#$1"^^ . + "taxonomy" . + . + "genpept" . + . + "cdpd" . + "Will Simpson" . + . + . + "ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^[A-Z]{6}(\\d{2})?$"^^ . + . + . + . + "https://www.ebi.ac.uk/chembl/compound/inspect/"^^ . + . + . + "The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer."^^ . + . + "http://www.proteinmodelportal.org/query/uniprot/"^^ . + . + "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"^^ . + . + "MIPModDB" . + . + . + . + . + "http://purl.obolibrary.org/obo/EO_"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/research/cog/cogcategory/$1"^^ . + . + "Cuban Registry of Clinical Trials" . + . + . + . + "STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots."^^ . + "structural biochemistry" . + "ino" . + . + . + . + . + "biomedical science" . + . + "research" . + "LOC_Os02g13300"^^ . + . + "ontology and terminology" . + . + . + . + "conferences" . + "^EB\\d+$"^^ . + . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + "0000003"^^ . + . + . + "Groundnut Trait Dictionary in template v5 - ICRISAT/ISRA/DARS - Sept 2015"^^ . + . + "false"^^ . + . + "^\\d{5}$"^^ . + "RBO is an ontology for the effects of radiation on biota in terrestrial and space environments."^^ . + . + . + "ontology" . + . + . + . + "http://www.w3.org/ns/shex#$1"^^ . + . + "Yaroslav Halchenko" . + . + "0000032"^^ . + . + . + "https://www.abmgood.com/search?query=$1"^^ . + . + . + . + . + . +_:Ndcd602300ff0433da46693e96d7101e7 "Crop Ontology Helpdesk" . + "ProGlycProt" . + "functional genomics" . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1=$1"^^ . + . + . + "^(imp|gen)\\d{5}$"^^ . + . + "Diseases Database" . + . + "true"^^ . + . + . + "https://swissmodel.expasy.org/repository/uniprot/$1"^^ . + "https://biomodels.net/vocab/idot.rdf#"^^ . + . + . + . + "phenolexplorer" . + . + . + . + "life science" . + . + . + . + "obo" . + . + "European Searchable Tumour Line Database" . + . + . + . + . + "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=$1"^^ . + . + . + "Wasila Dahdul" . + . + . + "ontology" . + "oa" . + "https://cropontology.org/rdf/CO_365:"^^ . + "life science" . + . + . + "Database of Macromolecular Movements" . + "^FOOD\\d+$"^^ . + . + "false"^^ . + "false"^^ . +_:Neb08671d822d4644a29d853b4a66d025 "tim.vandermeersch@gmail.com" . + "The gEAR portal is a website for visualization and analysis of multi-omic data both in public and private domains."^^ . + "ontology" . + "planp" . + . + . + "false"^^ . + . + . + . + . + . + "proteomics" . + . + . + . + . + "dna" . + . + . + . + . + "babelon" . + . + . + . + . + . + "M0001"^^ . + . + . + "00000022"^^ . + "jesper.friis@sintef.no" . + "biomedical science" . + "Neurovault is an online repository for statistical maps, parcellations and atlases of the brain. This collection references sets (collections) of images."^^ . + . + . + "iobc" . + . + "https://www.ncbi.nlm.nih.gov/nucleotide/"^^ . + . + . + . + . + . + . + . + "The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them."^^ . + . + "ontology" . + . + . + . + . + . + "protein" . + . + "false"^^ . + "drug" . + . + . + . + . + . + . + "span" . + . + "false"^^ . + "http://purl.obolibrary.org/obo/OVAE_$1"^^ . + "false"^^ . + . + . + . + "false"^^ . + "false"^^ . + . + "http://www.homd.org/modules.php?op=modload&name=GenomeList&file=index&link=detailinfo&seqid="^^ . + . + . + "false"^^ . + . + . + . + . + . + "obo" . + "false"^^ . + . + . + . + . + "pharmacology" . + "genome" . + "https://w3id.org/aio/"^^ . + . + "classification" . + "single nucleotide polymorphism" . + "biomedical science" . + "Genome assembly database" . + . + . + . + "SABIO-RK Reaction" . + . + . + . + "This vocabulary allows multi-dimensional data, such as statistics, to be published in RDF. It is based on the core information model from SDMX (and thus also DDI)."^^ . + . + . + "neuroscience" . + "Daniel Schober" . + . + "UniChem compound" . + "Information about the C57BL/6J. Includes genetic background and disease data."^^ . + . + "extraction_set"^^ . + . + . + . + "^\\d+$"^^ . + . + "^\\d{7}$"^^ . + "genome" . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "http://standards.iso.org/iso/15926/part14/$1"^^ . + . + "identifier for a fungus taxon in Index Fungorum"^^ . + . + "numpy"^^ . + . + "The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications."^^ . + "ala"^^ . + . + . + "embryo" . + . + . + . + "molecular biology" . + "hgnc.genefamily" . + "Liver Cancer Model Repository" . + . + "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id="^^ . + . + . + "false"^^ . + "^[1-9][0-9]*$"^^ . + "vfb" . + . + "P00266"^^ . + "UM-BBD_ruleID" . + "http://purl.obolibrary.org/obo/MFOEM_"^^ . + . + "roman@ebi.ac.uk" . + . + . + "https://bacdive.dsmz.de/strain/"^^ . + . + . + . + "covid19" . + . + . + "false"^^ . + . + . + . + "Torsten Schwede" . + . + . + . + . + . + . + . + . + "false"^^ . + . + "Gene Ontology Annotation Database" . + . + . + "nlm" . + . + "^\\d+$"^^ . + . + "HGNC gene symbol" . + . + . + "http://microsporidiadb.org/micro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "rxn00001"^^ . + . + . + . + . + . + . + . + . + "Cell Cycle Ontology" . + . + . + . + . + . + . + . + . + . + "https://zenodo.org/record/$1"^^ . + . + "https://arxiv.org/abs/"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/ZECO_$1"^^ . + "proco" . + "0000001"^^ . + "peptideatlas.dataset" . + "developmental biology" . + "http://www.probonto.org/ontology#PROB_"^^ . + . + . + . . - "spike.map" . - "cellosaurus.resource" . - "orthology" . - . - . - "http://www.chemspider.com/inchikey="^^ . - . - "gene" . - "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - . - "https://www.pgscatalog.org/pgs/"^^ . - "ontology" . - . - "Minimal Information about any Sequence" . - . - "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"^^ . - "health science" . - . - . - "https://www.echinobase.org/entry/gene/showgene.do?method=display&geneId=$1"^^ . - . - . - . - "GlycoMapsDB" . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "IA"^^ . - "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did="^^ . - . - "webelements" . - "bpdb" . - "http://purl.obolibrary.org/obo/EPIO_"^^ . - "1kfv"^^ . - "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."^^ . - "false"^^ . - . - . - . - "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . - . - . - . - "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"^^ . - . - . - "1000560"^^ . - "recombinant inbred rat" . - . - . - . - . - . - "stacia@stanford.edu" . - . - . - . - . - . - "X58356"^^ . - "InterLex" . - . - "biomedical science" . - "0002989"^^ . - . - "http://vita.mbc.nctu.edu.tw/search.php?acc=$1"^^ . - "ACM1_HUMAN"^^ . - . - . - . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid="^^ . - "pathway" . - . - "dolce" . - "Cell line databases/resources"^^ . - . - . - . - . - . - . - . - . - "interaction" . - "56586"^^ . - . - "http://purl.obolibrary.org/obo/CDNO_$1"^^ . - "^\\d+$"^^ . - "Jim Balhoff" . - . - . - "MarCat" . - . - "https://biopragmatics.github.io/providers/msigdb/"^^ . - . - . - "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid="^^ . - . - "false"^^ . - "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."^^ . - "MultiCellDS Digital Cell Line" . - . - "880798137"^^ . - "Bibliographic Reference Ontology" . - . - "false"^^ . - "systems biology" . - "https://easychair.org/cfp/"^^ . - "ontology" . - "false"^^ . - "^\\d{3}-\\d{3}-\\d$"^^ . - "Close to 5K Categorizations for drugs, similar to ATCC."^^ . + "smart" . + . + . + "Plasmodium Life Cycle" . + "A Systematic Annotation Package for Community Analysis of Genomes" . + . + . + "aop.events" . + . + . + "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . + . + "tritrypdb" . + . + "IUPAC Gold Book Compendium of Chemical Terminology" . + . + "false"^^ . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + "iNaturalist Observation" . + . + . + . + . + . + . + "AspGD Protein" . + . + . + . + . + "gene" . + "https://archive.softwareheritage.org/browse/swh:$1"^^ . + "https://lotus.naturalproducts.net/compound/lotus_id/$1"^^ . + . + . + . + . + . + . + "anatomy" . + "false"^^ . + . + . + "^[A-Z0-9]{4}$"^^ . + "0000404"^^ . + . + . + . + . + . + "life science" . + "FBcv" . + "false"^^ . + . + . + . + . + "anatomy" . + . + "tahh" . + . + . + "false"^^ . + "mediadive.medium" . + . + . + . + "false"^^ . + . + "obo" . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_anat_"^^ . + . + . + "ensembl.protist" . + "https://w3id.org/oc/meta/$1"^^ . + . + "false"^^ . + . + "http://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "http://www.orpha.net/ORDO/Orphanet_$1"^^ . + . + . + "http://purl.org/spar/pwo/$1"^^ . + "Database of Spatially Interacting Motifs in Proteins" . + . + . + "Global LEI Index" . + "mimodb" . + . + . + "^[-A-Za-z0-9\\_]*$"^^ . + . + . + . + "bcio" . + "gene" . + . + "http://www.kegg.jp/entry/"^^ . + "false"^^ . + "^\\d+$"^^ . + "http://www.w3.org/2001/XMLSchema#$1"^^ . + "co_367" . + . + "false"^^ . + . + . + "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."^^ . + . + . + . + . + . + . + . + "data quality" . + . + . + . + "uniprot.kw" . + . + "pdc.study" . + . + "taxonomy" . + . + "gene" . + "sperm" . + . + . + "otol" . + . + "Q0VCA6"^^ . + . + "Eric W. Deutsch" . + . + "mingxun.wang@cs.ucr.edu" . + "violinnet" . + "nmr" . + "http://purl.obolibrary.org/obo/GENO_$1"^^ . + . + "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/SCDO_"^^ . + . + . + . + "MicroScope is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis."^^ . + "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"^^ . + "00000000"^^ . + "obo" . + "ontology" . + "biomedical science" . + . + . + . + "Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project."^^ . + . + . + . + . + . + . + . + "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . + . + "adcad" . + . + "These are the terms that are improted for FOVT to describe vertebrate traits."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "kegg_genome" . + . + . + . + . + "0002066"^^ . + "gene" . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ligand_information.php?id="^^ . + "http://arabidopsis.info/StockInfo?NASC_id=$1"^^ . + . + . + . + . + . + . + . + . + . + "genome" . + . + . + "ontology" . + . + . + "http://www.w3.org/ns/dcat#"^^ . + "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."^^ . + "cba" . + "http://purl.obolibrary.org/obo/ECTO_$1"^^ . + "^\\d{4}$"^^ . + "true"^^ . + . + . + . + . + . + "data management" . + . + "Simple Knowledge Organization System eXtension for Labels" . + "119514"^^ . + . + . + "^\\w+$"^^ . + "https://ssbd.riken.jp/database/dataset/"^^ . + "https://bioportal.bioontology.org/ontologies/CCF/?p=classes&conceptid=http%3A%2F%2Fpurl.org%2Fccf%2F"^^ . + . + "The Gene Wiki is project which seeks to provide detailed information on human genes. Initial 'stub' articles are created in an automated manner, with further information added by the community. Gene Wiki can be accessed in wikipedia using Gene identifiers from NCBI."^^ . + . + "ontology" . + . + "bgee.stage" . + "PubChem_Compound_CID" . + "terms4FAIRskills" . + . + . + "Yoshiharu Y. Yamamoto" . + . + . + "false"^^ . + "^[a-z][a-zA-Z]+$"^^ . + "Human Plasma Membrane Receptome Families" . + "http://uri.neuinfo.org/nif/nifstd/nlx_$1"^^ . + . + "metagenomics" . + . + . + "^SLCTR/\\d{4}/\\d+$"^^ . + "https://bioregistry.io/rebase:"^^ . + . + "sciflection" . + . + . + "^PA\\d+$"^^ . + . + . + "33607"^^ . + . + . + . + . + "fly" . + . + . + "70"^^ . + . + "Li-San Wang" . + . + "data management" . + . + . + . + . + "http://cegg.unige.ch/orthodb/results?searchtext=$1"^^ . + . + . + "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . + . + "^\\d{4}-\\d+-\\d+-\\d+$"^^ . + . + . + "https://reactome.org/content/detail/"^^ . + . + . + . + "http://search.sisuproject.fi/#/variant/$1"^^ . + "https://sumlineknowledgebase.com/?page_id=$1"^^ . + . + . + . + . + . + . + "https://cgap.nci.nih.gov/Pathways/BioCarta/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/FBbt_"^^ . + . + . + . + . + . + . + . + "NIH RePORTER" . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "https://gpcrdb.org/protein/$1"^^ . + . + . + "OMIM" . + . + . + "health science" . + "pns12@hermes.cam.ac.uk" . + . + "Ontology of rat strains"^^ . + "genetics" . + . + "uniprot.disease" . + . + . + . + "botany" . + . + "false"^^ . + "false"^^ . + . + . + . + . + . + "0000031"^^ . + . + . + "Site groups are orthologous positions in human, mouse, rat, etc. where phosphorylations or other PTMs occur."^^ . + . + "co_340" . + "^\\w+$"^^ . + . + "Bioregistry Schema" . + "inxight" . + . + . + _:N820b1b954de9446f91f3dc21bc674d09 . + . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id="^^ . + . + "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."^^ . + "https://registry.healthresearch.ph/index.php/registry?view=research&layout=details&cid=$1"^^ . + . + . + . + "obo" . + . + . + "DragonDB Allele" . + . + "https://www.arraymap.org/pgx:"^^ . + . + "https://books.google.com/books?id="^^ . + "evolutionary biology" . + "rnao" . + . + . + "http://purl.obolibrary.org/obo/ICO_$1"^^ . + "https://www.re3data.org" . + "https://www.pirbright.ac.uk/node/$1"^^ . + . + "has URI pattern" . + "http://www.fludb.org/brc/fluSegmentDetails.do?ncbiGenomicAccession=$1"^^ . + . + . + . + . + "anatomy" . + . + . + . + "cdno" . + . +_:N21f8caeb1d264efd93eb87a9a39c96de "Ramesh Verna" . + . + . + "MagnitudeValueType"^^ . + "https://biopragmatics.github.io/providers/mba/"^^ . + "biomedical science" . + "http://purl.obolibrary.org/obo/ECAO_$1"^^ . + "NX_O00165"^^ . + . + . + . + "0001707"^^ . + . + "^\\d+$"^^ . + . +_:Ncff35745bc0b4cb4882876319048a670 "Onard Mejino" . + "germline" . + . + "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . + . + "https://terminology.hl7.org/CodeSystem-v3-$1"^^ . + . + . + . + . + . + . + . + "life science" . + "FAO/WHO_standards" . + "A subspace of Metabolic Atlas for compartment-specific records for metabolites."^^ . + . + . + "false"^^ . + . + "genomics" . + "sabiork.ec" . "true"^^ . - . - "1968"^^ . - . - . - "cell biology" . - . - "knowledge and information systems" . - "Rafael Richards" . - "Metabolomics Workbench stores metabolomics data for small and large studies on cells, tissues and organisms for the Metabolomics Consortium Data Repository and Coordinating Center (DRCC)."^^ . - "Digital archive of scholarly articles" . - . - . - . - . - . - . - . - "dna" . - . - "0000001"^^ . - "0000184"^^ . + . + "t3db" . + . + "did" . + "Hathitrust is a partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world."^^ . + "Gianni Cesareni" . + . + "phenomics" . + . + . + . + . + "Vertebrate Genome Annotation Database" . + . + . + . + . + . + "oma.grp" . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/compound/"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "epidemiology" . + "https://www.uniprot.org/unirule/$1"^^ . + "irefweb" . + . + "https://herv.img.cas.cz/s/"^^ . + . + . + . + . + . + . + . + . + "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id=$1"^^ . + . + . + . + . + "Spider Ontology" . + "neuroscience" . + "false"^^ . + . + . + . + "false"^^ . + . + . + "0000041"^^ . + "^\\d{7}$"^^ . + "repeatsdb.protein" . + . + _:Nec5a327b3e5848b4b67c4f1df2c7dada . + . + "13"^^ . + . + . + "dna" . + . + . + . + "variants" . + "LIPID_MAPS_instance" . + . + . + . + . + . + . + . + . + . + . + "entrez gene/locuslink" . + "owl" . + "Bernd Müller" . + . + . + . + . + "http://www.w3.org/2008/05/skos-xl#$1"^^ . + . + . + "medical informatics" . + . + "https://drugs.ncats.io/drug/"^^ . + . + . + . + . + . + "iceberg.ice" . + "BioSimulations is an open repository of simulation projects, including simulation experiments, their results, and data visualizations of their results. BioSimulations supports a broad range of model languages, modeling frameworks, simulation algorithms, and simulation software tools."^^ . + . + . + . + "0000140"^^ . + "Eukaryotic Linear Motif Resource" . + "https://gold.jgi.doe.gov/resolver?id="^^ . + . + . + . + . + "data management" . + . + . + "The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features."^^ . + . + . + "false"^^ . + "obo" . + . + . + . + "https://w3id.org/faircookbook/"^^ . + . + "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)"^^ . + "ontology" . + "preclinical studies" . + . + . + . + . + "natural science" . + "Thomas Lütteke" . + . + . + "^\\d+$"^^ . + . + "LO362836C"^^ . + . + "HGVM15354"^^ . + . + . + . + . + . + . + "bcrj" . + "^\\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"^^ . + "PomBase" . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/OMO_$1"^^ . + "steven.marsh@ucl.ac.uk" . + . + "^[A-Za-z0-9-]+$"^^ . + . + "false"^^ . + "classification" . + . + . + . + "gro-cpga" . + . + . + . + "https://nmrshiftdb.nmr.uni-koeln.de/molecule/$1"^^ . + . + . + . + "UniProtKB_VAR" . + "ontology" . + "AAindex" . + . + . + . + "ornaseq" . + "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . + "true"^^ . + "322"^^ . + "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."^^ . + . + "ontology" . + . + "medicine" . + . + "Japan Chemical Substance Dictionary" . + . + "Adverse Event Reporting Ontology" . + "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."^^ . + . + "nathan.baker@pnnl.gov" . + . + "live mouse" . + "ontology" . + . + "phenotype" . + . + . + "https://www.thermofisher.com/antibody/product/$1"^^ . + . + . + "http://purl.obolibrary.org/obo/"^^ . + "Wormbase Gene" . + . + . + . + . + . + "Scopus Work" . + . + . + . + "obo" . + "false"^^ . + . + "An ontology for non-coding RNA, both of biological origin, and engineered."^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . + "false"^^ . + "biosample" . + . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived."^^ . + "nstd102"^^ . + "biorxiv" . + . + "GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42)."^^ . + "conferences" . + "VMH metabolite" . + . + "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id="^^ . + "ontology" . + "OpenAlex" . + . + "Antibody Registry" . + "Bgee family" . + "structure" . + . + "false"^^ . + "protein" . + "stoeckrt@pcbi.upenn.edu" . + "aellenhicks@gmail.com" . + "sharesAuthorInstitutionWith"^^ . + . + "^[A-Z]C\\d{1,3}$"^^ . + "https://www.gwascentral.org/study/"^^ . + "false"^^ . + . + . + "Collembola Anatomy Ontology" . + . + "https://aopwiki.org/stressors/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + "https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid="^^ . + "oclc" . + . + . + "^\\d+$"^^ . + . + . + . + . + "^[0-9]+$"^^ . + "http://purl.obolibrary.org/obo/TO_"^^ . + "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology" . + . + . + . + "microbiology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "000000024"^^ . + "^IHW\\d+$"^^ . + "famplex" . + "https://bitbucket.org/$1"^^ . + . + "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."^^ . + "https://cellmodelpassports.sanger.ac.uk/passports/$1"^^ . + . + "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."^^ . + . + . + . + "Bilateria anatomy" . + . + . + . + . + . + . + . + "false"^^ . + . + . + "http://www.pseudomonas.com/feature/show/?locus_tag=$1"^^ . + . + "identifier of a compound in the UniChem database"^^ . + . + "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."^^ . + . + "http://www.sasbdb.org/data/$1"^^ . + . + . + "genome" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^ECMDB\\d+$"^^ . + . + . + . + "structural biology" . + . + . + . + "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."^^ . + . + . + . + . + . + . + "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . + . + "http://purl.obolibrary.org/obo/PD_ST_$1"^^ . + . + . + "easychair.topic" . + "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."^^ . + "https://rarediseases.info.nih.gov/diseases/$1/index"^^ . + "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."^^ . + . + . + "nih initiative" . + . + "https://www.rhea-db.org/rhea/$1"^^ . + . + . + "ecology" . + . + "imotdb" . + . + . + . + . + "6"^^ . + "protein" . + . + . + . + . + . + "http://viaf.org/viaf/$1"^^ . + . + . + . + "Ontology of Medically Related Social Entities" . + "CATH domain" . + . + . + . + "life science" . + . + . + . + . + "anatomy" . + . + . + "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."^^ . + . + "yetfasco" . + "ontology" . + "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . + . + . + "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . + "enviPath" . + . . - . - "Rahuman Sheriff" . - . - . - "BrainInfo is designed to help you identify structures in the brain. If you provide the name of a structure, BrainInfo will show it and tell you about it."^^ . - "false"^^ . - . - . - . - "gene" . - . - . - . - . - "norine" . - . - . - . - . - . - . - . - . - . + . + "co_325" . + "obo" . + . + . + . + . + "dsm-iv" . + "false"^^ . + . + "CBA: http://www.cba.ac.cn/ and the Shanghai Institutes for Biological Sciences (SIBS at http://www.sibs.ac.cn/) provide EBI with citation data not available in MEDLINE."^^ . + . + "obo" . + . + "ontology" . + . + . + "Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump"^^ . + "RepeatsDB Protein" . + . + . + "mutant" . + . + . + "jcm" . + . + "obo" . . - "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . - "pathway" . - . - "data mining" . - . - "The National Cancer Institute's Proteomic Data Commons (PDC) makes cancer-related proteomic datasets easily accessible to the public."^^ . - . - . - . - . - . - "oridb.schizo" . - "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$"^^ . - . - . - . - . - "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . - "genetree" . - . - "0000021"^^ . - . - . - "http://purl.obolibrary.org/obo/HTN_"^^ . - "LINCS_LDP" . - "stock" . - "tobias.schulze@ufz.de" . - "^[a-zA-Z]+.+$"^^ . - "http://purl.obolibrary.org/obo/CIO_$1"^^ . - . - . - . - . - . - . - "64ba"^^ . - . - "upper-level ontology" . - . - "ontology" . - _:N76f00e653b4248c9891b2f17b031ddbd . - . - "98034"^^ . - . - . - . - . - "Lentil ontology" . - . - "unique academic work identifier assigned in Scopus bibliographic database"^^ . - "phenomics" . - . - . - "FlyBase Reference Report" . - . - "http://multicellds.org/MultiCellDB/$1"^^ . - "true"^^ . - "https://aopwiki.org/stressors/$1"^^ . - . - "protein" . - "false"^^ . + . + . + . + "iNaturalist Place" . + . + "false"^^ . + . + . + . + . + "casspc" . + "http://registry.api.hq.identifiers.org/semanticApi/getRegistryOntology#$1"^^ . + "longevity" . + . + "false"^^ . + "obo" . + . +_:N9abc2b29d7c54644828f5ad866064c9e "jamsden@us.ibm.com" . + . + "phenotype" . + . + "MULT_4_VAR1_bovine"^^ . + . + "A0014"^^ . + . + . + "hasDbXref"^^ . + . + "APID Interactomes" . + . + "^UDB\\d{6}$"^^ . + . + . + . + "ndf-rt" . + "xuo" . + "https://data.bloodpac.org/ga4gh/drs/v1/objects/"^^ . + "chemistry" . + . + . + . + . + . + "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."^^ . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + "biomedical science" . + "http://www.antweb.org/specimen.do?name="^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/HEPRO_$1"^^ . + . + . + "bioinformatics" . + . + . + "NBC00001"^^ . + "CSTR is an identifier for Common Science and Technology Resources, to provide persistent identification services for the positioning, traceability, citation, statistics and evaluation of science and technology resources. "^^ . + . + "tropicalis" . + "^UP\\d{9}$"^^ . + "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . + "GO Evidence Code" . + . + "BitterDB Compound" . + . + "ontology" . + "Japan Registry of Clinical Trials" . + "neurobiology" . + . + . + . + . + . + "Epilepsy and Seizure Ontology" . + "http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid="^^ . + . + . + "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . + . + . + . + . + "false"^^ . + . + "translational medicine" . + . + "structrual bioinformatics" . + "biomedical science" . + "ramirez@macn.gov.ar" . + . + "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue=$1"^^ . + "Anatomical Entity Ontology" . + "^\\d+$"^^ . + . + "https://www.ncbi.nlm.nih.gov/protein/$1?report=genpept"^^ . + . + "File inside StoreDB"^^ . + "false"^^ . + . + . + . + "false"^^ . + "preclinical studies" . + . + "unists" . + . + . + . + "ligandbook" . + . + . + . + . + . + . + "https://www.swisslipids.org/#/entity/SLM:$1"^^ . + . + . + . + . + . + . + . + "classification" . + "obo" . + . + . + . + "false"^^ . + . + . + . + . + . + "aio" . + "false"^^ . + "TubercuList knowledge base" . + . + . + "http://stitch.embl.de/interactions/$1"^^ . + "genomics" . + "ecology" . + . + . + . + "^LTS\\d{7}$"^^ . + . + . + "https://www.ndexbio.org/viewer/networks/$1"^^ . + "^\\d{7}$"^^ . + . + . + . + . + "sharkipedia.trait" . + . + . + "immunology" . + "http://purl.obolibrary.org/obo/STATO_$1"^^ . + . + "https://cellbank.snu.ac.kr/english/sub/catalog.php?s_cellid=464&page=detail_info&CatNo=59&strQ=$1"^^ . + "20090303"^^ . + . + "http://purl.obolibrary.org/obo/COVOC_$1"^^ . + . + . + "DOULIX lab-tested standard biological parts, in this case, full length constructs."^^ . + . + "genomics" . + . + . + . + . + "https://www.flymine.org/come/entry?gn=$1"^^ . + . + "^\\d{7}$"^^ . + . + "biopragmatics/bioregistry/424"^^ . + . + . + . + "http://purl.obolibrary.org/obo/CLYH_"^^ . + . + . + . + "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."^^ . + . + . + "^[0-9][A-Za-z0-9]{3}[A-Za-z0-9][A-Za-z0-9]?[0-9]?[0-9]?$"^^ . + . + . + "false"^^ . + . + . + . + "life science" . + . + "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId="^^ . + . + . + . + "false"^^ . + . + "0400109"^^ . + "NAPP (Nucleic Acids Phylogenetic Profiling is a clustering method based on conserved noncoding RNA (ncRNA) elements in a bacterial genomes. Short intergenic regions from a reference genome are compared with other genomes to identify RNA rich clusters."^^ . + . + . + "^[A-Z0-9]+$"^^ . + . + "O80725"^^ . + . + "GitHub is an online host of Git source code repositories."^^ . + "BARC-013845-01256"^^ . + "^\\w+$"^^ . + . + . + . + . + "iro" . + "http://pax-db.org/#!protein/$1"^^ . + . + . + . + "janna.hastings@gmail.com" . + . + . + "chemistry" . + "sstoss" . + "g.gkoutos@gmail.com" . + . + . + "ontology" . + . + "https://cropontology.org/rdf/CO_346:"^^ . + . + . + . + "Identifier of an entry from the AAindex database."^^ . + . + "http://purl.org/cerif/frapo/"^^ . + . + "LiceBase" . + . + . + "The Community Research and Development Information Service (CORDIS) is the European Commission's primary source of results from the projects funded by the EU's framework programmes for research and innovation (FP1 to Horizon 2020)."^^ . + . + . + "ontology" . + . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to specific models."^^ . + "https://go.drugbank.com/salts/"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/OHD_"^^ . + . + "FDA Submission Tracking Number" . + "^\\d+$"^^ . + . + . + . + . + . + "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 wild strain information."^^ . + "chebi" . + . + . + . + . +_:N93953f5709f34a838912b45663c37bb8 "Michelle Futornick" . + . + . + . + "https://bioregistry.io/wikigenes:"^^ . + . + "cosmic.cell" . + "life science" . + . + . + "53504"^^ . + "http://www.narcis.nl/publication/RecordID/"^^ . + . + "obo" . + . + "obo" . + . + "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . + . + "pathway" . + . + . + . + "Cell line databases/resources"^^ . + . + "https://www.pombase.org/gene/"^^ . + "Orientations of Proteins in Membranes Database" . + . + . + "0000003"^^ . + . + "drks" . + "^\\d{7}$"^^ . +_:Nda1f307f111446f48481d11b881079b1 "Usha Mahadevan" . + . + . + . + . + . + "The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies. The resource contains genome profiles of more than 130'000 individual samples and represents about 700 cancer types, according to the NCIt \"neoplasm\" classification. Additionally to this genome profiles and associated metadata, the website present information about thousands of publications referring to cancer genome profiling experiments, and services for mapping cancer classifications and accessing supplementary data through its APIs."^^ . + . + . + . + . + . + . + . + "https://www.kazusa.or.jp/huge/gfpage/"^^ . + "Metabolite and Tandem Mass Spectrometry Database" . + . + . + "human" . + "KEGG Genome is a collection of organisms whose genomes have been completely sequenced."^^ . + "Identifier of an object from the ASTD database."^^ . + "ypo" . + . + "true"^^ . + . + . + "obo" . + "US4145692"^^ . + . + . + "^\\d{7}$"^^ . + "Database containing promotor sequences found in Saccharomyces cerevisiae."^^ . + . + . + . + . + . + "nif.grossanatomy" . + . + "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId="^^ . + "eu89h" . + . + "VFDB Gene" . + . + . + "false"^^ . + . + . + "structural biology" . + . + . + . + "obo" . + . + "^DG\\d+$"^^ . + . + "false"^^ . + . + "life science" . + . + "BioGRID Interactions" . + . + . + "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."^^ . + . + "https://www.checklistbank.org/dataset/3LR/taxon/"^^ . + . + "ontology" . + . + "Gramene QTL" . + . + "interaction" . + "lcsh" . + "Ontology about the development and life stages of the C. elegans"^^ . + . . - "microbiology" . - . - . - . - "false"^^ . - . - "giardiadb" . - "MEDLINE" . - . - "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."^^ . - "ontology" . - . - "PIR Superfamily Classification System" . - "ontology" . - "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . - . - "biology" . - "biology" . - . - . - . - . - . - "TogoVar (A comprehensive Japanese genetic variation database) is a database that has collected and organized genome sequence differences between individuals (variants) in the Japanese population and disease information associated with them."^^ . - "bioinformatics" . - "life science" . - "colao" . - "biomedical science" . - "^\\d{7}$"^^ . - "ontology" . - . - . - . - . - . - "A001094"^^ . - "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://www.mlcommons.org/mlc-id/$1"^^ . - . - . - . - . - "false"^^ . - . - . - "false"^^ . - . - . - "https://w3id.org/biolink/vocab/$1"^^ . - . - "life science" . - . - . - . - . - . - "genome" . - "A comprehensive set of radiology terms for use in radiology reporting, decision support, data mining, data registries, education and research.\n\nRadLex provides the foundation for vital data resources used in radiology:\n\n- The LOINC/RSNA Radiology Playbook\n- RadElement Common Data Elements\n-RadReport Radiology Reporting Templates\n\nThe development of RadLex has been supported by the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the cancer Biomedical Informatics Grid (caBIG) project."^^ . - . - . - . - . - . - "title"^^ . - . - . - "subject agnostic" . - . - . - . - . - . - "^[A-Z]+$"^^ . - "^\\d{7}$"^^ . - . - . - "thesaurus" . - . - . - . - . - . - "http://www.sasbdb.org/data/$1"^^ . - . - . - . - "000000159"^^ . - . - . - . - . - . - . - . - . - . - "http://virtualflybrain.org/reports/"^^ . - "NOAA Fisheries Species Directory" . - . - . - . - . - "developmental biology" . - . - "dietary restriction" . - "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."^^ . - . - . - . - . - . - . - "Transporter Classification Database" . - . - "false"^^ . - "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . - "tgd" . - "^SMP\\d+$"^^ . - . - . - "GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E."^^ . - "sequence" . - . - . - . - . - . - . - "http://bigg.ucsd.edu/models/universal/reactions/"^^ . - . - . - "https://registry.bio2kg.org/resource/$1" . - . - "CategorialBibliometricData"^^ . - "MarDB includes all sequenced marine microbial genomes regardless of level of completeness."^^ . - . - "false"^^ . - . - . - . - . - . - "mutant mouse strain" . - . - . - "false"^^ . - . - "^[a-z0-9]+$"^^ . - "neuroscience" . - "http://purl.obolibrary.org/obo/MFOMD_"^^ . - . - . - . - "Matt Yoder" . - "CHEBI" . - . - . - "Scopus Researcher" . - . - . - "https://www.flymine.org/come/entry?gn="^^ . - . - "GCST000035"^^ . - "help-swissmodel@unibas.ch" . - . - "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "agricultural engineering" . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . - . - . - "false"^^ . - . - . - . - "ZFIN serves as the zebrafish model organism database. This collection references all zebrafish biological entities in ZFIN."^^ . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - "CropMRepository" . - "https://dgrc.bio.indiana.edu/product/View?product=$1"^^ . - "true"^^ . - . - . - "false"^^ . - . - . - . - "davidos@ebi.ac.uk" . - . - "clinical decision support systems" . - "genomics" . - . - . - . - . - . - . - "TarBase" . - . - . - "Célia Michotey" . - "false"^^ . - "Cell line databases/resources"^^ . - "genetics" . - "http://www.kegg.jp/entry/"^^ . - . - "chemical" . - . - . - . - "UK Universities and Colleges Admissions Service" . - . - . - "ontology" . - . - . - "fisheries science" . - . - "false"^^ . - . - "pathwaycommons" . - "life science" . - "https://bioregistry.io/mesh.2013:"^^ . - . - . - . - . - "CPD-10330"^^ . - . - "http://purl.obolibrary.org/obo/OGI_$1"^^ . - . - . - "true"^^ . - "kegg.orthology" . - . - "registry" . - "https://www.biorxiv.org/content/10.1101/$1"^^ . - . - . - "WBls" . - . - . - . - . - . - . - "^G[0-9]{5}[A-Z]{2}$"^^ . - "life science" . - "https://www.ebi.ac.uk/interpro/set/pfam/$1"^^ . - "life science" . - . - . - . - "support@ccdc.cam.ac.uk" . - "http://purl.obolibrary.org/obo/VariO_"^^ . - . - . - "dunand@lrsv.ups-tlse.fr" . - . - . - . - "pombase" . - . - "https://go.drugbank.com/bio_entities/$1"^^ . - "pdb.ligand" . - . - . - "https://www.facebase.org/data/record/#1/isa:dataset/accession=$1"^^ . - "The 10th revision of the International Classification of Diseases (ICD) issued by the World Health Organization (WHO). ICD is formally named 'The International Statistical Classification of Diseases and Related Health Problems'. It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.\n\nNote that the WHO version of ICD-10 is distinct from the ICD-10-CM (Clinical Modification) issued by the U.S. National Center for Health Statistics for use in the United States."^^ . - . - . - "taxonomy" . - "false"^^ . - . - "PROV Namespace" . - "rrid" . - "MetaNetX compartment" . - . - . - . - "md.tyers@umontreal.ca" . - "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."^^ . - "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . - "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone="^^ . - . - "pharmacology" . - . - "umls.aui" . - . - "taxonomy" . - . - . - . - . - . - "cherry@genome.stanford.edu" . - . - "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . - . - . - . - "epidemiology" . - . - . - . - . - . - . - . - "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."^^ . - "Christian-Alexander Dudek" . - . - . - "hsa00190"^^ . - . - "This collection is a subset of UniProtKB that provides a means to reference the proteolytic cleavage products of a precursor protein."^^ . - . - . - "https://dgrc.bio.indiana.edu/product/View?product="^^ . - "ontology" . - "smiles" . - . - "kestrelo" . - "false"^^ . - . - . - "false"^^ . - "PRIDE Controlled Vocabulary" . - "Database of Spatially Interacting Motifs in Proteins" . - . -_:N226ad9bb06704cbfb4da47042ff528b0 "Crop Ontology Helpdesk" . - "Melanoma Molecular Map Project Biomaps" . - . - "r3d100010772"^^ . - . - "http://agroportal.lirmm.fr" . - . - . - "pmr.workspace" . - "eggnog" . - "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."^^ . - . - . - . - . + "owl" . + . + . + "PR000001"^^ . + . + . + . + "gene" . + "Animal Genome Chicken QTL" . + . + "12929"^^ . + "The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis."^^ . + "https://pk-db.com/data/$1"^^ . + "lipidbank" . + "http://jcggdb.jp/idb/jcggdb/$1"^^ . + . + . + "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID=$1"^^ . + . + . + . + "translational medicine" . + . + "ligandexpo" . + "bioinformatics" . + . + . + . + "false"^^ . + . + . + . + . + . + . + "https://web.expasy.org/cellosaurus/" . + . + . + . + "http://purl.obolibrary.org/obo/COB_$1"^^ . + "he Interaction Network Ontology (INO) is an ontology in the domain of interactions and interaction networks. INO represents general and species-neutral types of interactions and interaction networks, and their related elements and relations. INO is a community-driven ontology, aligns with BFO, and is developed by following the OBO Foundry principles."^^ . + "protein" . + "emea" . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + "https://cropontology.org/rdf/CO_370:"^^ . + . + "false"^^ . + "SugarBind" . + . + "http://purl.obolibrary.org/obo/EMAPA_$1"^^ . + . + . + "ontology" . + . + . + . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "genetics" . + . + . + "life science" . + . + "https://www.glycoepitope.jp/epitopes/$1"^^ . + . + . + . + . + . + . + . + "subject agnostic" . + . + . + "The human receptor families involved in signaling (with the exception of channels) are presented in the Human Plasma Membrane Receptome database."^^ . + . + "false"^^ . + "^\\d+\\.\\d+$"^^ . + . + "^(LCL|LDC|ES|LSC|LPC)-\\d+$"^^ . + . + . + "Degradome Database" . + . + . + "dbpedia" . + . + "^(\\d|\\w)+-\\d$"^^ . + . + "https://openalex.org/"^^ . + . + . + . + . + . + . + "ontology" . + . + "omid" . + . + . + "Chen Yang" . + . + . + . + "phylogenetics" . + "false"^^ . + . + . + "vdrc" . + . + "^\\d+$"^^ . + . + "protein" . + . + . + . + . + . + . + . + "https://www.brenda-enzymes.org/php/result_flat.php4?ecno="^^ . + "The Common Coordinate Framework (CCF) Ontology is an application ontology built to support the development of the Human Reference Atlas (HRA). It unifies vocabulary for HRA construction and usage—making it possible to ingest external data sources; supporting uniform tissue sample registration that includes the spatial positioning and semantic annotations within 3D reference organs; and supporting user-formulated cross-domain queries over tissue donor properties, anatomical structures, cell types, biomarkers, and 3D space. The CCF Ontology consists of three major ontologies. The Biological Structure Ontology records anatomical structures, cell types, and biomarkers (ASCT+B) and the relationships between them. The ASCT+B tables are authored by human experts using templated Google Sheets. The biomarkers, cell types, and anatomical structures are mapped to existing ontologies (Uberon/FMA, CL, HGNC) whenever possible. All relationships between anatomical structures and from cell types to anatomical structures are valid Uberon and CL relationships. The Spatial Ontology defines the shape, size, location, and rotation of experimental tissue and data major anatomical structures in the 3D Reference Object Library. The Specimen Ontology captures the sex, age, and other information on donors that provided tissue data used in the construction of the HRA."^^ . + "human health" . + "ontology" . + . + "decipher" . + "false"^^ . + . + "vfdb.genus" . + . + . + "^\\d{7}$"^^ . + . + "eolife" . + . + . + . + "bernd.mueller@zbmed.de" . + . + "The Cell Line Ontology 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."^^ . + . + . + "^[AEP]-\\w{4}-\\d+$"^^ . + "Small Angle Scattering Biological Data Bank (SASBDB) is a curated repository for small angle X-ray scattering (SAXS) and neutron scattering (SANS) data and derived models. Small angle scattering (SAS) of X-ray and neutrons provides structural information on biological macromolecules in solution at a resolution of 1-2 nm. SASBDB provides freely accessible and downloadable experimental data, which are deposited together with the relevant experimental conditions, sample details, derived models and their fits to the data."^^ . + "^CH_\\d+$"^^ . + "doco" . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "European Bank for induced pluripotent Stem Cells" . + . + "https://dataguids.org/ga4gh/dos/v1/dataobjects/"^^ . + . + "small molecule" . + _:Naf53a37095d24e73886a30c68eaa336f . + . + "grassbase" . + . + . + . + . + "http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=$1"^^ . + . + . + . + . + . + . + "http://www.kegg.jp/entry/$1"^^ . + . + . + "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."^^ . + . + . + "fernanda.dorea@sva.se" . + "61467"^^ . + . + . + "The Bibliographic Ontology Specification provides main concepts and properties for describing citations and bibliographic references (i.e. quotes, books, articles, etc) on the Semantic Web."^^ . + . + . + . + . + "johnbeverley2021@u.northwestern.edu" . + . + . + . + . + . + . + "balhoff@renci.org" . + . + "pubmed" . + . + "genetics" . +_:Ndf03f6d8403c435dbcd86c77420d1bf0 "custserv@nlm.nih.gov" . + . + "A user of FAIRsharing"^^ . + "https://cls.shop/"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/sao$1"^^ . + . + "mutant" . + . + . + "Citlalli Mejía-Almonte" . + . + . + "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"^^ . + . + . + . + . + . + . + . + . + "biology" . + . + "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."^^ . + "protein" . + "biomedical science" . + "https://fcs-free.org/fcs-database?$1"^^ . + . + . + . + . + "ecology" . + . + . + . + "obo" . + . + . + "false"^^ . + . + . + "http://bigg.ucsd.edu/compartments/"^^ . + . + "Zenodo is an open repository that allows researchers to deposit research papers, data sets, research software, reports, and any other research related digital artefacts."^^ . + . + . + . + . + . + "huanglin36@mail.sysu.edu.cn" . + "biology" . + . + . + . + "ontology" . + "false"^^ . + . + . + . + "anatomy" . + "https://wheat.pw.usda.gov/cgi-bin/GG3/report.cgi?class=reference&name="^^ . + . + . + . + "An ontology of Drosophila melanogaster anatomy."^^ . + . + . + . + . + "https://cropontology.org/rdf/CO_333:$1"^^ . + "^P\\d+$"^^ . + . + . + . + . + "false"^^ . + . + "BCRTi001-A"^^ . + . + . + . + "false"^^ . + "life science" . + . + . + . + "oma.hog" . + "^UCR\\d{5}$"^^ . + . + . + . + . + "^PWY\\w{2}\\-\\d{3}$"^^ . + "http://vocabularies.bridgedb.org/ops#$1"^^ . + . + . + . + "SNHG3"^^ . + "ontology" . + "anatomy" . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "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"^^ . + . + "data management" . + . + "developmental biology" . + . + . + "CIViC Molecular Profiles are combinations of one or more CIViC variants. Most Molecular Profiles are “Simple” Molecular Profiles comprised of a single variant. In most cases, these can be considered equivalent to the CIViC concept of a Variant. However, increasingly clinical significance must be considered in the context of multiple variants simultaneously. Complex Molecular Profiles in CIViC allow for curation of such variant combinations. Regardless of the nature of the Molecular Profile (Simple or Complex), it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional clinical relevance to be entered in CIViC."^^ . +_:Neb08671d822d4644a29d853b4a66d025 "Tim Vandermeersch" . + "alejandra.gonzalez.beltran@gmail.com" . + "ontology" . + "NLXRES covers digital resources. Most classes are high level types covering everything from databases and sourcecode to source code licenses and instrument supplier websites"^^ . + . + . + "ACTRN" . + "PubChem Element gives information on chemical elements like Hydrogen, with the local identifier corresponding to the atomic number."^^ . + . + . + "molecules" . + . + . + . + . + . + . + . + "System Science of Biological Dynamics project" . + . + . + . + "immunology" . + "http://gmd.mpimp-golm.mpg.de/profile/default.aspx?XemlId=$1"^^ . + . + "The Common Terminology Criteria for Adverse Events (CTCAE),[1] formerly called the Common Toxicity Criteria (CTC or NCI-CTC), are a set of criteria for the standardized classification of adverse effects of drugs used in cancer therapy. The CTCAE system is a product of the US National Cancer Institute (NCI)."^^ . + . + . + . + "anatomy" . + "https://www-is.biotoul.fr/scripts/ficheIS.php?name="^^ . . - . - "http://www.guidetopharmacology.org/GRAC/FamilyDisplayForward?familyId="^^ . - . - "Radiation Biology Ontology" . - . - . - . - . - "protein" . - . - . - "ecogene" . - . - "itmctr" . - . - . - "false"^^ . - . - "nuclear" . - . - "ontology" . - "life science" . - . - . - "^CTRI/\\d{4}/\\d{2}/\\d+$"^^ . - . - "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)."^^ . - "^\\d+$"^^ . - "lgai.cede" . - . - "Protein modification" . - . - "false"^^ . - . - . - . - . - . - "cell biology" . - . - "false"^^ . - "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models."^^ . -_:Nb01e8f454a334f6aa890c77212852321 "support@bioontology.org" . - . - "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=EN&Expert="^^ . - . - "miR-1"^^ . - . - . - "analytical chemistry" . - . - "hgnc.symbol" . - . - . - "awalker@apa.org" . - . - "Gainesville Core Ontology" . - . - . - . - "http://www.xmetdb.org/xmetdb/protocol/$1"^^ . - . - . - . - "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=$1"^^ . - "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes."^^ . - . - . - . - . - . - . - . - . - "false"^^ . - "obo" . - "http://purl.obolibrary.org/obo/VHOG_"^^ . - "deficiency" . - . - . - "false"^^ . - . - . - "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . - "grouping" . - . - "1000000"^^ . - "National stock center for X. laevis and X. tropicalis and training center for advanced technologies (e.g. husbandry, cell biology, imaging, genetics, transgenesis, genomics). [from RRID]"^^ . - . - . - "false"^^ . - . - . - . - "^Os\\S+g\\d{7}$"^^ . - . - "protein" . - . - "faseb list" . - "false"^^ . - . - . - . - . - "ontology" . - . - . - . - . - . - "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass="^^ . - "false"^^ . - . - . - . - . - . - . - . - "https://meshb.nlm.nih.gov/record/ui?ui=$1"^^ . - "false"^^ . - . - "http://purl.obolibrary.org/obo/UBERON_$1"^^ . - "http://www.scopus.com/record/display.url?origin=inward&eid=$1"^^ . - "rat" . - "apid.interactions" . - "h2o"^^ . - . - "Orphanet" . - "false"^^ . - _:N640b18da69e24f0fb18c32598a428ad3 . - "botany" . - . - "false"^^ . - . - . - . - . - "pathway" . - "unipathway.pathway" . - "mouse" . - "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."^^ . - . - . - . - . - . - "Sequencing Initiative Suomi" . - . - "http://purl.obolibrary.org/obo/XLMOD_$1"^^ . - . - "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . - . - . - "false"^^ . - "virology" . - . - . - "Michael K. Gilson" . - . - . - . - "bel" . - . - "stoeckrt@pcbi.upenn.edu" . - "http://cbg.garvan.unsw.edu.au/pina/interactome.oneP.do?showExtend=null&ac="^^ . - . - . - "Ensembl Gene" . - . - . - "homd.taxon" . - . - . - . - . + . + "ontology" . + . + . + . + "Scientific Information Retrieval and Exchange Network" . + . + . + . + "structural biology" . + . + . + "http://purl.dataone.org/odo/SENSO_$1"^^ . + "http://autism.mindspec.org/GeneDetail/$1"^^ . + . + "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . + "9606"^^ . + "AB016785"^^ . + . + . + "90806"^^ . + . + "Yeast Phenotype Ontology" . + . + . + . + . + "molecular" . + "^\\d{7}$"^^ . + . + "strain" . + . + . + "bsweeney@ebi.ac.uk" . + "Cooperative Patent Classification" . + "transgenic" . + "systems biology" . + . + . + . + . + . + "Beilstein" . + "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."^^ . + "The Signaling Gateway provides information on mammalian proteins involved in cellular signaling."^^ . + . + "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."^^ . + . + "atol" . + . + . + "SBML RDF Vocabulary" . + . + "biomedical science" . + "pathway" . + "false"^^ . + "http://www.candidagenome.org/cgi-bin/locus.pl?dbid="^^ . + . + . + . + . + "^\\d{4}$"^^ . + . + . + . + "IPR" . + "5621"^^ . + "16S rRNA gene database" . + "life science" . + . + . + "imaging" . + "GPST000024"^^ . + . + "Open Data Commons for Traumatic Brain Injury" . + . + "medicine" . + . + . + . + . + "go.model" . + . + . + . + . + . + . + "vasilevs@ohsu.edu" . + . + . + . + . + "false"^^ . + "Resource for the community to store, retrieve, search, reference, and reuse CellML models."^^ . + "animal" . + . + "http://database.deepsolar.space:18080/dbs/nlfff/"^^ . + "Vaccine Ontology" . + "protein" . + . + . + . + "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."^^ . + . + . + "beetlebase" . + . + . + . + "https://www.picb.ac.cn/limore/cellLines/single?para="^^ . + . + . + "thesaurus" . + "ComplexPortal" . + . + . + . + . + . + . + "computational biology" . + . + . + "xenbase" . + . + . + "google.patent" . + "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID="^^ . + "identifierPattern"^^ . + "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."^^ . + . + . + . + "The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism."^^ . + "Tom Gillespie" . + . + "http://ratmap.org/Showgene.php?gene_stable_id="^^ . + . + . + "^\\d{7}$"^^ . + "https://bioregistry.io/nsrrc:"^^ . + . + "false"^^ . + "http://purl.obolibrary.org/obo/ZEA_$1"^^ . + "data analysis service" . + . + "ChiCTR2300070727"^^ . + . + "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'."^^ . + . + "http://bioportal.bioontology.org/ontologies/$1"^^ . + . + . + . + "^\\d+$"^^ . + "SwissLipid" . + . + . + . + "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" . +_:N3b2786467c704005b88c4abc40a2e8e2 "Plant Ontology Administrators" . + . + . + . + "agriculture" . + "https://ontology.iedb.org/ontology/ONTIE_$1"^^ . + . + . + . + "A0001"^^ . + . + . + "protein structure" . + "creeas@gmail.com" . + . + . + . + "d.craik@imb.uq.edu.au" . + . + . + . + . + . + "The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate." . + "1374"^^ . + . + . + . + "^ST[0-9]{6}$"^^ . + "0000204"^^ . + . + . + . + "^\\d+$"^^ . + "https://www.ebi.ac.uk/intact/interaction/"^^ . + "dommino" . + "^(Q|P)\\d+$"^^ . + . + . + . + . + . + . + . + "01.01.005"^^ . + . + . + . + . + . + . + . + . + "zebrafish line" . + "TreeFam" . + "rs" . + "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . + "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id=$1"^^ . + "78073"^^ . + . + . + "^R-[A-Z]{3}-\\d+(-\\d+)?(\\.\\d+)?$"^^ . + "false"^^ . + . + "sdap" . +_:N2c2c85a20d454e07a2737aeb48617251 "helpdesk@cropontology-curationtool.org" . + "dna" . + . + . + . + . + . + . + "^([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+)?$"^^ . + "false"^^ . + . + "^[0-9A-Z]{4}[0-9A-Z]{14}[0-9A-Z]{2}$"^^ . + . + . + . + . + "Neural ElectroMagnetic Ontology" . + . + . + . + . + "Human Protein Atlas tissue profile information" . + "mesh" . + "false"^^ . + "https://senselab.med.yale.edu/ModelDB/ModelList?id=$1"^^ . + "^(?:\\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\\d+)?)$"^^ . + . + . + "ontology" . + "lei" . + . + . + . + "genome" . + "https://cellbank.nibiohn.go.jp/~cellbank/en/search_res_det.cgi?RNO=$1"^^ . + "translational medicine" . + . + "false"^^ . + . + . + "Glycan Naming and Subsumption Ontology" . + "sibo" . + "diseases" . + . + "icd10cm" . + "https://registry.identifiers.org/registry?query=MIR:"^^ . + "false"^^ . + . + "https://github.com/geneontology/go-site/blob/master/metadata/gorefs/README.md#goref"^^ . + . + . + . + "false"^^ . + . + . + . + . + . + . + "AntWeb" . + . + "p3db.protein" . + . + . + . + "knapsack" . + . + . + "Agricultural Online Access" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "00020134"^^ . + "false"^^ . + . + "Core Ontology for Biology and Biomedicine" . + . + "CHEMBL4303805"^^ . + . + . + "omia" . + "Rudolf T. Pillich" . + "domain" . + . + . + "protcom" . + . + . + . + . + . + "00000105"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "http://multicellds.org/MultiCellDB/"^^ . + "false"^^ . + . + . + . + . + "^\\d{7}$"^^ . + . + "http://aber-owl.net/ontology/$1/#/Browse/" . + . + "obo" . + "life science" . + . + "https://horizondiscovery.com/en/search?searchterm=$1"^^ . + . +_:N13bb372bbe454a47a953e75ba60f7f8d "Pierre Sprumont" . + . + . + "Bibliometric Data Ontology" . + "ordo.orphanet@inserm.fr" . + . + . + . + "comparative genomics" . + . + "PDB Structure" . + "software engineering" . + . + . + "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."^^ . + "enzyme" . + "http://purl.obolibrary.org/obo/OlatDv_$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)."^^ . + . + . . - "false"^^ . - . - . - . - . - . - . - "The TCTR was estabished in 2009 and has been operated by Clinical Research Collaboration Network (CRCN), an organization under the Medical Research Foundation, which is a non-profit organization, and financially supported by Thailand Center of Excellence for Life Sciences (TCELS). CRCN has been retitled the Medical Research Network (MedResNet) since June 15, 2012. (from homepage)"^^ . - . - "geoinformatics" . - "http://wodaklab.org/iRefWeb/interaction/show/"^^ . - . - . - . - . - . - . - . - . - . - _:N7462add7e86d4deea995dffb95f5cd6b . - . - . - . - . - . - . - "https://www.aapc.com/codes/cpt-codes/$1"^^ . - "http://www.nlm.nih.gov/medlineplus/ency/article/$1.htm"^^ . - "^[0-9a-fA-F]{8}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . - . - . - . - "Ecological terms"^^ . - "0440"^^ . - . - . - "false"^^ . - . - . - "BioNumbers" . - . - . - "Geonamaes" . - . - "https://www.animalgenome.org/CorrDB/q/?id=CorrID:"^^ . - . - . - "http://www.mmmp.org/MMMP/public/biomap/viewBiomap.mmmp?id=$1"^^ . - . - . - . - "phylogenetics" . - . - . - . - . - . - . - . - . - . - . - . - "Ontology for Avida digital evolution platform" . - . - . - . - . - . - . - "true"^^ . - . - . - . - "Coli Genetic Stock Center" . - . - . - . - . - . - "false"^^ . - "^\\d+$"^^ . - . - . - . - . - "William Hogan" . - . - . - "life science" . - . - . - . - . - . - "obo" . - . - . - "0100002"^^ . - "obo" . - . - . - . - "https://bioregistry.io/cubedb:"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - "Cell line collections (Providers)"^^ . - . - "molecular biology" . - . - "idomal" . - "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . - . - . - . - . - . - . - "https://chemkg.github.io/chemrof/"^^ . - . - "^\\w+$"^^ . - . - . - . - . - "true"^^ . - . - . - . - "UniProt Isoform" . - . - . - . - "rateRule"^^ . - . - . - . - "life science" . - "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . - . - . - "0100010"^^ . - . - "Collection"^^ . - . - . - . - . - . - . - . - . - "KEGG Orthology" . - "3"^^ . - . - . - . - . - "animal husbandry" . - "ricegap" . - . -_:N618fd1ab6a6a4e379c6d1f4f1cd3173d "Crop Ontology Helpdesk" . - . - "NIF Standard Ontology: Investigations" . - . - "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no="^^ . - . - . - . - "1122888"^^ . - . - . - . + . + "BirdBase" . + "https://www.webofscience.com/wos/woscc/full-record/WOS:"^^ . + . + . + . + "life science" . + . +_:Nc576373e3ad5403485c64e5f575d52d2 "Albert Goldfain" . + . + "Issaku Yamada" . + "Jennifer Smith" . + "https://plants.ensembl.org/id/$1"^^ . + . + . + . + "BCRC Strain Collection Catalog" . + "^MCDS_S_[a-zA-Z0-9]{1,10}$"^^ . + "opl" . + . + "biochemistry" . + . + . + . + "imgt.primerdb" . + . + . + . + . + . + "w.simpson@orcid.org" . + . + . + . + . + . + . + "false"^^ . + . + . + . + "Gary L Andersen" . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + . + . + . +_:Nec73fc3f397b45e4aa2ecdf3bfe3be4c "support@bioontology.org" . + . + "nutritional science" . + . + . + "961"^^ . + "LNC" . + . + . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/variation/$1"^^ . + "anatomy" . + . + . + . + . + "http://id.who.int/icd/entity/$1"^^ . + "ontology" . + "A_24_P98555"^^ . + . + . + "BEI Resources" . + "small molecule" . + . + . + . + "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."^^ . + . + . + . + "subject" . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/$1"^^ . + . + . + . + "true"^^ . + . + . + . + . + "hc.din" . + . + "false"^^ . + "obo" . + . + . + "anatomy" . + . + . + . + . + . + . + "http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=Project&ProjectID="^^ . + . + "^\\d+$"^^ . + . + "Digital Object Identifier" . + . + "false"^^ . + . + "drug metabolism" . + . + . + . + . + "FMA_RETIRED" . + "ICD10CM" . + . + "false"^^ . + "1050"^^ . + "cp" . + "Lepidoptera Anatomy Ontology" . + "organic molecular chemistry" . + . + "false"^^ . + "chemical" . + "CSP2005" . + . + "EG10173"^^ . + . + "ontology" . + . + . + . + "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . + . + "https://www.kerafast.com/Search?SearchTerm="$1""^^ . + "201022999"^^ . + . + . +_:Na6cd28f60aa44ebea3fa480cf4f65265 "ICARDA Ethiopia" . + "false"^^ . + "cvdo" . + "ontology and terminology" . + . + "embryonic stem cell" . + . + "^ZDB\\-\\w+\\-\\d+\\-\\d+$"^^ . + . + . + "spike00001"^^ . + . + . + "protein" . + . + . + . + "^\\d+$"^^ . + . + . + . + "pesticides" . + "https://www.cellosaurus.org/CVCL_$1"^^ . + . + . + "https://biopragmatics.github.io/providers/hog/$1"^^ . + . + "false"^^ . + . + . + . + . + "Funding, Research Administration and Projects Ontology" . + "true"^^ . + "FOOD00020"^^ . + . + . + . + "Simple Knowledge Organization System" . + "FaceBase Data Repository" . + . + "false"^^ . + . + . + "ontology" . + . + . + "UM-BBD_pathwayID" . + . + . + . + . + . + . + "kegg" . + . + . + . + "^GN_[A-Za-z0-9_:]+$"^^ . + . + . + . + "structure" . + "Snapshot" . + . + . + . + . + . + . + "cheminformatics" . + . + "ProtoNet ProteinCard" . + . + . + . + . + . + "biology" . + . + . + "https://bioregistry.io/diseasesdb:"^^ . + "^[A-Z0-9]{6,7}$"^^ . + . + . + "false"^^ . + . + . + "false"^^ . + "http://www.wikidata.org/entity/$1" . + . + "jason.stajich@ucr.edu" . + . + . + "icdom:8500_3"^^ . + . + . + . + . + . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name=$1"^^ . + "http://www.alzgene.org/geneoverview.asp?geneid=$1"^^ . + "stn" . + . + "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."^^ . + . + . + "small molecule" . + "12"^^ . + "molecular infection biology" . + "pathway" . + "biodiversity" . + . + . + "anne.morgat@sib.swiss" . + . + . + . + "AGRICOLA_ID" . + . + "false"^^ . + "http://www.orpha.net/ORDO/Orphanet_"^^ . + . + . + "protein" . + "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."^^ . + . + . + "ama-cpt" . + . + . + . + "The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."^^ . + . + . + . + . + "Merck Millipore (EMD Millipore)" . + . + . + . + "The Ontology of Genes and Genomes" . + "person" . + "glycomics" . + . + . + "computational chemistry" . + . + . + "83088"^^ . + "false"^^ . + "https://w3id.org/oc/corpus/$1"^^ . + "subject agnostic" . + . + . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/MONDO_"^^ . + "dna" . + . + . + . + "false"^^ . + . + "protein" . + . + "https://go.drugbank.com/reactions/$1"^^ . + . + "false"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/$1"^^ . + . + "1868"^^ . + . + "Population and Community Ontology" . + . + "metnetdb" . + . + "false"^^ . + . + "ontology" . + "false"^^ . + . + . + . + . + . + "ohmi" . + . + "https://apps.usgs.gov/thesaurus/term-simple.php?thcode=3&code=$1"^^ . + "false"^^ . + . + . + . + "Barry Smith" . + "false"^^ . + . + "JRBC Cell Bank" . + . + "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."^^ . + "00000001"^^ . + "bioinformatics" . + . + . . - . - "The NRFC was established at ICAR-National Bureau of Fish Genetic Resources, Lucknow in the form of a research project entitled ‘Establishment of a National Repository at NBFGR, Lucknow for conservation and characterization of fish cell lines’ during 09 November, 2010 to 08 November, 2014 with the financial support from Department of Biotechnology, Govt. of India, New Delhi. NRFC aims to receive, authenticate, store and supply the fish cell lines to the researchers and academicians for Research & Development works and to serve as a National Referral Centre for fish cell lines in the country. NRFC also aims to provide need-based support for training and education to stakeholders. (from homepage)"^^ . - . - . - . - "Theoretical explanation of to a purely spatiotemporal ontology of change and process, as part of a modular ontology of the dynamic features of reality."