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National Cancer Institute Center for Bioinformatics |
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Product Changes
The objective of this Protege 1.4 release is to harden the NCIEditTab plug-in for Protege so the project can go into an operation and maintenance mode of operation, in lieu of actively developing releases of the product containing new features. Protege 1.4 is planned to be the last major release of the NCIEditTab Protege plug-in.
New Feature Highlights
Although much of the work involved refactoring existing code to simplify maintenance and enhance performance in various spots, a number of new features have been introduced.
- Searching: The ability to use of negation (NOT operator) in queries in the LQT
- Searching: Lucene Match, Property Present, and Property Absent, added to the list of available search types in the LQT (which already includes Exact, Contains, Starts With, Ends With, and Sounds Like). The Lucene Match allows queries to be constructed with multiple query strings separated by boolean operators (NOT, AND), thereby extending the range and flexibility of lexical queries that can be conducted in the LQT.
- Property Restrictions: a simple GUI dialog for creating restrictions has been added to replace the Role expression dialog for simple restrictions; this is essentially the dialog used in the OWLClasses tab of Protege. The Role expression dialog now verifies that expressions have a valid Role Group format.
- Export of resultsets from the LQT for reports in a spreadsheet format now includes Superclasses. Reports can now also be generated for concepts that are input as a list of codes. Hence, the mechanisms for generating a resultset for outputting reports includes concepts specified a) from lexicographic searches (in the LQT tab), b) by their tree placement (Report Writer sub-tab), and c) by a list of codes (also from the Report Writer sub-tab).
- Batch Edits / Batch Loads: validation of complex properties and enumerations in property values.
- List of New Features and Bug Fixes (GForge items):
3954 Merging two concepts with incoming roles should not result in duplicates
5967 New concepts go to bottom of the sibling list, rather than alphabetical
7519 Changes ontology in database
8302 Need automatic cursors in filler windows
8407 Enter key does not close confirmation message box -- duplicate of #8611
8590 Allow user to modify Superclasses in Copy tab
8604 Improve load time of Edit tab
8609 Retain frame sizes after switching tabs
8610 Auto-select the previously selected Thesaurus
8629 Provide ability to disable right click menu options from main tree
10811 Restriction change frozen out
11018 catch client exception when server is down or being bounced
11110 PROMPT-Table wiew does not have ontologies' names
11114 PROMPT- 'Source knowledge bases' window inconsistency
11115 PROMPT- 'Table View' crashes after visting 'Show sources' window
11891 deleting classes can cause spurious values showing up in class browser
12358 PROMPT- Reject button in Tree view produces error message to the console
12815 Track the last modeler who modified the assignment
12817 Creating new workflow assignments
12935 text is not trimmed
13613 Does not change status of workflow to Updated when manager edits a concept
13848 Allow search on null in AQP
14404 If character in slot matches delimiter then export misaligns values
14480 Make NCIEdit subtabs configurable
14786 Focus jumps to new project after final row deleted
14805 Have batch load verify all STYs are correct when loading
15003 NCIWorkflow - reorder columns
15174 No copy option on right click menus for Split function
15175 (SEE COMMENTS) Invalid classification findings if premerge or pre-retire exists
