—

—

—

—

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 

5967

New concepts go to bottom of the sibling list, rather than alphabetical (C)

Approved

8851

Hardcoding of 'special' classes or properties in NCIEVSHistory and NCIConceptHistory plugins (C)

Approved

10811

Restriction change frozen out (C)

Approved

11018

catch client exception when server is down or being bounced (C)

Approved

11891

deleting classes can cause spurious values showing up in class browser (C)

Approved

13856

When client left open, log file grew to 4 GB (C)

Approved

16533

Unnecessary warning when leaving Copy or Edit pane (C)

Approved

18978

frame caching refactoring. (C)

Approved

18981

Switching subtabs in nciedittab is slow (C)

Approved

18988

Modifications to the reasoning server to support storage plug-ins (C)

Approved

18989

Add context information in reasoner client/server protocol to reject updates to unrelated ontologies (C)

Approved

18990

Reasoner URL as per-project preference (rather than per Protege Server) (C)

Approved

18995

Update C&P Custom Reasoner Plug-in to better integrate as a Protege Reasoner Plug-in (C)

Approved

18996

Update Reasoner Server the latest released version of Pellet 2 (C)

Approved

14480

Make NCIEdit subtabs configurable (E)

Approved

16120

Addition of a date tag to retired concepts and to merged concepts (E)

Approved

18663

Synchronization Errors for Domain Changes of Annotation Properties (CB)

Approved

18232

Language should be serialialized as xml:lang attribute (CH)

Approved

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

25466

Cannot edit or delete associations

Approved

18831

LQT needs label at bottom to identify protege instance (I)

18598

Changes Tab says No Action for property edits (H)

2950

String fillers on object properties - Stanford (H)

3945

Definition and Long Def property should only allow NCI as a source. (H)

7118

Restrict Delete action by date (H)

7520

Default editor_note & designNote when pre-retiring (H)

7618

Start-up time of Protege is slow (H)

8918

Allows paste of Preferred Name but can not delete. (H)

8947

Modal dialog does not stay on top (H)

8989

Selection of Properties in Report Writer (H)

8990

Report Writer output format. (H)

13848

Allow search on null in AQP. (H)

14786

Focus jumps to new project after final row deleted. (H)

14805

Have batch load verify all STYs are correct when loading. (H)

15174

No copy option on right click menus for Split function. (H)

15493

Default Task Description of new Workflow assignment has typo. (H)

15664

Assumption of role groups. (H)

15752

In copy pane, modify restriction does not remember filler value. (H)

16163

Addition of Superclass in Copy/Split/PreMerge - allow 'defining' superclass. (H)

16620

Report writer feature request. (H)

16775

Simplify adding a role. (H)

16839

Each change needs to be associated with an editor. (H)

16887

Add definition field to window when cloning a class. (H)

17210

LQP/AQP - selection and output of superclasses. (H)

17212

LQP/AQP - search for concepts lacking a property. (H)

17213

Selection criteria for concepts to be exported via LQP/AQP export function. (H)

17214

Report writer - add export function currently in LQP/AQP. (H)

17760

Workflow improvements. (H)

18177

Incorrect display of LQT search criteria. (H)

18536

Batch Load of new concepts interferes with other editors creating concepts. (H)

18616

Save of concept_history in NCI_DB format after Prompt should be altered or automated. (H)

18959

sort of inferred results panel. (H)

18982

gui refresh on switching apps back to protege. (H)

18997

Protege tab for reasoning server administration (including status information & kb reload). (H)

18999

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

19000

Reduce reasoning time for explanations which include domain or range axioms. (H)

2948

Domain and Range checks on property restrictions at edit time. (I)

3941

Duplicate Role Groups should not be allowed, even if roles are ordered differently. (I)

8302

Need automatic cursors in filler windows. (I)

8375

Display attributes in tree form on Copy tab. (I)

8590

Allow user to modify Superclasses in Copy tab (I)

8609

Retain frame sizes after switching tabs. (I)

8612

Display recently used classes in drop down of search. (I)

10987

Modify Name Superclass dialog should be eliminated. (I)

12337

Automated configuration of server project. (I)

12815

Track the last modeler who modified the assignment. (I)

12817

Creating new workflow assignments. (I)

12935

text is not trimmed. (I)

13951

Modal messages to other viewer. (I)

15003

NCIWorkflow - reorder columns (I)

16099

Complex property dialog layout goes crazy when a very long definition is entered. (I)

16100

Error message when full_syn has a tab or new line is confusing. (I)

16121

Button to make a concept defined. (I)

16152

Display of NCIEditTab Build Version. (I)

16255

Disable the Merge tab when the user is not allowed to merge. (I)

16347

Colors of text in copy, split, retire, merge and workflow panes are too dull. (I)

17570

Confusing message to the user when you drag the retiring concept into surviving concepts pane.(I)

18116

LQT export of results is exporting entire path. (I)

18164

query in changes tab search box gives ""Please enter an expressioin"" error". (I)

18583

Hierarchy View too cluttered. (I)

18961

queries in change tab. (I)

18998

Load explanation server from the Protege KB using the OWL API converter in Protege 3.4. (I)

—

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

[

caCORE:Other]

Portable ANSI-SQL compliant relational schemas

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 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

]

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.