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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.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { "@value": "CIViC Molecular Profile" }, "http://www.w3.org/2004/02/skos/core#exactMatch": { "@id": "https://registry.identifiers.org/registry/civic.mpid" }, "http://xmlns.com/foaf/0.1/homepage": { "@id": "https://civicdb.org/" }, "https://bioregistry.io/schema/#0000005": "559", "https://bioregistry.io/schema/#0000006": "https://civicdb.org/links/molecular_profile/$1", "https://bioregistry.io/schema/#0000008": "^[0-9]+$", "https://bioregistry.io/schema/#0000012": false, "https://bioregistry.io/schema/#0000019": { "@id": "https://orcid.org/0000-0002-6388-446X" }, "https://bioregistry.io/schema/#0000023": { "@value": "civic.molecularprofile" }, "https://bioregistry.io/schema/#0000024": "https://civicdb.org/links/molecular_profile/", "https://bioregistry.io/schema/#0000027": { "@id": "https://civicdb.org/links/molecular_profile/559" }, "https://bioregistry.io/schema/#0000029": { "@value": "civic.mpid" } }, { "@id": "https://fairsharing.org/FAIRsharing.zx2ztd", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/fairsharing" } }, { "@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": "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 download URL" }, "http://www.w3.org/2000/01/rdf-schema#range": { "@id": "http://www.w3.org/2001/XMLSchema#string" } }, { "@id": "https://bioregistry.io/registry/ncbi.assembly", "@type": "https://bioregistry.io/schema/#0000001", "http://purl.org/dc/terms/description": "A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/bioregistry" }, "http://www.w3.org/2000/01/rdf-schema#label": { "@value": "Assembly" }, "http://www.w3.org/2004/02/skos/core#exactMatch": [ { "@id": "https://registry.identifiers.org/registry/assembly" }, { "@id": "https://bioregistry.io/metaregistry/biocontext/NCBIAssembly" }, { "@id": "https://www.re3data.org/repository/r3d100012688" } ], "http://xmlns.com/foaf/0.1/homepage": { "@id": "https://www.ncbi.nlm.nih.gov/" }, "https://bioregistry.io/schema/#0000005": "GCF_000005845.2", "https://bioregistry.io/schema/#0000006": "https://www.ncbi.nlm.nih.gov/datasets/genome/$1", "https://bioregistry.io/schema/#0000008": "^[a-zA-Z0-9_\\.]+$", "https://bioregistry.io/schema/#0000012": false, "https://bioregistry.io/schema/#0000024": "https://www.ncbi.nlm.nih.gov/datasets/genome/", "https://bioregistry.io/schema/#0000027": { "@id": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2" }, "https://bioregistry.io/schema/#0000029": { "@value": "ncbi.assembly" } }, { "@id": "https://bioregistry.io/metaregistry/n2t/resolve/gxa.gene", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/n2t" } }, { "@id": "https://registry.identifiers.org/registry/paleodb", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/miriam" } }, { "@id": "https://bioregistry.io/metaregistry/n2t/resolve/greengenes", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/n2t" } }, { "@id": "https://orcid.org/0000-0002-8374-1941", "http://www.w3.org/2000/01/rdf-schema#label": { "@value": "Miguel A. 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\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. 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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). 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/ecocyc" }, { "@id": "https://bioregistry.io/registry/wormbase" }, { "@id": "https://bioregistry.io/registry/agrkb" }, { "@id": "https://bioregistry.io/registry/pharmgkb.disease" }, { "@id": "https://bioregistry.io/registry/flybase" }, { "@id": "https://bioregistry.io/registry/pombase" }, { "@id": "https://bioregistry.io/registry/civic.gid" }, { "@id": "https://bioregistry.io/registry/chebi" }, { "@id": "https://bioregistry.io/registry/civic.vid" }, { "@id": "https://bioregistry.io/registry/go" }, { "@id": "https://bioregistry.io/registry/chembl" }, { "@id": "https://bioregistry.io/registry/interpro" }, { "@id": "https://bioregistry.io/registry/ena.embl" }, { "@id": "https://bioregistry.io/registry/ucsc" }, { "@id": "https://bioregistry.io/registry/civic.aid" }, { "@id": "https://bioregistry.io/registry/ensembl" }, { "@id": "https://bioregistry.io/registry/gnomad" }, { "@id": "https://bioregistry.io/registry/zfin" }, { "@id": "https://bioregistry.io/registry/civic.eid" }, { "@id": "https://bioregistry.io/registry/panther.node" }, { "@id": "https://bioregistry.io/registry/brenda" }, { "@id": "https://bioregistry.io/registry/panther.family" }, { "@id": "https://bioregistry.io/registry/civic.tid" }, { "@id": "https://bioregistry.io/registry/eupath" }, { "@id": "https://bioregistry.io/registry/rgd" }, { "@id": "https://bioregistry.io/registry/uniprot" }, { "@id": "https://bioregistry.io/registry/bacdive" }, { "@id": "https://bioregistry.io/registry/pharmgkb.pathways" }, { "@id": "https://bioregistry.io/registry/sgd" }, { "@id": "https://bioregistry.io/registry/civic.sid" }, { "@id": "https://bioregistry.io/registry/panther.pathway" }, { "@id": "https://bioregistry.io/registry/pdb" }, { "@id": "https://bioregistry.io/registry/brenda.ligandgroup" }, { "@id": "https://bioregistry.io/registry/reactome" }, { "@id": "https://bioregistry.io/registry/hgnc" }, { "@id": "https://bioregistry.io/registry/orphanet.ordo" }, { "@id": "https://bioregistry.io/registry/orphanet" }, { "@id": "https://bioregistry.io/registry/rhea" }, { "@id": "https://bioregistry.io/registry/px" }, { "@id": "https://bioregistry.io/registry/bto" }, { "@id": "https://bioregistry.io/registry/mgi" }, { "@id": "https://bioregistry.io/registry/gbif" }, { "@id": "https://bioregistry.io/registry/civic.did" }, { "@id": "https://bioregistry.io/registry/pmc" }, { "@id": "https://bioregistry.io/registry/pharmgkb.gene" }, { "@id": "https://bioregistry.io/registry/brenda.ligand" }, { "@id": "https://bioregistry.io/registry/panther.pthcmp" }, { "@id": "https://bioregistry.io/registry/pharmgkb.drug" } ], "http://www.w3.org/2000/01/rdf-schema#label": { "@value": "Global Biodata Coalition - Global Core Biodata Resources" } }, { "@id": "https://orcid.org/0000-0001-9625-1899", "http://www.w3.org/2000/01/rdf-schema#label": { "@value": "Bill Duncan" }, "http://xmlns.com/foaf/0.1/mbox": { "@value": "wdduncan@gmail.com" } }, { "@id": "https://bioregistry.io/metaregistry/biocontext/ASPGD.PROTEIN", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/biocontext" } }, { "@id": "https://bioregistry.io/metaregistry/biocontext/IPI", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/biocontext" } }, { "@id": "https://registry.identifiers.org/registry/bugbase.protocol", "http://purl.org/dc/terms/isPartOf": { "@id": "https://bioregistry.io/metaregistry/miriam" } }, { "@id": "https://bioregistry.io/registry/aspgd.locus", "@type": "https://bioregistry.io/schema/#0000001", "http://purl.org/dc/terms/description": "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. 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