2018 Workshop 2
Agricultural microbiome data: data platforms, standards, and analytical tools needed for advancing our science (ICPP, Boston, MA)
Workshop Program (July 29, 10:30am-12:00pm, Room 206 Hynes Convention Center)
Welcome and Introductions
Linda Kinkel, University of Minnesota
Existing platforms: What is the state of the art for microbiome data? (45 minutes)
- The National Microbiome Data Collaborative (Lynn Shriml, University of Maryland, and Emiley Eloe-Fadrosh, JGI)
- The Joint Genome Institute (Susannah Tringe, JGI)
- The Genetics*Environmental*Management*Socioeconomic platform (Kevin Silverstein, University of Minnesota GEMS)
- LINbase classification and database (Boris Vinatzer, Virginia Tech)
- Questions and BRIEF discussion
A. Discussion One: Metadata
*What minimum information should be included in a standard metadata checklist for agricultural microbiome studies?
*Are metadata standards likely to vary among sub-domains of agricultural systems (e.g. soil vs. plant vs. post-harvest vs. insect microbiomes)?
*Are there metadata within existing microbiome databases that are not needed for agricultural microbiomes?
B. Discussion Two: Standards
*What standards are needed for: i) plant or soil sampling; ii) sample storage pre- or post-extraction; iii) extraction; iv) data processing; v) access to raw and/or processed data?
*Who should determine these and how should adoption or compliance with standards be encouraged (e.g. grant submission requirements, journal requirements, other)?
C. Discussion Three: Database needs
*What will success look like for a collective agricultural microbiomes database?
*What data types are going to be part of a database now and in the future?
*What role should the agricultural microbiomes research community play in database development?
D. Overall summary and next steps: wrap-up
List of participants
Kellye Eversole, USA
Leland Pierson, USA
Boris Vinatzer, USA
Gwyn Beattie, USA
Alejandra Huerta, USA
Audrey Kalil, USA
Ewa Lojkowska, POLAND
Marta Potrykus, POLAND
Deborah Samac, USA
Linda Kinkel, USA
Jose Pablo Dundore-Arias, USA
Neelam Redekar, USA
Sarah Castle, USA
Kenneth Frost, USA
Joshua Herr, USA
Anjali Iyer-Pascuzzi, USA
Thais Egreja, USA
Paul Schulze-Lefert, GERMANY
Jagdeep Kaur, USA
Bharath Prithiviraj, USA
Alejandro Rojas, USA
Kevin Silverstein, USA
Tijana Glavina del Rio, USA
James Tiedje, USA
Susannah Tringe, USA
Fiona Brennan, IRELAND
Joanne Emerson, USA
Lynn Schriml, USA
Sydney Everhart, USA
Rosalie Calderon, USA
Jhonson Leonard, USA