^^ . - . - "The Health Care Provider Taxonomy code set is an external, nonmedical data code set designed for use in an electronic environment, specifically within the ASC X12N Health Care transactions. This includes the transactions mandated under HIPAA.\n\nThe taxonomy code is a unique alphanumeric code, ten characters in length. The code set is structured into three distinct \"Levels\" including Provider Grouping, Classification, and Area of Specialization.\n\n - **Level I, Provider Grouping** A major grouping of service(s) or occupation(s) of health care providers. For example: Allopathic & Osteopathic Physicians, Dental Providers, Hospitals, etc.\n - **Level II, Classification** A more specific service or occupation related to the Provider Grouping. For example, the Classification for Allopathic & Osteopathic Physicians is based upon the General Specialty Certificates as issued by the appropriate national boards. The following boards will however, have their general certificates appear as Level III areas of specialization strictly due to display limitations of the code set for Boards that have multiple general certificates: Medical Genetics, Preventive Medicine, Psychiatry & Neurology, Radiology, Surgery, Otolaryngology, Pathology.\n - **Level III, Area of Specialization** A more specialized area of the Classification in which a provider chooses to practice or make services available. For example, the Area of Specialization for provider grouping Allopathic & Osteopathic Physicians is based upon the Subspecialty Certificates as issued by the appropriate national boards."^^ . - "false"^^ . - "MMP3888430"^^ . - "disdriv" . - . - "AC119"^^ . - . - . - "https://cropontology.org/rdf/CO_346:$1"^^ . - "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."^^ . - "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."^^ . - . - . - . - "ensembl.bacteria" . - "genetics" . - . - . - "life science" . - . - "kegg.pathway" . - "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."^^ . - "https://www.ebi.ac.uk/biomodels/"^^ . - "P53350"^^ . - "http://bioportal.bioontology.org/ontologies/$1"^^ . - "metanetx.chemical" . - "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."^^ . - . - "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=$1"^^ . - "obo" . - . - . - . - "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."^^ . - "structure" . - . - . - "AOPWiki (Stressor)" . - "A download link for the given resource" . - . - "http://mods.rna.albany.edu/mods/modifications/view/$1"^^ . - "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id="^^ . + "false"^^ . + . + . + . + . + . + . + "https://cropontology.org/rdf/CO_347:$1"^^ . + . + "gnome" . + "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . + . + "wujm@bjmu.edu.cn" . + . + . + "hannele.laivuori@helsinki.fi" . + . + . + . + . + "https://go.drugbank.com/salts/$1"^^ . + . + . + "http://id.nlm.nih.gov/mesh/vocab#$1"^^ . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "mmo" . + . + . + . + . + . + . + . + "ThermoFisher is a life sciences supply vendor."^^ . + "XB-GENE-922462"^^ . + . + . + "anatomy" . + . + . + "genome" . + . + . + . + "obo" . + . + . + . + . + . + . + "molecules" . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO="^^ . + "https://bionumbers.hms.harvard.edu/bionumber.aspx?id=$1"^^ . + "^\\d+$"^^ . + . + . + . + "Laurent Duret" . + . + . + . + "false"^^ . + . + . + "DOOR (Database for prOkaryotic OpeRons) contains computationally predicted operons of all the sequenced prokaryotic genomes. It includes operons for RNA genes."^^ . + "molecular biology" . + . + "false"^^ . + "false"^^ . + "https://biopragmatics.github.io/providers/schem/"^^ . + "true"^^ . + "https://senselab.med.yale.edu/ModelDB/ModelList?id="^^ . + . + . + "^\\w+(\\.\\d+)$"^^ . + . + "KEGG Metagenome" . + . + . + . + . + . + "https://taibnet.sinica.edu.tw/eng/taibnet_species_detail.php?name_code="^^ . + . + "protein" . + . + . + . + "OIDs provide a persistent identification of objects based on a hierarchical structure of Registration Authorities (RA), where each parent has an object identifier and allocates object identifiers to child nodes."^^ . + . + . + . + "The JRC Data Catalogue gives access to the multidisciplinary data produced and maintained by the Joint Research Centre, the European Commission's in-house science service providing independent scientific advice and support to policies of the European Union."^^ . + . + . + . + "false"^^ . + "ontoneo" . + . + . + . + "The European Registry of Materials is a simple registry with the sole purpose to mint material identifiers to be used by research projects throughout the life cycle of their project."^^ . + . + . + "genetic resource" . + . + . + . + . + . + "hpo" . + "Virtual International Authority File" . + . + . + "wikidata" . + . + . + . + "ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information."^^ . + . + "ontology" . + . + . + "https://pubchem.ncbi.nlm.nih.gov/substance/"^^ . + "OPMI is a biomedical ontology in the area of precision medicine and its related investigations. It is community-driven and developed by following the OBO Foundry ontology development principles."^^ . + "environmental science" . + "neurobiology" . + "The Protein Ensemble Database is an open access database for the deposition of structural ensembles, including intrinsically disordered proteins."^^ . + "http://purl.obolibrary.org/obo/NIF_CELL_"^^ . + "biomedical science" . + "Contains information about cells and data sheets related to transfection."^^ . + "^[A-Z]{14}\\-[A-Z]{10}(\\-[A-Z])$"^^ . + . + "polcaes@gmail.com" . + . + "http://purl.obolibrary.org/obo/T4FS_$1"^^ . + . + . + . + . + "false"^^ . + "^(\\d{8}|(\\w+\\d+\\w+))$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_IME.php?ime_id=$1_IME"^^ . + . + "Alzforum_mut" . + . + "5688061"^^ . + . + . + "dunand@lrsv.ups-tlse.fr" . + . + . + . + . + "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName="^^ . + . + "0000006"^^ . + "false"^^ . + "http://elm.eu.org/elms/elmPages/$1.html"^^ . . - "vertebrate" . - "FuTRES Ontology of Vertebrate Traits" . - . - . - . - . - . - . - . - . - . - "^\\d{3}\\.\\d{2}$"^^ . - "violinID" . - . - . - . - "false"^^ . - . - . - "000000001"^^ . - . - . - . - "eagle-i" . - . - . - . - . - . - . - "bioinformatics" . - . - . - . - "false"^^ . - "hdr" . - . - . - "keilbeck@genetics.utah.edu" . - "gene" . - . - . - "hivreagentprogram" . - "hpm.peptide" . - "^PA\\d+$"^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/SEP_$1"^^ . - . - . - "https://www.merckmillipore.com/catalogue/item/"^^ . - . - . - . - "The localization and quantitation atlas of the yeast proteome" . - "SMP0000219"^^ . - . - . - "genomic sequence" . - . - . - . - . - . - . - . - "https://www.webelements.com/"^^ . - "NLXSUB covers subcellular entities similar to the cellular component branch of the Gene Ontology (GO)."^^ . - . - . - . - . - "false"^^ . - . - "https://www.ebi.ac.uk/ega/studies/$1"^^ . - . - . - . - . - "https://cellmodelpassports.sanger.ac.uk/passports/"^^ . - "19210-3"^^ . - . - "beta-carotene"^^ . - . - . - . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/MFOMD_$1"^^ . + "protocol" . + . + . + . + "One of the many goals of the BCBC was to develop and maintain databases of useful research resources. A total of 813 different scientific resources were generated and submitted by BCBC investigators over the 14 years it existed. Information pertaining to 495 selected resources, judged to be the most scientifically-useful, has been converted into a static catalog, as shown below. In addition, the metadata for these 495 resources have been transferred to dkNET in the form of RDF descriptors, and all genomics data have been deposited to either ArrayExpress or GEO. [from homepage]"^^ . + "Arabidopsis Information Portal" . + "dragondb.dna" . + "zebrafish" . + "bioregistry.collection" . + . + "https://www.wikidata.org" . + . + . + . + . + . + . + "0000003"^^ . + "cell biology" . + . + . + "^\\d+$"^^ . + . + . + . + . + "https://www.disprot.org/idpo/IDPO:$1"^^ . + "biomedical science" . + "01027931310-01022252312"^^ . + . + "1018"^^ . + "http://www.genoscope.cns.fr/agc/microscope/mage/info.php?id="^^ . + . + "obo" . + . + . + . + . + "pfey@northwestern.edu" . + . + . + . + . + "http://iflastandards.info/ns/fr/frbr/frbrer/"^^ . + "false"^^ . + . + "http://www.nematodes.org/nembase4/cluster.php?cluster="^^ . + "life science" . + . + . + "^\\d+$"^^ . + . + . + . + "01001"^^ . + . + "life science" . + . + "1"^^ . + . + "mgiglio@som.umaryland.edu" . + . + . + . + . + . + . + . + . + "https://rism.online/"^^ . + "seed" . + . + "ngl" . + . + "http://www.subtiwiki.uni-goettingen.de/wiki/index.php/"^^ . + . + . + . + "https://doulix.com/constructs/$1"^^ . + . + . + . + . + . + . + . + . + "genetically modified pig" . + "Gemina Symptom Ontology" . + "A vocabulary about resources, similar to bioregistry.schema, venn, idot, etc."^^ . + . + "CHEBI"^^ . + . + . + "Information for ligands in the BRENDA database."^^ . + . + "false"^^ . + "Regulation of Transcription Ontology" . + . + "false"^^ . + "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode=$1"^^ . + "AgentIdentifierScheme"^^ . + . + . + "2639"^^ . + . +_:N947c2ef4044f49f18bd9f0caf7c87ee6 "Intellectual.PropertyServices@ama-assn.org" . + . + "18"^^ . + . + . + . + . + . + . + . + . + . + . + "DataNode"^^ . + . + "The NHMRC Australian PhenomeBank (APB) is a non-profit repository of mouse strains used in Medical Research. The database allows you to search for murine strains, housed or archived in Australia, carrying mutations in particular genes, strains with transgenic alterations and for mice with particular phenotypes. 1876 publicly available strains, 922 genes, 439 transgenes The APB has two roles: Provide and maintain a central database of genetically modified mice held in Australia either live or as cryopreserved material; Establish and maintain a mouse strain archive. Strains are archived as cryopreserved sperm or embryos. [from RRID]"^^ . + "Patrice Buche" . + "obo" . + . + "Homologous Organ Groups" . + . + . + . + . + "ontology" . + . + "nomen" . + "false"^^ . + . + . + . + . + "plasmid" . + . + . + "false"^^ . + . + "https://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1"^^ . + . + "j.a.moore@dundee.ac.uk" . + "63"^^ . + . + "https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl#$1"^^ . + . + . + . + "SKIP001214"^^ . + . + . + "sequence" . + . + . + . + . + . + . + "hoelzel" . + . + . + "genome" . + . + . + . + . + "The Library of Network-Based Cellular Signatures (LINCS) Program aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents. The LINCS small molecule collection is used as perturbagens in LINCS experiments. The small molecule metadata includes substance-specific batch information provided by each LINCS Data and Signature Generation Center (DSGC)."^^ . + "^DI-\\d{5}$"^^ . + . + "MycoBrowser smegmatis" . + "Dylan McGagh" . + "false"^^ . + "hl7.v2codesystem" . + . + . + . + . + "biomedical science" . + "http://purl.obolibrary.org/obo/LABO_"^^ . + . + . + . + . + . + . + "FlyBase Gene" . + "00001"^^ . + "human disease model" . + . + "neurology" . + . + . + . + . + "5359"^^ . + . + "Digital archive of scholarly articles" . + . + _:Nd0e161fdfff74c018182a797e85a4917 . + . + . + "molecular genetics" . + "PathBank" . + "Sugar Kelp trait ontology" . + "radiology" . + . + "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . + . + . + "0000109"^^ . + "false"^^ . + "ontology" . + . + . + "false"^^ . + "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."^^ . + "https://www.wormbase.org/species/c_elegans/rnai/"^^ . + . + "0000041"^^ . + . + . + "NLXBR covers brain regions from the PHT00 macaque parcellation, Paxinos, Huang, and Tog The Rhesus Monkey Brain In Stereotaxic Coordinates (1999)."^^ . + . + "biochemistry" . + "DB-0174"^^ . + . + . + "agriculture" . + . + "phylogenetics" . + "P00024"^^ . + . + . + "has prefix" . + "27267"^^ . + . + . + . + "dna" . + "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."^^ . + "epidemiology" . + "https://dbpedia.org/ontology/"^^ . + . + "https://data.4dnucleome.org/biosources/$1"^^ . + "T30002"^^ . + . + "structure" . + . + "health science" . + . + "comparative genomics" . + . + . + . + . + . + "false"^^ . + . + "eaglei" . + . + "false"^^ . + . + "false"^^ . + "Broad Fungal Genome Initiative" . + . + . + . + "https://pharmacodb.ca/datasets/"^^ . + "CATH Protein Structural Domain Superfamily" . + "LexicalMatching"^^ . + "GOLD metadata" . + . + . + . + "^[0-9]+$"^^ . + . + "ontology" . + . + . + . + . + . + "Protein Model Portal" . + . + "ChemIDplus" . + . + . + "56586"^^ . + "envipath" . + "http://purl.obolibrary.org/obo/VSAO_$1"^^ . + "- 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."^^ . + . + . + . + "http://modelseed.org/biochem/compounds/"^^ . + . + . + "epidemiology" . + . + "https://www.genecards.org/cgi-bin/carddisp.pl?gene=$1"^^ . + . + . + . + . + . + . + . + . + "Chris Mungall" . + . + . + "5282"^^ . + . + "H00076"^^ . + . + . + . +_:Nec5a327b3e5848b4b67c4f1df2c7dada "more.info@allotrope.org" . + . + . + "EC" . + "obo" . + "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."^^ . + "false"^^ . + . + . + "https://biopragmatics.github.io/providers/peff/$1"^^ . + . + . + "life science" . + . + "0000000"^^ . + . + . + . + . + . + . + . + "2404"^^ . + "241"^^ . + "http://uri.neuinfo.org/nif/nifstd/"^^ . + . + . + "false"^^ . + . + . + . + . + . + . + . + "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. "^^ . + "fisheries science" . + . + . + . + . + "https://raw.githubusercontent.com/github/linguist/master/lib/linguist/languages.yml#"^^ . + . + . + . + . + . + . + "false"^^ . + . + "The Coleoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of beetles in biodiversity research."^^ . + "ASRP1423"^^ . + . + . + . + "http://purl.org/spar/pro/$1"^^ . + . + . + . + "An OBO-compliant ontology representing the entities referenced by the SDGs, their targets, and indicators."^^ . + "experimental plant" . + "^\\d+$"^^ . + . + . + "false"^^ . + . + "Paul Fabry" . + . + . + "false"^^ . + . + . + . + . + "artificial intelligence" . + "Viral Bioinformatics Resource Center" . + . + . + . + . + . + . + "sequence" . + . + . + . + "NBK331"^^ . + . + "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . + "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."^^ . + "structure" . + "http://aps.unmc.edu/AP/database/query_output.php?ID=$1"^^ . + "https://www.uniprot.org/proteomes/$1"^^ . + . + . + "life science" . + "Jennifer C. Giron" . + "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . + . + . + "obo" . + . + . + "ENSG00000026508"^^ . + . + . + "^\\w+$"^^ . + "http://www.vbase2.org/vgene.php?id=$1"^^ . + . + "cutg" . + "worm" . + . + "transcriptomics" . + "^\\d+$"^^ . + . + "^\\d+$"^^ . + . + "life science" . + "MycoBrowser leprae" . + . + . + "gene" . + "APID (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). Interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier."^^ . + . + . + . + . + . + . + . + . + "^CNP\\d{7}$"^^ . + . + . + "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."^^ . + . + . + "neurobiology" . + "chemistry" . + . + . + . + "protein" . + "http://igsn.org/"^^ . + . + "http://purl.obolibrary.org/obo/OOSTT_$1"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "068078"^^ . + . + "false"^^ . + . + . . - "Uber-anatomy ontology" . - . - . - "Tatsuya Kushida" . - . - . - "Stefanie Seltmann" . - . - "dmendez@ebi.ac.uk" . - . - . - . - . - . - . - . - . - "plasmid" . - . - . - . - . - . - . - . - . - "false"^^ . - . - "genetic engineering" . - . - . - . - . - . - . - "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . - "sweetrealm" . - . - "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://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - . - "biomedical science" . - . - "https://go.drugbank.com/bio_entities/"^^ . - . - "ontology" . - . - . - . - "false"^^ . - . - "https://www.eionet.europa.eu/gemet/en/concept/"^^ . - . - . - "The Unified Medical Language System is a repository of biomedical vocabularies. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank."^^ . - . - . - . - . - . - . - . - . - . - . -_:N848769ba5c1f4a738b2435e71207d3ee "johardi@stanford.edu" . - . - . - "mwitt@purdue.edu" . - . - . - "^(E|D|S)RR[0-9]{6,}$"^^ . - "Cell line collections (Providers)"^^ . - . - "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/"^^ . + "http://scipion.i2pc.es/ontology/CRYOEM_$1"^^ . + "corum" . + . + "life science" . + . + "http://www.proteinmodelportal.org/query/uniprot/$1"^^ . + "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://bioregistry.io/cubedb:"^^ . + "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use."^^ . + . . - "uniprot.keyword" . - . - . - . - . - . - "live mouse" . - "ontology" . - "eukaryotic" . - "Katy Börner" . - . - "Clytia hemisphaerica Development and Anatomy Ontology" . - . + . + "false"^^ . + "http://kinase.bioinformatics.tw/showall.jsp?type=Kinase&info=Gene&name=$1&drawing=0&sorting=0&kinome=1"^^ . + "Nonribosomal Peptides Database" . + "http://www.w3.org/2003/11/swrl#"^^ . + . + "The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process."^^ . + . + . + . + "Clement Jonquet" . + . + "http://purl.obolibrary.org/obo/PRIDE_"^^ . + . + "General Multilingual Environmental Thesaurus" . + "life science" . + "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IMR&id="^^ . + . + . + . + . + "CRISPRdb" . + . + . + "https://metacyc.org/META/NEW-IMAGE?type=REACTION&object="^^ . + . + . + . +_:Ncacac89b73af4494b2963250287dad6c "Stephan Schurer" . + . + "lbctr" . + "SAO describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules."^^ . + . + "molecular microbiology" . + . + "false"^^ . + . + . + "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."^^ . + . + . + . + "false"^^ . + "KEGG Drug Group" . + . + "BioLegend" . + "World Wildlife Fund Ecoregion" . + . + . + . + . + "http://rna.rega.kuleuven.be/cgi-bin/rnamods/rnashow.pl?$1"^^ . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + . + "life science" . + "The international standard for identifying health measurements, observations, and documents."^^ . + . + . + "pubchem.element" . + . + . + "ProtClustDB" . + "http://purl.obolibrary.org/obo/RO_"^^ . + . + "icdc" . + . + "obo" . + . + . + "4447"^^ . + "J55.713G"^^ . + "registry" . + "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."^^ . + . + . + . + "ontology" . + . + . + "lpt" . + "http://purl.obolibrary.org/obo/WBPhenotype_$1"^^ . + "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."^^ . + "bibliography" . + . + "http://purl.obolibrary.org/obo/TAHE_$1"^^ . + . + . + . + . + . + . + . + "A terminology published by the American Psychiatric Association (APA) for the classification of mental disorders using a common language and standard criteria. [wikipedia]"^^ . + "genetics" . + . + . + . + "xeni.kechagioglou@lifewatch.eu" . + "https://www.ncbi.nlm.nih.gov/snp/$1"^^ . + . + . + . + "true"^^ . +_:N9753b3307f82484cbd3fe4a409beaccf "bert.van.nuffelen@tenforce.com" . + . + "CH_001923"^^ . + . + "^DTXSID\\d+$"^^ . + . + . + "Provides structured controlled vocabularies for the annotation of expressed sequences with respect to anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation and treatment."^^ . + . + . + . + . + . + "hinv.protein" . + "http://www.chemspider.com/inchikey="^^ . + . + . + "SCC111"^^ . + . + . + "http://www.genome.jp/dbget-bin/www_bget?cpd:$1"^^ . + . + . + "Philipp.Bucher@sib.swiss" . + . + "https://lobid.org/gnd/"^^ . + . + . + "0000984"^^ . + . + "worm" . + "Therapies (often drugs) in CIViC are associated with Predictive Evidence Types, which describe sensitivity, resistance or adverse response to therapies when a given variant is present. The Therapy field may also be used to describe more general treatment types and regimes, such as FOLFOX or Radiation, as long as the literature derived Evidence Item makes a scientific association between the Therapy (treatment type) and the presence of the variant."^^ . + . + "EDI_244000"^^ . + . + . + . + . + "https://www.fao.org/fishery/en/species/"^^ . + . + . + . + . + "bcp47" . + "0000509"^^ . + . + "Universal Natural Products Database" . + "^[CN]*\\d{4,7}$"^^ . + "ontology" . + "cameo" . + . + "https://reaxys.emolecules.com/cgi-bin/more?vid=$1"^^ . + "https://www.wikidata.org/wiki/Property:$1"^^ . + . + . + . + . + . + "http://www.ymdb.ca/compounds/$1"^^ . + . + . + . + . + "comparative genomics" . + . + . + . + "interaction" . + . + "https://purl.dataone.org/odo/SALMON_$1"^^ . + . + . + "^\\d+$"^^ . + "environmental science" . + . + "NLXRES" . + . + . + . + . + . + . + . + . + "biology" . + . + . + . + . + . + . + "DUO is an ontology which represent data use conditions."^^ . + . + . + "https://omim.org/MIM:$1"^^ . + "http://purl.org/spar/pro/"^^ . + "^\\d+$"^^ . + . + . + "http://linkedlifedata.com/resource/umls/id/$1"^^ . + . + . + "http://cdb.ics.uci.edu/cgibin/ChemicalDetailWeb.py?chemical_id=$1"^^ . + . + . + "Cell line collections (Providers)"^^ . + . + . + "https://cropontology.org/rdf/CO_331:"^^ . + "http://sideeffects.embl.de/drugs/"^^ . + "^r\\d+$"^^ . + "Represents chemical kinetic reaction mechanisms."^^ . + . + . + . + . + . + . + "interaction" . + "medicinal chemistry" . + . + "obo" . + . + "semantic web" . + . + "matus.kalas@uib.no" . + . + . + . + . + "life science" . + . + . + . + "Willy Wong" . + . + . + "false"^^ . + "https://cropontology.org/rdf/CO_324:$1"^^ . + "sed-ml.level-1.version-1"^^ . +_:Nab17e8af5a024810b922e139a33dedf0 "Crop Ontology Helpdesk" . + . + . + . + "false"^^ . + . + "false"^^ . + "baoym@big.ac.cn" . + . + . + . + . + . + "uo" . + . + . + "botany" . + "cubedb" . + . + . + . + . + "https://w3id.org/seo#$1"^^ . + "https://prefix.cc/$1" . + "false"^^ . + "Activity Streams" . + "1537"^^ . + . + . + "10020.2"^^ . + . + "5112"^^ . + "Bgee organ" . + . + . + "false"^^ . + . + . + . + "https://transyt.bio.di.uminho.pt/reactions/"^^ . + "AcknowledgementCondition"^^ . + "oncotree" . + . + . + "citlalli.mejiaalmonte@gmail.com" . + "^MIMAT\\d{7}$"^^ . + "phylomedb" . + . + "^\\d+$"^^ . + "false"^^ . + . + "BTO" . + . + . + "A10BA02"^^ . + . + . + . + "structure" . + . + . + . + . + . + "The SciCrunch Registry holds metadata records that describe digital resources, e.g., software, databases, projects and also services. Most of these are produced as a result of government funding and are available to the scientific community. Resources are manually curated to make sure the information is accurate. We also use a web crawler to find literature mentions for the resources."^^ . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "Gm00047"^^ . + "skos" . + . + . + . + . + . + "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."^^ . + "dal.alghamdi92@gmail.com" . + . + . + "https://www.ebi.ac.uk/unichem/compoundsources?type=uci&compound="^^ . + . + . + . + . + "obo" . + "false"^^ . + . + "The Japan Chemical Substance Dictionary is an organic compound dictionary database prepared by the Japan Science and Technology Agency (JST)."^^ . + . + . + . + "carrine.blank@umontana.edu" . + . + . + . + . + . + "^(\\w+)?\\d+$"^^ . + . + . + . + "https://www.biolegend.com/Default.aspx?ID=6664&productid=$1"^^ . + . + "Networked Knowledge Organization Systems/Services/Structures" . + . + . + . + "help-swissmodel@unibas.ch" . + . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "comparative genomics" . + . + . + . + . + "^\\d+$"^^ . + "biostudies" . + . + . + . + . + . + . + "Wyeth W. Wasserman" . "https://w3id.org/nfdi4cat/voc4cat_$1"^^ . - "http://cgsc.biology.yale.edu/Site.php?ID="^^ . - "http://purl.org/dc/elements/1.1/$1"^^ . - . - . - . - "^\\d{7}$"^^ . - "agriculture" . - "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym=$1"^^ . - . - . - "PSI Extended File Format" . - . - . - . - . - . - "subject agnostic" . - . - . - "National Microbiome Data Collaborative" . - "genome" . - . - . - . - . - . - "^[AEP]-\\w{4}-\\d+$"^^ . - "ECOCYC"^^ . - . - "^\\d+\\.\\d+$"^^ . - . - . - . - . - . - . + "http://yetfasco.ccbr.utoronto.ca/showPFM.php?mot="^^ . + . + "false"^^ . + . + . + _:N2079c6c1c21d4ad782eb69b0c991d0ee . + "http://uri.neuinfo.org/nif/nifstd/nlx_subcell_$1"^^ . + . + . + "National Uniform Claim Committee Taxonomy" . + . + "drug discovery" . + . + . + . + "An ontology for dengue fever."^^ . + . + "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId="^^ . + . + . + . + . + . + "developmental biology" . + . + "^\\d+$"^^ . + . + "Troy Pells" . + . + . + . + . + "ecao" . + . + . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/CDAO_$1"^^ . + "AD834"^^ . + "ontology" . + . + . + . + . + "https://pubchem.ncbi.nlm.nih.gov/substance/$1"^^ . + "https://glycopost.glycosmos.org/entry/"^^ . + "image" . + . + . + . + "life science" . + "64ba"^^ . + . + "^bt\\d+$"^^ . + . + . + . + . + . + . + "https://www.re3data.org/repository/"^^ . + "ontology and terminology" . + . + . + . + . + "false"^^ . + . + "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=$1"^^ . + "obo" . + "variant" . + . + "ontology" . + . + . + . + "OMIMPS" . + . + . + "ontology" . + "github" . + "^\\d+$"^^ . + . + "environmental science" . + . + "UniRule" . + . + . + "The bioRxiv is a preprint server for biology"^^ . + . + . + . + "civic.tid" . + "http://www.jcvi.org/charprotdb/index.cgi/view/$1"^^ . + . + . + "false"^^ . + "https://www.eionet.europa.eu/gemet/en/concept/$1"^^ . + "pharmgkb.pathways" . + . + . + . + "http://rdfs.org/ns/void#"^^ . + "http://www.pharmgkb.org/drug/$1"^^ . + . + . + . + . + . + . + . + "https://www.jax.org/strain/"^^ . + . + "Database of Genotypes and Phenotypes" . + "eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories)."^^ . + . + . + . + "health science" . + . + "frim1"^^ . + . + . + . + . + "6b1"^^ . + . + . + . + . + "obib" . + . + . + . + . + . + "42840"^^ . + "^RID\\d+$"^^ . + "ontology" . + "Python"^^ . + . + "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences."^^ . + . + "0100002"^^ . + . + . + "agriculture" . + . + . + "A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies." . + . + "rebec" . + . + . + . + . + "anatomy" . + . + "immunology" . + "^RBR-\\w+$"^^ . + . + . + "Elementary Multiperspective Material Ontology" . + . + . + . + . + . + "https://drs.microbiomedata.org/objects/$1"^^ . + . + . + . + "https://www.ncbi.nlm.nih.gov/genome/"^^ . + . + . + "^\\d+$"^^ . + . + . + . + . + . + "http://stitch.embl.de/interactions/"^^ . + . + . + "00007294"^^ . + . + . + . + . + . + . + . + . + "dragondb.allele" . + "false"^^ . + "Health Canada Clinical Trials Database" . + . + . + . + . + . + . + . + "ontology" . + "structure" . + . + . + "ontology" . + "Logical Observation Identifiers Names and Codes" . + . + "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . + "http://n2t.net/ark:$1"^^ . + "^(UMR|UMS|UMI|UPR|URA|USR|GDR|EA|FR|SNC|ERL|FRC|FRE|IFR|MOY)\\d+$"^^ . + "https://envipath.org/package/"^^ . + . + "Chemical Entity Materials and Reactions Ontological Framework" . + . + . + . + . + . + . + . + . + . + "https://www.storedb.org/store_v3/download.jsp?fileId=$1"^^ . + "Trushar Shah" . + . + "obo" . + . + . + . + . + "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family."^^ . + "MO000027"^^ . + . + . + . + . + . + "ontology" . + . + . + . + . +_:N1d6d2989305b482cad5c4f3d8442073c "j@deltaflow.com" . + . + "0000121"^^ . + . + . + . + . + . + "false"^^ . + . + . + "ahamosh@jhmi.edu" . + . + "http://purl.obolibrary.org/obo/ICO_"^^ . + "The VIAF® (Virtual International Authority File) combines multiple name authority files into a single OCLC-hosted name authority service. The goal of the service is to lower the cost and increase the utility of library authority files by matching and linking widely-used authority files and making that information available on the Web."^^ . + . + . + . + "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID="^^ . + . + "obo" . + "Internet Standard -- IETF Request for Comments" . + . + "^[0-9]+$"^^ . + "http://purl.obolibrary.org/obo/MC_"^^ . + . + "life science" . + . + . + . + . + "false"^^ . + . + . + . + . + "alzheimer's disease" . + . + "http://scicrunch.org/resolver/SCR_$1"^^ . + "cytology" . + "Eukaryotic Promoter Database" . + . + . + . + "n.lenovere@gmail.com" . + "storedb" . + "0000000"^^ . + . + "http://jcggdb.jp/idb/jcggdb/"^^ . + "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."^^ . + . + "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."^^ . + "small molecule" . + . + "Higher-level classifications of COG Pathways"^^ . + "Rhea, the Annotated Reactions Database" . + . + "http://www-bionet.sscc.ru/sitex/index.php?siteid="^^ . + . + "protein" . + . + . + . + . + . + . + "biomedical science" . + . + . + "false"^^ . + . + . + "Bibliographic data for all the journals, books, audiovisuals, computer software, electronic resources and other materials that are in the library's holdings."^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/ZFS_$1"^^ . + . + . + . + . + . + . + "http://sweetontology.net/matrMineral/"^^ . + . + . + . + . + . + . + . + "EV_0100011"^^ . + . + "https://drs.microbiomedata.org/objects/"^^ . + "Genotype-Tissue Expression" . + . + "VB.Ob.3736.GRSM125"^^ . + "obo" . + "ontology" . + . + "true"^^ . + . + . + "https://www.ebi.ac.uk/gxa/experiments/"^^ . + "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank."^^ . + "ontology" . + . + . + . + "http://proteomecentral.proteomexchange.org/usi/?usi=mzspec:"^^ . + . + . + "^[A-Za-z0-9]+$"^^ . + . + . + . + . + . + "Alliance of Genome Resources Knowledge Base" . + . + . + "https://prosite.expasy.org/$1"^^ . + . + . + . + "false"^^ . + "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."^^ . + "SNOMED_CT_US_2018_03_01" . + "https://proteinensemble.org/$1"^^ . + "http://purl.dataone.org/odo/SENSO_"^^ . + . + "mop" . + "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."^^ . + "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."^^ . + "Anatomy, development and life cycle stages - planula, polyp, medusa/jellyfish - of the cnidarian hydrozoan species, Clytia hemiphaerica."^^ . + . + "biomedical science" . + . + . + . + . + . + "Pankaj Jaiswal" . + . + . + . + "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_="^^ . + . + . + . + . + . + "physiology" . + . + . + "https://w3id.org/oc/meta/"^^ . + . + . + . + . + . + "0000000"^^ . + "https://uniresolver.io/#did:$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."^^ . + "obo" . + "patent" . + . + "PKDB00198"^^ . + . + "046"^^ . +_:N13bb372bbe454a47a953e75ba60f7f8d "pierre.sprumont@unifr.ch" . + . + . + . + . + "genome" . + . + . + "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . + . + . + . + . + "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."^^ . + . + "ihw" . + . + "Ecological terms"^^ . + "http://purl.obolibrary.org/obo/FYPO_"^^ . + . + "dc.terms" . + . + "true"^^ . + . + . + "false"^^ . + "proteomics" . + "omop" . + . + . + "false"^^ . + . + . + . + . + "bitterdb.rec" . + . + . + . + . + "http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?ipid=$1"^^ . + "chemical" . + "An ontology used to describe data resources in the Arctic Data Center (https://arcticdata.io)."^^ . + . + "OpenCitations Corpus" . + . + "biolegend" . + . + . + . + "ChEMBL" . + . + . + . + . + . + . + "tanja.bekhuis@tcbinfosci.com" . + . + . + . + "molecular biology" . + "false"^^ . + . + . + "biosamples" . + "false"^^ . + . + _:Nc6e5fcb883644175825da682379a1cd8 . + . + "life science" . + . + "false"^^ . + . + . + . + . + "http://neuromorpho.org/neuron_info.jsp?neuron_name="^^ . + . + . + "doi" . + . + . + "BM0456"^^ . + . + . + . + . + . + "ctgov" . + . + . + . + . + "eukaryotic Subcellular Localization database" . + . + . + _:N2c2c85a20d454e07a2737aeb48617251 . + . + . + . + "nextProt" . + "ontology" . + . + . + . + . + . + . + . + "structure" . + . + . . - . - "epidemiology" . - . - . - . - . - . - "imdrf" . - . - . - . - . - . - . - "Yiming Bao" . - . - "dna" . - . - . - "epcc" . - . - . - . - . - . - "2842"^^ . - . - . - . - . - . - . - . - "false"^^ . - "^[Ss][Aa][Ss][A-Za-z0-9]{3}[0-9]$"^^ . - "life science" . - "data analysis service" . - . - . - . - . -_:N3abf7e22f0e74131a3b6b2ff255f1b2b "helpdesk@cropontology-curationtool.org" . - . - . - "tm.shah@cgiar.org" . - . - "Human developmental anatomy, abstract version" . - "ontology" . - "cell biology" . - . - . - . - "false"^^ . - "Ontology of Biological and Clinical Statistics" . - "Ensembl Fungi, the Ensembl database for accessing genome-scale data from fungi." . - "hc.trial" . - . - . - . - . - . - "chemistry" . - . - . - "LCSCCPN"^^ . - . - . - "taxonomy" . - . - . - "epigenetics" . - . - . - . - . - . - "NCBI PubChem database of bioassay records" . - "domain" . - . - "^[AEP]-\\w{4}-\\d+$"^^ . - "BAC045"^^ . - . - "nmrshiftdb2" . - . - . - . - . - "false"^^ . - "XB-GENE-922462"^^ . - "^HGVPM\\d+$"^^ . - . - . - . - . - . - . - "false"^^ . - . - . - "rwinslow@jhu.edu" . - "obo" . - . - "protein" . - "false"^^ . - "vendor" . - . - . - . - "bioinformatics" . - . - . - "InTextReferencePointer"^^ . - . - "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . - . - "genome" . - . - . - . - . - . - "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . - . - "^\\d+$"^^ . - . - "Cell line collections (Providers)"^^ . - "bcrj" . - . - . - . - . - . - "false"^^ . - . - . - . - . - . - "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . - "https://www.datanator.info/metabolite/"^^ . - "http://purl.obolibrary.org/obo/BSPO_$1"^^ . - "medicine" . - . - . - "life science" . - . - "00005254"^^ . - . - "An ontology of information entities, originally driven by work by the Ontology of Biomedical Investigation (OBI) digital entity and realizable information entity branch."^^ . - . - . - "rlwalls2008@gmail.com" . - . - "^PRO_[0-9]{10}$"^^ . - . - "ontology" . - "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . - "KEGG Disease" . - "classification" . - . - "Healthcare Common Procedure Coding System" . - . - . - . - . - "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/$1"^^ . - "false"^^ . - "Omar Harb" . - . - "FAIRsharing Subject Ontology" . - . - "interaction" . - "TIGR protein families" . - . - . - "Rice Genome Annotation Project" . - "false"^^ . - . - . - "Lynn Schriml" . - "0000111"^^ . - . - . -_:Ncbaba8be38314faa87e015c819d05226 "SEP developers via the PSI and MSI mailing lists" . - "http://www.chemspider.com/inchikey=$1"^^ . - "438782"^^ . - "http://purl.obolibrary.org/obo/MIRO_"^^ . - "Biological Collections Ontology" . - "Nicolas Le Novère" . - . + "protein" . + "http://www.pharmgkb.org/disease/$1"^^ . + "E12768"^^ . + . + . + "false"^^ . + . + . + "life science" . + "ERR436051"^^ . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upc?upid=$1"^^ . + "genomics" . + "structure" . + "002368"^^ . + . + "genomics" . + . + . + . + "http://www.t3db.org/toxins/"^^ . + "false"^^ . + "Mungbean ontology" . + . + "The interacting motif database or iMOTdb , lists interacting motifs thatare identified for all structural entries in the PDB. The conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting the common motifs shared among all superfamily members."^^ . + . + . + . + . + "Five Stars of Online Research Articles Ontology" . + . + "pid" . + . + . + . + "Antimicrobial Peptide Database" . + . + . + "^EGAS\\d{11}$"^^ . + . + "PepBank is a database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored."^^ . + . + . + . + . + "A0118748"^^ . + . + . + . + . + . + . + "protein" . + . + "false"^^ . + . + . + . + . + "00000268"^^ . + . + "agriculture" . + . + "http://www.rnasoft.ca/sstrand/show_results.php?molecule_ID="^^ . + "false"^^ . + "metabolomics" . + "pdro" . + "false"^^ . + . + "hipsci" . + "^\\d{7}$"^^ . + . + "https://www.gtexportal.org/home/gene/$1"^^ . + . + . + . + "^[0-9a-z_:\\.-]+$"^^ . + . + . + . + "PepBank Peptide Database" . + . + . + . + "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/$1"^^ . + "https://www.re3data.org/repository/$1"^^ . + . + "bibliography" . +_:Ne9b68ac1ba7b4ba383f8a00484713304 "interhelp@ebi.ac.uk" . + . + . + "skm" . + . + . + "http://purl.obolibrary.org/obo/EPO_"^^ . + . + "hsdb" . + . + . + . + . + . + "obo" . + "^\\d+$"^^ . + . + "ontology" . + "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." . + . + "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."^^ . + . + "false"^^ . + . + . + . + "VEGA" . + . + "Werner Müller" . + . + . + . + . + "expressed sequence tag" . + "ASTD" . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + "http://rgd.mcw.edu/rgdweb/report/qtl/main.html?id=$1"^^ . + "^\\d{6}$"^^ . + . + "clinical studies" . + . + . + . + "A controlled vocabulary to support the study of transcription in the mouse brain"^^ . + "602"^^ . + . + "receptome.family" . + "P29894"^^ . + "Fossilworks Taxon" . + . + . + . + "http://epsf.bmad.bii.a-star.edu.sg/cube/db/data/$1/"^^ . + . + . + . + "dr.sebastian.koehler@gmail.com" . + . + . + . + "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://gmd.mpimp-golm.mpg.de/ReferenceSubstances/$1"^^ . + "protein" . + . + . + "unimod" . + . + "dna" . + . + . + "http://4dx.embl.de/4DXpress/reg/all/cview/gene.do?geneID=$1"^^ . + "SMP" . + . + . + "animal husbandry" . + . + "36010371"^^ . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=c&compID=$1"^^ . + . + . + "http://www.wikigenes.org/e/gene/e/$1.html"^^ . + "Search Tool for Interactions of Chemicals" . + . + . + "ensembl.metazoa" . + "classification" . + "mtbd" . + . + . + "spike.map" . + "https://fairsharing.org/$1"^^ . + "conferences" . + . + . . - "doap" . - "zenodo" . - . - . - "obo" . - . - "data governance" . - . - "molecular biology" . - . - "giant.plankton@gmail.com" . - "^SKIP\\d+$"^^ . - . - "false"^^ . - . - "^\\d+$"^^ . - "ILX" . - . - . - "https://www.enzolifesciences.com/"^^ . - "1250"^^ . - . - . - . - "false"^^ . - . - . - "117"^^ . - . - "Entrez Gene" . - . - . - . - . - . - . - . - "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"^^ . - "http://purl.obolibrary.org/obo/FBbi_"^^ . - "YBR125c"^^ . - . - "https://www.phenxtoolkit.org/protocols/view/"^^ . - "Vaccine Adjuvant Compendium" . - . - . - . - . - . - . - "http://www.pharmgkb.org/drug/$1"^^ . - . - . - . - . - . - . - . - . - . - "https://bioregistry.io/pesticides:"^^ . - . - "false"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "Cancer cell LInes GEne fusions portAl" . - . - . - . - . - . - . - . - . - "mbaudis@me.com" . - . - . - . - "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . - "^\\w+\\_\\w+$"^^ . - . - . - "http://www.w3.org/2003/01/geo/wgs84_pos#$1"^^ . - . - . - . - "PlasmoDB" . - . - "false"^^ . - "1868"^^ . - . - . - "false"^^ . - "6038"^^ . - "^\\d{7}$"^^ . - "false"^^ . - . - . - "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/$1"^^ . - . - . - . - . - "ontology" . - . - "ena.embl" . - . - . - "An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings."^^ . - . - . - "false"^^ . - . - "co_348" . - . - "probonto" . - . - . - "Animal Genome Cattle QTL" . - "crop2ml" . - . - "false"^^ . - "conference" . - . - "Reference"^^ . - "earth science" . - . - . - . - . - "The W3C Web Annotation Working Group is chartered to develop a set of specifications for an interoperable, sharable, distributed Web Annotation architecture."^^ . - . - . - . - . - "https://cropontology.org/rdf/CO_367:$1"^^ . - . - . - "HUMAN16963"^^ . - "http://www.chemspider.com/Chemical-Structure.$1.html"^^ . - "true"^^ . - . - . - . - . - . - . - . - . - . - "ontology" . - . - . - . - . - "^\\d{9}$"^^ . - "proteomicsdb.peptide" . - . - . - . - . - "0020"^^ . - "NLXBR" . - . - . - . - "false"^^ . - . - "protein" . - . - . - . - . - . - "false"^^ . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "life science" . - . - "metabolomics" . - "The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.\n\nThis ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project's main page at http://evoio.org/wiki/MIAPA."^^ . - "NIF Standard Ontology: Digital Resources" . - . - . - "0000519"^^ . - "dg.6vts" . - "^\\d{5}$"^^ . - "false"^^ . - "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."^^ . - . - . - . - . - . - "Bjoern Peters" . - . - . - "http://rna.igmors.u-psud.fr/NAPP/Niveau2.php?specie=$1"^^ . - . - . - "virus" . - "http://purl.obolibrary.org/obo/FAO_$1"^^ . - "http://www.jstor.org/stable/$1"^^ . - "ontology" . - . - . - "https://www.gbif.org/species/"^^ . - "protein" . - "ontology" . - . - "false"^^ . - . - . - . - . - "obo" . - . - "false"^^ . - . - . - "scop.sccs" . - . - "comptox" . - . + . + . + "Spectral Database for Organic Compounds" . + . + "drugcentral" . + . + "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . + "Ontology for Biomedical Investigations" . + "https://licebase.org/?q="^^ . + . + . + . + "ncbi.assembly" . + "^[A-Z]+[0-9]+$"^^ . + . + . + "life science" . + . + "John Kunze" . + "gcst" . + "https://www.ncbi.nlm.nih.gov/dbvar/variants/"^^ . + "davidos@ebi.ac.uk" . + . + . + "interaction" . + "Phenotype And Trait Ontology" . + "animal physiology" . + . + "ontology" . + . + . + "ChemSpiderID" . + . + "http://www.jcvi.org/mpidb/experiment.php?interaction_id=$1"^^ . + "1"^^ . + . + "GiardiaDB" . + . + . + . + "The Cell Cycle DB" . + . + . + . . - . - . - . - . - "^[A-Z0-9]+$"^^ . - "^\\d+$"^^ . - . - "https://purl.dataone.org/odo/ADCAD_$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."^^ . - "disease" . - . - . - . - . - . - . - . - . - . - . - "https://pb.apf.edu.au/phenbank/strain.html?id=$1"^^ . - "dideo" . - "377369"^^ . - . - . - . - "https://w3id.org/seo#"^^ . - . - "PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation."^^ . - . - "315.1"^^ . - "jRCTs041220087"^^ . - "false"^^ . - . - . - "protein" . - . - . - . - "0000550"^^ . - "matthias.samwald@meduniwien.ac.at" . - . - . - . - . - "Plant Protein Phosphorylation DataBase (P3DB) is a database that provides information on experimentally determined phosphorylation sites in the proteins of various plant species. This collection references plant proteins that contain phosphorylation sites."^^ . - . - . - "1915"^^ . - . - "expressed sequence tag" . - . - . - . - "^[0-9]+$"^^ . - "http://bioinformatics.ramapo.edu/GRSDB2/geneview.php?geneID="^^ . - "EV_0100011"^^ . - "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . - . - . - . - . - "genomics" . - . - . - . - . - . - "^\\d+$"^^ . - . - "false"^^ . - . - "transport and kinetic data" . - . - "obo" . - . - . - "interactive portal" . - "false"^^ . - "bgee.family" . - . - "0004828"^^ . - . - . - . - . - "OntoBee" . - "CTD Disease" . - . - . - "false"^^ . - . - "zinc" . - "datanator.metabolite" . - . - . - . - . - . - . - . - . - . - . - . - "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."^^ . - "umls" . - . - . - . - "yrcpdr" . - . - "Kaggle is a platform for sharing data, performing reproducible analyses, interactive data analysis tutorials, and machine learning competitions."^^ . - . - "000204"^^ . - . - "4019477"^^ . - "https://www.flymine.org/flymine/report/ChromosomeBand/$1"^^ . - . - . - . - "biomedical science" . - "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://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . - . - . - "http://purl.obolibrary.org/obo/NCRO_$1"^^ . - . - . - . - "HL7 External Code Systems are stored within the greater OID system" . - . - "false"^^ . - . - "James C. Hu" . - "GXA Expt" . - . - "ontology" . - "The cBioPortal for Cancer Genomics" . - "http://www.nbrc.nite.go.jp/NBRC2/NBRCCatalogueDetailServlet?ID=NBRC&CAT=$1"^^ . - . - . - . - . - . - . - "https://bbp.epfl.ch/nexus/web/studios/public/topological-sampling/studios/data:$1"^^ . - . - . - "life science" . - . - "https://www.merckmillipore.com/catalogue/item/$1"^^ . - . - . - . - . - . - . - "ontology" . - "mirte" . - . - "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . - "bootstrep" . - . - "hoganwr@gmail.com" . - . - . - . - . - _:Ndd49303c904448229b8b238eb16b593d . - "false"^^ . - . - . - . - . - . - . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - "http://virus.zoo.ox.ac.uk/rnavirusdb/virus.php?id="^^ . - "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."^^ . - . - . - . - . - . - . - . - . - "Cellosaurus Publication" . - . - . - "ribocenter" . - "^\\d{7}$"^^ . - . - "https://permalink.obvsg.at/$1"^^ . - . - . + . + "metabolomics" . + . + "omit" . + "CONSO00010"^^ . + . + . + . + . + . + . + "transcript" . + "https://giardiadb.org/giardiadb/app/record/gene/$1"^^ . + "http://purl.obolibrary.org/obo/APOLLO_SV_$1"^^ . + . + "C023"^^ . + "http://gmd.mpimp-golm.mpg.de/Analytes/$1"^^ . + "false"^^ . + . + "Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . + . + "rna" . + . + . + . +_:Ncfadbc34f17648fd84f1b3281ce5bb0d "W. Ted Klein" . + . + "http://purl.obolibrary.org/obo/CARO_"^^ . + . + "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."^^ . + . + . + . + . + . + "http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/getSMAR.cgi?$1"^^ . + . + . + . + . + . + . + "false"^^ . + "^spike\\d{5}$"^^ . + "The Polygenic Score (PGS) Catalog is an open database of PGS and the relevant metadata required for accurate application and evaluation."^^ . + "foodon" . + "^\\d+$"^^ . + . + . + . + "chebi" . + "false"^^ . + . + "^\\d{7}$"^^ . + . + "10.1038/s41597-022-01807-3"^^ . + . + . "https://go.drugbank.com/metabolites/$1"^^ . - "FAIRSharing" . - . - . - . - "http://www.ars.usda.gov/research/publications/publications.htm?seq_no_115="^^ . - . - . - . - . - . - . - . - "^ACYPI\\d{6}(-RA)?$"^^ . - . - "The Dietary Restriction Gene Database" . - "qafeQTWIWmcC"^^ . - . - "dna" . - "http://purl.obolibrary.org/obo/SBO_$1"^^ . - . - . - . - . - . - "http://purl.obolibrary.org/obo/UPHENO_"^^ . - "^\\d{7}$"^^ . - . - . - "http://ontology.apa.org/apaonto/termsonlyOUT%20(5).owl#"^^ . - "00000000"^^ . - . - "https://www.addexbio.com/productdetail?pid="^^ . - . - "https://cropontology.org/rdf/CO_340:$1"^^ . - "The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. Its scope includes: Immortalized cell lines; naturally immortal cell lines (example: stem cell lines); finite life cell lines when those are distributed and used widely; vertebrate cell line with an emphasis on human, mouse and rat cell lines; and invertebrate (insects and ticks) cell lines. Its scope does not include primary cell lines (with the exception of the finite life cell lines described above) and plant cell lines."^^ . - "http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id="^^ . - . - . - "Sean May" . - "medicine" . - "organic molecular chemistry" . -_:Nc5efd8506e27413980b3c557b7d6565f "helpdesk@cropontology-curationtool.org" . - . - . - "obo" . - . - . - . - . - "life science" . - "life science" . - . - . - "^[A-Za-z_]+$"^^ . - . - . - . - . - . - . - "dr.shorthair@pm.me" . + . + "ontology" . + . + . + . + . + . + . + "true"^^ . + . + . + "^PED\\d{5}e\\d{3}$"^^ . + . + "http://drugcentral.org/drugcard/$1"^^ . + "agriculture" . + "obo" . + "^DBMET\\d+$"^^ . + . + . + . + "false"^^ . + . + "CATH superfamily" . + "Tim Robertson" . + . + "bioinformatics" . + "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."^^ . + . + . + "An ontology meant to define bibliographic records, bibliographic references, and their compilation into bibliographic collections and bibliographic lists, respectively."^^ . + . + . + "^\\d{7}$"^^ . + . + "http://hdl.handle.net/"^^ . + "true"^^ . + "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://www.ubio.org/browser/details.php?namebankID=$1"^^ . + . + . + "ontologies" . + . + . + . + "UniProt provides proteome sets of proteins whose genomes have been completely sequenced."^^ . + . + . + . + . + . + "https://tree.opentreeoflife.org/taxonomy/browse?id=$1"^^ . +_:Na6cd28f60aa44ebea3fa480cf4f65265 "helpdesk@cropontology-curationtool.org" . + "Gene Expression Ontology" . + . + . + . + "CORDIS Article" . + "ontology" . + . + . + "small molecule" . + "gene" . + . + . + . + . + . + . + . + "http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=$1"^^ . + . + "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid="^^ . + "elm" . + . + . + . + . + "https://uts.nlm.nih.gov/uts/umls/semantic-network/"^^ . + . + . + . + . + . + "https://worldwide.espacenet.com/classification?locale=en_EP#!/CPC=$1"^^ . + . + . + "http://geneontology.org/" . + "rhea" . + . + . + . + . + "life science" . + . + "Genetic and Rare Diseases Information Center" . + . + . + "0000030"^^ . + . + . + . + "https://biopragmatics.github.io/providers/sdis/$1"^^ . + . + "ontology" . + . + . + . + . + . + . + . + "subject agnostic" . + "http://purl.obolibrary.org/obo/HANCESTRO_"^^ . + . + "gene" . + . + "https://www.ebi.ac.uk/biosamples/sample/$1"^^ . + . + "https://stemcells.nindsgenetics.org?line=$1"^^ . + "Omar Harb" . + "Mark Jensen" . + "plant" . + "3851"^^ . + . + "life science" . + . + . + "biocyc" . + . + . + . + . + . + "false"^^ . + "medical informatics" . + . + . + . + . + . + . + . + . + "Entrez Gene" . + . + "false"^^ . + "https://bacteria.ensembl.org/id/"^^ . + "Identifier for a user in iNaturalist"^^ . + "jgi.proposal" . + . + "mint" . + "0001000"^^ . + . + . + . + "false"^^ . + . + . + . + "Fernanda Dorea" . + . + "https://gitlab.com/$1"^^ . + . + "false"^^ . + . + . + . + . + "pathway" . + "false"^^ . + "biomedical science" . + . + . + "developmental biology" . + . + . + . + . + "genome" . + . + . + . + "gene" . + . + . + "Hannele Laivuori" . + . + "^\\d{7}$"^^ . + "comparative genomics" . + . + "https://biopragmatics.github.io/providers/goche/$1"^^ . + . + "false"^^ . + . + . + . + . + . + "https://www.kazusa.or.jp/rouge/gfpage/$1"^^ . + . + . + . + . + "life science" . + "^[A-Z]{2}\\d+$"^^ . + . + . + . + . + . + . + . + "KEGG_DGROUP" . + . + . + . + "Harry E. Pence" . + . + "https://www.rrrc.us/Strain/?x=$1"^^ . + . + . + "53784"^^ . + . + . + "^(VT)?\\d{7}$"^^ . + "2"^^ . + "anatomy" . + "MaizeGDB" . + . + . + "life science" . + . + . + . + "The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]"^^ . + . + . + "massbank" . + "http://arabidopsis.org/servlets/TairObject?accession=Gene:$1"^^ . + . + . + . + . + . + . + . + "false"^^ . + "000009"^^ . + "https://www.ebi.ac.uk/gwas/studies/"^^ . + . + "metatlas.metabolite" . + "identifier of an entry in the NCI Drug Dictionary"^^ . + . + . + . + . + "The DrugBank database is a bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. This collection references target information from version 4 of the database."^^ . + "^\\d+$"^^ . + "bork@embl.de" . + "http://purl.jp/bio/4/id/"^^ . + . + . + "Models developed with the Virtual Cell (VCell) software prorgam."^^ . + . + "redfly" . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OBI_"^^ . + "The SNCTP (Swiss National Clinical Trials Portal) is the portal where clinical trials in Switzerland are published. It contains data from two sources: from BASEC, the national platform for submitting applications for research projects to ethics committees, and from the ICTRP (the WHO International Clinical Trials Registry Platform), which covers the 17 primary registries worldwide. The ICTRP clinical trials shown on the SNCTP are limited to those conducted in Switzerland; there is also an option to display trials conducted in one of Switzerland's neighbouring countries. [from homepage]"^^ . + . + . + . + "Clytia hemisphaerica Development and Anatomy Ontology" . + . + . +_:N380682f09f724f709aeda330a6daf3ea "WikiData Support" . + "Pennsieve" . + "0807.4956v1"^^ . + "http://www.cellresource.cn/cellsearch.aspx?sc=1&where=$1"^^ . + . + "The Rouge protein database contains results from sequence analysis of novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project."^^ . + . + . + "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id=$1"^^ . + . + . + "http://purl.obolibrary.org/obo/SWO_$1"^^ . + . + "false"^^ . + . + "ontology and terminology" . + . + "protein" . + "BLL"^^ . + . + "false"^^ . + . + . + "50018"^^ . + . + . + . + . + . + "0000009"^^ . + "3SBPLMKKVEVR"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "noaa.cameo" . + . + . + . + "NCI2004_11_17" . + . + "disprot.region" . + . + . + "The cBioPortal for Cancer Genomics" . + . + . + . + . + . + "false"^^ . + "phipo" . + . + . + "^Gm\\d+$"^^ . + "^\\d*$"^^ . + "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."^^ . + . + "^\\d{6}$"^^ . + "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id=$1"^^ . + "protein" . + "sequence alignment" . + "UniProt Cross-ref database" . + "forest management" . + "http://purl.obolibrary.org/obo/HP_"^^ . + . + "WikiPathways Ontology" . + "^\\d{7}$"^^ . + . + . + "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."^^ . + "false"^^ . + . + . + "obo" . + . + "http://purl.obolibrary.org/obo/IDO_"^^ . + "gene" . + . + "ontology" . + . + "development" . + . + . + . + "http://www.ontologyrepository.com/CommonCoreOntologies/$1"^^ . + . + . + . + "4238"^^ . +_:Ndcd602300ff0433da46693e96d7101e7 "helpdesk@cropontology-curationtool.org" . + . + . + . + "hammer"^^ . + . + . + . + "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . + . + . + . + . + . + "^\\d+$"^^ . + "genome" . + . + . + "0001021"^^ . + . + "The dbSNP database is a repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms."^^ . + . + "genome" . + "^[CD]\\d+$"^^ . + "https://datanator.info/reaction/"^^ . + "OpenCitations Meta Identifier" . + "WiCell Research Institute Cell Collection" . + . + . + . + "https://cropontology.org/rdf/CO_325:$1"^^ . + "false"^^ . + . + . + . + . + . + "https://biopragmatics.github.io/providers/diseaseclass/$1"^^ . + . + "icd10" . + . + "nrfc" . + . + "^\\d{7}$"^^ . + . + . + . + . + "ChEBI Data Sources" . + . + "immunology" . + . + . + "^\\d{7}$"^^ . + "drosophila" . + . + "nlx.anat" . + "Joshua Orvis" . + "obo" . + "https://dataguids.org/ga4gh/dos/v1/dataobjects/$1"^^ . + "Hypertension Ontology" . + . + "computational biology" . "sequence" . - "http://www-snorna.biotoul.fr/plus.php?id="^^ . - "dictybase.est" . - "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.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid="^^ . - "A structured controlled vocabulary for the anatomy of fungi."^^ . - "Distributed Archives for Neurophysiology Data Integration" . - "https://flybase.org/reports/FBrf"^^ . - . - . - "https://goldbook.iupac.org/terms/view/$1"^^ . - . - "https://bioregistry.io/schema/#$1"^^ . - . - . - . - "http://www.w3.org/2006/time#"^^ . - . - . - . - "Narcis Fernandez-Fuentes" . - . - "^\\d+$"^^ . - . - . - "ECOLI:CYT-D-UBIOX-CPLX"^^ . - . - . - . - . - . - . - "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$"^^ . - "http://arabidopsis.org/servlets/TairObject?accession=Gene:"^^ . - . - "protein" . - "HL7 External Code Systems" . - "obo" . - . - "lcnaf" . - . - . - . - . - "National Drug File - Reference Terminology" . - "chemical" . - "life science" . - "https://www.dsmz.de/collection/catalogue/details/culture/"^^ . - "NCI_Thesaurus" . - "0000189"^^ . - "cell" . - . - "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . - "pathology" . - . - . - . - "^\\d{7}$"^^ . - "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . - . - . - . - "The identifier for an observation in iNaturalist"^^ . - . - . - "^[A-Za-z0-9_-]+$"^^ . - "trnadbce" . - "http://wasabi.lutzonilab.net/pub/displayTaxonInfo?aftol_id="^^ . - "https://glytoucan.org/Structures/Glycans/"^^ . - . - . - . - "DTO integrates and harmonizes knowledge of the most important druggable protein families: kinases, GPCRs, ion channels and nuclear hormone receptors."^^ . - . - . - "genotyping" . - . - "hpath" . - . - "http://www.w3.org/2003/01/geo/wgs84_pos#"^^ . - "Continuous Automated Model Evaluation" . - "201022999"^^ . - . - . - . - "gene" . - "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . - "biodiversity" . - "https://athena.ohdsi.org/search-terms/terms/"^^ . - . - . - . - "762"^^ . - . - "PRINTS compendium of protein fingerprints" . - . - . - . - . - "http://purl.obolibrary.org/obo/TAHE_"^^ . - . - . - . - "human geography" . - . - . - . - . - . - "https://bbp.epfl.ch/nexus/web/studios/public/"^^ . - "andreadega/systems-biology-compiler"^^ . - "false"^^ . - . - "Conference Ontology" . - "http://www.wikigenes.org/e/gene/e/$1.html"^^ . - "https://www.vmh.life/#reaction/$1"^^ . - . - . - . - . - . - "^\\d+$"^^ . - "chemidplus" . - . - "ontology" . - "npass" . - "bitterdb.rec" . - . - "https://abrc.osu.edu/stocks/number/SALK_"^^ . - . - . - "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions"^^ . - "tarbase" . - . - . + . + "systems biology" . + "DragonDB Locus" . + . + . + "https://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID="^^ . + . + . + . + . + . "Ontology for Biobanking" . - "xpo" . - "http://www.cathdb.info/cathnode/"^^ . - . - . - . - . - . - "false"^^ . - . - . - "Adnan Malik" . - . - "https://nsrrc.missouri.edu/nsrrc$1info/"^^ . - . - "jimhu@tamu.edu" . - . - . - . - . - . - . - . - . - "false"^^ . - . - "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . - "false"^^ . - "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."^^ . - . - . - . - . - . - . - . - . - . - . - . - "cognitive neuroscience" . - . + "cheminf" . + . + "http://purl.obolibrary.org/obo/CMF_$1"^^ . + . + . + "false"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OGMS_$1"^^ . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + "d4e2515"^^ . + . + . + . + . + "PM0012345"^^ . + "https://www.scopus.com/affil/profile.uri?afid="^^ . + . + "100101"^^ . + . + . + "http://bacmap.wishartlab.com/organisms/$1"^^ . + "agricultural engineering" . + . + . + "GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match."^^ . + . + "co_327" . + . + "dna" . + "sty" . + . + . + "The General Formal Ontology is a top-level ontology for conceptual modeling, which is being constantly further developed by Onto-Med. It includes elaborations of categories like objects, processes, time and space, properties, relations, roles, functions, facts, and situations. Moreover, we are working on an integration with the notion of levels of reality in order to more appropriately capture entities in the material, mental, and social areas."^^ . + "ontology" . + "chemidplus" . + "obo" . + "https://easychair.org/cfp/topic.cgi?tid=$1"^^ . + "edam.format" . + "suzia@stanford.edu" . + . + "^\\d{8}$"^^ . + . + "http://www.bioinsilico.org/cgi-bin/CAPSDB/getCAPScluster?nidcl=$1"^^ . + . + . + . + . + "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id=$1"^^ . + . + "^\\w{4}$"^^ . + "false"^^ . + . + . + . + . + "0003003"^^ . + . + "^\\d{7}$"^^ . + . + . + "Cell Line Ontology" . + . + "^\\d+$"^^ . + . + "ontology" . + . + "false"^^ . + . + . + . + . + . + "ontology" . + . + "Sol Genomics Network" . + . + . + "zenodo" . + "^\\d{8}$"^^ . + "genome" . + . + . + "computational biology" . + . + . + . + . + "life sciences" . + . + . + . + . + "https://gudmap.org/id/$1"^^ . + "ontology" . + . + "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname="^^ . + . + . + . + . + "MatrixDB Association" . + "YeTFasCo" . + . + "goccid" . + . + . + "https://bioregistry.io/cabri:"^^ . + "^\\d{7}$"^^ . + "Dr. Duke's Phytochemical and Ethnobotanical Databases chemical" . + . + . + "0000021"^^ . + . + "https://hdl.handle.net/hdl:20.500.12633/$1"^^ . + . + . + . + "MetaCyc Reaction" . + "http://eggnog.embl.de/version_3.0/cgi/search.py?search_term_0="^^ . + . + . + . + "^[A-Za-z_0-9]+$"^^ . + "obo" . + . + "^DB\\d{5}$"^^ . + . + "Rahuman Sheriff" . + . + . + . + . + . + "Sheeba Samuel" . + . + . + . + "0000590"^^ . + "GR_GENE" . + "^[a-zA-Z0-9\\-:#/\\.]+$"^^ . + "false"^^ . + . + "http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=$1"^^ . + . + "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."^^ . + . + . + . