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

Georgios V Gkoutos1, Eain C J Green, Simon Greenaway

  • 1Bioinformatics Group, MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK. g.gkoutos@har.mrc.ac.uk

Bioinformatics (Oxford, England)
|November 20, 2004
PubMed
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We developed CRAVE (Concept Relation Assay Value Explorer), a new tool for visualizing multiple biological ontologies. This helps link genome data to organism function by exploring phenotypic information.

Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Linking genome sequence to organism function is a key challenge in modern biology.
  • Phenotypic characterization of mutations is crucial for understanding gene function.
  • Efficiently expressing phenotypic information necessitates the combinatorial use of ontologies.

Purpose of the Study:

  • To address the lack of tools for visualizing combined ontologies.
  • To introduce CRAVE (Concept Relation Assay Value Explorer) for managing and visualizing multiple ontologies.

Main Methods:

  • CRAVE is a web-accessible JAVA application.
  • It utilizes a MySQL database and a JAVA persistent middleware layer (Chameleon).
  • Ontology data is mapped into JAVA classes and interlinked objects for efficient access.

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Main Results:

  • CRAVE enables simultaneous display and linking of multiple ontologies.
  • It supports advanced searching capabilities, including Boolean operations.
  • The application facilitates the exploration of complex relationships within biological data.

Conclusions:

  • CRAVE provides a novel solution for visualizing and querying multiple ontologies.
  • This tool aids in linking genomic information to organismal function through phenotype analysis.
  • It enhances the ability to manage and interpret complex biological datasets.