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

G. V. Gkoutos; E. C. Green; S. Greenaway; A. Blake; A. M. Mallon; J. M. Hancock

doi:10.1093/bioinformatics/bti147

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

G. V. Gkoutos, E. C. Green, S. Greenaway, A. Blake, A. M. Mallon, J. M. Hancock

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

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 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.

Original language	English
Pages (from-to)	1257-1262
Number of pages	6
Journal	Bioinformatics
Volume	21
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/bti147
Publication status	Published - 1 Apr 2005

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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 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.",

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AU - Gkoutos, G. V.

AU - Green, E. C.

AU - Greenaway, S.

AU - Blake, A.

AU - Mallon, A. M.

AU - Hancock, J. M.

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

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