Aug 23rd, 2016 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Aug 23rd, 2016
  • Time: 8:15am PDT (GMT-7)
  • Attendees: LC, AM, JE, CM, MAL, BS, DWS, BtSinn, Dario, GG
  • Regrets: EA, PJ

Recordings:


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

PJ attending NSF meeting Sept 7-8th

Plant and Cell Physiology Database manuscript

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

  • 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

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

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