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h1. Protégé 1.4 Scope Document
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*Author:* \[EVS:Project Manager/Technical Lead\]
*Email:* \[EVS:Email address for Scope Document contact\]
*Team:* \[EVS:For example caDSR, EVS, caGRID, and so on.\]
*Contract:* \[EVS:Contract number\]
*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 \\ ||
| --- | \--\- \\ | --- | --- \\ |
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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. 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.

h2. Vision and Needs

The *objective of this release* of Protégé 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 Protégé.

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 desirable "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.

h2. Current Solution

Protégé 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.

h2. Iteration B0 (merge into trunk)

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

h2. Iteration B1 (refactoring and hardening)

|| 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 |

h2. Iteration B2 (1.3 and 1.4 bug fixes)

|| GForge number \\
(hyperlinked) || Brief description of item \\ || (Approved or Proposed) \\ ||
| 16191 | Export of inferred Ontology - Tweaks to output file (A) | \--\-\\ |
| 18611 | insertion of Brackets in Preferred Name Display | Approved |
| 18599 | Language display (B) | Approved |
| 18319 | port EVS history plugin to support db inclusions (B) | Approved |
| 3954 | Merging two concepts with incoming roles should not result in duplicates (B) | Approved |
| 15889 | Merging two concepts with incoming properties should not result in duplicates (B) | Approved |
| 15175 | Invalid classification findings if premerge or pre-retire exists (B) | Approved |
| 15381 | Adding restrictions and the Advanced Query (B) | Approved |
| 13613 | 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 |
| 9101 | Automated creation of EVS{~}HISTORY~ and CONCEPT{~}HISTORY~ tables on first use (B) | Approved |
| 9298 | Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work (B) | Approved |
| 11115 | PROMPT\- 'Table View' crashes after visting 'Show sources' window (B) | Approved |
| 12358 | PROMPT\- Reject button in Tree view produces error message to the console (B) | Approved |
| 14404 | If character in slot matches delimiter then export misaligns values (B) | Approved |
| 16873 | History records created on classification in client--server mode (B) | Approved |
| 16983 | Duplicates Items displayed on the main menu. (B) | Approved |
| 17450 | 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 |

h2. Iteration B3 (highly desirable nice to have features)

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

h2. 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." | --- |

h2. 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 \\ |
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|| 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 vertica.  Contract management, coordination, testing, documentation \\ |
| Gilberto Fragoso \\ | Government Lead \\ | Technical resource from Bioinformatics vertical \\ |

h2. Technical Environment

This product uses the following technical components which have been derived from the current [NCICB Technology Stack|https://gforge.nci.nih.gov/docman/index.php?group_id=27&selected_doc_group_id=460&language_id=1].

|| 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 \\ |


h2. Product Dependencies

This release is dependent on the caCORE components or products documented in the [CORE Product Dependency Matrix|https://wiki.nci.nih.gov/x/hIx8].

\[EVS:Provide additional explanation as applicable. For example, "The EVS vocabulary systems are used by the Java client to retrieve and validate concept information for naming and defining meanings."\]

h2. 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 \\ ||
| --- | --- | --- |

h2. 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|https://wiki.nci.nih.gov/x/Cg5y] 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:* \\ | \[EVS:Name and URL of each related document\] \\ |

h2. 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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