Ontology Working Group Meeting, Tuesday April 28th, 2015

Planteome Ontology Working Group Meeting

• Time: Apr 28, 2015 8:30 AM (GMT-7:00) Pacific Time (US and Canada)
• Connection: Join from PC, Mac, iOS or Android: https://zoom.us/j/666739728

• File:Ontology WG 4-28-15 audio.m4a
• File:Ontology WG 4-28-15 video.mp4

Who: LC, PJ, EA, LV, CM, DWS

Updates from CO team

EA upcoming travel in May:

• LV has been progressing on several crop trait dictionaries, working with the plant breeders:
  • cowpea TD - discussing with the users, waiting for feedback
  • pigeon pea TD- Training was done with the breeders at the BMS, requested more traits, added 12 new, submitted revisions to Preasad, then it will be uploaded. Done offline, via email and dropbox
  • rice- no news from RH

Note: Discussion of the workflow: Working with Julian Pietragalla, Technical Support Officer of the BMS ([1]). Julian is at CIMMYT, deals with the data standards for the BMS.

• EA and LV are going to CIMMYT for all next week (May 3-8th?) to meet with the BMS folks and make revisions to the Trait Dictionaries. All the crops are on the list, wheat, maize, the legumes, etc
• Also will be working on better guidelines to fill in the TDs

PJ Question: Are there already vocabularies in place to annotate the germplasm/GWAS datasets, etc? Is there a list of traits that we can get to match with the TDs and the ref TO?. CIMMYT researchers are part of TCAP/maizeCAP projects? How can we address the needs for the top priority traits that are needed.

• Link to Crop Information & Genomics page
• Genebank staff will be gone, will be meeting with Rosemary and Kate: their role is the harmonization of the metadata
• BMS is being tested for use at CIMMYT, new initiative, integrated with the

GRIN Global System

• Also, CIMMYT is implementing the GRIN Global system: [2]- the USDA system for tracking and cataloging germplasm, been deployed for past 2 years
• GRIN Global- Peter Brettling, developer Peter ?
  • You can search for the descriptors for the different plant species: [3]
• Would be good to have the Planteome ontologies integrated into the GRIN Global system

Example of Grin Global descriptors for wheat

Data Harmonization Workshop, DC May 11-15th

• Pankaj will attend [4]
• Organizer: Cheryl Porter (AgMIP)
• Has been working with EA on the variables for crop modeling, would be good to have the Planteome ontologies integrated into the AgMIP variables

DivSeek Update

• EA elected to the Steering Committee.
• One of the main focuses will be data standards, information management
• They are aware of the Planteome ontologies,
• Ruth Bastow will be taking part as well (?)

Updates from OSU- Positions

• Curator position: Interviews starting this week
• CM offering to assist reviewing candidates
• Software developer position under review, probably will start interviews mid-May

Progress on transition to Github

• See: https://github.com/Planteome
• created repos for CGIAR rice, maize, wheat and cassava- may need to revise names
• Will remove from SVN

Updates on Amigo 2.0

See link: dev.planteome.org Tabled for next meeting:

Next meeting date May 12th

• PJ will be in DC, EA?