I believe that pathology procedures belong in the Procedure domain. And the OMOP vocabulary mostly agrees with me. For example, if you look in the OMOP vocabulary, SNOMED code 39228008 ‘Surgical pathology procedure’ is in the ‘Procedure’ domain.
http://athena.ohdsi.org/search-terms/terms/4213297
I have worked with pathology data within OMOP. This is how I believe that pathology data should be represented in OMOP:
- The pathology procedure belongs in the ‘PROCEDURE_OCCURRENCE’ table.
- The pathology report that records the pathology findings of the pathology procedure belongs in the ‘NOTE’ table.
- The pathology report in the ‘NOTE’ table should be related to the pathology procedure in the ‘PROCEDURE_OCCURRENCE’ table via the note_event_id/note_event_field_concept_id (or via FACT_RELATIONSHIP in CDM 5.X).
- The pathology findings (like anatomic site, histology, grade, staging and lymphatic invasion, etc.) belong in the ‘MEASUREMENT’ domain/table.
- The pathology findings in the ‘MEASUREMENT’ domain/table should related to the pathology procedure in the ‘PROCEDURE_OCCURRENCE’ table via ‘FACT_RELATIONSHIP’.
I have an open ticket related to this here:
The upshot of my ticket is that I believe pathology procedure concepts should be uniformly moved into the ‘Procedure’ domain and that the definition of a procedure should be modified as follows:
“The PROCEDURE_OCCURRENCE table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient, OR A SPECIMEN EXTRACTED FROM THE PATIENT, to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization.”
One current issue is that pathology procedure concepts are scattered accross multiple domains:
| SNOMED Code | SNOMED URL | OHDSI URL | Name | Domain |
|---|---|---|---|---|
| 108259003 | SNOMED International Browser | Athena | Autopsy pathology procedure AND/OR service | Procedure |
| 127801007 | SNOMED International Browser | Athena | Body fluid analysis | Measurement |
| 26086007 | SNOMED International Browser | Athena | Bone marrow laboratory procedure (procedure) | Measurement |
| 73735000 | SNOMED International Browser | Athena | Cytogenetic procedure | Procedure |
| 77485009 | SNOMED International Browser | Athena | Cytopathology procedure or service | Procedure |
| 15719007 | SNOMED International Browser | Athena | Fine needle aspirate with routine interpretation and report | Measurement |
| 64444005 | SNOMED International Browser | Athena | Flow cytometry | Procedure |
| 426329006 | SNOMED International Browser | Athena | Fluorescence in situ hybridization | Procedure |
| 33468001 | SNOMED International Browser | Athena | Hematology procedure | Measurement |
| 4192879 | SNOMED International Browser | Athena | Hematopathology | Observation |
| 108262000 | SNOMED International Browser | Athena | Molecular biology method | Procedure |
| 116148004 | SNOMED International Browser | Athena | Molecular genetics procedure | Procedure |
| 59000001 | SNOMED International Browser | Athena | Surgical pathology consultation and report on referred slides prepared elsewhere | Observation |
| 39228008 | SNOMED International Browser | Athena | Surgical pathology procedure | Procedure |