UMLS Tab - Revision history

JenniferVendetti: migrated documentation over from old cim3 wiki

2008-11-05T23:42:41Z

migrated documentation over from old cim3 wiki

JenniferVendetti at 23:35, November 5, 2008

2008-11-05T23:35:35Z

JenniferVendetti at 23:21, November 5, 2008

2008-11-05T23:21:19Z

JenniferVendetti at 23:20, November 5, 2008

2008-11-05T23:20:51Z

JenniferVendetti at 23:16, November 5, 2008

2008-11-05T23:16:58Z

JenniferVendetti: added instructions for setting the umls.dbyear property

2008-10-23T23:12:57Z

added instructions for setting the umls.dbyear property

JenniferVendetti: adding content

2007-09-27T01:22:39Z

adding content

JenniferVendetti: added screenshot

2007-09-19T22:01:50Z

added screenshot

JenniferVendetti: added content under more information section

2007-09-18T23:53:27Z

added content under more information section

JenniferVendetti: added license info

2007-09-18T23:44:25Z

added license info

@@ Line 65: / Line 65: @@
 * Press enter or click on the search button.
 * Closely matched terms are shown in the table, and the detailed information for the first term in the table is shown in the center pane.
@@ Line 117: / Line 143: @@
 The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.
-<br /><br />
+<br /><br /><br />
 </div>

@@ Line 20: / Line 20: @@
 The UMLS Tab is a customized interface for browsing and searching the UMLS from within Protege, and directly annotating a Protege ontology with information from the UMLS.  New instances and classes can be created in Protege or slot values added by directly importing search results from the UMLS.
 === Introduction to the UMLS ===
@@ Line 37: / Line 38: @@
 * The knowledge in the table and relation display can be navigated easily
 * UMLS content can be added selectively to Protege

← Older revision		Revision as of 23:21, November 5, 2008
Line 89:		Line 89:

	The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.		The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.
		+	<br /><br />
	</div>		</div>
−	~~<br /><br />~~

@@ Line 17: / Line 17: @@
 <div style="float:left; width:100%;">
 == Documentation ==
-'''Please note: This documentation contains screenshots of an outdated version of Protege called Protege-2000. The UMLS Tab still works with the latest version of Protege and despite the outdated screenshots, this documentation is still useful.'''
+''Please note: This documentation contains screenshots of an outdated version of Protege called Protege-2000. The UMLS Tab still works with the latest version of Protege and despite the outdated screenshots, this documentation is still useful.''
 The UMLS Tab is a customized interface for browsing and searching the UMLS from within Protege, and directly annotating a Protege ontology with information from the UMLS.  New instances and classes can be created in Protege or slot values added by directly importing search results from the UMLS.
@@ Line 30: / Line 30: @@
 The UMLS Tab is designed to query the UMLS directly through UMLS Knowledge Source Server. The UMLS Tab is a customized interface for:
 * Viewing a remote knowledge base within Protege
 * Directly annotating an ontology in Protege with information from the remote knowledge base
@@ Line 38: / Line 37: @@
 * The knowledge in the table and relation display can be navigated easily
 * UMLS content can be added selectively to Protege
@@ Line 65: / Line 61: @@
 It is also possible that the UMLSKS system may be down for maintenance or be encountering problems. If the UMLSKS is encountering problems, you can contact them (custserv@nlm.nih.gov) and notify them of the problem.
 == UMLS Releases ==
@@ Line 80: / Line 77: @@
    <li>Double-click in the Value column to edit the value of the UMLS release.</li>
 </ul>
 == License ==
@@ Line 85: / Line 83: @@
 Anyone who wishes to use this plug-in should be aware that the [http://www.nlm.nih.gov/nlmhome.html National Library of Medicine] requires a signed license agreement in order to use or access UMLS content. The license is free of charge and you are responsible for abiding by the license terms, which protect the rights of the providers of some component vocabularies. You can obtain a copy of the [http://www.nlm.nih.gov/research/umls/license.html license agreement] from the [http://umlsinfo.nlm.nih.gov/ UMLS Information Web site].
 == Level of Support ==
@@ Line 91: / Line 90: @@
 The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.
 </div>

@@ Line 14: / Line 14: @@
 |Description=Allows users to search the National Library of Medicine's Unified Medical Language System (UMLS) and annotate Protege ontologies with terms, concept IDs, synonyms, relations, and other information from the UMLS.
 }}
 <div style="float:left; width:100%;">
-== More Information ==
+== Documentation ==
 The UMLS Tab is a customized interface for browsing and searching the UMLS from within Protege, and directly annotating a Protege ontology with information from the UMLS.  New instances and classes can be created in Protege or slot values added by directly importing search results from the UMLS.
-=== Troubleshooting Connection Problems ===
+=== Introduction to the UMLS ===
 Many people report problems connecting to the UMLSKS servers in the form of remote or connect exceptions. Examples of what these exceptions might look like are:
@@ Line 41: / Line 66: @@
 It is also possible that the UMLSKS system may be down for maintenance or be encountering problems. If the UMLSKS is encountering problems, you can contact them (custserv@nlm.nih.gov) and notify them of the problem.
-=== UMLS Releases ===
+== UMLS Releases ==
 The user interface of the UMLS Tab does not allow you to specify which release version of Metathesaurus data to query. As a workaround, we have provided an additional property in the Protege.lax file called "UMLSTab.dbyear" that allows you to specify the desired Metathesaurus release number. The default value is 2004AA. A [http://www.nlm.nih.gov/research/umls/archive/archive_home.html list of release numbers] can be found in the documentation section of the UMLS portion of the National Library of Medicine's Web site.
@@ Line 56: / Line 81: @@
 </ul>
-=== License ===
+== License ==
 The UMLS Tab and its source code (like Protege) are freely available under the open source [http://www.mozilla.org/MPL/MPL-1.1.html Mozilla Public License].
 Anyone who wishes to use this plug-in should be aware that the [http://www.nlm.nih.gov/nlmhome.html National Library of Medicine] requires a signed license agreement in order to use or access UMLS content. The license is free of charge and you are responsible for abiding by the license terms, which protect the rights of the providers of some component vocabularies. You can obtain a copy of the [http://www.nlm.nih.gov/research/umls/license.html license agreement] from the [http://umlsinfo.nlm.nih.gov/ UMLS Information Web site].
-=== Level of Support ===
+== Level of Support ==
 This plug-in is no longer under active development. Since the Protege community continues to express interest in the UMLS Tab, the Protege team will answer questions about the tab (as time permits) via the [http://mailman.stanford.edu/mailman/listinfo/protege-discussion protege-discussion mailing list]. We also recompile the UMLS Tab to make sure that it works with each new version of Protege.
 The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.
 </div>

