Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Workshop: Cattle/Sheep
            

INTEGRATION AND USE OF GENE ONTOLOGY TERMS IN AN ANIMAL LIVESTOCK GENOMICS DATABASE

¹ USDA/ARS U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, NE 68933

Gene Ontology (GO) has the potential to provide a wide variety of scientists an efficient means to access and exploit livestock ESTs. GO is a controlled vocabulary that is completely invariant across species. In addition, GO is understandable to a broad range of scientists and end-users and provides a functional genomics framework for categorizing, relating, and querying genes and gene products. We have integrated GO terms and livestock ESTs to create a biologically rich context within which to analyze phenotypic and genotypic data on cattle and swine. Our approach is to relate publicly available information about genes and gene products associated with man and model organisms with similar gene and gene products in cattle and swine. TIGR livestock ESTs are compared to the NCBI Genbank non-redundant nucleotide database and the results imported into a relational database with a Perl script. Another Perl script extracts and incorporates information from the associated RefSeq and LocusLink sources (including GO terms) into our database. Using simple queries, GO terms, and the GO Perl API, new and useful positional candidate gene information is generated.