ontologies
GFVO
Genomic Feature and Variation Ontology (GFVO)
OWL
No license
Last submission date June 30, 2020
Summary
Classes
Properties
Instances
Notes
Mappings
Widgets
Sparql

General information

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). See more...
Initial created on June 22, 2014. For additional information, contact Joachim Baran (kim@codamono.com).

Languages

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FAIR score
Beta

Total score : 269.0 ( 56.0%)
See details

Ontology relations network

Submissions

Metrics

Identifiers

URI

http://www.biointerchange.org/gfvo#
http://www.biointerchange.org/gfvo#

Other identifier

https://doi.org/10.7717/peerj.933
https://doi.org/10.7717/peerj.933

Dates

Creation date

June 22, 2014

Submission date

June 30, 2020

Persons and organizations

Contact

Joachim Baran

Creator

Joachim Baran

Contributor

Joachim Baran
Francesco Strozzi
Robert Hoehndorf
Karen Eilbeck
Toshiaki Katayama
Raoul J. P. Bonnal
Michel Dumontier
Begum Durgahee
Christopher Mungall
Takatomo Fujisawa
Erick Antezana

Other links

Projects and usage information

Projects using GFVO

Agrisemantics Map of Data Standards
Agronomic Linked Data
Computational Biology Institute

Known usage

GFVO is presented here for annotating and representing genomic feature and variation dataset contents.

Methodology and provenance

Created with

OWL API

Community

Repository

https://github.com/BioInterchange/Ontologies
https://github.com/BioInterchange/Ontologies

Bug database

https://github.com/BioInterchange/Ontologies/issues
https://github.com/BioInterchange/Ontologies/issues

Notes

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.

Content

Preferred namespace prefix

gfvo

Example of resource

http://www.biointerchange.org/gfvo#BaseQuality
http://www.biointerchange.org/gfvo#BaseQuality

Visits

Views of GFVO

No views available for GFVO.