sheridancbio
commented
3 years ago cc: @ritikakundra @rmadupuri
Open sheridancbio opened 3 years ago
sheridancbio
commented
3 years ago cc: @ritikakundra @rmadupuri
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).