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=Peptide"^^ . + . + . + . + "http://europepmc.org/articles/$1"^^ . + . + . + . + . + "http://www.bioinfo.org/NONCODEv4/show_rna.php?id=$1"^^ . + . + . + . + "owlstar" . + . + . + . + . + "dna" . + . + . + "unique identifiers" . + . + . . - "genome" . - . - "H3.03.00.0.00007"^^ . - "http://tables.pseudogene.org/[?species_name]/"^^ . - . "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organ_details&organ_children=on&organ_id="^^ . - . - . - "^EBI\\-[0-9]+$"^^ . - . - . - "Analyses of microbiome data within MGnify"^^ . - . - . - . - . - . - "InChI" . - "https://www.brenda-enzymes.de/ligand.php?brenda_group_id=$1"^^ . - . - "gene" . - . - . - "http://purl.obolibrary.org/obo/XPO_$1"^^ . - . - . - . - . - "https://www.alliancegenome.org/accession/$1"^^ . - . - "^[1-9]\\d{0,5}$"^^ . - "COL3A1"^^ . - . - . - "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]"^^ . - "^\\d{7}$"^^ . - . - . - . - . - "sequence" . - "neuroscience" . - "false"^^ . - . - "intact" . - . - "AD834"^^ . - . - . - "100000"^^ . - . - . - "https://www.kegg.jp/entry/$1"^^ . - . - . - . - . - . - . - . - "^GC[AF]_[0-9]{9}\\.[0-9]+$"^^ . - . - . - . - . - "yeastract" . - . - "false"^^ . - . - . - . - . - "http://www.jstor.org/stable/"^^ . - "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . - . - . - "http://purl.obolibrary.org/obo/CLO_$1"^^ . - . - . - "DragonDB Allele" . - . - "DP00003"^^ . - "https://rarediseases.info.nih.gov/diseases/$1/index"^^ . - . - . - "OSR00185W"^^ . - "http://mods.rna.albany.edu/mods/modifications/view/"^^ . - "https://cstr.cn/$1"^^ . - . - "environmental science" . - "vfb" . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/protein/"^^ . - . - . - "https://bacdive.dsmz.de/strain/$1"^^ . + . + . + . + . + . + . + . + "GlycoNAVI" . + "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."^^ . +_:N820b1b954de9446f91f3dc21bc674d09 "J.Bard@ed.ac.uk" . + "true"^^ . + . + . + . + . + . + . + . + . + "human genetics" . + . + "B00162"^^ . + "chemistry" . + . + "http://www.noncode.org/NONCODERv3/ncrna.php?ncid=$1"^^ . + "BioNumbers" . + "co_334" . + . + "Mental Disease Ontology" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + "structure" . + "ProteomicsDB is an effort dedicated to expedite the identification of the human proteome and its use across the scientific community. This human proteome data is assembled primarily using information from liquid chromatography tandem-mass-spectrometry (LC-MS/MS) experiments involving human tissues, cell lines and body fluids. Information is accessible for individual proteins, or on the basis of protein coverage on the encoding chromosome, and for peptide components of a protein. This collection provides access to individual proteins."^^ . + "false"^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family="^^ . + . + . + "http://www.iresite.org/IRESite_web.php?page=view&entry_id="^^ . + . + . + "^bkc[0-9]*$"^^ . + . + . + "CHEMROF is an ontological framework for Chemical Entities Mixtures Reactions Ontological Framework. This OWL ontology is an automated Translation of the source LinkML schema, https://w3id.org/chemrof"^^ . + . + . + "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)."^^ . + "0005926"^^ . + "CIViC Evidence" . + . + "http://purl.org/spar/cito/"^^ . + . + . + "https://cordis.europa.eu/article/id/$1"^^ . + "genetics" . + "^T3D\\d+$"^^ . + "https://www.scopus.com/affil/profile.uri?afid=$1"^^ . + . + . + . +_:N5331d9cae68249828b269d4d462c8f93 "Julie Thompson" . + . + . + "http://www.genomesize.com/result_species.php?id="^^ . + "^\\d{7}$"^^ . + . + "mathematics" . + "^\\d{7}$"^^ . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/HTN_$1"^^ . + . + . + "NeuroVault Collection" . + . + . + . + "biosystems" . + . + . + "insdc.gca" . + . + "epidemiology" . + "Environment Ontology for Livestock" . + . + . + "proteomics" . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + . + "true"^^ . + . + "eukaryotic" . + . + . + "COG Pathways" . + . + . + . + . + . + "https://bioregistry.io/genpept:"^^ . + "^P\\w+$"^^ . + . + "https://www.confident-conference.org/index.php/Event_Series:$1"^^ . + . + . + . + . + . + . + . + . + "human genetics" . + "KEGG BRITE is a collection of hierarchical classifications (see new hierarchies and last updates) representing our knowledge on various aspects of biological systems. In contrast to KEGG PATHWAY, which is limited to molecular interactions and reactions, KEGG BRITE incorporates many different types of relationships."^^ . + "E5.11.2.0.0.0.4"^^ . + "re3data" . + "^\\d{7}$"^^ . + "t4fs" . + . + . + "^\\d+$"^^ . + "obo" . + . + "f.quaglia@ibiom.cnr.it" . + . + . + . + "MetaNetX chemical" . + "ChEMBL-Cells" . + "^\\d+$"^^ . + "IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively."^^ . + . + . + "^[a-zA-Z0-9\\-:#\\.]+$"^^ . + . + . + "lotus" . + . + . + . + . + "http://purl.obolibrary.org/obo/PD_ST_"^^ . + "chemistry" . + "45539"^^ . + "ncats.drug" . + . + "UniProt Protein" . + "Handle" . + . + "http://www.unimod.org/modifications_view.php?editid1=$1"^^ . + . + . + . + . + "Miguel A. Fortuna" . + . + . + "Michael Witt" . + "life science" . + . + "Kim Durante" . + "00042"^^ . + . + . + . + . + . + . + "drosophila" . + . + . + . + . + . + . . - . - . - "mw.study" . - . - "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."^^ . - "ontology" . - "https://civicdb.org/links/sources/$1"^^ . - . - "cio" . - . -_:N865baaa49d124e84968635b53d7122b6 "Jonathan Bard" . - "mutant" . - . - "Insect Resistance Ontology" . - "domain" . - . - . - . - "http://purl.obolibrary.org/obo/XLMOD_"^^ . - . - "CC-BY-1.0"^^ . - "gpcrdb" . - . - "greengenes" . - . - . - "BacMap Map" . - . - . - . - . - "Computer Retrieval of Information on Science Projects Thesaurus" . - . - "0001"^^ . - "https://europepmc.org/article/CTX/$1"^^ . - "life science" . - . - . - . - . - "Marc_Ciriello@hms.harvard.edu" . - . - "http://www.w3.org/2002/07/owl#$1"^^ . - . - . - "hl7.v3codesystem" . - "phylogeny" . - "false"^^ . - . - . - . - . - "^KW-\\d{4}$"^^ . - "false"^^ . - "interaction" . - . - . - . - . - . - "https://drugs.ncats.io/drug/$1"^^ . - . - . - . - . - "http://search.sisuproject.fi/#/variant/"^^ . - "12345"^^ . - . - . - . - . - "http://rest.bmrb.wisc.edu/bmrb/$1/html"^^ . - . - . - . - . - "https://bioregistry.io/phosphopoint.kinase:"^^ . - . - . - . - . - . - "WikiGenes" . - . - "The Ion Channel Electrophysiology Ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. "^^ . - . - . - . - . - "FMAID" . - "https://icd.codes/icd10cm/"^^ . - "physiology" . - . - "sep" . - "anatomy" . - . - "https://commonchemistry.cas.org/detail?cas_rn="^^ . + "^\\d+$"^^ . + "Publons Researcher" . + . + "Jade Hotchkiss" . + "false"^^ . + . + "^A[A-Z]+\\d+$"^^ . + "Uberon Property" . + . + . + . + "NextDb is a database that provides information on the expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans. This was done through EST analysis and systematic whole mount in situ hybridization. Information available includes 5' and 3' ESTs, and in-situ hybridization images of 11,237 cDNA clones."^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/"^^ . + . + . + . + "An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries." . + . + . + . + "CL0192"^^ . + . + "anatomy" . + . + . + . + . + "^[A-Za-z]+$"^^ . + "http://purl.obolibrary.org/obo/NCRO_"^^ . + . + . + . + "Montana Smith" . + . + "obo" . + "microbial" . + "^\\d+$"^^ . + . + . + . +_:Nb5a54a1ea36043279d2fbde29f909ebc "Crop Ontology Helpdesk" . + . + . + "1001"^^ . + . + "http://www.yeastract.com/view.php?existing=locus&orfname=$1"^^ . + "XUO" . + "http://solgenomics.net/phenome/locus_display.pl?locus_id=$1"^^ . + "https://neurovault.org/images/$1"^^ . + . + "https://pharmacodb.ca/tissues/$1"^^ . + . + . + "obo" . + . + "pathway" . + "issaku@noguchi.or.jp" . + . + "Southwestern Environmental Information Network" . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "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 Drosophila data."^^ . + . + "http://purl.obolibrary.org/obo/FAO_$1"^^ . + . + "false"^^ . + . + "nist" . + "Curated contextual database gathering samples related to SARS-CoV-2 virus and covid-19 disease."^^ . + . + . + . + . + "false"^^ . + "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=$1"^^ . + . + . + "upa" . + . + . + . + . + "usageNote"^^ . + . + . + . + "noaa" . + . + . + . + . + "FuTRES Ontology of Vertebrate Traits" . + "46977"^^ . + . + "https://cropontology.org/rdf/CO_330:"^^ . + "life science" . + . + . + . + . + "The IUPHAR Compendium details the molecular, biophysical and pharmacological properties of identified mammalian sodium, calcium and potassium channels, as well as the related cyclic nucleotide-modulated ion channels and transient receptor potential channels. It includes information on nomenclature systems, and on inter and intra-species molecular structure variation. This collection references individual receptors or subunits."^^ . + "MIRIAM Legacy Registry Identifier" . + "https://www.ebi.ac.uk/interpro/set/pfam/"^^ . + . + "https://animaldiversity.org/accounts/"^^ . + . + . + "Data format that can be used in conjunction with the Simulation Experimental Description Markup Language (SED-ML)."^^ . + . + "pw" . + . + . + . + . + "epigenetics" . + . + _:Ne9b68ac1ba7b4ba383f8a00484713304 . + . + . + "false"^^ . + "^CE\\d{5}$"^^ . + . + "Protein Structural Change Database" . + . + . + . + "Prefix Commons" . + "A registry of code systems (each are small vocabularies themselves) used by HL7 international, related to FHIR."^^ . + "https://www.metanetx.org/equa_info/$1"^^ . + . + "A resource for Dictyostelid discoideum (a soil-dwelling amoeba) genomics"^^ . + "itiswebmaster@itis.gov" . + . + "life science" . +_:N2079c6c1c21d4ad782eb69b0c991d0ee "J.Bard@ed.ac.uk" . + . + "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. "^^ . + . + "ADM1"^^ . + . + . + "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . + "data management" . + . + . + "vfdb.gene" . + "Jakob Voß" . + "https://www.alzforum.org/mutations/$1"^^ . + "European Medicines Evaluation Agency" . + "https://w3id.org/semapv/vocab/$1"^^ . + . + . + . +_:N799549267e7545d0961160c005e4ec68 "Vivian Lee" . + . + . + . + "false"^^ . + "true"^^ . + . + . + "vendor" . + "true"^^ . + . + . + "false"^^ . + "http://www.hmdb.ca/metabolites/$1"^^ . + "false"^^ . + . + . + . + . + "mwitt@purdue.edu" . + "^\\S+$"^^ . + "gtex" . + . + "Genomes Online Database" . + . + "https://rnacentral.org/rna/"^^ . + . + "obo" . + "https://www.ebi.ac.uk/metagenomics/analyses/$1"^^ . + "ontology" . + "subject agnostic" . + . + "ICD-9-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States."^^ . + . + "pharmacy" . + . + . + . + . + "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)."^^ . + "Ensembl Bacteria" . + "SP_SL" . + . + . + "Oryza Tag Line" . + . + . + . + . + . + . + . +_:N497517396e9a4f43959d71e6099fbdfd "CTCAE Help" . + . + . + . + . + "life science" . + . + . + "https://registry.bio2kg.org" . + "https://bioregistry.io/metaregistry/prefixcommons/$1"^^ . + "jonrkarr@gmail.com" . + "^[AEP]-\\w{4}-\\d+$"^^ . + . + . + . + . + "https://dandiarchive.org/dandiset/$1"^^ . + "ontology" . + . + . + "uniprot.tissue" . + "http://purl.obolibrary.org/obo/HANCESTRO_$1"^^ . + "SNOMEDCTCT_2019_03_01" . + "false"^^ . + . + "rs17852708"^^ . + "fluticasone"^^ . + . + "An ontology for describing the phenology of individual plants and populations of plants, and for integrating plant phenological data across sources and scales."^^ . + . + . + . + "structure" . + "datanator.gene" . + "https://www.proteomicsdb.org/#human/proteinDetails/$1/summary"^^ . + "http://sbi.imim.es/cgi-bin/archdb//loops.pl?loop=$1"^^ . + . + . + "bsu:BSU01340"^^ . + . + . + . + . + "false"^^ . + . + . + . + . + "^F\\d{4}$"^^ . + . + "http://purl.obolibrary.org/obo/OMP_"^^ . + "Contains entries for various database identifiers" . + "false"^^ . + "molecules" . + . + . + "ontology" . + "plant" . + "1"^^ . + . + "https://www.proteomicsdb.org/#human/proteinDetails/$1"^^ . + . + "microRNA Ontology" . + "^[1-9]\\d*$"^^ . + . + . + "nucleotide" . + "http://func.mshri.on.ca/yeast/genes/list_functional_scores/$1"^^ . + "Scopus Researcher" . + "Database of Sequence Tagged Sites" . + "protein" . + "DAPK1"^^ . + . + "^T\\d{3}$"^^ . + . + "false"^^ . + . + . + . + . + "Platynereis stage ontology" . + "false"^^ . + "false"^^ . + "false"^^ . + . + . + . + "HBB"^^ . + . + "^\\d{7}$"^^ . + . + "sgn" . + . + . + . + "Cell Signaling Technology Antibody" . + . + "http://crispr.i2bc.paris-saclay.fr/cgi-bin/crispr/SpecieProperties_db.cgi?Taxon_id[]="^^ . + "Pennsieve is a publicly accessible Scientific Data Management and publication platform. The platform supports data curation, sharing and publishing complex scientific datasets with a focus on integration between graph-based metadata and file-archival. The platform provides a \"peer\"-reviewed publication mechanism and public datasets are available through its Discover Web Application and APIs. "^^ . + "silvio.peroni@unibo.it" . + "^CA\\d+$"^^ . + . + "dwelter.ontologist@gmail.com" . + . + . + . + . + . + . + "ontology" . + "obo" . + . + "DDB0191090"^^ . + "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."^^ . + . + . + "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."^^ . + "GenAge is a database of human and model organism genes related to longevity and aging, maintained by the Human Ageing Genomics Resources (HAGR) group."^^ . + "DisProt region" . + "R-BTA-418592"^^ . + . + . + . + . + "true"^^ . + "An ontology for describing the steps in the workflow associated with the publication of a document or other publication entity."^^ . + . + . + . + . + "proteomics" . + . + "https://modeldb.science/"^^ . + . + . + . + . + "genetics" . + "insertion" . + . + . + . + . + . + . + . + . + . + "false"^^ . + "biology" . + "dna" . +_:Nc61e1ba3fdf94e6781d9d9a9ab3cfda2 "chebi-help@ebi.ac.uk" . + "GLIDA Ligand" . + "CLAO is an ontology of anatomical terms employed in morphological descriptions for the Class Collembola (Arthropoda: Hexapoda)."^^ . + . + "NEMBASE is a comprehensive Nematode Transcriptome Database. NEMBASE4 includes robust protein predictions (NemPep4), and protein families for 63 nematode species, over 600,000 ESTs and over 250,000 proteins."^^ . + . + . + "ontology" . + . + "uniparc" . + . + . + . + . + "anatomy" . + . + . + . + "^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\\.[0-9]))?))$"^^ . + . + . + . + . + . + . + "gene expression" . + . + . + . + "identifier for the defunct/merged Publons website; URL redirects to Web of Science's P8372 (WOSID)"^^ . + . + . + . + . + . + "molecular biology" . + . + "vgnc" . + . + . + "https://cropontology.org/rdf/CO_358:"^^ . + . + . + . + . "pmr" . - . - "GDS1234"^^ . - "SpBase, is designed to present the results of the genome sequencing project for the purple sea urchin. THe sequences and annotations emerging from this effort are organized in a database that provides the research community access to those data not normally presented through NCBI and other large databases."^^ . - "dron" . - . - "The Virus Infectious Disease Ontology" . - . - . - . - "false"^^ . - . - . - . - . - . - "The Extensible Markup Language (XML) is a subset of SGML that is completely described in this document. Its goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. XML has been designed for ease of implementation and for interoperability with both SGML and HTML."^^ . - . - . - . - . - . - "164750"^^ . - . - . - "false"^^ . - "2.1.1"^^ . - . - . - . - "^spike\\d{5}$"^^ . - . - "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . - . - "is deprecated" . - . - . - . - "ontology" . - "VirGen a comprehensive viral genome resource, which organizes the ‘sequence space’ of viral genomes in a structured fashion. It has been developed with an objective to serve as an annotated and curated database for complete viral genome sequences."^^ . - . - . - . - . - "co_337" . - . - . - "1"^^ . - . - "https://www.ncbi.nlm.nih.gov/sra/$1"^^ . - . - . - . - "preclinical studies" . - "The HGNC (HUGO Gene Nomenclature Committee) provides an approved gene name and symbol (short-form abbreviation) for each known human gene. All approved symbols are stored in the HGNC database, and each symbol is unique. HGNC identifiers refer to records in the HGNC symbol database."^^ . - "biology" . - . - . - "http://www.gramene.org/db/ontology/search?id=GRO:"^^ . - . - "false"^^ . - . - . - . - "ACYPI000159"^^ . - . - . - . - . - "^\\d+$"^^ . - . - . - . - "stitch" . - . - . - . - . - "http://purl.obolibrary.org/obo/TAXRANK_"^^ . - "Gene"^^ . - . - "Drug Target Ontology" . - "data science" . - "^\\d{7}$"^^ . - . - "This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]"^^ . - . - "^ILMN_\\d+$"^^ . - . - "Locus Reference Genomic" . - . - "false"^^ . - "dctypes" . - . - . - "infectious disease medicine" . - "https://www.clinicaltrials.gov/study/$1"^^ . - "http://purl.obolibrary.org/obo/WBbt_$1"^^ . - . - . - . - . - "NRFC051"^^ . - . - . - . - "HMS LINCS Compound" . - . - . - "genome" . - "Hans Ienasescu" . - "^\\d+$"^^ . - . - . - "one" . - . - "life science" . - . - . - "Provisional Cell Ontology" . - "obo" . - . - . - "Adrien Rougny" . - "Alzforum Mutations" . - "https://cordis.europa.eu/project/id/"^^ . - "dbpedia" . + "false"^^ . + . + . + . + "flopo" . + . + . + . + "biogrid" . + "characterisation data heat" . + "BioContext contains modular JSON-LD contexts for bioinformatics data." . + . + . + . + "http://purl.bioontology.org/ontology/IDODEN_"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_anat_$1"^^ . + . + . + . + . + . + "Aspergillus Genome Database" . + . + "http://geneontology.org/docs/gene-product-information-gpi-format/#$1"^^ . + "SitEx" . + . + "FMAID" . + "GRIN URL" . + . + . + . + . + . + . + . + . + . + "The Ambystoma Genetic Stock Center (AGSC) maintains a breeding colony of Mexican axolotls (Ambystoma mexicanum) and distributes axolotl embryos, larvae, and adults to laboratories and classrooms throughout the United States and abroad. [from homepage]"^^ . + . + "^YMDB\\d+$"^^ . + "https://bioregistry.io/polbase:"^^ . + . + . + . + . + . + "TopFind" . + . + . + "^\\d+$"^^ . + . + "http://multicellds.org/MultiCellDB/$1"^^ . + . + "^KCT\\d+$"^^ . + "cgrove@caltech.edu" . + "obo" . + . + "phylogenomics" . + "Molecular Interaction Database" . + "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."^^ . + . + . + "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id="^^ . + . + . + "e0333"^^ . + . + . + "scdo" . + "http://orion.rnet.missouri.edu/~nz953/DOMMINO/index.php/result/show_network/$1"^^ . + "bioinformatics" . + "Mondo Disease Ontology" . + . + . + . + "https://web-ast.dsi.cnrs.fr/l3c/owa/structure.infos_admin?&p_lab=$1&p_origine_appel=u"^^ . + "https://www.scopus.com/sourceid/"^^ . + "henriette007@ebi.ac.uk" . + . + . + . + "SCC111"^^ . + "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "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."^^ . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + "haendel@ohsu.edu" . + "miR-1"^^ . + . + . + . + "obstetrics" . + . + "structure" . + "false"^^ . + "pennsieve" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "https://aopwiki.org/events/"^^ . + "ontology" . + . + . + . + . + . + . + "^\\d+$"^^ . + "false"^^ . + . + "roundworm" . + . + "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."^^ . + . + "Experimental condition ontology" . + "TransportDB" . + . + "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://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=$1"^^ . + . + "4000027"^^ . + . + "^\\d{7}$"^^ . + . + "http://www.bindingdb.org/compact/$1"^^ . + "data governance" . + . + . + . + "drugbank.metabolite" . + . + . + "https://cryptodb.org/cryptodb/app/record/gene/"^^ . + . + "Bitbucket is a Git-based source code repository hosting service owned by Atlassian."^^ . + "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."^^ . + . + . + "http://purl.obolibrary.org/obo/PROCO_"^^ . + "https://publons.com/publon/$1"^^ . + "https://www.ebi.ac.uk/pdbsum/$1"^^ . + . + "http://purl.obolibrary.org/obo/PCO_"^^ . + "phenotype" . +_:N8f29cebc16e44d6c87f3a1f551121218 "pbrooks@hcfa.gov" . + . + "The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are 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."^^ . + "obo" . + . + . + "104674"^^ . + "fibroblast" . + . + "false"^^ . + "http://purl.obolibrary.org/obo/MIAPA_"^^ . + . + . + "http://www.ebi.ac.uk/cmpo/CMPO_"^^ . + . + . + "https://catalog.bcrc.firdi.org.tw/BcrcContent?bid="^^ . + . + . + . + "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc="^^ . + . + . + . + . + . + "http://metarray.ucsc.edu/cgi-bin/intron/yirIntrondb?orfName=$1"^^ . + "small molecule" . + . + . + . + "data science" . + . + . + . + "MycoBank is an online database, documenting new mycological names and combinations, eventually combined with descriptions and illustrations."^^ . + "computer science" . + . + "http://www.inoh.org/ontology-viewer/cgi-bin/InohOVAttr.php?type=IEV&id="^^ . + . + . + . + "TreeBASE" . + "sperm" . + "^\\d+$"^^ . + "^SEQF\\d+$"^^ . + "biochemistry" . + . + "^\\S+$"^^ . + . + . + . + "BIOZIL" . + "^PIRSF\\d{6}$"^^ . + . + "cath.domain" . + "PR" . + . + . + . + . + . + . + "https://www.xenbase.org/entry/"^^ . + . + . + . + . + . + "Human Disease Ontology" . + . + . + . + . + . + . + . + "http://database.deepsolar.space:18080/dbs/nlfff/$1"^^ . + . + . + . + "^\\d{7}$"^^ . + "Orthology Ontology" . + "ontology" . + "false"^^ . + "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . + . + "drug metabolism" . + "subject agnostic" . + . + . + "^\\d+$"^^ . + . +_:Ne1ca309b1b3c4995b4f70b52b7a65a7e "Crop Ontology Helpdesk" . + "http://purl.obolibrary.org/obo/PDRO_"^^ . + . + "Cell line databases/resources"^^ . + . + "false"^^ . + . + . + . . - . - "https://www.re3data.org" . - "^\\d{1,7}$"^^ . - "false"^^ . - . - "Golm Metabolome Database Analyte" . - . - "false"^^ . - . - "http://vocabularies.bridgedb.org/ops#$1"^^ . - "Supplier of mice for research purposes. [from RRID]"^^ . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/miRNAdetails.php?ID=$1"^^ . - _:Ne9d7876377624aa795c29d593ee4a373 . - . - "ontology" . - . - . + . + . + . + . + . +_:N368ac74c696846f0a3f1d215ab684b1f "gb-admin@ncbi.nlm.nih.gov" . + . + . + . + "disease" . + "^\\d+$"^^ . + . + . + "pharmacogenomics" . + "Jacqueline.Campbell@usda.gov" . + "http://purl.obolibrary.org/obo/OBA_$1"^^ . + . + "^\\d+$"^^ . + "http://bioinfo.iitk.ac.in/MIPModDB/result.php?code=$1"^^ . + . + "ontology" . + . + . + . + . + . + . + . + . + "Quantities, Units, Dimensions, and Types Ontology" . + . + . + . + . + . + "ensembl" . + . + . + . + . + "false"^^ . + "^SIGNOR\\-[A-Z]+\\d+$"^^ . + "https://shop.vbc.ac.at/vdrc_store/$1.html"^^ . + . + . + . + . + "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."^^ . + . + "Rice annotation Project database" . + . + . + . + "Observation"^^ . + . + "http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=$1"^^ . + "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . + . + . + . + . + "Marijane White" . + . + "Jingshan Huang" . + "UniProt Keywords" . + . + "https://w3id.org/seo#"^^ . + "NXPFA" . + . + . + "pride" . + . + "pcl" . + . + "virsi1909"^^ . + . + "anatomy" . + "005012"^^ . + . + "A vocabulary for representing latitude, longitude and altitude information in the WGS84 geodetic reference datum"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "^(MAM\\d{5}\\w)|(MAR\\d{5})$"^^ . + . + . + . + . + . + . + "false"^^ . + "An ontological version of MIABIS (Minimum Information About BIobank data Sharing)"^^ . + "AGROVOC" . + . + "false"^^ . + "Yeast-cell-cycle-Irons-J-Theor-Biol-2009"^^ . + . + . + "false"^^ . + . + "false"^^ . + "ontology" . + . + . + . + . + . + . + . + "6000122"^^ . + . + "15"^^ . + . + . + "GeneCards" . + . + . + "Integrated Canine Data Commons" . + . + "rs11603840"^^ . + . + . + "Human Proteome Map" . + "Protein Ensemble Database ensemble" . + . + "linguistics" . + . + "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."^^ . + . + . + . + . + "^F\\d+$"^^ . + . + . + "sh" . + . + "cell biology" . + . + . + "T039"^^ . + "https://bioregistry.io/reo:"^^ . + . + . + "0000004"^^ . + . + . + "1731"^^ . + . + . + . + "false"^^ . + "^\\S+$"^^ . + . + "upheno" . + . + "faseb list" . + . + . + "protein" . + . + . + . + . + . + . + . + "false"^^ . + "model" . + . + "IPD-IMGT/HLA" . + . + . + . + "https://mmp.sfb.uit.no/databases/mardb/#/records/$1"^^ . + "fdb8a927-45c3-48b7-9743-cbb5e16837fa"^^ . + . + . + "IntAct protein interaction database" . + . + "^MSBNK-[0-9a-zA-Z_]+-[A-Z0-9_]+$"^^ . + . + "https://www.sharkipedia.org/trends/$1"^^ . + . + "biomedical science" . + . + . + . + . + "The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species."^^ . + . + "Zhiliang Hu" . + "false"^^ . + "hinv.locus" . + "antibody" . + . + . + . + . + "An ontology of phenotypes covering microbes"^^ . + "JCRB1355"^^ . + "ontology" . + . + . "virology" . - . - . - "false"^^ . - "https://www.e-cyanobacterium.org/experiments-repository/?action=detail&id="^^ . - . - . -_:N80cd99ec595a4d0599dce7bf309e7f23 "AGROVOC Team" . - . - . + . + "giardiadb" . + . + . + "http://purl.obolibrary.org/obo/GOREL_"^^ . + . + . + . + "http://geneontology.org/docs/gene-product-information-gpi-format/#"^^ . + "life science" . + . + . + . + "^\\d+$"^^ . + . + . + . + "genome" . + . + . + . + . + "http://cicblade.dep.usal.es:8080/APID/Interactions.action?protein=$1"^^ . + . + . + "https://bioregistry.io/chemspider:"^^ . + "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name="^^ . + . + "https://orcid.org/$1"^^ . + "life science" . + . + . + . + "Resources used in the semantic web, inspired by [this list](https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml) in BioContext." . + . + . + . + . + . + . + "Simon Cox" . + "Cell line collections (Providers)"^^ . + "false"^^ . + "drugs" . + "earth science" . + "^\\d{7}$"^^ . + "genetic analysis" . + . + . + "https://ximbio.com/reagent/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/AERO_$1"^^ . + . + . + "^[a-zA-Z0-9_\\.]+$"^^ . + "Dublin Core Elements (1.1)" . + . + . + . + "cellular neuroscience" . + . + . + . + . + "false"^^ . + . + . + . + "gpcrnava" . + . + "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."^^ . + . + . + . + . + . + "https://portal.gdc.cancer.gov/cases/"^^ . + . + "None"^^ . + . + "health science" . + . + . + "sitex" . + "DBPedia Ontology" . + . + . + . + . + "http://senselab.med.yale.edu/NeuronDB/NeuronProp.aspx?id=$1"^^ . + . + . + . + . + "pypi" . + . + "protein" . + . + "https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm="^^ . + "Support Email" . + . + "https://www.ebi.ac.uk/ena/data/view/"^^ . + . + "false"^^ . + . + . + . + . + "wosid" . + "^\\d{7}$"^^ . + . + . + . + "classification" . + . + . + . + "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."^^ . + . + . + "life science" . + . + "go.resource" . + . + . + "genome" . + . + "dev.ga4ghdos" . + . + . + "http://www.cazy.org/$1.html"^^ . + "^\\d{1,7}\\-\\d{2}\\-\\d$"^^ . + . + . + . + "03212fd7_abfd_4828_9c8e_62c293052d4b"^^ . + . + . + . + . + "cattleqtldb" . + . + . + "760050"^^ . + "https://www.ncbi.nlm.nih.gov/nlmcatalog/$1"^^ . + . + . + . + . +_:Nffebff26bbc4479fa3f91e9a82d84254 "helpdesk@cropontology-curationtool.org" . + . + "NP_012345"^^ . + "biro" . + "pictar-vert" . + "Frédéric Bastian" . + . + . + . + . + . + "false"^^ . + . + . + . + "KW-1273"^^ . + "dentistry" . + . + . + . + "Ensembl" . + . + "true"^^ . + "https://cropontology.org/rdf/CO_337:$1"^^ . + . + . + . + . + . + . + "biochemistry" . + . + . + "23"^^ . + . + . + . + . + "biology" . + "141"^^ . + . + "https://www.kazusa.or.jp/rouge/gfpage/"^^ . + . + . + "International repository of Adverse Outcome Pathways."^^ . + . + "http://exac.broadinstitute.org/gene/$1"^^ . + . + "https://omia.org/OMIA"^^ . + "The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan."^^ . + . + "gold.genome" . + "SNR17A"^^ . + . + . + "kegg.compound" . + "02069237"^^ . + "0000070"^^ . + . + "^ENC[A-Za-z]{2}[0-9]{3}[A-Za-z]{3}$"^^ . + . + . + . + . + . + . + . + . + . + "Collection of European paediatric cardiac coding files"^^ . + . + . + . + . + . + "OriDB Schizosaccharomyces" . + . + "proteomics" . + . + . + . + "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."^^ . + . + "true"^^ . + "00030692-0FE1-4A1B-955E-A2E55D659267"^^ . + . + "Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types."^^ . + . + . + . + "Ruili Huang" . + "http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?prints_accn=$1&display_opts=Prints&category=None&queryform=false®expr=off"^^ . + "false"^^ . + . + . + . + . + . + . + "0000015"^^ . + . + . + "http://purl.obolibrary.org/obo/PLO_$1"^^ . + . + . + "Suggested Ontology for Pharmacogenomics" . + "genetics" . + . + "protozoan" . + . + . + "Plant Trait Ontology" . + "MESHD" . + "https://www.ncbi.nlm.nih.gov/snp/"^^ . + . + "http://www-deletion.stanford.edu/cgi-bin/YDPM/YDPM_search.cgi?thelist=$1"^^ . + "traits" . + "http://europepmc.org/articles/"^^ . + . + "false"^^ . + . + . + . + "WikiGenes" . + . + "ABE-0009634"^^ . + "https://lincs.hms.harvard.edu/db/antibodies/"^^ . + "ncats.bioplanet" . + . + "http://purl.obolibrary.org/obo/OHPI_$1"^^ . + . + . + "protein" . + . + "https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2022/php/detail.php?mirtid="^^ . + . + . + . + "CAPS-DB is a structural classification of helix-cappings or caps compiled from protein structures. The regions of the polypeptide chain immediately preceding or following an alpha-helix are known as Nt- and Ct cappings, respectively. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps."^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + "dragondb.protein" . + . + "MobiDB" . + . + . + "Petra Fey" . + "Integrated Taxonomic Information System" . + . + . + "19333"^^ . + "https://cropontology.org/rdf/CO_347:"^^ . + . + . + "Inge.Jonassen@uib.no" . + "relationships" . + . + "molecular physical chemistry" . + . + "http://purl.bioontology.org/ontology/HCPCS/"^^ . + . + . + . + "http://purl.obolibrary.org/obo/OGG_$1"^^ . + . + . + . + . + . + . + . + . + . +_:N380682f09f724f709aeda330a6daf3ea "info@wikidata.org" . + "http://www.maizegdb.org/cgi-bin/displaylocusrecord.cgi?id="^^ . + "AEO_RETIRED" . + . + "https://polbase.neb.com/polymerases/$1#sequences"^^ . + . + "^\\d+$"^^ . + "^/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$"^^ . + "The International Traditional Medicine Clinical Trial Registry (ITMCTR) is a non-profit online register of clinical trials being conducted in the field of traditional medicine. It isoperated by the China Academy of Chinese Medical Sciences and The China Center For Evidence Based Traditional Chinese Medicine. It is recognized as a Primary Registry of WHO, and contributes data to the WHO ICTRP. (from website)"^^ . + . + . + . + . + . + . + . + "https://foodb.ca/foods/$1"^^ . + "false"^^ . + "2023"^^ . + . + . + . + "knowledge and information systems" . + "EC-CODE" . + "1.10.8.10"^^ . + . + . + "Leigh Carmody" . + "true"^^ . + "0000215"^^ . + . + . + . + . + "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/$1"^^ . + "storedb.study" . + "false"^^ . + . + . + "baeverma@jcvi.org" . + . . - . - "^\\d+$"^^ . - . - . - "hmsl_id" . - "literalForm"^^ . - . - "dna" . - "25011"^^ . - . - "pocketome" . - . - "0000138"^^ . - . - . - . - "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."^^ . - "00000001"^^ . - "dbd" . - "https://www.nsf.gov/awardsearch/showAward?AWD_ID=$1"^^ . - "EC" . - . - . - . - "Collembola Anatomy Ontology" . - "This meta-ontology is self-describing. OBO metamodel properties are described using OBO metamodel properties"^^ . - . - . - . - "gene" . - . - . - . - "Pocketome is an encyclopedia of conformational ensembles of all druggable binding sites that can be identified experimentally from co-crystal structures in the Protein Data Bank. Each Pocketome entry corresponds to a small molecule binding site in a protein which has been co-crystallized in complex with at least one drug-like small molecule, and is represented in at least two PDB entries."^^ . - . - "biochemistry" . - "^InChI\\=1S?\\/[A-Za-z0-9\\.]+(\\+[0-9]+)?(\\/[cnpqbtmsih][A-Za-z0-9\\-\\+\\(\\)\\,\\/\\?\\;\\.]+)*$"^^ . - "geonames" . - "peff" . - "preclinical studies" . - "obo" . - "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."^^ . - "0000196"^^ . - . - . - "EDI_244000"^^ . - "^0[1-9]+0[0-9]+-0[1-9]+0[0-9]+$"^^ . - . - "dna" . - . - . - . - "Iranian Registry of Clinical Trials" . - . - "https://glyconavi.org/hub/?id="^^ . - "n2t" . - "TransportDB is a relational database describing the predicted cytoplasmic membrane transport protein complement for organisms whose complete genome sequence are available."^^ . - . - "https://bioregistry.io/fbol:"^^ . - . - "Unimod is a public domain database created to provide a community supported, comprehensive database of protein modifications for mass spectrometry applications. That is, accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all types of natural and artificial modifications. Other important information includes any mass change, (neutral loss), that occurs during MS/MS analysis, and site specificity, (which residues are susceptible to modification and any constraints on the position of the modification within the protein or peptide)."^^ . - . - "structure" . - . - . - "UK Provider Reference Number" . - "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - . - . -_:Nd62b24d3a8fe48d892050a1d27e387a3 "MedDRA MSSO" . - . - . - . - "FundRef" . - . - . - . - "Rat Resource and Research Center" . - . - "^m\\w+$"^^ . - . - "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://tritrypdb.org/tritrypdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . - "health science" . - "https://www.inaturalist.org/taxa/"^^ . - . - "small molecule" . - "false"^^ . - . - . - . - "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."^^ . - . - . - "^([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])$"^^ . - . - "false"^^ . - "75"^^ . - . - . - "false"^^ . - "Common Science and Technology Resources" . - . - "UniProt journal" . - . - . - . - "GNPS is a web-based mass spectrometry ecosystem that aims to be an open-access knowledge base for community-wide organization and sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS)"^^ . - "ProDom is a database of protein domain families generated from the global comparison of all available protein sequences."^^ . - . - . - . - "https://cropontology.org/rdf/CO_327:$1"^^ . - "aftol.taxonomy" . - "obo" . - . - "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."^^ . - . - . - . - . - . - "co_321" . - . - . - . - . - . - "NCBI Taxonomy" . - . - "http://database.deepsolar.space:18080/dbs/nlfff/"^^ . - . - . - "gene" . - "NCI Thesaurus" . - "EBI-366083"^^ . - . - . - . - . - . - . + "0000038"^^ . + . + . + "false"^^ . + . + . + "NLXINV includes funding agencies and some terms related to documenting scientific investigations data acquisition and analysis."^^ . + "s_mart_db" . + . + "alfred" . + "http://purl.obolibrary.org/obo/CDAO_"^^ . + "http://purl.obolibrary.org/obo/ECOCORE_$1"^^ . + . + . + . + . + "DragonDB is a genetic and genomic database for Antirrhinum majus (Snapdragon). This collection refers to allele information."^^ . + . + . + "ehdaa2" . + . + . + . + . + "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://www.molbase.com/en/index.php?app=search&search_keyword="^^ . + . + . + . + . +_:N1f3b094ee6cb47f5989b2a702e1e10e8 "NLM Customer Service" . + "gfo" . + . + . + "UniProtKB" . + . + "beiresources" . + . + . + . + "ncbigi" . + . + . + . + . + . + . + "An ontology for the standardization of terminology and integration of knowledge about Sickle Cell Disease."^^ . + . + . + "false"^^ . + "gene" . + . + "DataCollection"^^ . + . + . + . + . + "http://chemdb.niaid.nih.gov/CompoundDetails.aspx?AIDSNO=$1"^^ . + . + . + . + "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId="^^ . + . + . + . + . + "FAIRsharing Subject Ontology" . + . + "http://purl.obolibrary.org/obo/CLYH_$1"^^ . + . + . + . + "gbif" . + . + . + . + "Donny Winston" . + "https://coconut.naturalproducts.net/compound/coconut_id/$1"^^ . + "life science" . + . + . + . + . + "emsl.project" . + "^\\d{7}$"^^ . + "^\\w+$"^^ . + . + . + . + . + . + . + . + . + . + "false"^^ . + "Illumina Probe Identifier" . + . + . + . + . + . + . + . + "The Terminology for Description of Dynamics (TEDDY) is an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology."^^ . + . + . + "false"^^ . + . + "WoRMS-ID for taxa" . + . + . + "https://bioregistry.io/dashr.expression:"^^ . + . + "lrg" . + . + . + . + . + . + . + . + . + "Animal Genome QTL" . + "Chris Stoeckert" . + "https://www.ebi.ac.uk/QuickGO/GProtein?ac="^^ . + . + "Vaccine administered code set" . + "false"^^ . + "ontology" . + "Human Intermediate Filament Database" . + . + . + . + "NA06985"^^ . + . + . + "false"^^ . + "life science" . + . + . + . + . + . + "2842"^^ . + "BRENDA is a collection of enzyme functional data available to the scientific community. Data on enzyme function are extracted directly from the primary literature The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data."^^ . + "false"^^ . + "protein" . + "GR:0080039"^^ . + . + . + "^\\d+$"^^ . + "RO_proposed_relation" . + "ShareLoc" . + . + "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice=$1"^^ . + "^\\d{7}$"^^ . + . + "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]."^^ . + "^\\d{6}$"^^ . + "VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis."^^ . + "^\\d+$"^^ . + . + . + "genotype" . + . + . + . + . + "http://www.cellsignal.com/reference/pathway/$1.html"^^ . + "KEGG Reaction Class" . + . + "The Medical Dictionary for Regulatory Activities (MedDRA) was developed by the International Council for Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH)to provide a standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans. It is used within regulatory processes, safety monitoring, as well as for marketing activities. Products covered by the scope of MedDRA include pharmaceuticals, biologics, vaccines and drug-device combination products. The MedDRA dictionary is organized by System Organ Class (SOC), divided into High-Level Group Terms (HLGT), High-Level Terms (HLT), Preferred Terms (PT) and finally into Lowest Level Terms (LLT)."^^ . + . + "http://mycobrowser.epfl.ch/smegmasearch.php?gene+name="^^ . + "Confident makes descriptive metadata on conferences and other formats of scientific events permanently accessible in a high quality through automated processes and scientific data curating."^^ . + . + . + . + "kegg.pathway" . + . + . + . + . + . + "Computer Retrieval of Information on Science Projects Thesaurus" . + . + "Adnan Malik" . + "RYYVLZVUVIJVGH-UHFFFAOYSA-N"^^ . + . + "^\\d+$"^^ . + "^\\d+$"^^ . + . + "0000546"^^ . + . + . + . + "geonames.feature" . + "dna" . + . + "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."^^ . + . + "enzyme" . + "pubchem.assay" . + . + . + "owl" . + "false"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "ontology" . + . + . + . + . + "obo" . + . + "1200031"^^ . + . + . + . + "life science" . + . + . + "http://purl.obolibrary.org/obo/OARCS_"^^ . + . + . + . + . + . + "SPAR Ontologies" . + . + . + . + . + "ctibor.skuta@img.cas.cz" . + . + . + . + "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."^^ . + "policy" . + . + . + . + . + . + . + . + . + "omics" . + . + "pwo" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/COVIDO_$1"^^ . + . + "identifier for a chemical compound per EINECS or ELINCS"^^ . + . + "Medical Action Ontology" . + "bridgedb" . + . + "enzyme" . + "Phenoscape Publication" . + . + "AmoebaDB" . + . + . + . + . + "diseasesdb" . + "^\\d{7}$"^^ . + . + "The German Clinical Trials Register (DRKS) is the German WHO primary registry. It is competent for the registration of all patient-oriented clinical trials conducted in Germany. The DRKS now contains well over 14,000 studies. Currently, around 2,000 studies are added annually. (from website)"^^ . + . + . + . + "Xenobiotics Metabolism Database" . + "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)."^^ . + . + . + . + . + . + "^TS-\\d{4}$"^^ . + "Philip.Stroemert@tib.eu" . + . + "false"^^ . + . + "http://plugins.biogps.org/cgi-bin/wp.cgi?id="^^ . + "http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name="^^ . + . + "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."^^ . + . + "genome" . + . + "false"^^ . + . + "phenotype" . + . + "Richard Scheuermann" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OHMI_"^^ . + "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID="^^ . + . + "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://cropontology.org/rdf/CO_321:$1"^^ . + . + . + "diseaseclass" . + . + . + . + . + "00000674"^^ . + . + . + "biomedical science" . + . + "H-InvDb Locus" . + "MJoachimiak@lbl.gov" . + . + . + . + . + "http://purl.obolibrary.org/obo/RNAO_$1"^^ . + . + . + "PIRSF000100"^^ . + . + "false"^^ . + . + "computational biology" . + . + . + . + . + . + . + . + "0000029"^^ . + . + . + "Taxonomic rank vocabulary" . + "gene" . + . + "https://www.ebi.ac.uk/metabolights/$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."^^ . + . + "false"^^ . + "om" . + "0000001"^^ . + . + . + . + . + . + . + "true"^^ . + . + "tgv139393198"^^ . + . + . + "http://string.embl.de/interactions/$1"^^ . + "http://purl.obolibrary.org/obo/SYMP_"^^ . + "DailyMed" . + "http://purl.obolibrary.org/obo/NCRO_$1"^^ . + "https://biopragmatics.github.io/providers/msigdb/"^^ . + . + "taxonomy" . + "http://purl.obolibrary.org/obo/VTO_$1"^^ . + "virology" . + "https://biomedit.ch/rdf/sphn-ontology/sphn#$1"^^ . + "biology" . + . + . + . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + . + "biomedical science" . + . + . + . + "Q5BJF6-3"^^ . + . + . + . + . + . + . + . + . + "Alzheimer Gene Database" . + . + "SitEx is a database containing information on eukaryotic protein functional sites. It stores the amino acid sequence positions in the functional site, in relation to the exon structure of encoding gene This can be used to detect the exons involved in shuffling in protein evolution, or to design protein-engineering experiments."^^ . + . + . + . + "Metabolites in the Xenobiotics Metabolism Database."^^ . + . . - . - "01N50ZZ"^^ . + . + . + . + "^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9])|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])$"^^ . + "ontology" . + . + . + . + . + . + "ontology" . + . + . + . + "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://github.com/"^^ . + . + . + . + "foodex2" . + . + . + "https://datanator.info/reaction/$1"^^ . + . + "http://clipserve.clip.ubc.ca/topfind/proteins/"^^ . + . + . + "enzymology" . + "The Bioinorganic Motif Database" . + . + . + . + "pathway" . + . + "subject agnostic" . + . + . + . + "ontology" . + . + "computer science" . + "^Rv\\d{4}(A|B|c)?$"^^ . + "The Lepidoptera Anatomy Ontology contains terms used for describing the anatomy and phenotype of moths and butterflies in biodiversity research."^^ . + . + . + . + _:Nda1f307f111446f48481d11b881079b1 . + "^DP\\d{5}r\\d{3}$"^^ . + "e.arnaud@cgiar.org" . + . + . + . + . + "https://aopwiki.org/aops/$1"^^ . + . + "http://purl.obolibrary.org/obo/PPO_"^^ . + . + "http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/gpcr_information.php?id=$1"^^ . + . + . + . + . + "biochemistry" . + . + . + "https://gnomad.broadinstitute.org/variant/"^^ . + . + . + . + . + . + "https://www.clinicaltrialsregister.eu/ctr-search/search?query="^^ . + . + "reto" . + . + "rnajunction" . + . + . + . + . + . + "jstor" . + . + "true"^^ . + "txpo" . + . + . + . + . + . + "obo" . + . + "genes" . + "false"^^ . + . + "torsten.schwede@unibas.ch" . + . + "0000054"^^ . + . + . + . + . + "false"^^ . + . + . + "obo" . + . + . + . + "false"^^ . + . + . + . + "false"^^ . + "http://purl.org/pav/$1"^^ . + . + "http://ciliate.org/index.php/feature/details/"^^ . + "Identifier used by the Cancer Chemotherapy National Service Center."^^ . + "http://purl.obolibrary.org/obo/EPIO_"^^ . + . + . + . + . + . + "signor" . + "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#$1"^^ . + . + "https://repo.napdi.org/study/$1"^^ . + . + "Odor Molecules DataBase" . + . + . + "bioinformatics" . + "ontology" . + . + . + . + . + . + . + . + "SO-Pharm (Suggested Ontology for Pharmacogenomics) is a domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. SO-Pharm articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables to represent pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables to represent patient and more largely panel included in trials, and populations. SO-Pharm enables the representation of measured items on this patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains."^^ . + . + . + . + . + . + "IHW09326"^^ . + . + . + . + . + "biomedical science" . + "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."^^ . + . + . + . + . + . + . + "https://alfred.med.yale.edu/alfred/recordinfo.asp?UNID="^^ . + . + "life science" . + "Jennifer L Harrow" . + "mmp.cat" . + "life science" . + . + "ICD9CM_2005" . + . + . + . + . + . + . + . + . + . + . + . + "http://stormo.wustl.edu/ScerTF/details/$1"^^ . + . + . + "http://www.pseudomonas.com/feature/show/?locus_tag="^^ . + . + . + . + . + . + . + "ASPL0000349247"^^ . + . + "https://www.uniprot.org/locations/$1"^^ . + . + . + "^\\w+$"^^ . + . + . + "^\\d+$"^^ . + "http://www.drugbank.ca/drugs/$1"^^ . + . + . + _:Nac74b2e569134e4aa3278a0ee126d26d . + . + . + "genome" . + "mixs" . + . + . + . + . + . + "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."^^ . + . + . + . + . + . + . + . + . + . + "http://genome.crg.es/datasets/abs2005/entries/$1.html"^^ . + . + "expression" . + "http://purl.obolibrary.org/obo/NGBO_"^^ . + . + . + "false"^^ . + "gene expression" . + . + . + . + . + "A database to support glycobiology and glycomics research. Its main focus is on 3D structures, including 3D structure models as well as references to PDB entries that feature carbohydrates."^^ . + . + "The COVID-19 epidemiology and monitoring ontology" . + . + . + . + . + . + . + . + "SNP500Cancer" . + . + . + . + . + . + "rna" . + . + "OTTHUMG00000169812"^^ . + "metascience" . + . + . + "http://purl.obolibrary.org/obo/REO_$11"^^ . + . + . + "ontology" . + . + "^MMP\\d+.\\d+$"^^ . + "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."^^ . + "agrovoc" . + . + "enzyme" . + . + . + "http://www.mycobank.org/Biolomics.aspx?Table=Mycobank&MycoBankNr_=$1"^^ . + "vido" . + "^5\\d{4}$"^^ . + . + . + . + "microbial" . + . + . + . + . + "false"^^ . + "Christine Pourcel" . + . + . + "hasOpenAccessRating"^^ . + . + . + . + "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."^^ . + . + . + . + . + . + "genetics" . + "The conference-ontology is a new self-contained ontology for modelleing knowledge about conferences. The conference-ontology adopts best ontology design practices (e.g., Ontology Design Patterns, ontology reuse and interlinking) and guarantees interoperability with SWC ontology and all other pertinent vocabularies. (from homepage)"^^ . + . + . + . + "life science" . + "0000001"^^ . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . "life science" . - . - . - . - . - . - . - "development" . - . - . - . - . - . - . - "^\\d+$"^^ . - . - "obo" . - . - . - "ontology" . - "An experimental run, served thrugh the ENA"^^ . - "false"^^ . - . - . - . - "odam" . - "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"^^ . - "biological Process Inference from eXperimental Interaction Evidence/Microarray Experiment Functional Integration Technology" . - . - "true"^^ . - "International Traditional Medicine Clinical Trial Registry" . - . - . - "preclinical studies" . - . - . - "model" . - "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."^^ . - . - . - "life science" . - . - "http://www.cellresource.cn/cellsearch.aspx?sc=1&where="^^ . - "811"^^ . - . - . - "NCT00222573"^^ . - . - "http://bioportal.bioontology.org/ontologies/MEDDRA?p=classes&conceptid=$1"^^ . - "ontology" . - "molbase" . - "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:$1"^^ . - "^ISRCTN\\d+$"^^ . - . - . - . - . - . - . - . - "life science" . - . - "mouse" . - "http://purl.org/spar/deo/$1"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "https://cropontology.org/rdf/CO_335:"^^ . - "ncats.bioplanet" . - "biomedical science" . - "000140" . - . - . - . - . - . - "Benchmark Energy & Geometry Database" . - . - . - . - "pesticides" . - . - . - "false"^^ . - "^\\d+$"^^ . - "MassBank is a federated database of reference spectra from different instruments, including high-resolution mass spectra of small metabolites (<3000 Da)."^^ . - "BLL"^^ . - . - "^\\d+$"^^ . - . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "^\\d+$"^^ . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + "277.9"^^ . + "^\\d+$"^^ . + . . - "http://purl.obolibrary.org/obo/OGSF_"^^ . - "microbiology" . - . - . - . - . - . - . - "proteomics" . - . - . - . - "life science" . - . - . - "Melissa Haendel" . - . - . - . - . - "false"^^ . - . - "Tree of Life Web Project" . - . - "https://www.deciphergenomics.org/syndrome/"^^ . - . - "cdd" . - . - . - "http://ratmap.org/Showgene.php?gene_stable_id=$1"^^ . -_:Na592003593484832bee836301b205107 "vladimir.n.mironov@gmail.com" . - "https://n2t.net/$1:$2" . - . - . - . - . - . - . - . - . - . - "collagenmutdb" . - . - . - . - "0376"^^ . - "https://viralzone.expasy.org/$1"^^ . - "^\\d+$"^^ . - "Surjeet Kumar Arya" . - . - . - . - . - "^\\d+$"^^ . - . - "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym="^^ . - "https://www.ndexbio.org/viewer/networks/"^^ . - . - . - . - "KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number system) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG relational database with additional annotation of reaction hierarchy and sequence data links."^^ . - "false"^^ . - . - "cido" . - "^(SMP|PW)\\d+$"^^ . - . - . - "biomedical science" . - "genome" . - "clb" . - . - "false"^^ . - "Pfam" . - . - . - . - . - "http://scicrunch.org/resolver/SCR_$1"^^ . - "^4DN[A-Z]{2}[A-Z0-9]{7}$"^^ . - . - "biomedical science" . - . - . - . - . - "This ontology represents concepts related to homology, as well as other concepts used to describe similarity and non-homology."^^ . - . - . - . - "http://multicellds.org/MultiCellDB/"^^ . - "protein" . - . - . - . - . - "Starting in the fall of 2007, a collaborative group of influenza researchers have established an influenza ontology. The influenza ontology is an application ontology. Consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)"^^ . - . - "https://books.google.com/books?id="^^ . - "0000080"^^ . - . - "br/1"^^ . - . - . - "paxdb.organism" . - "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"^^ . - . - . - "data management" . - . - "sio" . - "TP53"^^ . - . - "^[A-Z0-9]{5}\\d+$"^^ . - . - . - . - "genetics" . - . - "qualities" . - . - "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . - . - . - . - . - "bcgo" . - . - . - . - "00000"^^ . - "https://www.wikidata.org" . - . - . - "Livestock Breed Ontology" . -_:N95d3105b2cdf4400a57957c9d02ead48 "albertgoldfain@gmail.com" . - "isbn" . - . - . - . - "http://qudt.org/schema/qudt#$1"^^ . - "https://www.ncbi.nlm.nih.gov/research/cog/cog/"^^ . - . - . - . - . - . - . - . - . - "true"^^ . - . - . - . - . - "VegBank" . - "https://www.vmh.life/#gene/"^^ . - "CIViC Therapy" . - "Karen Eilbeck" . - "organic chemistry" . - . - . - . - . - . - "24867"^^ . - "false"^^ . - . - "http://www.gramene.org/db/literature/pub_search?ref_id="^^ . - "http://purl.obolibrary.org/obo/"^^ . - . - "interaction" . - "CIViC gene" . - "0000040"^^ . - . - "miRNEST" . - . - "SNOMEDCT_US_2018_03_01" . - . - "589462"^^ . - . - . - "^\\d+$"^^ . - . - . - "https://bioregistry.io/vipr:"^^ . - . - "BioKC (Biological Knowledge Curation), is a web-based collaborative platform for the curation and annotation of biomedical knowledge following the standard data model from Systems Biology Markup Language (SBML)."^^ . - . - . - "genome" . - "Database containing promotor sequences found in Saccharomyces cerevisiae."^^ . -_:N226ad9bb06704cbfb4da47042ff528b0 "helpdesk@cropontology-curationtool.org" . - . - . - . - "gcst" . - . - . - . - . - . - "false"^^ . - "Genetic and Rare Diseases Information Center" . - . - . - . - "chemical biology" . - . - . - . - "obo" . - "dbvar.variant" . - . - "biomedical science" . - "Unimod protein modification database for mass spectrometry" . - "An organization in FAIRsharing, including universities, labs, etc."^^ . - "genomics" . - . - . - "http://purl.obolibrary.org/obo/SPD_"^^ . - . - "http://fossilworks.org/?a=referenceInfo&reference_no="^^ . - . - "biomedical science" . + . + . + . + . + "60316"^^ . + . "sedml.format" . - "https://go.drugbank.com/metabolites/"^^ . - . - . - . - . - "genecards.geneloc" . - . - "medicine" . - . - . + . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + "SpBase" . + . + . + . + "^\\d+$"^^ . + . + . + . + "4DN" . + . + . + . + . + "https://www.ebi.ac.uk/gxa/genes/$1"^^ . . - . + "https://www.fishbase.ca/summary/"^^ . + . + . + "subtiwiki" . + . + . + . . - . - . - . - . - . - "Aromatic"^^ . - "false"^^ . - . - . - . - . - "chemistry" . - . - "The Alan Wood’s Pesticides is a compendium of pesticides which contain nomenclature data sheets for more than 1700 different active ingredients."^^ . - . - . - "false"^^ . - "inhibitors" . - . - . - "true"^^ . - . - . - "HBG004341"^^ . - "true"^^ . - "The World-2DPAGE database" . - . - . - . - . - "Dataset"^^ . - . - . - . - . - "Molbase provides compound data information for researchers as well as listing suppliers and price information. It can be searched by keyword or CAS indetifier."^^ . - . - "datf" . - "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID=$1"^^ . - . - "^GLDS-\\d+$"^^ . - . - . - . - . - "^\\w+(\\.)?\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - "The Bibliographic Ontology" . - . - "nif.std" . - . - . - "umbbd.reaction" . - . - . - "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."^^ . - . - "false"^^ . - "genome" . - . - "false"^^ . - . - . - . - . - . - . - . - . - "mmmp.biomaps" . - . - . - . - "life science" . - . - . - . - "https://fungidb.org/fungidb/app/record/gene/$1"^^ . - "KESTREL Ontology" . - "http://purl.obolibrary.org/obo/PSO_"^^ . - . - . - . - . - "nanotechnology" . - . + . + _:N45e4474439d94b1c85c9d3a15c3a1d47 . + . + . + "genome" . + . + "stato" . + . + . + "DisProt is a database of intrisically disordered proteins and protein disordered regions, manually curated from literature."^^ . + "biology" . + . + . + "The Dietary Restriction Gene Database" . + "^\\d+$"^^ . + . + . + . + . + "false"^^ . + "life science" . + . + . + . + . + . + . + . + "BeAn 70563"^^ . + . + . + "ontology" . + "Célia Michotey" . + "EB0170"^^ . + "^(bsg-[dscp]?\\d{6})|(FAIRsharing\\.\\w+)$"^^ . + . + "fbdv" . + . + . + "SNOMEDCT_US_2021_09_01" . + . + . + . + "Brian Aevermann" . + "genome" . + . + "https://www.genenames.org/cgi-bin/gene_symbol_report?match="^^ . + . + "OrthoDB" . + . + . + . + . + . + "Chickpea ontology" . + . + . + "molecules" . + . + . + . + "KEGG Reaction" . + . + "false"^^ . + . + . + . + . + . + "Dataset"^^ . + . + . + . + . + . + "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."^^ . + "life science" . + . + . + . + "pathogen" . + . + . + "cd00400"^^ . + "https://www.ebi.ac.uk/miriam/main/$1"^^ . + . + "UTRdb" . + . + _:N947c2ef4044f49f18bd9f0caf7c87ee6 . + "0019030"^^ . + "FCB005"^^ . + . + . + . + "MMsINC" . + "http://www.grenoble.prabi.fr/obiwarehouse/unipathway/ucr?upid=$1"^^ . + . + . + . + . + "CTX" . + "false"^^ . + . + . + "http://bigg.ucsd.edu/compartments/$1"^^ . + . + "genotyping" . + . + "MarRef" . + "http://emmo.info/emmo#EMMO_$1"^^ . + "grsdb" . + . + . + "https://biomedit.ch/rdf/sphn-ontology/sphn#"^^ . + . + . + . + "protein" . + . + . + "LCSCCPN"^^ . + . + . + . + "clinvar.record" . + "^MAM\\d{5}\\w$"^^ . + "true"^^ . + . + . + . + . + "214100"^^ . + . + "NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons."^^ . + "https://flybase.org/reports/FBtc$1"^^ . + . + . + . + . + "false"^^ . + "03yrm5c26"^^ . + . + . + . + . + . + . + . + . + . + "https://flowrepository.org/id/$1"^^ . + . + . + . + "false"^^ . + "https://www.inaturalist.org/users/$1"^^ . + "D00001"^^ . + . + "880798137"^^ . . - . - "ucsc" . - . - "http://www.kegg.jp/entry/"^^ . - . - . - . - . - "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."^^ . - . - . - . - . - "small molecule" . - . - . - "http://webapps2.ucalgary.ca/~groupii/cgi-bin/intron.cgi?name=$1"^^ . - "false"^^ . - "protein" . - . - "GeoNames" . - . - . - "The Symptom Ontology has been developed as a standardized ontology for symptoms of human diseases."^^ . - . - . - . - "Peer Bork" . - "gene" . - . - . - . + . + . + . + . + . + "plo" . + . + . + . + . + "github" . + . + . + . + . + . + . + "pathways" . + . + . + "gene" . + . + . + "ab-1-ha"^^ . + . + . + . + . + . + "genomics" . + . + . + . + "identifier for an organisation in author affiliations per Scopus"^^ . + . +_:N17235b39f30847fc8a5e42bdd6482ff2 "PhenX Admin" . + . + . + . + . + . + . + . + . + . + "zoology" . + . + . + . + . + . + "PRJDB3"^^ . + . + . + . + . + "true"^^ . + . + . + "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."^^ . + . + "protein" . + . + "ontology" . + "https://neurovault.org/collections/$1"^^ . + . + "Regulatory Elements Database for Drosophila" . + "false"^^ . + "^\\w+$"^^ . + . + . + "Ceri Van Slyke" . + "ubio.namebank" . + . + "0000057"^^ . + . + "domain" . + . + "Causal_Graphical_Model"^^ . + . + "dna" . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_br_"^^ . + "cell lines" . + "false"^^ . + . + . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "ndc" . + . + . + "^\\d+$"^^ . + . + . + . + . + "Mike Cherry" . + . + . + . + . + . + . + . + "biochemistry" . + . + . + . + . + . + "classification" . + . + . + "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id="^^ . + "obcs" . + . + . + . + "https://www.uniprot.org/keywords/"^^ . + . + . + . + . + . + . + . + "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."^^ . + . + "ChemDB" . + . + "mo" . + "false"^^ . + . + "aap-1"^^ . + "E00002"^^ . + . + "ARBA00000001"^^ . + . + . + "biomodels.kisao" . + . + "false"^^ . + . + . + "ctd.chemical" . + "https://cropontology.org/rdf/CO_326:$1"^^ . + . + "anatomy" . + . + "false"^^ . + . + . + . + . + . + . + . + "PIR Superfamily Classification System" . + . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/gene/detail/$1"^^ . + . + . + "10087"^^ . + . + . + . + . + "ontology" . + . + "http://www.signaling-gateway.org/molecule/query?afcsid="^^ . + "paul.fabry@usherbrooke.ca" . + . + "https://biopragmatics.github.io/providers/pba/"^^ . + . + . + . + . + . + "The cell line vocabulary inside FlyBase"^^ . + . + . + . + "https://www.clinicaltrials.gov/study/$1"^^ . + . . - "nlx.sub" . - "https://pubchem.ncbi.nlm.nih.gov/compound/$1"^^ . - . - "The mission of the Clinical Trials Registry-India (CTRI) is to ensure that all clinical trials conducted in India are prospectively registered, i.e. before the enrolment of the first participant. Additionally, post-marketing surveillance studies, BA/BE studies as well as clinical studies as part of PG thesis are also expected to be registered in the CTRI. (from homepage)\n\nNote that the identifier in this semantic space is not the one used in the webpages"^^ . - . - . - . - "http://www.viprbrc.org/brc/viprStrainDetails.do?strainName=$1&decorator=arena"^^ . - . - . - "0003003"^^ . - . - "0000001"^^ . - "Adriano Rutz" . - "http://purl.obolibrary.org/obo/GSSO_$1"^^ . - "taxonomy" . - "82"^^ . - "ecyano.experiment" . - . - . - "ontology" . - . - "NASA GeneLab" . - . - . - . - . - . - . - "regulation" . - . - "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." . - . - . - . - "ena" . - . - . - . - . + "0000050"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "^\\d+$"^^ . + . + "CutDB" . + . + . + "https://bioregistry.io/collection/"^^ . + . + . + "ontology" . + "Library of Congress Subject Headings (LCSH) has been actively maintained since 1898 to catalog materials held at the Library of Congress. (from homepage)"^^ . + "http://www.scopus.com/record/display.url?origin=inward&eid=$1"^^ . + . + . + "^MCDS_L_[a-zA-Z0-9]{1,10}$"^^ . + . + . + "The dbEST contains sequence data and other information on \"single-pass\" cDNA sequences, or \"Expressed Sequence Tags\", from a number of organisms."