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title	Document Information

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*Author:* \[Project Manager/Technical Lead\]
*Email:* \[Email address for Scope Document contact\]
*Team:* \[For example caDSR, EVS, caGRID, and so on.\]
*Contract:* \[Contract number\]
*Client:* NCI CBIIT
National Institutes of Heath
US Department of Health and Human Services

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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) Protege Release 1.4. 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 Protege 1.4 is to harden Protege so the project can go into an operation and maintenance mode of operation in lieu of actively developing new releases of the product containing new features. Protege 1.4 is planned to be the last major release of Protege.

This release will be performed over five iterations:

Iteration B0 - will focus on merging the 1.3 branch with trunk and will not include the explanation server and explanation tabs.

Iteration B1 - will be a refactoring and hardening iteration focused on making improving and stabilizing the code base.

Iteration B2 - will focus on bugs that were discovered during QA of the 1.3 release and need to be resolved. Any critical 1.4 release bugs found at this point will be fixed as well.

Iteration B3 - will focus on highly desireable "Nice to Have" features.

Iteration B4 - will be dedicated to fixing defects found in 1.4 that are "must haves". Since 1.4 is currently planned to be the last major release, all critical fixes need to be resolved.

Current Solution

Protege 1.3 is in production currently and a Protege 1.3.0.1 patch release is scheduled to be released before Protege 1.4 is released.

Iteration B0

GForge number (hyperlinked)	Brief description of item	(Approved or Proposed)
	Merge the 1.3 branch with trunk and create a 1.4 branch.	Approved

Iteration B1

GForge number (hyperlinked)	Brief description of item	(Approved or Proposed)
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

Iteration B2

GForge number (hyperlinked)	Brief description of item	(Approved or Proposed)
	Export of inferred Ontology - Tweaks to output file (A)
	insertion of Brackets in Preferred Name Display	Approved
	Language display (B)	Approved
	port EVS history plugin to support db inclusions (B)	Approved
	Merging two concepts with incoming roles should not result in duplicates (B)	Approved
	Merging two concepts with incoming properties should not result in duplicates (B)	Approved
	Invalid classification findings if premerge or pre-retire exists (B)	Approved
	Adding restrictions and the Advanced Query (B)	Approved
	Does not change status of workflow to Updated when manager edits a concept (B)	Approved
16140	Copy Tab allows save of class with duplicate restrictions (B)	Approved
16753	Retain slot delimiters in LQT export (B)	Approved
16926	:ROLE concrete - Prompt bug fix (B)	Approved
16928	Ampersands in property values affecting copy/clone function (B)	Approved
	Automated creation of EVS_HISTORY and CONCEPT_HISTORY tables on first use (B)	Approved
	Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work (B)	Approved
	PROMPT- 'Table View' crashes after visting 'Show sources' window (B)	Approved
	PROMPT- Reject button in Tree view produces error message to the console (B)	Approved
	If character in slot matches delimiter then export misaligns values (B)	Approved
	History records created on classification in client--server mode (B)	Approved
	Duplicates Items displayed on the main menu. (B)	Approved
	Loss of Concepts form the Hierarchy (B)	Approved
17777	AQP sometimes returns an incomplete result set (B)	Approved
17926	Ontology imports cause data problems when loading the explanation server from a Protege database (B)	Approved
18163	Triple click on Change History causes UnsupportedOperationException (B)	Approved
18210	User can drag and drop a concept which has not been pre-merged into a merge pane. (B)	Approved
18497	RuntimeException when you click 'Edit form of type...' button on Edit tab (B)	Approved
18533	Changes Tab does not reflect items created in Batch Load. (B)	Approved
18588	Lucene query tab default setting will not search PATO (B)	Approved
18589	LQP view class buttons do not appear for class in PATO. (B)	Approved
18820	Package status not being updated in workflow. (B)	Approved
18929	A classifier run tags all concepts with protege:inferred properties. (B)	Approved
18930	PROMPT tab allows start of compare even when another compare is running. (B)	Approved

