PCGR integrates a variety of different datasets relating to precision cancer medicine, that often use different ontologies when it comes to diseases or phenotypes. We have cross-referenced a variety of ontologies (DiseaseOntology, EFO, OncoTree, UMLS, ICD-10) that are in use in the oncology domain, and organized all the various tumor subtypes into 30 different main tumor sites (see also https://github.com/sigven/phenOncoX).
Below you can browse all the various phenotype terms (including
specific tumor subtypes) that are associated with each of the primary
sites. This as a guide to choose the primary tumor type when running
PCGR for a given sample (option --tumor_site).