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Adding in ontology changes section III from the 1.0 version of the document, as a starting point. We can update as necessary.

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sjm222 2010-06-22 21:04:55 +00:00
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doc/upgrade-1.1.txt
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@ -117,7 +117,73 @@ will be reflected in the search index.
III. Ontology Changes
>>>>>> TBD
Changes to the VIVO core ontology may require corresponding
modifications of the knowledge base instance data and local ontology
extensions.
When Apache Tomcat starts up following the upgrade, it will initiate
a process to examine the knowledge base and apply necessary changes.
Not all of the modifications that may be required can be automated,
so manual review of the knowledge base is recommended after the
automated upgrade process. The automated process will make only
the following types of changes:
Class or Property renaming
All references to the class (in the subject or object position) will
be updated to the new name. References to the property will be
updated to the new name.
Class or Property deletion
All individuals in a deleted class will be changed to
belong to the nearest available superclass (which may be owl:Thing).
All statements using a deleted property will be changed
to use the nearest available superproperty. If there is no available
superproperty then the statement will be deleted from the
knowledge base. Note that all removed and added data
is recorded in the files in the changedData directory.
Class or Property addition
If a newly added class has a superclass and there are
individuals in that superclass, then a note will be
added to the log file suggesting review of those individuals to
see if they should be reasserted in the newly added class.
If a newly added property has a superproperty and there are
statements using the superproperty, then a note will be added to
the log file suggesting review of those statements to see if they
should be reasserted using the newly added property.
Annotation property default values
It a site has modified the value of a vitro annotation (such as
displayRankAnnot or displayLimitAnnot) so that it is
no longer using the default, then that setting will be left unchanged.
If a site is using the default value of a vitro annotation, and the
default has been changed in the new version of the ontology, then
the new default value will be propagated to the knowledge base.
The ontology alignment process will create the following files in the
Tomcat webapps/vivo/WEB-INF directory:
ontologies/update/logs/knowledgeBaseUpdate.log
a log of a summary of updates that were made to the knowledge base and notes
about some recommended manual reviews. This file should end with
"Successfully finished processing ontology changes".
ontologies/update/logs/knowledgeBaseUpdate.error.log
a log of errors that were encountered during the upgrade process. This file
should be empty if the upgrade was successful.
ontologies/update/changedData/removedData.n3
an N3 file containing all the statements that were removed from the knowledge base.
ontologies/update/changedData/addedData.n3
an N3 file containing all the statements that were added to the knowledge base.
After Apache Tomcat is started, these files should be reviewed to verify that
the automated upgrade process was executed successfully.
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