We propose to develop MouseCyc, a biochemical pathway genome database for the mouse that is integrated with well-curated information on phenotypes, gene expression data, functional annotations, and mammalian homology for mouse genes that is available from the Mouse Genome Informatics(MGI) database. The results of the proposed work will provide the scientific community a view of mouse genetic and genomic data in the context of biochemical and metabolic processes. This functionality will further enhance the value of the mouse as a model system for understanding human biology and disease processes. To implement MouseCyc we will use a robust software suite called Pathway Tools that has components for the creation, curation, and visualization of organism-specific biochemical pathway data. Once MouseCyc is implemented, we will curate pathway data for the mouse using information from the published scientific literature, other databases and, where appropriate, subject matter experts. Access to MouseCyc will be provided using web-based data query and browsing capabilities that are included in the Pathway Tools software development kit. The databases will also serve as a source of curated mouse pathway data for other pathway representation and modeling projects. We will work collaboratively with the developers of the Pathway Tools software to implement mechanisms to support comparisons of human and mouse pathways based on curated gene homology and conserved synteny relationships. Relevance to Public Health The MouseCyc database will serve as a publicly accessible internet resource that the scientific community will use to analyze mouse genetic and genomic data in the context of biochemical and metabolic processes. Priority for data curation and representation in the database will be given to those genes in the laboratory mouse that have counterparts in humans that are known to be involved in disease. The visualization and query interfaces for MouseCyc will further enhance the value of the mouse as a model system for understanding human biology and disease processes.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG003622-03
Application #
7351830
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Bonazzi, Vivien
Project Start
2006-04-01
Project End
2010-01-31
Budget Start
2008-02-01
Budget End
2010-01-31
Support Year
3
Fiscal Year
2008
Total Cost
$240,043
Indirect Cost
Name
Jackson Laboratory
Department
Type
DUNS #
042140483
City
Bar Harbor
State
ME
Country
United States
Zip Code
04609
Bult, Carol J; Drabkin, Harold J; Evsikov, Alexei et al. (2011) The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics 12:371
Evsikov, Alexei V; Dolan, Mary E; Genrich, Michael P et al. (2009) MouseCyc: a curated biochemical pathways database for the laboratory mouse. Genome Biol 10:R84