MII Implementation Guide Microbiology - Local Development build (v2027.0.0-ballot2) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Specimen

Report - Specimen

Ballot question 1 — can you supply a Specimen resource for every result? Every investigation profile in this module requires Observation.specimen, as the HL7 EU Lab Semantic Workgroup does — it asks for an explicit Specimen even where the LOINC code already carries the material.

German laboratory practice reports that a Specimen resource is frequently not produced. If that holds widely, the two ways out point in opposite directions: relax Observation.specimen to 0..1 and let pre-coordinated LOINC codes carry the material, or keep the requirement and accept that some senders cannot conform.

Specimens are represented by Specimen, which derives from MII_PR_Biobank_Specimen_Bioprobe_Core of the MII Biobank module — a base profile written for exactly this purpose, which modules derive from rather than implement directly. Observation.specimen of every investigation profile references it.

The following elements are particularly relevant for the microbiological use cases:

• Specimen.type[sct]
  Should be populated with the specimen type. This applies even where the material is already pre-coordinated in the LOINC code used, so that the specimen type is available in a structured form and independently of the Observation code.

• Specimen.collection.collected[x]
  Gives the time of specimen collection. If that is not known, the time of specimen receipt may be documented instead.

• Specimen.parent
  Represents the relationship to the specimen from which another specimen was derived or taken, e.g. for further-processed materials or materials obtained from primary specimens.

Specimen.processing: staining

Up to 2027.0.0-ballot.rc2 the biobank base profile required the extension temperaturbedingungen on every Specimen.processing element — a requirement from the storage of biosamples, without meaning for laboratory processing, and one a derived profile could not relax. This guide raised it as a ballot question; the base profile relaxed it to 0..1 in its 2027.0.0-ballot, which this module now depends on, and the question is settled.

The staining technique is nevertheless not given under Specimen.processing.procedure, as the HL7 EU Lab Semantic Workgroup proposes, but in an extension on the Observation, extension[faerbung], with the same codes — see Microscopy, where ballot question 2 sets out the reasoning.

Incubation duration and temperature

Ballot question 3 — is incubation representable via Specimen.processing? FHIR provides for it there and the MII has the pieces, so the modelling is settled. We ask whether it is implementable at your site.

The elements, measured against R4 core and the biobank module on 2026-09-10:

• Duration — Specimen.processing.time[x] as a Period. Specimen.processing has no Duration element of its own (Specimen.collection.duration refers to collection), so start and end are the FHIR-native form. That is precisely what the European data model asks for when it notes that its candidate LOINC code 80581-2 "mandates for start/enddate" — with a Period the requirement is met and no new LOINC code is needed.
• Temperature — the extension MII_EX_Biobank_Temperaturbedingungen, whose context is Specimen.processing and whose value is a Range. The right element and the right datatype for "35-37 degrees C", and optional since the base profile's 2027.0.0-ballot.

If no Specimen resource is produced (ballot question 1), Specimen.processing is out of reach, and the alternative would be extensions on Observation.method, which qualify the technique in the resource that reports the result. This module does not represent incubation until the answer is in.