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Protégé 1.5 Scope Document


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Document Information

Author: Gilberto Fragoso/ Bob Dionne
Team: EVS Protege
Contract: Contract number
National Institutes of Heath
US Department of Health and Human Services

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CBIIT or Stakeholder Organization

Sherri De Coronado


Government Sponsor


Gilberto Fragoso 6/18/2015Government SponsorCBIIT
Kumar Kuntipuram 6/18/2015Government SponsorLeidos Biomedical Research Inc.

The purpose of this document is to collect, analyze, and define high-level needs and features of the National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) Protégé Release 1.5. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product. The use-case and supplementary specifications document will detail how the framework will fulfill these needs.

Vision and Needs

The objective of this release of Protégé 1.5 is to harden the existing Protege 3.4 so the project can go into an operation and maintenance mode of operation whilst new development is occurring on Protégé 5. This release builds on the technology stack upgrade that's already in production and will entail one and possibly two iterations:

Iteration 1 - will include all the JIRA bug fixes enumerated below

Iteration 2 - Possible new JIRA items will be added in addition to any new bugs exposed by iteration 1.

Iteration 1 (1.5.0)

JIRA ticket

Brief description of item

(Approved or Proposed)


Associations are not able to be copied in the copy tab.


1430Add a cancel search buttonDeferred
1442Performance issues with long running queriesApproved
1432Batch Editor commits 'NA' to filler valuesApproved
1431Administrator should have rights to edit retired conceptsApproved
1424Can't Batch Delete Original N&S ParentApproved
1423Language on Definition not displayed in Edit TabApproved
1457Initial Editing of Preferred Class Name is not being recognizedApproved
1454Incorrect label on "Preretire" buttonApproved
1455Warning message spelling error when performing PreRetireApproved
1450Disable WorflowApproved
1445Batch Edit not treating FULL_SYN the same as Batch LoadApproved
1443Report Writer fails if a bad code is in the inputApproved
1448Empty qualifiers should not be allowed on batch editApproved
1447Duplicate restrictions discarded but still write to the evs_history tableApproved
1446It is possible to create duplicate rolesApproved
1439Allow code to be selected and copy/pasted from the edit paneApproved
1427If you click on 'No results found.' an error is thrown and comes up on the consoleApproved
1415When cloning not escaping definition if invalid class nameApproved


Iteration 2 (1.5.1)

JIRA ticket

Brief description of item

(Approved or Proposed)


Umlaut in a :NAME in a batch load file creates a term with a bad :NAME


1467Right Clicking on Class Name and Sub-Class name the Create Workflow Task Menu Pops upApproved
1468Closing "Enter Class Identifiers" by Clicking "X" Causes Java ErrorApproved
1465Disallow save of self concept as the parent concept (superclass)Approved
1457Initial Editing of Preferred Class Name using the Shift Key + Letter is not being recognized.Approved
34Output Duplicates for Input DuplicatesApproved
1461Copy tab functional discrepancyApproved
1433Have default Editor_Note and DesignNote on retiring merge partner point to the code.Approved
1460Ability to select "lucene match" as a default searchApproved
1471After save the GUI focus goes to the New Project... iconApproved
1440Assign STY to concept in Batch Load fileApproved
1407Sorting FeatureApproved
1436ByCode issue - Partonomy Tree dialog shows role codesApproved
1437ByCode issue - Partonomy Tree tab unable to create tree in byCode vocabApproved
1413Change of Semantic_Type value after changing PTsApproved


Stakeholder Summary

Customer Name



NCI CBIIT EVS Content Editorial Team

EVS Content Management

Primary Users of Protege. Utilize Protege to edit EVS content

CBIIT Staff/Contractor Name





Oversees NCI CBIIT Application Infrastructure


Director of CORE Engineering

Oversees NCICB caCORE Software Engineering


EVS Product Manager

Directs EVS Projects

Sherri de Coronado

Contract Project Officer

Management/technical resource from Bioinformatics vertica.  Contract management, coordination, testing, documentation

Gilberto Fragoso

Government Lead

Technical resource from Bioinformatics vertical

Technical Environment

This product uses the following technical components which have been derived from the current NCICB Technology Stack.



Client Application

The Protege client is java based and provides a complete editing environment for Protege databases, call ontologies.  It uses the same plugin architecture to support extensions, called Tabs.  For example, the NCI Edit Tab, Workflow, Changes, and Prompt, are examples of plugin tabs.

Java 1.8.x

Application Server


Database Server


Operating System

Any that supports Java: Windows, Linux, OS X


Portable ANSI-SQL compliant relational schemas

Product Dependencies

The runtime product has no dependencies other than the ones stated under Technical Environment.



Document History



Document Version:

Click the Info tab. View the Recent Changes or click the link to view the page history.

Last Modified:

Refer to the first line displayed in the document window.

Project JIRA site:

JIRA - Protege Issue Tracker

Most current version:

Unless the display includes a notice that you are viewing a previous version, you are viewing the most current version of this Scope Document for the release indicated in the title.

Revision history:

Click the Info tab. In the Recent Changes area, click the link to view the page history.

Review history:

Click the Info tab. In the Recent Changes area, note the developer who made each change and the date and time. Refer to the Key People Directory for their roles. Click the link to view any page or to view the page history, and then click the link for a page. When the page opens, view the comments and changes made in that version.

Related documents:

Name and URL of each related document

Project Information

CBIIT Management




Product Manager

Oversees development of the product: features, functions, definition of stakeholders, priorities within the scope, timeframe for release


Engineering Manager

Oversees NCICB caCORE software engineering practices, conducts design reviews, guides technical development


Product Line Manager

Oversees NCICB caCORE product line. Responsible for overall product integration, major and minor release cycles. Supports Product Manager.


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