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h1. Protégé 1.4.1 Scope Document
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{panel:title=Document Information}
*Author:* Jason Lucas/Gilberto Fragoso
*Email:* lucasjr@mail.nih.gov
*Team:* EVS
*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 \\ ||
|--- |--- \\ |--- |--- \\ |
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 1.4.1. 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 1.4.1 is to provide bugs fixes found in previous Protégé releases as well as completing feature request for formatting of the complex properties and improving performance for batch edits.
This release will be performed over one main development iteration and a second iteration to cover any items found in UAT:
Iteration B0 - Development of Scoped Features and Bug Fixes
Iteration B1 - Bug fixes found from user acceptance testing
h2. Current Solution
Protege 1.4 is currently in production.
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h2. Iteration B0
h3. Feature Requests
|| GForge number \\
(hyperlinked) || Brief description of item \\ || (Approved or Proposed) \\ ||
| [18997|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=18997&group_id=174&atid=822] | Protege tab for reasoning server administration (including status information and kb reload) | Approved |
| [22870|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22870&group_id=174&atid=822] | Would like to do 'property present' LQT queries with object properties | Approved |
| [2948|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=2948&group_id=174&atid=822] | Domain and Range checks on property restrictions at edit time | Approved |
| [23003|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23003&group_id=174&atid=822] | Not able to have a NOT query in the nested query | Approved |
| [23297|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23297&group_id=174&atid=822] | Restrict access to OWLClasses tab | Approved |
| [23516|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23516&group_id=174&atid=822] | the changes ontology sees changes involving internal protege classification slots (e.g. protege:inferredSuperclassOf) | Approved |
| [21375|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=21375&group_id=174&atid=822] | Use of parseType=Literal for complex properties | Approved |
| [18533|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=18533&group_id=174&atid=822] | Changes Tab does not reflect items created in Batch Load | Approved |
| [16324|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16324&group_id=174&atid=822] | Need indication of classifier run | Approved |
| [16121|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16121&group_id=174&atid=822] | Button to make a concept defined | Approved |
| [6082|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=6082&group_id=174&atid=822] | BACK and FORWARD Buttons | Approved |
h3. Bug Fixes
|| GForge number \\
(hyperlinked) || Brief description of item \\ || (Approved or Proposed) \\ ||
| [24801|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24801&group_id=174&atid=822] | Focus of editor switches while creating restrictions | Approved |
| [22400|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22400&group_id=174&atid=822] | LQT results don't have search criteria appended at the end of the file. | Approved |
| [22680|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22680&group_id=174&atid=822] | Restrictions added flagged as changes to Restriction classes in Prompt | Approved |
| [24503|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24503&group_id=174&atid=822] | LQT nested query causes error dialog | Approved |
| [24435|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24435&group_id=174&atid=822] | fitering inherited restrictions | Approved |
| [24343|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24343&group_id=174&atid=822] | Cannot edit restriction that has an apostrophe in the filler value | Approved |
| [24301|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24301&group_id=174&atid=822] | Add Individual button should only be enabled when hasValue is selected | Approved |
| [23284|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23284&group_id=174&atid=822] | Batch edit to delete associations needs full association rdfs:ID | Approved |
| [24196|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24196&group_id=174&atid=822] | Restore nci-specific export function in inferred tree widget | Approved |
| [19404|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19404&group_id=174&atid=822] | Link which opens when an unstructured proposal is imported, opens an xml. | Approved |
| [20587|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20587&group_id=174&atid=822] | infinite loop in Report Writer | Approved |
| [22969|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22969&group_id=174&atid=822] | Report Writer fails on rerun after a cancel | Approved |
| [22984|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22984&group_id=174&atid=822] | null pointer in Protege OWL layer | Approved |
| [23006|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23006&group_id=174&atid=822] | Can't change tabs unless focus is on a concept | Approved |
| [23204|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23204&group_id=174&atid=822] | After split one of the classes ended up with owl:thing as the only parent | Approved |
| [23276|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23276&group_id=174&atid=822] | In Copy pane, the Preferred_Name and PT are automatically sync'ed with an improper AQ. | Approved |
| [23431|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23431&group_id=174&atid=822] | Editing a role with Cardinality requires reselecting Cardinality | Approved |
| [23529|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23529&group_id=174&atid=822] | Report Writer shows anon class defined by conjunction of NandS | Approved |
| [23716|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23716&group_id=174&atid=822] | Report Writer incapable of generate completed report | Approved |
| [23613|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23613&group_id=174&atid=822] | CompleteableCache throws a nullpointer exception | Approved |
| [23057|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23057&group_id=174&atid=822] | Lucene indexing failure with database data | Approved |
