6. Organism Observation (and nested related observations) - Healthedata1/OO-on-FHIR-Micro-Profile GitHub Wiki
This Profile on Observation defines the Observation of Organism(s) isolated for a culture.
The point of a culture is isolate and identify the bug(s) in a specimen. This profile represents the finding (isolation of) a organism as well as the links to related observatins on the isolated organism such as colony count, growth characteristics and susceptibility results.
Based on DAF-Core/US-Core plus additional USlab (LRI) and US-Core Micro Report constraints (in italics):
Each Observations must include:
- a status
- a category code of ‘laboratory’
- micro category code as translation
- a LOINC code for the MIC measurement.
- a patient
- performing organization
- a coded result value for an organism that was isolated NOTE:need to name the US-core slices in ordere to remove slices - this only adds another slice may be simpler to change US-core to invarients to alow downstream slicing see GFORGE #12178
Each micro atomic observation must support:
(stuff from LRI OBX and OBR)
- an identifier (Filler/Placer) - Discuss whether this is a must support - not an LRI requirement
- a time indicating when the specimen was collected
- a time indicating when the measurement was reported
- the specimen
- a specimen rejection reason This is really a data absent reason and should go there instead of an extension on Obs - consider a DAR profile
- references to related observations for colony count, growth characteristics and susceptibility results and other observations.
Terminology considerations ( note need help from community to work these out)
This profile uses the same set of codes that are found in the microreport profile
For the concepts representing the possible Organisms that may isolated use the SNOMED CT microorganism heirarchy. [SCTID=264395009]