Ontology Working Group Meeting, Tuesday June 9th, 2015

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Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada) Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/834566681

  • Who will attend: LC, MAL, DWS, PJ, BS
  • Others?: , CM, GG
  • Regrets: JE, EA

Agenda

Summary from last meeting May 26th ::

  • Report form UN meeting- BS- need links to publication
  • Updates underway to the Trait Template (Leo)
  • Discussion of the id space for Crop Ontologies
  • Discussion of the hierarchy of the CO Vocabs- not a problem if the terms have logical def'ns, just import as flat file.
  • Mapping to TO with Agreement Maker Light - see below
  • Progress on AmiGO2 browser development: http://dev.planteome.org/amigo
  • Updates on the transition to Github: https://github.com/Planteome

Other Updates, etc

  • Hiring:
    • OSU: Offer has been made, waiting for confirmation, undergraduate student hired for summer, another one joining in August
    • NYBG:

- Offer has been made, waiting for confirmation, graduate student will be joining to help with the imaging work

- working with the AISO-Bisque team to generate images.

- Idea to do a use case study involving in situ analysis- leaf development or procambium development

Report from Bioversity team

Introduce new Crop_Ontology_Pages on the wiki (MAL)

  • Marie-Angelique has created an informative page on the wiki with information about the structure and format of the CO vocabularies.
  • Current structure of the Trait template (v.4)
  • Future structure of the Trait Template (v.5)

Mappings from CO to TO: MAL

From last meeting:

  • Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
  • Import as OWL or OBO, * Needs to make the product using owl files??
  • Add mapping to terms, structure or words

Results of mapping to Wheat Ontology CO:321

  • The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
  • The manually created Xrefs to TO can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)
  • The AML tool found about 73 mapping, case independent
  • Results: color coding:
    • Green- Xref and AML in agreement
    • Orange- Xref and AML NOT in agreement
    • No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.
  • Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once.
  • Examples of lack of agreement:

CO term: CO:321:0000040 grain size Xref: to seed size TO:0000391- AML maps it to: TO:0000397 grain size


Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- mainly in the wheat file

Updates on work on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)


Discussion of Timeline and Plan

Next Meeting Tuesday June 23rd

Back to the Planteome_Ontology_Development_and_Coordination_Working_Group page

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