How to access accompanying clinical data for the CCDI-MCI collection?

Support Data
1

Hello, we have downloaded the HE slides images from Molecular Characterization Initiative of the National Cancer Institute’s Childhood Cancer Data Initiative. However, we didn’t find the clinical or genetic information of these slides. Could you please kindly share how we can get and correlate these clinical informations with slide images? Thanks!

1 Like
2

See:

3

@beatrice thank you for reaching out with this question!

In addition to the resources shared above by @dclunie, which you should most definitely explore, a subset of clinical data is available directly in IDC along with the images. You are not the first one asking this question, and I will follow up with the details. I need some time to prepare that detailed response.

Note that we do not have any genetic/genomic information about IDC. The only way I am aware of to access it right now is through the resources mentioned by David.

4

@beatrice I updated this notebook to include an example how to access metadata describing anatomic structure and patient diagnosis, which for the CCDI-MCI collection is included in DICOM attributes: IDC-Tutorials/notebooks/pathomics/slide_microscopy_metadata_search.ipynb at master · ImagingDataCommons/IDC-Tutorials · GitHub

In short, idc-index python package, as of version 0.7.4, includes DICOM information from the AdmittingDiagnosesSequence as well as PrimaryAnatomicStructure in the sm_index table. The tutorial notebook referenced above demonstrates how to use idc-index for subsetting the slides, and how to download the selection.

If you are not a programmer, and you need to select slides by diagnosis without writing any code, please let us know!

6

Option 1: Download Participant IDs and Upload to CCDI

  1. Visit the IDC Slide Microscopy Summary:

  2. Download the list of participant IDs.

  3. Go to the CCDI Explore Page:

  4. Upload your list of participant IDs under the “Demographics” section.

  5. The application will filter the results for you.

  6. From these filtered results, you can download each tab of the table for the selected metadata that is presented.

  7. For all metadata on the study, go to the study tab, and select the download icon in the Access column for each study of interest.

Option 2: Use the CCDI Hub to Apply Filters

  1. Access the CCDI Explore Page

  2. Apply Filters:

  3. On the left side, find the filter panel and click on the “Study” tab.

  4. Select phs002790 MCI under the dbGaP accession to limit the datasets to this specific study.

  5. Download the Manifest Metadata:

  6. Go to the “Studies Table” tab.

  7. Click the download icon in the Access column to download the manifest metadata as a XLSX file.

  8. Review the Data:

  9. Open the XLSX file in Excel and apply filters to focus on your specific interests.

  10. Alternatively, you can download data from each table tab individually on the CCDI Hub and combine them as needed.

1 Like