The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.

Tim E Putman
Kevin Schaper
Nicolas Matentzoglu
Vincent P Rubinetti
Faisal S Alquaddoomi
Corey Cox
J Harry Caufield
Glass Elsarboukh
Sarah Gehrke
Harshad Hegde
Justin T Reese
Ian Braun
Richard M Bruskiewich
Luca Cappelletti
Seth Carbon
Anita R Caron
Lauren E Chan
Christopher G Chute
Katherina G Cortes
Vinícius De Souza
Tommaso Fontana
Nomi L Harris
Emily L Hartley
Eric Hurwitz
Julius O B Jacobsen
Madan Krishnamurthy
Bryan J Laraway
James A McLaughlin
Julie A McMurry
Sierra A T Moxon
Kathleen R Mullen
Shawn T O'Neil
Kent A Shefchek
Ray Stefancsik
Sabrina Toro
Nicole A Vasilevsky
Ramona L Walls
Patricia L Whetzel
David Osumi-Sutherland
Damian Smedley
Peter N Robinson, The Jackson Laboratory
Christopher J Mungall
Melissa A Haendel
Monica C Munoz-Torres

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.