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TCGA Imaging Data Integration with cBioPortal

This document describes the process of acquiring TCGA imaging studies from the NCI Imaging Data Commons (IDC) and integrating them as patient resources in cBioPortal's TCGA Pan Cancer Atlas 2018 studies. The images can be viewed using OHIF (radiology) and SLIM (pathology) viewers within the portal.

Data Structure in IDC

IDC organizes imaging data hierarchically:

Collections → Patients → Studies → Series → Instances
  • Study: One complete imaging exam for a patient, regardless of modality (e.g., "CT Chest with Contrast", "MRI Brain"). One patient could have undergone multiple imaging studies over time.
  • Series: Individual image batches within a study (e.g., different CT scan sections or sequences)

Note: While a single study may contain multiple imaging modalities, data was extracted at the study level and then split by modality for cBioPortal integration. This modality-level organization allows users to selectively access specific imaging types (e.g., CT scans vs. H&E slides) for each patient.

Available Imaging Modalities

Code Modality Viewer Resource ID Resource Tab Name
CR Computed Radiography OHIF IDC_OHIF_CR Computed Radiography
CT Computed Tomography OHIF IDC_OHIF_CT CT Scan
DX Digital Radiography OHIF IDC_OHIF_DX Digital Radiography
MG Mammography OHIF IDC_OHIF_MG Mammography
MR Magnetic Resonance OHIF IDC_OHIF_MR Magnetic Resonance
NM Nuclear Medicine OHIF IDC_OHIF_NM Nuclear Medicine
PT Positron Emission Tomography OHIF IDC_OHIF_PT PET Scan
SM Slide Microscopy (H&E) SLIM IDC_SLIM H&E Slide

Note: Annotation (ANN), Segmentation (SEG) and Structured Report (SR) are excluded as standalone resources since they are automatically loaded with their parent imaging studies in OHIF. Other (OT) modality is also excluded.

Implementation Steps

Generate Resource Files

Patient-level resource files are generated for each TCGA Pan Cancer study by:

  1. Downloading TCGA imaging metadata from IDC using the idc-index package
  2. Linking patients to their imaging studies via OHIF and SLIM viewer URLs

Script: generate_imaging_resources.py

Output Files

For each TCGA Pan-Cancer Atlas 2018 study, two files are generated:

  1. data_resource_patient.txt: Links patients to their imaging studies

    • Columns: PATIENT_ID, RESOURCE_ID, URL

  2. data_resource_definition.txt: Defines the resource types available in the study

    • Columns: RESOURCE_ID, DISPLAY_NAME, RESOURCE_TYPE, DESCRIPTION, OPEN_BY_DEFAULT, PRIORITY

Viewer URLs

  • OHIF Viewer (for radiology imaging): https://viewer.imaging.datacommons.cancer.gov/viewer/{StudyInstanceUID}
  • SLIM Viewer (for slide microscopy): https://viewer.imaging.datacommons.cancer.gov/slim/studies/{StudyInstanceUID}