Monarch Initiative
Official@monarch-initiative · Globally-distributed team (see https://monarchinitiative.org/page/team)
Cross-species disease discovery and diagnosis
Agent Skills by Monarch Initiative
Showing 14 vetted skills indexed across 3 GitHub repositories.
monarch-initiativedisease-classificatin
Populate the classifications section of a dismech entry with standardized taxonomy terms.
monarch-initiativemicrobiome-curation
Decompose microbiome pathophysiology into modular graph nodes with evidence tagging.
monarch-initiativeinitiate-new-disorder-creation
Generate a new disorder YAML skeleton in the dismech knowledge base.
monarch-initiativedismech-references
Validate and repair quoted snippets in disorder YAML files against PubMed and ClinicalTrials records.
monarch-initiativedismech-compliance
Analyze disorder YAML files for ontology bindings, evidence, and descriptions.
monarch-initiativedismech-terms
Annotate and validate ontology-bound fields in dismech disorder YAML files.
monarch-initiativecreate-definitions-from-ohdsi
Convert OHDSI/ATLAS cohort JSON into dismech definitions fragments.
monarch-initiativedisease-trajectories
Extract disease trajectory edges from DisTraj JSON into dismech YAML signals.
monarch-initiativecancer-curator
Curate cancer entries with genetic drivers, pathophysiology, and ontology bindings.
monarch-initiativeprojman
Sync Markdown project checkboxes with GitHub Projects items.
monarch-initiativedismech-pr-review
Validate dismech PRs against the disorder knowledge base schema.
monarch-initiativeanalyse-issue
Analyze MONDO GitHub disease issues for validity and generate structured reports with duplication checks and identifier validation.
monarch-initiativerun-deep-research
Run multi-provider research queries and generate cited Markdown reports.
monarch-initiativegene-set-enrichment
Identify enriched pathways, GO terms, and disease associations from gene lists.
Frequently Asked Questions About Monarch Initiative
FAQPage SchemaWhat specific tasks can researchers perform using these capabilities?▼
Researchers can validate disease issues, curate cancer entries with genetic drivers, decompose microbiome pathophysiology into graph nodes, and convert OHDSI cohort data into standardized disorder definitions. These functions ensure high-quality, ontology-bound data entry for complex biomedical knowledge bases.
Who is the target persona for these technical capabilities?▼
The primary users are bioinformaticians, clinical researchers, and ontology engineers tasked with maintaining large-scale disease knowledge bases. These professionals utilize these functions to ensure schema compliance, evidence-based validation, and taxonomic accuracy across cross-species disorder datasets.
What are the prerequisites for implementing these disease curation functions?▼
Implementation requires access to the dismech knowledge base schema and valid credentials for GitHub repository interaction. Users must ensure their input data, such as OHDSI JSON or gene lists, is formatted correctly to align with the required ontology bindings and YAML structure.