| [23631|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23631&group_id=174&atid=822] | Refresh of screen after classification slow and using up desktop resources | Approved |
| [22879|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22879&group_id=174&atid=822] | BatchEditor gives a false positive | Approved |
| [23530|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23530&group_id=174&atid=822] | Cannot edit the concept from workflow | Approved |
| [23969|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23969&group_id=174&atid=822] | Batch edit takes a long time | Approved |
| [22434|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22434&group_id=174&atid=822] | database accumulates garbage over a period of time | Approved |
| [22405|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22405&group_id=174&atid=822] | NPE when selecting row from PROMPT differences table | Approved |
| [20018|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20018&group_id=174&atid=822] | During a batch edit a new definition is accepted even without the qualifiers. | Approved |
| [13586|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=13586&group_id=174&atid=822] | Can the Read-Only view look like the Review pane (have one page with all class info)? | Approved |
| [22781|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22781&group_id=174&atid=822] | Protege 1.4 loads ndf-rt with exceptions, property tab has the ugly widget | Approved |
| [15632|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15632&group_id=174&atid=822] | Inability to reject and/or ignore suggestions from the classifier | Approved |
| [22786|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22786&group_id=174&atid=822] | Expands the first top level node under owl:Thing when add Restriction | Approved |
| [6067|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=6067&group_id=174&atid=822] | rethink and redesign workflow of pre-merge/pre-retire | Approved |
| [18033|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=18033&group_id=174&atid=822] | Make Changes tab show login and log out | Approved |
| [23495|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23495&group_id=174&atid=822] | Slow performance when creating new concepts including split and copy | Approved |
h2. Iteration B1
|| GForge number \\
(hyperlinked) || Brief description of item \\ || (Approved or Proposed) \\ ||
| [25466|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=25466&group_id=174&atid=822] | Cannot edit or delete associations | Approved |
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 \\ |
|--- |--- |--- |
\\
\\
|| 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 \\ |
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 \\ ||
| [7369|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=7369&group_id=174&atid=822] | Include a domain in the classification report |--- |
| [7679|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=7679&group_id=174&atid=822] | (make configurable) Default search parameters for Advanced Search are not default for search w/in search |--- |
| [8373|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=8373&group_id=174&atid=822] | Word wrap attributes in Copy tab |--- |
| [8787|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=8787&group_id=174&atid=822] | Controls can be pushed off to side of dialog with long attr |--- |
| [9298|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=9298&group_id=174&atid=822] | Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work |--- |
| [9572|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=9572&group_id=174&atid=822] | Need to see the 'retired' designation for concepts found in part of AQP |--- |
| [12337|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=12337&group_id=174&atid=822] | Automated configuration of server project |--- |
| [20906|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20906&group_id=174&atid=822] | Protege incorrectly exporting names with quotes |--- |
| [21549|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=21549&group_id=174&atid=822] | Single quote mark around multi-word parents |--- |
| [21738|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=21738&group_id=174&atid=822] | Hierarchy is not refreshing the D when retire concept |--- |
| [21946|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=21946&group_id=174&atid=822] | Incorrect unretire functionality |--- |
| [22090|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22090&group_id=174&atid=822] | Tool Tab compression and disappearance |--- |
| [22104|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22104&group_id=174&atid=822] | search string appears empty when invoked from restriction dialog box |--- |
| [22785|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22785&group_id=174&atid=822] | Only exports the first page of results in LQT search |--- |
| [22902|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=22902&group_id=174&atid=822] | Create a restriction with retired individual. |--- |
| [23385|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=23385&group_id=174&atid=822] | update protege/workflow and SWM to handle new XML Literal complex properties |--- |
| [24803|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24803&group_id=174&atid=822] | Edit of Preferred_Name does not always sync the NCI PT |--- |
| [24805|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24805&group_id=174&atid=822] | Edit of Preferred_Name in Copy tab caused two rdfs:labels |--- |
| [24870|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24870&group_id=174&atid=822] | trouble with saving upper/lowercase variants in the FS slot |--- |
| [24878|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24878&group_id=174&atid=822] | Deprecated concepts are editable |--- |
| [24929|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24929&group_id=174&atid=822] | Restriction domain checking does not work correctly for referenced classes |--- |
| [24955|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=24955&group_id=174&atid=822] | Rejection of changes to Retired Concept branch caused deletion of newly retired classes |--- |
| [26195|https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=26195&group_id=174&atid=822] | Variability in Batch Loading Times |--- |
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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