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| Resource element (CodeableConcept) | FHIR ValueSet | SNOMED CT attribute | SNOMED CT range | Comments | Comparison |
|---|---|---|---|---|---|
Specimen.type Suggest rename to .substance | https://www.hl7.org/fhir/v2/0487/index.html A v2 value set reused for FHIR | JTC Suggestion: Expand the range of 370133003 |Specimen substance (attribute)| to incorporate the hierarchies listed. DK: 118168003 |Specimen source morphology (attribute)| has <<49755003 |Morphologically abnormal structure (morphologic abnormality)| as range and 118170007 |Specimen source identity (attribute)| has << 260787004 |Physical object (physical object)| in its range. | < 105590001 |Substance (substance)| (in which case method and site should also be populated) OR < 49755003 |Morphologically abnormal structure (morphologic abnormality)| OR < 260787004 |Physical object (physical object)| | 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). | (^500121000057102 |urval provtyp laboratoriemedicin|) AND (<<123038009 |Specimen|:370133003 |Specimen substance|=*), n=44 |
| < 123038009 | Specimen (specimen) | | Pre or post coordinated concept which would preclude the population of other code fields. | ^500121000057102 refset with specimen concepts from Swedish microbiology labs, n=77 | |||
| Specimen.collection.method | https://www.hl7.org/fhir/valueset-specimen-collection-method.html Extensional ValueSet | 118171006 | Specimen procedure (attribute) | | < 71388002 | Procedure (procedure) | | (^500121000057102 |urval provtyp laboratoriemedicin|) AND (<<123038009 |Specimen|:118171006 |Specimen procedure|=*), n = 24 | |
Specimen.collection.bodySite Suggest rename to .source YGA suggests adding this rather than renaming so as to avoid overloading an element with heterogenous data. JTC agrees. | Include codes from | 118169006 | Specimen source topography (attribute) | | < 49755003 Morphologically abnormal structure | Previously << 442083009 | Anatomical or acquired body structure | Update 17 March: Not sure where this attempt to broaden collection site has come from. It's not showing as permissible in the MRCM. SV thinks the V2 mapping might be relevant ie https://www.hl7.org/fhir/v2/0487/index.html again also https://www.hl7.org/fhir/specimen-mappings.html#v2 | (^500121000057102 |urval provtyp laboratoriemedicin|) AND (<<123038009 |Specimen|:118169006 | Specimen source topography (attribute) |=*), n=48 500091000057101 additional refset with 66 body sites |
Specimen.collection.method JTC: Duplicate row? See two rows above | Note that the method would encompass the device used in obtaining the specimen <706041008 |Device for body fluid and tissue collection/transfer/processing (physical object)| | ||||
| 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) | JTC: The use of this attribute here is incorrect as the definition of 118171006 | Specimen procedure (attribute) | is "... identifies the procedure by which a specimen is obtained.", not what is done with the specimen after collection | << 71388002 | Procedure (procedure) | | (^500121000057102 |urval provtyp laboratoriemedicin|) AND (<<123038009 |Specimen|:118171006 |Specimen procedure|=*), n = 24 | |
| Specimen.processing.additive-->Substance.code | Include codes from Include codes from | primitive, e.g. 445295009 | Blood specimen with edetic acid (specimen) | | << 105590001 | Substance (substance) | | ||
| Specimen.container.type | Include codes from | Attribute type missing here? JTC: Is not a defining attribute so shouldn't be modelled as an attribute to the specimen. | ?? << 434711009 | Specimen container (physical object) | - only has 3 children. Useful values are distributed elsewhere. Consider << 706437002 |Container (physical object)| still doesn't contain test tube however! Also 706046003 | Specimen receptacle (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 ?? Catered for by Specimen.source | 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 FHIR is not interested in specifying the class of subject, it would just link to the instance of the particular person resource.
| (^500121000057102 |urval provtyp laboratoriemedicin|) AND (<<123038009 |Specimen|:118170007 | Specimen source identity (attribute) |=*), n=5 All "source identities" were devices, e.g. catheter tip, | |
Specimen.type ?? Catered for by Specimen.source | 118168003 | Specimen source morphology (attribute) | JTC: This SNOMED attribute is a "modifier" of the Specimen substance | << 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 ?? Catered for by Specimen.substance (previously type) | 370133003 | Specimen substance (attribute) | | << 105590001 | Substance (substance)| |
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