OBOE Ontology Extensions Meeting Agenda
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MINUTES
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|DATE               | August 12, 2011                                          |
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|TYPE OF MEETING    | Ontology Development, Annotations                        |
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|CALL IN            |                                                          |
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|NOTES              | Everyone                                                 |
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|ATTENDEES          | Shawn Bowers, Ben Leinfelder, Chris Jones, Matt Jones,   |
|                   | Margaret O'Brien, Mark Schildhauer                       |
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Discussion topics
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1. Modeling entities as specializations of superclasses with added characteristics

• This is largely done via intersection (e.g. LivingOrganism AND PopulationSample)
• Presents some difficulty when the intersecting 'entity' is more like a characteristic
  • LifeStage (move this to Characteristic)
    • FishLifeStage
      • SmoltStage (value)
    • MammalLifeStage
    • AlgaeLifeStage
    • PopulationSample
  • SmoltStage AND PopulationSample == SmoltPopulationSample
    • (SmoltStage is really just a characteristic of a salmonid (actually of any fish))
    • a 'Smolt' is a salmonid possessing the smolt stage characteristics
  • Some modeling choices:
    • SmoltStageFish (just a class)
    • hasLifeStage property and LifeStage value partition
    • SmoltStageFish = Fish and only hasLifeStage Smolt
      
      

A      E=SmoltStageFish
Tag#   C=Length
1      15.1
2      16.3

B    
Tag# C=FishLifeStage  C=Length
1    smolt            15.1         <- conditional annotation assigns E=SmoltStageFish
2    adult            16.3         <- conditional annotation assigns E=AdultStageFish


attribute=color value=red (so, red is an entity?!)
attribute=lifestage value=smolt (so, smolt is an entity?!)

MeasurementType = FishLifeStageMeasurementType
    FishLifeStageMeasurementType = 
       hasEntity only Fish
       hasCharacteristic only LifeStage
       hasValue only FishLifeStageValue
Trick here: how to relate hasLifeStage (obj. prop.) with LifeStage (characteristic class)

Conclusion: model these as classes (Entity), e.g., SmoltStageFish, and later can add additional properties to the ontologiy that clarify why the classes are subclasses, which might be useful in searching; in the meantime, can use the class in annotations, as shown in tables A and B above

2. Using oboe-taxa

• TaxonConcept (from DSW) is added
• Hear back from Matt re: contacting Rich Pyle
• Are specific taxon concepts to be modeled as individuals of TaxonConcept??
  • TaxonConcept
    • Genus (Individual)
    • Species (Individual)
    • etc?
  • If so, how do we use 'Species' in OBOE extensions, since we need to subclass it?
  • If not, what is Species a subclass of? Is it related to TaxonConcept?
    
    

Conclusion: We'll use the current scientific names to define species concepts, and will keep equivalence classes that use vernacular names.

3. Added oboe-ecology, oboe-biology

• Could use some discussion on the merits of this
• What about terms that have more to do with the scientific process
  • Sample
  • others?
• OWL classes defining 'Organism', 'Fish' etc. are hard to find
  • Do we want to subscribe to DwC 'IndividualOrganism'? (or at least use similarConceptAsClass)

Conclusion: 
oboe-ecology: put habitats here.
oboe-biology: fuzzy organism names go here, like "Fish", Kelp", "Algae". then subclass these in the extension with species binomials.