title: CRAVE: a database, middleware and visualization system for phenotype ontologies.
abstract: 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.
authors.affiliation: Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK. g.gkoutos@har.mrc.ac.uk
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
authors.forename: Eain C J
authors.initials: EC
authors.lastname: Green
authors.forename: Simon
authors.initials: S
authors.lastname: Greenaway
authors.forename: Andrew
authors.initials: A
authors.lastname: Blake
authors.forename: Ann-Marie
authors.initials: AM
authors.lastname: Mallon
authors.forename: John M
authors.initials: JM
authors.lastname: Hancock
mesh_terms: 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