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Protégé 1.4.2 Scope Document

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Document Information

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

Sign off

Date

Role

CBIIT or Stakeholder Organization

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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 1.4.2. 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 1.4.2 is to provide bugs fixes found in previous Protégé releases as well as validating functionality that had been developed in previous releases but never tested. Then fixing any defects that come out of that testing.

Current Solution

Protege 1.4.1.1 is currently in production.

Feature Requests

GForge number
(hyperlinked)

Brief description of item

(Approved or Proposed)

16191 

Export of inferred Ontology - Tweaks to output file

Approved

18998 

Load explanation server from the Protege KB using the OWL API converter in Protege 3.4

Approved

18999

Serialize state at explanation server shut-down so start-up can be incremental since previous run

Approved

22785 

Only exports the first page of results in LQT search

Approved

23385 

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

Approved

24359 

Batch jobs performance improvements

Approved

24360

Batch jobs robustness

Approved

24461 

Allow multiple domains and ranges

Approved

26328

Report Writer outputs extra instances in 'Property value present' query

Approved

26416 

Unable to get filler values from roles in query export

Approved

26548

A button to refresh the class hierarchy tree in the class browser pane.

Approved

26567

Disable Tooltips for NCI ontologies.

Approved

26568

Add a Complete button to workflow subtab

Approved

26569

Remove Unnecessary scripts from Protege Server / Explanation Server Folder

Approved

26570

Lucene query tab default setting will not search PATO

Approved

26571

Export of Annotations are viewed by OWLAPI as ObjectProperties

Approved

26573 

Start or restart of the Explanation server has lost the time/date reference

Approved

26605

In all NCI Editor Tabs except the Edit tab concept name property is not displayed properly

Approved

26606

Edit set as default instead of Load Please

Approved

26634 

“by code” (rdf:ID is meaningless)

Approved

26666

Configurability

Approved

26668

wiki collaboration

Approved

26669

Runtime classification

Approved

27029

Results panel callable from the explanation tab

Approved

28860

:NAME needs to be added to pull down list of Attributes w/ID in Report Writer

Approved

29103

Prevent save of a class that has less than 2 N&S conditions.

Approved

Bug Fixes

GForge number
(hyperlinked)

Brief description of item

(Approved or Proposed)

7679 

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

9298

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

11082 

Change of Focus after Retire

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

22181 

Convert project to format seems to run twice

22902

Create a restriction with retired individual in premerge only

23457

lucene search option falls off pull down list not sure of the trigger

23527

Explanation server syncronization issue with retire action

23564

protege:readOnly=true behavior is unexpected

23581 

Inconsistant reject button availability

23582

PROMPT Tree View reject gave null pointer exception

23710 

Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions

23795 

Legacy_Concept_Name should not transfer during merge

23874 

User's Guide goes to Protege 2000 page

23876 

Cannot change case of PT and PN

24274

inheritance of role restrictions is no longer working correctly

24432

Strange behavior on Preferred Name change

24445 

Failure of Lucene to index at runtime

24503

LQT nested query causes error dialog

24803

Edit of Preferred_Name does not always sync the NCI PT

24837

Search using contains is very slow

24955

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

25019 

Selection of display slot for individuals is not scrollable

25464

Properties that have spaces cannot be edited in the Edit tab

25645

identifiable?

25646 

SPCA contrib source

25769

Error Message displays association error, yet performs edit

25840

Strange output during Explanation Server restart

26169 

Duplicate Full Syn atom could not be deleted via NCI Editor Tab

26432 

unable to find concept

26463 

Remove hard-coding of LONG_DEFINITION and other deprecated complex properties

26478

Cannot add role after editing a parent due to loss of focus in class browser

26512

"Increase or Decrease Font Size" causes Edit Tab increment

26540

extra prefix string when exporting ALT-DEFINITION and DEFINITION

26682

report writer fails to produce output

26715

EditTab not persisting complex properties correctly

26759

GO_Annotation props not showing in correct panel

27037

Allows duplicated roles to be added with batch processing

27038 

Different “Reviewer Name” is displayed

27041

"Delete Parent" is allowed to delete last parent when batch processing.

