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Create RDF, TSV, and YAML exports (#70)
Closes #69
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| identifier name description resources author_names author_orcids | ||
| 0000001 "Resources mentioned in ""Sharing biological data: why, when, and how""" "These resources were listed in ""Sharing biological data: why, when, and how"", 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." biostudies|bmrb|cellimage|ega.dataset|ega.study|emdb|empiar|genbank|geo|idr|insdc.sra|massive|panorama|pdb|peptideatlas.dataset|pride|ssbd.dataset|ssbd.project Charles Tapley Hoyt 0000-0003-4423-4370 | ||
| 0000002 Semantic Web Context Resources used in the semantic web, based on https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml. ac|dcat|dcterms|dctypes|faldo|foaf|idot|oa|oboinowl|owl|prov|rdf|rdfs|void|xsd Charles Tapley Hoyt 0000-0003-4423-4370 |
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| '0000001': | ||
| authors: | ||
| - name: Charles Tapley Hoyt | ||
| orcid: 0000-0003-4423-4370 | ||
| description: 'These resources were listed in "Sharing biological data: why, when, | ||
| and how", 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.' | ||
| identifier: '0000001' | ||
| name: 'Resources mentioned in "Sharing biological data: why, when, and how"' | ||
| resources: | ||
| - biostudies | ||
| - bmrb | ||
| - cellimage | ||
| - ega.dataset | ||
| - ega.study | ||
| - emdb | ||
| - empiar | ||
| - genbank | ||
| - geo | ||
| - idr | ||
| - insdc.sra | ||
| - massive | ||
| - panorama | ||
| - pdb | ||
| - peptideatlas.dataset | ||
| - pride | ||
| - ssbd.dataset | ||
| - ssbd.project | ||
| '0000002': | ||
| authors: | ||
| - name: Charles Tapley Hoyt | ||
| orcid: 0000-0003-4423-4370 | ||
| contextName: semweb | ||
| description: Resources used in the semantic web, based on https://github.com/prefixcommons/biocontext/blob/master/registry/semweb_context.yaml. | ||
| identifier: '0000002' | ||
| name: Semantic Web Context | ||
| resources: | ||
| - ac | ||
| - dcat | ||
| - dcterms | ||
| - dctypes | ||
| - faldo | ||
| - foaf | ||
| - idot | ||
| - oa | ||
| - oboinowl | ||
| - owl | ||
| - prov | ||
| - rdf | ||
| - rdfs | ||
| - void | ||
| - xsd |
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| metaprefix name homepage description download example provider registry resolver provider_formatter resolver_formatter | ||
| biolink Biolink Model Registry https://raw.githubusercontent.com/biolink/biolink-model A modeling paradigm-specific registry of prefixes and their URL expansions https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml doi False True False | ||
| bioportal BioPortal Prefixes https://bioportal.bioontology.org/ The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry CHEBI True True False https://bioportal.bioontology.org/ontologies/$1 | ||
| bioregistry Bioregistry https://bioregistry.io The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database. https://bioregistry.io/api/registry/ chebi False True True https://bioregistry.io/registry/$1 https://bioregistry.io/$1:$2 | ||
| fairsharing FAIRSharing https://fairsharing.org/ A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. FAIRsharing.62qk8w True True False https://fairsharing.org/$1 | ||
| go Gene Ontology Registry http://geneontology.org/ A database-specific registry supporting curation in the Gene Ontology https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml CHEBI False True False | ||
| miriam Identifiers.org https://identifiers.org 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). https://registry.api.identifiers.org/resolutionApi/getResolverDataset chebi False True True https://registry.identifiers.org/registry/$1 https://identifiers.org/$1:$2 | ||
| n2t Name-to-Thing https://n2t.net An ARK resolver as well as resolver built with common prefxies as in Identifiers.org https://n2t.net/e/cdl_ebi_prefixes.yaml chebi False True True https://n2t.net/$1:$2 | ||
| ncbi National Center for Biotechnology Information Registry https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ A database-specific registry supporting curation in the NCBI GenBank and related NCBI resources ECOCYC False True False | ||
| obofoundry OBO Foundry http://www.obofoundry.org/ The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. http://www.obofoundry.org/registry/ontologies.yml chebi False True False http://www.obofoundry.org/ontology/$1 | ||
| ols Ontology Lookup Service https://www.ebi.ac.uk/ols 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. chebi True True False https://www.ebi.ac.uk/ols/ontologies/$1 | ||
| prefixcommons Prefix Commons https://prefixcommons.org A registry of commonly used prefixes in the life sciences and linked data https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/commons_context.jsonld CHEBI False True False | ||
| uniprot.database UniProt Cross-ref database https://www.uniprot.org/database/ The cross-references section of UniProtKB entries displays explicit and implicit links to databases such as nucleotide sequence databases, model organism databases and genomics and proteomics resources. https://www.uniprot.org/database/?format=rdf 0174 False True False https://www.uniprot.org/database/DB-$1 | ||
| wikidata Wikidata Property https://www.wikidata.org An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries. P683 True True False https://www.wikidata.org/wiki/Property:$1 |
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|---|---|---|
