My research group is converting EHR data from General Practice and I’m having difficulty trying to map the data from Pap smears/Cervical screening tests. Our raw data (simplified) looks like this:
Patient Number: 123
Test Type: Either CST or Pap Smear
HPV result: Either positive or negative
Endocervical Cells result: Either present or absent
HPV Types detected: HPV-16, HPV-18, HPV Other in some combination
It’s straightforward to map the HPV Types detected - there’s appropriate Meas Value concepts for each combination and a Measurement concept for the DNA test. However, there doesn’t appear to be Meas Value concepts for ‘HPV Positive’, ‘HPV Negative’, ‘Endocervical cells present’, ‘Endocervical cells absent’ - the best matches I could find via Athena are instead Condition concepts:
4173570 / Cervical smear - endocervical cells absent
4056547 / Cervical smear - endocervical cells present
44810558 / Cervical smear - human papillomavirus negative
44810559 / Cervical smear - human papillomavirus positive
My understanding is that only Meas Value concepts are permitted to be used in the value_as_concept_id field, so these concepts aren’t appropriate. It does seem a bit odd to me that these clinical finding concepts are classed as Conditions rather than Measurements!
I wondered if there was perhaps a Measurement concept like ‘Test for presence of endocervical cells in cervical smear’ which then expects Meas Value concepts like e.g. 45884086 / Absent or 45879438 / Present as the value_as_concept_id, but if so I haven’t been able to find it.
Any advice much appreciated!