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
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
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"/>