3.Gram Stain Profile - Healthedata1/OO-on-FHIR-Micro-Profile GitHub Wiki

This Profile on Observation defines the gram stain observations for a culture.

There are two potential patterns for reporting a Gram Stain results: 1) a single observation on the cytologic description -e.g. 'Gram Positive Bacilli' 2) a pair of observations describing the relative number as well as the cytologic descripion - e.g. 'Many Gram Positive Bacilli'. This profile describes the structure for the second case.

Based on DAF-Core/US-Core plus additional USlab (LRI) and US-Core Micro Report constraints (in italics):

Each Gram stain Observation must include:

  1. a status
  2. a category code of ‘laboratory’
  • micro category code as translation
  1. a LOINC code, if available, which tells you what is being measured
  2. performing organization
  3. a patient
  4. a pair of result components with: - LOINC code and a component result code for the relative number and - LOINC code and a component result code for the cytologic description

Each Gram stain Observation must include: must support:

(stuff from LRI OBX and OBR)

  1. an identifier (Filler/Placer) - Discuss whether this is a must support - not an LRI requirement
  2. a time indicating when the specimen was collected
  3. a time indicating when the measurement was reported
  4. the specimen
  5. 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

(note: the LRI requirement for AOE vs results category is not needed for this profile since is implicitly a result profile)

Terminology considerations ( note need help from community to work these out)

For Observation.code & Observation.component.code - extensible binding to LOINC with METHOD_TYP = 'Gram stain`

For Observation.component.valueCodeableConcept - extensible binding to SNOMED CT qualifier codes for Rare, Few, Moderate and Many.

For Observation.component.valueCodeableConcept - extensible binding to SNOMED CT concept codes for: ( This is too big a Valueset right now- need to identify the relevent 20 or so terms.)

View US-Core Gram Stain StructureDefinition