Oct 11th, 2016 Ontology Working Group Meeting: Difference between revisions

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=Agenda=
=Agenda=


* Suggest adding a new relation between the morphology trait and a quality trait
== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is a children resulting in dual parentage
Many of these are currently is a children resulting in dual parentage


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* is_a pericarp morphology trait (TO:0000945)
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)
* is_a fruit quality trait (TO:0002728)
== Harmonisation between TO and PO ==
PO defines classes with sometimes a lot of synonyms (broad and narrow).
e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?
* use subClassOf instead of equivalentClass for the DP when narrow synonyms
* keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
* keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?
== CO mappings ==
* 8 crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the planteome release. New crops added: sweet potato, maize, soybean and pigeonpea.
* statistics are available here: https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing
* attempt of a visualisation here: mariealaporte.github.io (avoid this if you have ocean sickness!). Feedback welcome.


= Upcoming Meetings and Workshops=
= Upcoming Meetings and Workshops=

Revision as of 22:45, 7 October 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Oct 11th, 2016
  • Time: 8:15am PDT (GMT-7)
  • Connection details: Join from PC, Mac, Linux, iOS or Android:
  • Attendees:
  • Regrets: rest

Recordings:

Agenda

Suggest adding a new relation between the morphology trait and a quality trait

Many of these are currently is a children resulting in dual parentage

e.g. pericarp texture (TO:0002623):

  • is_a pericarp morphology trait (TO:0000945)
  • is_a fruit quality trait (TO:0002728)

Harmonisation between TO and PO

PO defines classes with sometimes a lot of synonyms (broad and narrow). e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001) In TO, the classes 'fruit weight' and 'grain weight' exist. How to harmonise that?

  • use subClassOf instead of equivalentClass for the DP when narrow synonyms
  • keep only 'fruit weight'. 'grain weight' will then become a synonym of 'fruit weight'
  • keep 'fruit weight' in TO. 'grain weight' will then be in CO and imported in TO. The CO class 'grain weight' will use the same DP than 'fruit weight' + a taxon constraint. Related question: should all the CO class have a taxon constraint? or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?

CO mappings

Upcoming Meetings and Workshops

IC-FOODS Conference November 7-9,2016 Davis, California

4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016

Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA

http://www.intlpag.org/

  • October 31 early registration deadline
  • Deadline for workshop abstract submissions is December 2, 2016.
  • Deadline for changes to program (posting speakers) is November 30, 2016
  • Poster Abstracts Submission Deadline is October 28, 2016

Phenome 2017, Feb 10th to 14th, 2017

http://www.phenome2017.org/#homepage

  • DWS will attend- evo devo presentation
  • CM will attend and present Planteome and pheno-BLASTing

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

Workshop proposal accepted

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