mouse-phenome-database

Overview

The Mouse Phenome Database (MPD), maintained at the Jackson Laboratory, catalogs standardized phenotype measurements across inbred, recombinant inbred (e.g., BXD), and Collaborative Cross / Diversity Outbred mouse panels. It aggregates 520+ projects spanning metabolic, cardiovascular, behavioral, hematological, and immunological traits. The REST API at https://phenome.jax.org/api is free, requires no authentication, and is documented at https://phenome.jax.org/about/api. MPD measurement IDs (measnum) are project-scoped 5-digit integers — there is no global "measnum 10001 = body weight" mapping; valid measnums must be discovered per project via the measureinfo endpoint.

When to Use

• Selecting inbred strains with extreme phenotypes (highest/lowest fasted glucose, body weight, heart rate, etc.) as experimental models
• Pulling individual-animal data from BXD / CC / DO panels for QTL mapping with R/qtl2 or similar tools
• Comparing strain means and variance across metabolic, behavioral, or cardiovascular measures for genetic background studies
• Finding MPD projects that measure a trait of interest using ontology terms (MP, VT, MA) or free-text descriptions
• Validating mouse strain nomenclature (canonical JAX names ↔ stock numbers ↔ MGI IDs) before submitting orders or analyses
• Looking up coordinates and annotations for mouse genes in the MPD/MGI cross-reference
• Use monarch-database instead for disease-gene-phenotype knowledge graphs (HPO ↔ MP ↔ disease)
• Use ensembl-database instead for transcript-level mouse gene annotations and variant consequence prediction

Prerequisites