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

Journal Article · 23 November 2023 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad1082 · OSTI ID:2221875

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

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.

• Sponsoring Organization: USDOE
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2221875
• Alternate ID(s): OSTI ID: 2349058
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 52; ISSN 0305-1048
• Publisher: Oxford University PressCopyright Statement
• Country of Publication: United Kingdom
• Language: English