Genomic Feature and Variation Ontology

Last uploaded: June 30, 2020
Details
Acronym GFVO
Visibility Public
Description 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).
Status Production
Format OWL
Contact Joachim Baran, kim@codamono.com
Additional Metadata
URIhttp://www.biointerchange.org/gfvo#
bug Databasehttps://github.com/BioInterchange/Ontologies/issues
deprecatedfalse
endpoint
example Identifierhttp://www.biointerchange.org/gfvo#BaseQuality
ContributorsBegum Durgahee, Michel Dumontier, Joachim Baran, Francesco Strozzi, Raoul Bonnal, Karen Eilbeck, Toshiaki Katayama, Chris Mungall, Takatomo Fujisawa, Robert Hoehndorf, Erick Antezana
CreatorsJoachim Baran
has Formality Levelhttp://w3id.org/nkos/nkostype#ontology
Ontology Syntaxhttp://www.w3.org/ns/formats/RDF_XML
has Prior Versionhttp://data.agroportal.lirmm.fr/ontologies/GFVO/submissions/3
is Of Typehttp://omv.ontoware.org/2005/05/ontology#DomainOntology
known UsageGFVO is presented here for annotating and representing genomic feature and variation dataset contents.
Natural Language
notesBest 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.
ontology Related Tohttp://data.agroportal.lirmm.fr/ontologies/FALDO, http://data.agroportal.lirmm.fr/ontologies/SIO
preferred Namespace Prefixgfvo
Release date2014-06-22T18:03:02+02:00
repositoryhttps://github.com/BioInterchange/Ontologies
URI Lookup Endpointhttp://data.agroportal.lirmm.fr/search?ontologies=GFVO&require_exact_match=true&q=
used Ontology Engineering ToolOWL API
version1.0.2
Submissions
Views of GFVO

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Links
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FAIR Scores beta
Total score : 267.0 ( 55.0% ) details
Metrics
Classes 102
Individuals 0
Properties 33
Maximum depth 6
Maximum number of children 8
Average number of children 2
Classes with a single child 13
Classes with more than 25 children 0
Classes with no definition 0
Visits
includedInDataCatalog
Projects using GFVO

Agrisemantics Map of Data Standards

Agronomic Linked Data

Computational Biology Institute