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GEL Cancer diagnosis terminology mappings.adoc

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Infoflex XML to openEHR diagnosis, morphology and topography mappings

an McNicoll <[email protected]> v1.0.0, 5-Nov-2017

Terminology system mappings

When mapping terminology identifiers you must use a combination of the xml tag name and snomed-version to map to the terminology attribute in openEHR FLAT JSON.

e.g as in …​

gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:0|terminology": "ICD-O-3",

  • morphology-icd ⇒ …​|terminology": "ICD-O-3"

  • morphology-snomedct ⇒ …​|terminology": "SNOMED-CT"

  • morphology-snomedrt ⇒ …​|terminology": "SNOMED-RT"

  • topography-icd ⇒ …​|terminology": "ICD-O-3"

  • topography-snomedct ⇒ …​|terminology": "SNOMED-CT"

  • topography-snomedrt ⇒ …​|terminology": "SNOMED-RT" -

  • diagnosis-icd ⇒ …​|terminology": "ICD-10"

  • diagnosis-snomed-ct ⇒ …​|terminology":"SNOMED-CT"

ℹ️
 For morphology-snomed and topography-snomed, the mapping depends on the snomed-version specified.

SNOMED Version Mapping table

  • 01 (SNOMED II) ⇒ ..|terminology": "SNM2"

  • 02 (SNOMED 3) ⇒ ..|terminology": "SNOMED3"

  • 03 (SNOMED 3.5) ⇒ ..|terminology": "SNM198"

  • 04 (SNOMED RT) ⇒ ..|terminology": "SNOMED-RT"

  • 05 (SNOMED CT) ⇒ ..|terminology": "SNOMED-CT"

  • 99 (Not Known) ⇒ ..|terminology": "SNOMED-NK"

Pattern: topography-icd

<gelCAN:topography>
 <gelCAN:topography-icd>C00.9</gelCAN:topography-icd>
</gelCAN:topography>
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|code": "C00.9",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|value": "C00.9",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|terminology": "ICD-O-3",

Pattern: topography-snomedct

<gelCAN:topography>
 <gelCAN:topography-snomedct>891345</gelCAN:topography-snomedct>
</gelCAN:topography>
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|code": "891345",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|value": "891345",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|terminology": "SNOMED-CT",

Pattern: topography-snomedrt

<gelCAN:topography>
 <gelCAN:topography-snomedrt>891345</gelCAN:topography-snomedrt>
</gelCAN:topography>
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|code": "891345",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|value": "891345",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|terminology": "SNOMED-RT",

Pattern: topography-snomed (01 -SNOMED 2)

<gelCAN:topography>
  <gelCAN:topography-snomed>tf1qYs</gelCAN:topography-snomed>
    <gelCAN:snomed-version>01</gelCAN:snomed-version>
  </gelCAN:topography-snomed>
</gelCAN:topography>
FLATJSON
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|code": "tf1qYs",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|value": "tf1qYs",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/topography|terminology": "SNM2",

Pattern: morphology-icd

  <gelCAN:morphology>
    <gelCAN:morphology-icd>8020/3</gelCAN:morphology-icd>
  </gelCAN:morphology>

Flat JSON:

 "gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:0|code": "8020/3",
 "gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:0|value": "8020/3",
 "gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:0|terminology": "ICD-O-3",

Pattern: morphology-snomed (SNOMED Not Known)

<gelCAN:morphology-snomed>
 <gelCAN:morphology-snomed>M80203</gelCAN:morphology-snomed>
 <gelCAN:snomed-version>99</gelCAN:snomed-version>
</gelCAN:morphology-snomed>

FLAT JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|code": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|value": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|terminology": "SNOMED-NK",

NB. The value of 'terminology' will depend on snomed-version - see mappings above.

Pattern: morphology-snomed (SNOMED RT)

<gelCAN:morphology-snomed>
 <gelCAN:morphology-snomed>M80203</gelCAN:morphology-snomed>
 <gelCAN:snomed-version>4</gelCAN:snomed-version>
</gelCAN:morphology-snomed>

FLAT JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|code": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|value": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|terminology": "SNOMED-RT",

NB. The value of 'terminology' will depend on snomed-version - see mappings above.

Pattern: morphology-snomedct (SNOMED CT)

<gelCAN:morphology>
  <gelCAN:morphology-snomedct>M80203</gelCAN:morphology-snomedct>
</gelCAN:morphology>

FLAT JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|code": "828978",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|value": "828978",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|terminology": "SNOMED-CT",

Pattern: morphology-snomedrt (SNOMED RT)

 <gelCAN:morphology>
   <gelCAN:morphology-snomedrt>M80203</gelCAN:morphology-snomedrt>
 </gelCAN:morphology>

FLAT JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|code": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|value": "CEpqB8",
"gel_cancer_diagnosis/problem_diagnosis:0/cancer_diagnosis/morphology:16|terminology": "SNOMED-RT",

Pattern: diagnosis-icd

<gelCAN:diagnosis-icd>C16.1</gelCAN:diagnosis-icd>

Flat JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/diagnosis|code" : "C16.1",
"gel_cancer_diagnosis/problem_diagnosis:0/diagnosis|value" : "C16.1",
"gel_cancer_diagnosis/problem_diagnosis:0/diagnosis|terminology" : "ICD-10",
ℹ️
 Because the openEHR diagnosis can only carry a single 'defining_code' (as an ICD-10 code), any other codes such as SNOMED-CT codes must be carried as 'mappings' in openEHR

Pattern: diagnosis-snomed-ct

<gelCAN:diagnosis-snomed-ct>828978</gelCAN:diagnosis-snomed-ct>

Flat JSON:

"gel_cancer_diagnosis/problem_diagnosis:0/_mapping:0|match" : "=",
"gel_cancer_diagnosis/problem_diagnosis:0/_mapping:0/target|code" : "828978",
"gel_cancer_diagnosis/problem_diagnosis:0/_mapping:0/target|terminology" : "SNOMED-CT",
ℹ️
 Because the openEHR diagnosis can only carry a single 'defining_code' (as an ICD-10 code), any other codes such as SNOMED-CT codes must be carried as 'mappings' in openEHR