Leigh C. Carmody - MAxO development and tool implementation for the annotation of rare disease
Channel: Biocuration Conference 2023
Date: 2023-06-21

*Session:* April 25 - Applications 2 - 01

*Abstract:* A rare disease (RD) affects fewer than one in 2000 individuals. Finding relevant clinical literature about strategies to manage RD patients is often difficult. Responding to this need, the Medical Action Ontology (MAxO) was developed to provide structured vocabulary for medical procedures, interventions, therapies, and treatments for disease. While MAxO’s initial use case is to annotate RD, it can be broadly applied to common and infectious diseases. Currently, MAxO contains over 1387 terms added by manual curation using the Protégé OWL editor and ROBOT templates or by semi-automated curation using Dead Simple Design Patterns (DOSDP). Ontologies from the Open Biological and Biomedical Ontology Foundry (OBO Foundry) were used to axiomatize many terms and help give MAxO structure. Ontologies imported include Uber-anatomy Ontology (UBERON), Ontology for Biomedical Investigations (OBI), Chemical Entities of Biological Interest (ChEBI), Food Ontology (FOODON), Human Phenotype Ontology (HP), and Protein Ontology (PRO). An annotation database is currently under development to capture the medical actions and treatments used for RD. Three types of annotations are being curated (1) diagnosis annotations (MAxO-HP); these annotations are diagnostic terms, such as laboratory tests or diagnostic imaging procedures, that are used to observe or measure phenotypic abnormalities. These annotations are disease agnostic since the modality for assessing an abnormal phenotypic feature such as ‘Agenesis of the corpus callosum’ (HP:0001274) or ‘Hypertelerosm’ (HP:0000316)does not depend on the underlying disease. (2) RD-associated phenotypes are also annotated withmedical actions to capture how symptoms are treated in the context of a particular disease. For example, in Tumor Predisposition Syndrome where patients are prone to lung adenocarcinomas, the medical recommendation is to avoid radiation, including avoiding chest X-rays and computerized tomography (CT) so as not to exacerbate the condition. Therefore, medical recommendation annotations (e.g. ‘avoid CT scans’’ (MAXO:0010321) and ‘radiographic imaging avoidance’ (MAXO:0001127) are specific to the phenotypes (e.g ‘lung adenocarcinoma’ (HP:0030078) associated with that particular disease (e.g ‘BAP1-related tumor predisposition syndrome ’, MONDO:0013692). (3) Disease-specific annotations (MAxO-RD): these are either curative treatments or treatments that alleviate disease-associated phenotypes by directly affecting the disease cause. For example, gene therapy (MAXO:0001001) directly targets the gene variant causing the RD and thereby affects all phenotypes associated with the disease. The POET website (https://poet.jax.org/) houses MAxO annotations. Once fully established, the medical and research community will be invited to contribute to MAxO annotation database. While our initial efforts are focused on annotating RD, future annotations could be collected for common diseases. All community-added annotations will be verified before being published. All annotations will be available on the Human Phenotype Ontology website (hpo.jax.org). MAxO is open-source and freely available under a Creative Commons Attribution license (CC-BY 4.0) (https://github.com/monarch-initiative/MAxO; https://obofoundry.org/ontology/maxo).