The fundamental genetic similarity between mice and humans allows researchers to infer a human gene's function based on studies with laboratory mice. Identifying essential clues on gene function provided by model organisms has proved to be a powerful approach to gain knowledge on both human disease and mammalian biology.
Large-scale pan genomic community projects using mice like the International Mouse Phenotyping Consortium (IMPC) aim to generate and phenotypically characterize knockout mutant strains for every protein-coding gene in the mouse. Other resources like the Mouse Genome Informatics resource (MGI) collects and integrates literature curated information about genotypes and phenotypes in laboratory mice.
GenoBridge systematically maps between syntenic regions of the mouse and human genomes, supporting the discovery of functional conservation and helping with the validation/prioritization of candidate disease genes or regions.
GenoBridge was developed using Perl and Mysql scripts deposited in SVN integrating data from several main databases (Ensembl MGI, and GWAS) in a data warehouse (Mysql). Apache Solr was used for database integration, faceted search, dynamic clustering and indexing. We generated approximately 3.8 million documents in SolR allowing dynamic search of mouse and human genotype/phenotype data.
- Resources and data types integrated:
- Ensembl (http://www.ensembl.org/): Genome databases for vertebrates and other eukaryotic species
- GWAS catalogue (http://www.ebi.ac.uk/gwas/): Curated, literature-derived collection of all published genome-wide association studies
- MGI and IMPC: Mouse genotype/phenotype databases
- Human/Mouse variation Human/Mouse variation associated overlapping gene or nearest gene
- Human/Mouse gene associated annotation (genomic coordinates, gene ID, gene symbol...)
- Human/Mouse phenotypic annotations
- A detailed description of GenoBridge is included in the report on deliverable 3.4 Harmonisation of semantic standards supporting use cases from WP7 and WP10