{"doi":"10.7717/peerj.933","title":"GFVO: the Genomic Feature and Variation Ontology","abstract":"Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology's GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.","journal":"PeerJ","year":2015,"id":2970,"datarank":0.42106900098744415,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.12918247862914714,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.12918247862914714,"corpus_percentile":50.040683482506104,"corpus_rank":615,"citation_count":6,"citer_count":3,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6172,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-05-05","fair_score":61.25,"fair_percentile":92.70008795074759,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":33139,"name":"Bibi Sehnaaz Begum Durgahee","orcid":null,"position":1,"is_corresponding":false},{"id":4104,"name":"Karen Eilbeck","orcid":"0000-0002-0831-6427","position":2,"is_corresponding":false},{"id":19085,"name":"Erick Antezana","orcid":"0000-0002-2497-8236","position":3,"is_corresponding":false},{"id":12963,"name":"Robert Hoehndorf","orcid":"0000-0001-8149-5890","position":4,"is_corresponding":false},{"id":74,"name":"Michel J. Dumontier","orcid":"0000-0003-4727-9435","position":5,"is_corresponding":false},{"id":19089,"name":"Joachim Baran","orcid":null,"position":0,"is_corresponding":true}],"reference_count":36,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"26019997","pmcid":"PMC4435477","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":80.0,"fair_i":50.0,"fair_r":50.0,"fair_zscore":1.4508,"fair_rationale":{"fair_score":61.25,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper does not explicitly provide rich machine-readable metadata for itself beyond standard bibliographic details, though the ontology is available in RDF/XML."}]},"A":{"name":"Accessible","score":80.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"The paper clearly states the ontology's base URI, GitHub repository, BioPortal index, and a separate documentation webpage, providing a complete access protocol."}]},"I":{"name":"Interoperable","score":50.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":1.0,"signal":null,"rationale":"The ontology uses standard formats (OWL, RDF/XML), aligns with established ontologies (SIO, SO), and employs standard identifiers (URIs, DOIs)."}]},"R":{"name":"Reusable","score":50.0,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.833,"signal":null,"rationale":"The ontology is publicly available under a CC0 license, with clear access instructions and documentation, but the paper lacks a formal data-availability statement for the ontology itself and does not fully detail reproducibility of the paper's analysis."}]}},"suggestions":["Include a formal data-availability statement in the paper that explicitly states the ontology is available and under which license.","Add machine-readable metadata (e.g., schema.org annotations) to the paper's HTML version to improve findability.","Provide a persistent identifier (e.g., DOI) for the ontology version used in the paper.","Include a reproducibility section that describes how to recreate the ontology from the specification or how to verify the examples.","Document the exact version of the ontology used in the paper and link to a specific release on GitHub."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:52:16.829011Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}