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Protégé 1.4.1 Scope Document
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| * Author: *Jason Lucas/Gilberto Fragoso/Bob Dionne *Fragoso lucasjr@mail.nih.gov *
EVS *
[EVS:Contract number \] *
NCI CBIIT
Institutes of Heath
Department of Health and Human Services
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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)
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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.
Vision and Needs
The objective of this release of
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Protégé 1.4.1 is
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to provide bugs fixes found in
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previous Protégé releases as well
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as completing feature request for formatting of the complex properties and improving performance for batch edits.
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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
Current Solution
Protege 1.4 is currently in production.
Iteration B0
GForge number | Brief description of item | (Approved or Proposed) |
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7369 | Merge the 1.3 branch with trunk and create a 1.4 branch. | Approved |
Iteration B1 ()
Feature Requests
GForge number | Brief description of item | (Approved or Proposed) |
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Iteration B2 (1.3 and 1.4 bug fixes)
GForge number | Brief description of item | (Approved or Proposed) |
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16191 |
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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 EVSHISTORY and CONCEPTHISTORY 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 |
Iteration B3 (highly desireable nice to have features)
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GForge number (hyperlinked)
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Brief description of item
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(Approved or Proposed)
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18831
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LQT needs label at bottom to identify protege instance (I)
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18598
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Changes Tab says No Action for property edits (H)
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2950
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String fillers on object properties - Stanford (H)
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3945
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Definition and Long Def property should only allow NCI as a source. (H)
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7118
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Restrict Delete action by date (H)
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7520
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Default editornote & designNote when pre-retiring (H)
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7618
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Start-up time of Protege is slow (H)
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8918
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Allows paste of Preferred Name but can not delete. (H)
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8947
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Modal dialog does not stay on top (H)
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8989
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Selection of Properties in Report Writer (H)
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8990
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Report Writer output format. (H)
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13848
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Allow search on null in AQP. (H)
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14786
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Focus jumps to new project after final row deleted. (H)
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14805
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Have batch load verify all STYs are correct when loading. (H)
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15174
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No copy option on right click menus for Split function. (H)
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15493
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Default Task Description of new Workflow assignment has typo. (H)
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15664
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Assumption of role groups. (H)
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15752
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In copy pane, modify restriction does not remember filler value. (H)
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16163
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Addition of Superclass in Copy/Split/PreMerge - allow 'defining' superclass. (H)
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16620
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Report writer feature request. (H)
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16775
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Simplify adding a role. (H)
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16839
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Each change needs to be associated with an editor. (H)
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16887
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Add definition field to window when cloning a class. (H)
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17210
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LQP/AQP - selection and output of superclasses. (H)
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17212
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LQP/AQP - search for concepts lacking a property. (H)
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17213
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Selection criteria for concepts to be exported via LQP/AQP export function. (H)
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17214
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Report writer - add export function currently in LQP/AQP. (H)
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17760
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Workflow improvements. (H)
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18177
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Incorrect display of LQT search criteria. (H)
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18536
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Batch Load of new concepts interferes with other editors creating concepts. (H)
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18616
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Save of concepthistory in NCIDB format after Prompt should be altered or automated. (H)
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18959
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sort of inferred results panel. (H)
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18982
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gui refresh on switching apps back to protege. (H)
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18997
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Protege tab for reasoning server administration (including status information & kb reload). (H)
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18999
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Serialize state at explanation server shut-down so start-up can be incremental since previous run. (H)
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19000
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Reduce reasoning time for explanations which include domain or range axioms. (H)
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2948
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Domain and Range checks on property restrictions at edit time. (I)
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3941
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Duplicate Role Groups should not be allowed, even if roles are ordered differently. (I)
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8302
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Need automatic cursors in filler windows. (I)
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8375
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Display attributes in tree form on Copy tab. (I)
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8590
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Allow user to modify Superclasses in Copy tab (I)
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8609
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Retain frame sizes after switching tabs. (I)
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8612
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Display recently used classes in drop down of search. (I)
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10987
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Modify Name Superclass dialog should be eliminated. (I)
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12337
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Automated configuration of server project. (I)
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12815
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Track the last modeler who modified the assignment. (I)
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12817
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Creating new workflow assignments. (I)
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12935
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text is not trimmed. (I)
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13951
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Modal messages to other viewer. (I)
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15003
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NCIWorkflow - reorder columns (I)
