OMOP2OBO Measurement Mappings

OMOP2OBO Measurement Mappings V1.0

The mappings in this repository were created between OMOP standard measurement concepts (i.e., LOINC) to the Human Phenotype Ontology (HPO), Chemical Entities of Biological Interest (CheBI), Vaccine Ontology (VO), National Center for Biotechnology Information Taxon Ontology (NCBITaxon), Protein Ontology (PRO), Cell Ontology (CL), and the Uber-anatomy Ontology (UBERON).

For each measurement, all levels of the test result (results above, below, and within a reference range) were mapped, not only those deemed clinically relevant. Results outside of a reference range, but not currently deemed clinically relevant (as advised by the literature or consultation via domain expert), were annotated to the nearest relevant ontology concept ancestor. For example, when annotating the results of a test for Asparagus IgE Ab RAST class [Presence] in Serum (LOINC:15547-3), a result above a reference range would be annotated with an increased anti-plant-based food allergen IgE antibody level (HP:0410228). While a low level of this antibody may not be deemed clinically relevant, it is still outside of the provided reference range and thus was annotated to the nearest applicable concept ancestor, abnormal immunoglobulin level (HP:0010701). There is one exception to this rule: all measured drugs and toxins (entities not normally found in the human body) with normal results (results that were not outside of a given reference range) were annotated to the same HP concept as the clinically relevant result and logically negated. For example, Amphetamine [Presence] in Urine by Screen (LOINC:19343-3), a positive finding was mapped to a positive urine amphetamine test (HP:0500112) and a negative finding was mapped to a positive urine amphetamine test and logically negated (NOT HP:0500112).

LOINC2HPO currently aligns LOINC to HP. The current work extends existing LOINC2HPO annotations to match the OMOP2OBO mappings in the following two ways: (1) annotations were updated if new and/or more specific concepts had been added to the HP; and (2) existing mappings were expanded to include the measurement substance (body fluids, tissues, and organs via Uberon), the entity being measured (chemicals, metabolites, or hormones via ChEBI; cell types via CL; and proteins and protein complexes via PR), and the species of the measured entities (organism taxonomy via NCBITaxon). Consistent with LOINC2HPO, all measurements lacking sufficient specimen detail (those measured in non-specific body substances) were annotated as “Unspecified Sample” and all measurements without a valid result type were annotated as “Not Mapped test Type”. All modifications to the original LOINC2HPO annotations were meticulously recorded in the mapping evidence field enabling users to easily identify when an original LOINC2HPO annotation had been updated.

For this OMOP domain, the owl:complementOf (“not