Laboratory Measurements
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). Two types of data were combined prior to performing mapping on this domain:
- The first wave of data was pulled from
CHCOcontained only those concepts that were used at least once in clinical practice. This set contained a total of1,606LOINC concepts or4,425lab test results (more information on how lab test results were identified below). - The initial set of
CHCOdata were supplemented by adding the latestLOINC2HPOannotations. The current annotation set (annotations.tsv; last updated06/07/2020) was downloaded from the develop branch of the LOINC2HPO GitHub repository on08/12/2020). Of the3,119unique codes obtained fromLOINC2HPO(7,421unique results),631overlapped with theOMOPmeasurement terms retrieved fromCHCOand were excluded. An additional11concepts were excluded due to being deprecated. The final set of processed terms included2,477unique LOINC concepts or6,844lab test results.
Identifying LOINC Scale and Result Type
- All lab test scale types (i.e. ordinal, nominal, quantitative, qualitative, narrative, doc, and panel) were initially eligible to be mapped. The scale type of each lab test was identified by parsing the free-text text in the concept synonym field for the presence of any of the scale types listed above.
- Result type was identified using a two-step approach. First, we analyzed the reference ranges available in the patient data. If at least one numeric result was reported, the result type was recorded as
Normal/Low/Highand if apositiveornegativeresult was reported it was recorded asPositive/Negative. Then, for all lab tests without a reference range in the data, the result type was obtained by parsing the free-text in the concept synonym field. For all tests with an ordinal scale type, if the keywordspresenceorscreenwere identified, the result type was reported asPositive/Negative. All tests with a quantitative scale type were given the result typeNormal/Low/High. All other scale types were annotated withUnknown Result Type.
SQL Queries
- CHCO Measurements Used in Practice (
GitHub Gist) - Standard LOINC2HPO Concepts Not Used In Practice (
GitHub Gist)
An example of the output data produced by these queries is shown below (click on image to enlarge it):
OMOP Measurement concept ids were mapped to:
- Phenotypes (Human Phenotype Ontology (HPO))
- Anatomical entities (Uber-Anatomy Ontology (UBERON))
- Organisms (NCBI Organism Taxonomy (NCBITaxon))
- Proteins (Protein Ontology (PRO))
- Chemicals, hormones, and enzymes (Chemical Entities of Biological Interest (CHEBI))
- Cells (Cell Ontology (CL))
An example of the mappings generated for the concepts in the table above shown below (click on image to enlarge it):
