monarch-database SKILL.md skillA
monarch-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/monarch-database@git:20260528.3e3f998Pins git:20260528.3e3f998 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/databases/monarch-database/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.3e3f998, committed May 28, 2026
- Size
- 26,569 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking. For GWAS use gwas-database; for clinical pathogenicity use clinvar-database.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# monarch-database ## Overview The Monarch Initiative integrates disease-phenotype-gene relationships from 30+ biomedical databases (OMIM, Orphanet, ClinVar, MGI, ZFIN, Reactome) into a unified knowledge graph. The REST API at `https://api.monarchinitiative.org/v3/api` provides access to associations between genes, diseases, and phenotypes using MONDO disease IDs, Human Phenotype Ontology (HPO) terms, and standard gene identifiers. No authentication is required; the service is free for academic use. ## When to Use - Mapping a disease (MONDO ID) to all associated causal genes and their evidence sources - Retrieving phenotype profiles (HP terms) for a disease to build phenotypic similarity models - Ranking candidate genes by phenotypic similarity to a patient's HPO symptom list - Querying cross-species gene-phenotype associations (mouse, zebrafish, fly) for model organism comparisons - Exploring rare disease gene-phenotype networks for diagnostic candidate generation - Resolving entity metadata (gene symbol, disease name, phenotype label) from a MONDO/HP/HGNC ID …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/monarch-database@sha256:aff1e11cbb45a1daThe line at the top of this page pins the label git:20260528.3e3f998, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_kcuw42jsa4scwa6j)
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Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (26569 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_kcuw42jsa4scwa6j GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/monarch-database GET https://markdownregistry.com/api/v1/blob/aff1e11cbb45a1da2a19a704c2e0037f4619673389a7aaa8cbd8ca18451de056
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.