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Bioinformatics Advance Access published online on November 18, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti147
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 3, 2004
Revised November 5, 2004
Accepted November 11, 2004

Article

CRAVE: a database, middleware and visualisation system for phenotype ontologies

Georgios V. Gkoutos 1*, Eain C. J. Green 1, Simon Greenaway 1, Andrew Blake 1, Ann-Marie Mallon 1, and John M. Hancock 1

1 Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire, OX11 0RD, UK

* To whom correspondence should be addressed.
Georgios V. Gkoutos, E-mail: g.gkoutos{at}har.mrc.ac.uk


  Abstract

Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterising phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualise combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies.

Results: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's API. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Availability: Direct access: http://www.mgu.har.mrc.ac.uk/CRAVE/.


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E. C. J. Green, G. V. Gkoutos, H. V. Lad, A. Blake, J. Weekes, and J. M. Hancock
EMPReSS: European Mouse Phenotyping Resource for Standardized Screens
Bioinformatics, June 15, 2005; 21(12): 2930 - 2931.
[Abstract] [Full Text] [PDF]


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