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El Vira specifications

Information


Unique identifier OMICS_26522
Name El Vira
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An ontology.
Input format OWL
Output format OWL EL,RL,QL
Operating system Unix/Linux
Programming languages Groovy
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Robert Hoehndorf

Publication for El Vira

El Vira citations

 (3)
library_books

An ontology approach to comparative phenomics in plants

2015
Plant Methods
PMCID: 4359497
PMID: 25774204
DOI: 10.1186/s13007-015-0053-y

[…] We downloaded all the ontologies from the OBO Foundry [,] or their respective download site (see Table ), and used El Vira (version 0.2) [] to transform ontologies from an OWL DL profile into an OWL EL profile. The application of OWL EL files facilitates faster reasoning over the combined ontologies and is consist […]

library_books

Integrating systems biology models and biomedical ontologies

2011
BMC Syst Biol
PMCID: 3170340
PMID: 21835028
DOI: 10.1186/1752-0509-5-124

[…] tial quantifier in the formalization of process- and function-based annotations and we import only ontologies (including our upper-level ontology) that we converted into the OWL EL fragment using the EL Vira software []. Investigating alternative formalizations of the constraints employed in the SBML Harvester to improve query performance and expressiveness is an important subject for future resea […]

call_split

PhenomeNET: a whole phenome approach to disease gene discovery

2011
Nucleic Acids Res
PMCID: 3185433
PMID: 21737429
DOI: 10.1093/nar/gkr538
call_split See protocol

[…] The software we produce uses the OWL API () and is written in Groovy. We use the EL Vira software () to convert the generated OWL files to the OWL EL subset and enable tractable automated reasoning over the combined ontologies. To query the ontology, we combine the CB reasoner () […]

Citations

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El Vira institution(s)
Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge, UK; Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, Ottawa, ON, Canada; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing street, Cambridge, UK; The Jackson Laboratory, Bar Harbor, ME, USA
El Vira funding source(s)
Supported by the European Commission’s 7th Framework Programme, RICORDO project (grant number 248502); by a NSERC Discovery Grant; by the European Bioinformatics Institute; by an National Institutes of Health (grant number R01 HG004838-02); and by BBSRC (grant BBG0043581).

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