Ontology Working Group Meeting, Tuesday April 7th, 2015

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Who: LC, EA, LV, JE

  • Link to recording- Video:
  • Link to recording- Audio:


1. Updates on hiring etc

At the Crop Ontology in Montpellier, the postdoctoral position has been offered to Marie Angelique Laporte. She will probably join the team around mid April.

OSU- review of applicants is underway

NYBG- no report as yet

2. Guidelines for writing good definitions- Barry Smith Barry presented a short slide set- see attached: outlining the best practices for ontology design and writing definitions.

see presentation: File:TO BS 4-7-15.pdf

- need for genus- differentia format, single parentage of terms

- proposed idea for TO: 2 versions:

- editors version "asserted"- species neutral and widely applicable

- public/ live version- "inferred" version- containing the species specific definitions


3. Finalizing the response to Clement and Pierre @ the LIRMM Bioportal instance.

- clarified a few points, EA will send out tomorrow

4. Leo- update on revisions to Rice Trait Ontology, issues with using SVN

- working with RSH, but he is quite busy

- EA sent RSH the name of person who might be able to help- Berta?

- trouble shooting issues of SVN access with JE, possible call on THurs am if still on going

  • Discussion about how to deal with the revising on definitions in the CGIAR ontologies- current definitions are displayed in the Fieldbook and are in there format that the breeders are used to. Could we possibly have an additional field for the " ontology definition" ?
  • Could the backend be modified so that the comment is displayed in the field book rather than the def'n ? Then we could rewrite the def'ns in ontology language and move the breeders def'n to the comment field.
  • Another alternative is to have the ontology in OBO or owl and create a script that exports the breeder version to the trait template for import into the IBP Fieldbook. ????
  • Additional discussion about updating the links to the TO terms - where is the best place to link them? Currently going to Gramene TO.
  • Probably should go to the TO on live planteome site, but it is really out of date. April 2013.
  • TO dev site lacks the annotations

5. Plans for Trait Ontology revisions, work on CGIAR wheat and maize trait ontology

  • RS and KD are really busy right now with the tool out of the new IBP version (clarify?)
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