27043

OLD_PARENTS and OLD_ROLEs ought to be added simultaneously

27076

batch delete definitions fails

27078 

“Required field” for FULL_SYN is not enforced when doing Batch Processing.

27079

“Required field” for DEFINITION or ALT_DEFINITION is not enforced when doing Batch Processing.

27248

deleting a role takes rdfs:label (preferred name) and should take rdfs:ID

27755 

Trouble with usage of datatype properties

27757

Spotty Synchronization of NCIEditor Hierarchy with Explanation and OWLClasses Tabs

27855

Enable the use of rdfs:comment

27969

New strange behavior on PT change

28088

Preretire fails if redirect or remove two of the same restrictions pointing to the preretiree

28123

Generate Report with attributes does not display Definition or FULL_SYN

28127

AQP export needs to escape comma everywhere

28265 

rename a class and rename it back leads to loss of type information.

28284

Tabs in Edit Tab Preferences can't be removed. (Tabs in Edit Tab Preferences can't be added).

28312

"Delete FULL_SYN" in batch processing doesn't work

28335

Batch delete of Semantic_Type fails

28364 

Need to be able to configure Property Value Query in the LQP

28400

Performance Issues

28416

New concept with existing rdf:ID fails to be created, insufficient error message.

28417

Can only shutdown protege server through the Administer Server GUI

28532

There is error message when batch processing special characters "& and <" fails.

28553 

Classification Optimization

28586

Reasoner Error While Classifying in Standalone Mode

28589 

New scenarios that have strange behavior on PT change

29097

Performance testing

29102

Preretire causes multiplication of OLD_SOURCE_ROLEs from referencing classes

29145

Figure out if LQP result display timing is okay for a number of search scenarios.

29147 

LastUsageInvocationHandler being called with a high frequency

29193

Restrictions drop off when toggling from primitive to defined related to concurrency

29236

Split and Copy don't work in protege ByCode 1.4.2.174.

29258

Typo in Batch Load parent causes infinitely repeating exception

29286 

Qualifiers of Complex Properties don't display (ByCode)

29289

Legacy_Concept_Name ReadOnly works but it is passed to new concepts

29290

Retired concept is not listed under Retired Concepts

29342

Changing Preferred name makes 2nd rdfs:label be added. (NCIt - ByCode)

29344

There is no check-box next to Retire in the "Edit Tab Preferences"

29346

Cannot Edit Concept assigned in NCI Workflow (NPO)

29357

java.lang.NullPointerException is displayed in console windows after check /uncheck Copy, Split, Merge, or Retire  in Preference.

 

29358

Association Edit/Delete failed.

29383 

Does not retain assignment of workflow task from creation dialog

29445 

report writer fails to produce correct output for no attributes

29463 

The record number in the batch log may not match with the "line number" of the input file.

29464 

An invalid value is able to be added into the property Contributing_Source by the batch processing

29550

Need to use Display slot in Explanation tab panel

29552

After merge, redirected filler values are not updated by the Explanation Server

29565

A user was able to premerge two classes into a third class during concurrent editing

29569

Duplicate restrictions after merge with restriction pointing to surviving concept

29571 

Invalid messagebox/warning to user when modify a concept with N&S restrictions

29646

Review panel from LQT pane displays class name as "foo"

29707

Exceptions are thrown when closing "Select a property" dialog-box nested in "Edit an Object-Valued Property" dialog-box.

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

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.

[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

22104 

search string appears empty when invoked from restriction dialog box

23565 

refactoring namespaces

24510 

Need a fail-safe for creating codes for properties

28509 

Edit tab does not handle & or < properly

29143 

role groups not handled when toggling prim/defined

29358 

(NPO) Association Edit/Delete failed.

29513 

Improved formatting of batch load with error

29517

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

29665 

"Create Workflow Task" doesn't work" in 1.4.2.223 ByCode.

29720 

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

29752 

Generate Reports shows undesirable internal values

29753 

Extra box character shows in generated report

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:

Project GForge site link; 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.

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