^^ . + . + "co_346" . + . + . + "biology" . + . + . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?uid=$1"^^ . + "scopus.author" . + "https://www.kazusa.or.jp/huge/gfpage/$1"^^ . + . + "humanities" . + "https://mmp.sfb.uit.no/databases/marfun/#/records/"^^ . + . + "NameBank is a \"biological name server\" focused on storing names and objectively-derived nomenclatural attributes. NameBank is a repository for all recorded names including scientific names, vernacular (or common names), misspelled names, as well as ad-hoc nomenclatural labels that may have limited context."^^ . + . + "0000504"^^ . + "^\\d+$"^^ . + . + . + . + . + . + "co_323" . + "obo" . + . + . + . + . + "Scholarly Contributions and Roles Ontology" . + . + "beta cell" . + "^\\d+$"^^ . + . + "http://purl.obolibrary.org/obo/OBA_"^^ . + . + "cheminformatics" . + "The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community (from https://gnomad.broadinstitute.org)."^^ . + . + . + . + . + . + "botany" . + . + . + "biomedical science" . + . + . + . + . + . + "37232"^^ . + . + "An ontology of core ecological entities" . + "life science" . + "Interlinking Ontology for Biological Concepts" . + . + . + "Software Package Data Exchange License" . + "FamPlex" . + "https://rfam.xfam.org/family/$1"^^ . + . + "^\\d{8}$"^^ . + . + . + "https://lincs.hms.harvard.edu/db/cells/$1"^^ . + . + "medicine" . + "false"^^ . + "false"^^ . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_chem_$1"^^ . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://genelab-data.ndc.nasa.gov/genelab/accession/$1"^^ . + . + . + "DrugBank Drug Category" . + "Alex Bateman" . + . + . + . + . + "false"^^ . + "http://www.depod.bioss.uni-freiburg.de/showp.php?gene="^^ . + . + "^\\d+$"^^ . + "Data Science Ontology" . + . + "protein" . + . + . + . + "C. elegans ORFeome cloning project" . + . + . + . + "Archival Resource Key" . + "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession="^^ . + "abcd" . + . + "bioproject" . + . + "^\\d+$"^^ . + "MicrobeamManipulation"^^ . + "ontology" . + . + "false"^^ . + . + . + "^\\w+(\\_)?\\d+(\\.\\d+)?$"^^ . + "anatomy" . + "life science" . + . + . + . + . + "chembl" . + . + . + . + "MetaNetX compartment" . + . + . + . + . + "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id=$1"^^ . + "http://intron.ucsc.edu/cgi-bin/yeast4.3/intronreports.pl?outputformat=full&orfName=$1"^^ . + "genome" . + . + "^TTDS\\d+$"^^ . + "ZDB-GENE-041118-11"^^ . + "Alpha Tom Kodamullil" . + "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."^^ . + "false"^^ . + . + . + "version control" . + "antweb" . + . + "Vertebrate Breed Ontology is an ontology created to serve as a single computable resource for vertebrate breed names."^^ . + . + "Web of Science ID (work)" . + . + "life science" . + . + . + . + . + "090201"^^ . + . + . + . + "ontology and terminology" . + "NLXORG" . + "^\\d+$"^^ . + . + . + . + "false"^^ . + "ICD9CM_2006" . + . + "Ctenophore Ontology" . + "https://gen3.biodatacatalyst.nhlbi.nih.gov/ga4gh/drs/v1/objects/$1"^^ . + "rtecs" . + . + "https://glygen.org/glycan/$1"^^ . + . + . + . + . + . + . + "http://qudt.org/schema/qudt#$1"^^ . + . + "http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=$1"^^ . + "Tribolium Genome Database -- Insertion" . + "Michelle Giglio" . + . + . + "false"^^ . + . + . + "^\\d+(\\.[A-Z])?(\\.\\d+)?(\\.\\d+)?(\\.\\d+)?$"^^ . + . + . + "http://metlin.scripps.edu/metabo_info.php?molid=$1"^^ . + . + . + "classification" . + "medicine" . + "AgrO is an ontlogy for representing agronomic practices, techniques, variables and related entities"^^ . + . + . + . + . + . + . + . + . + "dna" . + "Q2207226"^^ . + . + "c elegans" . + . + . + . + . + . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=$1"^^ . + . + "ontology" . + "false"^^ . + "false"^^ . + . + "https://bioregistry.io/dragondb.dna:"^^ . + "Coverage of the terminology appearing in JMLA was extended with terms from MeSH, NCI Thesaurus (NCI), Emtree, the HTA Database Canadian Repository [international repository for health technology assessment], and Robert Sandieson's synonym ring for research synthesis. Collected terms were enriched with terms from the NCI Metathesaurus. Variants include synonyms for preferred terms, singular and plural forms, and American and British spellings. Definitions, if they exist, are mainly from MeSH, NCI, Emtree, and medical dictionaries."^^ . + "noncodev3" . + . + . + "http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA="^^ . + . + . + . + . + "map" . + "SM_UB-81"^^ . + . + . + . + . + "^\\d+$"^^ . + . + "homd.seq" . + . + "COMBINE specifications" . + . + "DIP-743N"^^ . + . + . + "4005"^^ . + . + . + "Annika Jahnke-Bornemann" . + . + . + "0002533"^^ . + "mamo" . + . + . + "http://purl.obolibrary.org/obo/MAXO_$1"^^ . + "ontology" . + "Rosa2"^^ . + "false"^^ . + . + "https://shareloc.xyz/#/ontology/vocabulary/SHARELOC_$1"^^ . + . + "http://wheat.pw.usda.gov/report?class=gene;name="^^ . + _:N380682f09f724f709aeda330a6daf3ea . + "ontology" . + "sabiork.reaction" . + "eupath" . + . + "http://rdfs.org/ns/void#$1"^^ . + "ontology" . + "dna" . + "obo" . + "^\\d{7}$"^^ . + . + . + "obo_rel" . + "Trish Whetzel" . + . + "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . + . + . + "http://purl.obolibrary.org/obo/SEP_"^^ . + . + "snap" . + . + . + . + "false"^^ . + . + . + . + . + "fabio" . + "https://metazoa.ensembl.org/id/$1"^^ . + . + "genetics" . + . + "illumina.probe" . + . + . + . + "https://bioregistry.io/proteomicsdb.protein:"^^ . + . + . + "rgd" . + "anatomy" . + "https://tetrahymena.vet.cornell.edu/display.php?stockid="^^ . + "agriculture" . + "^B\\d+$"^^ . + . + . + . + "biomedical science" . + . + "Carsten Linder" . + "anatomy" . + . + . + . + "https://bioregistry.io/go.rule:"^^ . + . + "false"^^ . + . + . + "sao" . + "Sustainable Development Goals Interface Ontology" . + . + . + "CHEBI" . + "Literature references in Gramene"^^ . + "MTHICD9_2006" . + . + . + "genomics" . + "Environmental conditions, treatments and exposures ontology" . + "https://abrc.osu.edu/stocks/number/SALK_"^^ . + . + "ICARDA - TDv5 - Sept 2018"^^ . + "false"^^ . + . + . + . + . + "ncit" . + "https://www.internationalgenome.org/data-portal/sample/"^^ . + . + . + . + "^ISRCTN\\d+$"^^ . + . + . + "NLFFF Database" . + . + . + . + "plasmodb" . + . + "FBdv" . + "hao" . + "CNBG_0001"^^ . + . + . + "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary"^^ . + . + . + "Gene Wiki" . + "pierre-alain.binz@chuv.ch" . + . +_:N4d553228bdc9474894f812f565b509c7 "j.bard@ed.ac.uk" . + "PRI10"^^ . + . + . + . + . + . + "KEGG Glycan" . + . + . + . + . + . + "http://www.bioinfo.org/NONCODEv4/show_rna.php?id="^^ . + "nb100-56351"^^ . + "http://purl.obolibrary.org/obo/IPR_$1"^^ . + "functional genomics" . + . + . + "http://func.mshri.on.ca/fly/genes/list_functional_scores/"^^ . + "false"^^ . + . + . + . + . + . + . + . + "^A\\d+$"^^ . + "cell biology" . + . + . + . + . + . + . + . + . + . + . + "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 Open Data Commons for Spinal Cord Injury is a cloud-based community-driven repository to store, share, and publish spinal cord injury research data."^^ . + . + "Decentralized Biomedical Ontology" . + "hdr" . + "uniprot.location" . + "Biological Spatial Ontology" . + . + . + "ontology" . + "pesticideinfo" . + "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."^^ . + "Information about research projects that NSF has funded since 1989 can be found by searching the Award Abstracts database. The information includes abstracts that describe the research, and names of principal investigators and their institutions. The database includes both completed and in-process research."^^ . + . + "true"^^ . + "Zenodo" . + "ontology" . + "obo" . + "^KIAA\\d{4}$"^^ . + "GOLD genome" . + . + . + . + . + . + . + . + "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."^^ . + "dna" . + . + "joerg.overmann@dsmz.de" . + . + . + "chemistry" . + "obo" . + . + . + "anatomy" . + "http://purl.obolibrary.org/obo/FIX_$1"^^ . + . + "http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_frame_disp.cgi?sdbsno="^^ . + . + . + "false"^^ . + "RiceNetDB is currently the most comprehensive regulatory database on Oryza Sativa based on genome annotation. It was displayed in three levels: GEM, PPIs and GRNs to facilitate biomolecular regulatory analysis and gene-metabolite mapping."^^ . + "protein" . + . + . + . + . + . + . + "false"^^ . + . + . + . + "3"^^ . + "A vocabulary for cattle, chicken, horse, pig, and sheep breeds."^^ . + . + "co_360" . + . + . + . . - . - . - "false"^^ . - . - "ChemSpider is a collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources."^^ . - "An ontology designed to support the semantic annotation of epidemiology resources"^^ . - . - "^\\d+$"^^ . - . - . - . - "false"^^ . - "life science" . - "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)."^^ . - . - "Mingxun Wang" . - "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID="^^ . - . - . - . - . - "Ontology for Immune Epitopes" . - . - . - . - "UMLS_CUI" . - _:Nd59148a3af5b498cbb0a2d1ceae31300 . - . - "life science" . - . - . - "https://cropontology.org/rdf/CO_337:$1"^^ . - . - . - . - . - "An ontology to capture confidence information about annotations."^^ . - . - . - . - . - "jgraybeal@stanford.edu" . - . - "http://oncotree.mskcc.org/api/tumorTypes/search/code/"^^ . - "hbvar" . - "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."^^ . - "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."^^ . - . - . - . - . - . - "h_aktPathway"^^ . - . - . - "bigg.reaction" . - . - . - . - . - "https://www.alzforum.org/mutations/"^^ . - "ACHN"^^ . - . - "OTTHUMG00000169812"^^ . - . - . - . - . - . - . - "jgi.proposal" . - . - . - . - . - "false"^^ . - "aphidbase.transcript" . - "vbrc" . - . - . - "http://compbio.cs.queensu.ca/cgi-bin/compbio/search/main.cgi?search_mode=id&id_type=snp_id&id_val=$1"^^ . - "SED-ML model format" . - "https://bioregistry.io/hivreagentprogram:"^^ . - "https://icd.codes/icd10cm/$1"^^ . - . - "amalik@ebi.ac.uk" . - "Carissa Park" . - "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . - . - "clyh" . - . - "https://bioregistry.io" . - "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did=$1"^^ . + . + . + . + . + . + . + "false"^^ . + "0000091"^^ . + . + "ontology" . + . + "0000010"^^ . + . + "natural science" . + . + . + . + "microscope" . + . + . + . + . + . + . + "B2067"^^ . + "http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=$1"^^ . + . + "gene" . + . + "Food-Biomarker Ontology" . + "enzyme" . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_chem_"^^ . + "health" . + "DDB_G0267522"^^ . + "http://purl.org/gc/"^^ . + . + . + . + "http://birdgenenames.org/cgnc/GeneReport?id=$1"^^ . + . + . + . + "100"^^ . + "^\\d+$"^^ . + . + . + . + . + "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."^^ . + . + . + . + "A structured controlled vocabulary of the anatomy of mosquitoes."^^ . + . + . + "^DRSC\\d+$"^^ . + . + . + "environmental science" . + "ML0224"^^ . + . + . + "http://purl.obolibrary.org/obo/BOOTSTREP_$1"^^ . + . + . + . + "false"^^ . + . + "3000045"^^ . + . + . + "http://yeastrc.org/pdr/viewProtein.do?id="^^ . + . + "taxonomy" . + . + "false"^^ . + . + . + . + . + "https://cropontology.org/rdf/CO_350:"^^ . + . + . + . + . + . + "456789"^^ . + . + . + "gene" . + "taxonomy" . + "^\\d+$"^^ . + . + . + . + "^\\d+$"^^ . + . + . + "true"^^ . + . + . + . + . + . + . + "BioContext" . + _:N9abc2b29d7c54644828f5ad866064c9e . + . + "https://www.pgscatalog.org/pgs/"^^ . +_:N21f8caeb1d264efd93eb87a9a39c96de "helpdesk@cropontology-curationtool.org" . + . + . + . + "false"^^ . + . + . + . + . + "MAR11851"^^ . + . + "^\\d+$"^^ . + . + . + . + "uspto" . + . + . + "https://sumlineknowledgebase.com/?page_id="^^ . + . + . + . + . + . + "shacl" . + "http://purl.org/spar/cito/$1"^^ . + "https://www.uniprot.org/arba/$1"^^ . + "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC=$1"^^ . + . + "Guide to Pharmacology Ligand" . + . + . + . + . + "false"^^ . + . + . + "http://www.marinespecies.org/aphia.php?p=taxdetails&id="^^ . + . + . + . + "false"^^ . + . + . + . + "http://www.hgmd.cf.ac.uk/ac/gene.php?gene="^^ . + "N1899"^^ . + "PNS12@cam.ac.uk" . + "https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid="^^ . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id="^^ . + "life science" . + . + "false"^^ . + "obo" . + "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."^^ . + . + "Morphological and physiological measurement records generated from clinical and model organism research and health programs."^^ . + . + "false"^^ . + "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."^^ . + . + "proteins" . + "has local unique identifier example" . + . + . + . + . + . + . + "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."^^ . + . + "BioKC" . + . + "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"^^ . + . + . + . + . + . + . + . + . + "ISRCTN10175490"^^ . + _:N21f8caeb1d264efd93eb87a9a39c96de . + "http://foodb.ca/compounds/$1"^^ . + "The Provider Characteristics code set is for use with health care provider information for enrollment and credentialing transactions and their corresponding responses. It is intended to provide codified responses to questions presented to a health care provider applying to or registering with an entity and to report the outcome of such application or registration. It may also be used for responses to inquiries regarding provider participation or registration in a program or plan."^^ . + . + . + "life science" . + . + "https://purl.uniprot.org/uniprot/$1"^^ . + . + . + "chromosome" . + . + . + "jrsmith@mcw.edu" . + . + . + . + . + "subject agnostic" . +_:Nab17e8af5a024810b922e139a33dedf0 "helpdesk@cropontology-curationtool.org" . + . + . + . + . + . + . + . + . + . + . + . + . + "0004828"^^ . + "true"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + "ontology" . + "60025709"^^ . + . + . + . + "SPCC13B11.01"^^ . + . + "H-InvDb Transcript" . + "false"^^ . + . + . + . + . + . + . + . + _:N02158d1ce8ce424abc89d4bad17cc26b . + . + . + "^(c|k)\\d{7}$"^^ . + . + . + "interlex" . + "preclinical studies" . + . + . + "forest management" . + "true"^^ . + "The International Harmonization of Nomenclature and Diagnostic criteria" . + . + . + "EC number" . + "589462"^^ . + . + . + . + . + . + "http://www.chemspider.com/$1"^^ . + "GWAS Catalog" . + "http://www.isni.org/isni/$1"^^ . + . + . + . + . + . + "cl3603"^^ . + . + "CLV_MEL_PAP_1"^^ . + . + "https://www.scopus.com/authid/detail.uri?authorId="^^ . + . + . + . + "pier.buttigieg@awi.de" . + "^\\w+(\\-)?\\w+(\\-)?\\w+$"^^ . + . + "A subspace of Metabolic Atlas for reactions."^^ . + . + . + . + "life science" . + . + "http://purl.obolibrary.org/obo/PSO_$1"^^ . + . + . + "false"^^ . + . + "^\\d+$"^^ . + . + "ontology" . + . + "Ontology of Host Pathogen Interactions" . + . + "biomedical science" . + "The main contact person for a registry" . + . + "UM-BBD_enzymeID" . + . + . + "2A"^^ . + . + . + . + . + . + "https://www.pombase.org/gene/$1"^^ . + . + . + "CTD Gene" . + "https://biopragmatics.github.io/providers/icepo/$1"^^ . + "KG09531"^^ . + "biodiversity" . + . + . + "PseudoGene" . + "^\\d{7}$"^^ . + . + . + "Human Proteome Map Peptide" . + . + . + "napp" . + . + . + . + . + . + "http://www.proteinatlas.org/$1"^^ . + "false"^^ . + . + "true"^^ . + "false"^^ . + . + . + "pharmgkb.drug" . + . + . + "https://bioregistry.io/dragondb.locus:"^^ . + "https://lotus.naturalproducts.net/compound/lotus_id/"^^ . + . + . + "The Philippine Health Research Registry (PHRR), managed by the Philippine Council for Health Research and Development, is a tool for good governance to promote transparency and accountability in health research. PHRR is a publicly accessible database on newly approved health researches. It includes clinical trials and non-clinical studies conducted in the Philippines. The registry is compliant with the World Health Organization (WHO) standard for clinical trials registry. [from website]"^^ . + . + . + "Human Metabolome Database" . + . + . + "ons" . + "http://darcsite.genzentrum.lmu.de/darc/view.php?id=$1"^^ . + . + . + . + . + . + "MCDS_L_0000000001"^^ . + . + . + "^\\d{7}$"^^ . + "SNOMEDCTCT" . + "^[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://mampol.uab.es/cgi-bin/MamPol_s2.pl?Accession=$1"^^ . + . + . + "grouping" . + . + "demographics" . + . + . + . + "true"^^ . "ncbi.gi" . - . - . - . - "genome" . - "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://dictybase.org/db/cgi-bin/feature_page.pl?primary_id=$1"^^ . - "false"^^ . - . - "ramirez@macn.gov.ar" . - "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."^^ . - "rna" . - . - "0000029"^^ . - . - "https://protists.ensembl.org/id/"^^ . - "KEGG Reaction Class" . - . - . - . - . - . - . - . - . - . - . - . - . - "false"^^ . - "publishing" . - . - . - "data management" . - . - . - "false"^^ . - "Joint Genome Institute Proposals" . - "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . - "small molecule" . - . - . - . - . - "worm" . - . - . - "genefarm" . - "PED00017e001"^^ . - . - . - "http://purl.obolibrary.org/obo/CIDO_$1"^^ . - "CRediT (Contributor Roles Taxonomy) is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output."^^ . - "^\\d+$"^^ . - . - "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."^^ . - . - "wikipedia" . - . - . + "protein" . + . + . + . + "ATTC" . + "adw" . + . + . + . + . + "g.gkoutos@bham.ac.uk" . + . + . + "ontology" . + . + . + . + "^PM\\d{7}$"^^ . + . + "75121530"^^ . + . + "2200950"^^ . + . + "FuncBase Human" . + . + "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."^^ . + . + . + . + . + "false"^^ . + . + . + . + "http://lincsportal.ccs.miami.edu/cells/#/view/"^^ . + . + . + "9002859"^^ . + . + "http://purl.obolibrary.org/obo/CIO_"^^ . + . + "identifier for a tree species of the United States and Canada on the Leafsnap electronic field guide"^^ . + "ontology" . + "false"^^ . + . + . + . + "1"^^ . + "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available."^^ . + . + . + . + . + . + . + "proteomics" . + . + "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="^^ . + . + "obo" . + . + . + . + . + "Lorenz Reimer" . + . + . + "obo" . + "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."^^ . + "Nucleotide Sequence Database" . + . + . + "organism supplier" . + "MultiCellDS Digital Cell Line" . + "http://plasmodb.org/plasmo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + . + "DisProt" . + . + . + "lincs" . + "^\\d{7}$"^^ . + . + "false"^^ . + "Milton H. Saier, Jr." . + . + . + . + . + . + . + "MC" . + "https://massbank.jp/RecordDisplay?id="^^ . + . + "^\\d{7}$"^^ . + "http://purl.obolibrary.org/obo/FLU_"^^ . + "Hazardous Substances Data Bank" . + . + . + . . - . - "^BSU\\d{5}$"^^ . - . - . - "protozoan" . - . - "2022.07.08.499378"^^ . - . - "false"^^ . - "MEROPS Entry" . - "interaction" . - "false"^^ . - . - . - . - . - . - . - "ChEMBL_ID" . - . - . - . - "AOPWiki" . - . - "false"^^ . - . - . - . - . - "genomics" . - . - . - . - "social science" . - "treebase" . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . - . - "nucc.taxonomy" . - "pibase" . - "ontology" . - "1000"^^ . - "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . - "chemistry" . - . - . - "false"^^ . - . - . - "false"^^ . - . - "http://arabidopsis.info/StockInfo?NASC_id="^^ . - . - "ontology" . - . - . - . - "CropMRespository is a database of soil and crop biophysical process models."^^ . - . - "false"^^ . - "Fababean ontology" . - . - . - "https://www.inaturalist.org/users/$1"^^ . - . - . - . - "https://www.ncbi.nlm.nih.gov/clinvar/submitters/"^^ . - "false"^^ . - "^\\d{7}$"^^ . - "Gender, Sex, and Sexual Orientation Ontology" . - . - "https://biomodels.net/vocab/idot.rdf#$1"^^ . - . - . - "THE1B"^^ . - "^[A-Z]+[0-9]+$"^^ . - . - "These are the terms that are improted for FOVT to describe vertebrate traits."^^ . - "false"^^ . - . - "^(GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?$"^^ . - . - . - . - . - . - . - . - "^.*/.*$"^^ . - "http://purl.obolibrary.org/obo/WBbt_"^^ . - . + . + . + "Dongsheng Cao" . + "false"^^ . + . + . + . + . + "life science" . + . + "Minimum Anformation About a Phylogenetic Analysis Ontology" . + . + . + "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."^^ . + "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."^^ . + "kcris" . + "cancer" . + "http://www.arachnoserver.org/toxincard.html?id=$1"^^ . + . + "Database of Quantitative Cellular Signaling: Pathway" . + "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."^^ . + . + . + . + . + . + "http://genomics.senescence.info/diet/details.php?id=$1"^^ . + . + "functional genomics" . + . + . + "https://www.kegg.jp/entry/"^^ . + . + "idpo" . + . + . + "MSV000082131"^^ . + . + "false"^^ . + . + . + . + "false"^^ . + "James C. Hu" . + . + "false"^^ . + "false"^^ . + "biomedical science" . + . + "donny@polyneme.xyz" . + "https://discover.pennsieve.io/package/"^^ . + "https://cropontology.org/rdf/CO_348:"^^ . + . + . + . + "http://purl.org/spar/datacite/$1"^^ . + "https://cryptodb.org/cryptodb/app/record/gene/$1"^^ . + . + . + . + . + "agriculture" . + "false"^^ . + . + . + "CHEBI" . + . + . + "http://purl.obolibrary.org/obo/NBO_"^^ . +_:Ncfadbc34f17648fd84f1b3281ce5bb0d "ted@tklein.com" . + . + "Ontology for Immune Epitopes" . + . + "obo" . + "http://purl.obolibrary.org/obo/HOM_"^^ . + . + . + . + . + . + . + . + . + "EchoBASE post-genomic database for Escherichia coli" . + "obo" . + . + "^[A-Z0-9]+$"^^ . + . + "https://w3id.org/oc/oci/$1"^^ . + "http://purl.obolibrary.org/obo/DUO_$1"^^ . + "WWF" . + "Cell Lines Service" . + . + "ontology" . + . + . + "false"^^ . + . + . + . + . + "lars.holm.nielsen@cern.ch" . + . + . + . + . + . + . + . + . + . "An ontology of Drosophila melanogaster developmental stages."^^ . - . - . - "00001"^^ . - . - "life science" . - . - "false"^^ . - . - . - . - . - . - . - . - "Database of experimentally verified IRES structures" . - "ontology" . - . - . - . - . - . - "IPR" . - . - . - "swh" . - . - . - "http://cegg.unige.ch/orthodb/results?searchtext="^^ . - "^(\\w+)?\\d+$"^^ . - "^\\d+$"^^ . - "ttd.target" . - . - . - . - "BibliographicRecord"^^ . - "JAX Mice is a catalogue of mouse strains supplied by the Jackson Laboratory."^^ . - . - "antibodies" . - . - . - "https://euclinicaltrials.eu/app/#/view/$1"^^ . - "bioregistry.collection" . - . - . - . - . - . - . - "adms" . - . - . - . - . - . - "bs" . - "neurobiology" . - . - . - "CMPO is a species neutral ontology for describing general phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations."^^ . - . + . + "http://trichdb.org/trichdb/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + "ximbio" . + "Re3data is a global registry of research data repositories that covers research data repositories from different academic disciplines." . + . + . + . + "ontology" . + "botany" . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + . + "fungidb" . + "^ITMCTR\\d+$"^^ . + "Registry of programming languages for the Linguist program for detecting and highlighting programming languages."^^ . + . + "1000001"^^ . + . + . + . + "As a scientific user facility, the Environmental Molecular Sciences Laboratory (EMSL) provides expertise, instrumentation, and resources to 250 projects each year. Current and past projects supported through a variety of EMSL user proposal avenues are publicly searchable on the EMSL website. Project pages provide details including:\n- Research team and institution\n- The EMSL project DOI\n- Link to project data available in EMSLs Data Portal\n- Project type"^^ . + "biosimulations" . + "life science" . + "fbbi" . + "false"^^ . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "http://bgee.unil.ch/bgee/bgee?page=anatomy&action=organs&stage_children=on&stage_id=$1"^^ . + . + . + . + . + . + "AntWeb is a website documenting the known species of ants, with records for each species linked to their geographical distribution, life history, and includes pictures."^^ . + . + "^PRJ[DEN][A-Z]\\d+$"^^ . + "ClinVar Variation" . + . + "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."^^ . + "^(\\w+(\\-\\w+)?(\\.\\w+)?)?\\d{4,7}(\\.\\d+(v\\d+)?)?$"^^ . + . + "obo" . + . + . + . + . + . + "vz" . + "ontology" . + . + "The OBO namespace is the top-level namespace used by Open Biological and Biomedical Ontology (OBO) Foundry ontologies."^^ . + "life science" . + "hovergen" . + "allyson.lister@oerc.ox.ac.uk" . + . + "1"^^ . + . + "Cancer Cell Line Encyclopedia Cells" . + "ChEMBL" . + . + "RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization."^^ . + . + . + "sheepqtldb" . + . + "http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=geneInfo&gid=$1"^^ . + "^\\d+$"^^ . + . + "false"^^ . + "cellosaurus.resource" . + "charprot" . + "false"^^ . + . + . + . + . + . + "The NMPDR provided curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma."^^ . + . + "false"^^ . + . + "P3DB Site" . + . + . + "^PASS\\d{5}$"^^ . + . + . + . + . + . + . + . + . + "^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}\\-[0-9a-fA-F]{12}$"^^ . + . + . + "0000634"^^ . + "7499841"^^ . + . + . + . + "obo" . + "408"^^ . + "obo" . + . + "Reference"^^ . + . + "https://www.gbif.org/species/"^^ . + . + . + . + . + . + "PharmGKB" . + "biomedical science" . + "https://w3id.org/faircookbook/$1"^^ . + . + "Name Reaction Ontology" . + . + . + . + . + . + . + . + . + . + . + . + . + "dna" . + . + . + . + "Protein and Associated NucleotideDomains with Inferred Trees" . + . + . + . + . + . + . + "^\\w+$"^^ . + . + . + "umbbd.enzyme" . + . + "false"^^ . + . + . + . + "dctypes" . + . + . + "Pathway Commons" . + . + "false"^^ . + . + . + . + . + . + . + . + "http://alk.ibms.sinica.edu.tw/cgi-bin/miRNA/virus.cgi?tax_id="^^ . + . + . + "biomedical science" . + "false"^^ . + "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."^^ . + "SciCrunch Registry" . + . + . + . + . + "^\\d+$"^^ . + . + "5013"^^ . + "BSU29180"^^ . + . + . + . + . + . + . + . + . + "oci" . + . + "Bitbucket" . + . + . + "MimoDB" . + . + "https://doi.org/$1"^^ . + . + "Paula.Duek@sib.swiss" . + . + . + "The Lebanese Clinical Trials Registry is an online register of clinical trials being undertaken in Lebanon. It includes trials that target humans from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. (from homepage)"^^ . + . + "obo" . + "BE0000048"^^ . + "functional genomics" . + . + "itis" . + . + . + . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id=$1"^^ . + . + "http://lgsun.grc.nia.nih.gov/cgi-bin/pro3?sname1="^^ . + "taxonomy" . + "http://www.weizmann.ac.il/molgen/loqate/gene/view/$1"^^ . + . + "^\\d+$"^^ . + "Bioinformatics Resource Center for Invertebrate Vectors of Human Pathogens" . + . + . + . + . + "OriDB Saccharomyces" . + . + . + "false"^^ . + . + "The Bibliographic Ontology" . + . + . + . + . + . + . + . + . + . + . + . + "https://massbank.jp/RecordDisplay?id=$1"^^ . + . + "https://health-products.canada.ca/ctdb-bdec/brand/?submissionNo="^^ . + . + "SoyBase is a repository for curated genetics, genomics and related data resources for soybean."^^ . + "Integrated Microbial Genomes Taxon" . + "anatomy" . + "life science" . + . + "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"^^ . + "An experimental run, served thrugh the ENA"^^ . + . + . + . + . + . + . + . + "http://nematode.lab.nig.ac.jp/db2/ShowCloneInfo.php?clone=$1"^^ . + "ngbo" . + . + . + "chemistry" . + . + "Prefix.cc" . + . + "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster="^^ . + "Robert Druzinsky" . + . + "genome" . + . + "alzforum.mutation" . + . + . + . + . + . + "Oral Health and Disease Ontology" . + . + . + . + . + "Nomenclature Consortium around Chicken genes (analogous to the HGNC for humans)"^^ . + "http://purl.obolibrary.org/obo/DOID_"^^ . + . + "ITMCTR2023000002"^^ . + "protein" . + . + "KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks."^^ . + . + . + "https://civicdb.org/links/molecular_profile/"^^ . + "AS000060"^^ . + . + . + . + . + . + . + . + . + . + . + "clinical studies" . + . + . + "http://www.oid-info.com/get/2.16.840.1.113883.6" . + "https://www.ensembl.org/id/$1"^^ . + "bioinformatics" . + "https://cstr.cn/"^^ . + . + . + . + "An expanded example URL for a resource or metaresource." . + . + . + . + "false"^^ . + "Magnaporthe grisea, the causal agent of rice blast disease, is one of the most devasting threats to food security worldwide and is a model organism for studying fungal phytopathogenicity and host-parasite interactions. The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae."^^ . + "^\\d{7}$"^^ . + . +_:N897a2f3e7af8401db8644acbfa753ed9 "johardi@stanford.edu" . + . + . + "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass="^^ . + "Chemical Component Dictionary" . + . + "false"^^ . + . . - . - . - . - . - . - "http://www.bioassayontology.org/bao#BAO_"^^ . - . - . - . - "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."^^ . - . - . - "Animal Genome Sheep QTL" . - "http://www.crop2ml.org/cropmdb/$1"^^ . - "HBB"^^ . - "false"^^ . - . - . - "^[a-z0-9]{8}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{4}-[a-z0-9]{12}$"^^ . - . - . - . - . - "false"^^ . - "fobi" . - "https://www.isrctn.com/"^^ . - . - . - . - "UniProtKB-KW" . - "epigenetics" . - "depends on" . - "molecules" . - . - . - . - . - "http://addgene.org/$1"^^ . - "Maize gross anatomy" . - . - . - . - . - "http://multicellds.org/MultiCellDB/"^^ . - "University hospital Medical Information Network Clinical Trial Registry" . - . - "http://purl.obolibrary.org/obo/TAHE_$1"^^ . - . - . - "false"^^ . - "NIF Standard Ontology: OEN Terms in Neurolex" . - . - . - . - "^[0-9]+$"^^ . - . - "Heather Piwowar" . - . - "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea"^^ . - . - "ontology" . - . - "protein" . - . - . - . - "MicroScope" . - . - . - "Spectral Database for Organic Compounds" . - "^\\d{8}$"^^ . - . - "hsdb" . - "dna" . - . - "scomp" . - . - . - . - . - . - . - . - . - . - "https://w3id.org/BCI-ontology#$1"^^ . - . - . - "T3D0001"^^ . - . - . - . - "tair.gene" . - . - . - . - "Vaccine administered code set" . - . - . - "http://biocyc.org/getid?id=$1"^^ . - . - "Catalogue of Life in Taiwan" . - . - "co_334" . - . - . - . - "reaction" . - . - . - . - . - "^[A-Za-z0-9]+$"^^ . - "drduke" . - "http://redfly.ccr.buffalo.edu/?content=/view_detail.php&crm_id=$1"^^ . - "Sequence types and features ontology" . - . - . - "false"^^ . - "identifier for an academic research group issued by the CNRS"^^ . - . - . - . - . - "PROSITE" . - . - . - "neuroname" . - "false"^^ . - "developmental biology" . - "habronattus" . - . - . - . - . - . - "http://iflastandards.info/ns/fr/frbr/frbrer/"^^ . - . - . - . + "obo" . + "interaction" . + "ab275461"^^ . + . + . + . + "https://www.datascienceontology.org/concept/$1"^^ . + . + "IA"^^ . + "false"^^ . +_:N9753b3307f82484cbd3fe4a409beaccf "Bert Van Nuffelen" . + "http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?"^^ . + . + . + . + "small molecule" . + "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. "^^ . + . + "http://www.mirbase.org/cgi-bin/mirna_summary.pl?fam=$1"^^ . + "AA0001"^^ . + "1004" . + . + . + . + . + . + "biomedical science" . + "Brain Architecture Knowledge Management System Neuroanatomical Ontology" . + "gmd.analyte" . + . + "The GO reference collection is a set of abstracts that can be cited in the GO ontologies (e.g. as dbxrefs for term definitions) and annotation files (in the Reference column). It provides two types of reference; It can be used to provide details of why specific Evidence codes (see http://identifiers.org/eco/) are assigned, or to present abstract-style descriptions of \"GO content\" meetings at which substantial changes in the ontologies are discussed and made."^^ . + "http://purl.org/spar/biro/"^^ . + "50-00-0"^^ . + . + . + . + "genome" . + . + "bigg.model" . + . + "false"^^ . + "The Antibody Registry provides identifiers for antibodies used in publications. It lists commercial antibodies from numerous vendors, each assigned with a unique identifier. Unlisted antibodies can be submitted by providing the catalog number and vendor information."^^ . + . + "KEGG Genes" . + "234"^^ . + . + "Pierre-Alain Binz" . + "https://www.gwascentral.org/marker/"^^ . + . + . + "bioinformatics" . + "^\\d+$"^^ . + . + . + . + "https://flybrain-ndb.virtualflybrain.org/fmi/xsl/browserecord.xsl@-lay=NDB&Accession+number.op=eq&Accession+number=$1&-find=-find.html"^^ . + . + . + "The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. The database provides a range of search, navigation, and comparison functions. This datatype provides access to pathways."^^ . + . + . + . + . + "small molecule" . + . + . + . + "https://urgi.versailles.inra.fr/gnpis/#result/term="^^ . + "^[a-zA-Z_][a-zA-Z0-9\\-_]+$"^^ . + "Elvira Mitraka" . + . + "https://ligandbook.org/package/"^^ . + . + . + . + . + . + . + . + . + . + . + "Descriptive Ontology for Linguistic and Cognitive Engineering" . + . + . + "population genetics" . + . + . + "http://www.ubio.org/browser/details.php?namebankID="^^ . + . + . + "http://vega.sanger.ac.uk/[?species_name]/Gene/Summary?g=$1"^^ . + . + "civic.vid" . + . + "The United States Patent and Trademark Office (USPTO) is the federal agency for granting U.S. patents and registering trademarks. As a mechanism that protects new ideas and investments in innovation and creativity, the USPTO is at the cutting edge of the nation's technological progress and achievement."^^ . + . + . + . + . + . + "^[A-Za-z-0-9]+$"^^ . + . + "ontology" . + . + . + "cell biology" . + . + "http://metnetonline.org/browse_pathway2.php?pthID="^^ . + "life science" . + . + "true"^^ . + . + . + . + "false"^^ . + "life science" . + . + . + . + "^\\d{7}$"^^ . + . + "https://grch38.togovar.org/variant/$1"^^ . + . + "9001411"^^ . + "false"^^ . + . + "reagents" . + . + . + . + . + . + "0110974"^^ . + "Enzo Life Sciences" . + "data_1664"^^ . + . + "1"^^ . + . + . + "Thorsten Henrich" . + . + . + . + "G8944"^^ . + . + . + . + . + . + . + . + . + . + . + . + "true"^^ . + . + "Dictyostelium discoideum anatomy" . + "niaid.chemdb" . + "ToxoDB" . + "false"^^ . + . + . + . + . + . + . + "^\\d+$"^^ . + "biomedical science" . + "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://www.cbioportal.org/study/summary?id="^^ . + . + . + "genomics" . + . + . + . + "Allotrope Merged Ontology Suite"^^ . + "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."^^ . + . + "2200934"^^ . + . + "https://cropontology.org/rdf/CO_323:"^^ . + . + . + "life science" . + . + "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."^^ . + "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."^^ . + "false"^^ . + "General Standard for Food Additives Online Database" . + "http://lincsportal.ccs.miami.edu/SmallMolecules/#/view/"^^ . + "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."^^ . + . + "gexo" . + "RiceNetDB Gene" . + . + "http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=$1"^^ . + . + . + . + "ICD-10-CM is the official system of assigning codes to diagnoses and procedures associated with hospital utilization in the United States issued by the National Center for Health Statistics (NCHS) and Centers for Medicare & Medicaid Services (CMS)."^^ . + "https://nanocommons.github.io/identifiers/registry#$1"^^ . + "true"^^ . + . + . + "The Paleobiology Database seeks to provide researchers and the public with information about the entire fossil record. It stores global, collection-based occurrence and taxonomic data for marine and terrestrial animals and plants of any geological age, as well as web-based software for statistical analysis of the data."^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "epidemiology" . + . + . + . + "nucleotide" . + . + . + . + . + . + . + "mjyoder@illinois.edu" . + . + "antibodies" . + . + . + . + . + . + "The reviewer of a prefix" . + . + . + . + . + . + . + . + "http://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20MetaThesaurus&code=$1"^^ . + . + . + "gene" . + . + . + "true"^^ . + . + "https://www.imanislife.com/?s="^^ . + . + . + . + "true"^^ . + . + . + . + "https://glytoucan.org/Structures/Glycans/"^^ . + . + . + . + . + . + . + . + "obo" . + "pdbj" . + . + . + . + . + . + "2.7.1.1"^^ . + "JRC Data Catalogue" . + "The Bloomington Drosophila Stock Center collects, maintains and distributes Drosophila melanogaster strains for research."^^ . + "^JCRB\\d+$"^^ . + . + . + . + . + "ontology" . + "fr" . + . + . + "umls.st" . + . + "Life cycle stages for Mus Musculus"^^ . + . + . + . + . + . + . + . + . + . + "^[\\w\\-.]{3,}$"^^ . + . + . + . + . + . + "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="^^ . + "Enrique Blanco" . + "http://www.flyrnai.org/cgi-bin/RNAi_gene_lookup_public.pl?gname=$1"^^ . + . + . + "https://drks.de/search/en/trial/"^^ . + "^[A-Za-z_0-9]+$"^^ . + "0440"^^ . + . + . + . + "sasbdb" . + . + "http://purl.org/cerif/frapo/$1"^^ . + . + . + . + . + "http://www.pathoplant.de/detail.php?accNo=$1"^^ . + . + "CTRI/2023/04/052053"^^ . + . + "NodeShape"^^ . + . + "false"^^ . + . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid=$1"^^ . + "obo" . + . + . + "http://clipserve.clip.ubc.ca/topfind/proteins/$1"^^ . + "mutant mouse strain" . + . + "provenance"^^ . + . + . + . + "Veterans Administration National Drug File" . + . + . + . + . + "LMPR0102010012"^^ . + . + . + . + . + . + "doi" . "A collaborative project intended to create an encyclopedia documenting all living species known to science"^^ . - . - . - . - "false"^^ . - . - "mtbd" . - "vbo" . - "0187632"^^ . - "false"^^ . - . - "false"^^ . - . - "83088"^^ . - "sael" . - . - . - . - "http://www.ecogene.org/gene/"^^ . - "recombinant host" . - . - . - "^\\d+$"^^ . - . - "http://www.ubio.org/browser/details.php?namebankID=$1"^^ . - . - "Internal identifiers form the LSP for ChEBML compound classes (e.g., combining various salts and ions)"^^ . - "pazar" . - . - "16"^^ . - . - . - . - "http://purl.obolibrary.org/obo/PATO_"^^ . - . - . - "clinvar.variation" . - . - . - "The NIH registration number should be used on all NIH competing applications and annual progress reports to identify the stem cell line proposed for use. Identify the specific line(s) from the Registry using the NIH Registration Number (e.g., 0001), in the specified location in the application (from homepage)"^^ . - . - "Animal Genome Pig QTL" . - "FuncBase Mouse" . - "ontology" . - "environmental science" . - . - . - "The Human Gene Mutation Database (HGMD) collates data on germ-line mutations in nuclear genes associated with human inherited disease. It includes information on single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation entry is unique, and includes cDNA reference sequences for most genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases."^^ . - . - "^\\d+$"^^ . - "^EGAD\\d{11}$"^^ . - . - "meddra" . - . - "biomedical science" . - "NeuroVault Image" . - "http://www.pazar.info/cgi-bin/tf_search.cgi?geneID="^^ . - "638309541"^^ . + . + "Iranian Registry of Clinical Trials" . + "taxid" . + . + . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . + "Sweet Potato Trait Dictionary in template v5 - CIP - November 2019"^^ . . -_:N7f8648ca4c8c4d6b9724d8d656769f4d "Pierre Sprumont" . - . - . - "^\\d+$"^^ . - . - . - . - . - "structure" . - . - . - . - "^[A-Z_0-9]+$"^^ . - . - "cell biology" . - . - . - . - "^HGVST\\d+$"^^ . - . - "Gramene QTL" . - "anatomy" . - . - "http://greengenes.lbl.gov/cgi-bin/show_one_record_v2.pl?prokMSA_id=$1"^^ . - "vendor" . - "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . - . - "ontology" . - "knowledge and information systems" . - "http://purl.org/cerif/frapo/"^^ . - . - "string" . - "5.1"^^ . - "The Animal Quantitative Trait Loci (QTL) database (Animal QTLdb) is designed to house publicly all available QTL and single-nucleotide polymorphism/gene association data on livestock animal species. This collection references cattle QTLs."^^ . - . - "C0026339"^^ . - "265"^^ . - . - . - "biomedical science" . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - "100101"^^ . - . - . - . - "^UCR\\d{5}$"^^ . - "^r3d\\d{9,9}$"^^ . - . - . + . + . + . + . + "depod" . + "Melanie Courtot" . + "https://books.google.com/books?id=$1"^^ . + . + "dbo" . + . + . + "An ontology of research resources such as instruments. protocols, reagents, animal models and biospecimens."^^ . + . + . + . + "^\\d+$"^^ . + . + "http://vbrc.org/gene_detail.asp?gene_id=$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + . + "1484"^^ . + . + "A structured controlled vocabulary of the anatomy of Amphibians. Note that AAO is currently being integrated into Uberon."^^ . + . + . + "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#"^^ . + "ontology" . + . + . + . + "Ontology Lookup Service" . + . + . + "Dublin Core Types" . + "epidemiology" . + "gene" . + . + . + . + "http://purl.obolibrary.org/obo/DDANAT_"^^ . + . + . + . + . + . + "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="^^ . + . + . + . + "Identifiers.org Registry" . + . + "prosite" . + "snoRNABase" . + . + "https://doi.org/"^^ . + . + . + "https://scicrunch.org/resolver/RRID:"^^ . + . + "4779"^^ . + . + "MedlinePlus Health Topics" . + "umbbd.reaction" . + "animal genetics" . + . + . + . + . + "transgenic" . + "miriam.resource" . + . + . + . + "ped.ensemble" . + . + "ontology" . + "ontology" . + "National Center for Biotechnology Information Registry" . + . + "false"^^ . + . + "SNCTP000005580"^^ . + "9"^^ . + "Concept used by ModelDB, an accessible location for storing and efficiently retrieving computational neuroscience models."^^ . + "OBO in OWL" . + . + . + . + . + . + . + . + "0000088"^^ . + "https://www.clinicaltrialsregister.eu/ctr-search/search?query=$1"^^ . + . + "https://cells.ebisc.org/$1"^^ . + . + "OntoCAPE is a large-scale ontology for the domain of Computer Aided Process Engineering (CAPE). Represented in a formal, machine-interpretable ontology language, OntoCAPE captures consensual knowledge of the process engineering domain in a generic way such that it can be reused and shared by groups of people and across software systems. On the basis of OntoCAPE, novel software support for various engineering activities can be developed; possible applications include the systematic management and retrieval of simulation models and design documents, electronic procurement of plant equipment, mathematical modeling, as well as the integration of design data from distributed sources."^^ . + "false"^^ . + "http://metlin.scripps.edu/metabo_info.php?molid="^^ . + "sequence" . + . + "ISBN-10" . + "rna" . + . + "ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters."^^ . + "protein" . + . + "http://purl.obolibrary.org/obo/IDOMAL_"^^ . + "Human Reference Atlas Common Coordinate Framework Ontology" . + "Web-application assembling the largest in vitro drug screens in a single database, and allowing users to easily query the union of studies released to date. Query by cell line."^^ . + . + . + "aism" . + "mihail.anton@chalmers.se" . + . + . + "^\\d+\\-\\d+\\-\\d+$"^^ . + . + "odc.sci" . + . + "research" . + . + . + . + . + "cell biology" . + "http://www.w3.org/ns/shex#"^^ . + "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . +_:N4d553228bdc9474894f812f565b509c7 "Jonathan Bard" . + . + . + . + . + "http://purl.enanomapper.org/onto/ENM_"^^ . + . + . + "https://civicdb.org/links/evidence/"^^ . + . + . + "protein complexes" . + . + "^[A-Z-a-z0-9]+$"^^ . + . + . + . + . + "arba" . + . + "false"^^ . + . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:"^^ . + "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."^^ . + . + "mgi" . + . + . + "small molecule" . + . + . + "chemistry" . + "ontology" . + . + "astrophysics and astronomy" . + . + . + "^AT.G[0-9]{5}$"^^ . + "false"^^ . + "LINCS Data" . + "https://civicdb.org/links/variant_group/$1"^^ . + "gold standard" . + "Bgee stage" . + . + "runbiosimulations" . + "cell biology" . + "gene expression" . + "0471491039"^^ . + . + . + . + . + . + . + . + "biology" . + . + . + "This ontology models classes and relationships describing deep learning networks, their component layers and activation functions, as well as potential biases."^^ . + "pgdso" . + . + "has canonical prefix" . + . + . + "false"^^ . + . + . + . + "ontology" . + "OUYCCCASQSFEME-MRVPVSSYSA-N"^^ . + . + "ontology" . + . + "The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes."^^ . + . + . + "Consensus CDS" . + . + "^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\\d+)|(NZ_[A-Z]{2,4}\\d+))(\\.\\d+)?$"^^ . + . + "Uberon" . + . + "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."^^ . + . + . + "ALX-210-175"^^ . + . + . + . + "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . + . + "nfdi4chem.ontocape" . + "NAD%20biosynthesis"^^ . + "civic.gid" . + . + "grid" . + . + "https://mobidb.org/"^^ . + "nlx" . + . + "false"^^ . + . + . + . + "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."^^ . + . + . + "mao" . + . + . + "^\\d{7}$"^^ . + . + . + "adrienrougny@gmail.com" . + . + . + "WBRNAi00086878"^^ . + "ontology" . + "structure" . + . + "pathoplant" . + . + . + "molecular medicine" . + . + "http://purl.obolibrary.org/obo/AEON_"^^ . + . + . + . + . + "Current Procedural Terminology, more commonly known as CPT®, refers to a medical code set created and maintained by the American Medical Association — and used by physicians, allied health professionals, nonphysician practitioners, hospitals, outpatient facilities, and laboratories to represent the services and procedures they perform. No provider of outpatient services gets paid without reporting the proper CPT® codes. [Description taken from this site](https://www.aapc.com/codes/cpt-codes-range/)]"^^ . + "Coli Genetic Stock Center" . + . + "^[a-z0-9\\-]+$"^^ . + . + "topalis@imbb.forth.gr" . + . + . + . + . + . + "AgroPortal" . + . + . + . + . + . + "^UPC\\d{5}$"^^ . + . + "clinical studies" . + "https://proteinensemble.org/"^^ . + "STOREDB at University of Cambridge" . + "cath" . + . + . + . + . + . + . + . + . + "neurobiology" . + . + "^\\d+-\\d+$"^^ . + . + "organic chemistry" . + . + "anatomy" . + . + "false"^^ . + . + "biology" . + . + . + "selventa" . + . + . + "biomedical science" . + "Primate Brain Atlas" . + "prefLabel"^^ . + "^PED\\d{5}$"^^ . + "chemistry" . + . + . + "http://www.cghtmd.jp/CGHDatabase/mapViewer?hid=$1&aid=%t&lang=en"^^ . + "owl" . + . + . + . + . + "0000000"^^ . + . + . + . + . + . + . + . + . + "2-s2.0-0030770923"^^ . + . + . + . + "knockout" . + "protein" . + . + . + "https://www.ncbi.nlm.nih.gov/nucest/"^^ . + . + . + . + "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"^^ . + "snornabase" . + . + "http://purl.obolibrary.org/obo/CHEBI_$1"^^ . + "http://www.humanproteomemap.org/spectrum.php?pep_id="^^ . + . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayEntry&p1="^^ . + "metabolomics" . + . + . + "viperdb" . + . + . + . + "gene" . + . + . + . + . + "973a9333-fec7-46dd-8eb5-25738f06ee54"^^ . + . + "systems biology" . + . + . + "life science" . + . + . + . + . + "co_347" . + . + . + . + . + . + . + . + "false"^^ . + "Rodent Unidentified Gene-Encoded Large Proteins" . + "Mark Gerstein" . + . + . + . + . + . + . + "LIPID MAPS" . + "orphanet.ordo" . + "ontology" . + "life science" . + "Research Resource Identification" . + . + "medicine" . + . + "22RV1_12_2019"^^ . + "^\\d{4,}((_[asx])?_at)$"^^ . + . + . + . + . + . + . + "12969"^^ . + . + "^\\d{7}$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/AERO_"^^ . + . + . + . + "Human Endogenous Retrovirus Database" . + . + "0000013"^^ . + "bdsc" . + . + "http://purl.org/spar/bido/$1"^^ . + . + . + . + . + . + "KEGG" . + . + "mmp.ref" . + "00000180"^^ . + . + . + . + "KESTREL Ontology" . + . + . + "http://purl.obolibrary.org/obo/SO_"^^ . + "http://erop.inbi.ras.ru/result2.php?PepName=$1"^^ . + . + "comparative neurobiology" . + . + "eugenes@iubio.bio.indiana.edu" . + "BioSchemas" . + . + . + . + "The Kinetic Simulation Algorithm Ontology (KiSAO) is an ontology that describes simulation algorithms and methods used for biological kinetic models, and the relationships between them. This provides a means to unambiguously refer to simulation algorithms when describing a simulation experiment."^^ . + . + "Narcis Fernandez-Fuentes" . + . + . + . + "VIPERdb is a database for icosahedral virus capsid structures . The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration."^^ . + . + . + . + . + . + . + . + . + . + . + . + "FlyBase" . + "gene" . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/imotdb/imotdb.cgi?sfcode="^^ . + . + "Regulation of Gene Expression Ontology" . + . + . + "false"^^ . + "ThoracicArtery"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + "http://scop.berkeley.edu/sid="^^ . + . + . + . + . + . + . + "^\\d{7}$"^^ . + "https://ontology.iedb.org/ontology/ONTIE_"^^ . + "TAIR Gene" . + "true"^^ . + "https://fairsharing.org/" . + . + "david.wishart@ualberta.ca" . + . + "0000184"^^ . + . + . + . + "false"^^ . + "ontology" . + . + . + "http://purl.obolibrary.org/obo/MAO_"^^ . + "false"^^ . + . + . + "ICEs have also been reported capable to mobilize other genetic elements, such as the chromosome-borne integrative and mobilizable elements (IMEs), cis-mobilizable elements (CIMEs), plasmids and etc. IMEs and CIMEs are also important vehicles for the spread of antiobiotic resistances and virulence factors. However, unlike ICE, IMEs and CIMEs are commonly devoid of conjugal apparatus, thus have to hijack the machinery of other conjugative elements."^^ . + "https://w3id.org/BCI-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."^^ . + . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + . + "TRQ"^^ . + . + . + . + "ontology" . + . + . + . + . + . + "^[a-z_A-Z0-9]+$"^^ . + . + . + "life science" . + "obo" . + . + . + . + "chemistry" . + . + "Tetrahymena Stock Center" . + . + . + "obo" . + . + . + . + . + "Guy Cochrane" . + . + "Rutger Vos" . + . + . + . + . + "botany" . + . + "earth science" . + "0000029"^^ . + . + "https://www.ebi.ac.uk/intact/interaction/$1"^^ . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1;class=DNA"^^ . + . + "false"^^ . + "false"^^ . + . + . + "Planarian Phenotype Ontology" . + . + . + . + "13"^^ . + . + "Pigeonpea ontology" . + . + "78"^^ . + . + . + . + "false"^^ . + "Mouse pathology ontology" . + . + . + . + . + . + . + . + "subject agnostic" . + "https://www.ebi.ac.uk/ega/datasets/"^^ . + . + "homologene" . + "langual" . + "life science" . + "Human Dephosphorylation Database" . + . + "^[a-z_A-Z0-9]+$"^^ . + . + . + "Includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them."^^ . + . + . + "Human Dermatological Disease Ontology" . + . + "ontology" . + . + . + "SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies."^^ . + "RTECS is a compendium of data extracted from the open scientific literature. The data are recorded in the format developed by the RTECS staff and arranged in alphabetical order by prime chemical name. Six types of toxicity data are included in the file: (1) primary irritation; (2) mutagenic effects; (3) reproductive effects; (4) tumorigenic effects; (5) acute toxicity; and (6) other multiple dose toxicity. Specific numeric toxicity values such as LD50, LC50, TDLo, and TCLo are noted as well as species studied and route of administration used. For each citation, the bibliographic source is listed thereby enabling the user to access the actual studies cited. No attempt has been made to evaluate the studies cited in RTECS. The user has the responsibility of making such assessments."^^ . + . + "Ath_AT1G01030.1"^^ . + . + . + . + "anatomy" . + . + . + "Basic Register of Thesauri, Ontologies & Classifications" . + . + "http://psb.kobic.re.kr/STAP/refinement1/result.php?search="^^ . + . + . + . + "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."^^ . + . + . + . + . + . + "clinicaltrial" . + . + "protein" . + "http://purl.org/spar/scoro/"^^ . + . + . + "ontology" . + . + "dggr" . + . + "http://www.p3db.org/phosphosite.php?id=$1&ref=0"^^ . + . + "Lutz Fischer" . + . + . + . + "geonames" . + . + "mouse" . + . + "http://purl.obolibrary.org/obo/OBI_$1"^^ . + "david.gloriam@sund.ku.dk" . + "model" . "https://repeatsdb.org/structure/"^^ . - "International Standard Book Number" . - . - . - "https://biopragmatics.github.io/providers/hog/"^^ . - "ID in NIAID ChemDB"^^ . - . - . - . - "27106865"^^ . - . - "preclinical studies" . - . - . - . - "0000006"^^ . - "Common Core Ontologies" . - . - "rna_sstrand" . - . - . - . - "protein" . - . - . - . - "^MI\\d{7}$"^^ . - "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."^^ . - . - . - . - . - "genome" . - . - . - . - . - "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."^^ . - "BiGG Compartment" . - . - . - . - . - . - "biologics" . - . - "David Sehnal" . - "kegg.genes" . - . - "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."^^ . - . - "^\\d{7}$"^^ . - . - . - . - . - "false"^^ . - . - . - . - "Cell Line Ontology" . - . - . - "ontology" . - . - . - "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/$1"^^ . - . - . - "pathway" . - . - "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics."^^ . - "genome" . - "Taxonomic rank vocabulary" . - . - "sequence" . - . - "charprot" . - . - "https://gpcrdb.org/protein/"^^ . - "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."^^ . - "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=ep&enzymeID="^^ . - . - "http://www.hipaaspace.com/Medical_Billing/Coding/National.Drug.Codes/"^^ . + "1200"^^ . + . + . + . +_:Nb5a54a1ea36043279d2fbde29f909ebc "helpdesk@cropontology-curationtool.org" . + . + . + . + . + . + "cthoyt@gmail.com" . + . + . + . + . + "ontology" . + . + . + "Bactibase" . + "ontology" . + . + . + . + . + . + "rrrc" . + . + "https://www.yeastgenome.org/locus/"^^ . + . + . + . + "http://ctdbase.org/detail.go?type=gene&acc=$1"^^ . + . + . + . + . + "http://tfclass.bioinf.med.uni-goettingen.de/?tfclass=$1"^^ . + . + "BioPortal is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies."^^ . + "GARD" . + . + . + "Database of researchers to track publications, citation metrics, peer reviews, and journal editing work."^^ . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. This collection references ligands."^^ . + "functional genomics" . + . + . + . + . + . + "false"^^ . + "NONCODE v4 Gene" . + . + . + "http://www.noncode.org/NONCODERv3/ncrna.php?ncid="^^ . + . + . + "MMs00000001"^^ . + . + . + "pharmacodb.cell" . + . + "biomaterial manufacture" . + . + . + "^\\d{5}$"^^ . + . + . + "http://purl.obolibrary.org/obo/MIRO_$1"^^ . + "https://www-is.biotoul.fr/scripts/ficheIS.php?name=$1"^^ . + . + . + . + . + . + "http://w3id.org/nkos/"^^ . + . + . + . + . + "CDC2"^^ . + . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/experiment.php?action=view&expt_id="^^ . + . + "^\\d+$"^^ . + . + . + "Global Proteome Machine Database" . + "https://entomology.ca.uky.edu/content/$1"^^ . + . + . + "false"^^ . + "life science" . + "false"^^ . + . + . + . + "Allen Institute Ontologies" . + . + "subject agnostic" . + . + . + . + . + . + . + "http://lipidbank.jp/cgi-bin/detail.cgi?id=$1"^^ . + . + . +_:N9e7c97749a6f4045a68fcff83d0fafd5 "edd@usefulinc.com" . + . + "^0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$"^^ . + . + . + . + "csp" . + "vt" . + "seo" . + "http://peroxibase.toulouse.inra.fr/browse/process/view_perox.php?id="^^ . + "gene" . + "false"^^ . + "ncbitaxon" . + "PANTHER Pathway Component" . + . + "statistics" . + . + . + "spectrometry" . + . + . + "false"^^ . + . + . + . + . + . + "A type for entries in the Bioregistry's metaregistry." . + . + . + . + . + "https://www.bgee.org/gene/"^^ . + . + . + . + . + . + . + . + . + "biomodels.teddy" . + . + "^\\w+$"^^ . + . + "hoso" . + . + . + . + . + . + . + "preprints" . + "KEGG-path" . + . + "MEDRA" . + . + . + . + "true"^^ . + . + . + . + . + . + . + . + . + "emapa" . + "http://www.hprd.org/protein/"^^ . + . + "human" . + . + "biology" . + . + . + . + . + . + . + "uberon" . + _:Naa71f4b9d1a3472aafbbf8cea9abd883 . + "Project"^^ . + "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."^^ . + . + . + . + "http://purl.obolibrary.org/obo/SCDO_$1"^^ . + "^\\d+$"^^ . + . + . + "http://purl.obolibrary.org/obo/CMF_"^^ . + "genetics" . + . + . + "https://pubchem.ncbi.nlm.nih.gov/source/hsdb/"^^ . + "life science" . + "^\\d+$"^^ . + . + . + . + "^\\d{8}$"^^ . + . + "epidemiology" . + . + "http://purl.obolibrary.org/obo/UO_"^^ . + . + "matt@tislab.org" . + . + . + "false"^^ . + . + "false"^^ . + . + . + "http://edamontology.org/data_"^^ . + "11"^^ . + . + . + . + . + "https://www.biocatalogue.org/services/$1"^^ . + . + . + . + . + "https://data.4dnucleome.org/experiment-set-replicates/$1"^^ . + . + . + "http://www.umbbd.ethz.ch/servlets/rule.jsp?rule="^^ . + . + "60141"^^ . + . + "animal husbandry" . + "https://webchem.ncbr.muni.cz/Platform/ValidatorDb/ByStructure/"^^ . + . + . + . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + "false"^^ . + . + "Curated Drug-Drug Interactions Database - Drug" . + . + . + . + . + . + . + . + . +_:Nba7394e70eed46019c593a60ce48ec28 "Allen Institute for Brain Science" . + . + . + . + . + . + "1"^^ . + "BioCarta Pathway" . + "SMP0000219"^^ . + . + . "C. elegans Small Molecule Identifier Database" . - . - . - "12300"^^ . - "^\\d+$"^^ . - "easychair.topic" . - . - . - "tgbugs@gmail.com" . - . - "PDB_CHEM_ID" . - "dermo" . - "0000003"^^ . - . - . - . - "amoebadb" . - . - . - . - "Planarian Anatomy and Schmidtea mediterranean Developmental Stage Ontology" . - "The Sequencing Initiative Suomi (SISu) project is an international collaboration to harmonize and aggregate whole genome and exome sequence data from Finnish samples, providing data for researchers and clinicians. The SISu project allows for the search of variants to determine their attributes and occurrence in Finnish cohorts, and provides summary data on single nucleotide variants and indels from exomes, sequenced in disease-specific and population genetic studies."^^ . - . - . - . - . - . - . - "The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB."^^ . - . - "http://stitch.embl.de/interactions/"^^ . - . - . - "Grape Ontology including OIV and bioversity descriptors. INRA July 2017"^^ . - . - . - "false"^^ . - "false"^^ . - "bibo" . - "PharmGKB" . - . - "^\\d+$"^^ . - "Rice Genome Annotation Project" . - "http://www.cs.tau.ac.il/~spike/maps/$1.html"^^ . - . - "SciCrunch Registry" . - "obo" . - . - . - . - . - "Identifiers.org namespace" . - "dsmz_mutz-id:ACC 291"^^ . - "^[0-9]+$"^^ . - . - . - . - . + . + "https://www.gwascentral.org/phenotype/"^^ . + . + . + "expression" . + . + . + . + "http://www.drugbank.ca/drugs/"^^ . + . + . + "life science" . + . + "1009107926"^^ . + . + . + "^[\\d.]