Document Type
Article
Publication Date
12-8-2023
Original Citation
Carmody L,
Gargano M,
Toro S,
Vasilevsky N,
Adam M,
Blau H,
Chan L,
Gomez-Andres D,
Horvath R,
Kraus M,
Ladewig M,
Lewis-Smith D,
Lochmüller H,
Matentzoglu N,
Munoz-Torres M,
Schuetz C,
Seitz B,
Similuk M,
Sparks T,
Strauss T,
Swietlik E,
Thompson R,
Zhang X,
Mungall C,
Haendel M,
Robinson P.
The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. Med. 2023;4(12):913-27.
Keywords
JGM, Humans, Biological Ontologies, Rare Diseases, Software, Computer Simulation
JAX Source
Med. 2023;4(12):913-27.
ISSN
2666-6340
PMID
37963467
DOI
https://doi.org/10.1016/j.medj.2023.10.003
Grant
This study was supported by the National Institutes of Health (NIH): NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04. R.H. is a Wellcome Trust Investigator (109915/Z/15/Z), who receives support from the Medical Research Council (UK) (MR/V009346/1), the Addenbrookes Charitable Trust (G100142), the Evelyn Trust, the Stoneygate Trust, the Lily Foundation, Action for AT and an MRC strategic award to establish an International Centre for Genomic Medicine in Neuro- muscular Diseases (ICGNMD) MR/S005021/1. This research was supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014). The views ex- pressed are those of the authors and not necessarily those of the NIHR or the Depart- ment of Health and Social Care.
Abstract
BACKGROUND: Navigating the clinical literature to determine the optimal clinical management for rare diseases presents significant challenges. We introduce the Medical Action Ontology (MAxO), an ontology specifically designed to organize medical procedures, therapies, and interventions.
METHODS: MAxO incorporates logical structures that link MAxO terms to numerous other ontologies within the OBO Foundry. Term development involves a blend of manual and semi-automated processes. Additionally, we have generated annotations detailing diagnostic modalities for specific phenotypic abnormalities defined by the Human Phenotype Ontology (HPO). We introduce a web application, POET, that facilitates MAxO annotations for specific medical actions for diseases using the Mondo Disease Ontology.
FINDINGS: MAxO encompasses 1,757 terms spanning a wide range of biomedical domains, from human anatomy and investigations to the chemical and protein entities involved in biological processes. These terms annotate phenotypic features associated with specific disease (using HPO and Mondo). Presently, there are over 16,000 MAxO diagnostic annotations that target HPO terms. Through POET, we have created 413 MAxO annotations specifying treatments for 189 rare diseases.
CONCLUSIONS: MAxO offers a computational representation of treatments and other actions taken for the clinical management of patients. Its development is closely coupled to Mondo and HPO, broadening the scope of our computational modeling of diseases and phenotypic features. We invite the community to contribute disease annotations using POET (https://poet.jax.org/). MAxO is available under the open-source CC-BY 4.0 license (https://github.com/monarch-initiative/MAxO).
FUNDING: NHGRI 1U24HG011449-01A1 and NHGRI 5RM1HG010860-04.
Comments
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).