OBOE Ontology Extensions Meeting Agenda
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MINUTES
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+-------------------+----------------------------------------------------------+
|DATE               |October 14, 2011                                          |
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|TYPE OF MEETING    | Ontology Development, Annotations                        |
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|CALL IN            | EVO                                                      |
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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. Salmon ontology work
 * Review the salmon OBOE extension at http://ecoinformatics.org/oboe-ext/salmon.1.0/oboe-salmon.owl

2. Creating annotations
 * See https://code.ecoinformatics.org/code/semtools/trunk/dev/sms/examples/Salmon/
 * Problems encountered
   * Creating annotations with Morpho fails to save locally, and saving to fred fails due to log in issues.  Ben - ideas on this? 
     * Ben is looking into bespin being down
     * Use Annotations menu to Save locally (unintuitive?)
   * Annotations are viewable in 'full annotation' view, not 'column annotation' view in Morpho
     * The <sms:map> dataObject attribute was set to '1', not '0', which was incorrect (zero-based list)
   * Hand-written Annotation syntax
     * Documentation in the XSD file would be helpful
     * Examples should be updated

3. Detailed subclasses vs object properties
 * Dilemna - do we create entity classes that are specific to entities that are being observed with highly detailed properties?
 * Example: see https://code.ecoinformatics.org/code/semtools/trunk/dev/sms/examples/Salmon/cjones-eml.21.1.xml
   * We've created classes such as LiveSmoltSteelheadPopulationSample
   * We haven't created LiveHatcherySteelheadNoIdentifierPopulationSample
   * or LiveHatcherySteelheadLeftRedIdentifierPopulationSample
 * These classes are increased specializations based on the protocol at hand
 * Discuss the use of object properties
   * PopulationSample and hasMember only Steelhead and etc ...
   * example property to discuss
     * hasMember
     * memberOf (and all other partonomy-type relationships)
     * hasOrigin 
     * originatesFrom (relating to Wild vs Hatchery Origin)

4. Annotation syntax support in the SMS library
 * Our examples include data that have multiple codes in a single data column that need to conditionally be mapped to observed entities.
   * Example, COHO, STHD, SOCK
   * What classes do we need to modify?
 * Constants (metadata fields need to be supported in the annotations)
   * Example: site name that applies across all observations
   * MapType in the annotation schema requires 'dataObject' and 'attribute' attributes. Does this need to change?
   * Discuss the syntax, and how these can be pulled into an integrated dataset from a materialized model

5. Namespaces
 * http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl#Entity vs
 * http://ecoinformatics.org/oboe/oboe.1.0/Entity
 * http://ecoinformatics.org/oboe-ext/salmon.1.0/oboe-salmon.owl#ChinookSalmon vs
 * http://ecoinformatics.org/oboe-ext/salmon.1.0/ChinookSalmon
 * Decision: Via IRC discussion, we will use the syntax that includes the owl file name in the class URI 

6. Standards
 * How should we model subclasses of Standard?
   * Example: IdentifierType is an enumerated list of types of fish grouping identifiers (marks). I've made the values NamedIndividuals of IdentifierType.  Is this correct?

7. Version freezing


<observation label="...">
   <entity id="..."/>
   <measurement label="m1">
      <characteristic id="..."/>
      <standard id="IdentifierType"/>
   </measurement>
</observation>

<map attribute="col-name" measurement="m1" 
     if="col-name eq 1" value="BismarkBrownDye"/>