+$"^^ . + "http://senselab.med.yale.edu/OdorDB/Data/$1/?db=5"^^ . + . + "PharmacoDB Tissues" . + . + . + . + . + . + . + "46946"^^ . + . + . + "supfam" . + . + . + . + "http://purl.obolibrary.org/obo/VO_$1"^^ . + "https://world-2dpage.expasy.org/repository/$1"^^ . + "Animal Genome Cattle QTL" . + . + . + "life science" . + "UCR00513"^^ . + . + . + . + "false"^^ . + . + . + "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"^^ . + . + . + . + "^[SCTAGMNU]\\d+$"^^ . + . + "life science" . + . + . + "Egon Willighagen" . + "http://www.ebi.ac.uk/efo/EFO_$1"^^ . + . + . + . + . + . + "GlycomeDB" . + . + "false"^^ . + . + . + "http://www.allergome.org/script/dettaglio.php?id_molecule=$1"^^ . + "^\\w\\d+$"^^ . + . + . + "0000001"^^ . + "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . + "dna" . + "https://ensaiosclinicos.gov.br/rg/$1"^^ . + . "8cf84adb-b4db-4807-ac98-0004247c35df"^^ . - "provides for" . - "http://www.pharmgkb.org/drug/"^^ . - . - . + "Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to taxonomic information in Gramene."^^ . + "obo" . + "idoden" . + . + . + "Database of small human noncoding RNAs" . + "https://biopragmatics.github.io/providers/peff/"^^ . + "A type for entries in the Bioregistry's registry." . + "NCI" . + . + . + . + . + . + "gdc" . + "^RPCEC\\d+$"^^ . + "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."^^ . + . + . + "HGVST1828"^^ . + "Simon Jupp" . + "8639.1"^^ . + "obo" . + . + . + . + . + . + "GitHub Issue" . + . + . + . + "^ENST\\d{11}$"^^ . + "Biological Collections Ontology" . + . + "1000003"^^ . + . + "4900"^^ . + "http://purl.obolibrary.org/obo/OGG_"^^ . + . + . + "An ontology for data retrieval and exchange in the fields of multiple DNA/RNA alignment, protein sequence and protein structure alignment."^^ . + "0001410"^^ . + "^\\d{7}$"^^ . + . + "^(C|D)\\d{6,9}$"^^ . + . + . + "ProtoNet Cluster" . + . + . + "Wikidata" . + . + "false"^^ . + . + "srao" . + "false"^^ . + "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."^^ . + "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp=$1"^^ . + "https://www.ebi.ac.uk/chembl/entity/"^^ . + . + . + . + . + . + . + . + . + . + . + . + "marine biology" . + "The namespace name http://www.w3.org/ns/prov# is intended for use with the PROV family of documents that support the interchange of provenance on the web."^^ . + "Laia Subirats" . + "obo" . + . + "Ontology for Nutritional Studies" . + . + . + "^\\d{7}$"^^ . + "identifier for a scientific journal, in the UniProt database"^^ . + "obo" . + . + . + . + "An alternative or synonymous prefix" . + . + . + "selventa" . + . + "MicrosporidiaDB" . + . + "A Semantic Web Rule Language Combining OWL and RuleML" . + . + . +_:N9abc2b29d7c54644828f5ad866064c9e "Jim Amsden" . + . + . + . + "SR0000178"^^ . + "https://bioregistry.io/skm:"^^ . + . + . + . + . + "https://www.langual.org/langual_thesaurus.asp?termid="^^ . + . + "10531"^^ . + "200282"^^ . + . + "proteomics" . + . + . + . + "molecular chemistry" . + . + "European Registry of Materials" . + . + . + . + "PMCID" . + . + . + "Saccharomyces genome database pathways" . + "MaizeGDB is the maize research community's central repository for genetics and genomics information."^^ . + "PF11779"^^ . + . + . + "The set of prefixes used in the Cellosaurus resource" . + . + "SNP to Transcription Factor Binding Sites" . + . + "phenomics" . + "mathematics" . + "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://bioregistry.io/metaregistry/scholia/$1"^^ . + . + . + "Genomics Cohorts Knowledge Ontology" . + "regulation" . + . + . + "0000196"^^ . + . + . + . + "metabolomics" . + "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."^^ . + . + . + . + . + . + . + "Transcription Factor Database" . + . + . + "OntoBee" . + "https://biopragmatics.github.io/providers/diseaseclass/"^^ . + . + . + . + . + . + "voss@gbv.de" . + . + "computational neuroscience" . + . + . + "uniprot.ptm" . + . + . + . + . + "rrid" . + "100010"^^ . + "rna" . + "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."^^ . + "agriculture" . + . + "http://www.marinespecies.org/aphia.php?p=taxdetails&id=$1"^^ . + "https://bioregistry.io/abs:"^^ . + "^\\d{1,7}$"^^ . + . + . + . + . + . + . + "false"^^ . + . + "SNOMED_CT" . + "http://cancer.sanger.ac.uk/cosmic/gene/overview?ln=$1"^^ . + . + . + "false"^^ . + . + . + "gene" . + "eagle-i" . + . + . + "genomics" . + "comparative genomics" . + "false"^^ . + "Henning Hermjakob" . + "obo" . + "0000101"^^ . + . + . + . + . + "The Natural Product-Drug Interaction Research Data Repository, a publicly accessible database where researchers can access scientific results, raw data, and recommended approaches to optimally assess the clinical significance of pharmacokinetic natural product-drug interactions (PK-NPDIs)."^^ . + . + . + . + "Cell line collections (Providers)"^^ . + . + . + "The International Classification of Diseases (ICD) is designed to promote international comparability in the collection, processing, classification, and presentation of mortality statistics."^^ . + . + "repeatsdb.structure" . + . + . + . + "molecule" . + . + "^\\d{8}$"^^ . + . + . + . + "http://imgt.org/IMGTPrimerDB/Check_PrDB.pl?numacc0=$1&origin=view&source=PrList"^^ . + "^[0-9]*$"^^ . + "https://cropontology.org/rdf/CO_336:"^^ . + . + "mouse strain" . + "https://smid-db.org/smid/$1"^^ . + . + . + "biology" . + "022586"^^ . + . + . + . + . + . + . + "glycomapsdb" . + . + . + . + "https://progenetix.org/services/ids/$1"^^ . + . + "^(Gi|Gc)\\d+$"^^ . + "Bambara groundnut ontology" . + . + . + . + "LDS-1110"^^ . + . + "https://www.ncbi.nlm.nih.gov/nucest/$1"^^ . + "life science" . + "PhosphoSite is a mammalian protein database that provides information about in vivo phosphorylation sites. This datatype refers to residue-level information, providing a information about a single modification position in a specific protein sequence."^^ . + . + "http://www.w3.org/2002/07/owl#"^^ . + "pav" . + . + "The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules."^^ . + "PED00017e001"^^ . + "The database of Genotypes and Phenotypes (dbGaP) archives and distributes the results of studies that have investigated the interaction of genotype and phenotype."^^ . + "The Human Protein Reference Database (HPRD) represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."^^ . + "chemistry" . + . + . + . + "Network of Different Plant Genomic Research Projects" . + . + "NIHhESC-10-0083"^^ . + . + . + "^Y[A-Z]{2}\\d+[CW]$"^^ . + "apd" . + "ncim" . + . + "http://bactibase.hammamilab.org/"^^ . + . + . + "http://idp1.force.cs.is.nagoya-u.ac.jp/IDEAL/ideal.php?id="^^ . + . + . + . + . + "false"^^ . + "aeo" . + . + . + . + . + "biomedical science" . + . + . + "hgnc.family" . + . + "http://www.ebi.ac.uk/astd/geneview.html?acc=$1"^^ . + . + "23fa7b4b-9d68-429b-aece-658b11124bb3#2017-03-24T18:43:16.886826-05:00"^^ . + . + . + "antibody" . + "vac" . + . + . + . + "genecards" . + "This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and the Genome Browser that provides an integrated display of annotation data."^^ . + . + . + . + . +_:Ne1ca309b1b3c4995b4f70b52b7a65a7e "helpdesk@cropontology-curationtool.org" . + . + _:N4b239e856348428b86c8044d5a72bbff . + "Document Components Ontology" . + "Plant Growth and Development Stage" . + . + . + . + . + "developmental biology" . + . + "comparative genomics" . + . + "http://www.kegg.jp/entry/"^^ . + . + . + . + "http://www.signaling-gateway.org/molecule/query?afcsid=$1"^^ . + "https://bartoc.org/en/node/"^^ . + "http://purl.obolibrary.org/obo/GENO_"^^ . + . + . + . + "A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . + "life science" . . - . - "^\\d+$"^^ . - . - "life science" . - "^\\d+$"^^ . - . - "bioregistry"^^ . - . + . + . + "Enzyme Commission Code" . + . + . + "clingene" . + . + . + "ontology" . + . + "^TIGR\\d+$"^^ . + "miaa" . + "bko" . + . + . + . + . . - "LNC" . - . - "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."^^ . - "false"^^ . - "2.16.840"^^ . - "https://biosimulations.org/projects/"^^ . - "uniref" . - "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . - . - "life science" . - . - . - "developmental biology" . - . - "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 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."^^ . - . - "https://discover.pennsieve.io/package/$1"^^ . - . - "http://genolist.pasteur.fr/SubtiList/genome.cgi?external_query+$1"^^ . - "g.gkoutos@gmail.com" . - . - "imgt.ligm" . - "http://bis.zju.edu.cn/ricenetdb/genedetails.php?ID=$1"^^ . - "Michel Dumontier" . - "false"^^ . - . - . + . + . + "^\\d{7}$"^^ . + . + . + "CoVoc Coronavirus Vocabulary" . + "https://www.diseasesdatabase.com/ddb$1.htm"^^ . + . + "obo" . + . + . + . + . + . + "metanetx.compartment" . + . + . + "agriculture" . + "This ontology is generated from the manually created specifications in the dbpedia mappings wiki. each release of this ontology corresponds to a new release of the dbpedia data set which contains instance data extracted from the different language versions of wikipedia. for information regarding changes in this ontology, please refer to the dbpedia mappings wiki."^^ . + . + . + . + "^ERM[0-9]{8}$"^^ . + . + . + . + "Orphanet Rare Disease Ontology" . + . + "http://purl.obolibrary.org/obo/PHIPO_$1"^^ . + . + "mgilson@health.ucsd.edu" . + _:Nc729bd6327734c5b8747f5b552404699 . + . + . + . + "^[0-9]{8}$"^^ . + "human" . + "The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology."^^ . + . + . + . + "inaturalist.observation" . + . + . + . + "vto" . + "H-InvDb Protein" . + . + . + "https://bioregistry.io/imgt.primerdb:"^^ . + "data management" . + . + . + "0010039"^^ . + "SLCTR/2023/010"^^ . + "Uber Anatomy Ontology" . + . + . + . + "model" . + . + "grouping" . + . + . + . + "rna-seq" . + . + . + . + . + . + . + "RC00001"^^ . + . + . + . + . + . + "1044544"^^ . + . + "Asset Description Metadata Schema Vocabulary" . + . + "^\\d+$"^^ . + "SCOP(e) concise classification string" . + . + "https://swbiodiversity.org/seinet/taxa/index.php?taxon="^^ . + . + . + "^CTRI/\\d{4}/\\d{2}/\\d+$"^^ . + . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID=$1"^^ . + . + "biomedical science" . + "subject agnostic" . + . + . + "https://www.ensembl.org/id/"^^ . + "http://purl.obolibrary.org/obo/WBbt_"^^ . + "The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character."^^ . + . + "false"^^ . + . + . + . + . + . + . + "computer science" . + "topics" . + "^[0-9][A-Za-z0-9]{3}$"^^ . + . + "NITE Biological Resource Center" . + "rna" . + . + . + . + . + "http://scipion.i2pc.es/ontology/CRYOEM_"^^ . + . + . + . + "arraymap" . + "Kyoto Stock Center" . + "0000000"^^ . + . + "biochemistry" . + . + . + . + . + "webelements" . + . + . + . + . + . + . + . + . + "G77500AY"^^ . + "schober@imbi.uni-freiburg.de" . + . + . + . + "fix" . + "Dublin Core Metadata Initiative Terms" . + . + "metanetx.chemical" . + "http://purl.obolibrary.org/obo/PECO_$1"^^ . + . + . + . + "^\\d{7}$"^^ . + "obo" . . - "051"^^ . - "genetics" . - . - "antibodyregistry" . - . - "neuroscience" . - "^DB\\d{5}$"^^ . - . - "false"^^ . - "deo" . - "life science" . - . - "false"^^ . - . - . - . - . - . - "obo" . - "Richard Boyce" . - . - . - "pfey@northwestern.edu" . - "veterinary medicine" . - "^DDB\\d+$"^^ . - . - . - "http://dictybase.org/gene/$1"^^ . - . - . - . - . - . - . - . - "obo" . - . - . - . - "PSI-MI" . - . - . - . - . - . - . - . - . - "ontology" . - . - . - . - "true"^^ . - . - . - . - "Computational and Informatics Resources for Glycoscience" . - "^\\d+$"^^ . - . - . - "rpillich@ucsd.edu" . - "MESHD" . - . - "co_338" . - . - . - . + . + . + . + . + . + "http://icd9cm.chrisendres.com/index.php?action=search&srchtext="^^ . + . + "cito" . + . + . + . + . + "stem cell" . + . + . + . + . + . + "An anatomical and developmental ontology for ctenophores (Comb Jellies)"^^ . + "false"^^ . + "HEX1"^^ . + . + . + "^\\d{3}$"^^ . + . + "true"^^ . + "nmr" . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/strain/inducedMutationLine/detail/"^^ . + "http://purl.obolibrary.org/obo/GOREL_$1"^^ . + . + "Web Elements" . + "neurodegeneration" . + . + "AURKA"^^ . + . + . + . + . + . + . + . + "foaf" . + . + . + . + . + . + . + . + . + "frederique.lisacek@isb-sib.ch" . + "http://purl.obolibrary.org/obo/AAO_"^^ . + "http://antibodyregistry.org/AB_"^^ . + "life science" . + . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"^^ . + . + . + . + . + . + "repository" . + . + "false"^^ . + "true"^^ . + "ontology" . + "false"^^ . + . + . + . + . + . + . + . + "http://rhesus.amu.edu.pl/mirnest/copy/details.php?id="^^ . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page_CIME.php?cime_id=$1_CIME"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/OGMS_"^^ . + . + . + . + . + . + "false"^^ . + . + "false"^^ . + . + "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. "^^ . + . + "Ontology for computer aided process engineering" . + . + "obo" . + "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."^^ . + . + "https://www.uniprot.org/tissues/"^^ . + . + . + . + . + "EU Clinical Trials" . + "SEQF1003"^^ . + "genotype" . + "y3ax-8bq3-60"^^ . + "https://www.sharkipedia.org/species/"^^ . + "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&taxon_oid=$1"^^ . + "health science" . + "^[1-9]\\d*$"^^ . + "^FCB\\d{3}$"^^ . + . + . + "false"^^ . + "Crystallographic Information Framework" . + "inn" . + "^[\\w\\-:,]{3,64}$"^^ . + . + "EAWAG Biocatalysis/Biodegradation Database" . + . + . + . + . + . + _:N8f29cebc16e44d6c87f3a1f551121218 . + . + . + . + . + . + . + . + . + . + . + . + . + "http://purl.org/net/orth#"^^ . + "https://urgi.versailles.inra.fr/gnpis/#result/term=$1"^^ . + "http://www.bootstrep.eu/ontology/GRO#"^^ . + . + . + "^\\d{7}$"^^ . + "false"^^ . + . + "Sequence-Structural Templates of Single-member Superfamilies" . + "https://vectorbase.org/gene/"^^ . + . + . + . + . + . + . + "PeptideAtlas" . + . + "health science" . + . + "http://www.interfil.org/details.php?id=$1"^^ . + "https://mmp.sfb.uit.no/databases/mardb/#/records/"^^ . + . + "functional genomics" . + . + . + "Toxin and Toxin Target Database" . + "false"^^ . + . + . + "ontology" . + "^\\d+$"^^ . + "myco.lepra" . + . + . + . + . + . + "false"^^ . + . + . + "synthetic biology" . + . + . + . + . + . + "dpo" . + . + . + . + . + "http://purl.obolibrary.org/obo/LIPRO_$1"^^ . + . + . + "UM-BBD compound" . + . + . + "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."^^ . + . + . + . + "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."^^ . + . + . + "genome" . + . + "http://avis.princeton.edu/pixie/viewgraph.php?graphID=$1"^^ . + "http://www.receptome.org/families/Frameset_family.asp?ProtType=Receptor&FamId=$1"^^ . + . + "vario" . + . + "epidemiology" . + . + "phenotype" . + . + . + . + . + . + . + . + "fly" . + "Nanbyo Disease Ontology (NANDO) is the ontology creating a comprehensive hierarchical controlled vocabulary for intractable and rare disease (i.e., nanbyo) representation in Japan."^^ . + "neurophysiology" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "4390079"^^ . + "development" . + . + "An ontology representing the structure of model card reports - reports that describe basic characteristics of machine learning models for the public and consumers."^^ . + . + "https://www.ins.gob.pe/ensayosclinicos/rpec/recuperarECPBNuevo.asp?val=&NroPag=1&flg=0&ver=EN&numEC="^^ . + . + "^(MNX[CD]\\d+|BOUNDARY|IN|OUT)$"^^ . + . + . + . + . + . + . + . + "ontology and terminology" . + . + . + "http://gmd.mpimp-golm.mpg.de/Analytes/"^^ . + "Molecular database for the identification of fungi" . + "false"^^ . + . + "ExAC Transcript" . + . + . + . + . + . + . + "mondo" . + . + . + "https://www.genedb.org/gene/"^^ . + . + . + "false"^^ . + "https://cropontology.org/rdf/CO_348:$1"^^ . + . + "^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$"^^ . + . + . + . + . + . + . + "classification" . + . + "^\\w+(\\.)?\\d+$"^^ . + "http://purl.obolibrary.org/obo/ECO_"^^ . + . + "Influenza Virus Database" . + . + . + . + . + . + . + . + . + . + "mathematics" . + "KEGG Pathways Database" . + . + "systems biology" . + . + . + . + "http://purl.obolibrary.org/obo/FOBI_$1"^^ . + . + . + . + . + . + . + . + . + "Medical Data Models" . + "http://caps.ncbs.res.in/cgi-bin/pass2//show_sf.py?sf_id=$1"^^ . + "anatomy" . + . + "false"^^ . + "data management" . + . + . + "The GPCR NaVa database describes sequence variants within the family of human G Protein-Coupled Receptors (GPCRs). GPCRs regulate many physiological functions and are the targets for most of today's medicines. The acronym NaVa stands for Natural Variant, which means any (non-artificial) variant that occurs in humans."^^ . + "false"^^ . + . + "rna" . + "BioSimulators" . + . + "nihhesc" . + "virology" . + . + . + "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)."^^ . + . + . + "https://cropontology.org/rdf/CO_370:$1"^^ . + "DrugBank Metabolite" . + . + "EP0311"^^ . + . + . + "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."^^ . + "595"^^ . + "http://iflastandards.info/ns/fr/frbr/frbrer/$1"^^ . + "true"^^ . + . + . + . + "false"^^ . + . + . + "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"^^ . + . + "supply" . + . + . + . + "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid=$1"^^ . + "The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ended, the Data Coordination Centre at EMBL-EBI has received continued funding from the Wellcome Trust to maintain and expand the resource. IGSR was set up to do this and has the following aims: ensure the future access to and usability of the 1000 Genomes reference data; incorporate additional published genomic data on the 1000 Genomes samples; and expand the data collection to include new populations not represented in the 1000 Genomes Project."^^ . + . + "^[-0-9a-zA-Z]+(@[-0-9a-zA-Z]+)?$"^^ . + "LinkML" . + . + . + "Compositional Dietary Nutrition Ontology" . + . + . + . + . + . + . + "false"^^ . + . + "Os01g0883800"^^ . + . + . + "life science" . + . + . + . + "https://vocab.org/vann/"^^ . + . + "scientist" . + "false"^^ . + . + "728"^^ . + "Healthcare Organizations and Services Ontology" . + . + . + . + "^PACTR\\d+$"^^ . + "International Classification of Diseases for Oncology" . + "0000400"^^ . + . + "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."^^ . + "false"^^ . + "descriptor" . + . + . + . + . + "protein" . + . + "https://jcoin.datacommons.io/ga4gh/drs/v1/objects/"^^ . + . + . + . + . + . + "P53350"^^ . + "https://www.ebi.ac.uk/metagenomics/projects/"^^ . + . + "taxonomy" . + "aBq"^^ . + "false"^^ . + . + "infectious disease medicine" . + "http://www.mgc.ac.cn/cgi-bin/VFs/genus.cgi?Genus="^^ . + . + . + "207LH0002X"^^ . + . + "https://cropontology.org/rdf/CO_367:$1"^^ . + . + "STOREDB at University of Cambridge" . + . + . + "0000773"^^ . + "BN000065"^^ . + . + . + . + . + . + "developmental biology" . + . + . + "sequence" . + "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."^^ . + . + . + . + . + . + . + . + "massive" . + "Darren Natale" . + "ls-c35719-120"^^ . + . + . + . + . + "TogoVar" . + "http://purl.obolibrary.org/obo/CLAO_$1"^^ . + . + "https://ocid.ontochem.com/prefname?ocid="^^ . + "https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=$1"^^ . + "functional genomics" . + "genetics" . + . + . + "virology" . + "https://cropontology.org/rdf/CO_340:$1"^^ . + . + "morpheus" . + . + . + "hms.lincs.dataset" . + . + . + . + . + . + "^\\d+$"^^ . + . + "ontology" . + "https://biopragmatics.github.io/providers/cemo/"^^ . + "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"^^ . + . + "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)."^^ . + "imp10873"^^ . + "pass2" . + . + "https://www.ncbi.nlm.nih.gov/dbvar/studies/$1"^^ . + "flybase" . + . + . + . + . + . + . + . + . + . + . + "https://www.jax.org/strain/$1"^^ . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code=$1"^^ . + "http://bioportal.bioontology.org/ontologies/MAMO/?p=classes&conceptid=http://identifiers.org/mamo/MAMO_"^^ . + "chemical" . + "http://purl.obolibrary.org/obo/PGDSO_$1"^^ . + "structure" . + . + . + . + . + . + "https://sciflection.com/$1"^^ . + . + . + . + . + . + . + . + . + . + "P4355"^^ . + . + "PhenX Toolkit" . + . + . + "dashr" . + . + . + . + . + . + . + . + . + "^\\w+$"^^ . + "http://drugcentral.org/drugcard/"^^ . + "MultiCellDS collection" . + . + . + . + . + "false"^^ . + . + . + . + "tair.locus" . + "63189"^^ . + . + . + . + . + "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."^^ . + . + "http://purl.obolibrary.org/obo/ECO_$1"^^ . + . + . + . + . + . + . + . + "structure" . + . + "ontology" . + . + "AICARTRANSIMPCYCLO-CPLX"^^ . + "atmospheric science" . + . + . + . + "environmental science" . + . + . + . + . + . + . + . + . + "chemical" . + . + . + "0020"^^ . + "false"^^ . + "provides for" . + "https://cropontology.org/rdf/CO_324:"^^ . + "Roman Laskowski" . + . + "RepeatsDB is a database of annotated tandem repeat protein structures. This collection references structural entries in the database."^^ . + . + . + "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://biopragmatics.github.io/providers/uniprot.ptm/"^^ . + . + . + . + . + . + . + "Nathan Baker" . + "http://www.mgc.ac.cn/cgi-bin/ShiBASE/ShiBASE_query.cgi?synonym="^^ . + . + "National Drug Code" . + . + . + . + "true"^^ . + "http://sabiork.h-its.org/newSearch?q=ecnumber:"^^ . + . + . + . + "obo" . + . + . + "Ekaterina Chuprikova" . + . + . + . + "0000066"^^ . + "false"^^ . + . + . + . + . + "http://immunet.cn/bdb/index.php/mimoset/"^^ . + . + . + "ViolinNet" . + . + . + . + "https://cropontology.org/rdf/CO_360:"^^ . + . + . + "https://bioregistry.io/phosphopoint.kinase:"^^ . + . + . + . + "false"^^ . + . + . + "wd" . + . + "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."^^ . + . + . + . + "http://vegbank.org/cite/$1"^^ . + . + "ega.study" . + . + "gene" . + . + "http://sabiork.h-its.org/kineticLawEntry.jsp?viewData=true&kinlawid="^^ . + . + . + "false"^^ . + . + "togovar" . + "^\\d{7}$"^^ . + "^\\d{7}$"^^ . + "false"^^ . + . + . + "^\\d+$"^^ . + . + "false"^^ . + . + . + "3DMET is a database collecting three-dimensional structures of natural metabolites."^^ . + "false"^^ . + "Lipid Ontology" . + "protein" . + . + . +_:Ne99dc73b20714efa88f5c99a1754101f "helpdesk@cropontology-curationtool.org" . + . + . + . + "Chicken Gene Nomenclature Consortium" . + "EST database maintained at the NCBI." . + "182"^^ . + "false"^^ . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "http://www.whocc.no/atcvet/atcvet_index/?code="^^ . + "https://herv.img.cas.cz/s/$1"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/MF_"^^ . + . + "https://w3id.org/aio/$1"^^ . + "false"^^ . + . + "false"^^ . + . + . + . + . + "Multispecies fish anatomy ontology. Originally seeded from ZFA, but intended to cover terms relevant to other taxa"^^ . + . + . + "^SM\\d{5}$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/SBO_"^^ . . - "H-InvDb Locus" . - "life science" . - . - . - "^\\d+$"^^ . - . - . - . - "DBrodbelt@RVC.AC.UK" . - . - . - "https://www.langual.org/langual_thesaurus.asp?termid=$1"^^ . - . - . - . - . - . - . - "N1899"^^ . - . - . - "ontology" . - "pier.buttigieg@awi.de" . - "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'."^^ . - . - . - . - . - . - . - . - . - "http://ensembl.org/glossary/ENSGLOSSARY_"^^ . - . - "Aspergillus Genome Database" . - . - . - . - . - "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId=$1"^^ . - . - "GO Chemicals" . - . - "Metabolic Network Exchange Database" . - . - "ontology" . - . - "http://purl.org/gc/$1"^^ . - "obo" . - "glida.gpcr" . - . - . - . - "Genome Properties" . - . - . - . - . - . - . - . - . - "A web-developer centric archive of prefixes and URI prefixes" . -_:N1e52be9bd7ce42428f19eb8361ffc581 "American Medical Association" . - . - . - . - "485991"^^ . - "gramene.growthstage" . - . - . - . - . - . - . - . - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . - "1731"^^ . - "http://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=GeneDetail&gene_oid="^^ . - . - . - "https://www.animalgenome.org/QTLdb/q?id=QTL_ID:$1"^^ . - "cpc" . - . - "http://hdl.handle.net/"^^ . - "false"^^ . - . - . - "^\\d+$"^^ . - . - . - "NCI Data Commons Framework Services" . - "ncbibook" . - . - "http://purl.obolibrary.org/obo/OHMI_"^^ . - "Database of protein-protein complexes" . - . - "^\\d+$"^^ . - . - "bandrow@gmail.com" . - . - . - . - . - . - "Thai Clinical Trials Registry" . - "biomedical science" . - "http://purl.obolibrary.org/obo/MCO_$1"^^ . - . - "The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. " . - . - . - . - . - "^\\d+$"^^ . - . - "https://biopragmatics.github.io/providers/goche/$1"^^ . - "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name="^^ . - . - . - . - . - "pina" . - "false"^^ . - "oma.protein" . - "^\\d{7}$"^^ . - . - . - . - . - . - "data integration" . - . - . - "LinJ.20.0070"^^ . - "NIF Cell" . - "UCR00226"^^ . - . - . - "^[a-z0-9\\_]+$"^^ . - . - . - . - . - . - "jaxmice" . - "https://bartoc.org/" . - . - . - . - "http://dicom.nema.org/resources/ontology/DCM/"^^ . - . - . - "uniparc" . - "biology" . - . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/TAHH_"^^ . - . - "http://uri.neuinfo.org/nif/nifstd/birnlex_$1"^^ . - . - . - . - . - . - . - "genomics" . - . - . - . - . - . - . - . - . - "https://www.ebi.ac.uk/complexportal/complex/$1"^^ . - . - "registry" . - . - . - "false"^^ . - . - . - . - "DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) is a foundational ontology developed as part of the WonderWeb Foundational Ontologies Library (WFOL). The development of this library has been guided by the need of a reliable set of foundational ontologies that can serve as 1) astarting point for building other ontologies, 2) a reference point for easy and rigorous comparisons among different ontological approaches, and 3) a rigorous basis for analyzing, harmonizing and integrating existing ontologies and metadata standards (by manually mapping them into some general module(s) in the library). DOLCE is the first module of WFOL and it is not a candidate for a universal standard ontology. Rather, it is intended as a starting point for comparing and elucidating the relationships with the other modules of the library, and also for clarifying the hidden assumptions underlying existing ontologies or linguistic resources such as WordNet. As reflected by its acronym, DOLCE has a clear cognitive bias, in the sense that it aims at capturing the ontological categories underlying natural language and human commonsense. DOLCE is an ontology that focuses on particulars in the sense that its domain of discourse is restricted to them. The project is complete, though the ontology remains available for use."^^ . - "SMP0000219"^^ . - . - "envipath" . - . - . - . - "Bgee gene" . - "false"^^ . - "biomedical science" . - . - . - . - . - . - . - . - . - "https://dandiarchive.org/dandiset/$1"^^ . - . - "http://purl.obolibrary.org/obo/DOID_"^^ . - . - . - . - "civic.mpid" . - . - . - . - "https://www.ebi.ac.uk/metabolights/$1"^^ . - "Microarray experimental conditions" . - . - "false"^^ . - . - . - "false"^^ . - . - "https://biopragmatics.github.io/providers/mba/$1"^^ . - . - . - . - . - . - "ontology" . - . - . - "MediaDive Ingredient" . - "^\\d+$"^^ . - . - . - . - . - . - "foodb" . - "https://hdl.handle.net/hdl:20.500.12582/"^^ . - . - . - "plasmodb" . - . - . - "^([\\dA-Z]\\d{2}(\\.\\d{1,3}|))|(\\d{2}(\\.\\d{1,2}|))$"^^ . - "Chinese Biological Abstracts" . - . - "oncotree" . - . - . - "http://pathway.yeastgenome.org/YEAST/new-image?type=PATHWAY&object=$1"^^ . - . - "phylogeny" . - "IP" . - . - "false"^^ . - . - "dsm-v" . - "ProteomeXchange" . - . - "repository" . - "computational biology" . - . - "Scopus Publication" . - "false"^^ . - "Glycosciences.DB" . - . - . - . - . - "false"^^ . - "dclunie@dclunie.com" . - "NONHSAT000001"^^ . - . - "Drosophila Phenotype Ontology" . - "^\\d{8}$"^^ . - "chemistry" . - . - . - . - . - . - "life science" . - "unipathway.compound" . - "Cambridge Structural Database" . - . - "https://www.geonames.org/$1"^^ . - . - . + . + . + "genomics" . + . + "https://www.cellbiolabs.com/search?keywords="^^ . + . + . + . + . + . + "refseq" . + "WBGene00000001"^^ . + . + "life sciences" . + . + "http://purl.obolibrary.org/obo/AISM_"^^ . + "https://legacy.vectorbase.org/ontology-browser?cv=MIRO&t=IRO:$1"^^ . + "http://purl.obolibrary.org/obo/OHD_$1"^^ . + . + "false"^^ . + . + "CHEMONTID" . + . + . + . + . + . + . + . + . + "computational biology" . + . + . + "Documentation of SMILES (Simplified Molecular Input Line Entry System), a line notation (a typographical method using printable characters) for entering and representing molecules and reactions."^^ . + . + "phylogenetics" . + "genomics" . + . + "Silvio Peroni" . + . + . + . . - . - . - . - . - . - "^\\d+$"^^ . - . - "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."^^ . - "nfdi4chem.osmo" . - "subject agnostic" . - . - "protein" . - . - "life science" . - . - "http://purl.obolibrary.org/obo/IPR_"^^ . - . - . + "OSMO is an ontologization and extension of MODA, a workflow metadata standard that constitutes a mandatory requirement within a number of European calls and projects in the context of materials modelling. OSMO was developed within the Horizon 2020 project VIMMP (Virtual Materials Marketplace) and is part of a larger effort in ontology engineering driven by the European Materials Modelling Council, with the European Materials and Modelling Ontology (EMMO) as its core. (from https://nfdi4cat.org/services/ontologie-sammlung/)"^^ . + . + . + . + "ontology" . + . + "24801"^^ . + . + . + . + "The Basic Register of Thesauri, Ontologies & Classifications (BARTOC) is a database of Knowledge Organization Systems and KOS related registries.\nThe main goal of BARTOC is to list as many Knowledge Organization Systems as possible at one place in order to achieve greater visibility, highlight their features, make them searchable and comparable, and foster knowledge sharing. BARTOC includes any kind of KOS from any subject area, in any language, any publication format, and any form of accessibility. BARTOC’s search interface is available in 20 European languages and provides two search options: Basic Search by keywords, and Advanced Search by taxonomy terms. A circle of editors has gathered around BARTOC from all across Europe and BARTOC has been approved by the International Society for Knowledge Organization (ISKO)."^^ . + . + . + . + "https://scicrunch.org/resolver/RRID:AGSC_"^^ . + "^[8-9]\\d{3}(/[0-3])?$"^^ . + "Medical Dictionary for Regulatory Activities" . + "p3db.site" . + . + "classification" . + . + "^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$"^^ . + . + "unichem" . + "https://foodb.ca/foods/"^^ . + "false"^^ . + "vhog" . + "ontology" . + . + . + . + . + . + "6200"^^ . + . + . + . + . + "^\\b[0-9a-f]{8}\\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\\b[0-9a-f]{12}\\b$"^^ . + "PD000596"^^ . + "agriculture" . + . + "http://oid-info.com/get/$1"^^ . + "obo" . + "https://mmp.sfb.uit.no/databases/marref/#/records/$1"^^ . + . + . + "life science" . + "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-$1"^^ . + . + "https://identifiers.org" . + . + . + "https://vcell.org/biomodel-"^^ . + "The Funder Registry is an open registry of persistent identifiers for grant-giving organizations around the world."^^ . + . +_:N7474ab215e6849ba97c110a221df4162 "helpdesk@cropontology-curationtool.org" . + . + . + "false"^^ . + . + . + . + . + . + . + "7123"^^ . + "ricegap" . + . + . + . + . + . + . + "hms.lincs.cell" . + _:N613e35d4094d47e4af9d8a0547acbfbf . + . + . + . + . + "ontology" . + . + "GeneTree" . + "https://uts.nlm.nih.gov/uts/umls/semantic-network/$1"^^ . + . + . + . + . + "false"^^ . + . + "^\\d{7}$"^^ . + "GT10"^^ . + . + . + "Assembling the Fungal Tree of Life - Taxonomy" . + . + . + . + . + . + . + . + . + . + "The antimicrobial peptide database (APD) provides information on anticancer, antiviral, antifungal and antibacterial peptides."^^ . + "skosxl" . + . + "http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid="^^ . + . + "https://www.ebi.ac.uk/ontology-lookup/?termId=PAR:$1"^^ . + . + "CY077097"^^ . + . + "http://www.probonto.org/ontology#PROB_$1"^^ . + . + . + . + . + . + "https://n2t.net/$1:"^^ . + . + . + "structure" . + . + . + . + "DateTimeDescription"^^ . + . + . + . + . + "dna" . + . + . + "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."^^ . + . + "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."^^ . + . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/" . + "false"^^ . + "genetic" . + . + "Cell Ontology" . + "Sebastien Moretti" . + . + . + . + . + . + . + . + . + . + . + "bioinformatics" . + . + "bmrb" . + . + . + . + . + . + "http://wodaklab.org/iRefWeb/interaction/show/$1"^^ . + "rna" . + . + . + . + . + . + . + . + . + "hgmd" . + . + "small molecule" . + . + . + . + "https://w3id.org/linkml/$1"^^ . + "53504"^^ . + . + . + . + "RoleInTime"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/DERMO_$1"^^ . + "https://biopragmatics.github.io/providers/goche/"^^ . + . + "snomedct" . + "The FAO Statistics Team (NFISS) of Fisheries and Aquaculture Division collates world capture and aquaculture production statistics at either the species, genus, family, or higher taxonomic levels in 3,169 statistical categories (2022 data release) referred to as species items. ASFIS list of species includes 13,417 species items selected according to their interest or relation to fisheries and aquaculture. For each species item stored in a record, codes (ISSCAAP group, taxonomic and 3-alpha) and taxonomic information (scientific name, author(s), family, and higher taxonomic classification) are provided. An English name is available for most of the records, and about one third of them have also a French and Spanish name. Information is also provided about the availability of fishery production statistics on the species item in the FAO databases. (from homepage)"^^ . + "anatomy" . + "4892"^^ . + "tissue" . + . + "https://www.nextprot.org/term/"^^ . + . + "NIF Standard Ontology: Molecules" . + . + "false"^^ . + "false"^^ . + . + "^TB[1,2]?:[A-Z][a-z]?\\d+$"^^ . + "UMLS_ICD9CM_2005_AUI" . + . + . + . + . + . + . + . + "RiceNetDB Protein" . + "Lars Holm Nielsen" . + . + . + . + . + . + . + . + . + . + . + "NMR Restraints Grid" . + "DBrodbelt@RVC.AC.UK" . + . + . + "http://www.bioassayontology.org/bao#BAO_"^^ . + . + . + . + . + . + . + "ontology" . + . + "false"^^ . + . + . + "https://pubchem.ncbi.nlm.nih.gov/classification/#hid="^^ . + . + "^\\d+$"^^ . + . + . + . + "structure" . + . + "https://shigen.nig.ac.jp/rice/oryzabase/reference/detail/$1"^^ . + "Resource Description Framework" . + . + "soybase" . + . + . + . + . + . + "Cell types that are provisionally defined by experimental techniques such as single cell transcriptomics rather than a straightforward & coherent set of properties."^^ . + . + . + . + "^[A-Z]{2,6}(e|i)[A-Za-z0-9]{3}-[A-Z]{1,2}(-[A-Za-z0-9]{1,2})?$"^^ . + . + . + . + "http://purl.obolibrary.org/obo/AMPHX_"^^ . + . + "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID=$1"^^ . + . + . + . + "HGVPM623"^^ . + "ped" . + . + . + . + "biology" . + . + . + . + "Simple Modular Architecture Research Tool" . + "^\\d{7}$"^^ . + . + . + . + . + . + . +_:N7905bc80f2e64f5990160fb6972ac478 "FALDO group" . + "biomedical science" . + . + . + . + . + "arXiv is an e-print service in the fields of physics, mathematics, non-linear science, computer science, and quantitative biology."^^ . + "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."^^ . + . + . + "http://igsn.org/$1"^^ . + "ontology" . + . + . + . + "false"^^ . + . + . + . + . + "http://asrp.cgrb.oregonstate.edu/db/sRNAdisplay.html?ASRP_id="^^ . + "cultured cell line" . + . + . + "translational medicine" . + . + "https://www.rebuildingakidney.org/id/"^^ . + "biopesticides" . + "molecular biology" . + "false"^^ . + . + . + . + . + . + "https://www.ncbi.nlm.nih.gov/medgen/"^^ . + "false"^^ . + . + "UniGene" . + . + "https://www.uniprot.org/locations/"^^ . + . + . + "subject agnostic" . + . + . + . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "ontology" . + . + . + . + . + . + . + "video resource" . + . + . + "luana.licata@gmail.com" . + . + "811"^^ . + . + . + . + "https://cropontology.org/rdf/CO_357:$1"^^ . + . + "imsr_em" . + "omim.ps" . + . + . + "life science" . + . + . + "https://www.ncbi.nlm.nih.gov/clinvar/submitters/$1"^^ . + . + "false"^^ . + . + . + . + "histology" . + "mmrrc" . + "gdsc" . + . + . + . + . + . + . + "false"^^ . + . + . + "dna" . + . + . + "http://purl.obolibrary.org/obo/PdumDv_"^^ . + . + . + "Common Science and Technology Resources" . + . + . + "false"^^ . + "protein" . + . + "gc" . + . + "0000001"^^ . + . + "protein" . + . + . + "http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?action=view&protocol_id=$1"^^ . + "developmental biology" . + . + . + . + "biogrid.interaction" . + . + "An OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation."^^ . + . + "101"^^ . + . + . + . + . + . + . + . + . + . + . + . + "genome" . + "glycosciences.db" . + . + . + . + "http://gpcr.biocomp.unibo.it/cgi-bin/predictors/esldb/dettagli.cgi?codice="^^ . + . + . + . + . + . + . + . + . + . + "MmusDv" . + . + . + . + "false"^^ . + "life science" . + . + . + . + . + "orthology assignment" . + "epidemiology" . + "life science" . + "MolMeDB" . + "HPA000698"^^ . + "https://www.flymine.org/come/entry?gn="^^ . + . + "interaction" . + . + "http://purl.obolibrary.org/obo/FYPO_$1"^^ . + "Ontology of Genetic Susceptibility Factor" . + . + "Insertion sequence elements database" . + "https://thebiogrid.org/interaction/$1"^^ . + . + . + . + "protein" . + "ontology" . + "The Drug-Drug Interactions Ontology" . + "ensembl.fungi" . + "pseudomonas" . + . + . + "life science" . + . + "gene" . + . + "anatomy" . + "Lebanon Clinical Trials Registry" . + "UPISO" . + "^\\d{7}$"^^ . + . + "cgsc" . + . + "ontology" . + "^\\d{6,7}$"^^ . + "The RNA Modification Database" . + . + "protein"^^ . + . + "natural science" . + . + "https://mobidb.org/$1"^^ . + "The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data pertains to unrelated individuals sequenced as part of various disease-specific and population genetic studies and serves as a reference set of allele frequencies for severe disease studies. This collection references gene information."^^ . + "The Cambridge Crystallographic Data Centre (CCDC) develops and maintains the Cambridge Stuctural Database, the world's most comprehensive archive of small-molecule crystal structure data. A CCDC Number is a unique identifier assigned to a dataset deposited with the CCDC."^^ . + . + . + "Amelanchier laevis"^^ . + . + . + . + . + . + "DirectiveInformationContentEntity"^^ . + . + "http://purl.org/spar/datacite/"^^ . + . + . + . + . + . + . + . + . + "dbsnp" . + . + "^S\\w+(\\.)?\\w+(\\.)?$"^^ . + "genomics" . + "dg.4dfc" . + . + . + . + "life science" . + . + . + . + . + . + "^[m,M]{2}[0-9]{5}[0-9]*$"^^ . + . + . + "http://hawaii.eagle-i.net/i/"^^ . + "^SD\\d+$"^^ . + "false"^^ . + . + . + "false"^^ . + "AU124"^^ . + . + . + . + . + . + "wormmart" . + . +_:N7474ab215e6849ba97c110a221df4162 "Crop Ontology Helpdesk" . + "REDflyis a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs)."^^ . + . + . + . + "46"^^ . + "https://www.storedb.org/store_v3/study.jsp?studyId=$1"^^ . + . + . + "http://data.crossref.org/fundingdata/funder/10.13039/$1"^^ . + . + "aero" . "https://massive.ucsd.edu/ProteoSAFe/QueryMSV?id=$1"^^ . - "P29894"^^ . - "knowledge and information systems" . - . - "clinvar.variant" . - . - . - . - . - . - . - . - "http://wheat.pw.usda.gov/report?class=gene;name="^^ . - . - "^M\\d{5}$"^^ . - . - "^A\\d+$"^^ . - . - . - . - . - . - . - "Terry Hayamizu" . - . - . - . - . - "protein" . - . + . + . + . + "marine biology" . + . + . + . + . + . + . + "colao" . + . + . + "obo" . + . + "https://jrct.niph.go.jp/en-latest-detail/$1"^^ . + . + . + . + . + . + "ConfIDent Event" . + . + . + . + . + . + . + "345201101230312003"^^ . + "darc" . + . + "false"^^ . + "Rfam database of RNA families" . + . + . + "ricenetdb.protein" . + "4dn.biosource" . + "microbiology" . + "false"^^ . + "orchard@ebi.ac.uk" . + . + "0000095"^^ . + "http://biomodels.net/rdf/vocabulary.rdf#"^^ . + "mirnest" . + . + _:Nf61f2d7c1ff54380bf84884a9c9d8f51 . + . + . + . + "obo" . + . + . + "ACHN"^^ . + "Elizabeth Arnaud" . + . + "senso" . + "https://nanbyodata.jp/disease/NANDO:$1"^^ . + . + . + "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]"^^ . + "ensemblglossary" . + "false"^^ . + . + "false"^^ . + . + . + . + . + . + . + "https://archive.gramene.org/db/ontology/search?id=GR_tax:$1"^^ . + "metaproteomics" . + . + "jrct" . + . + . + "A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology."^^ . + . + . + . + . + . + . + . + . + "http://www.ces.clemson.edu/compbio/protcom/print_file.cgi?pdbid=$1"^^ . + "structure" . + . + "Cell lines used in the Dependency Map (DepMap). Highly related to CCLE Cells."^^ . + "^\\d+$"^^ . + . + . + . + "obo" . + "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."^^ . + . + "chemistry" . + "762"^^ . + "miRNEST" . + . + "0000487"^^ . + . + . + . + . + "https://www.cameo3d.org/sp/targets/target/"^^ . + "http://purl.obolibrary.org/obo/NGBO_$1"^^ . + . + "Molecular Signatures Database" . + . + "BRENDA Tissue Ontology" . + . + . + "obo" . "false"^^ . - . - _:N50de7bbebb744373b98eaefc287f558e . - . - . - "Human Unidentified Gene-Encoded" . - . - "^[A-Za-z0-9+_.%-:]+$"^^ . - . - "^splash\\d[A-Z-a-z0-9]-[A-Za-z0-9]+-[A-Za-z0-9]+$"^^ . - "CRISPRdb" . - . - "International Molecular Exchange" . - . - "obo" . - . - "dc.elements" . - . - . - "drosophilidae" . - . - . - . - . - . - . - "obo" . - "false"^^ . - . - . - . - "1"^^ . - . - . - . - . - . - "0000319"^^ . - "'ocid' stands for \"Ontology Concept Identifiers\" and are 12 digit long integers covering IDs in topical ontologies from anatomy up to toxicology."^^ . - "Patrice Buche" . - "44259"^^ . - "dr.sebastian.koehler@gmail.com" . - . - . - . - . - . - . - . - . - . - "http://id.who.int/icd/entity/$1"^^ . - . - . - . - . - "ontology" . - "AGROVOC" . + . + . + "https://w3id.org/nfdi4cat/voc4cat_"^^ . + . + . + "taxonomy" . + "comparative genomics" . + "genome" . + . + . + "http://purl.bioontology.org/ontology/CSP/$1"^^ . + . + "National Academic Research and Collaborations Information System" . + . + "http://func.mshri.on.ca/fly/genes/list_functional_scores/$1"^^ . + . + . + . + . + "ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature."^^ . + . + "false"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + "^\\d{7}$"^^ . + "obo" . + "ontology" . + "http://purl.obolibrary.org/obo/CTENO_$1"^^ . + "development" . + . + . + . + . + . + . + "Bioschemas aims to improve the Findability on the Web of life sciences resources such as datasets, software, and training materials. It does this by encouraging people in the life sciences to use Schema.org markup in their websites so that they are indexable by search engines and other services. Bioschemas encourages the consistent use of markup to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed resources. [from BioSchemas.org]"^^ . + . + "^\\d+$"^^ . + "^\\d{7}$"^^ . + "genome" . + . + . + "genome" . + "4019477"^^ . + . + . + . + . + "6017782"^^ . + "addiehl@buffalo.edu" . + . + . + "Protein Model Database" . + "araport" . + . + . + . + . + . + . + . + "BioTools" . + ""^^ . + . + . + "MCDS_C_0000000001"^^ . + . + . + "^A_\\d+_.+$"^^ . + . + "pathway" . + "SNOMEDCT_US_2022_09_01" . + . + "cell lines" . + "^([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,})$"^^ . + "^C?\\d+$"^^ . + . + . + . + . + "Novus Biologicals" . + . + "pharmgkb.disease" . + "rdf" . + "https://www.brenda-enzymes.de/ligand.php?brenda_group_id="^^ . + . + "https://uniresolver.io/#did:"^^ . + "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://dtp.cancer.gov/dtpstandard/servlet/ChemData?searchtype=NSC&searchlist=$1"^^ . + _:N1d6d2989305b482cad5c4f3d8442073c . + . + . + . + . +_:N497517396e9a4f43959d71e6099fbdfd "ncictcaehelp@mail.nih.gov" . + "model" . + . + . + "http://www.w3.org/2006/time#"^^ . + "26753"^^ . + . + . + "https://biopragmatics.github.io/providers/scomp/"^^ . + . + . + . + . + . + "http://www.peptideatlas.org/PASS/$1"^^ . + . + "environmental science" . + . + . + "phenotype" . + . + . + . + . + . + "http://research.nhgri.nih.gov/apps/homeodomain/web/index.cgi?mode=view&view=proteins&id="^^ . + . + "Next Generation Biobanking Ontology" . + . + . + . + . + "functional genomics" . + "Ontology of standardized units"^^ . + . + . + "skip" . + "huang@southalabama.edu" . + . + "assays" . + . + . + . + "WBbt" . + . + "UniProt Proteomes" . + "A001094"^^ . + . + "YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes."^^ . + "UMIN000049383"^^ . + . + . + . + . + "neurobiology" . + . + . + . + . + . + . + "false"^^ . + "GM17027"^^ . + "ontology" . + . + . + . + . + "cpc" . + "^\\d{7}$"^^ . + . + . + "http://www.ebi.ac.uk/cmpo/CMPO_$1"^^ . + . + . + "Span" . + "https://www.nextprot.org/db/entry/"^^ . + . + "http://www.protonet.cs.huji.ac.il/requested/protein_card.php?protein_id="^^ . + "The Virus Pathogen Database and Analysis Resource (ViPR) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses. It provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, and host factor data. This collection references viral strain information."^^ . + . + . + "phenotyping" . + . + "0001998"^^ . + . + . + . + "Proteoform Atlas" . + . + "pmr.workspace" . + "^PTM-\\d{4}$"^^ . + "http://www.kegg.jp/entry/"^^ . + "irgsp" . + . + . + "Dendritic cell" . + "Common Core Ontologies" . + . + "The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase."^^ . + . + . + . + "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . + . + "ccdc" . + . + "http://bis.zju.edu.cn/ricenetdb/reactiondetails.php?ID="^^ . + . + . + "BatchelorC@rsc.org" . + "50885"^^ . + . + "gpmdb" . + . + . + . + . + "An ARK resolver as well as resolver built with common prefixes as in Identifiers.org" . + . + . + . + "https://mged.sourceforge.net/ontologies/MGEDontology.php#$1"^^ . + . + . + . + "hamap" . + . + . + "^[a-zA-Z0-9_\\-]+(/.*?)?$"^^ . + "transcriptomics" . + "ecto" . + . + . + "Anne Morgat" . + "David Osumi-Sutherland" . + . + "https://www.ebi.ac.uk/pride/archive/projects/"^^ . + . + . + . + . + "^\\d+$"^^ . + "Yongqunh He" . + . + "Database of homology-derived secondary structure of proteins" . + . + "false"^^ . + . + "https://portal.gdc.cancer.gov/cases/$1"^^ . + "false"^^ . + . + . + . + "68513255-fc44-4041-bc4b-4fd2fae7541d"^^ . + "^\\d{7}$"^^ . + "mmmp:biomaps" . + . + . + . + . + "0000001"^^ . + . + "William Hogan" . + . + . + . + "true"^^ . + . + "https://www.ebi.ac.uk/biostudies/studies/"^^ . + "gendis" . + "mpid" . + . + . + "false"^^ . + "false"^^ . + "chemical in the database supplied by National Oceanic and Atmospheric Administration"^^ . + "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."^^ . + . + "Ontology for Parasite LifeCycle" . + "University hospital Medical Information Network Clinical Trial Registry" . + "false"^^ . + . + . + "dna" . + "msaier@ucsd.edu" . + . + . + . + . + "https://progenetix.org/services/ids/"^^ . + "HUPO-PSI cross-linking and derivatization reagents controlled vocabulary" . + . + . + . + "obo" . + "montana.smith@pnnl.gov" . + "^\\d{7}$"^^ . + . + "false"^^ . + "andreas.ledl1@fhnw.ch" . + "oryzabase.mutant" . + "genomics" . + "FlyBase_Cell_line" . + . + "genome" . + . + "The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can"^^ . + "hog" . + "^[a-z][a-z0-9_]+[a-z0-9]$"^^ . + . + . + "ontology" . + . + . + . + . + . + . + . + "http://www.pantree.org/node/annotationNode.jsp?id=$1"^^ . + . + "https://registry.bio2kg.org/resource/$1" . + "civic.aid" . + "biologics" . + "microbiology" . + "https://neurovault.org/collections/"^^ . + . + . + "SL-0002"^^ . + . + "http://www.membranetransport.org/protein.php?pOID=mmar1&pSynonym=$1"^^ . + "https://www.ebi.ac.uk/gwas/studies/$1"^^ . + . + . + . + . + "false"^^ . + "The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC).[2][3][4] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations."^^ . + "InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences."^^ . + . + . + . + "0778"^^ . + . + . + . + . + . + "insdc.sra" . + . + . + . + "knowledge and information systems" . + . + "^(hsa-(let|mir)-\\w+(-\\w+)?)|(piR-\\d+)|(chr\\w+.tRNA\\d+-\\w+)|(chr\\w+.tRNA\\d+-\\w+-tRF\\d)|((SNORD|SNORA|ACA|HBII|HBI|U)(-)?\\w+)|(HY\\d\\+(-L\\d+)?)|((LSU|SSU|5S)(-rRNA_Hsa)?(-L\\d+)?)$"^^ . + . + . + . + . + . + "http://tolweb.org/"^^ . + "prov" . + . + "https://www.ncbi.nlm.nih.gov/bioproject/?term=$1"^^ . + . + "cas" . + . + . + "interaction" . + . + . + "http://planttfdb.cbi.pku.edu.cn/tf.php?sp=Ath&did="^^ . + "protein" . + . + "National Microbiome Data Collaborative" . + "agriculture" . + . + . + . + "http://cerevisiae.oridb.org/details.php?id="^^ . + . + "https://mips.helmholtz-muenchen.de/corum/?id=$1"^^ . + "https://www.ncbi.nlm.nih.gov/clinvar/submitters/"^^ . + "Haruki Nakamura" . + "drug discovery" . + "http://purl.obolibrary.org/obo/MmusDv_$1"^^ . + "BIOMD" . + "macie" . + . + . + . + "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."^^ . + . + "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)."^^ . + "pharmacodb.tissue" . + . + . + "http://www.drugtargetontology.org/dto/DTO_"^^ . + "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."^^ . + . + . + . + "Terminology for Description of Dynamics" . + . + . + . + . + "dbvar.variant" . + "ontology" . + . + "Amphibian taxonomy" . + "funcbase.yeast" . + . + . + . + . "life science" . - . -_:Neb149b8fd9b444d5a596c99172b80614 "custserv@nlm.nih.gov" . - . - . - . - . - . - "pw" . - "false"^^ . - . - "ontology" . - . - . - "http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=$1"^^ . - "drugbank.metabolite" . - . - . - . - . - "zfin" . - "false"^^ . - "clingene" . - . - . - . - . - "goccid" . - "health monitoring" . - "pactr" . - . - "4b848c342a4f4abc871bdf8a09a60807"^^ . - "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."^^ . - . - "genomics" . - . - . - "http://www.depod.bioss.uni-freiburg.de/showp.php?gene=$1"^^ . - . - . - . - . - . - . - . - . - "BCRC Strain Collection Catalog" . - "false"^^ . - . - . - . - "false"^^ . - . - . - "The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. The data were previously provided by the miRNA Registry. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR)."^^ . - . - . - "occ" . - "SUPERFAMILY" . - . - "The DBD (transcription factor database) provides genome-wide transcription factor predictions for organisms across the tree of life. The prediction method identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains from Pfam and SUPERFAMILY. It does not include basal transcription factors or chromatin-associated proteins."^^ . - "iceberg.family" . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d{7}$"^^ . - . - . - "^\\d{7}$"^^ . - "PubChem Substance ID (SID)" . - "^(data|topic|operation|format)\\_\\d{4}$"^^ . - . - "http://www.bioguo.org/AnimalTFDB/family.php?fam="^^ . - "0000187"^^ . - . - . - "unii" . - "doid" . - . - . - "Overview of the Web Ontology Language (OWL) which provides an introduction to OWL by informally describing the features of each of the sublanguages. "^^ . - . - "MultiCellDS collection" . - "Sharkipedia is an open source research initiative to make all published biological traits and population trends on sharks, rays, and chimaeras accessible to everyone."^^ . - . - "CLO" . - . - . - "chemistry" . - . - . - . - . - "RoleInTime"^^ . - "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC=$1"^^ . - "^\\w+$"^^ . - . - . - . - . - "http://uri.neuinfo.org/nif/nifstd/nlx_"^^ . - . - . - . - . - . - . - . - . . - . - . - . - "http://www.kegg.jp/entry/"^^ . - "http://purl.obolibrary.org/obo/MRO_$1"^^ . - . - . - "kegg_genomes" . - . - "ordo" . - . - "4195"^^ . - "https://bioregistry.io/gabi:"^^ . - . - . - "^SIGNOR\\-[A-Z]+\\d+$"^^ . - . - "^[0-9]+$"^^ . - . - "NBK331"^^ . - . - "pathway" . - . - . - "https://data.kidsfirstdrc.org/ga4gh/drs/v1/objects/"^^ . - . - . - "Identifier for a journal article in the fossilworks website"^^ . - . - "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."^^ . - "uniprot.resource" . - . - . - . - . - . - . - . - "ontology" . - . - . - "ddinter.interaction" . - . - . - . - . - "vandf" . - . - . - "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."^^ . - . - . - . - . - . - . - "c4o" . - . - . - "to" . - . - "obo" . - "comparative genomics" . - "false"^^ . - . - . - "http://purl.uniprot.org/annotation/$1"^^ . - "SNOWMEDCT_US_2018_03_01" . - "dna" . - "https://www.metabolome-express.org/datasetview.php?datasetid=$1"^^ . - . - "https://flybase.org/reports/"^^ . - "metabolomics" . - "false"^^ . - "pubchem_id" . - "obo" . - . - "VirOligo" . - . - . - . - . - . - . - "false"^^ . - . - "Animal TFDB Family" . - "false"^^ . - . + "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 Phenotype."^^ . + . + "https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/"^^ . + "UniProt" . + . + . + "3"^^ . + . + . + "grouping" . + "John-Marc Chandonia" . + . + . + "false"^^ . + . . - . - . - . - . - "http://www.cathdb.info/cathnode/$1"^^ . - "chembank" . - . - . - "false"^^ . - "ontology" . - "67"^^ . - . - . - . - "4f0fa9b6-514f-4ff4-98cc-0009bc08eb80"^^ . - . - . - . - "https://www.ebi.ac.uk/ols4" . - . - . - . - . - . - . - . - "ontology" . - "0000121"^^ . - "protein" . - . - . - "https://www.ebi.ac.uk/ena/browser/view/"^^ . - "Guy Cochrane" . - "msig" . - . - . - . - "http://www.case.edu/EpilepsyOntology.owl#"^^ . - . - . - . - "https://www.kerafast.com/Search?SearchTerm="$1""^^ . - . - . - . - . - "http://immunet.cn/bdb/index.php/mimoset/"^^ . - . - . - "medicine" . - "^\\d+$"^^ . - . - "computational biology" . - . - . - . - . - . - "lipid" . - . - . - . - "HGNC_GROUP" . - . - "https://viperdb.org/Info_Page.php?VDB=$1"^^ . - . - . - . - . - . - . - . - . - . - . - "1784"^^ . - "ClinVar archives reports of relationships among medically important variants and phenotypes. It records human variation, interpretations of the relationship specific variations to human health, and supporting evidence for each interpretation. Each ClinVar record (RCV identifier) represents an aggregated view of interpretations of the same variation and condition from one or more submitters. Submissions for individual variation/phenotype combinations (SCV identifier) are also collected and made available separately. This collection references submissions, and is based on SCV accession."^^ . - . - . - . - . - "https://reactome.org/content/detail/"^^ . - . - . - . - . - . - . - . - . - . - "biomedical science" . - . - . - . - . - "Cell Lines in PubChem"^^ . - "earth science" . - . - "0000449"^^ . - . - "^\\d+$"^^ . - . - . - . - "biology" . - . - . - . - "234"^^ . - "https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId="^^ . - . - . - . - . - "metabolomics" . - . - . - "systems biology" . - . - . - . - . - "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch="^^ . - . - "https://jjj.bio.vu.nl/models/$1"^^ . - . - . - . - . - "false"^^ . - . - . - . - "agriculture" . + "false"^^ . + . + "^\\d+$"^^ . + . + "true"^^ . + . + . + "431472"^^ . + . + . + "behavior" . + "^\\w+_COVID19_[-\\w]+$"^^ . + . + "health science" . + . + . + "Reaxys" . + "mgnify.analysis" . + . + . + "biochemistry" . + "false"^^ . + . + . + . + "database" . + "cardiology" . + . + . + . + . + . + . + . + . + "Peer Bork" . + . + . + . + . + "maizegdb.locus" . + . + "Ada Hamosh" . + . + "protein trap" . + "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."^^ . + . + . + . + . + . + "false"^^ . + "https://www.ncbi.nlm.nih.gov/gtr/conditions/$1"^^ . + . + "taxonomy" . + "taxonomy" . + . + "https://cameochemicals.noaa.gov/chemical/"^^ . + "https://www.findacode.com/code.php?set=ICD10PCS&c=$1"^^ . + . + "C34"^^ . + . + . + . + "http://purl.obolibrary.org/obo/APO_"^^ . + "https://fairsharing.org/users/$1"^^ . + "obo" . + "The NCBI Bookshelf provides free online access to books and documents in life science and healthcare. Search, read, and discover. "^^ . + . +_:Nc7f4b51b50d3443c910d77680c53fbc7 "helpdesk cropontology" . + "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."^^ . + . + "rbk" . + . + . + "Cell line collections (Providers)"^^ . + . + . + "http://purl.uniprot.org/isoforms/$1"^^ . + "0000128"^^ . + "ExAC Variant" . + "elisa-kits" . + "false"^^ . + . + "Ontology of Host-Microbiome Interactions" . + . + . + . + . + . + . + . + . + . + "http://influenza.psych.ac.cn/search/detail.jsp?segment.gb_id="^^ . + . + . + . + . + "false"^^ . + "https://cancer.sanger.ac.uk/cell_lines/sample/overview?id=$1"^^ . + . + . + . + . + "biochemistry" . + . + . + "true"^^ . + "https://www.kegg.jp/entry/$1"^^ . + "http://www.phytozome.net/genePage.php?crown&method=0&search=1&detail=1&searchText=locusname:"^^ . + . + . + "obo" . + . + "^\\d+$"^^ . + "life science" . + "dictybase.est" . + "life science" . + "unite" . + "https://omim.org/MIM:PS$1"^^ . + "jiezheng@pennmedicine.upenn.edu" . + . + . + . + . + . + . + "A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data."^^ . + . + . + "1150"^^ . + . + . + "false"^^ . + . + . + . + . + "The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. PANTHER tree is a key element of the PANTHER System to represent ‘all’ of the evolutionary events in the gene family. PANTHER nodes represent the evolutionary events, either speciation or duplication, within the tree. PANTHER is maintaining stable identifier for these nodes."^^ . + "The Vaccine Adjuvant Compendium (VAC) was established in 2020 by the NIAID Division of Allergy, Immunology, and Transplantation to foster collaborations between NIAID-supported adjuvant researchers and the broader scientific community. The VAC displays adjuvant characteristics or metadata defined through NIAID-supported adjuvant studies to help vaccine developers identify suitable adjuvants for various vaccine indications, including immune-mediated and infectious diseases. In addition, the VAC welcomes the inclusion of adjuvant metadata generated by other research programs."^^ . + . + . + "vcell" . + . + "false"^^ . + . + "obo" . . - . - . - . - . - . - . - "An application ontology for use with miRNA databases."^^ . - . - . - "http://purl.obolibrary.org/obo/NCRO_"^^ . - . - . - "^\\d{7}$"^^ . - "false"^^ . - . - "https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG"^^ . - . - "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."^^ . - "MediaDive Medium" . - "^(cl|tum)\\d+$"^^ . - . - . - "http://www.protonet.cs.huji.ac.il/requested/cluster_card.php?cluster="^^ . - . - "^\\w+$"^^ . - . - "somatic" . - . - . - . - . - . - . - . - "CranioMaxilloFacial ontology" . - . - . - "biology" . - "time" . - . - . - "LIPID MAPS" . - "Cowpea Trait Dictionary in template v5 - IITA - August 2015"^^ . - . - "false"^^ . - . - . - . - . - . - "FAIRsharing.62qk8w" . - . - . - "21692"^^ . - . - "roleo" . - . - "1000100"^^ . - . - . - . - "anatomy" . - . - "violinId" . - . - . - "^NBK\\d+$"^^ . - . - "Comprehensive hierarchy of extinct and extant vertebrate taxa."^^ . - "C0020004/4992"^^ . - . - . - . - . - "^8\\d{4}$"^^ . - . - . - "SNOMEDCT_US_2021_07_31" . - . - "interaction" . - . - . - "false"^^ . - "http://toxodb.org/toxo/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id=$1"^^ . - . - "structure" . - . - . - . - . - . - "^[A-Z][a-z]{2}_([A-Za-z]{3}[0-9]{6})|([A-Za-z0-9\\._\\-#]*)$"^^ . - "C. elegans development ontology" . - "GALEN" . - "proteomics" . - "https://civicdb.org/links/gene/"^^ . - . + "Each OCI (Open Citation Identifier) has a simple structure: oci:-, where “oci:” is the identifier prefix, and is used to identify a citation as a first-class data entity - see https://doi.org/10.6084/m9.figshare.7127816.v2 for additional information. In each OCI, the first is the identifier for the citing bibliographic resource, while the second is the identifier for the cited bibliographic resource."