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

**URL:** <https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636>\
**Category:** Data\
**Tags:** ccdi\_mci\
**Created:** [October 11, 2024, 3:24am UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636 "2024-10-11T03:24:39Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![beatrice](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.canceridc.dev/beatrice/32/501_2.png) [@beatrice](https://discourse.canceridc.dev/u/beatrice)\
**Post date:** [October 11, 2024, 3:24am UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636/1 "2024-10-11T03:24:39Z")

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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!

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**Author:** ![dclunie](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.canceridc.dev/dclunie/32/174_2.png) [@dclunie](https://discourse.canceridc.dev/u/dclunie)\
**Post date:** [October 11, 2024, 5:59am UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636/2 "2024-10-11T05:59:45Z")

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See:

- [Molecular Characterization Initiative for Childhood Cancers - NCI](https://www.cancer.gov/research/areas/childhood/childhood-cancer-data-initiative/programs/molecular-characterization#where-can-these-data-be-accessed)
- [CCDI Hub](https://ccdi.cancer.gov/MCI#Accessing_MCI_Data)

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**Author:** ![fedorov](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.canceridc.dev/fedorov/32/3_2.png) [@fedorov](https://discourse.canceridc.dev/u/fedorov)\
**Post date:** [October 11, 2024, 2:10pm UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636/3 "2024-10-11T14:10:46Z")

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@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.

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**Author:** ![fedorov](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.canceridc.dev/fedorov/32/3_2.png) [@fedorov](https://discourse.canceridc.dev/u/fedorov)\
**Post date:** [October 18, 2024, 9:49pm UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636/4 "2024-10-18T21:49:35Z")

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@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](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/pathomics/slide_microscopy_metadata_search.ipynb)

In short, [`idc-index` python package](https://github.com/ImagingDataCommons/idc-index), 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!

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**Author:** ![Bahar](https://avatars.discourse-cdn.com/v4/letter/b/77aa72/32.png) [@Bahar](https://discourse.canceridc.dev/u/Bahar)\
**Post date:** [November 26, 2024, 3:26pm UTC](https://discourse.canceridc.dev/t/how-to-access-accompanying-clinical-data-for-the-ccdi-mci-collection/636/6 "2024-11-26T15:26:19Z")

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**Option 1: Download Participant IDs and Upload to CCDI**

1. **[Visit the IDC Slide Microscopy Summary](https://lookerstudio.google.com/reporting/e4795618-80ad-4cfe-a668-89a8090d560b/page/NM1rD)**:

2. Download the list of participant IDs.

3. **Go to the [CCDI Explore Page](https://ccdi.cancer.gov/explore)**:

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.