—

---

—

---

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

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.

—

—

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

—

NCI CBIIT EVS Content Editorial Team

EVS Content Management

Primary Users of Protege.  Utilize Protege to edit EVS content

—

—

—

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

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

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 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

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.