GaP FAQ Archive

This book contains actual questions asked by dbGaP users. We have tried to compile questions and answers that are representative of the entire spectrum of questions that our users ask, regardless of whether or not they are frequently asked. It is therefore likely that the question you have now, or a variant of it, may have been asked before, and may be in this book. The book will be updated with new questions regularly.

The questions and their answers have been edited for clarity and to protect the privacy of our users.

Contents

• Data Content
  Created: October 21, 2008; Last Update: March 23, 2009.
  • Individual-level Data: General Questions
    Created: October 21, 2008; Last Update: March 23, 2009.
    • Data Available through the dbGaP
    • De-identification of Data
    • Available Data File Format
    • TCGA Data Availability
  • Analytical Tool Availability
    Created: October 21, 2008; Last Update: March 23, 2009.
    • Tool for analyzing individual level data remotely
    • Tool for analyzing summary level data
• Data Access Requests
  Created: October 21, 2008; Last Update: December 11, 2013.
  • Starting Point to Applying for dbGaP Data
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Demo Videos and Overview
    • Access Individual Level Data
    • The dbGaP and eRA Account
    • Institutional eRA Account
    • DUNS Number
    • Principal Investigator (PI) Role Is Required
    • For NIH Staff
    • Allow up to Two Days for New or Changed eRA Commons Account Information to Become Effective
  • Authorized Access System Login
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Login Page Redirect
    • Troubleshoot Login Problems
    • Reset Login Passwords
    • New Password Works at eRA but not at dbGaP
  • Data and Other Information Related to Controlled Access
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Authorized Access Related Information
    • IRB Requirement
    • Data Use Restrictions
    • Data Use Certification (DUC)
    • Data Manifest
    • Data Manifest of Sequencing (BAM, SRA, etc.) Data
  • Applying for Controlled Access Data
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Overview
    • Information of Data Available for Download
    • SRA Data Availability
    • A Brief Step-by-Step for Filling Out the Data Access Request
    • Check Status of Submitted Data Requests
    • Time Estimate for Data Access Committee (DAC) Review
    • Signing Official (SO) and IT Director
    • Select Datasets by Consent Groups
    • No Need to Complete the Request in a Single Session
    • How to Write the Research Use Statement
    • Examples of Research Use Statements
    • IRB Requirement
    • For Institutional Review Board (IRB)-Related Questions Contact the Data Access Committee (DAC)
    • Add or Update Institutional Review Board (IRB) Approval Documents
  • Revise, Amend, and Update Existing Application
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Revise Data Access Request
    • Recall is required before Making Changes to Project under SO Review
    • Changing Signing Official
    • Changing the Principal Investigator (PI) for Project
    • Transferring Data Request to a Different Institution
    • Adding New Lab Members from the Same Institution
    • Requested Wrong Data Sets
    • Change User Profile
  • Contact Information
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Contacting dbGaP
    • Contacting Data Access Committee (DAC)
    • Contact for Short Read Archive (SRA ) Related Questions
    • Contact for SRA Toolkit Related Questions
  • Expiration Date, Renewal, Project Suspension, and Closeout
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Data Request and Project Expiration Date
    • Renewal Procedure
    • Annual Report
    • Project Closeout
  • Account Suspension
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Why is My Account Suspended and How Do I Fix This Issue?
  • Collaborators
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Collaborators within Primary PI’s Institution
    • Collaborators outside Primary PI’s Institution
    • Collaborators who Contract with the Primary PI’s Institution
    • Add or Remove Collaborators
  • Signing Officials (SO)
    Created: October 21, 2008; Last Update: December 11, 2013.
    • Lost Passwords
    • How to Sign Off on a Data Access Request?
    • Changing Signing Official
• Downloading and Extracting dbGaP Data
  Created: October 22, 2008; Last Update: August 12, 2013.
  • Downloading Data
    Created: October 22, 2008; Last Update: August 12, 2013.
    • Aspera Connect
    • Download Procedure
    • How to Add Downloaders to Projects?
    • How to Become a Downloader?
    • Download Procedure for Downloader
    • Expired Download Package
    • FTP Site Availability for Downloads
  • Decrypting and Extracting Data
    Created: October 22, 2008; Last Update: August 12, 2013.
    • File Decryption
    • SRA to BAM format conversion
    • SRA fastq-dump Utility
  • Data Sample and Subject ID Mapping
    Created: October 22, 2008; Last Update: August 12, 2013.
    • Sample and Subject ID Mapping of Pheno, Genotype, and Sequencing Data
    • The Description of Sample, Subject IDs Used in dbGaP Data Files
• General Information regarding dbGaP Data Access
  Created: October 21, 2008; Last Update: December 7, 2011.
  • Data Sharing Policy
    Created: October 21, 2008; Last Update: December 7, 2011.
    • Data Sharing Policy
  • Informed Consent for Genomic Research
    Created: October 21, 2008; Last Update: December 7, 2011.
  • Citing dbGaP in a Publication
    Created: October 21, 2008; Last Update: December 7, 2011.
  • Is the Data I’m looking for Authorized (Controlled) or Public Access?
    Created: October 21, 2008; Last Update: December 7, 2011.
    • Questionnaires
  • Summary-Level Data
    Created: October 21, 2008; Last Update: December 7, 2011.
    • Is Authorized Access Required for Viewing Summary-Level data?
    • Embargo Release Dates
  • Is Institutional Affiliation Required for Data Access?
    Created: October 21, 2008; Last Update: December 7, 2011.
• Searching dbGaP
  Created: October 22, 2008; Last Update: March 23, 2009.
  • Is the Material I Need in Public Access or Authorized (Controlled) Access?
    Created: October 22, 2008; Last Update: March 23, 2009.
    • Questionnaires
  • How to Search for Specific Information in a Particular Study
    Created: October 22, 2008; Last Update: March 23, 2009.
    • Finding Variables Represented in a Specific Study.
• Submitting to dbGaP
  Created: October 21, 2008; Last Update: April 4, 2014.
  • Beginning the Submission Process
    Created: October 21, 2008; Last Update: April 4, 2014.
  • NIH ICs that Support GWAS
    Created: October 21, 2008; Last Update: April 4, 2014.