mouse-phenome-database
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.
npx skills add BioTender-max/awesome-bio-agent-skills --skill mouse-phenome-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
The skill enables querying the Jackson Laboratory Mouse Phenome Database (MPD) through its REST API to access projects, strains, measures, strain means (unadjusted), LS-means (adjusted), per-animal values, and ontology-based measures. It supports locating measures by project, pulling strain-level statistics, and validating strain nomenclature, with guidance to use monarch-database and ensembl-database for related knowledge and annotations.
How it works
It lays out a structured usage of the MPD REST API, including examples and code snippets that perform the following concrete actions:
- List projects and filter by investigator, projsym, projid, mpdsector, largecollab, or panelsym; access project measures via /pheno/measureinfo/{projsym} and find measures with varname, descrip, units.
- Retrieve per-project strain data via /projects/{projsym}/strains and pull per-animal datasets from /projects/{projsym}/dataset.
- Access publications and strain lists for a project using /projects/{projsym}/publications and /projects/{projsym}/strains.
- Discover measures with /pheno/measureinfo/{selector} where selector can be a projsym or measnum; view fields like measnum, varname, descrip, units, sex, age.
- Get strain means with /pheno/strainmeans/{selector} returning rows containing measnum, varname, strain, sex, mean, sd, sem, cv, nmice, zscore; optionally obtain LS-means with /pheno/lsmeans/{selector}.
- Retrieve per-animal values with /pheno/animalvals/{measnum} returning animal_id, strain, sex, value, zscore, etc.
- Discover measures by ontology with /pheno/measures_by_ontology/{ont_term}, supporting options like this_term_only, omit_baseline, collapse_series.
- Validate and normalize strains with /straininfo to compare JAX nomenclature and MPD metadata.
- Access gene coordinates with /geneinfo/{symbol} returning coordinates, strand, MGI ID, description.
When to use it
- When selecting strains with extreme phenotypes or when mapping traits to MPD projects.
- When pulling individual-animal data for QTL mapping or mixed-effects modeling.
- When comparing strain means or LS-means across cohorts or projects.
- When locating candidate measures by ontology terms (MP, VT, MA) for targeted phenotype discovery.
- When validating strain nomenclature before ordering or analysis, and when seeking gene coordinates or annotations for MPD-associated data.
What it can touch
- The REST API endpoints at https://phenome.jax.org/api for projects, strains, dataset, publications, measureinfo, strainmeans, lsmeans, animalvals, measures_by_ontology, straininfo, and geneinfo.
Caveats
- Measures (measnum) are project-scoped; there is no global mapping. Valid measnums must be discovered per project via the measureinfo endpoint.
- Selector usage is project symbol or measnum; unrecognized selectors yield a 400 JSON error detailing the selector requirement.
- Rate limits: the examples suggest reasonable pacing (e.g., sleep between requests) but no hard published limit; bursts should be avoided to prevent throttling.
- License declared as CC-BY-4.0 for the MPD data; usage should comply with attribution requirements.
# 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 fr
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Module 1: Browse Projects — /projects
- Module 2: Project Detail — /projects/{projsym}/...
- Module 3: Measure Discovery — /pheno/measureinfo/{selector}
- Module 4: Strain Means — /pheno/strainmeans/{selector}
- Module 5: Per-Animal Values — /pheno/animalvals/{measnum}
- Module 6: Ontology-Based Measure Discovery — /pheno/measuresbyontology/{ontterm}
- Module 7: Strain Nomenclature — /straininfo
- Module 8: Gene Info — /geneinfo/{symbol}
- Key Concepts
pip install requests pandas matplotlib
What does the mouse-phenome-database skill do?
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill mouse-phenome-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.