CRAVE: a database, middleware and visualization system for phenotype ontologies.
BACKGROUND
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.
Gkoutos
Georgios V
GV
Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK. g.gkoutos@har.mrc.ac.uk
Green
Eain C J
EC
Greenaway
Simon
S
Blake
Andrew
A
Mallon
Ann-Marie
AM
Hancock
John M
JM
D000465:Algorithms; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D010641:Phenotype; D014584:User-Computer Interface