DI_20091022
iPG2P Data Integration
October 22, 2009, 4pm EDT
Attendees: Doreen Ware, Damian Gessler, Jerry Lu, Pankaj Jaiswl, Doina Caragea, Qi Sun, Ruth Grene, Eva Huala, Chris Jordan, Jim Jones, Steve Welch, Lukas Mueller, Karla Gendler
Action Items:
- Eva, Lukas, Pankaj, Qi Sun: What are standards of exchange for genome sequence? for metadata? What are file formats?
Agenda/Notes:
- Introduction of participants
- Introduce Confluence as collaboration environment
- iPlant suppport staff (support@iplantcollaborative.org) to deal with problems
- iPG2P Working Group review
- Preliminary review of NGS needs based on workflow
- InitialTasks.ppt
- Is it possible to produce a single output that can be used by all groups? Other groups will need to define what is needed in the format though.
- Qi Sun: Probably won't have single file format as each group will provide own format but we need to focus on cross-repository search and also how do we integrate across species and working on different platforms?
- Chris Jordan: is it possible to archive all the data in one format but then transform into each format type that is needed? Looking for ways to minimize number of formats internally.
- Jim Jones: what is the scope of this project? Is the main scope aimed at G2P effort and what are the sources of data (DNA, RNA, phenotype information)?
- Main scope is aimed at G2P effort
- Will international reserach centers be a contact for data sources?
- Welch: modeling group has begun to identify what metadata is necessary for formats
- Identification of Action Items
- All: look at NGS Workflow
- reference genome seuqence and annotations (TAIR, Solanceae group): going to end up being a resource that links to you and links back; needs to link to model organism database
- What are standards of exchange for genome seq?
- What are standards of exchange for metadata?
- How do we want to get attributes from model organism databases and how to feed it back?
- Eva and Lukas being targeted initially
- review existing repositories and formats that exist
- for Lukas, very viable option as they have a lot of genoytping and pheontyping info
- Eva, Lukas, Pankaj, Qi Sun
- How to go between sequence information and pheontype information
- First push is to align to reference genomes so need to ID people who work with reference genomes
- What are the file formats and data exchange standards?
- What about phenotype info w/o reference genome?
- All: look at NGS Workflow
- Set date for next meeting
- Thursday, November 12, 2009 12pm PST (3pm EST)
WebEx:
Topic: iPG2P Data Integration Intro Meeting
Date: Thursday, October 22, 2009
Time: 1:00 pm, Mountain Standard Time (GMT -07:00, Arizona)
Meeting Number: 752 894 132
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