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Contents of this Page

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At a Glance Details
  • Version Number and Release Date: 1.4.3, February 2011 (NCI Protégé 1.4 requires Protégé 3)
  • Installation Level: Intermediate - technical assistance may be required, download may require supporting infrastructure or software
  • System Requirements: Protégé runs on platforms that support JDK version 1.4. This includes all modern versions of MS Windows (NT/2000/XP), the common versions of Unix including Linux, Solaris, AIX, and HP-UX, and Mac OS X.

Tool Overview


NCI Protégé is a collection of Protégé plug-ins developed for the NCI-specific editing environment. Protégé is an open-source development environment for ontologies and knowledge based systems. The OWL plug-in extends the environment to support the Web Ontology Language (OWL). Refer to the Protégé page for more information.

NCI Protégé is a collection of Protégé plug-ins used to edit the NCI Thesaurus. NCI Protégé provides a customized OWL editing environment, including additional editing and querying capabilities that are not available in the Protégé OWL plug-in. The NCI-specific plug-ins have been implemented as a tabbed interface. Beginning with NCI Protégé 1.3.0. this tool allows imports of ontologies in database mode and enables collaborators to begin "federating" ontologies.

NCI Protégé runs in a client-server environment. Current editors will want to download the client only. Others may wish to download for review or download and install the entire client-server package. Links to both are provided in the tool downloads.


Installation and Downloads

The distribution package can be found on the GForge files archive page.

The package contains the following (this may vary slightly for different versions):

  • The installation folders for the client, Explanation server and Protégé server.
  • A metaproject which contains accounts for editor and administrator by default.
  • Test BiomedGT and NCIThesaurus OWL files to load.
  • An import-repository folder containing OWL files to set up a local ontology repository.
  • A ReadMe file with instructions on how to configure all the necessary scripts from scratch.

When you install a new release, you must configure a new database project, following the instructions on Protege Software Updates and Configuring New Database Project. These instructions reflect the NCI EVS server environment (directory structures, filenames, server hostnames, etc). It is not required, but it is probably easiest, to set up the same directories in a new environment.

Download for an NCI editor

If you are an NCI editor, you will only need to download the appropriate client, from the list on the GForge archive downloads page.

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NCI Protégé Forum and Support

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What's New

The final version of NCI Protégé (1.4.3) to be built on the Protégé 3.4 code base from Stanford has been released. The status of NCI Protégé is now maintenance mode. Only major bugs that appear in production will be fixed. Future versions of NCI Protégé are being considered for the Protege 4 code base.


The EVS Protégé distribution includes the NCIEditTab Protégé plug-in editing client (and other plug-ins), a highly concurrent Protégé server (modified from the base Stanford distribution), and an Explanation server that includes the Pellet reasoner.

Client Environment

The client environment includes:

  • NCIEditTab plug-in, supporting basic editing functionality as well as complex edits (merge, split, retirement, and cloning), batch jobs, report writing, and tree-like views of graphs built along transitive relationships (e.g. part_of). It supports XMLLiterals for complex properties as per configuration, and tracks editing history independently of the change ontology, which is used in support of Prompt.
  • LuceneQuery tab plug-in, supporting a variety of search modes (including negation) on annotations and restrictions as well as indexed Lucene "match" and "sounds like" searching, plus reporting support for the result sets.
  • Explanation tab plug-in, providing a description logic entailment-explanation facility integrated with an incremental classifier; classification results are available to all the clients in the client-server environment.
  • Workflow tab plug-in, supporting basic workflow/assignment functionality, and communications to Semantic Media Wiki if set up for collaborative development.


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NCI Protégé Presentations

The information and links in this section are no longer being updated and are provided for reference purposes only.

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NCI Protégé Documentation and Training

The information and links in this section are no longer being updated and are provided for reference purposes only.

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