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.
authors.affiliation: Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University , Stanford, CA , USA.
authors.forename: Joachim
authors.initials: J
authors.lastname: Baran
authors.affiliation: Department of Biomedical Informatics, School of Medicine, University of Utah , Salt Lake City, UT , USA.
authors.forename: Bibi Sehnaaz Begum
authors.initials: BS
authors.lastname: Durgahee
authors.affiliation: Department of Biomedical Informatics, School of Medicine, University of Utah , Salt Lake City, UT , USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Eilbeck
authors.affiliation: Department of Biology, Norwegian University of Science and Technology , Trondheim , Norway.
authors.forename: Erick
authors.initials: E
authors.lastname: Antezana
authors.affiliation: Computer, Electrical and Mathematical Sciences & Engineering Division and Computational Bioscience Research Center, King Abdullah University of Science and Technology , Thuwal , Kingdom of Saudi Arabia.
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.affiliation: Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University , Stanford, CA , USA.
authors.forename: Michel
authors.initials: M
authors.lastname: Dumontier
keywords: Bioinformatics; Genomics; Ontology