An ontological definition of disease enables each type of disease to be
singularly classified in a formalized structure. By intention, the use of
disease ontology terms should facilitate a cross-link of information between
separate disease-related knowledge resources for a given domain.
However, multiple disease ontology frameworks have been developed for human
disease (i.e. OncoTree,
Experimental Factor Ontology (EFO),
Disease Ontology (DO), UMLS, ICD-10),
and they are used to different extents across knowledge resources in the
oncology domain, such as the following:
- gene-disease associations
- drug-disease indications
- variant-disease associations
In order to integrate such knowledge resources, there is henceforth a need
to cross-link or map the entries across disease ontologies to the extent it
is possible.
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 December 2025, the following ontology versions are used to create the mapping:
- OncoTree (2025_10_03)
- Experimental Factor Ontology v3.84.0 (2025-11-17)
- Disease Ontology (v2025-11-25)
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.
sigven AT ifi.uio.no
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