Difference between revisions of "Annotator Dataset Workflow Howto"

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(New page: == Chapter 1: Synchronizing Data with BioPortal == * The synchronization with BioPortal data should be performed regularly (currently scheduled bi-weekly or on-demand). * The synchron...)
 
(Replaced content with "As of Virtual Appliance v2.2, populating the Annotator Dataset is done automatically when an ontology is processed.")
 
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==  Chapter 1: Synchronizing Data with BioPortal ==
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As of Virtual Appliance v2.2, populating the Annotator Dataset is done automatically when an ontology is processed.
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* The synchronization with BioPortal data should be performed regularly (currently scheduled bi-weekly or on-demand). 
 
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* The synchronization (Incremental Update) should be done in separate environment from Staging & PROD.
 
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<pre>
 
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Environment for OBS Data Population
 
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Instance of tomcat : ncbodev-obs
 
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Instance of DB : ncbodev-obsdb1.sunet
 
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</pre>
 
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* The steps are as following:
 
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<ol>
 
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<li>Remove out-dated ontologies from OBS Database (e.g. older version of ontologies that does not in BioPortal anymore). By invoking this Restlet, it will remove all the outdated ontology data and the associated entities such as concepts, terms, relations, semantic types and hierarchy information.
 
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<p><code>
 
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Query: Get List of ontologies to be removed  (old):
 
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http://ncbodev-obs:8080/obs_hibernate/admin/ontologies/list/old<br/>
 
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Run:
 
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http://ncbodev-obs:8080/obs_hibernate/admin/ontologies/remove
 
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</code></p></li>
 
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<li>Add new ontologies from BioPortal to OBS. By invoking this Restlet, it will add all the new ontology data and the associated entities such as concepts, terms, relations, semantic types and hierarchy information.
 
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<p><code>
 
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Query:  Get List of ontologies to be added (new):
 
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http://ncbodev-obs:8080/obs_hibernate/admin/ontologies/list/new<br/>
 
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Run:
 
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http://ncbodev-obs:8080/obs_hibernate/admin/ontologies/add
 
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</code></p></li>
 
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<li>Populate Concepts (For details, please refer to Chapter 2.1)
 
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<p><code>http://ncbodev-obs:8080/obs_hibernate/loaderBigConcepts/all</code></p></li>
 
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<li>Populate Hierarchy (For details, please refer to Chapter 2.2)
 
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<p><code>http://ncbodev-obs:8080/obs_hibernate/loaderBigPaths/all</code></p>
 
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<p>To monitor the progress and error, refer to:</p>
 
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<ol>
 
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<li>The "status" field in the table obs_ontology in OBS DB. (ncbo-dev-obsdb1.sunet)
 
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<li>Check the log in tomcat. (ncbodev-obs: /usr/local/tomcat5/logs)</li>
 
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</ol></li>
 
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<li>Create Dictionary: To run this, this step has to be complete: "3. Populate Concepts" (For details, please refer to Chapter 4)</li>
 
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<li>Create Mapping Data (For details, please refer to Chapter 6)</li>
 
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</ol>
 
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* When the update is complete, the snapshot of DB should be copied (or replicated) to Staging/PROD.
 

Latest revision as of 17:06, 14 January 2015

As of Virtual Appliance v2.2, populating the Annotator Dataset is done automatically when an ontology is processed.

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