15381 Adding restrictions and the Advanced Query
15493 Default Task Description of new Workflow assignment has typo
15664 Assumption of role groups
15752 In copy pane, modify restriction does not remember filler value
15889 Merging two concepts with incoming properties should not result in duplicates
15944 PROMPT: namespaces in Table view
16012 User is able to accept changes that classifier suggest for inconsistant class - leads to issue
16120 Addition of a date tag to retired concepts and to merged concepts
16140 Copy Tab allows save of class with duplicate restrictions
16152 Display of NCIEditTab Build Version
16161 Comment on the confirmation 'OK' box
16163 Addition of Superclass in Copy/Split/PreMerge - allow 'defining' superclass
16533 Unnecessary warning when leaving Copy or Edit pane
16775 Simplify adding a role
16873 History records created on classification in client--server mode
16887 Add definition field to window when cloning a class
16926 :ROLE concrete - Prompt bug fix
16983 Duplicates Items displayed on the main menu.
17128 Changes tab does not show up after changing the Look and feel.
17145 Protege freezes after chaning the Look and Feel the second time.
17210 LQP/AQP - selection and output of superclasses
17212 LQP/AQP - search for concepts lacking a property value
17213 Selection criteria for concepts to be exported via LQP/AQP export function
17214 Report writer - add export function currently in LQP/AQP
17450 Loss of Concepts form the Hierarchy
17570 Confusing message to the user when you drag the retiring concept into surviving concepts pane.
17760 Workflow improvements
17777 AQP sometimes returns an incomplete result set
18116 LQT export of results is exporting entire path
18163 Triple click on Change History causes UnsupportedOperationException
18164 query in changes tab search box gives 'Please enter an expressioin' error
18177 Incorrect display of LQT search criteria
18210 User can drag and drop a concept which has not been pre-merged into a merge pane.
18232 Language should be serialialized as xml:lang attribute
18497 RuntimeException when you click 'Edit form of type...' button on Edit tab
18536 Batch Load of new concepts interferes with other editors creating concepts
18589 LQP view class buttons do not appear for class in PATO
18599 Language display
18616 Save of concept_history in NCI_DB format after Prompt should be altered or automated
18831 LQT needs label at bottom to identify protege instance
18929 A classifier run tags all concepts with protege:inferred properties
18930 PROMPT tab allows start of compare even when another compare is running
18959 sort of inferred results panel
18961 queries in change tab
18978 frame caching refactoring
18981 switching subtabs in nciedittab is slow
18988 Modifications to the reasoning server to support storage plug-ins
18989 Add context information in reasoner client/server protocol to reject updates to unrelated ontologies
18990 Reasoner URL as per-project preference (rather than per Protege Server)
19000 Reduce reasoning time for explanations which include domain or range axioms
19024 Merge process by GUI changed between 1.2.3.25 and 1.3.0.172
19077 Not able to Split a concept :RuntimeException
19100 property tab, can't edit enumerations
19165 Display in Browser' dialog for editing Unstructured Proposals shows wrong URL
19308 OWL:Thing can be added as a filler value while adding a restriction or an association
19361 FULL_SYN with incorrect format cannot be fixed in NCI Editor Edit Tab
19499 Not able to drag and drop a concept in to Copy,Premerge,preretire,merge and retire pane.
19520 Project is closed when you check Drag and Drop, while on edit tab.
19522 Select Named Class does not reappear with a populated window after a search,so OWL:Thing gets added.
19722 Could add OWL:Thing as a filler value and also as an association.
19730 Error at save causes loss of all prior edits
19734 Focus is incorrect after edit of subclass in PreRetire
19792 LPQ gives duplicate results
19826 Confirmation box when Preferred_Name is changed
19850 Changing the Preferred Name in the copy tab does not change the NCI PT
19934 Partonomy Tree Tab does not work
19973 Nested Search fails with quantifier 'Only'.
19985 Defined Concepts in Hierarchy Browser not indicated
20018 During a batch edit a new definition is accepted even without the qualifiers.
20120 Problems editing a parent
20134 Exception on switching to the LQT tab from the Report Writer tab
20157 Couple of classes on the 'Select a name class' dialogue are expanded upto 2nd node.
20170 Configurability of Report Writer output
20173 Cloned concepts have incorrectly diaplayed PN.
20318 Lucene query tab will not search PATO
20323 Prompt: NCI Concept History -- management of properties
20420 Classification failed with a Reasoner error.
20478 Unwanted Rick-click options.
20510 Classes in the 'Select a named class' dialogue not sorted alphabetically.
20512 Right click menu options on the class browser can create, delete super classes.
20624 Concept History plugin of Prompt writes empty string on referencecode
20644 Case sensitivity when creating a copy.
20698 Inability to exit merge panel when a non-pre-merged concept is accidentally dropped into merge panel
20738 Cannot save/accept new child concept proposals imported from SMW
20754 Add support for associations to merge/retire
20914 Explanation tab should request one explanation initially, more only on user request
20928 search invoked from the drop down is missing magnifying glasses
20929 exporter is single quoting names from browser text
21196 Lang is not displayed for a full syn or a definition.
21271 Need to filter property choices so that only valid options are available.
21301 Right click edit full syn in Copy pane unecessarily prompts warning messagebox
21317 Empty Definition tags created on the New concept pane of Copy tab.
21323 Modifying rdfs label does not update PN or PT full_syn
21446 On the retire pane after clicking retire and before clicking save, a user can add properties to the retiring concept.
21474 LQP Report inverted the query output
21481 Copying the Preferred_Name from the main GUI enables the Save button
21570 Able to edit a Retired Concept in a bulk process
21576 Invalid Filler Value Errors
21578 Unusual characters in cloned definition cause blank definition
21579 Validating complex properties in batch edit
21598 Multiple confirmation messages after a preretire save
21629 APQ popup window still not labeled with terminology
21630 Merge and retire cannot be completed because of protegeinferred:Sub/SuperclassOf
21631 Clone without DEF gives empty <def-definition> but other qualifiers are present i.e. <def-source>, <Definition_Review_Date>
21633 Hierarchy not displaying trees in alphabetical order
21650 Lucene configuration-- minus 1 value does not function properly
21651 Explanation Tab not in sync with Hierarchy Browser in NCIEditor tab
21689 Strange behavior on Preferred Name change
21712 Editor allows editing of retired concepts
21856 Explanation server takes over 90 min to start
21896 follow up bug #21650--Lucene Config setting -1
21900 If clone a concept with no definition it does not retain the provided one
22005 Restriction-based queries not working
22010 carriage return allowed in property field?
22021 Loss of Concepts form the Hierarchy with bad modeling
22027 unable to bring concept upto Edit panel after failed BulkEdit
22114 batch load/edit need to capture EVS History
22333 BFO concepts with BGT subclasses have duplicate rdfs properties after prompt and file export
22400 LQT results don't have search criteria appended at the end of the file.
22404 Batch load causes NPE
22723 Problem with property creation
22856 lucene query incorrectly filters properties for search.
23143 unable to save concept with Def_Curator property
23205 Concept deleted when trying to replace owl:thing as a parent
Important Remaining Issues
- Description of the issue including special circumstances and workarounds. GF tracker number hyperlinked to the tracker. Note: Write for the intended audience.
Indented commentary if needed (example). Continue the previous pattern for each issue.
CORE Product Dependencies
Refer to the CORE Product Dependency Matrix for the caCORE SDK and other software technologies on which this release of this product relies.
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