RESUMO
UNLABELLED: Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. AVAILABILITY: Direct access: http://www.empress.har.mrc.ac.uk CONTACT: e.green@har.mrc.ac.uk.
Assuntos
Bases de Dados Genéticas , Genômica/métodos , Camundongos/classificação , Camundongos/genética , Fenótipo , Animais , Sistemas de Gerenciamento de Base de Dados , Europa (Continente) , Internet , Padrões de Referência , Interface Usuário-ComputadorRESUMO
The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sources. This produces a framework with greater flexibility, power and economy than previous approaches. We discuss some of the issues this approach raises.
Assuntos
Biologia Computacional/métodos , Camundongos/genética , Fenótipo , Animais , Biologia Computacional/normas , Modelos Animais de Doenças , Genótipo , Humanos , Informática Médica , Camundongos/fisiologia , Vocabulário ControladoRESUMO
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.
