NCI Protégé 1.4.0 Release Notes

National Cancer Institute Center for Bioinformatics
Protege 1.4.0 Release Notes
15 Sep 2009

Product Changes

The objective of this Protégé 1.4 release is to harden the NCIEditTab plug-in for Protégé 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. Protégé 1.4 is planned to be the last major release of the NCIEditTab Protégé 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 items 23284, 23276, and 23057 (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            Thesaurus
: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, being exported also. 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 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.

• 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, Protégé 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 issue is 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 issue is slated for modification in Protégé 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 Dollow 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