Aug 23rd, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Aug 23rd, 2016
• Time: 8:15am PDT (GMT-7)

• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/217118644

• Attendees: LC, AM, JE, CM, MAL, BS, DWS, BtSinn, Dario, GG
• Regrets: EA, PJ

Recordings:

• File:Ontology WG Meeting 8-23-2016 audio only.m4a
• File:Ontology WG Meeting 8-23-2016 video.mp4

Follow up from ICBO conference

• DWS
  • Working on the monocot matrix with Chelsea Specht- she sent it out to CM, DWS etc?
  • Matrix files can be translated to Nexus files
  • Character states and names of terminals start at '0'
  • Banana terms need work
  • Preparing images labeled with PO terms
  • In situs for gene expression can be associated to GO temrs
  • Line art good for recognition
  • Brandon and Dario working on the images
  • Meeting with JP et al again soon

• George:
  • Continuing to develop PlantPhenomeNet
  • High throughput phenotyping- with John Doonan at Aber.- proposal to standardize the terminology
  • Possible joint call from EuroCap
  • Luke continuing to work on AberOwl- special version for plants
  • GG will follow up with PJ about paperwork

• CM:
  • Need YAML template for TO..????
  • TermGenie should be working, it was down on Monday etc
  • New design patterns for TO could be incorporated??
  • From Mal: On OBOFoundry, NCBI taxonomy ontology lacks any authorities, open tracker for
  • CM: what is plan for EO? Lets change the abbreviation
  • Would like to see the CO ids registered

• AM:
  • Progress on the OOPS soon
  • Using simple patterns to create the terms, things like symptoms are more complicated, may have to be added manually

Updates from Planteome members

MAL: newest trait dictionaries being completed:

• wheat - in progress; MAL is doing the mapping

- Rosemary validated the mappings during the Montpellier workshop - MAL will create the OBO file after it is checked over, will add common name in the trait names

Upcoming Release

• currently fixing things and testing

Plant and Cell Physiology Database manuscript

• Addressing issues raised by the editors:
• Response to Plant and Cell Physiology @ Planteome Database
• deadline Sept 1
• draft will be circulated

Fall workshop planning

TBA...

Other items?

Scientific Advisory Board

• List of possible people:
  • Sandy Knapp
  • Lynn Schriml (Lynn Schriml- Google Scholar)
  • Sarah Mathews - Was at Harvard, but she has moved to CSIRO in Canberra, Australia
  • Ruth Bastow
  • others?

• LC will draft a letter and discuss with PJ
• Goals review progress, help improve, recommend us to funders
• Could have a meeting with them at the fall workshop

Upcoming Meetings and Workshops

GODAN Summit, New York City, Sept 15-16th, 2016

• http://summit.godan.info/

• Who is involved- will present an exhibit booth together:
  • Planteome- PJ will attend, also possibly LC?
  • Crop Ontology- Bioversity- EA will attend
  • Gramene
  • Agronomy Ontology- Medha
  • IC3-FOODS at UC Davis for Food Ontology
  • Agricultural Nutrition and Technology ontology (ANT)

• Materials for booth are being collected in DropBox folder:
  • Project logo in high resolution
  • Short slide show (~ 5 slides) to show your project's impact and applications
  • Any handouts like brochures

• Also can bring swag gifts such as tote bags, coffee mugs,pens,jump drives with your project materials on it, etc

4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016

• International Maize and Wheat Improvement Center (CIMMYT)
• El Batan, Texcoco, México (Near Mexico City)
• Early bird registration deadline: October 16, 2016

• http://www.cimmyt.org/event/4th-international-plant-phenotyping-symposium/

Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA

http://www.intlpag.org/

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

Workshop proposal accepted