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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

https://www.hl7.org/fhir/valueset-specimen-collection-method.html

Extensional ValueSet

< 71388002 | Procedure (procedure) |

1 Sept could we be more specific to 17636008 |Specimen collection (procedure)|?

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)|

1 SeptProcessing of the specimen may also be relevant - see 9265001 |Specimen processing (procedure)|

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.

< 49755003 Morphologically abnormal structure
OR < 442083009 Anatomical or acquired body structure
OR < 125676002 Person
OR < 133928008 Community
OR < 276339004 Environment
OR < 35359004 Family
OR < 49062001 Device

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)|

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

Random values exist: <<9265001 | Specimen processing (procedure) |

Sept 1 Note that a derived specimen can be indicated with the use of the parent element to point to a specimen that this specimen object came from, possibly in combination with a procedure object.

?? << 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.

https://www.hl7.org/fhir/v2/0371/index.html

A v2 value set reused for FHIR