DataRepositoryNotes

Overview

NA-MIC is using the Wiki to organize our analysis datasets, and to provide additional information about the meaning and history of the data. The Wiki is publically viewable, so no personally identifiable health information should go in the Wiki -- use the BIRN Repository for images and clinical metadata.

This page provides HowTo information about setting up and formatting data repository entries.

BIRN Repository

The Biomedical Informatics Research Network (BIRN) http://www.nbirn.net provides a secure password controlled infrastructure for managing research data that must be held confidential. BIRN is a collaborating project that shares many common investigators with NA-MIC. Where NA-MIC is primarily focusing on algorithm development and software engineering, BIRN is aimed at infrastructure development and cross-site calibration.

As a data repository, BIRN provides a number of important functions:

• password controlled access (contact Steve Pieper to request a NA-MIC account)
• per-file auditing of data transactions
• distributed / replicated data storage (i.e. multi-site) appearing as a single logical file hierarchy
• multiple data access and manipulation tools
  • the web-based portal
  • a java-based file browser with drag-and-drop to your local machine (the BIRN Virtual Data Grid)
  • an explorer-like windows client (inQ)
  • a set of unix-like command line tools (the 'Scommands')
  • an API for accessing the extra features of the BIRN repository
  • an experimental interface using AFS to mount BIRN as a local disk

To add data, first be sure you have proper IRB clearance to share the data. Typically this means that you will need to request additional permission to go beyond the original terms under which the data was collected. NA-MIC and BIRN are working to provide a secure infrastructure so IRBs can be comfortable allowing additional multi-institution research with the data.

Once the IRB is in place, upload the data to https://portal.nbirn.net/BIRN/cgi-bin/Projects/index.cgi?pid=NAMIC__0003&files=1

• Create a directory named for your site (called a "Collection" in BIRN terminology)
• Upload the files as a .tar.gz or .zip file
• Create a Wiki page describing the data you uploaded (see next section)

Wiki Pages

Use the wiki editing tools to provide a description of how the data was collected and how it should be interpreted. Please be as detailed as possible and include the scan parameters, subject selection criteria, etc. Ideally, publications describing the data should be uploaded.

Refer to the example pages in the data repository for examples.

• Refer to The MediaWiki User's Guide for more reading and editing help.

Note: you need to request a Wiki account to edit these pages. Currently anyone can get instant wiki account just by going here. If needed, we may restrict access in the future.

Images

You can upload images to the wiki to illustrate either the raw data or the type of derived data you can obtain from it. See the upload page for more information. See the slicer page for an example of how to reference an image from within a wiki page.

Documents

To facilitate sharing, the NA-MIC wiki has been modified to accept PDF files plus all the Microsoft Office document types (Word, Excel, PowerPoint). Use the same Special:Upload interface for documents that you use for images. See the existing examples in the DataRepository to see how these files can be referenced.