Skip to content
@monarch-initiative

Monarch Initiative

Cross-species disease discovery and diagnosis

Welcome to the Monarch Initative!

The Monarch Initiative is an international consortium that leads key biological and biomedical standards and semantic data integration technologies. Monarch resources and integrated data are also foundational to many downstream applications and contexts; we work closely with a variety of stakeholders and resource-development communities to capture feedback and make improvements. To maximize utility and impact, the Monarch platform is composed of multiple open-source, open-access components. We promote provenance and transparency, enhanced use of standards and new technologies and improved data accessibility, end-user utility, and data submission. Please visit the Monarch website to learn more and try our tools and resources: https://monarchinitiative.org/

If you need help or have questions about Monarch, please make a ticket at our helpdesk or email us at info@monarchinitiative.org.

Find ways to get involved at https://monarchinitiative.org/community/get-involved

See our pinned repositories below for quick access to our main code bases, or use the search bar to find a specific code repository.

monarch-logo-black-stacked

Pinned Loading

  1. mondo mondo Public template

    Mondo Disease Ontology

    Jupyter Notebook 326 65

  2. monarch-app monarch-app Public

    Monarch Initiative website and API

    Python 39 8

  3. koza koza Public

    Data transformation framework for LinkML data models

    Python 73 7

  4. dismech dismech Public

    Disease Mechanisms KB

    HTML 65 12

  5. helpdesk helpdesk Public

    The Monarch Initiative Helpdesk

    7 1

  6. ontogpt ontogpt Public

    LLM-based ontological extraction tools, including SPIRES

    Jupyter Notebook 1k 124

Repositories

Showing 10 of 315 repositories
  • bioinf-agent Public

    Bioinformatics install/pipeline agent with conda, Docker, and HPC support (experimental)

    monarch-initiative/bioinf-agent's past year of commit activity
    Python 0 BSD-3-Clause 1 0 1 Updated Oct 13, 2026
  • dismech Public

    Disease Mechanisms KB

    monarch-initiative/dismech's past year of commit activity
    HTML 65 BSD-3-Clause 12 1,137 (14 issues need help) 68 Updated Oct 13, 2026
  • kozahub Public

    Dashboard monitoring KozaHub ingest repository health

    monarch-initiative/kozahub's past year of commit activity
    Python 1 1 0 0 Updated Oct 13, 2026
  • monarch-app Public

    Monarch Initiative website and API

    monarch-initiative/monarch-app's past year of commit activity
    Python 39 BSD-3-Clause 8 239 (2 issues need help) 24 Updated Oct 13, 2026
  • mondo Public template

    Mondo Disease Ontology

    monarch-initiative/mondo's past year of commit activity
    Jupyter Notebook 326 CC-BY-4.0 65 458 (2 issues need help) 78 Updated Oct 12, 2026
  • genesets Public

    Fast ontology-aware gene set enrichment in Rust

    monarch-initiative/genesets's past year of commit activity
    Python 1 1 3 1 Updated Oct 12, 2026
  • dismech-owl Public
    monarch-initiative/dismech-owl's past year of commit activity
    Python 1 0 0 0 Updated Oct 12, 2026
  • dismech-evals Public

    Public corpus evaluation history, reusable model assessments, and recuration reports for DisMech

    monarch-initiative/dismech-evals's past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Oct 12, 2026
  • monarch-initiative/mondo-ingest-icd10who's past year of commit activity
    Python 0 0 0 0 Updated Oct 12, 2026
  • mechregistry Public

    A registry for *Mechs

    monarch-initiative/mechregistry's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Oct 12, 2026