Sept 22nd, 2015- Ontology Working Group Meeting

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Agenda

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

  • In attendance: LC, AM, EA, MAL, PJ, CM, BS


1. Ontology Development Meeting in Corvallis- November 2015

  • Discussion of scheduling and what would be covered:
  • Workshop (and other strategy meetups)
    • Agenda of workshop: Three parts:

1. Strategic planning (PIs)

  • can be on Zoom (difficult to schedule with that number of people.)

2. Curator training: GitHub, Protege, TermGenie

  • CM is fine training twice, exposure, then larger group
  • First training: week 2 Nov.
  • Second stage 2-3 days before or after PAG

3. Hands on curation/annotation

Date planning: Week 2 Nov (9th-13th) Issues

  • EA -will be traveling week 2 of Nov.
  • CM -week 1 doesn't work, week 2 works.
  • PJ - week1 in Dec doesn't work.
  • BS - comes for first/second half for a few days for the strategic planning.
  • PAG- will be used as a second meeting/continuation of the OSU workshop
    • continue strategy and OWL training for those who make it to OSU in Nov, and fill in people who couldn't make it.
    • PJ probably not going to PAG- or perhaps just for the weekend
    • Can use travel funding to fly curators out to PAG if they can't make OSU workshop


Please see the notes here: Planteome_Curator_workshop_Fall_2015

2.

3. Update from Bioversity:

  • Progress on mapping the CO vocabularies and creating cross products

On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?) 

  Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))

Intersection of a quality and either a Process or a Plant Entity.

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties (MAL)

Examples

Seed Color 

  color and ('inheres in' some seed)

Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

Aluminium Tolerance 

  'tolerant to' and ('inheres in' some ('aluminum nutrient regimen' and 'whole plant'))

Intersection of Tolerant to and a specifically dependent continuant that depends on both the presence of a plant and an aluminum nutrient regimen

Amylose content (of the tuberous root) 

  composition and ('inheres in' some (amylose and ('continuant part of' some 'tuberous root')))

Intersection of Composition and a specifically dependent continuant that exists only if ( the intersection of amylose and a continuant (which is a part of a tuberous root) )exists.

Flowering Time 

  time and ('s depends on' some (flowering and ('has participant' some 'flowering stage')))

Intersection of Time and a specifically dependent continuant that exists only if the intersection of (the Process Flowering and A Process that exists only the Flowering stage exists) exists

From OBA:

Plant trait: 

  'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)

Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color 

  'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')

Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

Next meeting: Sept_29th,_2015_Ontology_Working_Group_Meeting

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