1. First teleconference/web session Dec 11, 2015
Working Group 6 Criteria for Repository Inclusion: Standards, Interoperability, Sustainability, etc.
First teleconference/web session
Dec 11, 2015

2. Agenda 1. Introductions 2. Brief review of bioCADDIE
3. Goals for this group
Timeline
Discuss and check for understanding
4. Repositories/sources already indexed
5. The list of potential repositories/sources
6. Reactions, comments

3. WG6 – Current Membership
George Alter - ICPSR, University of Michigan
Dianne Babski - National Library of Medicine
Tanya Barrett - NCBI (GEO, BioSample, BioProject), GA4GH
Kei Cheung - Yale University
Tim Clark - Harvard Medical School, FORCE11 Data Citation Implementation Group
Larry Clarke - National Cancer Institute (NCI)
Ian Fore - NIH
Marek Grabowski - University of Virginia
Jeffrey Grethe - University of California San Diego
Chelsea Ju - University of California Los Angeles
Chirag Lakhani - Harvard Medical School
Matthew McAuliffe - Center for Information Technology NIH
Neil McKenna - Baylor College of Medicine
Lucila Ohno-Machado - University of California San Diego
Thomas Radman - NIH
Jim Rehg - Georgia Institute of Technology
Susanna-Assunta Sansone - University of Oxford and Nature Publishing Group
Alisa Surkis - New York University School of Medicine
Griffin Weber - Harvard Medical School
Justin Wood - University of California Los Angeles
John Yates - The Scripps Research Institute
Wenchao Yu - University of California Los Angeles
2/17/20192/17/2019
Supported by the NIH grant #xxxxxxxxx to the University of California, San Diego

4. Introductory Logistics
bioCADDIE Web Site
White paper
Under Resources
Working Groups Menu
Working Group 6 Or
Google “biocaddie wg6” !

5. bioCADDIE – Working Groups location on the web site

6. User Interface Prototype
UI webpage address:
datamed.biocaddie.org
User name: biocaddie
Password: biocaddie

7. WG6 - Goals GOAL ACTIVITIES/RESPONSIBILITIES DELIVERABLES
Obtain consensus from multiple NIH representatives on which data sets NIH wants to see indexed by bioCADDIE
Determine which features(criteria) these sets have in common for future selection of data sets
Determine process of review of criteria for newly proposed datasets
ACTIVITIES/RESPONSIBILITIES
Assemble an authoritative group of a minimum of 4 NIH officers and 4 bioCADDIE executive committee members to discuss criteria to select repositories using the DDI prototype.
Decide which repositories will be used for the prototype
DELIVERABLES
Recommended metadata for data inclusion
Contact information for NIH-selected data sets
Standard for persistence and preservation
Investigation of access requirements

8. Balancing Act for Criteria
What researchers/repositories can provide?
Which criteria program officers will endorse?
Metadata quality

9. Criteria for Inclusion in the Initial Prototype
Key data resources used by the community
Aligns with concept of the Commons Pilots
Cancer Genomics Cloud Pilots and Genomic Data Commons
Human Microbiome Project
Model organism databases
Facilitate development of indexing methodology
Ensure broad coverage of types of data
Examples not yet represented
Clinical data, Imaging data
“The long tail”?
The hardest to find
The Variety component of big data
There is good convergence between the bioCADDIE emphasis on indexing highly accessed datasets and the idea of the Commons. The Cancer Genomics Cloud Pilots and Genomic data commons both seek to make available data which are highly used by cancer researchers. These will not be in credits model funded cloud – but they are part of a broader Commons.

10. NIH representation on WG6
Represent NIH repositories
Intramural and extramural
Facilitate collaborations
Represent NIH program staff
Criteria they are willing to endorse in their programs

11. Background relevant to WG6
Metadata specification
Can repositories provide this?
Identifiers
A non-prescriptive approach
Does it work for repositories?
Core Development work
Pipeline for reading data from repositories
Material on all the above on website
How do we supplement this?

12. Repositories already in progress
Source
Status
PDB, GEO
Stable
BioProject, ArrayExpress, dbGAP, GEMMA
Ongoing
Library of Integrated Network-based Cellular Signatures (LINCS) program
Reviewing API details for structure
Inter-university Consortium forPolitical and Social Research (ICPSR)
Reviewing sample file for structure
Jeff to speak to

13. Future The next 10 repositories The overall list of repositories
In Google Docs
The overall list of repositories

14. Thank you!
Questions?