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PennTURBO / semantic-engine

TURBO semantic engine (Drivetrain). Transforms source-dependent RDF data into a source-independent, semantically rich RDF model.
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Classification of OMOP procedures #11

Closed turbomam closed 4 years ago

turbomam commented 4 years ago

OMOP procedures should at least classified as something more specific than planned process, but probably more general tan health care encounter

In the short term, I'll experiment with classifying them even more specifically. That will require creating or importing classes for things like 'colonoscopy' and 'intramuscular injection'

Another design pattern, similar to diagnoses and prescriptions, is that a instances of a procedure class would mention the SNOMED class.

turbomam commented 4 years ago

Globally switched to health care process.

The BioPortal recommender finds mapping from the SNOMED terms used in Synthea/OMOP, but almost all of them com from non-BFO ontologies like NCIT and OMIT (which mainly reuses MeSH terms as SDCs)

See two useful exceptions below:

concept_name concept_code vocabulary_id procedure_source_concept_id count OBO mapping
Documentation of current medications 4.28191E+14 SNOMED 765467 4755
Evaluation of uterine fundal height 274804006 SNOMED 4168236 2921
Auscultation of the fetal heart 225158009 SNOMED 4075363 2921
Subcutaneous immunotherapy 180256009 SNOMED 4107731 1512
Intramuscular injection 76601001 SNOMED 4295880 1425 http://purl.obolibrary.org/obo/OBI_0000934
Renal dialysis 265764009 SNOMED 4146536 1215
Physical examination 5880005 SNOMED 4240345 850 http://purl.obolibrary.org/obo/OGMS_0000057
Direct current cardioversion 180325003 SNOMED 4078793 705
Hemogram, automated, with RBC, WBC, Hgb, Hct, Indices, Platelet count, and manual WBC differential 104091002 SNOMED 4015052 661
Standard pregnancy test 252160004 SNOMED 4091461 520
turbomam commented 4 years ago

coarsely bucketed