Activity
From 03/14/2010 to 04/12/2010
04/12/2010
- 03:12 PM Bug #4922: DB-driven Annotation Manager
- implemented the "is not" operator for criteria. I'm not sure how useful it will be at this point given that searches ...
- 02:28 PM Bug #4922: DB-driven Annotation Manager
- Contexts are now processed recursively so that their transitive nature can be searched:
A rel B
B rel C
-----
A rel C... - 02:14 PM Bug #4922: DB-driven Annotation Manager
- Status:
The existing query methods have been re-implemented to use the db model.
If there's a "working" copy of the a...
04/09/2010
- 04:53 PM Bug #4922: DB-driven Annotation Manager
- Making good progress on this implementation. Really it's more of a hybrid - extending the in-memory version to only h...
04/07/2010
- 02:06 PM Bug #4935 (New): Lazily load semtools plugin
- While Morpho has a good framework for developing and loading plugins for the application, it does not have a way to e...
04/06/2010
- 04:19 PM Bug #4906: Annotation query implementation (SPARQL)
- we are dropping this in favor of a relational-db approach:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4922 - 04:18 PM Bug #4905: iTunes-inspired search UI
- Hey, this is all done now!
04/02/2010
- 02:25 PM Bug #4905: iTunes-inspired search UI
- Good news:
-there's now no dependency on Morpho for the AnnotationManager to query correctly.
-the row heights are ma...
04/01/2010
- 04:53 PM Bug #4844: Dynamically resize Ontology selection fields
- the tooltip is now much more helpful when the classname runs off the text area.
- 04:48 PM Bug #4844: Dynamically resize Ontology selection fields
- at the very least, the tooltip for them could read the full text so there's someway of seeing what the full classname...
- 03:53 PM Bug #4905: iTunes-inspired search UI
- The criteria are now actually driving the query.
I'm not happy with how there's a slight dependency on the morpho co... - 12:15 PM Bug #4922: DB-driven Annotation Manager
- I'm not sure the cardinality is right on that ERD model. In particular, shouldn't the Measurement--Characteristic ca...
- 11:21 AM Bug #4922: DB-driven Annotation Manager
- draft of the basic schema needed is here:
https://code.ecoinformatics.org/code/semtools/trunk/docs/design/AnnotationM...
03/31/2010
- 04:22 PM Bug #4922 (Resolved): DB-driven Annotation Manager
- The current AnnotationManager implementation reads XML serializations into Annotation objects in memory. Any operatio...
- 03:11 PM Bug #4906: Annotation query implementation (SPARQL)
- (In reply to comment #5)
> Expressivity/simplicity?
> Something that would allow us to retrieve a list of annotation
... - 02:53 PM Bug #4906: Annotation query implementation (SPARQL)
- Expressivity/simplicity?
Something that would allow us to retrieve a list of annotation [instances?/objects?] with a ... - 02:14 PM Bug #4906: Annotation query implementation (SPARQL)
- (In reply to comment #3)
> I think we were saying that an every annotation would be an Annotation Instance
> (in some... - 02:04 PM Bug #4906: Annotation query implementation (SPARQL)
- I think we were saying that an every annotation would be an Annotation Instance (in some yet-undefined ontology that ...
- 07:52 AM Bug #4906: Annotation query implementation (SPARQL)
- the current search implementation is simple and generous. some features that are desired:
-compound grouping conditio... - 07:58 AM Bug #4905: iTunes-inspired search UI
- -The UI (first draft?) is completed.
-The underlying search capabilities are not hooked up (no query is actually per... - 07:54 AM Bug #4889: Compound Search UI
- Consensus was to abandon this UI in favor of the iTunes-esque UI
- 07:45 AM Bug #4891: Rank annotation search results
- closing this - they are ranked. I'll be sure to keep this feature as the search capabilities are augmented (grouping,...
03/29/2010
- 01:24 PM Bug #4906: Annotation query implementation (SPARQL)
- I am not sure what it means here to materialize an annotation, but if it implies storing an annotation per se as an i...
- 11:33 AM Bug #4906 (Resolved): Annotation query implementation (SPARQL)
- Matt recommends materializing the Annotation and Ontology as instances in the OBOE model for running searches.
I nee... - 11:30 AM Bug #4905 (Resolved): iTunes-inspired search UI
- Compound search should be more flexible and allow 2-levels of any/all grouping.
Example query that should be express...
03/27/2010
- 07:58 AM Bug #4891: Rank annotation search results
- current scheme for each annotation:
-5 possible search criteria (Entity, Characteristic, Standard, Protocol, Context)...
03/25/2010
- 02:11 PM Bug #4890: findMatchingAnnotations(...) needs Context
- added to the UI.
One thing that could be improved is integration between the Observation Entity selection and the fir...
03/24/2010
- 02:33 PM Bug #4902: Annotations duplicated during editing
- Stale listeners were hanging around and responding to events that they should not have responded to - hence duplicati...
- 11:19 AM Bug #4902 (Resolved): Annotations duplicated during editing
- Still trying to track down the scenario in which this occurs. I believe it might have something to do with re-reading...
03/18/2010
- 11:25 AM Bug #4890: findMatchingAnnotations(...) needs Context
- Reopening but as a Morpho plugin bug.
Now that the annotation manager can search on context, we need to include it in... - 11:22 AM Bug #4890: findMatchingAnnotations(...) needs Context
- now you can provide a list of Triples (Entity, Relationship, Entity) as part of the search criteria.
03/17/2010
- 04:51 PM Bug #4891: Rank annotation search results
- [4:42pm] bowers: i'm not super big on using "or" and "and" in search
[4:42pm] bowers: i think it should all be "or" w... - 04:51 PM Bug #4891 (Resolved): Rank annotation search results
- "just like google"
- 04:48 PM Bug #4889: Compound Search UI
- Another recommendation: do away with AND/OR confusion and use the search results ranking to indicate how closely the ...
- 04:25 PM Bug #4889: Compound Search UI
- Include Context relationship searching. This needs to be added to the SMS AnnotationManager
- 04:00 PM Bug #4889 (Resolved): Compound Search UI
- Place-holding bug for work done on the search interface.
Initially there was a single screen for specifying Entity/C... - 04:45 PM Bug #4890: findMatchingAnnotations(...) needs Context
- [4:31pm] bowers: i think the madlib stuff could be reused for this ... although you might want a way to say that two ...
- 04:28 PM Bug #4890 (Resolved): findMatchingAnnotations(...) needs Context
- Likely the first of many enhancements to the AnnotationManager API.
We need to allow searching based on Context.
... - 11:36 AM Bug #4882: Use OBOE Measurement class to auto-fill other fields
- cutting installers for folks to check out this feature.
enter bugs as needed for tweaking
03/16/2010
- 03:50 PM Bug #4882: Use OBOE Measurement class to auto-fill other fields
- I've added a method to the SMS OntologyManager that can be used to look up the restrictions that are defined on the M...
03/15/2010
- 04:55 PM Bug #4882: Use OBOE Measurement class to auto-fill other fields
- i've casually been calling this a "Measurement template"
- 11:14 AM Bug #4882 (Resolved): Use OBOE Measurement class to auto-fill other fields
- By defining subclasses of OBOE's Measurement class (of Characteristic, uses Protocol, etc...) we can just have one wi...
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