Conditions
To create the mappings, clinical data was pulled in two waves from an OMOP (v5.0) PEDSNet (v3.0)-normalized instance of Children's Hospital of Colorado data (#15-0445). The first waved returned all condition concepts ids used at least 1 time in practice (n=29,129). The second wave returned all standard SNOMED-CT concepts not used in practice (n=109,719). Once the 29,129 concepts used in practice were removed, there 80,590 were standard SNOMED-CT concepts that had not been used in practice.
SQL Queries
- Condition Concepts Used in Practice (
GitHub Gist) - Standard SNOMED-CT Condition Concepts (
GitHub Gist)
An example of the output data produced by these queries is shown below (click on image to enlarge it):
OMOP Condition concept ids were mapped to:
- Phenotypes (Human Phenotype Ontology (HP))
- Diseases (MonDO Disease Ontology (MONDO))
An example of the mappings generated for the concepts in the table above shown below (click on image to enlarge it):
