URI*
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http://www.biointerchange.org/gfvo#
http://www.biointerchange.org/gfvo#
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Bug database
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https://github.com/BioInterchange/Ontologies/issues
https://github.com/BioInterchange/Ontologies/issues
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Contact*
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Joachim Baran (kim@codamono.com)
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Submission date
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June 30, 2020
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Deprecated
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false
See more...
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Description*
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The Genomic Feature and Variation Ontology (GFVO) is modeled to represent genomic data using the Resource Description Format (RDF). It is captures the contents of data files that adhere to the Generic Feature Format Version 3 (GFF3, http://www.sequenceontology.org/resources/gff3.html), the General Transfer Format (GTF, http://mblab.wustl.edu/GTF22.html), the Genome Variation Format Version 1 (GVF, http://www.sequenceontology.org/resources/gvf.html), and the Variant Call Format (VCF, http://vcftools.sourceforge.net/specs.html). The creation of the ontology was inspired by previous work of Robert Hoehndorf on RDF2OWL (http://code.google.com/p/rdf2owl).
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Documentation
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https://github.com/BioInterchange/Ontologies
https://github.com/BioInterchange/Ontologies
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Example of resource
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http://www.biointerchange.org/gfvo#BaseQuality
See more...
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Contributor
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Michel Dumontier Christopher Mungall Francesco Strozzi Joachim Baran Raoul J. P. Bonnal Robert Hoehndorf Takatomo Fujisawa Toshiaki Katayama Begum Durgahee Karen Eilbeck Erick Antezana |
Creator
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Joachim Baran |
Formality level
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http://w3id.org/nkos/nkostype#ontology
http://w3id.org/nkos/nkostype#ontology
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Representation language*
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OWL
See more...
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Syntax
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http://www.w3.org/ns/formats/RDF_XML
http://www.w3.org/ns/formats/RDF_XML
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Prior version
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|
Homepage
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https://github.com/BioInterchange/Ontologies
https://github.com/BioInterchange/Ontologies
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Other identifier
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https://doi.org/10.7717/peerj.933
https://doi.org/10.7717/peerj.933
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Indexed or included in catalog or repository
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http://aber-owl.net/ontology/GFVO
http://aber-owl.net/ontology/GFVO
http://bioportal.bioontology.org/ontologies/GFVO
http://bioportal.bioontology.org/ontologies/GFVO
https://agroportal.lirmm.fr/
agroportal.lirmm.fr
https://vest.agrisemantics.org/content/genomic-feature-and-variation-ontology
https://vest.agrisemantics.org/content/genomic-feature-and-variation-ontology
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Generic type
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http://omv.ontoware.org/2005/05/ontology#DomainOntology
http://omv.ontoware.org/2005/05/ontology#DomainOntology
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Known usage
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GFVO is presented here for annotating and representing genomic feature and variation dataset contents.
See more...
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Natural language
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Notes
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Best Practices
1.) The class hierarchy, object- and datatype-property hierarchies are modeled to match SIO's hierarchies.
2.) Every class and property has a label (rdfs:label) as well as a description (rdfs:comment). The description may contain an example of how a class/property is being applied.
3.) Classes that are directly related to either GFF3, GTF, GVF or VCF specification have a link-out to the specification's document as provenance indicator (via rdfs:isDefinedBy).
4.) Link-outs to Wikipedia are provided for classes whereever possible.
5.) Ontology terms are encoded in the URIs using camel case, i.e. letters following a white space in an ontology term are capitalized followed by the removal of the white space.
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Generally related to or relies on
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Preferred namespace prefix
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gfvo
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Creation date*
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June 22, 2014
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Repository
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https://github.com/BioInterchange/Ontologies
https://github.com/BioInterchange/Ontologies
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Status*
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production
See more...
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URI Lookup Endpoint
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http://agroportal.lirmm.fr/search?ontologies=GFVO&require_exact_match=true&q=
search?ontologies=GFVO&require_exact_match=true&q=
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Created with
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OWL API
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Version information
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1.0.2
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