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Type
ArticleAuthors
Baran, JoachimDurgahee, Bibi Sehnaaz Begum
Eilbeck, Karen
Antezana, Erick
Hoehndorf, Robert

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
2015-05-05Permanent link to this record
http://hdl.handle.net/10754/552560
Metadata
Show full item recordAbstract
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 PeerJPublisher
PeerJJournal
PeerJPubMed ID
26019997PubMed Central ID
PMC4435477Additional Links
https://peerj.com/articles/933Relations
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
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