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Nakken S (2024). phenOncoX: A phenotype ontology map for cancer. -R package version 0.7.9, https://sigven.github.io/phenOncoX. +R package version 0.8.0, https://sigven.github.io/phenOncoX.
@Manual{, title = {phenOncoX: A phenotype ontology map for cancer}, author = {Sigve Nakken}, year = {2024}, - note = {R package version 0.7.9}, + note = {R package version 0.8.0}, url = {https://sigven.github.io/phenOncoX}, }
phenOncoX is an R data package that attempts to address this challenge. In short, phenOncoX provides a global cross-mapped set of phenotype ontology terms attributed to cancer phenotypes.
The mapping established within phenOncoX is semi-manually curated, using OncoTree as the starting point for a list of UMLS phenotype terms per cancer subtype/primary site. Next, phenOncoX appends a number of phenotypes attributed to heritable cancer conditions. Furthermore, each cancer subtype entry in OncoTree is expanded with additional subtypes that are found in the UMLS child-parent hierarchy of disease terms.
For each entry in the final list of phenotype terms, we make cross-mappings with phenotype terms from EFO, DO, and the ICD10 classification.
As of early September 2024, the following ontology versions are used to create the mapping:
As of late October 2024, the following ontology versions are used to create the mapping:
The package offers a few pre-processed datasets, along with metadata, that the user can retrieve and use for their own projects or set-ups. The package utilizes the googledrive R package to download the pre-processed and documented datasets to a local cache directory provided by the user.
IMPORTANT NOTE: The mapping established by phenOncoX attempts to be comprehensive, but we acknowledge that the presence of missing or erroneous cross-references might still occur.