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
- Main Planteome website: http://planteome.org/
- Development site: http://dev.planteome.org/amigo
Issues being sorted out:
- Relations are not being recognized and displayed in AmiGO 2.0 (https://github.com/Planteome/planteome-ontology-browsers/issues/20)
- Synonym scopes are not being displayed- all the broad, narrow, realted and exact synonyms are being lumped together- (https://github.com/Planteome/planteome-ontology-browsers/issues/17)
Revisions to the biochemical trait TO:0000277 branch of the TO:
Revisions to the upper-level categories
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
