The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species-Reference-Cited by-同舟云学术

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

Published:2023-11-24 Issue:D1 Volume:52 Page:D938-D949
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Putman Tim E¹^ORCID,Schaper Kevin¹^ORCID,Matentzoglu Nicolas²^ORCID,Rubinetti Vincent P¹^ORCID,Alquaddoomi Faisal S¹^ORCID,Cox Corey¹^ORCID,Caufield J Harry³^ORCID,Elsarboukh Glass¹^ORCID,Gehrke Sarah¹^ORCID,Hegde Harshad³^ORCID,Reese Justin T³^ORCID,Braun Ian⁴^ORCID,Bruskiewich Richard M⁵^ORCID,Cappelletti Luca⁶^ORCID,Carbon Seth³^ORCID,Caron Anita R⁷^ORCID,Chan Lauren E⁸^ORCID,Chute Christopher G⁹^ORCID,Cortes Katherina G¹^ORCID,De Souza Vinícius⁷^ORCID,Fontana Tommaso¹⁰^ORCID,Harris Nomi L³^ORCID,Hartley Emily L⁴^ORCID,Hurwitz Eric¹^ORCID,Jacobsen Julius O B¹¹^ORCID,Krishnamurthy Madan¹^ORCID,Laraway Bryan J¹,McLaughlin James A⁷^ORCID,McMurry Julie A¹^ORCID,Moxon Sierra A T³^ORCID,Mullen Kathleen R¹^ORCID,O’Neil Shawn T¹^ORCID,Shefchek Kent A¹^ORCID,Stefancsik Ray⁷^ORCID,Toro Sabrina¹^ORCID,Vasilevsky Nicole A⁴^ORCID,Walls Ramona L⁴^ORCID,Whetzel Patricia L¹^ORCID,Osumi-Sutherland David⁷,Smedley Damian¹¹^ORCID,Robinson Peter N¹²^ORCID,Mungall Christopher J³^ORCID,Haendel Melissa A¹^ORCID,Munoz-Torres Monica C¹^ORCID

Affiliation:

1. Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus , Aurora , CO 80045 , USA

2. Independent Consultant, Semanticly , Athens , Greece

3. Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA

4. Data Collaboration Center, Critical Path Institute , Tucson , AZ 85718 , USA

5. STAR Informatics, Delphinai Corporation , Sooke , BC V9Z 0M3 , Canada

6. Biology, University of Fribourg , Fribourg , Switzerland

7. European Bioinformatics Institute (EMBL-EBI) , Hinxton CB10 1SD , UK

8. College of Public Health and Human Sciences, Oregon State University , Corvallis , OR 97331 , USA

9. Schools of Medicine, Public Health, and Nursing, Johns Hopkins University , Baltimore , MD 21205 , USA

10. Dipartimento di Informatica, Università degli Studi di Milano Statale , Milano , Italy

11. William Harvey Research Institute, Queen Mary University of London , London EC1M 6BQ , UK

12. The Jackson Laboratory for Genomic Medicine , Farmington , CT 6032 , USA

Abstract

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.

Funder

Office of the Director National Institute of Health

National Human Genome Research Institute

National Library of Medicine

U.S. Department of Energy

U.S. Department of Health and Human Services

Publisher

Oxford University Press (OUP)

Subject

Genetics

Link

https://academic.oup.com/nar/article-pdf/52/D1/D938/55040743/gkad1082.pdf