Jan 21st, 2016 Ontology Working Group Meeting

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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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