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Bioinformatics Advance Access originally published online on November 18, 2004
Bioinformatics 2005 21(7):1257-1262; doi:10.1093/bioinformatics/bti147
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

Motivation: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize 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 application programming interface. 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/

Contact: g.gkoutos{at}har.mrc.ac.uk


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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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