General info for using ABCD data

Important

Only users registered with a named application can use this data. Check with Dr Heather Whalley if you have any question. Watch this video to know more about data protection.

ABCD protocol papers
Data dictionary for release 2.0.1
A summary of ABCD study

Data location

  • Eddie: /exports/igmm/eddie/GenScotDepression/data/abcd/release2.0.1
  • Eddie datastore: /exports/igmm/datastore/GenScotDepression/data/abcd/release2.0.1
  • CMVM datastore:

Important

You should check with Dr. Heather Whalley to see if you have been added to the data usage agreement (i.e. permission to use the data). Once you have permission, contact Dr. Mark Adams for access to the GenScotDepression folder.

Data in these folders are the same. You can load from whichever location you prefer.

Within the data folder, you will be able to see:

  • i.files_from_web: raw curated data from the NDA database in plain text format (not recommended to use).
  • ii.docs: supporting documentations from the NDA database.
  • iii.data: curated data sorted by category. Data is stored in rds format (recommended).

Data download

This section describes procedures for downloading data used by data managers. Those who only wish to use the data can omit this section.

Data

Downloaded

In subfolder 'i.files_from_web'

Procedure:
- Go to: https://nda.nih.gov/abcd - Login with NDA credentials and go to 'my dashboard' - Click username at the topright of the page to go to your profile - Go to 'Data packages' and select the packages to download (add to 'My Data Packages' using tab 'Actions') - Click 'Download Manager' - Run the downloaded 'Download Manager' - Login with NDA credentials - Download data

Note

It takes a while before the added packages appears in your account. Large data may take up to around 30 mins.
Remember that including bulk data may take up a very large space

The latest curated data packages downloaded are: ABCDstudyNDA

Supporting documentations

Downloaded

In subfolder 'ii.docs'

Summary of the latested release
Check the hyperlinks 'DEAP-NDA variables mapping' and 'Release Notes' for more information about the current dataset.

Segment data by category

Functions need

  • Summary

    • process_files.R is the default R script for all main steps
    • baseline.R and baseline_imputation.R are functions for baseline measures
    • Other files are used by process_files.R

  • Files essential for process_files.R (all need manual check for each data release)

    • Instruments.ABCD_summary_web_dictionary.csv: This file should be created manually. Copy contents from URL
    • ls.category: a list of object names and categories, a master list of all object names that ABCD ever released
    • ls.category.PreiousVersionOnly: like ls.category, but contains the objects only release in a previous version
    • ls.category.CurrentVersion: like ls.category, but contains objects released in the lasted version
    • ls.faultyobjects: sometimes ABCD have objects that need to be removed (e.g. some imaging files from release 2.0, fixed in release 2.0.1)