Import data from ICDC

📘

Currently available version of ICDC data on CAVATICA has been updated with UBC02 - Basal and Luminal Molecular Subtypes in Naturally-Occurring Canine Urothelial Carcinoma Are Associated With Tumor Immune Signatures and Dog Breed.. For more information about the timeline and contents of each ICDC release, please see the ICDC website.

About ICDC

Integrated Canine Data Commons (ICDC), a cloud-based repository of canine cancer data and was established to further research on human cancers by enabling comparative analysis with canine cancer. The data in the ICDC is sourced from multiple different programs and projects; all focused on canine subjects. The data is harmonized into an integrated data model and then made available to the research community.

The process of importing files from ICDC to CAVATICA consists of the following two stages:

  • Downloading a manifest file from the ICDC website.
  • Importing files to CAVATICA based on the downloaded manifest file.

Please note that the Seven Bridges team strives to keep the data available for import on CAVATICA aligned with ICDC data updates. However, ICDC updates are not instantly available for import on CAVATICA. Find out the currently available release of ICDC data on CAVATICA and see the complete history of updates.

Downloading manifest files from ICDC

Manifest files that are downloaded from ICDC contain information about the data you want to import in the second stage of this process.

To download a manifest file from ICDC:

  1. Open the ICDC website.
  2. Click Cases on the main navigation bar at the top of the page.
  3. In the filters section on the left, select the criteria to narrow down the cases list.
14291429
  1. Scroll down to see the list of cases that match the filtering criteria.
14281428
  1. Check the boxes next to cases you want to select.
  2. Click Add Filtered Files Associated With Selected Case(s) in the bottom-left corner below the list.
  3. Click the MY FILES button in the top-right corner of the page. The button should also show a badge with the number of selected files.
509509
  1. Select the files which you want to download.
  2. Scroll down to the bottom of the page and click DOWNLOAD MANIFEST in the bottom-left corner.
    A CSV file is downloaded to your machine. Save the file as you will need it for the import procedure on CAVATICA.

Import files from ICDC to CAVATICA

  1. Navigate to a project on CAVATICA.
  2. Once in the project, click the Files tab.
  3. Click Add files > Import from a manifest file.
  4. In the Import files from dropdown, select Integrated Canine Data Commons (ICDC).
  5. Click Browse files and select the manifest file from your local machine, or drag and drop the file onto the marked area. Alternatively, if you have already uploaded your generated manifest file to a project, click Select manifest from project and select the file.
  6. (Optional) In the Add tags field add the keywords (tags) that describe the imported items.
  7. Resolve naming conflicts - Select the action to be taken if a naming conflict occurs. Available actions are Skip and Auto Rename. Read more about naming conflicts resolution.
  8. Click Import. The file import process starts and you are taken to the Files tab.

Metadata

The ICDC API provides easy and open access to ICDC metadata. One of the ways to get ICDC metadata on CAVATICA is to use Data Cruncher to query the ICDC API.

Reference files

The Public Reference Files repository on CAVATICA contains two ICDC-related files that are ready to be used in e.g. RNA-seq alignment workflows with ICDC data provided as inputs. Those files are:

  • Canis_familiaris.CanFam3.1.dna.toplevel.fa (reference genome)
  • Canis_familiaris.CanFam3.1.98.gtf (gene annotation file)

Did this page help you?