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| 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 |
| Home Page | https://github.com/BioInterchange/Ontologies |
| Publications Page | https://doi.org/10.7717/peerj.933 |
| Documentation Page | |
| Categories | |
| Groups | Rice Data Interoperability working group |
Additional Metadata
| URI | http://www.biointerchange.org/gfvo# |
|---|---|
| Natural Language | |
| Release date | 2014-06-22T18:03:02+02:00 |
| known Usage | GFVO is presented here for annotating and representing genomic feature and variation dataset contents. |
| 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. |
| Contributors | Begum Durgahee, Michel Dumontier, Joachim Baran, Francesco Strozzi, Raoul Bonnal, Karen Eilbeck, Toshiaki Katayama, Chris Mungall, Takatomo Fujisawa, Robert Hoehndorf, Erick Antezana |
| Creators | Joachim Baran |
| has Formality Level | http://w3id.org/nkos/nkostype#ontology |
| has License | CC0 [https://creativecommons.org/publicdomain/zero/1.0/]. |
| is Of Type | http://omv.ontoware.org/2005/05/ontology#DomainOntology |
| used Ontology Engineering Tool | OWL API |
| has Prior Version | GFVO/submissions/3 |
| deprecated | false |
| ontology Related To | FALDO, SIO |
| identifier | http://www.biointerchange.org/gfvo# |
| endpoint |  |
| URI Lookup Endpoint | http://data.agroportal.lirmm.fr/search?ontologies=GFVO&require_exact_match=true&q= |
| bug Database | https://github.com/BioInterchange/Ontologies/issues |
| example Identifier | http://www.biointerchange.org/gfvo#BaseQuality |
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Submissions
| Submission | Release Date | Upload Date | Downloads |
|---|---|---|---|
| unknown (Parsed, Indexed, Metrics, Annotator) | 06/22/2014 | 06/30/2020 | OWL | CSV | RDF/XML |
| 1.0.6 (Archived) | 10/18/2016 | 10/18/2016 | OWL |
| 1.0.5 (Archived) | 05/30/2016 | 05/30/2016 | OWL |
| 1.0.3 (Archived) | 06/22/2014 | 06/23/2015 | OWL |
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Projects Using This Ontology Create new project
| Project | Description | People | Institution |
|---|---|---|---|
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Agrisemantics Map of Data Standards
|
This Agrisemantics (previously called VEST-AgroPortal) Map of...
This Agrisemantics (previously called VEST-AgroPortal) Map of Data Standards provides a global map of existing vocabularies for the exchange of data in the field of food and agriculture. The directory is the result of the merging of records from two different sources: the VEST Registry (a registry of vocabularies of all types and all formats) and the AgroPortal (a repository of ontologies).
|
Valeria Pesce (valeria.pesce@fao.org)
Valeria Pesce (valeria.pesce@fao.org)
|
Food & Agriculture Organization |
|
Agronomic Linked Data
|
AgroLD is a RDF knowledge base that consists of data integrated...
AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. The aim of the Agronomic Linked Data (AgroLD) project is to provide a portal for bioinformatics and domain experts to exploit the homogenized data models towards efficiently generating research hypotheses.
|
Pierre Larmande (pierre.larmande@ird.fr)
Pierre Larmande (pierre.larmande@ird.fr)
|
IRD |
|
Computational Biology Institute
|
Modeling, processing and analysis of large scale data in biology, health, agronomy and environment.
Modeling, processing and analysis of large scale data in biology, health, agronomy and environment.
|
Pierre Larmande (pierre.larmande@ird.fr)
Pierre Larmande (pierre.larmande@ird.fr)
|
University of Montpellier, CNRS, CIRAD, INRIA, IRD, INRAE, SupAgro, INSERM |
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