Abstract: The Mouse Phenome Database (MPD; https://phenome.jax.org ) is a widely used resource that provides access to primary experimental data, protocols and analysis tools for mouse phenotyping studies. Data are contributed by investigators around the world and represent a broad scope of phenotyping endpoints and disease-related characteristics in naïve mice and those exposed to drugs, environmental agents or other treatments. MPD is engineered to facilitate interactive data exploration and quantitative analysis. It encompasses data from inbred strains and other reproducible panels, including HMDP, KOMP, Collaborative Cross (CC), CC-RIX, and founder strains, along with primary data from mapping populations, including historic mapping crosses and advanced high-diversity mouse populations such as Diversity Outbred mice. A new Study Intake Platform (SIP) for data contributors allows domain experts to submit and annotate their own data with relevant ontology terms. Data contributors also provide detailed information for protocols and animal environmental conditions to fulfill ARRIVE guidelines. Data are exposed to analysis tools within MPD and are available through APIs to other systems. We will demonstrate selected MPD tools, including GenomeMUSter (https://muster.jax.org), a new imputed SNP grid on 650+ strains of mice at 106+M locations, and a new GWAS metanalysis tool.

Bogue MA, Ball RL, Philip VM, Walton DO, Dunn MH, Kolishovski G, Lamoureux A, Gerring M, Liang H, Emerson J, Stearns T, He H, Mukherjee G, Bluis J, Desai S, Sundberg B, Kadakkuzha B, Kunde-Ramamoorthy G, Chesler EJ. Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes. Nucleic Acids Res. 2023 Jan 6;51(D1):D1067-D1074. doi: 10.1093/nar/gkac1007. PMID: 36330959; PMCID: PMC9825561.

Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res. 2024 Feb 7;34(1):145-159. doi: 10.1101/gr.278157.123. PMID: 38290977; PMCID: PMC10903950.

Funding provided by NIH DA028420, DA045401, AG066346.

Presented by:

Molly Bogue and Robyn Ball
Other senior members of the MPD team: Elissa Chesler, Vivek Philip, Dave Walton
The Jackson Laboratory