Jan 21st, 2016 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Thursday Jan. 21st, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/757453328

  • Attendees: TBA
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  • [[File:|thumb| ]]

Report on the PAG Workshop with CG Collaborators Monday Jan 11th

- 29 attendees


Revisions to the biochemical trait TO:0000277 branch of the TO:

Revisions to the upper-level categories

Biochemical branch TO

Previously mentioned December 8th meeting

current upper level terms:

  • TO:0000283 biological process related trait
  • TO:0000282 enzymatic activity and protein content related trait
  • TO:0000281 metabolite content related trait
  • TO:0000465 mineral and ion content related trait
  • TO:0020080 stover organic matter digestability

Suggest reducing to:

  • mineral and ion content trait
  • metabolite content trait
  • biological process trait

content/concentration/amount

Biochemists definitions:

  • concentration = amount/ VOLUME
  • content = amount/MASS

PATO defs:

  • ‘concentration of’ -A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
  • 'amount' -The number of entities of this type that are part of the whole organism.

-Requested a revision of the 'amount' definition

  • The number of entities of this type that are part of another entity.

Options:

Merge content and concentration terms

  • this would allow for an overall reduction of terms.
  • Might be problematic due to changing definitions of terms with existing annotations (eg:)

Add new parent term 'amount'. Make content and concentration terms children of this parent (see image)

  • Results in an overall addition of terms
  • Adds unnecessary parent to cases where both content and concentration terms don't exist