Deprecate sphn:ICDODiagnosis and introduce aidava:Topography and aidava:Morphology

[KateSerafimova]

Background

In SPHN there is a subclass of Diagnosis, called sphn:ICDODiagnosis. It has properties sphn:hasTopographyCode and sphn:hasMorphologyCode, which allow coding system ICD-O-3 Topography and ICD-O-3 Morphology, accordingly. These properties can be useful, but with wider range that will also include SNOMED codes.

Change Detail

[UPDATED]

The suggested change is to Deprecate sphn:ICDODiagnosis and add new class - aidava:OncologyDiagnosis, that will be a subclass of sphn:Diagnosis. As the OncologyDiagnosis in the 2024/1 version of SPHN, this class is to be equivalent to SNOMED 363346000 | Malignant neoplastic disease (disorder) |.

New property to be added to aidava:OncologyDiagnosis:

• sphn:hasBodySite with range sphn:BodySite - extend the domain of sphn:hasBodySite

Why is this change needed?

In MUG data there are the following data points: [topography]

1. Topography with valueset ICD-10 (C50.4, C50.9, C50.9..) -> to be mapped with hasCode of OncologyDiagnosis
2. Localization (Left/Right)
3. Lower Inside Tumor Localization (yes/no)
4. Lower External Tumor Localization (yes/no)
5. Central Tumor Localization (yes/no)
6. Upper Inner Tumor localization (yes/no)
7. Upper External Tumor localization (yes/no)

Having BodySite for OncologyDiagnosis will allow to map Localization to Laterality and the following codes to Body Site:

• 19100000 |Structure of lower inner quadrant of breast (body structure)|
• 33564002 |Structure of lower outer quadrant of breast (body structure)|
• 49058007 |Structure of central portion of breast (body structure)|
• 77831004 |Structure of upper inner quadrant of breast (body structure)|
• 76365002 |Structure of upper outer quadrant of breast (body structure)|

The ICD-10 code of the Topography can be mapped to hasCode of OncologyDiagnosis:

• 373090000 |Primary malignant neoplasm of breast lower inner quadrant (disorder)|
• 373091001 |Primary malignant neoplasm of breast lower outer quadrant (disorder)|
• 353521000119108 |Primary malignant neoplasm of central portion of female right breast (disorder)|
• 373089009 |Primary malignant neoplasm of breast upper inner quadrant (disorder)|
• 373088001 |Primary malignant neoplasm of breast upper outer quadrant (disorder)|

In MUG data there is listing of datapoints, that can be mapped to disorders or morphologic abnormalities in SNOMED. These can be mapped also to hasCode of OncologyDiagnosis:

1. IDC NST - 408643008 | Infiltrating duct carcinoma of breast (disorder) |
2. ILC - 722524005 | Primary invasive pleomorphic lobular carcinoma of breast (disorder) |
3. Specialized Invasiv Carcinoma
4. Morbidity Paget - 2985005 |Paget's disease, mammary (morphologic abnormality)| or 403946000 |Paget's disease of nipple (disorder)|
5. Inflammatory Breast Cancer - 254840009 | Inflammatory carcinoma of breast (disorder) |
6. DCIS - 109889007 | Ductal carcinoma in situ of breast (disorder) |

In UM data the following data points with possible values are listed:

• Topography: DCIS, LCIS, DCIS + LCIS, Other namely
• Histology in situ component: DCIS, LCIS, DCIS + LCIS
• Histology invasive breast cancer: Ductal carcinoma, Lobular carcinoma, Scirrhous adenocarcinoma, Tubular carcinoma, Cystic adenocarcinoma, Colloid carcinoma, Medullar carcinoma, Paget's disease

Here I think, that Histology invasive breast cancer values can be mapped to hasCode of OncologyDiagnosis.

What is the impact if this change isn't made?

Two new classes will be introduced so many relations are to be added, mainly related to Diagnosis.

Additional Information

Resource on how the ICD-O-3 codes are build shows what the topography and morphology components include: Topography: the location (site) of the tumor in the body

• Primary
• Subsite

Morphology (histology, cytology): the appearance of the tumor when examined under the microscope.

• Cell type
• Behavior
• Differentiation (grading)

[rcelebi]

In the SPHN 2024 candidate version, 'ICDODiagnosis' is replaced with 'OncologyDiagnosis,' and this new class includes 'hasBodySite,' which can be used to add Topography information. For Morphology, 'hasCode' in 'OncologyDiagnosis' can still be used. Details regarding change in SPHN: https://git.dcc.sib.swiss/sphn-semantic-framework/sphn-schema/-/blob/release-candidate-2024-1/dataset/documentation-2024.1/OncologyDiagnosis_2024.1_final.pdf

[rcelebi]

• In the WP2 on December 21, 2023, we agreed that SPHN 2024 candidate version provides a good solution for this issue. This change needs to be implemented in the AIDAVA reference ontology.

[KateSerafimova]

The disorders listed are actually composite in SNOMED CT, so they include the body structure

373090000 |Primary malignant neoplasm of breast lower inner quadrant (disorder)|
373091001 |Primary malignant neoplasm of breast lower outer quadrant (disorder)|
353521000119108 |Primary malignant neoplasm of central portion of female right breast (disorder)|
373089009 |Primary malignant neoplasm of breast upper inner quadrant (disorder)|
373088001 |Primary malignant neoplasm of breast upper outer quadrant (disorder)|

[todorprimov]

to be included in the next release