^^ . + "Confidence Information Ontology" . + . + "Salmon Ontology" . + . + "small molecule" . + . + "obo" . + "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."^^ . + "http://purl.obolibrary.org/obo/PROPREO_"^^ . + . + . + . + . + "hom" . + "false"^^ . + "cho"^^ . + "tobias.schulze@ufz.de" . + . + "sphn" . + . + "agriculture" . + "Human Oral Microbiome Database" . + . + . + . + . + "1038233"^^ . + . + . + "health science" . + "kyinno" . + . + "BacDive" . + . + "^\\d+$"^^ . + . + "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."^^ . + "Sigma Aldrich" . + . + "http://purl.obolibrary.org/obo/PSDO_"^^ . + . + . + . + "false"^^ . + "false"^^ . + "DataONE ontology of Carbon Flux measurements for MsTMIP and LTER Use Cases"^^ . + . + . + . + "merops.clan" . + "false"^^ . + "00026f50-858a-446b-8ed9-b0e3ecd7b20e"^^ . + . + . + . + . + . + . + "The Veterinary Nomenclature (VeNom) is a standard set of clinical veterinary terms for use in referral veterinary hospital electronic patient records and first opinion veterinary practice management systems."^^ . + "false"^^ . + . + . + . + . + . + . + "proteomics" . + "genomic" . + "Protein Alignment organised as Structural Superfamily" . + . + . + "obo" . + "dclunie@dclunie.com" . + . + . + . + . + . + . + "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."^^ . + . + . + "Chemical Methods Ontology" . + "animal genetics" . + . + "vann" . + . + . + . + . + "BacMap Biography" . + . + . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "protein" . + . + "046-19"^^ . + "A comprehensive listing of post-transcriptionally modified nucleosides from RNA -"^^ . + "Neural ElectroMagnetic Ontology (NEMO) describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters). FAIRsharing curators have been unable to contact the project developers, and as such this record has been marked as Uncertain. Please contact us if you have any information on this resource."^^ . + "Open Data Commons for Spinal Cord Injury" . + . + "dna" . + . + . + "This namespace is about Neuroscience Multi-Omic data, specially focused on that data generated from the BRAIN Initiative and related brain research projects."^^ . + "https://giardiadb.org/giardiadb/app/record/gene/"^^ . + "AY321118"^^ . + . + . + "An ontology to describe entities related to cardiovascular diseases"^^ . + . + . + "ZEA_0015177"^^ . + "International repository of Adverse Outcome Pathways."^^ . + . + . + . + . + . + "https://www.ebi.ac.uk/arrayexpress/arrays/$1"^^ . + _:N098f5affb8dd45a592472db7bcd9e9e5 . + . + . + "primary health care" . + "^PF\\d{5}$"^^ . + . + . + "imgt.ligm" . + . + "http://www.nematodes.org/nembase4/cluster.php?cluster=$1"^^ . + . + . + . + . + . + . + "Hans Ienasescu" . + . + "jrc-eurl-ecvam-chemagora"^^ . + "http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID="^^ . + "Describes typical Computational Chemistry experiments, including Molecular Publications, Molecular Systems, Molecular Calculations"^^ . + . + . + "^\\d+$"^^ . + . + "The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined."^^ . + "^[0-9A-Za-z\\-.]+$"^^ . + "^(ENSFM|ENSGTV:)\\d+$"^^ . + . + . + . + "https://w3id.org/reproduceme#$1"^^ . + "SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes."^^ . + "PXD002255::ES_XP_Ubi_97H_HCD_349:scan:9617:LAEIYVNSSFYK/2"^^ . + . + . + "OMA HOGs" . + "http://webprod3.hc-sc.gc.ca/dpd-bdpp/info.do?lang=eng&code="^^ . + . + . + . + . + . + . + "Flybase Cell Line" . + . + . + "http://sabiork.h-its.org/reacdetails.jsp?reactid="^^ . + . + . + "fobi" . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID="^^ . + . + . + "77"^^ . + . + "epidemiology" . + "http://string.embl.de/interactions/"^^ . + . + . + "Richard Boyce" . + . + "CASID" . + "false"^^ . + "genome" . + . + "https://cropontology.org/rdf/CO_356:"^^ . + . + "http://hdl.handle.net/$1"^^ . + "knowledge and information systems" . + . + "false"^^ . + . + "Mouse Brain Atlas" . + . + "^[SED]R[APRSXZ]\\d+$"^^ . + "TTD Target" . + . + . + "http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum="^^ . + "^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\\S+)*$"^^ . + . + "^[1-9][0-9]*$"^^ . + . + . + . + . + . + . + . + . + "AP011135"^^ . + . + "Mouse adult gross anatomy" . + "bcgo" . + "genomics" . + "structure" . + "owl" . + . + . + "http://www.genomesonline.org/cgi-bin/GOLD/GOLDCards.cgi?goldstamp="^^ . + "^\\d{7,}$"^^ . + "dg.4503" . + . + "Electron Microscopy Public Image Archive" . + . + . + . + . + . + "rx00408"^^ . + "ISO 15926-14" . + "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."^^ . + . + . + . + . + . + "https://neurovault.org/images/"^^ . + . + "ukprn" . + . + "false"^^ . + "Ontology of species-neutral phenotypes observed in pathogen-host interactions."^^ . + . + . + . + . + "false"^^ . + . + "http://mycobrowser.epfl.ch/leprosysearch.php?gene+name=$1"^^ . + . + "combine.specifications" . + "oryzabase.gene" . + . + "Korean Cell Line Bank" . + "human" . + . + . + . + . + . + . + "International Histocompatibility Workshop cell lines" . + . + . + . + "https://mint.bio.uniroma2.it/index.php/detailed-curation/?id=MINT-"^^ . + . + . + . + . + . + "subject agnostic" . + . + "ontology" . + . + "npass" . + . + "http://purl.obolibrary.org/obo/MFO_"^^ . + . + "https://comptox.epa.gov/dashboard/"^^ . + . + . + . + "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."^^ . + "https://idr.openmicroscopy.org/search/?query=Name:idr$1"^^ . + "fbrf" . + . + . + "https://fairsharing.org/users/"^^ . + "pathway" . + "bioinformatics" . + . + . + . + . + . + "Silvio C.E. Tosatto" . + . + . + "biomedical science" . + . + "virology" . + . + . + . + "ConfIDent Event Series" . + "The Livestock Product Trait Ontology (LPT) is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to products produced by or obtained from the body of an agricultural animal or bird maintained for use and profit."^^ . + . + "EBI-366083"^^ . + . + . + . + . + . + . + . + . + "100"^^ . + "SNOMEDCT_US_2018_09_01" . + "^\\d{1,9}$"^^ . + . + "KEGG Enzyme" . + . + . + "false"^^ . + . + . + . + . + . + "genetics" . + "sael" . + . + . + "PTN000000026"^^ . + "French National Center for Scientific Research - Research Group Identifier" . + "Gramene protein" . + . + . + . + "agriculture" . + "hp" . + . + "^\\d+$"^^ . + "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://www.novusbio.com/products/$1"^^ . + "http://purl.obolibrary.org/obo/DOID_$1"^^ . + "https://bioregistry.io/collection/$1"^^ . + "ontology" . + "fyeco" . + "http://multicellds.org/MultiCellDB/"^^ . + . + . + "Adrien Coulet" . + . + . + "gold standard" . + "embryonic stem cell line" . + . + . + . + . + "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum."^^ . + . + . + "kegg.brite" . + . + "0001009"^^ . + "anatomy" . + . + . + . + "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."^^ . + . + . + . + "CRISP" . + . + "Cell Signaling Technology is a commercial organisation which provides a pathway portal to showcase their phospho-antibody products. This collection references pathways."^^ . + . + . + "dna" . + "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."^^ . + "http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index&mirnas="^^ . + . + "http://purl.obolibrary.org/obo/OHMI_$1"^^ . + . + "DBG2 Introns" . + . + "^[a-zA-Z0-9-]+$"^^ . + . + . + "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."^^ . + "nbrc" . + "data analysis service" . + . + "PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains."^^ . + . + "https://cropontology.org/rdf/CO_334:$1"^^ . + . + "earth science" . + . + . + "true"^^ . + . + . + "NLXMOL covers molecules, proteins, and molecular roles, similar to entities in the Protein Ontology, UniProt, and ChEBI, with a focus on those of particular relevance in the nervous system."^^ . + . + . + . + . + "0000205"^^ . + "http://ddinter.scbdd.com/ddinter/interact/"^^ . + . + "multicellds" . + . + . + . "http://www.vbase2.org/vgene.php?id="^^ . - "false"^^ . - . - . - "^\\d\\w+$"^^ . - . - . - . - . - . - "https://cropontology.org/rdf/CO_324:"^^ . - "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). The following designations are used as part of local unique identifiers:\n\n- `PC`: positive control\n- `NC`: negative control\n- `AS`: antiserum\n- `PV`: plant viruses\n- `RT`: recommended test\n- `ACC`: human or animal cell line\n- `DSM`: microorganism cell line"^^ . - "WB_REF" . - . - . - "http://flypush.imgen.bcm.tmc.edu/pscreen/details.php?line="^^ . - . - "knowledge and information systems" . - "https://omim.org/MIM:$1"^^ . - . - "^[CN]*\\d{4,7}$"^^ . - "The Cuban Public Registry of Clinical Trials (RPCEC) is a website with a database of clinical trials, with national coverage. It was established in 2007 under the leadership of the National Coordinating Center of Clinical Trials (CENCEC) and with INFOMED collaboration. (from homepage)"^^ . - "dg.anv0" . - "false"^^ . - . - "biomedical science" . - . - "Europe PMC Preprints" . + . + "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."^^ . + . + . + . + . + . + "false"^^ . + "false"^^ . + . + . + "Scientific Evidence and Provenance Information Ontology" . + . + "https://www.ncbi.nlm.nih.gov/research/cog/pathway/$1"^^ . + "0000055"^^ . + "ICD10" . + . + . + "pesticides" . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "ontology" . + "dsmz" . + "Deutsche Sammlung von Mikroorganismen und Zellkulturen" . + . + . + "^P(X|R)D\\d{6}$"^^ . + "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."^^ . + "metadata" . + . + "gene" . + . + . + . + "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."^^ . + . + . + . + . + . + . + . + . + "Philipp Bucher" . + "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."^^ . + "protein" . + . + . + "Echinobase supports the international research community by providing a centralized, integrated and easy to use web based resource to access the diverse and rich, functional genomics data of echinoderm species."^^ . + "obo" . + . + . + "phylogenetics" . + . + "ontology" . + . + "http://www.case.edu/EpilepsyOntology.owl#$1"^^ . + . + . + . + . + "Health Canada, through its Clinical Trials Database, is providing to the public a listing of specific information relating to phase I, II and III clinical trials in patients. The database is managed by Health Canada and provides a source of information about Canadian clinical trials involving human pharmaceutical and biological drugs. [from website]"^^ . + . + . + . + . + "^[1-9]\\d{0,5}$"^^ . + . + . + . + "http://igrcid.ibms.sinica.edu.tw/cgi-bin/cell_line_view.cgi?cl_name="^^ . + "326705068"^^ . + . + . + . + . + . + . + "https://gpcrdb.org/protein/"^^ . + "Shapes Constraint Language" . + . + . + . + "https://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/$1.php"^^ . + "true"^^ . + . + . + . + . + "^\\d+$"^^ . + "0001807"^^ . + . + . + . + "false"^^ . + "omiabis" . + . + "laevis" . + . + "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."^^ . + . + . + . + "^\\w+$"^^ . + . + . + "https://nanocommons.github.io/identifiers/registry#"^^ . + "http://www.begdb.com/index.php?action=oneMolecule&state=show&id=$1"^^ . + "doqcs.model" . + "false"^^ . + "http://purl.obolibrary.org/obo/EHDAA_$1"^^ . + . + . + . + "http://purl.obolibrary.org/obo/GECKO_$1"^^ . + . + . + . + "biolink" . + . + . + "Datanator Gene" . + "Christian-Alexander Dudek" . + . + . + "environmental science" . + "biomedical science" . + . + . + . + . + . + "Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management."^^ . + . + . + . + "regulation" . + "Xenopus Anatomy Ontology" . + . + . + . + . + . + "https://cropontology.org/rdf/CO_339:"^^ . + . + . + "preclinical studies" . + . + "ontology" . + . + . + "^[A-Za-z0-9_-]+$"^^ . + . + "CHEBI" . + "Sean May" . + . + "false"^^ . + . + "ontology" . + "https://www.gtexportal.org/home/gene/"^^ . + . + . + . + "archdb" . + "ontology" . + . + "Discovery tool for biomedical research resources available at institutions throughout the U.S."^^ . + "0010316"^^ . + . + . + . + "^\\d{7}$"^^ . + . + . + "ebf69ca24298b28b2361e7d43eb52d6c"^^ . + "http://vita.mbc.nctu.edu.tw/search.php?acc="^^ . + . + . + . + . + . + "Pesticide Properties DataBase" . + "A database-specific registry supporting curation in the Gene Ontology" . + . + . + "gwascentral.marker" . + . + "brenda.ligand" . +_:N098f5affb8dd45a592472db7bcd9e9e5 "Eionet Helpdesk" . + . + "https://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=$1"^^ . + "Mouse Developmental Stages" . + . + "http://purl.obolibrary.org/obo/OlatDv_"^^ . + "http://purl.obolibrary.org/obo/$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."^^ . - . - . - . - . - . - . - . - . - . - . - "Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. [from RRID]"^^ . - . - . - . - . - . - . - . - "SRX000007"^^ . - "biomedical science" . - "adrienrougny@gmail.com" . - . - . - . - . - "false"^^ . - "PharmGKB Drug" . - . - . - "microscope" . - "https://www.geonames.org/"^^ . - . - . - "co_347" . - "false"^^ . -_:Nffb883398fd44d7f8657b94b6b3a1812 "Animal Diversity Web technical staff" . - . - "life science" . - "http://purl.obolibrary.org/obo/UO_$1"^^ . - . - . - . - "clustering" . - . - "Documentation of GO that provides a description of some of the commonly used relationships and conventions in GO."^^ . - . - "This is a dot notation used to concisely describe a SCOP(e) class, fold, superfamily, and family. For example, a.39.1.1 references the 'Calbindin D9K' family, where 'a' represents the class, '39' represents the fold, '1' represents the superfamily, and the last '1' represents the family."^^ . - . - "neurobiology" . - . - . - . - "101"^^ . - . - "beetlebase" . - "http://pombe.oridb.org/details.php?id="^^ . - . - . - . - "^[a-zA-Z0-9_\\(\\_\\)\\[\\]]+$"^^ . - "proteomics" . - . - "15"^^ . - "false"^^ . - . - . - "Legacy disease classes that later became MONDO"^^ . - . - . - . - . - "biocuration" . - . - "Vertebrate trait ontology" . - . - . - "hc.din" . - . - . - . - . - . - "The Research Resource Identification Initiative provides RRIDs to 4 main classes of resources: Antibodies, Cell Lines, Model Organisms, and Databases / Software tools" . - "^\\d{7}$"^^ . - . - "ChemDB is a chemical database containing commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds."^^ . - "^\\w+$"^^ . - . - "frapo" . - . - . + . + "aftol.taxonomy" . + "http://purl.obolibrary.org/obo/XAO_$1"^^ . + . + "https://mediadive.dsmz.de/medium/"^^ . + "molecules" . + "ontology" . + . + "karel.berka@upol.cz" . + . + . + . + "Minimal Information About Anatomy ontology" . + "^RC\\d+$"^^ . + . + . + . + . + "Microbial Conditions Ontology is an ontology..."^^ . + . + "reaction" . + "bfo" . + . + . + . + . + . + . + . + . + . + "The covid-19 epidemiology and monitoring ontology (cemo) provides a common ontological model to make epidemiological quantitative data for monitoring the covid-19 outbreak machine-readable and interoperable to facilitate its exchange, integration and analysis, to eventually support evidence-based rapid response."^^ . + . + "ontology" . + . + . + "false"^^ . + "^\\d{6}$"^^ . + . + . + . + "Zach Landis-Lewis" . + "0000080"^^ . + . + . + . + . + "nucleardb" . + . + "false"^^ . + "animal husbandry" . + . + "Scholia Registry" . + . + . + "http://purl.obolibrary.org/obo/ENVO_$1"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "http://ascl.net/$1"^^ . + . + . + "Teleost taxonomy ontology" . + . + . + . + . + . + "002678"^^ . + . + . + . + . + "26957"^^ . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "NeuronDB" . + . + . + . + "false"^^ . + "false"^^ . + . . - . - "Anatomical Entity Ontology" . - "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://www.whocc.no/atcvet/atcvet_index/?code="^^ . - . - . - . - . - . - . - "aBq"^^ . - "https://cropontology.org/rdf/CO_357:$1"^^ . - . - . - "http://purl.obolibrary.org/obo/MC_"^^ . - "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."^^ . - . - "Identifiers.org Registry" . - . - . - . - "http://virtualflybrain.org/reports/$1"^^ . - . - . - "CQG5"^^ . - "M00002"^^ . - "mirtarbase" . - . - "duo" . - . - . - "false"^^ . - . - . - . - . - . - . - "ssbd.project" . - . - "Online Computer Library Center WorldCat" . - "https://massbank.jp/RecordDisplay?id="^^ . - . - . - . - . - . - "The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS). MIxS identifiers are for terms describing an aspect of an environmental sample."^^ . - . - "^\\w+$"^^ . - . - . - . - . - "sperm" . - "true"^^ . - "anatomy" . - "cellbank.australia" . - . - . - . - "bioinformatics" . - "cob" . - . - . - . - "http://purl.obolibrary.org/obo/RNAO_"^^ . - . - . - "https://nanbyodata.jp/disease/NANDO:"^^ . - "^\\w+$"^^ . -_:N917df5114e6348d2a23df4152c26f3d5 "Anita Ghebeles" . - "http://www.w3.org/2004/02/skos/core#"^^ . - . - "false"^^ . - "http://purl.obolibrary.org/obo/OARCS_"^^ . - . - "^[SCTAGMNUI]\\d{2}\\.([AB]\\d{2}|\\d{3})$"^^ . - "0005147"^^ . - . - . - . - "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . - . - . - . - . + . + "http://pbil.univ-lyon1.fr/cgi-bin/view-tree.pl?query=$1&db=HOVERGEN"^^ . + "SCV000151292"^^ . + "0154"^^ . + . + . + . + "http://purl.obolibrary.org/obo/OPMI_$1"^^ . + . + . + "RBR-6qvdftm"^^ . + . + . + "UniPathway Reaction" . + . + . + "Ribocentre is designed to contain comprehensive information of all natural ribozymes."^^ . + "Cellular Phenotypes" . + . + . + "^T3\\d+$"^^ . + . + "anatomy" . + . + . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/CMO_$1"^^ . + "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://eds.gene.le.ac.uk/home.php?select_db="^^ . + "GSTA1"^^ . + . + "http://immunet.cn/bdb/index.php/mimoset/$1"^^ . + . + "ontology" . + "false"^^ . + . + "^\\d{7}$"^^ . + . + "eukaryotic" . + "anatomy" . + . + . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PORO_$1"^^ . + . + "peroxibase" . + . + "georgeta.bordea@u-bordeaux.fr" . + . + "encode" . + . + "duret@biomserv.univ-lyon1.fr" . + "sequence" . + . + . + . + "Jianjiong Gao" . + "false"^^ . + "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."^^ . + . + . + . + "cghdb" . + . . - "ecao" . - . - . - . - . - "PicTar" . - "0000046"^^ . - "Prefixes useful in annotating documentation provenance." . - . - . - "ontology" . - . - "E-cyanobacterium model" . - . - "Association-Rule-Based Annotator (ARBA), a multiclass, self-training annotation system for automatic classification and annotation of UniProtKB proteins. This replaces the previous rule-based SAAS system."^^ . - . - "0000001"^^ . - . - "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."^^ . - . - . - "https://www.ncbi.nlm.nih.gov/protein/"^^ . - . - . - "obo" . - . - "genome" . - . - "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."^^ . - "nutritional science" . - . - "https://publons.com/publon/"^^ . - "ontology" . - . - . - . + "enzymology" . + . + "http://www.fossilworks.org/cgi-bin/bridge.pl?a=taxonInfo&taxon_no=$1"^^ . + _:N9c645ce04f594b14a09661a17b0ccc23 . + . + "edong@umich.edu" . + "agsd" . + . + "^\\d+$"^^ . + . + . + . + "http://www.ymdb.ca/compounds/"^^ . + . + . + . + "1000160"^^ . + "https://w3id.org/semapv/vocab/"^^ . + . + . + . + . + "http://www.humanproteomemap.org/protein.php?hpm_id="^^ . + . + "genome" . + . + . + . + . + . + . + . . - . - "ontology" . - . - . - . - "enzyme" . - . - "stian@soiland-reyes.com" . - "BioLegend" . - "anatomy" . - "atmospheric science" . - . - . - . - "ipi" . + . + . + . + "NIF Standard Ontology: Investigations" . + "https://registry.identifiers.org/registry?query=MIR:$1"^^ . + . + . + "protein" . + . + . + . + "^000\\d{5}$"^^ . + "^SIGNOR-\\d+$"^^ . + "re3data" . + "false"^^ . + . + . + "RHEA" . + . + . + "mathias.uhlen@scilifelab.se" . + "life science" . + . + . + . + . + . + . + . + . + . + "ftp://hgdownload.cse.ucsc.edu/goldenPath/"^^ . + . + . + "http://yeastrc.org/pdr/viewProtein.do?id=$1"^^ . + "planttfdb" . + "http://scicrunch.org/resolver/SCR_"^^ . + . + . + . + . + "507568"^^ . + . + . + "PeptideAtlas Dataset" . + . + . + . + "Ontology Concept Identifiers" . + . + . + . +_:N45e4474439d94b1c85c9d3a15c3a1d47 "Crop Ontology Helpdesk" . + . + "https://bioregistry.io/hovergen:"^^ . + . + . + . + . + . + . + . + . + "go.chemical" . + . + . + "false"^^ . + . + . + "http://purl.obolibrary.org/obo/FOVT_$1"^^ . + . + . + . + . + . + "http://purl.obolibrary.org/obo/PCL_"^^ . + . + . + . + . + . + "https://bioregistry.io/flybrain.ndb:"^^ . + . + . + . + "https://www.webofscience.com/wos/woscc/full-record/WOS:$1"^^ . + . + "GWAS Central Study" . + . + "http://www.conoserver.org/?page=card&table=protein&id="^^ . + "https://permalink.obvsg.at/"^^ . + . + "jla1@sanger.ac.uk" . + . + . + . + "Conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms."^^ . + "The Assembling the Fungal Tree of Life (AFTOL) project is dedicated to significantly enhancing our understanding of the evolution of the Kingdom Fungi, which represents one of the major clades of life. There are roughly 80,000 described species of Fungi, but the actual diversity in the group has been estimated to be about 1.5 million species."^^ . + "A 16S rRNA gene database which provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies."^^ . + . + "https://www.inaturalist.org/users/"^^ . + "^\\d{7}$"^^ . + . + "microbiology" . + "https://bioregistry.io/genecards.genenote:"^^ . + . + . + "kegg.reaction" . + . + . + . + "https://www.flymine.org/flymine/report/ChromosomeBand/$1"^^ . + "model organism database" . + . + "^\\d+$"^^ . + "50943"^^ . + . + "obv" . + "MetaCyc" . + "salmon" . + "CryptoDB" . + . + . + . + . + . + . + . + "false"^^ . + "developmental biology" . + . + . + . + . + . + . + "Description of a Project" . + "false"^^ . + . + "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."^^ . + . + "Christopher Baker" . + "ENSG00000169174"^^ . + . + . + . + "genome" . + . + . + . + . + . + . + "AADB12"^^ . + "false"^^ . + . + . + . + . + . + "Legacy disease classes that later became MONDO"^^ . + . + "COSMIC Cell Lines" . + . + "DrugBank Condition" . + . + "protein" . + "http://bioinformatics.hsanmartino.it/hypercldb/$1.html"^^ . + . + "Image Data Resource" . + "PAp00000009"^^ . + . + . + "strain" . + "http://purl.org/ontology/bibo/"^^ . + "2000191"^^ . + . + . + . + . + . + . + "maxo" . + . + . + . + "Provides the worldwide dog research community a variety of data services including access to genes, genomes, SNPs, breed/disease Traits, gene expression experiments, dog-guman homology, and literatur. In addition, iDog provides online tools for performing genomic data visualization and analyses."^^ . + "false"^^ . + "^\\d+$"^^ . + . + . + . + "jcsd" . + . + . + . + "ro" . + . + . + . + "life sciences" . + . + "transgenic" . + . + . + "obo" . + . + "5"^^ . + "molecular infection biology" . + . + "http://purl.obolibrary.org/obo/EMAP_$1"^^ . + . + _:N08c690e074974bdfb9dbf805d1627267 . + . + . + "^\\d{3}$"^^ . + . + . + "^\\w{3,15}[-_]\\w[\\w.-]{3,128}$"^^ . + . + "kegg.dgroup" . + . + "An application ontology built for beta cell genomics studies."^^ . + "7345"^^ . + . + "^\\d+$"^^ . + "protein" . + . + "structure" . + "bibliometrics" . + . + "^\\d{7}$"^^ . + . + . + "false"^^ . + "false"^^ . + . + . + . + "molecule" . + "Cell Biolabs cell line products" . + . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases allow the access to information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + "25782"^^ . + . + "An ontology of human and animal behaviours and behavioural phenotypes"^^ . + "br/1"^^ . + "^\\d+$"^^ . + . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_br_$1"^^ . + . + . + . + . + "false"^^ . + . + "expression" . + . + . + . + "neuroscience" . + "http://sideeffects.embl.de/se/$1"^^ . + . + . + "jcrb" . + . + "false"^^ . + "false"^^ . + . + "genome" . + "false"^^ . + "^HBG\\d+$"^^ . + . + . + . + . + . + "anatomy" . + "https://go.drugbank.com/metabolites/"^^ . + . + "http://www.w3.org/ns/activitystreams#$1"^^ . + . + "ICD9_2005" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + . + "http://www.mmrrc.org/catalog/getSDS.php?mmrrc_id="^^ . + . + . + . + . + . + "npo" . + . + . + . + "false"^^ . + "ontology" . + "developmental biology" . + . + "Saccharomyces cerevisiae promoter database" . + "false"^^ . + "A structured controlled vocabulary for the phenotypes of Ascomycete fungi."^^ . + . + "icdo" . + "AB0"^^ . + "vegbank" . + . + "Clinical Trials Ontology" . + . + "^[A-Z0-9]{6,7}$"^^ . + . + . + . + "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . + "assetConcepts"^^ . + . + "NIF Gross Anatomy" . + "Enzo Life Sciences is an antibody vendor."^^ . + . + . + "Beet Ontology ontology" . + . + . + . + "dsmz_mutz-id:ACC 291"^^ . + "9-1-1 Complex"^^ . + "Liliana Andres Hernandez" . + "http://www.w3.org/ns/oa#"^^ . + "http://purl.obolibrary.org/obo/BCO_"^^ . + . + _:Na6cd28f60aa44ebea3fa480cf4f65265 . + "Brendan MacLean" . + . + "VirGen" . + . + . + "Network Data Exchange" . + "reagent" . + "false"^^ . + . + . + "^\\d+$"^^ . + . + "Selventa Complexes" . + . + "784"^^ . + . + . + "554"^^ . + . + "Eukaryotic Genes" . + . + . + "Xenbase" . + "Integrated Genomic Resources of human Cell Lines for Identification" . + . . - . - "MassIVE" . - . - . - "amphx" . - . - "Pier Luigi Buttigieg" . - . - "RNA Virus Database" . - . - "false"^^ . - "MicrobeamManipulation"^^ . - . - "http://purl.bioontology.org/ontology/VANDF/$1"^^ . - . - . - "neurophysiology" . - "Shorthand representations of languages and their subtypes"^^ . - . - . - . - "OArCS is an ontology describing the Arthropod ciruclatory system."^^ . - . - "false"^^ . - . - "http://purl.obolibrary.org/obo/CHMO_"^^ . - "^UDB\\d{6}$"^^ . - . - "^\\d{6}$"^^ . - . - . - "dictyBase Expressed Sequence Tag" . - . - . - . - . - "Vocabulary used in the RDF representation of SBML models."^^ . - "false"^^ . - "^\\d+$"^^ . - . - "false"^^ . - "https://www.ebi.ac.uk/ols4/ontologies/sio/terms?short_form=$1"^^ . - . - . - "false"^^ . - "false"^^ . - "Google Books" . - "false"^^ . - . - . - "https://www.ebi.ac.uk/interpro/genomeproperties/#"^^ . - "https://meshb.nlm.nih.gov/record/ui?ui="^^ . - . - "LINCS Data" . - . - "true"^^ . - "false"^^ . - . - . - . - . - . - "Integrated Canine Data Commons" . - . - "^([0-9a-fA-F]){8}(-([0-9a-fA-F]){4}){3}-([0-9a-fA-F]){12}$"^^ . - "TP53-47"^^ . - . - "^AT.G[0-9]{5}$"^^ . - . - "genetics" . - "anatomy" . - "emdb" . - . - . - "false"^^ . - "http://uri.neuinfo.org/nif/nifstd/nlx_qual_$1"^^ . - "https://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?ID="^^ . - . - "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)."^^ . - . - "omics" . - . - . - . - "gianni.cesareni@torvergata.it" . - . - . - . - . - . - . - "Diseases Database" . - "false"^^ . - . - . - "drug" . - . - . - . - . - . - . - . - "biology" . - "PD10000"^^ . - . - "gene" . - . - "false"^^ . - . - "http://www.nematodes.org/nembase4/cluster.php?cluster=$1"^^ . - "prosite" . - "^\\d{7}$"^^ . - . - . - "true"^^ . - . - "http://purl.obolibrary.org/obo/ZP_$1"^^ . - "http://lincsportal.ccs.miami.edu/cells/#/view/"^^ . - . - . - . - "National Drug Code" . - "eurofir" . - . - . - . - "https://www.vmh.life/#gene/$1"^^ . - . - "https://www.disprot.org/idpo/IDPO:"^^ . - . - . + "topics" . + "https://vac.niaid.nih.gov/view?id="^^ . + _:Nfa7ed40a90074ec19376c04d4c9a1c78 . + "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 4 and relates to individual transcripts."^^ . + . + . +_:N08c690e074974bdfb9dbf805d1627267 "eVOC mailing list" . + . + . + . + . + . + . + "Li7"^^ . + . + "false"^^ . + . + "https://europepmc.org/article/CTX/$1"^^ . + "bcrc" . + "false"^^ . + "false"^^ . + . + . + "https://www.emsl.pnnl.gov/project/$1"^^ . + . + . + "https://w3id.org/biolink/vocab/"^^ . + . + . + . + . + . + "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."^^ . + . + "sov:WRfXPg8dantKVubE3HX8pw"^^ . + . + "gard" . + . + "http://purl.obolibrary.org/obo/kestrelo_$1"^^ . + "life science" . + . + "rna" . + . + . + "^\\w+$"^^ . + . + "false"^^ . + . + . + . + "http://www.gramene.org/db/protein/protein_search?protein_id=$1"^^ . + . + . + . + . + "co_333" . + . + . + . + "^\\d+$"^^ . + . + . + . + "drsc" . + . + . + . + . + . + . + . + . + . + "lynn.schriml@gmail.com" . + . + "Chemical Analysis Ontology" . + . + "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."^^ . + . + "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."^^ . + . + . + . + "preclinical studies" . + . + . + . + "NDFI4Chem Collection" . + "false"^^ . + . + . + "domain" . + . + "ApiDB_PlasmoDB" . + "wawong@gmail.com" . + "false"^^ . + . + "https://www.kegg.jp/entry/$1"^^ . + . + "genome" . + "depmap" . + . + "true"^^ . + . + "structure" . + . + . + . + . + . + "The PubChem Classification Browser allows you to browse the distribution of PubChem data among nodes in the hierarchy of interest, thereby providing an aggregate view of PubChem data. It also allows you to search for PubChem records annotated with the desired hierarchy/term, providing a powerful way to quickly find the subset of PubChem records."^^ . + "50583"^^ . + "bel" . + "ontology" . + . + . + . + . + "multicellds.cell_line" . + . + . + "false"^^ . + "http://purl.obolibrary.org/obo/CTENO_"^^ . + . + . + . + "^[1-9]\\d*$"^^ . + "William Hayes" . + . + . + . + . + "A comprehensive compendium of human long non-coding RNAs"^^ . + . + . + . + "MicroScope" . + "euclinicaltrials" . + "false"^^ . + "topdb" . + "false"^^ . + . + . + . + "genome" . + "gramene.taxonomy" . + "false"^^ . + . + . + "false"^^ . + "FAIRsharing Organization" . + "Minimal Viable Identifier" . + . + "Transcriptional Regulatory Element Database" . + . + "^\\d+$"^^ . + "false"^^ . + "https://www.ebi.ac.uk/merops/cgi-bin/famsum?family=$1"^^ . + . + "Endogenous Regulatory OligoPeptide knowledgebase-Moscow" . + . + "false"^^ . + . + "Núria Queralt Rosinach" . + "^\\d+$"^^ . +_:N93953f5709f34a838912b45663c37bb8 "futo@stanford.edu" . +_:Ne9b68ac1ba7b4ba383f8a00484713304 "InterPro Help" . + . + "http://purl.obolibrary.org/obo/OPL_"^^ . + "ANOVA"^^ . + "^\\d+$"^^ . + . + . + . + . + . + . + . + . + . + "https://gitlab.com/"^^ . + . + "0011124"^^ . + "developmental biology" . + . + "sdbs" . + "ontology" . + . + "ontology" . + . + "false"^^ . + "false"^^ . + "0000295"^^ . + . + "obo" . + "447860"^^ . + . + . + "false"^^ . + "ccle.cell" . + . + . + . + . + . + "odor" . + . + . + "Wormpep" . + "The State of Alaska's Salmon and People Ontology" . + "false"^^ . + . + . + "false"^^ . + "zeco" . + "ontology" . + . + "genome" . + . + . + . + . + "bigg.metabolite" . + . + . + . + "https://mediadive.dsmz.de/ingredients/"^^ . + . + . + "^\\d{7}$"^^ . + . + . + "2GC4"^^ . + . + "SD00043"^^ . + "hsa-let-7a"^^ . + "^CHEMBL\\d+$"^^ . + . + . + . + "^TCTR\\d+$"^^ . + "chemistry" . + "help@emdatabank.org" . + "scopus.work" . + "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.obolibrary.org/obo/TADS_$1"^^ . + "drugs" . + . + "false"^^ . + "https://cropontology.org/rdf/CO_346:$1"^^ . + "qualities" . + "fernanda.farinelli@gmail.com" . + . + "smiles" . + . + . + "gobp" . + "https://biopragmatics.github.io/providers/msigdb/$1"^^ . + "ontology" . + . + . + "https://idr.openmicroscopy.org/search/?query=Name:idr"^^ . + . + "https://aopwiki.org/events/$1"^^ . + "KEGG Drug" . + . + . + "http://www.genomesize.com/result_species.php?id=$1"^^ . + . + . + . + . + . + "classification" . + "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."^^ . + . + . + . + . + "Brachiaria (forages) ontology TD v5 - Version Oct 2016"^^ . + "https://flybase.org/reports/FBrf$1"^^ . + . + . + . + "https://omim.org/MIM:"^^ . + . + "http://purl.org/gc/$1"^^ . + "software engineering" . + . + . + . + . + "https://bioregistry.io/registry/$1" . + . + "https://genome.jgi.doe.gov/portal/lookup?keyName=proposalId&groupOnly=1&app=Info&keyValue="^^ . + . + "nkos" . + . + "false"^^ . + . + . + "jeffvin.wong@utoronto.ca" . + . + . + "The Variation Ontology (VariO) is an ontology for the standardized, systematic description of effects, consequences and mechanisms of variations. It describes the effects of variations at the DNA, RNA and/or protein level."^^ . + . + "mouse" . + "Cell Cycle Database is a collection of genes and proteins involved in human and yeast cell cycle"^^ . + "http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM="^^ . + "compulyeast" . +_:Nee4e59f3e724439c8721b03d893e8269 "MedDRA MSSO" . + . + . + "confident.event" . + "pathway" . + . + . + . + . + . + . + "https://www.biocatalogue.org/services/"^^ . + . + "http://purl.obolibrary.org/obo/MmusDv_"^^ . + . + . + . + . + . + . + . + . + . + "https://bioregistry.io/cazy:"^^ . + "http://www.cvrgrid.org/files/ECGOntologyv1.owl#ECG_"^^ . + . + . + "http://purl.obolibrary.org/obo/BOOTSTREP_"^^ . + "Types of named geographic features. Applicable also to many unnamed features but reflects the level of detail traditionally shown on maps, so some feature types specified in scientific studies may not be well represented here. Not highly specific."^^ . + "cell lines" . + . + "Database that provides a central location for scientists to browse uniquely observed proteoforms and to contribute their own datasets."^^ . + . + "life science" . + "farming systems research" . + "Human developmental anatomy, abstract" . + . + . + "^\\d+$"^^ . + "systems biology" . + . + "false"^^ . + . + . + "bibo" . + . + "Database of Arabidopsis Transcription Factors" . + . + . + . + . + . + "life science" . + "microbial" . + "false"^^ . + . + _:Nf15094c178294dd0b15e5d36b3dbb2d6 . + . + "^TF\\w+$"^^ . + "Mouse gross anatomy and development, timed" . + "http://purl.obolibrary.org/obo/HSO_"^^ . + "^\\d+$"^^ . + "International Standard Name Identifier" . + "9008500"^^ . "https://fungi.ensembl.org/id/$1"^^ . - . - . - . - . - . - . - . + . + . + . + "AAC"^^ . + . + . + "http://www.w3.org/2003/01/geo/wgs84_pos#"^^ . + . + . + "false"^^ . + "^\\d{7}$"^^ . + "1664"^^ . + "https://grants.nih.gov/stem_cells/registry/current.htm?ID=$1"^^ . + "https://smpdb.ca/view/"^^ . + "EntrezGene" . + . + "BiGG Model" . + . + . + " KEGG DGROUP contains structurally and functionally related groups of D number entries in KEGG DRUG. There are five types of drug groups.\n\n Chemical - grouped as identical chemical structures with minor variations of salts, hydration states, etc.\n Structure - grouped as similar chemical structures having the same skeleton, etc.\n Target - grouped by drug targets\n Class - drug classes often representing similar mechanisms of action\n Metabolism - grouped by substrates, inhibitors and inducers of drug metabolizing enzymes and transporters\n\nChemical groups are often used for identifying essentially the same active ingredients of drugs in different countries."^^ . + "false"^^ . + "false"^^ . + "An online database of inorganic compounds, MolBase was constructed by Dr Mark Winter of the University of Sheffield with input from undergraduate students."^^ . + "life science" . + . + . + . + "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID="^^ . + . + . + . + "The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target."^^ . + . + . + . + "false"^^ . + . + "Japan Collection of Microorganisms" . + . + . + "ontology" . + "astd" . + "false"^^ . + "false"^^ . + "^\\d{7}$"^^ . + . + . + . + . + . + . + . + "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."^^ . + "false"^^ . + . + . + . + "Homeodomain Research" . + . + . + "genome" . + . + . + . + . + . + . + . + "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project."^^ . + . + . + "false"^^ . + . + "http://ecoportal.lifewatch.eu" . + . + "Q9UKQ2"^^ . + "shex" . + "transcriptomics" . + . + . + . + "PXD000500"^^ . + . + "International repository of Adverse Outcome Pathways."^^ . + . + . + "namerxn" . + . + . + . + "ddanat" . + . + "Golm Metabolome Database Profile" . + . + . + . + . + "hilmar.lapp@duke.edu" . + "^\\d{7}$"^^ . + . + "molecular microbiology" . + "A structured controlled vocabulary for the anatomy of fungi."^^ . + . + "PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. It provides alignments, phylogentic trees and tree-based orthology predictions for all encoded proteins."^^ . + . + "proteomics" . + . + "false"^^ . + "https://go.drugbank.com/indications/"^^ . + "Universal Spectrum Identifier" . + . + . + . + . + . + . + . + . + . + . + "biology" . + . + "imke.tammen@sydney.edu.au" . + "Henriette Harmse" . + . + . + . + "PubMed" . + . + . + _:N8a1cf018ca2c4c11bf7f165adebf9721 . + . + "epidemiology" . + . + . + . + "^NRFC\\d+$"^^ . + "Comprehensive Resource of Mammalian protein complexes" . + . + . + . + . +_:N12268bc5728c47d7a4381e5d54096fd5 "Michael J. Lincoln MD" . + "nucleotide" . + . + . + . + "http://purl.obolibrary.org/obo/HAO_$1"^^ . "genprop" . - "Application ontology for human cell types, anatomy and development stages for the Human Cell Atlas."^^ . - . - "ontology" . - "environmental science" . - . - "cell" . - "Danielle Welter" . - . - . - "bgee.gene" . - "The Peruvian Clinical Trials Registry - REPEC is a non-profit online information system developed in 2007 by INS. It is a publicly accessible prospective registry aimed at providing information about clinical trials underway in Peru. REPEC also includes Registries for Trial Sites, Institutional Research Ethics Committees, Sponsors and Contract Research Organizations. REPEC contains records of clinical trials since 1995. Since December 14, 2012, the Peruvian National Institute of Health, by means of the General Office for Research and Technological Transfer (OGITT), has started a process to improve REPEC and to join the WHO International Clinical Trials Registry Platform (ICTRP) and to be acknowledged as a Primary Registry. More information about primary registries is available in ICRTP at http://apps.who.int/trialsearch/. (from website)"^^ . - . - . - . - "https://www.isrctn.com/$1"^^ . - . - "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."^^ . - . - . - "http://emmo.info/emmo#EMMO_$1"^^ . - . - "Gazetteer" . - . - . - . - "NCT" . - . - "knowledge and information systems" . - . - "http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=$1"^^ . - . - . - . - . - . - . - "^MGYA\\d+$"^^ . - . - . - "https://n2t.net/$1:"^^ . - . - . - . - "genetic engineering" . - . - . - . - "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."^^ . - "anzctr" . - . - . - "signor" . - . - . - "false"^^ . - . - "0000001"^^ . - . - . - . - . - . - . - . - . - "false"^^ . - . - "false"^^ . - . - . - . - "Eric W. Deutsch" . - "anatomy" . - "ssbd.dataset" . - "595"^^ . - . - . - . - . - "mirex" . - . - . - . - . - . - "https://sed-ml.org/urns.html#language:$1"^^ . - . - . - "domain" . - . - . - . - . - . - "http://purl.obolibrary.org/obo/RBO_$1"^^ . - . - . - "false"^^ . - . - "Nucleotide Sequence Database" . - "false"^^ . - "false"^^ . - . - . - . - . - . - . - . - "^\\d+$"^^ . - "^(\\d|\\w)+-\\d$"^^ . - . - "biomedical science" . - "https://bioregistry.io/resolve/github/issue/$1"^^ . - "^\\d+$"^^ . - . - . - . - . - . - . - . - "ncim" . - . - . - . - . - "life science" . - . - "RDF Schema" . - . - . - "145"^^ . - "false"^^ . - . - . - . - . - . - . - "0000411"^^ . - . - . - . - "obo" . - . - . - "secondary_attack_rate"^^ . - "CNBG_0001"^^ . - . - . - "Oryzabase Strain" . - . - . - "^PED\\d{5}$"^^ . - . - "Kim Durante" . - . - . - . - . - "ontology" . - . - . - "1537"^^ . - "0.7-123"^^ . - . - "MNXM1723"^^ . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF genes."^^ . - . - "obo" . - . - "fetal fibroblast" . - . - . - "http://www.gramene.org/db/genes/search_gene?acc="^^ . - . - "ecyano.model" . + . + . + "http://www.pathguide.org/fullrecord.php?organisms=all&availability=all&standards=all&order=alphabetic&DBID=$1"^^ . + . + "obo" . + "cdna" . + . + . + . + . + "PerkinElmer cell line collection" . + "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)."^^ . + . + . + "fideo" . + "http://dicom.nema.org/resources/ontology/DCM/$1"^^ . + . + . + . + "biomedical science" . + . + . + "https://meshb.nlm.nih.gov/record/ui?ui="^^ . + . + . + "eukaryotic" . + . + . + . + . + . + . + . + "ontology" . + . + "dictyBase Expressed Sequence Tag" . + . + . + . + . + . + . + . + "protein" . + . + . + . + . + . + . + . + . + "lucas.leclere@obs-vlfr.fr" . + . + . + "dan5@georgetown.edu" . + . + . + . + "^SKIP\\d+$"^^ . + "meddra" . + . + . + "^\\d{7}$"^^ . + . + . + "3G6A5W338E"^^ . + . + "Citation Counting and Context Characterisation Ontology" . + "DOAP is a project to create an XML/RDF vocabulary to describe software projects, and in particular open source projects."^^ . + "https://www.glycoepitope.jp/epitopes/"^^ . + "obo" . + "^[1-9]\\d{0,5}$"^^ . + . + "LK99"^^ . + . + "genetics" . + . + . + "^\\d+$"^^ . + "goa" . + "false"^^ . + "http://www.spbase.org/SpBase/search/viewAnnoGeneInfo.php?spu_id="^^ . + . + . + . + "https://glyconavi.org/hub/?id="^^ . + "neurovault.collection" . + . + "whimar@ohsu.edu" . + . + . + "NCIT" . + . + . + . + "genome" . +_:Ne50f13c462df4890baab17f28398c834 "Cynthia.Hake@cms.hhs.gov" . + . + . + "System Science of Biological Dynamics dataset" . + . + . + "Statistical Torsional Angles Potentials" . + . + . + . + "insdc" . + . + . + . + . + "https://rnaloops.cs.put.poznan.pl/search/details/"^^ . + . + "https://www.facebase.org/data/record/#1/isa:dataset/accession="^^ . + . + "KEGG GLYCAN, a part of the KEGG LIGAND database, is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways."^^ . + . + . + "br/0601"^^ . + . + "SNOMEDCT_US_2018_03_01" . + . + "^\\d+$"^^ . + "identifier for chemicals linked to information on occurrence in plants"^^ . + . + . + . + "https://cropontology.org/rdf/CO_326:"^^ . + . + . + . + "http://mona.fiehnlab.ucdavis.edu/#/spectra/splash/"^^ . + "ACTRN12623000498695"^^ . + "life science" . + . + . + . + . + "WikiPathways" . + . + . + . + . + "biocarta.pathway" . + "^\\d+$"^^ . + . + "56"^^ . + "A miscellaneous ontology of terms used for curation in FlyBase, including the DPO."^^ . + . + . + . + . + . + "http://splicenest.molgen.mpg.de/cgi-bin/splicegraph.cgi?cluster=$1"^^ . + "fish" . + "^\\d+$"^^ . + . + . + . + . + . + "nlx.dys" . + . + . + . + . + "Sharkipedia Trend" . +_:Neadaa30113554d4c98ff0c2fc706641b "Stephan Schurer" . + "Cryo Electron Microscopy ontology" . + . + "https://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1="^^ . + . + . + "Jörg Wicker" . + . + "0010034"^^ . + "adult" . + " Christos Louis" . + . + "https://utrdb.cloud.ba.infn.it/cgi-bin/utrdb/utrdb?e=$1"^^ . + . + . + . + . + . + . + "TVAG_386080"^^ . + . + . + . + . + "immunology" . + . + . + . + "preclinical studies" . + "false"^^ . + . + . + . + . + "Uber-anatomy ontology" . + "dna" . + . + "^JCGG-STR\\d{6}$"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "^\\w+$"^^ . + "https://bioinfo-mml.sjtu.edu.cn/ICEberg2/feature_page.php?ice_id="^^ . + . + . + "ontology" . + "data integration" . + "f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + . + . + "https://signor.uniroma2.it/relation_result.php?id="^^ . + . + . + . + "ecology" . + . + . + . + "^[WAICV]\\d{2,}$"^^ . + . + . + . + "DrugBank" . + "false"^^ . + . + . + . + . + . + . + . + . + "12345"^^ . + "Blake A Sweeney" . + . + "ccrid" . + "longevity" . + . + . + . + . + "Identifiers.org Terms" . + . + "The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation."^^ . + "ontology" . + . + "human" . + . + . + . + "https://www.genenames.org/cgi-bin/genefamilies/set/$1"^^ . + "https://bioregistry.io/vipr:"^^ . + . + . + "developed by ICARDA - Dec 2018"^^ . + "gene" . + "false"^^ . + "genome" . + "medicine" . + "^\\d{7}$"^^ . + . + . + "Drosophila Genomics Resource Center" . + . + "toprea@salud.unm.edu" . + . + . + . + . + . + "1000"^^ . + . + . + . + . + . + . . - . -_:Necdcf0cef45e47968707a7dee8f4a0d2 "Jonathan Bard" . - "137"^^ . - . - . - . - . - "ontology" . - . - "https://repeatsdb.org/structure/$1"^^ . - "ChEBI Integrated Role Ontology" . - "vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project. The mapping to species-specific anatomical ontologies is provided as a separated file: http://bgee.unil.ch/download/organ_association_vHOG.txt This mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available."^^ . - . - . - "enzyme" . - "https://www.nsf.gov/awardsearch/showAward?AWD_ID="^^ . - . - . - "^\\d{7}$"^^ . - . - . - . - . - . - "https://www.encodeproject.org/$1"^^ . - . - . - . - "false"^^ . - "https://www.uniprot.org/diseases/"^^ . - . - "^\\d{7}$"^^ . - "SPCC13B11.01"^^ . - . - . - . - "Unipathway" . - . - . - "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="^^ . - "https://cropontology.org/rdf/CO_327:"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - "pathway" . - . - "^[a-z][a-zA-Z]+$"^^ . - "https://www.re3data.org/repository/"^^ . - "cheminformatics" . - . - . - "sequence" . - . - . - . - . - "Ximbio" . - . - . - . + "004435"^^ . + "http://mycobrowser.epfl.ch/marinosearch.php?gene+name=$1"^^ . + . + . + . + . + . + . + "ontology" . + . + . + . + . + . + . + "obo" . + . + . + . + . + . + "rnamods" . + . + "https://proteinensemble.org/"^^ . + . + "myco.smeg" . + "2.16.840.1.113883.6.88" . + . + . + "LSM-6306"^^ . + . + "NLXMOL" . + . + "false"^^ . + "false"^^ . + "version Dec 2019"^^ . + . + . + "http://www.kegg.jp/entry/$1"^^ . + "ontology" . + . + . + "chebi" . + "Kerafast cell lines" . + . + . + . + . + "obo" . + . + . + "plant" . + "AAA35559"^^ . + "MGnify is a resource for the analysis and archiving of microbiome data to help determine the taxonomic diversity and functional & metabolic potential of environmental samples. Users can submit their own data for analysis or freely browse all of the analysed public datasets held within the repository. In addition, users can request analysis of any appropriate dataset within the European Nucleotide Archive (ENA). User-submitted or ENA-derived datasets can also be assembled on request, prior to analysis."^^ . + "vita" . + "noncodev4.gene" . + . + . + "^[A-Z]+[0-9]+$"^^ . + "FlyMine Chromosome Band" . + . + . + . + . + "DSSTox_Generic_SID" . + "covoc" . + . + . + "proteomicsdb.peptide" . + "FAIRsharing.62qk8w" . + "http://purl.obolibrary.org/obo/RXNO_"^^ . + . + . + "https://viralzone.expasy.org/"^^ . + . + "Robert Court" . + . + "williams.antony@epa.gov" . + . + . + . + . + . + "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID="^^ . + "http://www.ecogene.org/gene/$1"^^ . + . + . + "false"^^ . + "http://vbrc.org/gene_detail.asp?gene_id="^^ . + . + "false"^^ . + . + . + . + "false"^^ . + . + . + . + . + "caro" . + . + . + . + . + . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "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."^^ . + . + . + "bel" . + "false"^^ . + . + . + . + . + "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 )."^^ . + "po" . + "true"^^ . + "International coverage of the world's leading research organisations, indexing 92% of funding allocated globally."^^ . + . + "ArrayGroup"^^ . + . + "http://www.ncbi.nlm.nih.gov/clinvar/"^^ . + "0007404"^^ . + . + . + . + . + . + "ZFA_RETIRED" . + . + . + . + "Conference Ontology" . + . + "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."^^ . + . + "systems biology" . + . + "https://www.ebi.ac.uk/interpro/genomeproperties/#$1"^^ . + . + . + . + . + . + "^\\d{7}$"^^ . + . + . + . + . + "obo" . + . + "https://www.ncbi.nlm.nih.gov/pubmed/$1"^^ . + . + . + "MIMIC-III is a dataset comprising health-related data associated with over 40,000 patients who stayed in critical care units of the Beth Israel Deaconess Medical Center between 2001 and 2012"^^ . + . + "^\\d{7}$"^^ . + "https://tripod.nih.gov/bioplanet/detail.jsp?pid=bioplanet_$1"^^ . + "ontology" . + . + . + "http://purl.obolibrary.org/obo/MAT_"^^ . + . + "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=$1"^^ . +_:Nac74b2e569134e4aa3278a0ee126d26d "Jonathan Bard" . + . + . + "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."^^ . + "biology" . + "has download URL" . + "grid.225360.0"^^ . + . + . + . + . + "785"^^ . + . + . + . + . + "http://bidd.nus.edu.sg/group/TTD/ZFTTDDetail.asp?ID="^^ . + . + . + . + . + . + . + "genome" . + "http://purl.obolibrary.org/obo/MOP_$1"^^ . + "rna" . + . + "https://bioregistry.io/kerafast:"^^ . + . + "http://purl.obolibrary.org/obo/FLU_$1"^^ . + . + . + . + . + . + "FuncBase Fly" . + . + "gitlab" . + "Bactibase is a database describing the physical and chemical properties of bacteriocins from gram-negative and gram-positive bacteria."^^ . + . + "^[0-9]+$"^^ . + . + . + . + . + . + . + "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 public place to process, interpret and share GC/MS metabolomics datasets."^^ . + . + "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."^^ . + "FlowRepository" . + . + . + "intact" . + . + "^\\d+$"^^ . + . + . + . + . + . + "Hölzel is a life science reagent vendor based in Cologne, Germany. As a distributor, they offer products suitable for many kinds of research areas such as oncology, neuroscience, immunology, and more. Their portfolio consists of antibodies, recombinant proteins, inhibitors, ELISA-kits as well as other assays, arrays and kits. Their inhibitor portfolio can be easily accessed via the CAS-register catalog."^^ . . - . - "SNOMECT" . - . - . - . - . - . - "ontology" . - . - . - . - . - "0000049"^^ . - . - . - "Insertion sequence elements database" . - "^\\d+$"^^ . - "^\\d+$"^^ . - . - . - . - "Epilepsy Ontology" . - "ncbi.genome" . - . - . - . - . - . - . - "http://purl.obolibrary.org/obo/PRIDE_$1"^^ . - "false"^^ . - "JCOIN" . - . - . - "homologene" . - . - "^osa-miR\\d{3,5}[a-z]{0,1}$"^^ . - . - . - "j.a.moore@dundee.ac.uk" . - . - . - . - . - . - . - . - . - "neuroscience" . - . - "https://bdsc.indiana.edu/stocks/"^^ . - "development" . - . -_:Na592003593484832bee836301b205107 "Vladimir Mironov" . - . - "true"^^ . - . - . - "mamo" . - . - "gene" . - "proteomics" . - . - . - . - . - "http://bis.zju.edu.cn/ricenetdb/proteindetails.php?ID="^^ . - "Cell line collections (Providers)"^^ . - "^\\d{7}$"^^ . - "ruili.huang@nih.gov" . - "IUPHAR family" . - . - . - . - "life science" . - . - . - . - "https://umgear.org/p?id="^^ . - "A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus)."^^ . - . - . - "https://www.ebi.ac.uk/metagenomics/samples/"^^ . - "Mark Jensen" . - . - . - . - . - . - . - "VFDB is a repository of virulence factors (VFs) of pathogenic bacteria.This collection references VF information by Genus."^^ . - . - . - . - . - . - . - . - "gemet" . - . - . - "ASAP (a systematic annotation package for community analysis of genomes) stores bacterial genome sequence and functional characterization data. It includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources."^^ . - . - . - "false"^^ . - . - "gear" . - . - . - . - . - . - "hcvdb" . - . - . - "ontology" . - . - . - "knowledge and information systems" . - . - "kegg.ligand" . - . + . + "Australian New Zealand Clinical Trials Registry" . + "botany" . + . + . + . + "true"^^ . + . + "^\\d+$"^^ . + "aaeA"^^ . + . + . + . + . + . + "debio" . + "dna" . + . + "0000001"^^ . + "MMP0523"^^ . + "https://scicrunch.org/resolver/RRID:IMSR_TAC_"^^ . + . + . + "NOAA Fisheries Species Directory" . + . + . + . + . + "http://purl.obolibrary.org/obo/ENVO_"^^ . + . + . + . + "SIDER Drug" . + "false"^^ . + . + . + . + . + "http://purl.obolibrary.org/obo/COVIDO_"^^ . + . + . + . + . + . + . + "Semantic Web for Earth and Environment Technology Ontology" . + . + "4QHKG"^^ . + . + "An ontology for the description of Drosophila melanogaster phenotypes."^^ . + . + "^\\d+$"^^ . + "jak@ucop.edu" . + . + . + . + . + . + "true"^^ . + . + . + "^\\d+$"^^ . + . + "rdf" . + . + . + "th" . + . + "http://purl.obolibrary.org/obo/SWO_"^^ . + . + "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."^^ . + . + . + "adms" . + . + . + "https://www.e-cyanobacterium.org/bcs/entity/"^^ . + . + "^[0-9]+:[0-9]+$"^^ . + "^MSMEG\\w+$"^^ . + . + . + "ac" . + . + . + "21552"^^ . + "^LSM-\\d+$"^^ . + . + . + . + . + "false"^^ . + . + . + . + "CHMO, the chemical methods ontology, describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy prepare and separate material for further analysis, such as sample ionisation, chromatography, and electrophoresis synthesise materials, such as epitaxy and continuous vapour deposition It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI)."^^ . + "structure" . + "^(G|P|U|C|S)\\d{5}$"^^ . + . +_:N5601098de94f4d4fbeab59b9878b4d57 "loinc@regenstrief.org" . + . + "project management" . + "Common Bean ontology" . + "VEuPathDB ontology" . + "ontology" . + "genotyping" . + . + . + "false"^^ . + . + . + . + . + . + . + "This describes the metadata schema for the Gene Product Information (GPI) files in the Gene Ontology, i.e., the local unique identifiers in this identifier space refer to the columns in GPI files."^^ . + "http://seed-viewer.theseed.org/seedviewer.cgi?page=Subsystems&subsystem="^^ . + "InnateDB has been developed to facilitate systems level investigations of the mammalian (human, mouse and bovine) innate immune response. Its goal is to provide a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation."^^ . + . + . + . + . + . + . + . + . + . + "RiceNetDB miRNA" . + . + . + "109082"^^ . + "agriculture" . + . + . + "https://models.physiomeproject.org/workspace/$1"^^ . + "opm" . + "fbtc" . + . + "COMe (Co-Ordination of Metals) at the EBI represents an ontology for bioinorganic and other small molecule centres in complex proteins, using a classification system based on the concept of a bioinorganic motif."^^ . + "false"^^ . + "^GE\\d+$"^^ . + "MESHPP" . + "26"^^ . + . + . + "http://purl.uniprot.org/annotation/VAR_"^^ . + . + "genome" . + "false"^^ . + "life science" . + . + . + . + . + . + "InterPro" . + . + . + . + . + "http://purl.obolibrary.org/obo/MPATH_$1"^^ . + . + "genome" . + "Q-2958"^^ . + "biology" . + . + . + "life science" . + . + "http://purl.obolibrary.org/obo/VTO_"^^ . + . + . + . + . + "^\\d{7}$"^^ . + "genomics" . + . + . + . + "subject agnostic" . + "Foundational Model of Anatomy" . + . + . + "^rs[0-9]+$"^^ . + . + "nddf" . + "http://www.coloncanceratlas.org/search_cell_line?cell_line="^^ . + "https://biopragmatics.github.io/providers/scomp/$1"^^ . + . + "wwpdb" . + . + . + "https://bioregistry.io/bpdb:"^^ . + . + . + . + . + . + "The dictyBase database provides data on the model organism Dictyostelium discoideum and related species. It contains the complete genome sequence, ESTs, gene models and functional annotations. This collection references gene information."^^ . + . + . + . + . + . + . + . + "^\\d{7}$"^^ . + . + "false"^^ . + "^\\w+$"^^ . + "101"^^ . + "false"^^ . + . + "false"^^ . + . + "0000047"^^ . + "https://www.datanator.info/gene/"^^ . + "false"^^ . + "virology" . + . + . + . + "qafeQTWIWmcC"^^ . + "XLYOFNOQVPJJNP-UHFFFAOYSA-N,NBSCHQHZLSJFNQ-GASJEMHNSA-N--%3ENBIIXXVUZAFLBC-UHFFFAOYSA-N,WQZGKKKJIJFFOK-GASJEMHNSA-N"^^ . + "regulation" . + "sgd.pathways" . + . + . + . + . + "toxicology" . + "bioinformatics" . + "GE86325"^^ . + "ensembl.plant" . + "computational biology" . + . + "^TC\\d+$"^^ . + "BAC045"^^ . + . + "Carlos Oscar S. Sorzano" . + . + . + "Zebrafish Information Network Gene" . + "metascience" . + . + "493771"^^ . + "glida.gpcr" . + "biology" . + . + . + "dna" . + "reactions" . + "Matúš Kalaš" . + . + . + . + "https://www.vmh.life/#gene/$1"^^ . + . + "A Phenotypic Series is a tabular view of genetic heterogeneity of similar phenotypes across the genome."^^ . + . + . + . + . + "false"^^ . + . + . + . + "https://www.kegg.jp/entry/"^^ . + "https://entomology.ca.uky.edu/content/"^^ . + . + . + . + "Dr. Alpha Tom Kodamullil" . + "^[0-9]+$"^^ . + . + . + . + "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."^^ . + . + "Genetic Testing Registry" . + "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."^^ . + . + . + . + "biochemistry" . + . + "genome" . + "data management" . + . + . + . + . + "nlx.inv" . + . + . + . + . + "Banana ontology" . + . + . + . + . + . + "botany" . + . + . + . + "false"^^ . + . + . + . + . + "Cell line collections (Providers)"^^ . + . + . + "bioresource" . + . + "horizon_discovery" . + . + . + . + . + . + . + "bibliography" . + . + "false"^^ . + "http://purl.obolibrary.org/obo/IAO_"^^ . + . + "dso" . + "^CHEMBL\\d+$"^^ . + . + . + "Cell line collections"^^ . + "MIRIAM Registry is an online resource created to catalogue data types (Gene Ontology, Taxonomy or PubMed are some examples), their URIs and the corresponding resources (or physical locations), whether these are controlled vocabularies or databases."^^ . + . + "^MAR\\d{5}$"^^ . + . + "subject agnostic" . + . + . + . + . + . + . + . + "Cellosaurus Registry" . + . + "https://www.sharkipedia.org/species/$1"^^ . + . + . + . + . + "https://go.drugbank.com/bio_entities/$1"^^ . + . + "immunology" . + . + "clinical data" . + "Insect Cell Line Database" . + . + . + "iao" . + . + . + "0005250"^^ . + "to" . + "gwascentral.phenotype" . + . + "ontology" . + "Evan Patterson" . + . + "https://doulix.com/biomodules/"^^ . + "hpiwowar@gmail.com" . + . + . + . + "http://purl.obolibrary.org/obo/ECAO_"^^ . + "Vocabulary used in the RDF representation of SBML models."^^ . + . + "bind" . + . + _:Nee4e59f3e724439c8721b03d893e8269 . + "HOMD Sequence Metainformation" . + . + . + . + . + . + . + "https://www.clinicaltrials.gov/study/"^^ . + . + . + "https://www.ncbi.nlm.nih.gov/biosystems/$1"^^ . + . + . + . + . + "https://www.pesticideinfo.org/chemical/"^^ . + "virology" . + . + . + "AOPWiki (Stressor)" . + . + . + "International Standard Serial Number" . + . + "false"^^ . + . + . + . + "Jacqueline Campbell" . + . + "https://www.ebi.ac.uk/ena/browser/view/$1"^^ . + . + . + . + . + . + . + "131"^^ . + "16793"^^ . + "https://s3.us-east-2.amazonaws.com/lg.cede/$1"^^ . + . + . + "https://bioregistry.io/cnrs:"^^ . + . + "classification" . + "A controlled vocabulary to support the study of transcription in the developing mouse brain"^^ . + "exac.variant" . + . + . + "unipathway" . + . + "C0017565"^^ . + . + . + . + . + . + "https://bioregistry.io/metaregistry/cellosaurus/$1"^^ . + . + "bdgp.insertion" . + "mutant" . + . + "plwhetzel@gmail.com" . + . + "The Comparative Toxicogenomics Database (CTD) presents scientifically reviewed and curated information on chemicals, relevant genes and proteins, and their interactions in vertebrates and invertebrates. It integrates sequence, reference, species, microarray, and general toxicology information to provide a unique centralized resource for toxicogenomic research. The database also provides visualization capabilities that enable cross-species comparisons of gene and protein sequences."^^ . + . + . + . + . + "false"^^ . + . + "http://purl.obolibrary.org/obo/NOMEN_"^^ . + . + . + "insdc.run" . + . + . + . + . + . + "seed.reaction" . + "^\\w+\\_\\w+$"^^ . + . + . + "^\\d+$"^^ . + . + "pathway" . + "obo" . + . + . + . + "protein" . + "genome" . + "false"^^ . + . + "obo" . + "iRefWeb" . + . + . + . + "http://cerevisiae.oridb.org/details.php?id=$1"^^ . + . + "3304"^^ . + . + "https://www.ebi.ac.uk/interpro/entry/pfam/$1"^^ . + . + "structure" . + . + "http://purl.obolibrary.org/obo/WBbt_$1"^^ . + . + . + . + _:N0d15b74d2231418f80502274c743eb89 . + . + . + . + "UniProtKB-KW" . + . + "false"^^ . + . "NDF-RT combines the NDF hierarchical drug classification with a multi-category reference model. The categories are: Cellular or Molecular Interactions [MoA]; Chemical Ingredients [Chemical/Ingredient]; Clinical Kinetics [PK]; Diseases, Manifestations or Physiologic States [Disease/Finding]Dose Forms [Dose Form]; Pharmaceutical Preparations; Physiological Effects [PE]; Therapeutic Categories [TC]; and VA Drug Interactions [VA Drug Interaction]."