Ontology Working Group Meeting, Tuesday June 23rd, 2015

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Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)

Connection details: TBA

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

Summary from last meeting June 9th:

  • TBA...


Discussion of Timeline and Plan

Workshop

a. What will be the objective of the workshop? b. Who will be the attendees ? data manger, ontology curators, researchers I propose to consider: Use of Protégé; Discussion on Traits/trait mapping; Discussion on possible annotation pipelines and test on data sets

Mappings from CO to TO: MAL

From Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015 :

  • 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created Xrefs to TO can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date)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 (which is correct)

Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- Are these only in the wheat file right now?


Next Meeting Tuesday July 21st

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