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Protégé 1.3 Scope

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Document Information

Author: Charles Griffin
Email:
Team: EVS
Contract:
Client: National Cancer Institute Center for Biomedical Informatics and Information Technology
National Institutes of Heath
US Department of Health and Human Services

The purpose of this document is to collect, analyze, and define high-level needs and features of the NCI CBIIT Protégé Release 1.3. This document focuses on the functionalities proposed by the product stakeholders and target users in order to make it a better product.

Vision and Needs

The objective of this release of Protégé 1.3 is to introduce the database inclusion enhancements that will support owl:imports for federation.

This release will also incorporate defects fixes and other minor feature requests that were high priority items identified by the NCI editing team that were not able to be addressed in the Protégé 1.2.3 release.

Functional Requirements

Each enhancement, modification or new feature is described in detail in the following table.

GForge number
(hyperlinked)

Brief description of functional requirement
(enhancement or new feature)

Iteration
(Approved or Proposed)

caCORE:GF#12247

Database inclusion

1

caCORE:GF#8714

Admin component of protege server goes to sleep on extended inactivity periods

1

caCORE:GF#3435

Restriction INHERITED listing includes duplicate and superceded values

1

caCORE:GF#7518

Visibility of 'changes' ontology

1

caCORE:GF#8745

Removal of duplicate GO_Annotations from the Complex Properties

1

caCORE:GF#9298

Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work

1

caCORE:GF#14296

Copy tab panes don't have header labels

1

caCORE:GF#14557

Unnecessary warning dialog when saving with no semantic type set

1

caCORE:GF#15131

Cancel in classification progress dialog does not terminate the classification

1

caCORE:GF#15251

The order of items in config file is important

1

caCORE:GF#16191

Export of inferred Ontology - Tweaks to output file

1

caCORE:GF#16400

split tab allows creation of new roots

1

caCORE:GF#16076

Transaction didn't close in a class copy operation from the Copy panel

1

caCORE:GF#16058

Class Creation Problems

1

caCORE:GF#15788

Save Confirmation Popup Dialog blocks other editors

1

caCORE:GF#14973

class dissappears after editing(wind up under *Thing* ?)

1

caCORE:GF#16252

Lengthy and incorrect transactions in EditTab

1

caCORE:GF#16258

Can't retire some concepts that had referenced classes

1

caCORE:GF#15230

Error when Retiring a class with existing Editor_Note or DesignNote

1

caCORE:GF#14056

Permission allows delete of definition (see comments)

1

caCORE:GF#13842

Incremental Round Trip from Protege to Wiki

1

caCORE:GF#8682

Merged and Retired concepts are not properly tagged with Retired_Concept

1

caCORE:GF#14966

Business rule - Single restriction as N'S condition cannot be quantified by 'all'

1

caCORE:GF#11018

catch client exception when server is down or being bounced

1

caCORE:GF#14404

if character in slot matches delimiter then export misaligns values

1

caCORE:GF#15131

Cancel in classification progress dialog does not terminate the classification

1

caCORE:GF#15921

Explanation server synchronization issue

1

caCORE:GF#14939

Copy pane Preferred_Name issues after a modeling error

1

caCORE:GF#12066

Different displays of attributes in top and bottom pane of workflow

1

caCORE:GF#15913

Save should not be an option on the Merge panel until after a Merge or UnMerge

1

caCORE:GF#13712

SMW manifestation - If source not found, may enter BioCarta

1

caCORE:GF#12068

Apply the same restrictions as Protege on imported data from SMW

1

caCORE:GF#12935

text is not trimmed

1

caCORE:GF#9455

Editing the DEFINITION Annotation property

1

caCORE:GF#3537

Synchronization of rdfs:label and Preferred_Name

1

caCORE:GF#15247

Failure to cross check Preferred Term in Protege 1.2.3 release

1

caCORE:GF#15613

the start_explanation_server.sh script does not have appropriate commands

1

caCORE:GF#12131

Inconsistent naming used in Configuration dialog

1

caCORE:GF#12831

Removes/Corrupts Go_Annotation if have the exact same Long_Definition

1

Non-Functional Requirements

This section describes in detail all the related requirements which must be met for this release but do not add functionality. These requirements 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 non-functional requirement

Iteration
(Approved or Proposed)

None

None

None

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

Iteration
(Approved or Proposed)

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Support Activities are Performed by the EVS Operations Team

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Stakeholder Summary

Customer Name

Role

Interest/Need

NCI CBIIT EVS Content Editorial Team

EVS Content Management

Primary Users of Protege.  Utilize Protege to edit EVS content

CBIIT Staff/Contractor Name

Role

Responsibilities

George Komatsoulis

NCI CBIIT

Oversees NCI CBIIT Application Infrastructure

Avinash Shanbhag

Director of CORE Engineering

Oversees NCICB caCORE Software Engineering

Frank Hartel

EVS Product Manager

Directs EVS Projects

Sherri de Coronado

Contract Project Officer

Management/technical resource from Bioinformatics vertica. 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.

Component

Description

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

None

Database Server

MySQL

Operating System

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

[caCORE:Other]

Portable ANSI-SQL compliant relational schemas

Product Dependencies

This release is dependent on the caCORE components or products documented in the caDSR Technology Dependency Matrix.

[caCORE: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

caCORE:GF#14480

Make NCIEdit subtabs configurable - The requirements and design need to be flushed out in more detail before the team can move forward on this item.

1

Document History

Item

Information

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 Development 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:

Name and URL of each related document

Project Information

CBIIT Management

Role

Responsibilities

Frank Hartel

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.

Document Signoffs

CBIIT Management

Role

Stakeholder Management

Role

*Sign off

Date

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