^^ . - . - . - . - . - "false"^^ . - . - . - . - . - "Beta Cell Biology Consortium" . - . - . - . - . - . - . - . - "00073"^^ . - "structural bioinformatcs" . - . - . - "^\\w+$"^^ . - . - . - . - . - . - . - . - . - . - . - . - . - . - "^\\d+$"^^ . - . - . - . - . - . - . - . - . - . - "http://www.homd.org/modules.php?op=modload&name=HOMD&view=dynamic&oraltaxonid=$1"^^ . - "metascience" . - "0007404"^^ . - . - . - . - "https://www.cancer.gov/publications/dictionaries/cancer-drug/def/$1"^^ . - . - . -_:N9c76a2bea9b1468b8d223185d6d2be17 "gb-admin@ncbi.nlm.nih.gov" . - "compulyeast" . - . - "^[A-Z]{2}\\d+$"^^ . - "Kyoto Stock Center" . - "person" . - . - . - "1"^^ . - . - "^[1-9]\\d*$"^^ . + "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."^^ . + . + . + . + . + "ontology" . + . + . + . + . + . + "SAMEA2397676"^^ . + "false"^^ . + "SNOMEDCT_2020_03_01" . + . + . + . + . + . + "FB" . + . + . + . + . + . + . + . + . + "Lindsey N. Anderson" . + . + . + . + . + . + "https://bioregistry.io/resolve/github/pull/$1"^^ . + . + . "https://euhcvdb.ibcp.fr/euHCVdb/do/displayHCVEntry?primaryAC="^^ . - "gobpid" . - . - . - "molecular biology" . - . - . - "false"^^ . - "mmrrc" . - "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."^^ . - "rdo" . - . - . - "piroplasma" . - . - "http://noctua.geneontology.org/editor/graph/gomodel:$1"^^ . - . - "http://purl.obolibrary.org/obo/OGG_"^^ . - "nlx.oen" . - . - . - . - "https://www.drugbank.ca/categories/"^^ . - . - "http://purl.obolibrary.org/obo/AERO_"^^ . - "SNOMEDCT_US_2023_02_28" . - "human health" . - "murine" . - "http://caps.ncbs.res.in/cgi-bin/mini/databases/gendis/sf.cgi?code=$1"^^ . - . - "biodiversity" . - "^[A-Za-z0-9-]+$"^^ . - "PTM" . - . - . - . - "aio" . - . - . - . - "false"^^ . - . - . - . - . - "3546"^^ . - . - . - . - "P00747__P07355"^^ . - . - "http://purl.obolibrary.org/obo/WBls_$1"^^ . - . - "Annotated Regulatory Binding Sites" . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - . - "http://ontologies.dbmi.pitt.edu/edda/StudyDesigns.owl#"^^ . - "The Terminologia Histologica (TH) is the controlled vocabulary for use in cytology and histology. It was intended to replace Nomina Histologica. [wikipedia]"^^ . - "genomics" . - . - . - "Sharkipedia Trend" . - . - "ontology" . - "hogenom" . + . + "http://caps.ncbs.res.in/cgi-bin/mini/databases/SSTOSS/sstoss.cgi?code="^^ . + . + . + . + "chemistry" . + . + "0004486"^^ . + "false"^^ . + . + . + "https://cropontology.org/rdf/CO_366:$1"^^ . + . + . + "false"^^ . + . + . + "time" . + . + "structure" . + "BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests."^^ . + . + . + . + . + . + . + "Schema for the export of the Bioregistry as RDF"^^ . + "http://purl.obolibrary.org/obo/PLANA_"^^ . + . + . + "false"^^ . + . + . + . + "bioinformatics" . + "publons.researcher" . + "Animal natural history and life history" . + "Schema.org" . + . + . + "The Echinoderm Anatomy and Development Ontology" . + . + . + . + "sequence" . + . + "https://www.vmh.life/#reaction/$1"^^ . + "dna" . + . + . + . + "2224"^^ . + "Computational and Informatics Resources for Glycoscience" . + "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons."^^ . + . + . + "^J\\d{1,3}(\\.\\d{3})?(\\.\\d{1,3})?[A-Za-z]$"^^ . + . + . + . + . + . + "ontology" . + "biocatalogue.service" . + . + . + . + . + . + . + "Apple Ontology" . + "http://www.allergome.org/script/dettaglio.php?id_molecule="^^ . + "http://www.shigen.nig.ac.jp/rice/oryzabaseV4/devstageineachorgan/detail/"^^ . + . + . + . + . + . + "human geography" . + . + . + . + . + "Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD)."^^ . + "An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys."^^ . + . + . + "obo" . + "phylogenetics" . + . + . + . + "https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_"^^ . + . + . + . + . + . + . + . + . + "obo" . + . + . + . + . + "^([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])$"^^ . + "FoodEx2 is a comprehensive food classification and description system aimed at covering the need to describe food in data collections across different food safety domains."^^ . + "^A\\d+$"^^ . + "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."^^ . + "protein" . + . + "Health Canada Drug Identification Number" . + . + . + . + . + . + . + . + "structure" . + . + . + . + . + "https://sed-ml.org/urns.html#format:"^^ . + . + . + "chemical" . + "ontology" . + "hpath" . + "00001234"^^ . + . + "dsm-v" . + "dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d"^^ . + "http://purl.obolibrary.org/obo/FBcv_"^^ . + . + . + "false"^^ . + "agriculture" . + . + "http://www.phosphosite.org/proteinAction.do?id="^^ . + "false"^^ . + "elspeth@genenames.org" . + . + . + . + "http://mms.dsfarm.unipd.it/mmsinc/search/molecule.php?mmscode="^^ . + . + . + "post-translational modification" . + . + . + . + . + . + "rbo" . + "https://orcid.org/"^^ . + . + "ontology" . + "http://agroportal.lirmm.fr/ontologies/$1" . + "http://rice.plantbiology.msu.edu/cgi-bin/ORF_infopage.cgi?&orf=$1"^^ . + "https://www.scopus.com/authid/detail.uri?authorId=$1"^^ . + . + "anatomy" . + . + . + . + . + . + . + . + . + "subject agnostic" . + "15000"^^ . + "https://metabolicatlas.org/identifier/MetabolicAtlas/$1"^^ . + "https://data.4dnucleome.org/biosources/"^^ . + . + "false"^^ . + . +_:Ncff35745bc0b4cb4882876319048a670 "mejino@u.washington.edu" . + . + . "false"^^ . - "phenotype" . - "Cancer Cell Line Encyclopedia Cells" . - . - "obo" . - . - . - "Inge.Jonassen@uib.no" . - "EC-CODE" . - "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."^^ . - . - . - "imanis" . - "https://www.ebi.ac.uk/chembl/target/inspect/$1"^^ . - "https://www.checklistbank.org/dataset/"^^ . - . - "maria.gould@ucop.edu" . - "gwascentral.marker" . - "^CONSO\\d{5}$"^^ . - . - "D00123"^^ . - "life science" . - "life science" . - . - "1"^^ . - "^[0-9a-zA-Z\\-]+\\/[0-9a-zA-Z\\-]+$"^^ . - . - . - . - "false"^^ . + . + "NLXFUNC covers terms for cognitive function."^^ . + . + "https://www.cellbankaustralia.com/$1.html"^^ . + . + "GLIDA GPCR" . + "false"^^ . + . + . + "AY209920"^^ . + . + . + . + . + . + "100291"^^ . + . + . + "RSC3"^^ . + "http://arabidopsis.org/servlets/TairObject?accession=AASequence:$1"^^ . + . + . + . + "NLXCELL" . + "^\\d{7}$"^^ . + . + "Complex Portal" . + . + . + "false"^^ . + . + . + . + . + "false"^^ . + . + . + . + "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."^^ . + . + "FullySpecifiedAtom"^^ . + . + . + "false"^^ . + . + . + "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. "^^ . + . + "animal physiology" . + . + . + "biomedical science" . + "200906038218908385"^^ . + "plant" . + . + . + . + "https://bioregistry.io/cadsr:"^^ . + "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."^^ . + . + . + . + . + "botany" . + . + . + . + . + . + . + . + . + . + . + . + . + . + "EBI-2307691"^^ . + . + . + . + "lcnafid" . + "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."^^ . + "Blue Brain Project's published data as knowledge graphs and Web Studios."^^ . + "neurophysiology" . + "Health Data Research Innovation Gateway" . + "NCATS Drugs" . + . + "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . + "http://purl.obolibrary.org/obo/FOODON_$1"^^ . + . + . + . + . + . + "gene" . + "Melissa Haendel" . + . + . + "biology" . + . + "Index Fungorum" . + "helpdesk@cropontology-curationtool.org" . + . + "DB-0174" . + . + "GeneDB" . + . + . + . + . + . + "false"^^ . + . + . + . + "genomics" . + . + . + . + . + . + "http://purl.obolibrary.org/obo/DRON_"^^ . + . + . + . + . + . + "kuiper@bio.ntnu.no" . + "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."^^ . + . + "Software ontology" . + . + . + . + . + . + . + . + "false"^^ . + "https://www.deciphergenomics.org/syndrome/"^^ . + . + "phosphopoint.protein" . + "alzgene" . + "Zebrafish Experimental Conditions Ontology" . + . + . + . + . + . + . + . + "true"^^ . + . + . + . + . + . + . +_:N12268bc5728c47d7a4381e5d54096fd5 "michael.lincoln@va.gov" . + . + . + "nmdc" . + . + . + "https://bykdb.ibcp.fr/data/html/annotated/$1.html"^^ . + "false"^^ . + . + . + . + . + . + . + . + "clinical LABoratory Ontology" . + "ctd.gene" . + . + . + . + "false"^^ . + . + "subject agnostic" . + "https://www.enzolifesciences.com/"^^ . + . + "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."^^ . + "lgic" . + . + . + "novus" . + . + . + . + . + . + . + "protein" . + . + . + . + "rna" . + . + . + . + . + . + . + . + "http://nbn-resolving.org/resolver?identifier=$1&verb=redirect"^^ . + . + "false"^^ . + . + . + "^[0-9\\.]+$"^^ . + "ontology" . + . + . + . + . + "pathology" . + "http://snomed.info/id/"^^ . + . + . + "9606117"^^ . + "miw023@ucsd.edu" . + . + . + . + . + "true"^^ . + . + "subject agnostic" . + "https://tetrahymena.vet.cornell.edu/display.php?stockid=$1"^^ . + "rna" . + "^\\d+$"^^ . + "Diagnostic and Statistical Manual of Mental Disorders (5th Edition)" . + "0004"^^ . + . + . + . + . + . + . + "ddinter.drug" . + . + "https://github.com/combine-org/combine-specifications/blob/main/specifications/$1.md"^^ . + . + . + "Cellosaurus" . + . + . + . + . + . + . + "^\\d+$"^^ . + "Human Medical Genetics" . + . + . + . + "https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS/?p=classes&conceptid=http%3A%2F%2Fvocabularies.wikipathways.org%2Fwp%23"^^ . + . + . + . + . + "Neuronal cell types"^^ . + . + "emap" . + . + . + . + . + . + . + . + "yeastract" . + . + . + . + . + "http://www.w3.org/ns/activitystreams#"^^ . + . + . + . + "Database of Interacting Proteins" . + . + . + "obo" . + . + . + . + . + . + . + . + . + "ILX" . + . + . + "ADA"^^ . + . + "Chinese Biological Abstracts" . + "false"^^ . + "http://www.ncbi.nlm.nih.gov/clinvar/$1"^^ . + . + . + "Database of Genomic Structural Variation - Variant" . + . + "ROR (Research Organization Registry) is a global, community-led registry\nof open persistent identifiers for research organizations. ROR is jointly\noperated by California Digital Library, Crossref, and Datacite."^^ . + . + . + . + . + . + . + . + . + . + "benjamin_gyori@hms.harvard.edu" . + . + . + "Amanda Hicks" . + . + "Ctibor Škuta" . + "221058"^^ . + . + "Social Behavior in insects"^^ . + "CellBank Australia" . + . + . + "Health Surveillance Ontology" . + "^[a-f0-9]+$"^^ . + . + . + . + . + . + . + . + . + . + . + . + "1"^^ . + . + "^\\d{7}$"^^ . + . + . + "https://bioregistry.io/tokue:"^^ . + . + . + "Electron Microscopy Data Bank" . + . + . + "^KW-\\d{4}$"^^ . + . + "info@casrai.org" . + . + . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + "A CIViC Gene Summary is created to provide a high-level overview of clinical relevance of cancer variants for the gene. Gene Summaries in CIViC focus on emphasizing the clinical relevance from a molecular perspective rather than describing the biological function of the gene unless necessary to contextualize its clinical relevance in cancer. Gene Summaries include relevant cancer subtypes, specific treatments for the gene’s associated variants, pathway interactions, functional alterations caused by the variants in the gene, and normal/abnormal functions of the gene with associated roles in oncogenesis"^^ . + . + "https://vertebrate.genenames.org/data/gene-symbol-report/#!/vgnc_id/"^^ . +_:Nc729bd6327734c5b8747f5b552404699 "michael.lincoln@med.va.gov" . + . + . + . + "xml" . + "topological-sampling/studios/f0ba2f3e-aa6f-4264-8d18-8ee65cf6f61a"^^ . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + "ontology" . + . + . + . + "^\\d{8}$"^^ . + "botany" . + . + . + "http://purl.obolibrary.org/obo/BTO_$1"^^ . + "true"^^ . + . + . + . + "Yam ontology" . + . + "preprints" . + . + "chemistry" . + . + "^\\d+$"^^ . + "ontology" . + . + . + . + "40565"^^ . + . + . + "life science" . + "agriculture" . + . + . + "http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$1"^^ . + "0000485"^^ . + "https://www.re3data.org/repository/$1" . + . + "oborel" . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + . + "hinv.transcript" . + "ontology" . + . + . + . + . + "ontology" . + . + "http://func.mshri.on.ca/human/genes/list_functional_scores/"^^ . + . + "WB_REF" . + . + . + . + "SCOP(e) unique identifier. This is simply a number that may be used to reference any entry in the SCOP(e) hierarchy, from root to leaves (Fold, Superfamily, Family, etc.)."^^ . + "cheminformatics" . + . + . + . + "biomodels.kisao" . + "gene" . + . + . + "http://ctdbase.org/detail.go?type=chem&acc="^^ . + . + "PPDB is a comprehensive source of data on pesticide chemical, physical and biological properties. "^^ . + "https://odc-tbi.org/data/$1"^^ . + . + . + . + "Database of Clusters of Orthologous Genes grouped by pathways and functional systems. It includes the complete genomes of 1,187 bacteria and 122 archaea that map into 1,234 genera."^^ . + "GenInfo Identifier" . + . + . + . + . + . + "bpdb" . + . + "life science" . + . + . + . + "obo" . + "^\\d+$"^^ . + . + . + "YMDB00001"^^ . + . + . + "hdl" . + "Accession number of an entry from the BIND database."^^ . + . + . + . + . + . + "co_356" . + "genome" . + . + . + . + . + "https://cropontology.org/rdf/CO_359:$1"^^ . + . + . + "physiology" . + "sequence" . + . + "ontology" . + "^\\d+$"^^ . + . + "http://www.molbase.com/en/index.php?app=search&search_keyword=$1"^^ . + . + . + "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."^^ . + . + . + . + "mouse" . + . + "chemical biology" . + "ICEberg integrative and conjugative element" . + . + . + . + "reo" . + "0045310"^^ . + . + . + . + "fbql" . + "International Classification of Diseases, 10th Revision, Procedure Coding System" . + . + "https://dashr1.lisanwanglab.org/entry/hsa-mir-200a#$1#exprPerTissueTable"^^ . + . + "http://purl.obolibrary.org/obo/CHIRO_"^^ . + "MEROPS Entry" . + "https://drugs.ncats.io/drug/$1"^^ . + . + . + "BiGG Reaction" . + "Data Object Service" . + "Cell line databases/resources"^^ . + _:Nffebff26bbc4479fa3f91e9a82d84254 . + . + . + "nlfff" . + . + . + . + "false"^^ . + . + "false"^^ . + "https://www.ebi.ac.uk/ols/ontologies/teddy/terms?iri=http://identifiers.org/teddy/TEDDY_$1"^^ . + "obo" . + . + . + . + "^\\d{7}$"^^ . + . + . + . + "life science" . + "false"^^ . + . + "false"^^ . + . + "traditional medicine" . + "structure" . + "C. elegans Gross Anatomy Ontology" . + . + . + . + "Hathi Trust Digital Library" . + "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."^^ . + "botany" . + "^\\d{7}$"^^ . + . + . + . + "rna" . + "ontology" . + "registry" . + . + . + . + . + . + . + "NLXORG covers organisms."^^ . + . + . + . + . + "genome" . + . + "H3.03.00.0.00007"^^ . + . + "FBbt" . + "gene expression" . + . + . + . + . + "Ligand Expo" . + . + . + "http://piroplasmadb.org/piro/showRecord.do?name=GeneRecordClasses.GeneRecordClass&source_id="^^ . + "false"^^ . + "rbca.jackson@gmail.com" . + "https://www.ebi.ac.uk/cgi-bin/ipd/estdab/print_cell.cgi?ESTDAB-"^^ . + "http://purl.obolibrary.org/obo/VSAO_"^^ . + . + "^K[0-9]+$"^^ . + "http://antirrhinum.net/cgi-bin/ace/generic/tree/DragonDB?name=$1&class=Allele"^^ . + . + . + . + "dna" . + . + . + "0000069"^^ . + . + . + . + . + . + . + "decimal"^^ . + "has local unique identifier pattern" . + "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."^^ . + . + . + . + "ontology" . + "http://purl.obolibrary.org/obo/PHIPO_"^^ . + . + . + "amalik@ebi.ac.uk" . + "MassIVE" . + . + . + . + . + "https://icd.codes/icd10cm/$1"^^ . + . + . + "^\\d+$"^^ . + . + . + "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."^^ . + "161671"^^ . + "Agilent Probe" . + "obo" . + . + "https://bioregistry.io/prints:"^^ . + . + . + "IP" . + "^\\d{7}$"^^ . + . + . + . + . + "anatomy" . + . + . + "P01116"^^ . + . + "biochemistry" . + "mauno.vihinen@med.lu.se" . + . + . + "An identifier for institutions in the United Kingdom, used in GRID and ROR."^^ . + "life science" . + . + . + . . - . - . - . - . - . - "biopragmatics/bioregistry/416"^^ . - . - . - . - "gene" . - . - "ontology" . - . - . - . - . - "AntWeb" . - . - . - . - . - . - . - . - "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."^^ . - . - . - . - "KEGG Environ" . - . - . - . - "https://e-cyanobacterium.org/bcs/rule/$1"^^ . - . - "CIViC variants are usually genomic alterations, including single nucleotide variants (SNVs), insertion/deletion events (indels), copy number alterations (CNV’s such as amplification or deletion), structural variants (SVs such as translocations and inversions), and other events that differ from the “normal” genome. In some cases a CIViC variant may represent events of the transcriptome or proteome. For example, ‘expression’ or ‘over-expression’ is a valid variant. Regardless of the variant, it must have a Predictive, Prognostic, Predisposing, Diagnostic, Oncogenic, or Functional relevance that is clinical in nature to be entered in CIViC. i.e. There must be some rationale for why curation of this variant could ultimately aid clinical decision making."^^ . - "https://signor.uniroma2.it/relation_result.php?id="^^ . - . - "virmirdb" . - "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/"^^ . - . - . - . - "http://bidd.nus.edu.sg/group/TTD/ZFTTDDRUG.asp?ID=$1"^^ . - "An ontology for describing the administrative information of research projects, e.g., grant applications, funding bodies, project partners, etc."^^ . - "bgee.organ" . - . - . - "false"^^ . - . - . - . - "http://getentry.ddbj.nig.ac.jp/getentry/dad/"^^ . - "EP0311"^^ . - . - . - . - . - "http://www.obofoundry.org/" . - . - . - "Steven G. E. Marsh" . - "swissregulon" . - "niaest" . - . - . - . - "Soybean Trait Dictionary in template v5 - IITA - July 2015"^^ . - . - "pictar" . - "https://doulix.com/biomodules/$1"^^ . - . - . - . - . - . - "nutritional science" . - . - . - . - "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."^^ . - . - . - . - . - "An ontology of traits covering vertebrates"^^ . - . - . - "http://biobanknetwork.telethon.it/Sample/View?sampleId=$1"^^ . - . - "This ontology was built as part of the AKER project. It describes variables used in beet phenotyping (experimental properties and measurement scale) for each institution (INRAE, Geves, ITB) and breeding companies (Florimond Desprez). Curator: Dorothee Charruaud (ADRINORD - URGI) Daphne Verdelet (Florimond Desprez) - First submission in November 2017."^^ . - . - . - . - . - "http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="^^ . - . - . - . - . - "http://purl.obolibrary.org/obo/GO_"^^ . - "nasc" . - "^\\d+\\-\\d+\\-\\d+$"^^ . - "^CA\\d+$"^^ . - . - "projects_to"^^ . - . - . - "life science" . - . - . - . - . - . - . - . - . - . - . - . - . - "Collection of European paediatric cardiac coding files"^^ . - . - "http://viaf.org/viaf/"^^ . - "http://degradome.uniovi.es/cgi-bin/protease/"^^ . - . - . - . - "Mosquito insecticide resistance" . - . - . - . - "steven.marsh@ucl.ac.uk" . - . - . - . - . - . - . - . - . - "ChEBI"^^ . - "A structured controlled vocabulary of anatomies of the slime-mold Dictyostelium discoideum."^^ . - . - "http://trna.nagahama-i-bio.ac.jp/cgi-bin/trnadb/whole_detail.cgi?SID="^^ . - . - "PubMed Central" . - "PhosphoSite Residue" . - . - . - . - . - . - "Carlos Oscar S. Sorzano" . - _:N9c76a2bea9b1468b8d223185d6d2be17 . - . - . - . - "http://hpc-bioinformatics.cineca.it/fusion/cell_line/$1"^^ . - . - "9606"^^ . - . - "icd11" . - "^[1-9][0-9]{14}$"^^ . - "subject agnostic" . - . - . - . - . - . - . - . - . - "^[0-9]{8}$"^^ . - . - "proteins" . - . - . - "hagr.gendr" . - . - . - . - . - "RISM Online is a new service that will publish the bibliographic and authority data from the catalogue of the Répertoire International des Sources Musicales project."^^ . - "ontology" . - . - . - . - "56305849200"^^ . - "^\\d+$"^^ . - . - "ogi" . - . - . - . - . - "false"^^ . - . - . - . - . - . - . - . - . - "3771992"^^ . + "^EG\\d+$"^^ . + . + "Database of Genomic Structural Variation - Study" . + "true"^^ . + "chembl" . + . + "http://www.kegg.jp/entry/$1"^^ . + . + . + "Pierre-Yves LeBail" . + . + "http://rgd.mcw.edu/rgdweb/report/strain/main.html?id=$1"^^ . + . + . + "mice" . + "false"^^ . + . + . + "authoredBy"^^ . + . + . + "MEROPS Clan" . + "https://www.ncbi.nlm.nih.gov/protein/"^^ . + . + . + "iev" . + . + . + "molecular chemistry" . + . + "phosphosite.protein" . + "https://www.grid.ac/institutes/$1"^^ . + . + . + . + . + . + . + . + . + . + . + . + . + "20560"^^ . + "classification" . + "Comparative Data Analysis Ontology" . + . + . . - "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."^^ . - . - . - . - "http://purl.obolibrary.org/obo/CVDO_$1"^^ . - . - "^\\d+$"^^ . - . - "ShareLoc defines terms to annotate data sets from single molecule localization microscopy, including but not limited to: imaging technique, biological structures or molecules of interest, cell types, experimental condition, labeling method, fixation protocol, etc."^^ . - "torsten.schwede@unibas.ch" . - . - . - "false"^^ . - "Babelon is a simple standard for managing ontology translations and language profiles. Profiles are managed as TSV files, see for example https://github.com/obophenotype/hpo-translations/tree/main/babelon. The goal of Babelon as a data model and vocabulary is to capture the minimum data required to capture important metadata such as confidence and precision of translation."^^ . - . - . + . + . + . + . + . + "interaction" . + "false"^^ . + . + . + "false"^^ . + . + "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=$1"^^ . + . + "GitHub Pull Request" . + . + "Rat Genome Database seeks to collect, consolidate, and integrate rat genomic and genetic data with curated functional and physiological data and make these data widely available to the scientific community. This collection references quantitative trait loci (qTLs), providing phenotype and disease descriptions, mapping, and strain information as well as links to markers and candidate genes."^^ . + . + "^\\d+$"^^ . + "alignment" . + "Aquatic Sciences and Fisheries Information System" . + "E-MEXP-1712"^^ . + . + "https://comptox.epa.gov/dashboard/$1"^^ . + . + . + "igsn" . + "http://bipaa.genouest.org/apps/grs-2.3/grs?reportID=aphidbase_transcript_report&objectID="^^ . + . + "^MI\\d{7}$"^^ . + . + . + . + . + . + . + . + "true"^^ . + . + "http://www.ifomis.org/bfo/1.1/snap#"^^ . + . + . + "fd8d0743-344a-4758-bb97-f8ad84a37357"^^ . + . + "ExAC Gene" . + "pancreatic islet" . + "dbvar.studies" . + "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."^^ . + . + "ORCID" . + "hssp" . + "chemistry" . + . + "false"^^ . + . + "metadata" . + "giant.plankton@gmail.com" . + . + . + . + . + . + "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."^^ . + . + . + . + . + "rdfs" . + . + . + . + "http://zinc15.docking.org/substances/"^^ . + . + . + . + . + . + "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."^^ . + . + . + . + . + "true"^^ . + "Plant Ontology" . + . + . + "https://civicdb.org/links/variant_group/"^^ . + "daniel.gautheret@u-psud.fr" . + "http://www.gramene.org/db/ontology/search?id=GRO:$1"^^ . + "https://www.ebi.ac.uk/ena/browser/view/"^^ . + . +_:N890c5c3e89754d0e974e862d58120df2 "Bgee team" . + "pao" . + "The Gene Regulation Ontology (GRO) is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes."^^ . + "mouse" . + "http://purl.obolibrary.org/obo/RoleO_$1"^^ . + . + "systems biology" . + . + . + "probesanddrugs" . + . + . + . + . + "protein" . + . + . + . + . + "false"^^ . + "false"^^ . + . + "hcpcs" . + . + . + . + . + "false"^^ . + . + "gold.meta" . + "MarFun" . + . + "life science" . + . + . + . + . + . + . + . + . + . + . + . + "kegg.module" . + "EDAM Ontology" . + . + "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."^^ . + "false"^^ . + . + . + "true"^^ . + "ark" . + . + "uniprot.taxonomy" . + "ontology" . + . + "http://pmb-bordeaux.fr/getdata/json/$1/datapackage?links=1"^^ . + "https://www.ncbi.nlm.nih.gov/dbvar/variants/$1"^^ . + . + "life science" . + . + . + . + "^\\d{6}$"^^ . + . + . + "rsk00410"^^ . + "http://www.pathwaycommons.org/pc/record2.do?id="^^ . + . + . + . + . + . + "Close to 5K Categorizations for drugs, similar to ATCC."^^ . + . + "CAPS-DB" . + . + "URGI Contact" . + . + "KCT0008394"^^ . + . + . + . + . + . + . + . + "false"^^ . + . + "bibliography" . + . + . + . + "hpm.peptide" . + . + . + . + . + "https://hl7.org/fhir/us/$1"^^ . + . + "FlyBase internal citation identifiers"^^ . + "^\\w{5}\\.\\d{2}\\..*$"^^ . + . + "Tree of Life Web Project" . + "medicine" . + "molecular" . + . + . + "https://publons.com/publon/"^^ . + "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. "^^ . + . + "ChEMBL target" . + "Asiyah Yu Lin" . + . + "false"^^ . + . + . + . + "fetal fibroblast" . + "1.1.1.1"^^ . + "Habronattus courtship" . + . + . + . + . + . + . + "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"^^ . + . + "Rat Genome Database" . + . + . + . + "pid.pathway" . + "0058"^^ . + . + "pdbsum" . + "http://www.fao.org/gsfaonline/additives/details.html?id="^^ . + . + "Scopus affiliation ID" . + "Cell line collections (Providers)"^^ . + . + . + . + . + . + . + . + "^v2_[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}$"^^ . + "http://www.pantherdb.org/panther/family.do?clsAccession="^^ . + "life science" . + "^[1-9]\\d{0,11}$"^^ . + . + _:Ne1ca309b1b3c4995b4f70b52b7a65a7e . + . + . + . + . + . + . + "377369"^^ . + "CORDIS Project" . + "https://cropontology.org/rdf/CO_336:$1"^^ . + . + . + "false"^^ . + . + "The OBO Relation Ontology provides consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies."^^ . + . + . + . + . + . + . + "expression" . + . + "eukaryotic" . + . + "mouse embryonic stem cell line" . + "http://purl.obolibrary.org/obo/MAO_$1"^^ . + . + . + . + "http://uri.neuinfo.org/nif/nifstd/nlx_inv_"^^ . + . + . + . + . + . + . + "The Behaviour Change Intervention Ontology is an ontology for all aspects of human behaviour change interventions and their evaluation."^^ . + "11478"^^ . + "The Behaviour Change Intervention Ontology" . + . + . + "protein families" . + . + . + "mutation" . + . + "^\\d{7}$"^^ . + . + "Pazar Transcription Factor" . + . + . + . + . + . + "https://www.vmh.life/#metabolite/"^^ . + . + . + . + . + "239287"^^ . + . + "doi" . + "anatomy" . + . + . + "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."^^ . + . + . + . + "structure" . + . + "phylogeny" . + . + "developmental biology" . + "true"^^ . + . + "HsapDO:0000004"^^ . + "false"^^ . + . + "false"^^ . + . + . + "Hölzel Diagnostika" . + . + "gene" . + . + . + . + . + . + . + . + "^IID\\d+$"^^ . + "^\\d{4}$"^^ . + . + . + . + "wikipedia" . + . "^\\d{7}$"^^ . - "Meng LIU" . - . - "^\\d{7}$"^^ . - "http://www.cathdb.info/cathnode/"^^ . - "protein" . - "^\\d+$"^^ . - . - . - "http://purl.obolibrary.org/obo/DIDEO_$1"^^ . - "false"^^ . - "http://www.kegg.jp/entry/"^^ . - . - . - . - . - "Oryzabase Mutant" . - . - . - "complexportal" . - . - . - "computer science" . - . - "human" . - "genome" . - "https://bioregistry.io/genecards.genenote:"^^ . - . - . - "life science" . - . - . - . - "vaccines" . - "mcarthua@mcmaster.ca" . - . - . - "botany" . - . - . - . - . - . - . - . - "ontology" . - "animal physiology" . - . - . - . - . - . - . - . - "pharmacodb.dataset" . - "false"^^ . - . - . - . - . - "false"^^ . - "56"^^ . - . - "ENCSR163RYW"^^ . - . - . - "000000341"^^ . - "https://fungidb.org/fungidb/app/record/gene/"^^ . - . - . - . - . - . - . - . - . - . - . - "http://www.theworldavatar.com/ontology/ontokin/OntoKin.owl#$1"^^ . - . - . - . - . - . - . - "https://swissmodel.expasy.org/repository/uniprot/"^^ . - . - "gnome" . - . - "https://bioregistry.io/iceberg.cime:"^^ . - . - . - . - . - . - . - "Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank."^^ . - . - . - . - "hasPrimaryUriPattern"^^ . - . - . - . - . - "mlc" . - "immunology" . - _:N865baaa49d124e84968635b53d7122b6 . - . - . - . + . + "A vendor of antibodies and other biologics"^^ . + . + "protein" . + "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."^^ . + "CGH Data Base" . + "https://goldbook.iupac.org/terms/view/$1"^^ . + "http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=$1"^^ . + "clao" . + "ontology" . + . + "helpdesk@cropontology-curationtool.org" . + . + "TTHERM_00648910"^^ . + . + "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"^^ . + . + . + "false"^^ . + . + . + "610"^^ . + . + . + . + . + . + "true"^^ . + . + "Horizon Discovery cell line collection" . + . + "ISED catalogues the influenza sequence and epitope information obtained in countries worldwide and currently hosts a total of 49368 influenza A and 4761 influenza B virus sequence data including pandemic A/H1N1 2009 virus sequences collected in 42 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea."^^ . + . + . + "http://modelseed.org/biochem/reactions/"^^ . + . + . + . + . + . + "gene" . + . + . + . + . + . + . + . + "PA131"^^ . + . + "http://purl.obolibrary.org/obo/MPIO_"^^ . + . + . + . + "^LOC\\_Os\\d{1,2}g\\d{5}$"^^ . + . + . + . + . + . + . + "molecular biology" . + . + "false"^^ . + "nlx.res" . + "neurophysiology" . + . + . + . + . + . + . + . + "false"^^ . + . + . + . + . + . + . + "Contributor Role Ontology" . + . + . + . + "http://hpc-bioinformatics.cineca.it/fusion/cell_line/"^^ . + . + . + . + . + . + . + . + . + . + . + . diff --git a/exports/rdf/bioregistry.ttl b/exports/rdf/bioregistry.ttl index b616dd4a7..e2b8a0b31 100644 --- a/exports/rdf/bioregistry.ttl +++ b/exports/rdf/bioregistry.ttl @@ -30292,6 +30292,15 @@ bioregistry:emdb a bioregistry.schema:0000001 ; bioregistry.schema:0000027 emdb:EMD-1001 ; bioregistry.schema:0000029 "emdb" . +bioregistry:emea a bioregistry.schema:0000001 ; + rdfs:label "European Medicines Evaluation Agency" ; + dcterms:description "Product number for the European Medicines Agency"^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + foaf:homepage ; + bioregistry.schema:0000005 "EMEA/H/C/000181"^^xsd:string ; + bioregistry.schema:0000012 false ; + bioregistry.schema:0000029 "emea" . + bioregistry:emolecules a bioregistry.schema:0000001 ; rdfs:label "Reaxys eMolecules" ; dcterms:description "Catalog of purchasable reagents and building blocks"^^xsd:string ; @@ -35560,6 +35569,15 @@ bioregistry:sssom a bioregistry.schema:0000001 ; bioregistry.schema:0000027 sssom:mapping_justification ; bioregistry.schema:0000029 "sssom" . +bioregistry:stn a bioregistry.schema:0000001 ; + rdfs:label "FDA Submission Tracking Number" ; + dcterms:description "The pre-IND tracking number for submissions to the FDA"^^xsd:string ; + dcterms:isPartOf bioregistry.metaresource:bioregistry ; + foaf:homepage ; + bioregistry.schema:0000005 "125768"^^xsd:string ; + bioregistry.schema:0000012 false ; + bioregistry.schema:0000029 "stn" . + bioregistry:sty a bioregistry.schema:0000001 ; rdfs:label "UMLS Semantic Types Ontology" ; dcterms:description "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."^^xsd:string ; @@ -50874,6 +50892,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:edam.format, bioregistry:edam.operation, bioregistry:edam.topic, + bioregistry:emea, bioregistry:emmo, bioregistry:emmo.cif, bioregistry:emolecules, @@ -51132,6 +51151,7 @@ orcid:0000-0003-4423-4370 rdfs:label "Charles Tapley Hoyt" ; bioregistry:span, bioregistry:ssbd.dataset, bioregistry:ssbd.project, + bioregistry:stn, bioregistry:storedb.dataset, bioregistry:storedb.file, bioregistry:storedb.study, @@ -56961,6 +56981,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:emapa, bioregistry:emaps, bioregistry:emdb, + bioregistry:emea, bioregistry:emmo, bioregistry:emmo.cif, bioregistry:emolecules, @@ -57994,6 +58015,7 @@ bioregistry.metaresource:bioregistry a bioregistry.schema:0000002 ; bioregistry:stap, bioregistry:stato, bioregistry:stitch, + bioregistry:stn, bioregistry:storedb, bioregistry:storedb.dataset, bioregistry:storedb.file, diff --git a/exports/rdf/schema.jsonld b/exports/rdf/schema.jsonld index 7e042fe29..7290a3e04 100644 --- a/exports/rdf/schema.jsonld +++ b/exports/rdf/schema.jsonld @@ -43,439 +43,439 @@ }, "@graph": [ { - "@id": "https://bioregistry.io/schema/#0000019", + "@id": "https://bioregistry.io/schema/#0000023", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The responsible person for a resource" + "@value": "An alternative or synonymous 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": "has responsible" + "@value": "has alternative prefix" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@id": "http://www.w3.org/2001/XMLSchema#string" + }, + "http://www.w3.org/2000/01/rdf-schema#subPropertyOf": { + "@id": "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" + }, + "http://www.w3.org/2002/07/owl#equivalentProperty": { + "@id": "http://identifiers.org/idot/alternatePrefix" } }, { - "@id": "https://bioregistry.io/schema/#0000006", + "@id": "https://bioregistry.io/schema/#0000021", "@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": "The reviewer of a 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": "has provider formatter" + "@value": "has reviewer" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" - }, - "http://www.w3.org/2002/07/owl#equivalentProperty": [ - { - "@id": "http://identifiers.org/idot/accessPattern" - }, - { - "@id": "http://www.wikidata.org/entity/P1630" - }, - { - "@id": "http://vocabularies.bridgedb.org/ops#hasPrimaryUriPattern" - } - ] + "@id": "https://bioregistry.io/schema/#0000020" + } }, { - "@id": "https://bioregistry.io/schema/#0000010", - "@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": "A download link for the given 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 download URL" - }, - "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#string" + "@value": "Registry" } }, { - "@id": "https://bioregistry.io/schema/#0000026", + "@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": "An organization" + "@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 identifier space owner" + "@value": "has local unique identifier pattern" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000025" - } + "@id": "http://www.w3.org/2001/XMLSchema#string" + }, + "http://www.w3.org/2002/07/owl#equivalentProperty": [ + { + "@id": "http://identifiers.org/idot/identifierPattern" + }, + { + "@id": "http://www.wikidata.org/entity/P1793" + }, + { + "@id": "http://vocabularies.bridgedb.org/ops#hasRegexPattern" + } + ] }, { - "@id": "https://bioregistry.io/schema/#0000002", + "@id": "https://bioregistry.io/schema/#0000025", "@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": "An organization" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Registry" + "@value": "Organization" } }, { - "@id": "https://bioregistry.io/schema/#0000021", + "@id": "https://bioregistry.io/schema/#0000027", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "The reviewer of a prefix" + "@value": "An expanded example URL 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": "has reviewer" + "@value": "has resource example" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000020" + "@id": "http://www.w3.org/2001/XMLSchema#string" + }, + "http://www.w3.org/2002/07/owl#equivalentProperty": { + "@id": "http://rdfs.org/ns/void#exampleResource" } }, { - "@id": "https://bioregistry.io/schema/#0000020", - "@type": "http://www.w3.org/2000/01/rdf-schema#Class", + "@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 person" + "@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": "Person" + "@value": "has responsible" }, - "http://www.w3.org/2002/07/owl#equivalentClass": { - "@id": "http://xmlns.com/foaf/0.1/Person" + "http://www.w3.org/2000/01/rdf-schema#range": { + "@id": "https://bioregistry.io/schema/#0000020" } }, { - "@id": "https://bioregistry.io/schema/#0000005", + "@id": "https://bioregistry.io/schema/#0000028", "@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 pattern for expanded URIs 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 local unique identifier example" + "@value": "has URI pattern" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" }, "http://www.w3.org/2002/07/owl#equivalentProperty": [ { - "@id": "http://identifiers.org/idot/exampleIdentifier" + "@id": "http://rdfs.org/ns/void#uriRegexPattern" }, { - "@id": "http://purl.org/vocab/vann/example" + "@id": "http://www.wikidata.org/entity/P8966" }, { - "@id": "http://vocabularies.bridgedb.org/ops#idExample" + "@id": "http://identifiers.org/idot/accessIdentifierPattern" } ] }, { - "@id": "https://bioregistry.io/schema/#0000011", + "@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": "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": "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/#0000001" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "provides for" + "@value": "is deprecated" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "https://bioregistry.io/schema/#0000001" - } - }, - { - "@id": "https://bioregistry.io/schema/#0000003", - "@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" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Collection" + "@id": "http://www.w3.org/2001/XMLSchema#boolean" } }, { - "@id": "https://bioregistry.io/schema/#0000023", + "@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 alternative or synonymous prefix" + "@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 alternative prefix" + "@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/#0000020", + "@type": "http://www.w3.org/2000/01/rdf-schema#Class", + "http://purl.org/dc/terms/description": { + "@value": "A person" }, - "http://www.w3.org/2000/01/rdf-schema#subPropertyOf": { - "@id": "http://www.geneontology.org/formats/oboInOwl#hasExactSynonym" + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "Person" }, - "http://www.w3.org/2002/07/owl#equivalentProperty": { - "@id": "http://identifiers.org/idot/alternatePrefix" + "http://www.w3.org/2002/07/owl#equivalentClass": { + "@id": "http://xmlns.com/foaf/0.1/Person" } }, { - "@id": "https://bioregistry.io/schema/#0000016", + "@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": "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." + "@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 canonical" + "@value": "appears in" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000024", + "@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": "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." + "@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": "has URI prefix" + "@value": "has local unique identifier example" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" }, "http://www.w3.org/2002/07/owl#equivalentProperty": [ { - "@id": "http://purl.org/vocab/vann/preferredNamespaceUri" + "@id": "http://identifiers.org/idot/exampleIdentifier" }, { - "@id": "http://rdfs.org/ns/void#uriSpace" + "@id": "http://purl.org/vocab/vann/example" }, { - "@id": "http://www.w3.org/ns/shacl#namespace" + "@id": "http://vocabularies.bridgedb.org/ops#idExample" } ] }, { - "@id": "https://bioregistry.io/schema/#0000001", - "@type": "http://www.w3.org/2000/01/rdf-schema#Class", + "@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": "A type for entries in the Bioregistry's registry." + "@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/#0000002" }, "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Resource" + "@value": "has resolver formatter" + }, + "http://www.w3.org/2000/01/rdf-schema#range": { + "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { - "@id": "https://bioregistry.io/schema/#0000017", + "@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 data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" + "@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": "depends on" + "@value": "provides for" }, "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/#0000006", "@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": "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": "has local unique identifier pattern" + "@value": "has provider formatter" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" }, "http://www.w3.org/2002/07/owl#equivalentProperty": [ { - "@id": "http://identifiers.org/idot/identifierPattern" + "@id": "http://identifiers.org/idot/accessPattern" }, { - "@id": "http://www.wikidata.org/entity/P1793" + "@id": "http://www.wikidata.org/entity/P1630" }, { - "@id": "http://vocabularies.bridgedb.org/ops#hasRegexPattern" + "@id": "http://vocabularies.bridgedb.org/ops#hasPrimaryUriPattern" } ] }, { - "@id": "https://bioregistry.io/schema/#0000025", - "@type": "http://www.w3.org/2000/01/rdf-schema#Class", - "http://purl.org/dc/terms/description": { - "@value": "An organization" - }, - "http://www.w3.org/2000/01/rdf-schema#label": { - "@value": "Organization" - } - }, - { - "@id": "https://bioregistry.io/schema/#0000012", + "@id": "https://bioregistry.io/schema/#0000026", "@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 organization" }, "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 identifier space owner" }, "http://www.w3.org/2000/01/rdf-schema#range": { - "@id": "http://www.w3.org/2001/XMLSchema#boolean" + "@id": "https://bioregistry.io/schema/#0000025" } }, { - "@id": "https://bioregistry.io/schema/#0000022", - "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", + "@id": "https://bioregistry.io/schema/#0000003", + "@type": "http://www.w3.org/2000/01/rdf-schema#Class", "http://purl.org/dc/terms/description": { - "@value": "The main contact person for a registry" - }, - "http://www.w3.org/2000/01/rdf-schema#domain": { - "@id": "https://bioregistry.io/schema/#0000002" + "@value": "A type for entries in the Bioregistry's collections" }, "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": "Collection" } }, { - "@id": "https://bioregistry.io/schema/#0000027", + "@id": "https://bioregistry.io/schema/#0000029", "@type": "http://www.w3.org/1999/02/22-rdf-syntax-ns#Property", "http://purl.org/dc/terms/description": { - "@value": "An expanded example URL for a resource or metaresource." + "@value": "has canonical 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": "has resource example" + "@value": "has prefix" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" }, - "http://www.w3.org/2002/07/owl#equivalentProperty": { - "@id": "http://rdfs.org/ns/void#exampleResource" - } + "http://www.w3.org/2002/07/owl#equivalentProperty": [ + { + "@id": "http://www.w3.org/ns/shacl#prefix" + }, + { + "@id": "http://purl.org/vocab/vann/preferredNamespacePrefix" + }, + { + "@id": "http://identifiers.org/idot/preferredPrefix" + }, + { + "@id": "http://vocabularies.bridgedb.org/ops#systemCode" + } + ] }, { - "@id": "https://bioregistry.io/schema/#0000007", + "@id": "https://bioregistry.io/schema/#0000024", "@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": "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." }, "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 URI prefix" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" - } + }, + "http://www.w3.org/2002/07/owl#equivalentProperty": [ + { + "@id": "http://purl.org/vocab/vann/preferredNamespaceUri" + }, + { + "@id": "http://rdfs.org/ns/void#uriSpace" + }, + { + "@id": "http://www.w3.org/ns/shacl#namespace" + } + ] }, { - "@id": "https://bioregistry.io/schema/#0000018", + "@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": "Terms from the source appear in the target resource" + "@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. See examples [here](https://bioregistry.io/highlights/relations#canonical)." }, "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 canonical" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "https://bioregistry.io/schema/#0000001" } }, { - "@id": "https://bioregistry.io/schema/#0000028", + "@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": "The pattern for expanded URIs in the given 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": "has URI pattern" + "@value": "has download URL" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" - }, - "http://www.w3.org/2002/07/owl#equivalentProperty": [ - { - "@id": "http://rdfs.org/ns/void#uriRegexPattern" - }, - { - "@id": "http://www.wikidata.org/entity/P8966" - }, - { - "@id": "http://identifiers.org/idot/accessIdentifierPattern" - } - ] + } }, { - "@id": "https://bioregistry.io/schema/#0000029", + "@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": "has canonical prefix" + "@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": "has prefix" + "@value": "depends on" }, "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", + "http://purl.org/dc/terms/description": { + "@value": "A type for entries in the Bioregistry's registry." }, - "http://www.w3.org/2002/07/owl#equivalentProperty": [ - { - "@id": "http://www.w3.org/ns/shacl#prefix" - }, - { - "@id": "http://purl.org/vocab/vann/preferredNamespacePrefix" - }, - { - "@id": "http://identifiers.org/idot/preferredPrefix" - }, - { - "@id": "http://vocabularies.bridgedb.org/ops#systemCode" - } - ] + "http://www.w3.org/2000/01/rdf-schema#label": { + "@value": "Resource" + } } ] } \ No newline at end of file diff --git a/exports/rdf/schema.nt b/exports/rdf/schema.nt index d9b3b75ab..b80a85a23 100644 --- a/exports/rdf/schema.nt +++ b/exports/rdf/schema.nt @@ -1,133 +1,133 @@ - "has resolver formatter" . + . + "The responsible person for a resource" . + . + "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." . + . + . + . + "An alternative or synonymous prefix" . . - "Organization" . + . + . + "An expanded example URL for a resource or metaresource." . + . . - "The reviewer of a prefix" . - . - . - . - "A person" . - "An alternative or synonymous prefix" . - "Terms from the source appear in the target resource" . - . - . - "Registry" . - . - "A type for entries in the Bioregistry's collections" . - . - "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . - "has identifier space owner" . - . - "has resource example" . - . - . - "Resource" . - . - "provides for" . - . - . - . - "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . - . - . + "has local unique identifier pattern" . + "The pattern for identifiers in the given resource" . + "has prefix" . + "has local unique identifier example" . + "A download link for the given resource" . "The URL format for a resolver that contains $1 for the prefix and $2 for the identifier that should be resolved." . - . - . - . - "has canonical" . - "depends on" . - . + . . - "The pattern for identifiers in the given resource" . + "Organization" . "An organization" . - . - "has URI pattern" . - . - . - . - . - "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." . . - "Collection" . - "The responsible person for a resource" . - . . + . + . + . . - . - . . - . - "has responsible" . - . - . - "The pattern for expanded URIs in the given resource" . - "An identifier for a resource or metaresource." . - "has canonical prefix" . - "has download URL" . - . - . . - "has URI prefix" . - . - . - . - "appears in" . - . - . - "Person" . - . - . - . - . - . - . - . - . - "has alternative prefix" . - "has provider formatter" . - . - . - "The main contact person for a registry" . - . - . - . - . - . - . - . - . - "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . - . - "has local unique identifier pattern" . - . - "An expanded example URL for a resource or metaresource." . - "has local unique identifier example" . + . + . + . . + . . - . - . + . + "The URL prefix for a provider that does not $1 for the identifier (or metaidentifier) that should be resolved." . + "A type for entries in the Bioregistry's collections" . + "has URI pattern" . + . + "has canonical prefix" . "has responsible" . - . - "A download link for the given resource" . - . + . . - . - . - . - "A type for entries in the Bioregistry's registry." . - . + . + . "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." . - "An organization" . - "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." . - "has prefix" . - "is deprecated" . + "has provider formatter" . + . + . + . + . + . + . + "has canonical" . + . + . + "has resource example" . + "has resolver formatter" . + "A property connecting two prefixes that share an IRI where the subject is the non-preferred prefix and the target is the preferred prefix. See examples [here](https://bioregistry.io/highlights/relations#canonical)." . + . + "Terms from the source appear in the target resource" . "has reviewer" . "A type for entries in the Bioregistry's metaregistry." . + "depends on" . + . + . + . + "provides for" . + . + . + . + . + . + . + . + "has URI prefix" . + "The reviewer of a prefix" . . + . + . + . + "A type for entries in the Bioregistry's registry." . + . + . + . + . + . + . . + "is deprecated" . + . + . . - . - . + . + "Resource" . . - . - . + "Person" . + "The URL format for a provider that contains $1 for the identifier (or metaidentifier) that should be resolved." . + "appears in" . + "The pattern for expanded URIs in the given resource" . + . + "has download URL" . + "has responsible" . + . + . + "has alternative prefix" . + . + . + . + "Registry" . + "An organization" . + "An identifier for a resource or metaresource." . + . + . + . + . + . + "A person" . + . + . + . + . + "The main contact person for a registry" . + . + "has identifier space owner" . + . + . + "The data in resource denoted by the subject prefix depends on the data in the resources denoted by the object prefix" . + "Collection" . diff --git a/exports/registry/registry.json b/exports/registry/registry.json index a7f0f26e8..456fec0e2 100644 --- a/exports/registry/registry.json +++ b/exports/registry/registry.json @@ -16152,6 +16152,19 @@ ], "uri_format": "https://www.ebi.ac.uk/pdbe/entry/emdb/$1" }, + "emea": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "Product number for the European Medicines Agency", + "example": "EMEA/H/C/000181", + "homepage": "https://www.ema.europa.eu/en/medicines", + "name": "European Medicines Evaluation Agency", + "preferred_prefix": "emea" + }, "emmo": { "banana": "EMMO", "banana_peel": "_", @@ -53411,6 +53424,19 @@ ], "uri_format": "http://stitch.embl.de/interactions/$1" }, + "stn": { + "contributor": { + "email": "cthoyt@gmail.com", + "github": "cthoyt", + "name": "Charles Tapley Hoyt", + "orcid": "0000-0003-4423-4370" + }, + "description": "The pre-IND tracking number for submissions to the FDA", + "example": "125768", + "homepage": "https://www.fda.gov/media/128698/download", + "name": "FDA Submission Tracking Number", + "preferred_prefix": "stn" + }, "storedb": { "banana": "STOREDB", "contact": { diff --git a/exports/registry/registry.tsv b/exports/registry/registry.tsv index f723c6409..65ec010b3 100644 --- a/exports/registry/registry.tsv +++ b/exports/registry/registry.tsv @@ -519,6 +519,7 @@ emap Mouse gross anatomy and development, timed http://emouseatlas.org A structu emapa Mouse Developmental Anatomy Ontology http://www.informatics.jax.org/expression.shtml An ontology for mouse anatomy covering embryonic development and postnatal stages. ^\d+$ 26753 Terry.Hayamizu@jax.org http://purl.obolibrary.org/obo/EMAPA_$1 EMAPA_RETIRED False EMAPA 549 EMAPA EMAPA emapa emapa EMAPA emaps Mouse Developmental Anatomy Ontology with Theiler Stage https://www.informatics.jax.org/vocab/gxd/anatomy/ EMAPA identifiers refer to developmental stage-independent mouse anatomical features, for instance, EMAPA:35178 resolves to the MGI's Mouse Developmental Anatomy Browser. EMAPS is an extension to EMAPA which introduces terms for different developmental stages of this generic EMAPA entry. EMAPS identifiers are constructed such that they are a concatenation of the EMAPA ID and a Theiler Stage (TS) number. For instance, EMAPA:35178 in TS 23 becomes EMAPS:3517823 ^\d+$ 3517823 Terry.Hayamizu@jax.org https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPS:$1 False emdb Electron Microscopy Data Bank https://www.ebi.ac.uk/pdbe/emdb/ The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. The EMDB map distribution format follows the CCP4 definition, which is widely recognized by software packages used by the structural biology community. ^EMD-\d{4,5}$ EMD-1001 help@emdatabank.org https://www.ebi.ac.uk/pdbe/entry/emdb/$1 False EMDB 1146 emdb emdb r3d100010562 +emea European Medicines Evaluation Agency https://www.ema.europa.eu/en/medicines Product number for the European Medicines Agency EMEA/H/C/000181 False emmo Elementary Multiperspective Material Ontology https://emmo-repo.github.io EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub) 03212fd7_abfd_4828_9c8e_62c293052d4b jesper.friis@sintef.no http://emmo.info/emmo#EMMO_$1 False emmo.cif Crystallographic Information Framework https://www.iucr.org/resources/cif A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/) _space_group_symop.operation_xyz jesper.friis@sintef.no http://emmo.info/emmo/cif-core#$1 False emolecules Reaxys eMolecules https://reaxys.emolecules.com Catalog of purchasable reagents and building blocks ^\d+$ 491187 https://reaxys.emolecules.com/cgi-bin/more?vid=$1 False @@ -1646,6 +1647,7 @@ sstoss Sequence-Structural Templates of Single-member Superfamilies http://caps. stap Statistical Torsional Angles Potentials http://psb.kobic.re.kr/STAP/refinement/ STAP (Statistical Torsional Angles Potentials) was developed since, according to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, are less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. The refined NMR solution structures (statistical torsion angle potentials; STAP) in the database are refined from the Protein Data Bank (PDB). ^[0-9][A-Za-z0-9]{3}$ 1a24 http://psb.kobic.re.kr/STAP/refinement1/result.php?search=$1 False STAP stap stap stato The Statistical Methods Ontology http://stato-ontology.org/ STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots. ^\d{7}$ 0000288 alejandra.gonzalez.beltran@gmail.com http://purl.obolibrary.org/obo/STATO_$1 False STATO STATO STATO stato stato STATO stitch Search Tool for Interactions of Chemicals http://stitch.embl.de/ STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. ^\w{14}$ BQJCRHHNABKAKU http://stitch.embl.de/interactions/$1 False STITCH stitch stitch stitch +stn FDA Submission Tracking Number https://www.fda.gov/media/128698/download The pre-IND tracking number for submissions to the FDA 125768 False storedb Store DB https://www.storedb.org/ STOREDB database is a repository for data used by the international radiobiology community, archiving and sharing primary data outputs from research on low dose radiation. It also provides a directory of bioresources and databases for radiobiology projects containing information and materials that investigators are willing to share. STORE supports the creation of a low dose radiation research commons. ^(STUDY|FILE|DATASET)\d+$ STUDY1040 PNS12@cam.ac.uk https://www.storedb.org/?$1 False STOREDB storedb storedb r3d100011049 storedb.dataset STOREDB at University of Cambridge https://www.storedb.org/ Datasets inside StoreDB ^\d+$ 1251 https://www.storedb.org/?STOREDB:DATASET$1 True storedb storedb.file STOREDB at University of Cambridge https://www.storedb.org/ File inside StoreDB ^\d+$ 12929 https://www.storedb.org/store_v3/download.jsp?fileId=$1 False storedb diff --git a/exports/registry/registry.yml b/exports/registry/registry.yml index 8cf815b29..b1e66dde4 100644 --- a/exports/registry/registry.yml +++ b/exports/registry/registry.yml @@ -15065,6 +15065,17 @@ emdb: title: New electron microscopy database and deposition system year: null uri_format: https://www.ebi.ac.uk/pdbe/entry/emdb/$1 +emea: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: Product number for the European Medicines Agency + example: EMEA/H/C/000181 + homepage: https://www.ema.europa.eu/en/medicines + name: European Medicines Evaluation Agency + preferred_prefix: emea emmo: banana: EMMO banana_peel: _ @@ -49483,6 +49494,17 @@ stitch: title: 'STITCH: interaction networks of chemicals and proteins' year: 2007 uri_format: http://stitch.embl.de/interactions/$1 +stn: + contributor: + email: cthoyt@gmail.com + github: cthoyt + name: Charles Tapley Hoyt + orcid: 0000-0003-4423-4370 + description: The pre-IND tracking number for submissions to the FDA + example: '125768' + homepage: https://www.fda.gov/media/128698/download + name: FDA Submission Tracking Number + preferred_prefix: stn storedb: banana: STOREDB contact: diff --git a/exports/tables/summary.tex b/exports/tables/summary.tex index 3b41bf42c..b4b868689 100644 --- a/exports/tables/summary.tex +++ b/exports/tables/summary.tex @@ -1,16 +1,16 @@ \begin{table} -\caption{Overview statistics of the Bioregistry on 2023-10-16.} +\caption{Overview statistics of the Bioregistry on 2023-10-17.} \label{tab:bioregistry-summary} \begin{tabular}{lr} \toprule Category & Count \\ \midrule -Version & 0.10.63-dev \\ +Version & 0.10.64-dev \\ Registries Surveyed & 27 \\ Registries Aligned & 26 \\ -Prefixes & 1727 \\ +Prefixes & 1729 \\ Synonyms & 471 \\ -Cross-registry Mappings & 7816 \\ +Cross-registry Mappings & 7818 \\ Curated Mismatches & 52 \\ Collections and Contexts & 13 \\ Direct Contributors & 45 \\ diff --git a/src/bioregistry/data/external/aberowl/processed.json b/src/bioregistry/data/external/aberowl/processed.json index a40a9b29b..43858dfb0 100644 --- a/src/bioregistry/data/external/aberowl/processed.json +++ b/src/bioregistry/data/external/aberowl/processed.json @@ -3244,7 +3244,7 @@ }, "GO": { "description": "An ontology for describing the function of genes and gene products", - "download_owl": "http://aber-owl.net/media/ontologies/GO/1781/go.owl", + "download_owl": "http://aber-owl.net/media/ontologies/GO/1782/go.owl", "homepage": "http://geneontology.org/", "name": "Gene Ontology", "prefix": "GO" @@ -3391,7 +3391,7 @@ }, "HANCESTRO": { "description": "The Human Ancestry Ontology (HANCESTRO) provides a systematic description of the ancestry concepts used in the NHGRI-EBI Catalog of published genome-wide association studies.", - "download_owl": "http://aber-owl.net/media/ontologies/HANCESTRO/12/hancestro.owl", + "download_owl": "http://aber-owl.net/media/ontologies/HANCESTRO/13/hancestro.owl", "homepage": "https://ebispot.github.io/hancestro/", "name": "Human Ancestry Ontology", "prefix": "HANCESTRO" @@ -3702,7 +3702,7 @@ }, "HP": { "description": "A structured and controlled vocabulary for the phenotypic features encountered in human hereditary and other disease.", - "download_owl": "http://aber-owl.net/media/ontologies/HP/604/hp.owl", + "download_owl": "http://aber-owl.net/media/ontologies/HP/605/hp.owl", "homepage": "http://www.human-phenotype-ontology.org/", "name": "Human Phenotype Ontology", "prefix": "HP" @@ -6437,7 +6437,7 @@ }, "OMO": { "description": "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).", - "download_owl": "http://aber-owl.net/media/ontologies/OMO/8/omo.owl", + "download_owl": "http://aber-owl.net/media/ontologies/OMO/9/omo.owl", "homepage": "https://github.com/information-artifact-ontology/ontology-metadata", "name": "OBO Metadata Ontology", "prefix": "OMO" @@ -7253,7 +7253,7 @@ }, "PHIPO": { "description": "PHIPO is a formal ontology of species-neutral phenotypes observed in pathogen-host interactions.", - "download_owl": "http://aber-owl.net/media/ontologies/PHIPO/34/phipo.owl", + "download_owl": "http://aber-owl.net/media/ontologies/PHIPO/35/phipo.owl", "homepage": "https://github.com/PHI-base/phipo", "name": "Pathogen Host Interaction Phenotype Ontology", "prefix": "PHIPO" diff --git a/src/bioregistry/data/external/aberowl/raw.json b/src/bioregistry/data/external/aberowl/raw.json index 50c6abd61..13feb5b26 100644 --- a/src/bioregistry/data/external/aberowl/raw.json +++ b/src/bioregistry/data/external/aberowl/raw.json @@ -1 +1 @@ -[{"acronym":"BANDARQ","name":"CapsaBandarQ.com Capsa Online, Agen Bandar Q, Domino 99, Qiu Qiu Online, BandarQ","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"ONTOPARON_SOCIAL","name":"Ontology of amyotrophic lateral sclerosis, social module","status":"Unknown","topics":null,"species":null,"submission":null},{"acronym":"GEOSPECIES","name":"GeoSpecies Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":8,"download_url":"media/ontologies/GEOSPECIES/1/geospecies.owl","submission_id":1,"domain":null,"description":"This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. 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\r\nLineage(s)\r\n