Iteration B3

GForge number (hyperlinked)	Brief description of item	(Approved or Proposed)
	LQT needs label at bottom to identify protege instance (I)	Approved
	Changes Tab says No Action for property edits (H)	Approved
	2950 String fillers on object properties - Stanford (H)	Approved
3945	Definition and Long Def property should only allow NCI as a source. (H)	Approved
7118	Restrict Delete action by date (H)	Approved
7520	Default editor_note & designNote when pre-retiring (H)	Approved
7618	Start-up time of Protege is slow (H)	Approved
8918	Allows paste of Preferred Name but can not delete. (H)	Approved
8947	Modal dialog does not stay on top (H)	Approved
8989	Selection of Properties in Report Writer (H)	Approved
8990	Report Writer output format. (H)	Approved
13848	Allow search on null in AQP. (H)	Approved
14786	Focus jumps to new project after final row deleted. (H)	Approved
14805	Have batch load verify all STYs are correct when loading. (H)	Approved
15174	No copy option on right click menus for Split function. (H)	Approved
15493	Default Task Description of new Workflow assignment has typo. (H)	Approved
15664	Assumption of role groups. (H)	Approved
15752	In copy pane, modify restriction does not remember filler value. (H)	Approved
16163	Addition of Superclass in Copy/Split/PreMerge - allow 'defining' superclass. (H)	Approved
16620	Report writer feature request. (H)	Approved
16775	Simplify adding a role. (H)	Approved
16839	Each change needs to be associated with an editor. (H)	Approved
16887	Add definition field to window when cloning a class. (H)	Approved
17210	LQP/AQP - selection and output of superclasses. (H)	Approved
17212	LQP/AQP - search for concepts lacking a property. (H)	Approved
17213	Selection criteria for concepts to be exported via LQP/AQP export function. (H)	Approved
17214	Report writer - add export function currently in LQP/AQP. (H)	Approved
17760	Workflow improvements. (H)	Approved
18177	Incorrect display of LQT search criteria. (H)	Approved
18536	Batch Load of new concepts interferes with other editors creating concepts. (H)	Approved
18616	Save of concept_history in NCI_DB format after Prompt should be altered or automated. (H)	Approved
18959	sort of inferred results panel. (H)	Approved
18982	gui refresh on switching apps back to protege. (H)	Approved
18997	Protege tab for reasoning server administration (including status information & kb reload). (H)	Approved
18999	Serialize state at explanation server shut-down so start-up can be incremental since previous run. (H)	Approved
19000	Reduce reasoning time for explanations which include domain or range axioms. (H)	Approved
2948	Domain and Range checks on property restrictions at edit time. (I)	Approved
3941	Duplicate Role Groups should not be allowed, even if roles are ordered differently. (I)	Approved
8302	Need automatic cursors in filler windows. (I)	Approved
8375	Display attributes in tree form on Copy tab. (I)	Approved
8590	Allow user to modify Superclasses in Copy tab (I)	Approved
8609	Retain frame sizes after switching tabs. (I)	Approved
8612	Display recently used classes in drop down of search. (I)	Approved
10987	Modify Name Superclass dialog should be eliminated. (I)	Approved
12337	Automated configuration of server project. (I)	Approved
12815	Track the last modeler who modified the assignment. (I)	Approved
12817	Creating new workflow assignments. (I)	Approved
12935	text is not trimmed. (I)	Approved
13951	Modal messages to other viewer. (I)	Approved
15003	NCIWorkflow - reorder columns (I)	Approved
16099	Complex property dialog layout goes crazy when a very long definition is entered. (I)	Approved
16100	Error message when full_syn has a tab or new line is confusing. (I)	Approved
16121	Button to make a concept defined. (I)	Approved
16152	Display of NCIEditTab Build Version. (I)	Approved
16255	Disable the Merge tab when the user is not allowed to merge. (I)	Approved
16347	Colors of text in copy, split, retire, merge and workflow panes are too dull. (I)	Approved
17570	Confusing message to the user when you drag the retiring concept into surviving concepts pane.(I)	Approved
18116	LQT export of results is exporting entire path. (I)	Approved
18164	query in changes tab search box gives ""Please enter an expressioin"" error". (I)	Approved
18583	Hierarchy View too cluttered. (I)	Approved
18961	queries in change tab. (I)	Approved
18998	Load explanation server from the Protege KB using the OWL API converter in Protege 3.4. (I)	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
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CBIIT Staff/Contractor Name	Role	Responsibilities
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Technical Environment

This product uses the following technical components which have been derived from the current NCICB Technology Stack.

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Client Interface

Wiki Markup

\[Example, Internet Explorer 6.0 and above\]]]></ac:plain-text-body></ac:structured-macro>
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