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NIHVIVO-3841 some updates to update documentation

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stellamit 2012-06-27 19:35:59 +00:00
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doc/upgrade-1.5.html
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@ -141,8 +141,56 @@
<h3 id="#upgrade_process">III. Upgrade Instructions</h3> <h3 id="#upgrade_process">III. Upgrade Instructions</h3>
<h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1> <h1>BOGUS -- INSERT REAL STUFF HERE, EVENTUALLY</h1>
<h3 id="#kbm">IV. Knowledge Base Migration</h3> <h3 id="kbm">IV .Knowledge Base Migration</h3>
<p>
Changes to the VIVO core ontology may require corresponding
modifications to the knowledge base instance data and ontology annotations.
When VIVO first starts up following the upgrade, it will
initiate a process to examine the knowledge base and apply necessary
changes. The knowledge base migration process for release 1.5 will make
the following types of changes:
</p>
<dl>
<dt>
The vivo:ResearchLaboratory class has been removed. All instances of vivo:ResearchLaboratory will be
retyped to its superclass vivo:Laboratory.
</dt>
</dl>
<dl>
<dt>
Annotation property default values
</dt>
<dd>
If 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.
<br>
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.
</dd>
</dl>
<p>
In addition to the logs described in <strong>step 8</strong> of the <a href="#upgrade_process">previous section</a>, the knowledge base migration
process will log copies of all additions and deletions that were made to the knowledge base in the following files:
</p>
<dl>
<dt>
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/removedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were removed from the knowledge base.
</dd>
</dl>
<dl>
<dt>
<code>webapps/vivo/WEB-INF/ontologies/update/changedData/addedData.n3</code>
</dt>
<dd>
An N3 file containing all the statements that were added to the knowledge base.
</dd>
</dl>
<h3 id="termsofuse">V. Review the VIVO Terms of Use</h3> <h3 id="termsofuse">V. Review the VIVO Terms of Use</h3>
<p> <p>
VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name" VIVO comes with a "Terms of Use" statement linked from the footer. The "Site Name"