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

doc/upgrade-1.1.txt

@@ -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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