\r\nA class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage. \r\n

\r\nAnnotations\r\n

\r\nSpecific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
\r\nDEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
\r\nFULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
\r\nICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
\r\nICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
\r\nClass Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
\r\nPreferred_Name: A human-friendly and commonly used name in plain English.
\r\nSynonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
\r\nUMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they \"understand\" the meaning of the language of biomedicine and health.\r\n

\r\nRelationships (Object Properties)\r\n

\r\nRelationships are properties by which one class is related to another class in the ontology. For example, \"Population_Group\" (a class) has_susceptibility_to_disease (a relationship) \"Immune_Disorder\" (a class). This box may be empty if no relationship has been used for modeling. \r\n

\r\nDatatype Properties\r\n

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Allotrope Merged Ontology Suite

\r\n\r\n

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

\r\n\r\n

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

\r\n\r\n

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
\r\nrights: http://purl.allotrope.org/voc/copyright

\r\n \r\n

Please get the latest version of AFO from http://purl.allotrope.org

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A simplified list was deemed sufficient since the domain under study (cultural documents) will not have detailed medical information with regards to cause of death or health issues. But instead of accepting a list of general usage terms for causes of death or health issues that appear in some sources (e.g. Wikipedia, Wikidatak, etc.), a standardized, medical classification was selected so that it could be of use for future analysis regarding questions involving the intersection of health and culture.\r\n\r\nICD-10-SMoL was chosen since it was the latest version of this list (June, 2018). A stable version of ICD-11 was to be available in June 2018 but there was no ICD-11-SMoL available at this time.\r\n\r\nTo obtain the ICD10-SMoL:\r\nhttp://www.who.int/healthinfo/civil_registration/ICD_10_SMoL.pdf?ua=1","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2018-07-22T00:00:00Z","date_created":"2018-07-22T21:52:48Z","home_page":null,"version":"1.0","has_ontology_language":"OWL","nb_classes":21,"nb_individuals":141,"nb_properties":0,"max_depth":2,"max_children":20,"avg_children":10,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"GFFO","name":"Genetic Feature Format Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":4987,"download_url":"media/ontologies/GFFO/1/gffo.owl","submission_id":1,"domain":null,"description":"An ontology to represent genome feature annotations in gff3 format.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2022-03-28T00:00:00Z","date_created":"2022-03-28T15:58:06Z","home_page":"https://github.com/mpievolbio-scicomp/GenomeFeatureFormatOntology","version":"0.0.1","has_ontology_language":"OWL","nb_classes":1,"nb_individuals":0,"nb_properties":33,"max_depth":1,"max_children":1,"avg_children":1,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"HP_O","name":"Hypersensitivity pneumonitis ontology","status":"Classified","topics":null,"species":null,"submission":{"id":1673,"download_url":"media/ontologies/HP_O/1/hp_o.owl","submission_id":1,"domain":null,"description":"Hypersensitivity Pneumonitis Ontology involves the domain of knowledge of 1. diseases caused by organic dusts exposure including hypersensitivity pneumonitis as well as 2. organic dusts.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2018-07-17T00:00:00Z","date_created":"2018-07-17T08:06:43Z","home_page":"https://hypontology.herokuapp.com/","version":"1.0","has_ontology_language":"OWL","nb_classes":199,"nb_individuals":0,"nb_properties":7,"max_depth":8,"max_children":38,"avg_children":8,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"AI-RHEUM","name":"Artificial Intelligence Rheumatology Consultant System Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":279,"download_url":"media/ontologies/AI-RHEUM/9/ai-rheum.umls","submission_id":9,"domain":null,"description":"AI/RHEUM is used for the diagnosis of rheumatologic diseases. 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The BIM ontology is represented in three parts; (i) image vocabularies - which holds vocabularies for the annotation of an image and/or region of interests (ROI) inside an image, as well as vocabularies to represent the pre and post processing states of an image, (ii) text entities - covers annotations from the text that are associated with an image (e.g. image captions) and provides semantic representation for NLP algorithm outputs, (iii) a provenance model - that contributes towards the maintenance of annotation versioning. 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Food Ontology Knowledgebase (FOKB) is developed in English and Turkish that contains details of food ingredients such as their codes (e-codex or codex numbers) and also side effects of them such as allergy. Initially, the first stage of the research project was funded in 2013 by TUBITAK (The Scientific and Technological Research Council of Turkey- http://www.tubitak.gov.tr/en) – 1512 Progressive Entrepreneurship Support Program (Project No: 2120357, “Semantic-based Personal Safe Food Consumption System for Allergic Individuals via Smart Devices”) by the Semantica Trd. Ltd. Co (http://www.semantica.com.tr/en). The initial proposal of the first stage project is presented in Hindawi Publishing Corporation http://www.hindawi.com- The Scientific World Journal with the title “FoodWiki: Ontology-driven Mobile Safe Food Consumption System”. After that, another project as an extension of the first stage project was funded again by TUBITAK toward the end of 2014. 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","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2015-08-07T00:00:00Z","date_created":"2016-08-04T22:06:52Z","home_page":"http://www.aniseed.cnrs.fr/","version":null,"has_ontology_language":"OBO","nb_classes":880,"nb_individuals":0,"nb_properties":7,"max_depth":2,"max_children":371,"avg_children":88,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"MCO","name":"Microbial Conditions Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":2559,"download_url":"media/ontologies/MCO/2/mco.owl","submission_id":2,"domain":"experimental conditions","description":"Microbial Conditions Ontology is an ontology...","documentation":null,"publication":null,"publications":null,"products":[{"id":"mco.owl","ontology_purl":"http://purl.obolibrary.org/obo/mco.owl"},{"id":"mco.obo","ontology_purl":"http://purl.obolibrary.org/obo/mco.obo"}],"taxon":null,"date_released":"2019-05-20T13:24:27.583288Z","date_created":"2019-05-20T13:24:27.583312Z","home_page":"https://github.com/microbial-conditions-ontology/microbial-conditions-ontology","version":null,"has_ontology_language":"OWL","nb_classes":3384,"nb_individuals":0,"nb_properties":16,"max_depth":21,"max_children":179,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":"489fbeba542c9f4b2717f5a8a08893d4"}},{"acronym":"MDIM","name":"Mapping of Drug Names, ICD-11 and MeSH 2021","status":"Classified","topics":null,"species":null,"submission":{"id":4297,"download_url":"media/ontologies/MDIM/2/mdim.owl","submission_id":2,"domain":null,"description":"The Mapping of Drug Names, ICD-11 and MeSH 2021 (MDIM) provides owl:sameAs relationships of similar concepts for Drug Names from the DrugBank vocabulary (https://go.drugbank.com/releases/latest#open-data), the International Classification of Diseases Version 11 (https://icd.who.int/) and the Medical Subject Headings (http://id.nlm.nih.gov/mesh/). 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\r\nLineage(s)\r\n

\r\nA class may be related to its superclass through a true is_a relationship (e.g., Polymyositis is a Dermatomyositis, which is an Autoimmune_Disease, which is an Immune_Disorder). Based on description logic, a class inherits all the Relationships (Object Properties) and Datatype Properties (if any) assigned to its superclass. In a few occasions, a class may have more than one superclass and belongs to more than one lineage. \r\n

\r\nAnnotations\r\n

\r\nSpecific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. The following provides more detail on annotation information presented:
\r\nDEFINITION: A human-readable definition is provided for each class in the ontology and the displayed format is Owner|Definition (Source).
\r\nFULL_SYN: Synonym of a class in the ontology with type (PT: preferred term, SY: synonym) and source of this synonym indicated. Synonym|Type of Synonym|Source of Synonym is the format displayed.
\r\nICD-10_Code: Code of International Classification of Diseases and Related Health Problems, 10th revision. ICD-10 is a detailed description of known diseases and injuries. It is published by the World Health Organization (WHO) and is used worldwide for mortality statistics.
\r\nICD-9_Code: Code of International Classification of Diseases and Related Health Problems, 9th revision.
\r\nClass Name: Class_Name is used as a unique identifier by Protege-OWL, the environment where this ontology is being developed and therefore has to be OWL-compliant. Class_Name is composed of a string only made of digits, letters, underscores, and hyphens. A Class_Name cannot start with a digit.
\r\nPreferred_Name: A human-friendly and commonly used name in plain English.
\r\nSynonym: Synonym of a class in plain English, including those in plural form or British spelling. In contrast to FULL_SYN, no type nor source of synonym is indicated. Synonym is human-friendly and not OWL-compliant. A class may have multiple synonyms.
\r\nUMLS_CUI: Concept Unique Identifier in Unified Medical Language System that is produced and distributed by NLM. There are three UMLS Knowledge Sources: the Metathesaurus, the Semantic Network, and SPECIALIST Lexicon. The purpose of UMLS is to facilitate the development of computer systems that behave as if they \"understand\" the meaning of the language of biomedicine and health.\r\n

\r\nRelationships (Object Properties)\r\n

\r\nRelationships are properties by which one class is related to another class in the ontology. For example, \"Population_Group\" (a class) has_susceptibility_to_disease (a relationship) \"Immune_Disorder\" (a class). This box may be empty if no relationship has been used for modeling. \r\n

\r\nDatatype Properties\r\n

\r\nDatatype Properties are properties by which a class is related to a datatype. 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To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA.\r\nIf you have any comments, questions or suggestions, please contact Yann Le Franc at ylefranc(at)gmail.com.","documentation":"https://github.com/INCF/Computational-Neurosciences-Ontology--C.N.O.-/wiki","publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2015-11-17T02:21:21Z","date_created":"2015-11-17T02:21:21Z","home_page":null,"version":"version 0.5","has_ontology_language":"OWL","nb_classes":395,"nb_individuals":20,"nb_properties":40,"max_depth":11,"max_children":27,"avg_children":3,"classifiable":false,"nb_inconsistent":0,"indexed":false,"md5sum":null}},{"acronym":"TEO","name":"Time Event Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":9,"download_url":"media/ontologies/TEO/4/teo.owl","submission_id":4,"domain":null,"description":"The Time Event Ontology (TEO) is an ontology for representing events, time, and their relationships.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2012-04-26T07:00:00Z","date_created":"2012-04-27T16:21:15Z","home_page":null,"version":"1.0.8","has_ontology_language":"OWL","nb_classes":728,"nb_individuals":41,"nb_properties":91,"max_depth":9,"max_children":38,"avg_children":4,"classifiable":false,"nb_inconsistent":0,"indexed":false,"md5sum":null}},{"acronym":"OntoVIP","name":"Medical image simulation","status":"Unloadable","topics":null,"species":null,"submission":{"id":293,"download_url":"media/ontologies/OntoVIP/1/ontovip.owl","submission_id":1,"domain":null,"description":"The OntoVIP ontology was developed in the context of the Virtual Imaging Platform project (VIP), a french project supported by ANR (ANR-09-COSI-03 grant) aiming at sharing medical image simulation resources. \r\nThis ontology describes the content of the models used in medical image simulation. 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Allotrope Merged Ontology Suite

\r\n\r\n

The AFO is an ontology suite that provides a standard vocabulary and semantic model for the representation of laboratory analytical processes. The AFO suite is aligned at the upper layer to the Basic Formal Ontology (BFO). The core domains modeled include: Equipment, Material, Process, and Results.

\r\n\r\n

This version of Allotrope Foundation Ontology (AFO) has been prepared specifically for publication on the NCBO platform.

\r\n\r\n

license: http://purl.allotrope.org/voc/creative-commons-attribution-license
\r\nrights: http://purl.allotrope.org/voc/copyright

\r\n \r\n

Please get the latest version of AFO from http://purl.allotrope.org

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Food Ontology Knowledgebase (FOKB) is developed in English and Turkish that contains details of food ingredients such as their codes (e-codex or codex numbers) and also side effects of them such as allergy. Initially, the first stage of the research project was funded in 2013 by TUBITAK (The Scientific and Technological Research Council of Turkey- http://www.tubitak.gov.tr/en) – 1512 Progressive Entrepreneurship Support Program (Project No: 2120357, “Semantic-based Personal Safe Food Consumption System for Allergic Individuals via Smart Devices”) by the Semantica Trd. Ltd. Co (http://www.semantica.com.tr/en). The initial proposal of the first stage project is presented in Hindawi Publishing Corporation http://www.hindawi.com- The Scientific World Journal with the title “FoodWiki: Ontology-driven Mobile Safe Food Consumption System”. After that, another project as an extension of the first stage project was funded again by TUBITAK toward the end of 2014. It is titled “Artificial Intelligence-based Mobile System for Conscious Food Consumption through Ontology” and recorded with the project number 3140417 in cooperation with Semantica Internet and Software Services Trd. Ltd. Co. and Acıbadem Hospitals Group[1] in consultation with Asst. Prof. Dr. Duygu Çelik. Copyrights of the Food Ontology Knowledgebase (FOKB) and FoodWiki system are reserved by Semantica Trd. Ltd. Co and Acıbadem Hospitals Group (http://www.acibademinternational.com/)","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2015-04-01T00:00:00Z","date_created":"2015-04-27T18:56:49Z","home_page":null,"version":"v1.0","has_ontology_language":"OWL","nb_classes":62,"nb_individuals":1740,"nb_properties":46,"max_depth":4,"max_children":15,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"BAO","name":"BioAssay Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":772,"download_url":"media/ontologies/BAO/32/bao.owl","submission_id":32,"domain":null,"description":"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. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 1000 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc.). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.","documentation":"http://www.bioassayontology.org/","publication":"http://www.bioassayontology.org/","publications":null,"products":null,"taxon":null,"date_released":"2017-10-05T01:00:16Z","date_created":"2017-10-05T01:00:16Z","home_page":"http://www.bioassayontology.org/","version":"2.3.3","has_ontology_language":"OWL","nb_classes":7125,"nb_individuals":1,"nb_properties":223,"max_depth":13,"max_children":178,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"BAO-GPCR","name":"G Protein-Coupled Receptor BioAssays Ontology","status":"Unloadable","topics":null,"species":null,"submission":{"id":182,"download_url":"media/ontologies/BAO-GPCR/23/bao-gpcr.owl","submission_id":23,"domain":null,"description":"The G protein-coupled receptors (GPCRs) ontology (http://www.bioassayontology.org/bao_gpcr) describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. 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The ontology was developed as part of Information Artifact Ontology (IAO).","documentation":null,"publication":null,"publications":null,"products":[{"id":"omo.owl","ontology_purl":"http://purl.obolibrary.org/obo/omo.owl"}],"taxon":null,"date_released":"2023-10-16T12:55:03.885493Z","date_created":"2023-10-16T12:55:03.885501Z","home_page":"https://github.com/information-artifact-ontology/ontology-metadata","version":null,"has_ontology_language":"OWL","nb_classes":28,"nb_individuals":20,"nb_properties":0,"max_depth":9,"max_children":7,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":"4155e3a777e1ea5165738d10cc9f6eb2"}},{"acronym":"Spitali","name":"Dallendyshe","status":"Classified","topics":["Spitali"],"species":["Spitali"],"submission":{"id":2288,"download_url":"media/ontologies/Spitali/1/spitali.owl","submission_id":1,"domain":null,"description":"se di","documentation":"se di","publication":"se di","publications":null,"products":null,"taxon":null,"date_released":"2019-02-21T22:25:23.044763Z","date_created":"2019-02-21T22:25:23.044744Z","home_page":"Desktop","version":"se di","has_ontology_language":"OWL","nb_classes":21,"nb_individuals":92,"nb_properties":27,"max_depth":3,"max_children":5,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VEO","name":"Visualized Emotion Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":1130,"download_url":"media/ontologies/VEO/1/veo.owl","submission_id":1,"domain":null,"description":"Visual Emotion Ontology (VEO) is an ontology that links visualizations with specific emotions from the Ortony, Clore, and Collins' description of human emotions.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2017-12-27T00:00:00Z","date_created":"2017-12-27T16:20:48Z","home_page":null,"version":"0.5","has_ontology_language":"OWL","nb_classes":1012,"nb_individuals":44,"nb_properties":39,"max_depth":15,"max_children":35,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VHO","name":"VFB Helper Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":4697,"download_url":"media/ontologies/VHO/1/vho.owl","submission_id":1,"domain":null,"description":"Ontology of terms used for annotating data in Virtual Fly Brain, including anatomical templates.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2021-11-15T00:00:00Z","date_created":"2021-11-16T10:45:08Z","home_page":null,"version":null,"has_ontology_language":"OWL","nb_classes":9,"nb_individuals":0,"nb_properties":0,"max_depth":1,"max_children":9,"avg_children":9,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VHOG","name":"Vertebrate Homologous Organ Group Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":369,"download_url":"media/ontologies/VHOG/12/vhog.obo","submission_id":12,"domain":null,"description":"vHOG is a multi-species anatomical ontology for the vertebrate lineage, developed as part of the Bgee project.\r\nThe mapping to species-specific anatomical ontologies is provided as a separated file:\r\nhttp://bgee.unil.ch/download/organ_association_vHOG.txt\r\nThis mapping represents homology-strict relationships, in the sense of HOM:0000007 \"historical homology\". Each mapping has been manually reviewed, and we provide confidence codes and references when available.","documentation":"http://bgee.unil.ch/?page=documentation#sectionHomologyRelationships","publication":"http://www.unil.ch/dee/page31219_en.html","publications":null,"products":null,"taxon":null,"date_released":"2017-05-17T01:11:42Z","date_created":"2017-05-17T01:11:42Z","home_page":"http://bgee.unil.ch","version":"unknown","has_ontology_language":"OBO","nb_classes":1185,"nb_individuals":0,"nb_properties":1,"max_depth":8,"max_children":25,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VICO","name":"Vaccination Informed Consent Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":494,"download_url":"media/ontologies/VICO/10/vico.owl","submission_id":10,"domain":null,"description":"The Vaccination Informed Consent Ontology (VICO) is a community-driven ontology in the domain of vaccination/immunization informed consent.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2016-01-31T02:14:05Z","date_created":"2016-01-31T02:14:07Z","home_page":"https://github.com/VICO-ontology","version":"Arbor version; 1.0.52","has_ontology_language":"OWL","nb_classes":710,"nb_individuals":126,"nb_properties":94,"max_depth":18,"max_children":29,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VIDO","name":"Virus Infectious Disease Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":5510,"download_url":"media/ontologies/VIDO/3/vido.owl","submission_id":3,"domain":null,"description":"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. ","documentation":"https://github.com/infectious-disease-ontology-extensions/ido-virus","publication":"https://osf.io/5bx8c","publications":null,"products":null,"taxon":null,"date_released":"2020-06-05T00:00:00Z","date_created":"2022-11-28T03:58:43Z","home_page":"https://github.com/infectious-disease-ontology-extensions/ido-virus","version":"10-27-2022","has_ontology_language":"OWL","nb_classes":432,"nb_individuals":0,"nb_properties":32,"max_depth":10,"max_children":19,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VIO","name":"Vaccine Investigation Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":2503,"download_url":"media/ontologies/VIO/1/vio.owl","submission_id":1,"domain":null,"description":"VIO is an VO-extended ontology with the aim to standardize the metadata types in various vaccine investigation studies.","documentation":null,"publication":"https://sites.google.com/site/vdosworkshop/VDOS-2018","publications":null,"products":null,"taxon":null,"date_released":"2019-04-29T00:00:00Z","date_created":"2019-04-29T21:31:04Z","home_page":"https://github.com/vaccineontology/VIO","version":"Vision Release: 1.0.01","has_ontology_language":"OWL","nb_classes":80,"nb_individuals":0,"nb_properties":46,"max_depth":10,"max_children":15,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VIVO-ISF","name":"VIVO-Integrated Semantic Framework","status":"Classified","topics":null,"species":null,"submission":{"id":732,"download_url":"media/ontologies/VIVO-ISF/1/vivo-isf.owl","submission_id":1,"domain":null,"description":"The Integrated Semantic Framework ontology modules for VIVO (the VIVO-ISF ontology) provide a set of types (classes) and relationships (properties) to represent researchers and the full context in which they work. ","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2013-12-14T00:00:00Z","date_created":"2015-09-13T18:32:39Z","home_page":"vivoweb.org","version":"1.6","has_ontology_language":"OWL","nb_classes":414,"nb_individuals":14,"nb_properties":415,"max_depth":10,"max_children":35,"avg_children":3,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VO","name":"Vaccine Ontology","status":"Classified","topics":null,"species":null,"submission":{"id":6064,"download_url":"media/ontologies/VO/293/vo.owl","submission_id":293,"domain":"health","description":"VO is a biomedical ontology in the domain of vaccine and vaccination.","documentation":null,"publication":null,"publications":[{"id":"https://www.ncbi.nlm.nih.gov/pubmed/23256535","title":"Ontology representation and analysis of vaccine formulation and administration and their effects on vaccine immune responses"},{"id":"https://www.ncbi.nlm.nih.gov/pubmed/21624163","title":"Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology"}],"products":[{"id":"vo.owl","ontology_purl":"http://purl.obolibrary.org/obo/vo.owl"}],"taxon":null,"date_released":"2023-09-18T14:23:12.286726Z","date_created":"2023-09-18T14:23:12.286742Z","home_page":"http://www.violinet.org/vaccineontology","version":null,"has_ontology_language":"OWL","nb_classes":7912,"nb_individuals":167,"nb_properties":242,"max_depth":21,"max_children":881,"avg_children":6,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":"db074640929ea044272ed034d28129fd"}},{"acronym":"VODANACOVID","name":"VODANA-COVIDTERMS","status":"Classified","topics":null,"species":null,"submission":{"id":4851,"download_url":"media/ontologies/VODANACOVID/4/vodanacovid.skos","submission_id":4,"domain":null,"description":"Ontology containing the controlled terms and semantic properties used in the COVID-19 generic template used within different facilities in VODANA ","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2022-01-24T00:00:00Z","date_created":"2022-01-24T09:37:31Z","home_page":null,"version":"3.0","has_ontology_language":"SKOS","nb_classes":2,"nb_individuals":54,"nb_properties":5,"max_depth":1,"max_children":2,"avg_children":2,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}},{"acronym":"VFB_DRIVERS","name":"vfb_drivers","status":"Classified","topics":null,"species":null,"submission":{"id":6106,"download_url":"media/ontologies/VFB_DRIVERS/84/vfb_drivers.owl","submission_id":84,"domain":null,"description":"An ontology of Drosophila melanogaster drivers and expression patterns.","documentation":null,"publication":null,"publications":null,"products":null,"taxon":null,"date_released":"2023-10-09T01:22:06Z","date_created":"2023-10-09T01:22:16Z","home_page":null,"version":"2023-10-09","has_ontology_language":"OWL","nb_classes":33355,"nb_individuals":9,"nb_properties":103,"max_depth":7,"max_children":31626,"avg_children":1329,"classifiable":true,"nb_inconsistent":0,"indexed":true,"md5sum":null}}] \ No newline at end of file diff --git a/src/bioregistry/data/external/agroportal/processed.json b/src/bioregistry/data/external/agroportal/processed.json index c1726ec9f..585db706b 100644 --- a/src/bioregistry/data/external/agroportal/processed.json +++ b/src/bioregistry/data/external/agroportal/processed.json @@ -1033,11 +1033,10 @@ "description": "The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. EFO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We also add terms for external users when requested.", "example_uri": "http://www.orpha.net/ORDO/Orphanet_1390", "homepage": "http://www.ebi.ac.uk/efo/", - "license": "Copyright [2014] EMBL - European Bioinformatics Institute\nLicensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the\nLicense.", "name": "Experimental Factor Ontology", "prefix": "EFO", "repository": "https://github.com/EBISPOT/efo", - "version": "3.58.0" + "version": "3.59.0" }, "ENVO": { "contact": { diff --git a/src/bioregistry/data/external/agroportal/raw.json b/src/bioregistry/data/external/agroportal/raw.json index 9b860404a..40540cfc7 100644 --- a/src/bioregistry/data/external/agroportal/raw.json +++ b/src/bioregistry/data/external/agroportal/raw.json @@ -1151,7 +1151,6 @@ "https://data.agroportal.lirmm.fr/groups/RICE" ], "homepage": "http://www.ebi.ac.uk/efo/", - "license": "Copyright [2014] EMBL - European Bioinformatics Institute\nLicensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the\nLicense.", "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", @@ -1199,7 +1198,7 @@ "name": "Experimental Factor Ontology", "ontologyType": "https://data.agroportal.lirmm.fr/ontology_types/ONTOLOGY", "repository": "https://github.com/EBISPOT/efo", - "version": "3.58.0", + "version": "3.59.0", "viewingRestriction": "public" }, { diff --git a/src/bioregistry/data/external/biolink/processed.json b/src/bioregistry/data/external/biolink/processed.json index 8bb370c9e..626cd9204 100644 --- a/src/bioregistry/data/external/biolink/processed.json +++ b/src/bioregistry/data/external/biolink/processed.json @@ -318,10 +318,10 @@ "uri_format": "http://xmlns.com/foaf/0.1/$1" }, "foodb.compound": { - "uri_format": "http://foodb.ca/foods/$1" + "uri_format": "http://foodb.ca/compounds/$1" }, "foodb.food": { - "uri_format": "http://foodb.ca/compounds/$1" + "uri_format": "http://foodb.ca/foods/$1" }, "gff3": { "uri_format": "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#$1" diff --git a/src/bioregistry/data/external/biolink/raw.yaml b/src/bioregistry/data/external/biolink/raw.yaml index 843edcd83..e30e4874e 100644 --- a/src/bioregistry/data/external/biolink/raw.yaml +++ b/src/bioregistry/data/external/biolink/raw.yaml @@ -60,8 +60,8 @@ prefixes: ExO: 'http://purl.obolibrary.org/obo/ExO_' fabio: 'http://purl.org/spar/fabio/' foaf: 'http://xmlns.com/foaf/0.1/' - foodb.food: 'http://foodb.ca/compounds/' - foodb.compound: 'http://foodb.ca/foods/' + foodb.compound: 'http://foodb.ca/compounds/' + foodb.food: 'http://foodb.ca/foods/' FYECO: 'https://www.pombase.org/term/' FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#' diff --git a/src/bioregistry/data/external/bioportal/curation.tsv b/src/bioregistry/data/external/bioportal/curation.tsv index c6745bf63..e9fcb1379 100644 --- a/src/bioregistry/data/external/bioportal/curation.tsv +++ b/src/bioregistry/data/external/bioportal/curation.tsv @@ -102,7 +102,7 @@ CISAVIADO Ciona savignyi Anatomy and Development Ontology http://www.aniseed.cnr CKDO Chronic Kidney Disease Ontology clininf.eu The Chronic Kidney Disease Ontology was developed to assist routine data studies and case identification of CKD in primary care. CMDO Clinical MetaData Ontology http://www.snubi.org/software/cmo/ The Clinical MetaData Ontology is designed to be used to classify Common Data Elements (CDEs) from different studies and clinical documents. CDEs can be efficiently searched, shared and reused by using our ontology. CMR-QA Cardiovascular Magnetic Resonance Quality Assessment Ontology https://github.com/ernestojimenezruiz/CMR-QA-Semantic-Layer/ CMR-QA ontology aims at defining the semantics of free-text quality assessment annotations associated to Cardiac Magnetic Resonance (CMR) Imaging. -CN computer network Computer networks ontology +CN computer network CNO Computational Neuroscience Ontology CNO is a controlled vocabulary of terms used in Computational Neurosciences to describe models of the nervous system. This first release of CNO is an alpha version and should be further aligned with other ontologies accessible on Bioportal and should be made compliant with the OBO foundry recommendations. This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. If you have any comments, questions or suggestions, please contact Yann Le Franc at ylefranc(at)gmail.com. CNO_ACRONYM CNO_NAME test CO Crop Ontology diff --git a/src/bioregistry/data/external/bioportal/processed.json b/src/bioregistry/data/external/bioportal/processed.json index f60b3935c..056332fc4 100644 --- a/src/bioregistry/data/external/bioportal/processed.json +++ b/src/bioregistry/data/external/bioportal/processed.json @@ -1597,11 +1597,6 @@ "version": "0.4.5" }, "CN": { - "contact": { - "email": "demaidim@cs.man.ac.uk", - "name": "monademaidi" - }, - "description": "Computer networks ontology", "name": "computer network", "prefix": "CN" }, @@ -2816,7 +2811,7 @@ "description": "eLTER Controlled Lists are used in different environmental projects related to the eLTER community.", "name": "eLTER Controlled Lists", "prefix": "ELTER_CL", - "version": "1.0.8" + "version": "1.0.9" }, "EMAP": { "contact": { @@ -2909,7 +2904,7 @@ "description": "EnvThes", "name": "Thesaurus for long-term ecological research, monitoring, experiments", "prefix": "ENVTHES", - "version": "5.0.2" + "version": "5.0.3" }, "EO": { "contact": { @@ -3088,16 +3083,8 @@ "version": "0.3" }, "EUPATH": { - "contact": { - "email": "jiezheng@pennmedicine.upenn.edu", - "name": "Jie Zheng" - }, - "description": "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 & 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.", - "homepage": "https://github.com/EuPath-ontology/EuPath-ontology", "name": "VEuPathDB Ontology", - "prefix": "EUPATH", - "publication": "https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf", - "version": "2023-05-30" + "prefix": "EUPATH" }, "EVI": { "contact": { @@ -4508,7 +4495,7 @@ "description": "The value set for the Human Reference Atlas metadata records as part of the Human BioMolecular Atlas Program (HuBMAP) (https://hubmapconsortium.org)", "name": "Human Reference Atlas Value Set", "prefix": "HRAVS", - "version": "2.1.10" + "version": "2.1.11" }, "HRDO": { "contact": { @@ -6013,16 +6000,8 @@ "version": "0.330" }, "MEDDRA": { - "contact": { - "email": "mssohelp@meddra.org", - "name": "MedDRA MSSO" - }, - "description": "MedDRA is an international medical terminology with an emphasis on use for data entry, retrieval, analysis, and display. It applies to all phases of drug development, excluding animal toxicology, and to the health effects and malfunction of devices. An appendix includes concept descriptions which describe how a medical concept is interpreted, used, and classified within the MedDRA terminology. It is not intended as a medical definition. The concept descriptions are intended to aid the consistent and accurate use of MedDRA in coding, retrieval, and analysis.", - "homepage": "https://www.meddra.org/", "name": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)", - "prefix": "MEDDRA", - "publication": "https://www.meddra.org/msso-presentations", - "version": "2023AA" + "prefix": "MEDDRA" }, "MEDEON": { "contact": { @@ -7661,16 +7640,8 @@ "version": "2.0.50" }, "OMIM": { - "contact": { - "email": "custserv@nlm.nih.gov", - "name": "NLM Customer Service" - }, - "description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine", - "homepage": "http://www.ncbi.nlm.nih.gov/omim/", "name": "Online Mendelian Inheritance in Man", - "prefix": "OMIM", - "publication": "http://www.ncbi.nlm.nih.gov/omim/", - "version": "2023AA" + "prefix": "OMIM" }, "OMIT": { "contact": { @@ -10687,7 +10658,7 @@ "description": "An ontology of Drosophila melanogaster drivers and expression patterns.", "name": "vfb_drivers", "prefix": "VFB_DRIVERS", - "version": "2023-10-09" + "version": "2023-10-16" }, "VHOG": { "contact": { diff --git a/src/bioregistry/data/external/bioportal/raw.json b/src/bioregistry/data/external/bioportal/raw.json index 7bfb824bb..481f1c362 100644 --- a/src/bioregistry/data/external/bioportal/raw.json +++ b/src/bioregistry/data/external/bioportal/raw.json @@ -3797,7 +3797,7 @@ }, "name": "vfb_drivers", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "version": "2023-10-09" + "version": "2023-10-16" }, { "@id": "https://data.bioontology.org/ontologies/AURA", @@ -8821,7 +8821,7 @@ }, "name": "Thesaurus for long-term ecological research, monitoring, experiments", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "version": "5.0.2" + "version": "5.0.3" }, { "@id": "https://data.bioontology.org/ontologies/DMTO", @@ -10641,13 +10641,7 @@ "administeredBy": [ "https://data.bioontology.org/users/admin" ], - "contact": { - "email": "mssohelp@meddra.org", - "name": "MedDRA MSSO" - }, - "description": "MedDRA is an international medical terminology with an emphasis on use for data entry, retrieval, analysis, and display. It applies to all phases of drug development, excluding animal toxicology, and to the health effects and malfunction of devices. An appendix includes concept descriptions which describe how a medical concept is interpreted, used, and classified within the MedDRA terminology. It is not intended as a medical definition. The concept descriptions are intended to aid the consistent and accurate use of MedDRA in coding, retrieval, and analysis.", "flat": true, - "homepage": "https://www.meddra.org/", "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", @@ -10688,8 +10682,7 @@ }, "name": "Medical Dictionary for Regulatory Activities Terminology (MedDRA)", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "publication": "https://www.meddra.org/msso-presentations", - "version": "2023AA" + "summaryOnly": false }, { "@id": "https://data.bioontology.org/ontologies/FRMO", @@ -28491,7 +28484,7 @@ }, "name": "eLTER Controlled Lists", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "version": "1.0.8" + "version": "1.0.9" }, { "@id": "https://data.bioontology.org/ontologies/MADS-RDF", @@ -41404,12 +41397,7 @@ "administeredBy": [ "https://data.bioontology.org/users/admin" ], - "contact": { - "email": "custserv@nlm.nih.gov", - "name": "NLM Customer Service" - }, - "description": "Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine", - "homepage": "http://www.ncbi.nlm.nih.gov/omim/", + "flat": false, "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", @@ -41450,8 +41438,7 @@ }, "name": "Online Mendelian Inheritance in Man", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "publication": "http://www.ncbi.nlm.nih.gov/omim/", - "version": "2023AA" + "summaryOnly": false }, { "@id": "https://data.bioontology.org/ontologies/CN", @@ -41460,11 +41447,7 @@ "administeredBy": [ "https://data.bioontology.org/users/monademaidi" ], - "contact": { - "email": "demaidim@cs.man.ac.uk", - "name": "monademaidi" - }, - "description": "Computer networks ontology", + "flat": null, "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", @@ -41504,7 +41487,8 @@ "views": "https://data.bioontology.org/ontologies/CN/views" }, "name": "computer network", - "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY" + "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", + "summaryOnly": null }, { "@id": "https://data.bioontology.org/ontologies/EUPATH", @@ -41513,12 +41497,7 @@ "administeredBy": [ "https://data.bioontology.org/users/jzheng" ], - "contact": { - "email": "jiezheng@pennmedicine.upenn.edu", - "name": "Jie Zheng" - }, - "description": "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 & 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.", - "homepage": "https://github.com/EuPath-ontology/EuPath-ontology", + "flat": null, "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", @@ -41559,8 +41538,7 @@ }, "name": "VEuPathDB Ontology", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "publication": "https://pdfs.semanticscholar.org/888e/a51dbb138122d39c42f863f2a1ada7976db4.pdf", - "version": "2023-05-30" + "summaryOnly": false }, { "@id": "https://data.bioontology.org/ontologies/AIRBUS", @@ -47700,7 +47678,7 @@ }, "name": "Human Reference Atlas Value Set", "ontologyType": "https://data.bioontology.org/ontology_types/ONTOLOGY", - "version": "2.1.10" + "version": "2.1.11" }, { "@id": "https://data.bioontology.org/ontologies/PVONTO", diff --git a/src/bioregistry/data/external/ecoportal/curation.tsv b/src/bioregistry/data/external/ecoportal/curation.tsv index fea821dbb..47d125bd3 100644 --- a/src/bioregistry/data/external/ecoportal/curation.tsv +++ b/src/bioregistry/data/external/ecoportal/curation.tsv @@ -9,7 +9,7 @@ DWCDOE Darwin Core Degree of Establishment Controlled Vocabulary The Darwin Cor DWCEM Darwin Core Establishment Means Controlled Vocabulary The Darwin Core term establishmentMeans provides information about whether an organism or organisms have been introduced to a given place and time through the direct or indirect activity of modern humans. The Establishment Means Controlled Vocabulary provides terms that should be used as values for dwc:establishmentMeans and dwciri:establishmentMeans. DWCPW Darwin Core Pathway Controlled Vocabulary The Darwin Core term pathway provides information about the process by which an Organism came to be in a given place at a given time. The Pathway Controlled Vocabulary provides terms that should be used as values for dwc:pathway and dwciri:pathway. ENDEMISMS Endemisms Thesaurus Thesaurus on endemisms -ENVTHES Environmental Thesaurus https://github.com/LTER-Europe/EnvThes EnvThes compiles a set of terms in order to describe in a harmonised way data resulting from observations and measurements of ecosystem processes across different domain specific sciences. It is used by DEIMS-SDR for common keywords for annotation and quering metadata purposes. +ENVTHES Environmental Thesaurus EnvThes compiles a set of terms in order to describe in a harmonised way data resulting from observations and measurements of ecosystem processes across different domain specific sciences. It is used by DEIMS-SDR for common keywords for annotation and quering metadata purposes. EURIO eurio EURIO (EUropean Research Information Ontology) conceptualises, formally encodes and makes available in an open, structured and machine-readable format data about resarch projects funded by the EU's framework programmes for research and innovation. EUROSCIVOC EuroSciVoc European Science Vocabulary (EuroSciVoc) is the taxonomy of fields of science based on OECD's 2015 Frascati Manual taxonomy. It was extended with fields of science categories extracted from CORDIS content through a semi-automatic process developed with Natural Language Processing (NLP) techniques. EUROVOC EuroVoc Core Concepts EuroVoc is a multilingual, multidisciplinary thesaurus covering the activities of the EU. It contains terms in 24 EU languages, plus in three languages of countries which are candidate for EU accession. EuroVoc is managed by the Publications Office of the European Union, which moved forward to ontology-based thesaurus management and semantic web technologies conformant to W3C recommendations as well as latest trends in thesaurus standards. EuroVoc users include the European Union institutions, the Publications Office of the EU, national and regional parliaments in Europe, plus national governments and private users around the world. EcoPortal is currently hosting the core concepts of EuroVoc, including all their attributes, except alternative labels. diff --git a/src/bioregistry/data/external/ecoportal/processed.json b/src/bioregistry/data/external/ecoportal/processed.json index 0c02a9fc8..9b245b1ad 100644 --- a/src/bioregistry/data/external/ecoportal/processed.json +++ b/src/bioregistry/data/external/ecoportal/processed.json @@ -121,8 +121,6 @@ }, "ENVTHES": { "description": "EnvThes compiles a set of terms in order to describe in a harmonised way data resulting from observations and measurements of ecosystem processes across different domain specific sciences. It is used by DEIMS-SDR for common keywords for annotation and quering metadata purposes.", - "homepage": "https://github.com/LTER-Europe/EnvThes", - "license": "CC-BY-4.0", "name": "Environmental Thesaurus", "prefix": "ENVTHES", "version": "5.0.3" diff --git a/src/bioregistry/data/external/ecoportal/raw.json b/src/bioregistry/data/external/ecoportal/raw.json index a6b23ce2a..cd88239e7 100644 --- a/src/bioregistry/data/external/ecoportal/raw.json +++ b/src/bioregistry/data/external/ecoportal/raw.json @@ -214,8 +214,6 @@ "https://data.ecoportal.lifewatch.eu/categories/Ecology", "https://data.ecoportal.lifewatch.eu/categories/Environmental_Sciences" ], - "homepage": "https://github.com/LTER-Europe/EnvThes", - "license": "CC-BY-4.0", "links": { "@context": { "analytics": "http://data.bioontology.org/metadata/Analytics", diff --git a/src/bioregistry/data/external/fairsharing/processed.json b/src/bioregistry/data/external/fairsharing/processed.json index 1bd2c5ff9..5cda0d3ef 100644 --- a/src/bioregistry/data/external/fairsharing/processed.json +++ b/src/bioregistry/data/external/fairsharing/processed.json @@ -675,7 +675,7 @@ "FAIRsharing.27rndz": { "abbreviation": "GEO", "description": "The Geographical Entity Ontology (GEO) is an ontology of geographical entities (such as sovereign states and their administrative subdivisions) as well as various geographical regions (including but not limited to the specific ones over which the governments have jurisdiction).", - "homepage": "https://github.com/ufbmi/geographical-entity-ontology", + "homepage": "https://github.com/mcwdsi/geographical-entity-ontology", "license": "CC-BY-4.0", "name": "Geographical Entity Ontology", "publications": [], @@ -12972,8 +12972,8 @@ "orcid": "0000-0002-9881-1017" }, "description": "An ontology of drug products and packaged drug products.", - "homepage": "https://ontology.atlassian.net/wiki/display/DRON/Drug+Ontology+Home", - "license": "CC-BY-3.0", + "homepage": "https://github.com/mcwdsi/dron", + "license": "CC-BY-4.0", "name": "The Drug Ontology", "publications": [ { diff --git a/src/bioregistry/data/external/ncbi/raw.html b/src/bioregistry/data/external/ncbi/raw.html index aa905ab60..422f45edb 100644 --- a/src/bioregistry/data/external/ncbi/raw.html +++ b/src/bioregistry/data/external/ncbi/raw.html @@ -42,7 +42,7 @@ - +

@@ -4094,8 +4094,8 @@

INSDC Members

You are here: NCBI
- Support Center - + Support Center +

@@ -4301,8 +4301,8 @@

INSDC Members

- - + + diff --git a/src/bioregistry/data/external/obofoundry/processed.json b/src/bioregistry/data/external/obofoundry/processed.json index 1013fb825..92c1c4a6b 100644 --- a/src/bioregistry/data/external/obofoundry/processed.json +++ b/src/bioregistry/data/external/obofoundry/processed.json @@ -1837,7 +1837,7 @@ "contact.label": "Lynn Schriml", "contact.orcid": "0000-0001-8910-9851", "deprecated": true, - "description": "A gazetteer constructed on ontological principles", + "description": "A gazetteer constructed on ontological principles. The countries are actively maintained.", "domain": "environment", "download.obo": "http://purl.obolibrary.org/obo/gaz.obo", "download.owl": "http://purl.obolibrary.org/obo/gaz.owl", diff --git a/src/bioregistry/data/external/obofoundry/raw.yaml b/src/bioregistry/data/external/obofoundry/raw.yaml index 3cd5ca95e..f0e1ee047 100644 --- a/src/bioregistry/data/external/obofoundry/raw.yaml +++ b/src/bioregistry/data/external/obofoundry/raw.yaml @@ -8257,7 +8257,8 @@ ontologies: github: lschriml label: Lynn Schriml orcid: 0000-0001-8910-9851 - description: A gazetteer constructed on ontological principles + description: A gazetteer constructed on ontological principles. The countries are + actively maintained. domain: environment homepage: http://environmentontology.github.io/gaz/ id: gaz diff --git a/src/bioregistry/data/external/re3data/curation.tsv b/src/bioregistry/data/external/re3data/curation.tsv index 151754557..3c5233255 100644 --- a/src/bioregistry/data/external/re3data/curation.tsv +++ b/src/bioregistry/data/external/re3data/curation.tsv @@ -2820,7 +2820,7 @@ University of Nottingham researchers who have produced research data associated r3d100012410 QMU eData Repository https://eresearch.qmu.ac.uk/handle/20.500.12289/4 eData is a data repository where QMU researchers can store finished project data that, where appropriate, can be accessed and potentially re-used by other researchers. r3d100012411 St Andrews Research portal - Research Data https://risweb.st-andrews.ac.uk/portal/en/datasets/index.html The St Andrews research portal features the research activities within the University of St Andrews. r3d100012412 University of Strathclyde KnowledgeBase Datasets https://pureportal.strath.ac.uk/en/datasets/ The KnowledgeBase of the University of Strathclyde includes research data from the staff and students of the university. -r3d100012413 University of the Arts London Data Repository http://researchdata.arts.ac.uk/ "This Repository holds research data for all research projects where there is a need to store and share the supporting research. +r3d100012413 UAL Research Online https://ualresearchonline.arts.ac.uk/ "This Repository holds research data for all research projects where there is a need to store and share the supporting research. According to current Research Data Policy these records will include all data from projects funded by RCUK funders and in particular the AHRC." r3d100012414 UEL Research Repository https://repository.uel.ac.uk UEL Research Repository: the institutional repository of open access publications and research data at the University of East London. As a research archive, it preserves and disseminates scholarly work created by members of the University of East London. @@ -3461,7 +3461,8 @@ r3d100013142 Pyramids of the Steppe / Kazakhstan, Land of Seven Rivers http://re r3d100013143 Portable X-Ray fluorescence analysis of Late Bronze Age glass from Amarna http://repository.edition-topoi.org/collection/KBLT Cobalt was commonly used as a colourant in the Egyptian glass industries of the 18th dynasty, dark blue glass being a regular find at palatial and settlement sites, including Amarna and Malqata. The main source of cobalt ore used during this period has been identified in the Egyptian Western Desert, around the oases of Kharga and Dakhla. The data presented here was obtained in order to better understand the chaîne opératoire of Late Bronze Age glass production and -working, in particular with regard to cobalt ore. For this purpose, chemical analysis by portable X-Ray fluorescence (pXRF) was carried out in the field on contextualised archaeological material excavated at the site of Amarna, which cannot be exported from Egypt for analysis. In addition, glass and other vitreous materials from the same site, but without a more precise archaeological context, were analysed in the Egyptian Museum and Papyrus Collection, Berlin. The results of this study demonstrate how cobalt ore from various sub-sources was used in the known workshop sites at Amarna, resulting in a deeper understanding of raw materials use and exchange across this settlemen r3d100013144 The Uruk-Warka Survey http://repository.edition-topoi.org/collection/URUK "The small digitized archive comprises drawings and photos made by Hans J. Nissen, many of which were not included in the book, The Uruk Countryside. Most of the material consists of pottery, but other ceramic artifacts, stone and metal objects as well as inscribed bricks were also documented. All materials were recorded in the field. The goal of this website is to provide online access to this remaining archival documentation of the Uruk-Warka survey." -r3d100013148 Blackfynn Discover https://discover.blackfynn.com Blackfynn Discover is a repository for Neurology and Neuroscience datasets. This repository, funded by DARPA, the NIH, and others, provides a user-friendly solution for publishing large, complex datasets is a scalable and sustainable way. The platform aims to make data available in a meaningful way and to drive adoption of cloud-based analysis over large datasets. +r3d100013148 Pennsieve Discover https://discover.pennsieve.io/ "The Pennsieve platform is a cloud-based scientific data management platform focused on integrating complex datasets, fostering collaboration and publishing scientific data according to all FAIR principles of data sharing. +The platform is developed to enable individual labs, consortiums, or inter-institutional projects to manage, share and curate data in a secure cloud-based environment and to integrate complex metadata associated with scientific files into a high-quality interconnected data ecosystem. The platform is used as the backend for a number of public repositories including the NIH SPARC Portal and Pennsieve Discover repositories. It supports flexible metadata schemas and a large number of scientific file-formats and modalities." r3d100013152 Perdigao Field Experiment https://perdigao.fe.up.pt/ "Data repository of a meteorological experiment conducted in Perdigão, Portugal between December 15, 2016 to June 15, 2017. The Perdigao field project is part of a larger joint US/European multi-year program in Portugal. The project is partially funded by the European Union (EU) ERANET+ to provide the wind energy sector with more detailed resource mapping capabilities in the form of a new digital EU wind atlas. A major goal of the Perdigão field project is to quantify errors of wind resource models against a benchmark dataset collected in complex terrain. The US participation will complement this activity by identifying physical and numerical weaknesses of models and developing new knowledge and methods to overcome such deficiencies." r3d100013153 Australian Bureau of Meteorology data catalogue http://www.bom.gov.au/metadata/catalogue Meteorology, atmospheric science and oceanography, forecasts, current and historical observations for weather, water, space weather data; data analyses and reports. @@ -4464,3 +4465,4 @@ r3d100014251 Arias Montano https://rabida.uhu.es/dspace/ "Arias Montano, Institu In order to collect the data management plans of the research projects carried out by the research groups and centers of the University of Huelva, the collection ""Research data: complementary information"" was created in Arias Montano, Institutional Repository of Investigations https://rabida.uhu.es/dspace/handle/10272/14868" r3d100014252 SIPAM https://sipam.gov.pl/ "The main objective of the project is to digitize the data collected by the Maritime Administration and make it available for reuse by digitizing analog resources, integrating and harmonizing data and building a digital repository, and disseminating information about the resources collected in the system. The aim of the project is to make maritime administration data sets available on the Internet." +r3d100014253 Repository of the University of Life Sciences in Lublin https://repozytorium.up.lublin.pl/en The purpose of the Repository of the University of Life Sciences in Lublin is to disseminate the academic achievements of the University' employees and to promote research conducted at the University. The repository contains resources from various fields of life sciences. Only the community of the University is allowed to upload new records. diff --git a/src/bioregistry/data/external/re3data/processed.json b/src/bioregistry/data/external/re3data/processed.json index c73271223..e11fd6bf3 100644 --- a/src/bioregistry/data/external/re3data/processed.json +++ b/src/bioregistry/data/external/re3data/processed.json @@ -20569,9 +20569,12 @@ }, "r3d100012413": { "description": "This Repository holds research data for all research projects where there is a need to store and share the supporting research.\n\nAccording to current Research Data Policy these records will include all data from projects funded by RCUK funders and in particular the AHRC.", - "homepage": "http://researchdata.arts.ac.uk/", - "name": "University of the Arts London Data Repository", - "prefix": "r3d100012413" + "homepage": "https://ualresearchonline.arts.ac.uk/", + "name": "UAL Research Online", + "prefix": "r3d100012413", + "synonyms": [ + "University of the Arts London Data Repository" + ] }, "r3d100012414": { "description": "UEL Research Repository: the institutional repository of open access publications and research data at the University of East London. As a research archive, it preserves and disseminates scholarly work created by members of the University of East London.", @@ -25535,13 +25538,15 @@ } }, "r3d100013148": { - "description": "Blackfynn Discover is a repository for Neurology and Neuroscience datasets. This repository, funded by DARPA, the NIH, and others, provides a user-friendly solution for publishing large, complex datasets is a scalable and sustainable way. The platform aims to make data available in a meaningful way and to drive adoption of cloud-based analysis over large datasets.", - "homepage": "https://discover.blackfynn.com", - "name": "Blackfynn Discover", + "description": "The Pennsieve platform is a cloud-based scientific data management platform focused on integrating complex datasets, fostering collaboration and publishing scientific data according to all FAIR principles of data sharing.\nThe platform is developed to enable individual labs, consortiums, or inter-institutional projects to manage, share and curate data in a secure cloud-based environment and to integrate complex metadata associated with scientific files into a high-quality interconnected data ecosystem. The platform is used as the backend for a number of public repositories including the NIH SPARC Portal and Pennsieve Discover repositories. It supports flexible metadata schemas and a large number of scientific file-formats and modalities.", + "homepage": "https://discover.pennsieve.io/", + "name": "Pennsieve Discover", "prefix": "r3d100013148", + "synonyms": [ + "formerly: Blackfynn Discover" + ], "xrefs": { - "fairsharing": "FAIRsharing.PD1PEt", - "scr": "018068" + "scr": "021677" } }, "r3d100013152": { @@ -32328,5 +32333,15 @@ "Spatial Information System of the Maritime Administration", "System Informacji Przestrzennej Administracji Morskiej" ] + }, + "r3d100014253": { + "description": "The purpose of the Repository of the University of Life Sciences in Lublin is to disseminate the academic achievements of the University' employees and to promote research conducted at the University. The repository contains resources from various fields of life sciences. Only the community of the University is allowed to upload new records.", + "homepage": "https://repozytorium.up.lublin.pl/en", + "name": "Repository of the University of Life Sciences in Lublin", + "prefix": "r3d100014253", + "synonyms": [ + "Repozytorium Uniwersytetu Przyrodniczego w Lublinie", + "University of Life Sciences in Lublin Repository" + ] } } \ No newline at end of file