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

- http://planteome.org/outreach/workshops/PAG_2016

- 29 attendees ( link to spreadsheet: https://docs.google.com/spreadsheets/d/12Wl98Hy8LeQRZoDME2hDkqNgKqCjG89ymndJN84hP3I/edit?usp=docslist_api)

- Comments and feedback?

Update on browsers

Planteome.org

Dev.planteome

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

Revisions to the upper-level categories

Biochemical branch TO

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 (definition of 'metabolite' is sufficiently vague)
• biological process trait

metabolite content branch to be divided further in parallel to ChEBI

content/concentration/amount

Previously mentioned December 8th meeting

24 “concentration” terms

45 “content” terms

9 both

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 - new terms would be "amount"

• this would allow for an overall reduction of terms.

• Keeps the TO "measurement agnostic", in the reference ontology sense

• Might be problematic due to changing definitions of terms with existing annotations (none found on Planteome browser)

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