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Protégé 1.4.1 Scope Document

Contents
Document Information

Author: Jason Lucas/Gilberto Fragoso
Email: lucasjr@mail.nih.gov
Team: EVS
Contract: [EVS:Contract number]
Client: NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services

Sign off

Date

Role

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) Protégé Release 1.4.1. 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 1.4.1 is to provide bugs fixes found in previous Protégé releases as well as completing feature request for formatting of the complex properties and improving performance for batch edits.

This release will be performed over one main development iteration and a second iteration to cover any items found in UAT:

Iteration B0 - Development of Scoped Features and Bug Fixes

Iteration B1 - Bug fixes found from user acceptance testing

Current Solution

Protege 1.4 is currently in production.

Iteration B0

Feature Requests

GForge number
(hyperlinked)

Brief description of item

(Approved or Proposed)

18997

Protege tab for reasoning server administration (including status information and kb reload)

Approved

22870

Would like to do 'property present' LQT queries with object properties

Approved

2948

Domain and Range checks on property restrictions at edit time

Approved

23003

Not able to have a NOT query in the nested query

Approved

23297

Restrict access to OWLClasses tab

Approved

23516

the changes ontology sees changes involving internal protege classification slots (e.g. protege:inferredSuperclassOf)

Approved 

21375

Use of parseType=Literal for complex properties

Approved 

18533

Changes Tab does not reflect items created in Batch Load

Approved 

16324

Need indication of classifier run

Approved 

16121

Button to make a concept defined

Approved 

6082

BACK and FORWARD Buttons

Approved 

Bug Fixes

GForge number
(hyperlinked)

Brief description of item

(Approved or Proposed)

24801 

Focus of editor switches while creating restrictions

Approved

22400

LQT results don't have search criteria appended at the end of the file.

Approved

22680

Restrictions added flagged as changes to Restriction classes in Prompt

Approved

24503

LQT nested query causes error dialog

Approved

24435

fitering inherited restrictions

Approved

24343

Cannot edit restriction that has an apostrophe in the filler value

Approved

24301

Add Individual button should only be enabled when hasValue is selected

Approved

23284

Batch edit to delete associations needs full association rdfs:ID

Approved

24196

Restore nci-specific export function in inferred tree widget

Approved

19404

Link which opens when an unstructured proposal is imported, opens an xml.

Approved

20587

infinite loop in Report Writer

Approved

22969

Report Writer fails on rerun after a cancel

Approved

22984

null pointer in Protege OWL layer

Approved

23006

Can't change tabs unless focus is on a concept

Approved

23204

After split one of the classes ended up with owl:thing as the only parent

Approved

23276

In Copy pane, the Preferred_Name and PT are automatically sync'ed with an improper AQ.

Approved

23431

Editing a role with Cardinality requires reselecting Cardinality

Approved

23529

Report Writer shows anon class defined by conjunction of NandS

Approved

23716

Report Writer incapable of generate completed report

Approved

23613

CompleteableCache throws a nullpointer exception

Approved 

23057

Lucene indexing failure with database data

Approved 

23631

Refresh of screen after classification slow and using up desktop resources

Approved

22879

BatchEditor gives a false positive

Approved 

23530

Cannot edit the concept from workflow

Approved 

23969

Batch edit takes a long time

Approved 

22434

database accumulates garbage over a period of time

Approved 

22405

NPE when selecting row from PROMPT differences table

Approved 

20018

During a batch edit a new definition is accepted even without the qualifiers.

Approved 

13586

Can the Read-Only view look like the Review pane (have one page with all class info)?

Approved 

22781

Protege 1.4 loads ndf-rt with exceptions, property tab has the ugly widget

Approved 

15632

Inability to reject and/or ignore suggestions from the classifier

Approved 

22786

Expands the first top level node under owl:Thing when add Restriction

Approved 

6067

rethink and redesign workflow of pre-merge/pre-retire

Approved 

18033

Make Changes tab show login and log out

Approved 

23495

Slow performance when creating new concepts including split and copy

Approved

Iteration B1

GForge number
(hyperlinked)

Brief description of item

(Approved or Proposed)

25466

Cannot edit or delete associations

Approved

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)

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

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 vertical. 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.

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 CORE Product Dependency Matrix.

[EVS: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

7369

Include a domain in the classification report

7679

(make configurable) Default search parameters for Advanced Search are not default for search w/in search

8373

Word wrap attributes in Copy tab

8787

Controls can be pushed off to side of dialog with long attr

9298

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

9572

Need to see the 'retired' designation for concepts found in part of AQP

12337

Automated configuration of server project

20906

Protege incorrectly exporting names with quotes

21549

Single quote mark around multi-word parents

21738

Hierarchy is not refreshing the D when retire concept

21946

Incorrect unretire functionality

22090

Tool Tab compression and disappearance

22104

search string appears empty when invoked from restriction dialog box

22785

Only exports the first page of results in LQT search

22902

Create a restriction with retired individual.

23385

update protege/workflow and SWM to handle new XML Literal complex properties

24803

Edit of Preferred_Name does not always sync the NCI PT

24805

Edit of Preferred_Name in Copy tab caused two rdfs:labels

24870

trouble with saving upper/lowercase variants in the FS slot

24878

Deprecated concepts are editable

24929

Restriction domain checking does not work correctly for referenced classes

24955

Rejection of changes to Retired Concept branch caused deletion of newly retired classes

26195

Variability in Batch Loading Times

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:Project GForge site link]

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

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.


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