This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.As part of its annotation of genes knocked out in mouse embryonicstem cells, BayGenomics (www.baygenomics.ucsf.edu) provides linksto medical terms with which the human orthologs of the genes areassociated. This is accomplished by using the Medical SubjectHeadings (MeSH) linked with PubMed abstracts that describe the genein question. A tool called Meshlinker is used to browse the resultson the BayGenomics site. This functionality is in place for genesknocked out in the BayGenomics database but has not yet been portedto the International Gene Trap Consortium database (www.genetrap.org).Initially, my research project is to create an implementation ofMeshlinker for the IGTC web site. This involves: designing amodified database schema for Meshlinker to correspond with thedifferences between the BayGenomics and IGTC databases, load thedata itself to allow for fully functional data mining on the IGTCsite, and integrate the loading process into the IGTC pipeline toallow for future automated runs. Further direction will includelinking medical terminology ontologies other than MeSH to knocked-outgenes and using these linkages to ask interesting biologicalquestions.
Showing the most recent 10 out of 508 publications
