monarch-initiative

Use when asked to curate the next N disease curation issues already assigned to the current GitHub user. Filters open issues to those where the user is the sole assignee and no PR exists yet, picks the first N, then dispatches /curate in parallel for each. Accepts a positional integer N between 1 and 8.

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

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.

Use ONLY when the user explicitly asks to orchestrate parallel external agents (Codex or Claude Code) in tmux sessions via tp (tmux-pilot). Or when a user tells you that you're the boss or orchestrator. You can also use this if you are an operclaw agent. NEVER auto-invoke for a generic "do this in parallel" request. For in-process subagents, use superpowers:dispatching-parallel-agents instead.

Skill for populating the `classifications` top-level block of a dismech Disease entry. Covers Harrison's Part assignment, mechanistic nosology, lysosomal storage, IUIS immunodeficiency, channelopathy, and ICD-O morphology fields, with a lookup table from common clinical phrasing to controlled-vocabulary keys.

Use when claiming the next high-priority uncurated disease from the dismech priority dashboard. Picks the top-ranked disease in dashboard/priority.json that is not already covered in kb/disorders/, opens a GitHub curation issue, and assigns it to the current GitHub user. Accepts an optional integer 1–8 to claim N diseases at once.

Skill for adding and validating ontology term references in the dismech knowledge base. This skill should be used when working with disorder YAML files that need ontology term annotations (HPO for phenotypes, CL for cell types, GO for biological processes, MONDO for diseases, UBERON for anatomical entities). Use this skill when adding phenotype_term, cell_types term, biological_processes term, or other ontology-bound fields to disorder files.

Project management skill for markdown-based projects with GitHub Project sync. Use when: (1) viewing/managing projects in projects/ folder, (2) syncing project checkboxes to GitHub Projects, (3) picking up next work item from a project, (4) updating project status after completing work, (5) generating project dashboards. Replaces the older /pm command with enhanced GitHub integration.

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 improving knowledge base coverage.

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 scientific accuracy and preventing AI hallucinations.

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.

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.