Rare disease terminology can be complex, but Mondo helps standardize clinical documentation and link disparate knowledge sources within healthcare. Learn more in this 101 guide, authored by Patrick McCormick, MD, Staff Clinical Terminologist at IMO Health.
Table of Contents
What is Mondo?
The Monarch Disease Ontology (Mondo) is a logic-based structure that relates many disease knowledge sources and terminologies to each other from multiple industry-leading sources like OMIM, Orphanet, and ICD-10-CM. OMIM, or the Online Mendelian Inheritance in Man terminology set, is a catalogue of human genes, genetic disorders, and traits.
How or why is it used?
Both Mondo and OMIM are used by researchers, clinicians, and others in the biomedical community for rare disease research. Mondo aims to standardize data related to all diseases, such as genotype, phenotype, and other related knowledge. OMIM, an integral part of Mondo, serves as a tool supporting genetics research, clinical education, and the practice of clinical genetics, and aids in the understanding of potential relationships between diseases and genes.
What is its significance?
Mondo helps bridge the gaps between disparate disease information sources and provides an up-to-date database that cross-references knowledge sources and terminologies with precise semantics, noting if conditions are equivalent or related and thereby enabling systems and computational tools to interoperate. OMIM serves as a reference within Mondo, describing how specific genetic and environmental factors influence disease manifestations. Both help advance knowledge discovery, clinical diagnoses, and treatments for patients living with rare diseases.
How will IMO Health’s Mondo/OMIM integration help providers improve clinical documentation at the point of care?
With the addition of diseases from Mondo/OMIM to IMO Health’s lexicon, it is very likely that providers will be able to find diagnoses for their patients, regardless of rarity. This is on top of IMO Health’s already granular rare disease coverage, which includes the entirety of SNOMED CT® to the Orphanet reference set provided by SNOMED International (6,556 diagnoses as of January 2025). Some of the diagnoses recently added to IMO Health’s database have only been described in a handful of patients in the entire world. Melissa Haendel, PhD, FACMI at the University of North Carolina and co-founder of Mondo, emphasizes that “IMO Health is a critical partner in the clinical dissemination of the communities’ work to standardize rare and genetic disease diagnoses worldwide, ensuring more effective diagnostics for all.”
IMO Health is a critical partner in the clinical dissemination of the communities’ work to standardize rare and genetic disease diagnoses worldwide, ensuring more effective diagnostics for all.
Why does this matter for rare disease drug development in life sciences?
Accurate identification of patients can be one of the most costly aspects of drug trial enrollment, especially for therapeutics targeting rare disease populations. An IMO Health lexical is a constrained, discrete data element in the electronic health record (EHR) that is easier to find and query, compared to a rare disease mentioned in a clinical note.
How does Mondo’s structure make IMO Health’s clinical terminology more accessible?
The Mondo Terminology is a hierarchical representation of rare disease types that encapsulates clinical and research insight in a known structure called an ontology. This unique representation of detailed clinical and biological concepts enables users to leverage this knowledge and tailor patient queries to their needs.
Consider Ehlers-Danlos syndrome (MONDO:0020066), which has 43 descendants (or “children” and “grandchildren”) in the Mondo hierarchy as of January 2025. Instead of listing out dozens of individual diagnoses, a researcher could simply query all IMO Health lexicals mapped to this Mondo code or any of its descendants. Coupled with IMO Health’s support for text string matching and leveraging the SNOMED CT hierarchy, researchers have numerous ways to find patients diagnosed with rare diseases.
Another researcher might be interested in a narrower slice of the Ehlers-Danlos patient populations, such as spondylodysplastic Ehlers-Danlos syndrome (MONDO: 0007526), which has three direct subtypes in the Mondo ontology. They can leverage this more granular slice of the Mondo hierarchy instead of the broader one mentioned above.
How does support for Mondo help connect clinical care and research?
IMO Health is the premier clinical terminology used by most healthcare providers in the United States. Mondo has become the de facto standard in the research and life sciences community for rare diseases. By providing maps from point-of-care documentation to a language more familiar to the research and life sciences community, IMO Health’s efforts to incorporate Mondo allow for secondary use of clinical data that would otherwise be siloed or more difficult to access.
What relationships does Mondo maintain to further unlock this clinical data?
The Monarch Initiative, which maintains Mondo, also sustains the Human Phenotype Ontology (HPO). This includes a mapping between rare diseases (Mondo) and phenotypes (HPO), which are specific clinical findings specifically seen in rare, genetic diseases. Thus, providers with diagnoses tied to Mondo could be prompted to search for additional phenotypes that may not have been on their radars by leveraging these relationships. Mapping IMO lexicals to Mondo could also make it easier to discover new phenotypes associated with a specific rare disease that was previously unknown.
The Monarch Initiative also maintains relationships between Mondo rare diseases and causal genes (if known), using official HGNC (HUGO Genome Nomenclature Committee) gene symbols. This is another relationship users could potentially leverage with IMO Health lexicals mapped to Mondo.
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