Microsoft Word 2007
Durgahee, Bibi Sehnaaz Begum
KAUST DepartmentBio-Ontology Research Group (BORG)
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/552560
MetadataShow full item record
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.
CitationGFVO: the Genomic Feature and Variation Ontology 2015, 3:e933 PeerJ
PubMed Central IDPMC4435477
RelationsIs Supplemented By:
- Drug target ontology to classify and integrate drug discovery data.
- Authors: Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC
- Issue date: 2017 Nov 9
- DMTO: a realistic ontology for standard diabetes mellitus treatment.
- Authors: El-Sappagh S, Kwak D, Ali F, Kwak KS
- Issue date: 2018 Feb 6
- Genozip: a universal extensible genomic data compressor.
- Authors: Lan D, Tobler R, Souilmi Y, Llamas B
- Issue date: 2021 Aug 25
- Improving the Sequence Ontology terminology for genomic variant annotation.
- Authors: Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K
- Issue date: 2015
- EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
- Authors: Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P
- Issue date: 2013 May 15