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Bug #4768

UI for managing annotation ontologies

Added by ben leinfelder over 10 years ago. Updated over 10 years ago.

Status:
Resolved
Priority:
Normal
Category:
Morpho Plugin
Target version:
Start date:
02/06/2010
Due date:
% Done:

0%

Estimated time:
Bugzilla-Id:
4768

Description

There is a section of the config.xml that contains ontology URI (and URL) mappings for ontologies we want to load when Morpho starts. Right now it's the GCE and the SBC oboe extensions.
I want to make this list of ontologies configurable in the UI so that you can point to other ontolgies (either locally or remotely).
This same UI could be used to display the available ontologies that are managed by the Metacat server that we use for storing EML, Annotations, and ontologies.

PastedGraphic-1.pdf (65 KB) PastedGraphic-1.pdf ben leinfelder, 02/06/2010 10:32 PM

Related issues

Blocked by Semtools - Bug #4770: Load Annotations from Metacat in Annotation pluginNew02/06/2010

History

#1 Updated by ben leinfelder over 10 years ago

Soe more background (from an email I sent a while ago):
-----
I went to use the ontology browser in Morpho and realized that all the ontologies that are referenced are actually loaded from their URIs and not stored locally in Morpho or the SMS manager (unlike the annotation documents themselves which are stored locally).
I'm wondering how we should approach this so that it fits with Morpho's ability to do things offline.
We've talked about mapping logical URIs to local resources in the context of Metacat, and there's a way to do this logical/physical mapping in the API as it stands currently (but I'm just hardcoding the sample ontology URIs in the plugin right now).

Some thoughts:
-We should let users load (and unload?) ontologies and provide a mapping from URI to local resource (a la Protege).
-We'll want to automatically load any ontologies that are referenced in annotation documents being edited in Morpho (and prompt for the local resource if the URI does not resolve).
-How highly managed should the ontologies then be when mapped locally? When we import an ontology (OWL file) should Morpho cache it so it's not lost when users rearrange their local filesystem? The OWL file would then become yet another resource managed in Morpho's data store (just like an EML file or an Annotation file).

#3 Updated by Matt Jones over 10 years ago

You might see if the ontology manager/editor that Sean Riddle developed for Kepler could be reused in whole or part here.

#4 Updated by ben leinfelder over 10 years ago

created a very basic editor for the physical/logical mapping that is stored in Morpho's configuration.
It's just text fields - you are on your own for choosing filesystem paths and typing URLs. For the latter, I think that's fine, but a file chooser widget might be nice for local resources.
I'd also like you not to have to specify the physical URL if it is the same as the logical...but if it's blank, the configuration methods don't function properly.

#5 Updated by ben leinfelder over 10 years ago

now loading new ontologies and unloading ontologies that are removed from the configuration

#6 Updated by ben leinfelder over 10 years ago

done for this round of plugin development - will revisit when loading remote (metacat) ontologies as well

#7 Updated by Redmine Admin over 7 years ago

Original Bugzilla ID was 4768

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