Show simple item record

dc.contributor.authorBaran, Joachim
dc.contributor.authorDurgahee, Bibi Sehnaaz Begum
dc.contributor.authorEilbeck, Karen
dc.contributor.authorAntezana, Erick
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorDumontier, Michel
dc.date.accessioned2015-05-10T14:35:30Z
dc.date.available2015-05-10T14:35:30Z
dc.date.issued2015-05-05
dc.identifier.citationGFVO: the Genomic Feature and Variation Ontology 2015, 3:e933 PeerJ
dc.identifier.issn2167-8359
dc.identifier.pmid26019997
dc.identifier.doi10.7717/peerj.933
dc.identifier.urihttp://hdl.handle.net/10754/552560
dc.description.abstractFalling 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.
dc.publisherPeerJ
dc.relation.urlhttps://peerj.com/articles/933
dc.rightsThis is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
dc.subjectBioinformatics
dc.subjectGenomics
dc.subjectOntology
dc.titleGFVO: the Genomic Feature and Variation Ontology
dc.typeArticle
dc.contributor.departmentBio-Ontology Research Group (BORG)
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalPeerJ
dc.identifier.pmcidPMC4435477
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionStanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford, CA, USA
dc.contributor.institutionDepartment of Biomedical Informatics, School of Medicine, University of Utah, Salt Lake City, UT, USA
dc.contributor.institutionDepartment of Biomedical Informatics, School of Medicine, University of Utah, Salt Lake City, UT, USA
dc.contributor.institutionDepartment of Biology, Norwegian University of Science and Technology, Trondheim, Norway
dc.contributor.institutionStanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, Stanford, CA, USA
kaust.personHoehndorf, Robert
refterms.dateFOA2018-06-14T07:35:26Z


Files in this item

Thumbnail
Name:
peerj-933.pdf
Size:
575.8Kb
Format:
PDF
Description:
Main article
Thumbnail
Name:
GFVO_resubmission_2_supp.docx
Size:
517.2Kb
Format:
Microsoft Word 2007
Description:
Supplemental files
Thumbnail
Name:
Table_S1.xlsx
Size:
485.3Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files
Thumbnail
Name:
Table_S2.xlsx
Size:
480.5Kb
Format:
Microsoft Excel 2007
Description:
Supplemental files

This item appears in the following Collection(s)

Show simple item record