Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data.

Molly A. Bogue, The Jackson Laboratory
Vivek M. Philip, The Jackson Laboratory
David O Walton, The Jackson Laboratory
Stephen C. Grubb, The Jackson Laboratory
Matthew H Dunn, The Jackson Laboratory
Georgi Kolishovski, The Jackson Laboratory
Jake Emerson, The Jackson Laboratory
Gaurab Mukherjee, The Jackson Laboratory
Timothy M Stearns, The Jackson Laboratory
Hao He, The Jackson Laboratory
Vinita Sinha, The Jackson Laboratory
Beena Kadakkuzha, The Jackson Laboratory
Govindarajan Kunde-Ramamoorthy, The Jackson Laboratory
Elissa J Chesler, The Jackson Laboratory


The Mouse Phenome Database (MPD; is a widely accessed and highly functional data repository housing primary phenotype data for the laboratory mouse accessible via APIs and providing tools to analyze and visualize those data. Data come from investigators around the world and represent a broad scope of phenotyping endpoints and disease-related traits in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD houses rigorously curated per-animal data with detailed protocols. Public ontologies and controlled vocabularies are used for annotation. In addition to phenotype tools, genetic analysis tools enable users to integrate and interpret genome-phenome relations across the database. Strain types and populations include inbred, recombinant inbred, F1 hybrid, transgenic, targeted mutants, chromosome substitution, Collaborative Cross, Diversity Outbred and other mapping populations. Our new analysis tools allow users to apply selected data in an integrated fashion to address problems in trait associations, reproducibility, polygenic syndrome model selection and multi-trait modeling. As we refine these tools and approaches, we will continue to provide users a means to identify consistent, quality studies that have high translational relevance.