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, LC, PJ, JE, CM and EA

Regrets: JD

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; OBO Foundry
  • Chris Mungall, Seth Carbon; OBO foundry, GO, LBNL
  • Marie-Angélique Laporte, Leo Valette, Elizabeth Arnaud (remotely); Bioversity, Crop Ontology Project
  • Vilma Hualla, Omar Benites; Bioversity, CIP- Sweet Potato
  • Agbona Afolabi- Cassava; Bioversity, IITA
  • Karthika Rajendra- Lentil; Bioversity, ICARDA
  • Rex Nelson- SoyBase
  • Also Sinisa, Eugene, Botong, XuXu

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.

  • Final outcome of the workshop was the mapping of TD terms to the TO, making the TO a true reference ontology, starting with the 5 crops present at the workshop

Shorter term goal (for PAG meeting) is to have a working mappings of the 5 species (lentil, soybean, cassava, sweet potato, banana) that we had at the workshop.

  • Need to demonstrate to the breeders how TO can help (need to show the benefits of ontologies.)
  • Show them annotation data- needs to be put into the GAF2.0 formatting
  • Ideal would be ~5 germplasm phenotypes for each trait in the CO TDs, with the CO mapped to it
  • Need germplasm info: Name, source, ID, synonyms, and PHENOTYPES
  • note from EA: lentils have not been integrated in the BMS yet

Workflow Details

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
  • EA expresses need for a timeline- so CO contacts for each crop can know what to expect, and when
    • The CO curators are busy in the field, but we shouldn't need her assistance until after we work through what we have (Karthica)
    • The mapping from their side is 100 terms/week
    • The tougher and more time consuming part is fixing the TO.

TermGenie

  • TermGenie Instance for TO- Questions and Issues:
  • Comments, questions etc can be posted on this TO tracker Issue: [2]
  • Proposed workflow for new requesters (from CM):

1. Sign up for a persona account (from Termgenie) 2. Add a ticket to the TO tracker, include persona username, requesting TG permission. CM will take care of these.

AmiGO2

A demonstration version of the AmiGO2.0 Planteome browser has been set up with the TO and the lentil ontology, along with the mappings to the equivalent classes.

You can view it at: http://dev.planteome.org

Example: plant height trait

Questions and Comments:

  • This is an older version of the TO
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