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 in 1.4 involved refactoring existing code to simplify maintenance and enhance performance in various spots, a number of new features have been introduced in various areas. 

• Searching:  The ability to use 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 included 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.

Behavior To Be Aware Of

A number of GForge items were created that need additional comment. With the exception of GForge item 23284 (see below), which will be addressed in 1.4.1, the items listed here have been closed.

• 19949 Return of 60,082 results for a search

Searching complex properties or the rdf:ID (:NAME) with specific Contains queries will result in the entire vocabulary being returned, as if a single wildcard character was the query string. This is because complex properties contain embedded XML and the rdf:ID contains a full URI. For instance, the following searches will return the entire NCIt vocabulary

entity searched    query string
FULL_SYN            name
FULL_SYN            group
FULL_SYN            source
FULL_SYN            >
:NAME                 /
:NAME                 :
:NAME                 http
:NAME                 owl

Similarly, a Contains search for "reviewer" or "source" in DEFINITION will return all the concepts with a DEFINITION property.

By the same token, doing Exact searches on the above properties and the :NAME will fail unless the complex property value or URI is entered in its entirety.

• 23284 Batch edit to delete associations needs full association rdfs:ID

This is deemed an inconsistency in behavior and is slated for a fix in 1.4.1. For now, editors need to be aware that deleting associations in batch requires that the association's rdf:ID be entered in its entirety.

• 19970 Batch edit records with sequential escaped characters fail

Exporting a txt file containing escapable characters from Excel results in Excel's escape character, the double-quote, to be exported too. Files derived from these exports used for a batch edit will fail. The files need to be cleaned up by searching and fixing the misplaced double-quotes.

• 21973 Browser does not refresh after bulk load

To increase the performance of the bulk load, the event listeners are turned off during the batch load (and edit). This is by design and results in the behavior listed in the gforge.

• 21569 Bulk Load prevents others from moving around in Protege

This applies to GForge 21632 as well (Batch load of new concepts freezes GUI for other editors)

Although issues that affected the performance of batch loads and edits were examined and their effects minimized in the 1.4.0 release, changes in the edit filters to satisfy QA requirements canceled out the performance increase. As discussed in other venues, batch edits and batch loads need to be dealt with through guidelines. As of this time, batch loads are being restricted to specific time periods of the day after editors have been notified. Batch edits can be done without this restriction but notification must be sent out so that a) competing batch edits are not done at the same time, b) editors are aware that there might be an increased lag time in Protege's response due to the ongoing batch edit.

• 17711 Missing warning message to the user : causes protege to freeze.

• 22004 Error message appears during a bulk edit when there is an error in the input file. The bulk edit freezes until the OK button on the error message is pressed.

This issue has to do with concurrent edits being done by other editors on the same classes that are being batch-edited. The warning messages are the correct behavior, and can only be prevented if the classes are not edited by more than one person (or batch edit) at the same time.

• 17711 Missing warning message to the user : causes protege to freeze.

On selecting a "hasValue" modifier when owl:Thing is selected in the class widget, Protege appears to freeze. It is not frozen, the client is loading all the classes into the widget. Editors need to be aware that if "hasValue" is to be used, in the class widget the "class hierarchy" view must be selected, instead of the "instance" view.

• 23276 In Copy pane, the Preferred_Name and PT are automatically sync'ed with an improper AQ

A warning message is displayed on changing a PT or PN, e.g. like when an AQ is created. If the editor does not wish to change the PT/PN, canceling out of the action will restore the concept to its initial state and other edits will also be lost and they'll need to be recreated. This gforge is slated for modification in protege 1.4.1. For the time being, editors need to be aware of this behavior.

• 23057 Lucene indexing failure with database data

Searches in the LQT with "lucene match" might yield incorrect results if multiple concepts exist where the rdf:ID (the class name) only differs in case, e.g. "tocopherol" and "Tocopherol". The observed incorrect result is that only one class is returned instead of both. This is due to a fetch action on the database being done in a case-insensitive manner. This gforge is slated for modification in protege 1.4.1. Editors need to be aware that under these conditions "lucene match" searches (and "sounds like") won't be accurate.

List of New Features and Bug Fixes

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

Other Items Closed

• The defects in the following list were not reproducible, some of these were deemed fixed as a by-product of refactoring.

8947 Modal dialog does not stay on top
13856 When client left open, log file grew to 4 GB
18987 Cannot close project using File menu
19292 Prompt - Doesn't display changes in User tab
19569 ArrayIndexOutOfBoundsException when you edit concept for a package with a New change proposal
20073 Unable to create a new class.
20125 After editing for a while the Lucene menu at the top gets multiplied
20625 Export to WIKI fails
21445 Dragging a preretired concept into retire pane shows a message 'Concept has not been flagged for retirement'.
21484 Cannot retire a concept.
21645 Errors at export in ADQ

• The defects in the following list were either considered invalid or did not require a fix

8608 Add Cut, Copy, and Paste options to main tree that modifies Superclass
8918 Allows paste of Preferred Name but can not delete
11600 Automatically switches Restriction when select a Restriction Property
15182 Removal of XML tags from query export
17144 Definition under the Edit tab not visible when you choose CDE/Motif and Window under Look and Feel
17571 Search under the Class browser is not cleared after the search is done.
17926 Ontology imports cause data problems when loading the explanation server from a Protege database
18583 Hierarchy View too cluttered
19383 Problems configuring the LQP
19595 Welcome to Protege User's Guide link goes to the Geek
20300 PATO concepts not found when criteria has 'Exact match' but found with criteria 'contains'.
20475 Exception while adding property (right-click - Add Property) in the copy tab.
20480 Expanding OWL:Thing using right click menu
21084 Changes tab displays edits even after cleaning the changes ontology.
21541 Prompt log output is acting differently than expected
21624 Associations pointing to PATO concepts display ID not name

CORE Product Dependencies

No caCORE dependencies. This software is used for editing and maintaining NCI Thesaurus and BiomedGT

Release History