Skip to main content

cBioPortal

Category: Cancer study package

cBioPortal is a platform and study format for cancer genomics data. Convert-Pheno reads study metadata, patient and sample clinical tables, and case lists from a study package. This profile is implemented and regression-tested; timeline and molecular files are not converted.

RoleInput
Accepted inputStudy directory or ZIP package
Main outputBFF, PXF, OMOP-CDM
Mapping fileOptional for project-specific clinical fields
cBioPortal clinical study metadata, patient and sample tables, and case lists linked before conversion
Clinical files are discovered through cBioPortal metadata and linked by patient and sample identifiers

What You Need​

Supply either an unpacked study directory or a .zip archive. The package must contain:

  • meta_study.txt
  • one sample-clinical metadata file and its referenced data table
  • optionally, a patient-clinical table and case_lists/
convert-pheno -icbioportal study/ \
  -obff --entities individuals biosamples datasets cohorts \
  --out-dir bff_out/

PXF and OMOP-CDM output use the same input. See the cBioPortal recipes.

What Is Converted​

cBioPortal contentBFF content
study metadatadatasets
patient rowsindividuals
sample rows and patient linksbiosamples
case listscohorts
ONCOTREE_CODEOncoTree: disease and histological-diagnosis terms

Identifiers and links are checked before mapping. Duplicate identifiers or references to unknown patients and samples stop the conversion.

SAMPLE_TYPE values such as Primary are cBioPortal source categories, not necessarily ontology concepts. They remain in source provenance, while sampleOriginType stays Not Available unless a project mapping supplies a reviewed ontology term.

Use --no-source-info to omit the copied patient, sample, and study metadata. Structural links and mapped semantics remain.

Optional Project Mapping​

A Mapping V2 file with source.profile: cbioportal can map additional patient beacon.biosamples evaluates sample attributes. Source PATIENT_ID and SAMPLE_ID values cannot be rewritten because sample links and case lists depend on them.

See Mapping Files and cBioPortal to BFF for the detailed contract.

Current boundaries

The package is processed in memory. ZIP archives are read directly. Timeline and molecular files are not converted, and this filesystem-package route is not exposed through the HTTP(s) API.