monarch-initiative

Skill for curating cancer and neoplastic disease entries in the dismech knowledge base. Use this skill when creating or enhancing cancer entries, adding oncogene/tumor suppressor pathophysiology, curating histopathology findings, adding targeted therapy…

Skill for initiating new disorder YAML files in the dismech knowledge base. Use this skill when the user asks to create a new disorder entry. Also useful for enhancing existing entries.

Add, validate, repair, or review evidence references and exact-quote snippets in dismech KB YAML and deep-research reports. Use for PMID, DOI, NCT, ICTRP, or structured-source evidence; reference-cache generation; snippet failures; title snippets; bracket…

Select, add, validate, review, or repair ontology bindings and derived term caches in dismech. Use when changing term IDs, canonical labels, preferred_term values, enum meaning mappings, phenotype, cell-type, biological-process, disease, anatomy, exposure, or…

Write the prose of a GitHub PR body, issue comment, review body, or review reply in this repo. Use before posting anything to GitHub — opening a PR, summarizing or triaging an issue, replying to a reviewer, reporting what a scan found, or explaining why you…

Instructions for reviewing a dismech PR, in particular PRs relating to disorder curation, either creating new dismech entries or updating existing ones.

Skill for creating a new mechanism module in kb/modules/ (a conserved pathological process that recurs across disorders). Use when the user asks to create/curate a module, add an Xogenesis (pathological-structure-formation) module, or factor a recurrent…

Create, edit, review, or audit dismech disease groupings in kb/groupings/*.yaml. Use for Grouping records, member unions, grouping_basis and grouping_rationale, membership_criteria boolean logic, criteria_semantics, differentiating_mechanisms, grouping…

Use when asked to merge two MONDO terms — obsoleting one and transferring its metadata to the surviving term

Use when running any ODK-backed command in this repo — owltools, robot, make NORM, robot verify, or any other tool that lives inside the ODK docker image

Generate a formatted Mondo release announcement with statistics table from release diff reports

Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

Skill for analyzing and improving compliance in the MIC knowledge base. Use this when checking nutrient file completeness, identifying missing fields (ontology terms, evidence, descriptions), understanding weighted priority scoring, and systematically…

Skill for creating new nutrient YAML files from MIC website content. Use this when extracting a nutrient from lpi.oregonstate.edu/mic. Also useful for enhancing existing nutrient entries.

Skill for validating and repairing evidence references in the MIC knowledge base. Use this when working with evidence items in nutrient YAML files, validating that snippet text matches PubMed abstracts, and repairing misquoted evidence. Critical for ensuring…

Skill for adding and validating ontology term annotations in the MIC knowledge base. Covers CHEBI, FOODON, HP, GO, MONDO, UBERON, HGNC lookups. Use when adding term bindings to nutrient YAML files.

Perform gene set enrichment analysis using AI research providers. Analyzes lists of genes to identify biological themes, pathways, and functional associations.

Toolkit for performing deep research on complex topics using multiple AI research providers (OpenAI, Falcon, Perplexity, Consensus). Emphasizes explicit speed vs depth trade-offs.

Use when curating or reviewing a GO-term interpretation of a non-GO gene set (MSigDB C8/C2/H, literature disease-activity, or GWAS/CRISPR genetics) for the curation/ gold standard in this repo. Covers grounding in the real membership, OLS term verification,…

Use when evaluating a GO enrichment method or a GOA evidence variant (all vs IBA vs IBA+IEA vs no-contributes_to) against the curated benchmark in this repo — the IBA/evidence-ablation eval. Covers building queries.gmt, prepare_go_eval, running genesets-rs,…

Updates the Monarch Initiative publications page with latest data from Google Scholar. Use this when the user asks to update publications, refresh citation metrics, or add new papers to the publications page.

Extract and cross-reference foundation stock (ancestor breed) relations from kennel club registry websites for a given species. Use when the user wants to build or update foundation stock data from breed registry sources.

Run one research prompt across multiple deep research providers (via the Deep Research Client) and compare the results side by side — length and structure, citation counts, whether cited sources actually resolve, and whether they are relevant to the question.…