GFVO: the Genomic Feature and Variation Ontology

Abstract

Falling costs in genomic laboratory experiments have led to a steady increaseof genomic feature and variation data. Multiple genomic data formats exist forsharing these data, and whilst they are similar, they are addressing slightly differentdata viewpoints and are consequently not fully compatible with each other. Thefragmentation of data format specifications makes it hard to integrate and interpretdata for further analysis with information from multiple data providers. As asolution, a new ontology is presented here for annotating and representing genomicfeature 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 andenables linking of genomic annotations across datasets through common semanticsof genomic types and relations.Availability and implementation.The latest stable release of the ontology isavailable via its base URI; previous and development versions are available at theontology’s GitHub repository: https://github.com/BioInterchange/Ontologies;versions of the ontology are indexed through BioPortal (without externalclass-/property-equivalences due to BioPortal release 4.10 limitations); examplesand reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under theCC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0)and thereforede factowithin the public domain; the ontology can be appropriatedwithout attribution for commercial and non-commercial use.