← Older revision		Revision as of 23:12, October 23, 2008
Line 40:		Line 40:

	It is also possible that the UMLSKS system may be down for maintenance or be encountering problems. If the UMLSKS is encountering problems, you can contact them (custserv@nlm.nih.gov) and notify them of the problem.		It is also possible that the UMLSKS system may be down for maintenance or be encountering problems. If the UMLSKS is encountering problems, you can contact them (custserv@nlm.nih.gov) and notify them of the problem.
		+
		+	=== UMLS Releases ===
		+
		+	The user interface of the UMLS Tab does not allow you to specify which release version of Metathesaurus data to query. As a workaround, we have provided an additional property in the Protege.lax file called "UMLSTab.dbyear" that allows you to specify the desired Metathesaurus release number. The default value is 2004AA. A [http://www.nlm.nih.gov/research/umls/archive/archive_home.html list of release numbers] can be found in the documentation section of the UMLS portion of the National Library of Medicine's Web site.
		+
		+	To modify the UMLSTab.dbyear property in Protege:
		+
		+	<ul>
		+	<li>Select File \| Preferences...</li>
		+	<li>Click on the Property Files tab in the Preferences dialog.</li>
		+	<li>Click on the Protege.lax tab.</li>
		+	<li>Locate the entry for the UMLSTab.dbyear property in the Property Table.<br /><br />[[Image:Protege-preferences-dialog.jpg]]<br /><br />
		+	</li>
		+	<li>Double-click in the Value column to edit the value of the UMLS release.</li>
		+	</ul>

	=== License ===		=== License ===

@@ Line 2: / Line 2: @@
 |PluginType=Tab Widget
 |ForApplication1=Protege-Frames
 |HomepageURL=http://protegewiki.stanford.edu/index.php/UMLS_Tab
 |DeveloperID1=Qi Li

← Older revision		Revision as of 23:53, September 18, 2007
Line 13:		Line 13:
	\|Description=Allows users to search the National Library of Medicine's Unified Medical Language System (UMLS) and annotate Protege ontologies with terms, concept IDs, synonyms, relations, and other information from the UMLS.		\|Description=Allows users to search the National Library of Medicine's Unified Medical Language System (UMLS) and annotate Protege ontologies with terms, concept IDs, synonyms, relations, and other information from the UMLS.
	}}		}}
		+
		+	<div style="float:left; width:100%;">
		+	== More Information ==
		+
		+	=== License ===
		+	The UMLS Tab and its source code (like Protege) are freely available under the open source [http://www.mozilla.org/MPL/MPL-1.1.html Mozilla Public License].
		+
		+	Anyone who wishes to use this plug-in should be aware that the [http://www.nlm.nih.gov/nlmhome.html National Library of Medicine] requires a signed license agreement in order to use or access UMLS content. The license is free of charge and you are responsible for abiding by the license terms, which protect the rights of the providers of some component vocabularies. You can obtain a copy of the [http://www.nlm.nih.gov/research/umls/license.html license agreement] from the [http://umlsinfo.nlm.nih.gov/ UMLS Information Web site].
		+
		+	=== Level of Support ===
		+	This plug-in is no longer under active development. Since the Protege community continues to express interest in the UMLS Tab, the Protege team will answer questions about the tab (as time permits) via the [http://mailman.stanford.edu/mailman/listinfo/protege-discussion protege-discussion mailing list]. We also recompile the UMLS Tab to make sure that it works with each new version of Protege.
		+
		+	The source code for the UMLS Tab is available in the Protege Subversion repository. The URL to browse the code via a Web interface is: http://smi-protege.stanford.edu/svn/umls-tab/trunk/. The URL to download the source code with a Subversion client is: http://smi-protege.stanford.edu/repos/protege/umls-tab/trunk/.
		+	</div>

@@ Line 8: / Line 8: @@
 |Topic1=Biomedical Informatics
 |Topic2=Terminologies
 |Affiliation1=Stanford University
 |Affiliation2=Stanford Medical Informatics
 |Description=Allows users to search the National Library of Medicine's Unified Medical Language System (UMLS) and annotate Protege ontologies with terms, concept IDs, synonyms, relations, and other information from the UMLS.
 }}