Study Configuration
Define cBioPortal study metadata and generate
meta_study.txt plus cancer type metadata.meta_study.txtmandatory
cBioPortal Instancelocal
Target API responds at /api/info. Write/import operations may require server-side metaImport.
Preview: meta_study.txt
type_of_cancer: cervix
cancer_study_identifier: cervix_kcmc_moshi_2024
name: Cervical Cancer - KCMC Zonal Hospital, Moshi 2024
add_global_case_list: false
reference_genome: hg38
groups: KCMC_ONCOLOGY;KCMC_ADMIN
Source Data
Review data extracted from GynOnco/Track for cBioPortal staging.
Patients Extracted
247
All registered <= May 2026
Samples / Encounters
1,483
Total clinical events
Incomplete Records
58
Flagged in validation
Data Types Ready
6
Clinical, staging, path, Rx, lab, timeline
Clinical Data
Staging
Pathology
Treatment
Timeline
Molecular (HPV)
Field Mapping
Map GynOnco/Track fields to cBioPortal columns and datatypes.
24 mapped4 review2 unmapped
data_clinical_patient.txt - Patient AttributesPATIENT_ATTRIBUTES
| GynOnco/Track Field | cBioPortal Column | Datatype | Priority | Required | Status |
|---|
data_clinical_sample.txt - Sample AttributesSAMPLE_ATTRIBUTES
| GynOnco/Track Field | cBioPortal Column | Datatype | Priority | Required | Status |
|---|
Data Validation
Run cBioPortal dataset validation checks against staged files.
Passed Checks
41
Format, types, required fields
Warnings
3
Non-critical
Errors
0
No blockers
Files Validated
7
Mandatory files present
Validation ReportNo blocking errors
Generate cBioPortal Files
Export staged data into cBioPortal import directory structure.
Study Directory Structure
cervix_kcmc_moshi_2024/
|-- meta_study.txt
|-- meta_cancer_type.txt
|-- meta_clinical_patient.txt
|-- data_clinical_patient.txt
|-- meta_clinical_sample.txt
|-- data_clinical_sample.txt
|-- meta_timeline_diagnosis.txt
|-- data_timeline_diagnosis.txt
|-- meta_generic_assay_hpv.txt
|-- data_generic_assay_hpv.txt
`-- case_lists/cases_all.txt
File Generation Progress
Load to cBioPortal
Push staged study through API or server-side metaImport.
Method 1: API PushRecommended
Uses the local cBioPortal REST API registered in the platform. Write endpoints may require protected server-side import privileges.
GET/api/studiesList studies
GET/api/studies/{studyId}Check study
POSTmetaImport.pyServer-side study import
Method 2: metaImport Script
# Run on cBioPortal server
python3 metaImport.py \
-s ./cervix_kcmc_moshi_2024/ \
-u http://10.105.0.251:8080 \
-o -v