UMLS Tab

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UMLS Tab

by Qi Li, Philip Shilane

Screenshot

Type Tab Widget
Author(s) Qi Li, Philip Shilane
Last Update September 14, 2006
License Mozilla Public License
Homepage UMLS Tab website
For Application
Topic(s)
Affiliation

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.

Contents


Versions & Compatibility

This section lists available versions of UMLS Tab.

Version Compatible with Dependencies
UMLS Tab 2.0 Protege-Frames 3.3.1 UMLS Metathesaurus License Agreement

If you click on the button below to add a new version of UMLS Tab, you will be asked to define a page title for the new version. Please adhere to the naming convention of UMLS Tab X.X.X when you define the new page!

Changelog

Version Changes in this version
UMLS Tab 2.0 no change log was maintained for this version


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Please note: This documentation contains screenshots of an outdated version of Protege called Protege-2000. The UMLS Tab still works with the latest version of Protege and despite the outdated screenshots, this documentation is still useful.

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

The National Library of Medicine (NLM) sets up the Unified Medical Language System (UMLS). UMLS develops and distributes multi-purpose electronic "Knowledge Sources" and associated lexical programs. The UMLS sources are quite useful for users to set up their knowledge base in the medical domain. All of the concepts, terms, and semantic types in the UMLS come from lots of sources. In the UMLS Tab, users can query directly through the UMLS Knowledge Source server.

To learn more about the UMLS, please visit:

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
  • Searching UMLS sources by term name
  • Creating new Protege classes and instances with UMLS content
  • New instances and classes can be created in Protege and slot values can be added by directly importing search results from the UMLS Knowledge Source Server
  • The knowledge in the table and relation display can be navigated easily
  • UMLS content can be added selectively to Protege



Troubleshooting Connection Problems

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:

java.net.ConnectException: Operation timed out: connect

java.rmi.RemoteException: Connection refused; invalid client IP address

To successfully connect, please verify that you have completed the following items:

  • You are a registered UMLSKS user. If you have not registered, you may request an account on the home page of the UMLSKS Web site.
  • You have added your IP address to your account profile on the UMLSKS Web site. Instruction for doing this are as follows:
    • Go to the UMLSKS Web site.
    • Login to their site using your UMLSKS LoginID and password.
    • Click on the Views/Profiles link on the navigation bar that runs along the top of the page.
    • Add your static IP address to the "IP Address(es)" text area.
    • Click Update Changes to save your changes.
  • If you are running from behind a firewall, confirm that the firewall is configured to allow outside connection to the default RMI service port of 1099.

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 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:

  • Select File | Preferences...
  • Click on the Property Files tab in the Preferences dialog.
  • Click on the Protege.lax tab.
  • Locate the entry for the UMLSTab.dbyear property in the Property Table.

    Protege-preferences-dialog.jpg

  • Double-click in the Value column to edit the value of the UMLS release.

License

The UMLS Tab and its source code (like Protege) are freely available under the open source Mozilla Public License.

Anyone who wishes to use this plug-in should be aware that the 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 license agreement from the 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 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/.

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