LINKING DISEASE-RELATED GENE TO THE IGTC KNOCKOUT DATABASE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. As part of its annotation of genes knocked out in mouse embryonic stem cells, BayGenomics (www.baygenomics.ucsf.edu) provides links to medical terms with which the human orthologs of the genes are associated. This is accomplished by using the Medical Subject Headings (MeSH) linked with PubMed abstracts that describe the gene in question. A tool called Meshlinker is used to browse the results on the BayGenomics site. This functionality is in place for genes knocked out in the BayGenomics database but has not yet been ported to the International Gene Trap Consortium database (www.genetrap.org). Initially, my research project is to create an implementation of Meshlinker for the IGTC web site. This involves: designing a modified database schema for Meshlinker to correspond with the differences between the BayGenomics and IGTC databases, load the data itself to allow for fully functional data mining on the IGTC site, and integrate the loading process into the IGTC pipeline to allow for future automated runs. Further direction will include linking medical terminology ontologies other than MeSH to knocked-out genes and using these linkages to ask interesting biological questions.