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Protégé (Patch) Scope Document


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Document Information

Author:Jason Lucas/Gilberto Fragoso
Contract: Contract number
National Institutes of Heath
US Department of Health and Human Services

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CBIIT or Stakeholder Organization


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) Protege Patch release. 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 Protege Patch is to provide bugs fixes found in the 1.4.2 Protege release that was determined to be important but should not slow down the deployment of 1.4.2.

Current Solution

Protege 1.4.2 is currently in production.

Feature Requests

GForge number

Brief description of item

(Approved or Proposed)

Bug Fixes

GForge number

Brief description of item

(Approved or Proposed)


PreMerge "two concepts" after renaming them is not allowed.



Generate Reports shows undesirable internal values



Extra box character shows in generated report



Duplicate restrictions are found in the class BRCA1_wt_Allele.



Concept History Plugin - OLD_PARENT is deleted during save of concept history



Unalble to search from box by hitting return key



When invalid format is provided on a clone it doesn't retain previously entered Definition


General Support Activities

This section describes in detail all the related activities which must be performed for this release but do not add functionality. These activities are included in the scope and project plan due to level of effort or relative importance to the overall success of delivery of the release.

GForge number (hyperlinked)

Brief description of general support activity

(Approved or Proposed)

Example, "Level 2 Support, integration of help and training to the user community."

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



George Komatsoulis


Oversees NCI CBIIT Application Infrastructure

Avinash Shanbhag

Director of CORE Engineering

Oversees NCICB caCORE Software Engineering

Sherri de Coronado

Contract Project Officer

Management/technical resource from Bioinformatics vertical. Contract management, coordinateion, 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 1.5.x

Application Server


Database Server


Operating System

Any that supports Java: Windows XP, Linux, OS X


Portable ANSI-SQL compliant relational schemas

Product Dependencies

This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.

[Provide additional explanation as applicable. For example, "The EVS vocabulary systems are used by the Java client to retrieve and validate concept information for naming and defining meanings."]

Out of Scope Items

Items that are out of scope were evaluated as part of the initial scoping activities for this release, and subsequently not included in the final approved scope. These items are also documented in the cumulative backlog of requirements found on the product GForge site. They include out-of-scope functional requirements (enhancements or new features), bug fixes, non-functional requirements, and general support activities.

GForge number (hyperlinked)

Brief description of item moved from the in-scope section
with brief explanation added of why it was not included in this release

Iteration during which the item
was removed from in-scope

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 GForge site:

EVS Collaborative Terminology Dev Tools GForge project Docs archive, Files archive

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:

[EVS:Name and URL of each related document]

Project Information

CBIIT Management



Sherri de Coronado

Product Manager

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

Avinash Shanbhag

Engineering Manager

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

Denise Warzel

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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