Nov 24th, 2015 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting:

Date: Tuesday Nov. 24th, 2015 Time: 9am PST (GMT-8)

Attendees: - AM, MAL, Lol, PJ, JE ..... Regrets:

Review of recent Planteome Developers' Workshop, Nov 9th-13th, 2015 Corvallis, OR

Attendees:

  • Laurel Cooper, Pankaj Jaiswal, Austin Meier, Justin Elser, Justin Preece- Planteome project, OSU
  • Barry Smith
  • Chris Mungall, Seth Carbon
  • Marie-Angélique Laporte, Leo Valette, Elizabeth Arnaud (remotely)
  • Vilma Hualla, Omar Benites CIP- Sweet Potato
  • Agbona Afolabi- Cassava IITA
  • Karthika Rajendra- Lentil ICARDA
  • Rex Nelson- SoyBase
  • Also Sinisa, Eugene, Botong

*The overall goal is to enrich the Trait Ontology with terms that can be mapped to their equivalents in the various crop specific trait dictionaries.

Workflow Details

  • For test group- lentil (Karthica), Sweet Potato (Omar & Vilma), cassava (Aflola), banana (Leo), soybean (rex)
  • Work coordinated through GitHub site
  • Readme file on each GitHub repo should be filled in with this information


  • TD xls file - stay intact as a reference
  • Create a mapping spreadsheet- similar to “lentil-mapping-TO-CO_339.xls”- leaving the method and scale in and move to a tab in the google spreadsheet
  • Owl file with proposed mappings- MAL will extract mapping from owl files- add to mapping spreadsheet on gsheet. These are the ones the curators selected
  • MAL should put the computationally-derived mappings on the gsheet as well. That way we could review them
  • Curators should Open TO tracker Issues for terms they need added to TO:
    • Template for missing terms or ones that need revision:
    • Ref to CO term name and ID
    • entity and attribute
    • proposed TO term name
    • Proposed parent in TO
    • proposed TO definition
  • Optional information:
    • link to CO term on CO website
    • method and scale (is also on the gsheet)
    • literature citation

TermGenie

  • TermGenie Instance for TO- Questions and Issues:
  • Comments have been moved to new Issue: [2]
  • Proposed workflow for new requesters (from CM):

Sign up for a persona account (use the link above) Add a ticket to the TO tracker, include persona username, requesting TG permission. I will take care of these.


AmiGO2

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