aberowl: contact: ali.syed@kaust.edu.sa description: 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. download: http://aber-owl.net/api/ontology/?format=json example: CHEBI homepage: http://aber-owl.net name: AberOWL prefix: aberowl provider_uri_format: http://aber-owl.net/ontology/$1 resolver_type: lookup resolver_uri_format: http://aber-owl.net/ontology/$1/#/Browse/ agroportal: description: A vocabulary and ontology repository for agronomy and related domains. example: ENVO homepage: http://agroportal.lirmm.fr name: AgroPortal prefix: agroportal provider_uri_format: http://agroportal.lirmm.fr/ontologies/$1 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://github.com/biolink/biolink-model name: Biolink Model Registry prefix: biolink bioportal: description: The BioPortal is a less stringent registry of biomedical ontologies than the OBO Foundry example: CHEBI homepage: https://bioportal.bioontology.org/ name: BioPortal Prefixes prefix: bioportal provider_uri_format: https://bioportal.bioontology.org/ontologies/$1 bioregistry: contact: cthoyt@gmail.com 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 homepage: https://bioregistry.io name: Bioregistry prefix: bioregistry provider_uri_format: https://bioregistry.io/registry/$1 resolver_type: resolver resolver_uri_format: https://bioregistry.io/$1:$2 cellosaurus: contact: Amos.Bairoch@sib.swiss description: The set of prefixes used in the Cellosaurus resource example: 4DN homepage: https://web.expasy.org/cellosaurus/ name: Cellosaurus Registry prefix: cellosaurus cropoct: contact: helpdesk@cropontology-curationtool.org description: 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 download: https://github.com/bioversity/Crop-Ontology/blob/master/public/dump.json example: CO_010 homepage: https://www.cropontology.org name: Crop Ontology Curation Tool prefix: cropoct provider_uri_format: https://www.cropontology.org/ontology/$1 ecoportal: description: The LifeWatch ERIC repository of semantic resources for the ecological domain. example: ALIENSPECIES homepage: http://ecoportal.lifewatchitaly.eu name: EcoPortal prefix: ecoportal provider_uri_format: http://ecoportal.lifewatchitaly.eu/ontologies/$1 fairsharing: description: A curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies. example: FAIRsharing.62qk8w homepage: https://fairsharing.org/ name: FAIRSharing prefix: fairsharing provider_uri_format: https://fairsharing.org/$1 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 miriam: contact: hhe@ebi.ac.uk 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 homepage: https://identifiers.org name: Identifiers.org prefix: miriam provider_uri_format: https://registry.identifiers.org/registry/$1 resolver_type: resolver resolver_uri_format: https://identifiers.org/$1:$2 n2t: contact: cdl@www.cdlib.org description: An ARK resolver as well as resolver built with common prefixes as in Identifiers.org download: https://n2t.net/e/n2t_full_prefixes.yaml example: chebi homepage: https://n2t.net name: Name-to-Thing prefix: n2t provider_uri_format: 'https://n2t.net/$1:' resolver_type: resolver resolver_uri_format: 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 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 homepage: http://www.obofoundry.org/ name: OBO Foundry prefix: obofoundry provider_uri_format: http://www.obofoundry.org/ontology/$1 resolver_type: resolver resolver_uri_format: http://purl.obolibrary.org/obo/$1_$2 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 homepage: https://www.ebi.ac.uk/ols name: Ontology Lookup Service prefix: ols provider_uri_format: https://www.ebi.ac.uk/ols/ontologies/$1 ontobee: description: ' Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.' example: AGRO homepage: http://www.ontobee.org/ name: OntoBee prefix: ontobee provider_uri_format: http://www.ontobee.org/ontology/$1 resolver_type: lookup resolver_uri_format: http://www.ontobee.org/ontology/$1?iri=http://purl.obolibrary.org/obo/$1_$2 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_uri_format: https://prefixcommons.org/?q=$1 scholia: contact: faan@dtu.dk description: A frontend to Wikidata example: doi homepage: https://scholia.toolforge.org/ name: Scholia prefix: scholia resolver_type: lookup resolver_uri_format: https://scholia.toolforge.org/$1/$2 uniprot: 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' homepage: https://www.uniprot.org/database/ name: UniProt Cross-ref database prefix: uniprot provider_uri_format: https://www.uniprot.org/database/DB-$1 wikidata: description: An open, community-curated knowledgebase that contains several properties corresponding to resources listed in other biomedical registries. example: P683 homepage: https://www.wikidata.org name: Wikidata Property prefix: wikidata provider_uri_format: https://www.wikidata.org/wiki/Property:$1