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| biolink: | ||
| description: A modeling paradigm-specific registry of prefixes and their URL expansions | ||
| download: https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml | ||
| example: doi | ||
| homepage: https://raw.githubusercontent.com/biolink/biolink-model | ||
| name: Biolink Model Registry | ||
| prefix: biolink | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| bioportal: | ||
| description: The BioPortal is a less stringent registry of biomedical ontologies | ||
| than the OBO Foundry | ||
| example: CHEBI | ||
| formatter: https://bioportal.bioontology.org/ontologies/$1 | ||
| homepage: https://bioportal.bioontology.org/ | ||
| name: BioPortal Prefixes | ||
| prefix: bioportal | ||
| provider: true | ||
| registry: true | ||
| resolver: false | ||
| bioregistry: | ||
| description: The Bioregistry is integrative meta-registry of biological databases, | ||
| ontologies, and nomenclatures that is backed by an open database. | ||
| download: https://bioregistry.io/api/registry/ | ||
| example: chebi | ||
| formatter: https://bioregistry.io/registry/$1 | ||
| homepage: https://bioregistry.io | ||
| name: Bioregistry | ||
| prefix: bioregistry | ||
| provider: false | ||
| registry: true | ||
| resolver: true | ||
| resolver_url: https://bioregistry.io/$1:$2 | ||
| fairsharing: | ||
| description: A curated, informative and educational resource on data and metadata | ||
| standards, inter-related to databases and data policies. | ||
| example: FAIRsharing.62qk8w | ||
| formatter: https://fairsharing.org/$1 | ||
| homepage: https://fairsharing.org/ | ||
| name: FAIRSharing | ||
| prefix: fairsharing | ||
| provider: true | ||
| registry: true | ||
| resolver: false | ||
| go: | ||
| description: A database-specific registry supporting curation in the Gene Ontology | ||
| download: https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml | ||
| example: CHEBI | ||
| homepage: http://geneontology.org/ | ||
| name: Gene Ontology Registry | ||
| prefix: go | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| miriam: | ||
| description: 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). | ||
| download: https://registry.api.identifiers.org/resolutionApi/getResolverDataset | ||
| example: chebi | ||
| formatter: https://registry.identifiers.org/registry/$1 | ||
| homepage: https://identifiers.org | ||
| name: Identifiers.org | ||
| prefix: miriam | ||
| provider: false | ||
| registry: true | ||
| resolver: true | ||
| resolver_url: https://identifiers.org/$1:$2 | ||
| n2t: | ||
| description: An ARK resolver as well as resolver built with common prefxies as in | ||
| Identifiers.org | ||
| download: https://n2t.net/e/cdl_ebi_prefixes.yaml | ||
| example: chebi | ||
| homepage: https://n2t.net | ||
| name: Name-to-Thing | ||
| prefix: n2t | ||
| provider: false | ||
| registry: true | ||
| resolver: true | ||
| resolver_url: https://n2t.net/$1:$2 | ||
| ncbi: | ||
| description: A database-specific registry supporting curation in the NCBI GenBank | ||
| and related NCBI resources | ||
| example: ECOCYC | ||
| homepage: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/ | ||
| name: National Center for Biotechnology Information Registry | ||
| prefix: ncbi | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| obofoundry: | ||
| description: The mission of the OBO Foundry is to develop a family of interoperable | ||
| ontologies that are both logically well-formed and scientifically accurate. | ||
| download: http://www.obofoundry.org/registry/ontologies.yml | ||
| example: chebi | ||
| formatter: http://www.obofoundry.org/ontology/$1 | ||
| homepage: http://www.obofoundry.org/ | ||
| name: OBO Foundry | ||
| prefix: obofoundry | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| ols: | ||
| description: '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. ' | ||
| example: chebi | ||
| formatter: https://www.ebi.ac.uk/ols/ontologies/$1 | ||
| homepage: https://www.ebi.ac.uk/ols | ||
| name: Ontology Lookup Service | ||
| prefix: ols | ||
| provider: true | ||
| registry: true | ||
| resolver: false | ||
| prefixcommons: | ||
| description: A registry of commonly used prefixes in the life sciences and linked | ||
| data | ||
| download: https://raw.githubusercontent.com/prefixcommons/biocontext/master/registry/commons_context.jsonld | ||
| example: CHEBI | ||
| homepage: https://prefixcommons.org | ||
| name: Prefix Commons | ||
| prefix: prefixcommons | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| uniprot.database: | ||
| description: 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. | ||
| download: https://www.uniprot.org/database/?format=rdf | ||
| example: '0174' | ||
| formatter: https://www.uniprot.org/database/DB-$1 | ||
| homepage: https://www.uniprot.org/database/ | ||
| name: UniProt Cross-ref database | ||
| prefix: uniprot.database | ||
| provider: false | ||
| registry: true | ||
| resolver: false | ||
| wikidata: | ||
| description: An open, community-curated knowledgebase that contains several properties | ||
| corresponding to resources listed in other biomedical registries. | ||
| example: P683 | ||
| formatter: https://www.wikidata.org/wiki/Property:$1 | ||
| homepage: https://www.wikidata.org | ||
| name: Wikidata Property | ||
| prefix: wikidata | ||
| provider: true | ||
| registry: true | ||
| resolver: false |
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