Oct 11th, 2016 Ontology Working Group Meeting

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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: https://zoom.us/j/620296847
  • Attendees:
  • Regrets:

Recordings:

Agenda

New Taxon constraints added to PO

  • Prototype taxon constraints have been added to the plant Ontology
  • This will be an area where the botanical expertise of the NYBG group will be very helpful
  • Currently:
    • whole plant (PO:0000003): only_in_taxon NCBITaxon:33090 Viridiplantae {source="cjm"}
    • plant ovary (PO:0000004): only_in_taxon NCBITaxon:3398 Magnoliophyta {source="GO:0035670"}
    • microspore (PO:0020048):
  • microspores are present in 5 different taxa (flowering plants, gymnosperms, some of the ferns, selaginella, and isoetes). Those taxa don’t have a common ancestor.
  • How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:
    • In GO they name taxon unions (CM: but these are a real pain)
    • id: GO:0009766
    • name: primary charge separation
    • namespace: biological_process
    • def: "In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
    • is_a: GO:0022904 ! respiratory electron transport chain
    • relationship: only_in_taxon NCBITaxon_Union:0000007 {id="GOTAX:0000169"} ! Viridiplantae or Bacteria or Euglenozoa
    • relationship: part_of GO:0019684 ! photosynthesis, light reaction
  • The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....

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)

Harmonization 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

  • Eight crops have been mapped to TO so far: lentil, cassava, wheat and rice are part of the current Planteome release 1.0
  • New crops added: sweet potato, maize, soybean and pigeonpea


  • Statistics are available here: [[1]]
  • Attempt of a visualization: [[2]] (avoid this if you have ocean sickness!). Feedback is welcome


Redirect from old Plant Ontology Site


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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