Resource
https://www.hl7.org/fhir/specimen.html
Profile examples
https://simplifier.net/search?text=specimen&category=Profile&fhirVersion=STU3
Relevant Confluence pages
Pathology and Laboratory Medicine Clinical Reference Group
Resource – concept model mapping
Yellow rows denote SNOMED CT attributes where there is no specific FHIR counterpart.
| Resource element (CodeableConcept) | FHIR ValueSet | SNOMED CT attribute | SNOMED CT range | Comments |
|---|---|---|---|---|
Specimen.type Suggest rename to .substance | https://www.hl7.org/fhir/v2/0487/index.html A v2 value set reused for FHIR | << 105590001 |Substance (substance)| (in which case method and site should also be populated) | A ConceptMap exists: https://www.hl7.org/fhir/conceptmap-example-specimen-type.html Another set of specimen type codes used for biobanking, SPREC, is available here (tables 1 and 2). | |
| Suggest new element: Specimen.code | << 123038009 | Specimen (specimen) | | Pre or post coordinated concept which would preclude the population of other code fields. | ||
| Specimen.collection.method | https://www.hl7.org/fhir/valueset-specimen-collection-method.html Extensional ValueSet | 118171006 | Specimen procedure (attribute) | | << 71388002 | Procedure (procedure) | | |
Specimen.collection.bodySite Suggest rename to .source | Include codes from | 118169006 | Specimen source topography (attribute) | | << 49755003 Morphologically abnormal structure | Previously << 442083009 | Anatomical or acquired body structure | |
| Specimen.processing.procedure | https://www.hl7.org/fhir/valueset-specimen-processing-procedure.html A v2 value set reused for FHIR (Most probably nothing in SNOMED CT corresponding directly to those codes) | 118171006 | Specimen procedure (attribute) | | << 71388002 | Procedure (procedure) | | |
| Specimen.processing.additive-->Substance.code | Include codes from Include codes from | primitive | << 105590001 | Substance (substance) | | |
| Specimen.container.type | Include codes from | - | ?? << 434711009 | Specimen container (physical object) | ?? | ValueSet not adequate, e.g. 337386000 | Test tube (physical object) | not included. Generally, little content in SNOMED CT. Terminology requirements?? SPREC, linked above also has a set of container types. |
| Specimen.container.additiveCodeableConcept | https://www.hl7.org/fhir/v2/0371/index.html A v2 value set reused for FHIR | primitive | << 105590001 | Substance (substance) | | |
| Specimen.subject ?? | 118170007 | Specimen source identity (attribute) | | << 125676002 | Person | OR << 35359004 | Family | OR << 133928008 | Community | OR << 49062001 | Device | OR << 276339004 | Environment | | Overlapping semantics between FHIR and SNOMED CT | |
| Specimen.type ?? | 118168003 | Specimen source morphology (attribute) | | << 49755003 | Morphologically abnormal structure | | SNOMED CT distinguishes site, abnormal morphology, and substance when specifying the material contents of the specimen, while FHIR only has type and collection.bodySite | |
| Specimen.type ?? | 370133003 | Specimen substance (attribute) | | << 105590001 | Substance (substance) | |
