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.