Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

user wishes to map combination of ICDO Topology and ICDO Morphology codes #236

Open
sheridancbio opened this issue Feb 19, 2021 · 1 comment

Comments

@sheridancbio
Copy link
Contributor

When going from ICDO to oncotree code, the ontology-to-ontology mapping tool is unable to combine ICDO Topography and Morphology codes to select a more specific oncotree code. So, for example, the combination of "C15.9" (Esophagus, NOS) and "8070/3" (Squamous cell carcinoma, NOS) could if both used narrow the selection to the oncotree code for Esophageal Squamous Cell Carcinoma (ESCC) ...

but if only C15.9 is used, it could be mapped to any of these (as well as ESCC):
Adenocarcinoma of the Gastroesophageal Junction (GEJ)
Mucosal Melanoma of the Esophagus (ESMM)
Esophageal Adenocarcinoma (ESCA)
Esophagogastric Adenocarcinoma (EGC)
Esophageal Poorly Differentiated Carcinoma (EPDCA)

and if only 8070/3 is used, it could be mapped to any of these (as well as ESCC):
Lung Squamous Cell Carcinoma (LUSC)
Larynx Squamous Cell Carcinoma (LXSC)
Head and Neck Squamous Cell Carcinoma (HNSC)
Penile Squamous Cell Carcinoma (PSCC)
Oropharynx Squamous Cell Carcinoma (OPHSC)
Urethral Squamous Cell Carcinoma (USCC)
Bladder Squamous Cell Carcinoma (BLSC)
Cutaneous Squamous Cell Carcinoma (CSCC)
Anal Squamous Cell Carcinoma (ANSC)
Metaplastic Squamous Cell Carcinoma (MSCC)
Prostate Squamous Cell Carcinoma (PRSC)
Cervical Squamous Cell Carcinoma (CESC)
Oral Cavity Squamous Cell Carcinoma (OCSC)
Hypopharynx Squamous Cell Carcinoma (HPHSC)
Squamous Cell Carcinoma of the Vulva/Vagina (VSC)
Squamous Cell Carcinoma, NOS (SCCNOS)
Head and Neck Squamous Cell Carcinoma of Unknown Primary (HNSCUP)

I think ideally when going from ICDO codes to Oncotree codes, the tool should consider the combination of topography and morphology codes and select the exact oncotree code which corresponds to the combination of ICDO codes. If no exact match is found it could report the choices which matched only the topologic code, and the choices which matched only the mophologic code (to aid the user in a manual selection).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

1 participant