cBioPortal to BFF
This table summarizes the built-in clinical study mapping. Project-specific patient and sample columns can be added with an optional Mapping V2 file.
| cBioPortal source | BFF destination | Behavior |
|---|---|---|
| Study identifier | Dataset identifier | Preserved as the stable dataset identity |
| Study name and description | Dataset name and description | Copied from study metadata |
| Patient identifier | Individual identifier | Required and not rewritable by the optional mapping |
| Patient sex or gender | Individual sex | Common male, female, other, and unknown values are normalized |
| Patient survival status | Phenopackets vital-status provenance | Living/alive and deceased values are recognized when present |
| OncoTree code and cancer labels | Individual disease | One distinct disease term is emitted per patient |
| Sample identifier | Biosample identifier | Required and not rewritable by the optional mapping |
| Sample patient identifier | Biosample individual link | Must resolve to a known patient |
| OncoTree code and detailed cancer label | Biosample histological diagnosis | Emitted as an OncoTree: term |
| Sample type | Source provenance | Preserved exactly; not assumed to be an ontology concept |
| Case-list stable identifier and name | Cohort identifier and name | Preserved from each case-list descriptor |
| Case-list sample members | Cohort membership and size | Samples are resolved to distinct patient identifiers |
Required Defaults
BFF requires ontology terms for biosampleStatus and sampleOriginType.
cBioPortal clinical tables do not guarantee ontology identifiers for either
field, so the built-in mapping uses NCIT:C126101 (Not Available). An
optional mapping may replace these defaults with curated terms.
The source value SAMPLE_TYPE=Primary is not mapped to the generic NCIT term
whose label is also “Primary.” Label equality alone does not establish that a
source category represents specimen origin.
Source Provenance
With the default --source-info, generated records retain:
- patient attributes under
info.cbioportal.patient - sample attributes under
info.cbioportal.sample - study and attribute-definition metadata under dataset
info.cbioportal - case-list descriptors and resolved membership under cohort
info.cbioportal
--no-source-info removes copied source payloads. Resolved cohort membership
is retained because it is part of the converted relationship graph.
Optional Mapping
Use source.profile: cbioportal. Individual rules read patient columns and
biosample rules read sample columns. Dataset and cohort defaults can augment
the source-derived collection metadata. The package identifiers remain
authoritative so references cannot be broken by configuration.
See the cBioPortal format guide for commands and input scope.