Microbiology Updates

[alexmbennett2]

The structure of the microbiology data in FHIR is not the most straightforward. Go through and confirm the data is coming across fine. To test:

• Observation_micro_test
  • [x] If no organism attached to test, make sure some information is passed on (currently looks like it would just say there is a test that occurred)
  • [x] Check for duplicate organisms referenced
• Observation_micro_org
  • [x] Ensure all micro_org have a test
  • [x] Check for micro_org without any susceptibility refs
  • [x] Check for duplicate org generation
• Observation_micro_susc
  • [x] Check if the interpretation valueset, custom interpretation for every entry don't make sense. The MIMIC column that is used might allow for custom text entry

Misc questions

• [x] Do we need/want a Specimen resource
  • There is an id for specimen but not much else, still probably worth it
• [x] Do dilution values need to be stored in ObservaitonMicroSusc?
• [x] Add invariant to micro profiles to specify one of hasMember or valueString MUST be present
  • Maybe not necessary for ObservtionMicroSusc since no hasMember here
  • US core already has an invariant at the top level that covers this!

[alexmbennett2]

Notes for Observation_micro_test

• If there is a test with no organism, the MIMIC comments column will be stored as a valueString in FHIR.
  • For tests with no organism and no comment, a fixed value of 'No result present' will be input into valueString
• Distinct organisms are selected for each test by an initial group by to get distinct values

[alexmbennett2]

Notes for Observation_micro_org

• All micro_org have an associated test
• Some micro_org do not have suceptiblity results. These entries now have a valueString value with the microbioloyevents comments column pulled in. If the comments column is NULL, then a simple message 'No susceptibility results present' is input
• The group by in the sql script ensures no duplicate organisms are created

Notes for Observation_micro_susc

• interpretation codes are fixed to four values R, S, I, P

[alexmbennett2]

Added Specimen resource and referenced at the top level in ObservationMicroTest