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16099
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Complex property dialog layout goes crazy when a very long definition is entered. (I)
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16100
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Error message when fullsyn has a tab or new line is confusing. (I)
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16121
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Button to make a concept defined. (I)
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16152
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Display of NCIEditTab Build Version. (I)
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16255
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Disable the Merge tab when the user is not allowed to merge. (I)
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16347
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Colors of text in copy, split, retire, merge and workflow panes are too dull. (I)
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17570
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Confusing message to the user when you drag the retiring concept into surviving concepts pane.(I)
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18116
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LQT export of results is exporting entire path. (I)
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18164
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query in changes tab search box gives ""Please enter an expressioin"" error". (I)
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18583
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Hierarchy View too cluttered. (I)
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18961
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queries in change tab. (I)
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Protege tab for reasoning server administration (including status information and kb reload) | Approved | |
Would like to do 'property present' LQT queries with object properties | Approved | |
Domain and Range checks on property restrictions at edit time | Approved | |
Not able to have a NOT query in the nested query | Approved | |
Restrict access to OWLClasses tab | Approved | |
the changes ontology sees changes involving internal protege classification slots (e.g. protege:inferredSuperclassOf) | Approved | |
Use of parseType=Literal for complex properties | Approved | |
Changes Tab does not reflect items created in Batch Load | Approved | |
Need indication of classifier run | Approved | |
Button to make a concept defined | Approved | |
BACK and FORWARD Buttons | Approved |
Bug Fixes
GForge number | Brief description of item | (Approved or Proposed) |
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Focus of editor switches while creating restrictions | Approved | |
LQT results don't have search criteria appended at the end of the file. | Approved | |
Restrictions added flagged as changes to Restriction classes in Prompt | Approved | |
LQT nested query causes error dialog | Approved | |
fitering inherited restrictions | Approved | |
Cannot edit restriction that has an apostrophe in the filler value | Approved | |
Add Individual button should only be enabled when hasValue is selected | Approved | |
Batch edit to delete associations needs full association rdfs:ID | Approved | |
Restore nci-specific export function in inferred tree widget | Approved | |
Link which opens when an unstructured proposal is imported, opens an xml. | Approved | |
infinite loop in Report Writer | Approved | |
Report Writer fails on rerun after a cancel | Approved | |
null pointer in Protege OWL layer | Approved | |
Can't change tabs unless focus is on a concept | Approved | |
After split one of the classes ended up with owl:thing as the only parent | Approved | |
In Copy pane, the Preferred_Name and PT are automatically sync'ed with an improper AQ. | Approved | |
Editing a role with Cardinality requires reselecting Cardinality | Approved | |
Report Writer shows anon class defined by conjunction of NandS | Approved | |
Report Writer incapable of generate completed report | Approved | |
CompleteableCache throws a nullpointer exception | Approved | |
Lucene indexing failure with database data | Approved | |
Refresh of screen after classification slow and using up desktop resources | Approved | |
BatchEditor gives a false positive | Approved | |
Cannot edit the concept from workflow | Approved | |
Batch edit takes a long time | Approved | |
database accumulates garbage over a period of time | Approved | |
NPE when selecting row from PROMPT differences table | Approved | |
During a batch edit a new definition is accepted even without the qualifiers. | Approved | |
Can the Read-Only view look like the Review pane (have one page with all class info)? | Approved | |
Protege 1.4 loads ndf-rt with exceptions, property tab has the ugly widget | Approved | |
Inability to reject and/or ignore suggestions from the classifier | Approved | |
Expands the first top level node under owl:Thing when add Restriction | Approved | |
rethink and redesign workflow of pre-merge/pre-retire | Approved | |
Make Changes tab show login and log out | Approved | |
Slow performance when creating new concepts including split and copy | Approved |
Iteration B1
GForge number | Brief description of item | (Approved or Proposed) |
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Cannot edit or delete associations | Approved |
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18998
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Load explanation server from the Protege KB using the OWL API converter in Protege 3.4. (I)
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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 |
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— | Example, "Level 2 Support, integration of help and training to the user community." |
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Stakeholder Summary
Customer Name | Role | Interest/Need |
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NCI CBIIT EVS Content Editorial Team | EVS Content Management | Primary Users of Protege. |
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Utilize Protege to edit EVS content |
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CBIIT Staff/Contractor Name | Role | Responsibilities |
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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 |
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vertical. |
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Contract management, |
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coordination, testing, documentation | ||
Gilberto Fragoso | Government Lead | Technical resource from Bioinformatics vertical |
Technical Environment
This product uses the following technical components which have been derived from the current NCICB Technology Stack.
Component | Description |
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Client Application | The Protege client is java based and provides a complete editing environment for Protege databases, call ontologies. |
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It uses the same plugin architecture to support extensions, called Tabs. |
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For example, the NCI Edit Tab, Workflow, Changes, and Prompt, are examples of plugin tabs. | |
Application Server | None |
Database Server | MySQL |
Operating System | Any that supports Java: Windows XP, Linux, OS X |
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[caCORE:Other] | Portable ANSI-SQL compliant relational schemas |
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Product Dependencies
This release is dependent on the caCORE components or products documented in the CORE Product Dependency Matrix.
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[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."]
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 | Iteration during which the item |
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Include a domain in the classification report | — | |
(make configurable) Default search parameters for Advanced Search are not default for search w/in search | — | |
Word wrap attributes in Copy tab | — | |
Controls can be pushed off to side of dialog with long attr | — | |
Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work | — | |
Need to see the 'retired' designation for concepts found in part of AQP | — | |
Automated configuration of server project | — | |
Protege incorrectly exporting names with quotes | — | |
Single quote mark around multi-word parents | — | |
Hierarchy is not refreshing the D when retire concept | — | |
Incorrect unretire functionality | — | |
Tool Tab compression and disappearance | — | |
search string appears empty when invoked from restriction dialog box | — | |
Only exports the first page of results in LQT search | — | |
Create a restriction with retired individual. | — | |
update protege/workflow and SWM to handle new XML Literal complex properties | — | |
Edit of Preferred_Name does not always sync the NCI PT | — | |
Edit of Preferred_Name in Copy tab caused two rdfs:labels | — | |
trouble with saving upper/lowercase variants in the FS slot | — | |
Deprecated concepts are editable | — | |
Restriction domain checking does not work correctly for referenced classes | — | |
Rejection of changes to Retired Concept branch caused deletion of newly retired classes | — | |
Variability in Batch Loading Times | — |
Document History
Item | Information |
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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. |
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Project GForge site: | [EVS:Project GForge site link] |
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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. |
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Related documents: | [EVS:Name and URL of each related document] |
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Project Information
CBIIT Management | Role | Responsibilities |
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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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