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    GFVO: the Genomic Feature and Variation Ontology

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    Type
    Article
    Authors
    Baran, Joachim
    Durgahee, Bibi Sehnaaz Begum
    Eilbeck, Karen
    Antezana, Erick
    Hoehndorf, Robert cc
    Dumontier, Michel
    KAUST Department
    Bio-Ontology Research Group (BORG)
    Computational Bioscience Research Center (CBRC)
    Computer Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Date
    2015-05-05
    Permanent link to this record
    http://hdl.handle.net/10754/552560
    
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    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.
    Citation
    GFVO: the Genomic Feature and Variation Ontology 2015, 3:e933 PeerJ
    Publisher
    PeerJ
    Journal
    PeerJ
    DOI
    10.7717/peerj.933
    PubMed ID
    26019997
    PubMed Central ID
    PMC4435477
    Additional Links
    https://peerj.com/articles/933
    Relations
    Is Supplemented By:
    • [Software]
      Title: BioInterchange/Ontologies: Bioinformatics related ontologies.. Publication Date: 2012-10-11. github: BioInterchange/Ontologies Handle: 10754/668070
    ae974a485f413a2113503eed53cd6c53
    10.7717/peerj.933
    Scopus Count
    Collections
    Articles; Bio-Ontology Research Group (BORG); Computer Science Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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