National Cancer Institute Center for Bioinformatics |
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The objective of this release of Protégé 1.4.2 is to provide the remaining feature requests and bugs fixes found in previous Protégé releases that have been determined to be a priority for the final release of Protege. Currently, there is no development planned after the 1.4.2 release.
New Feature Highlights
A number of GForge items were created that need additional comment.
GForge number |
Brief description of item |
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Export of inferred Ontology - Tweaks to output file |
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Load explanation server from the Protege KB using the OWL API converter in Protege 3.4 |
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Serialize state at explanation server shut-down so start-up can be incremental since previous run |
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Only exports the first page of results in LQT search |
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update protege/workflow and SWM to handle new XML Literal complex properties |
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Batch jobs performance improvements |
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Batch jobs robustness |
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Allow multiple domains and ranges |
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Report Writer outputs extra instances in 'Property value present' query |
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Unable to get filler values from roles in query export |
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A button to refresh the class hierarchy tree in the class browser pane. |
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Disable Tooltips for NCI ontologies. |
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Add a Complete button to workflow subtab |
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Remove Unnecessary scripts from Protege Server / Explanation Server Folder |
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Lucene query tab default setting will not search PATO |
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Export of Annotations are viewed by OWLAPI as ObjectProperties |
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Start or restart of the Explanation server has lost the time/date reference |
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In all NCI Editor Tabs except the Edit tab concept name property is not displayed properly |
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Edit set as default instead of Load Please |
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“by code” (rdf:ID is meaningless) |
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Configurability |
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wiki collaboration |
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Runtime classification |
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Results panel callable from the explanation tab |
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:NAME needs to be added to pull down list of Attributes w/ID in Report Writer |
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Prevent save of a class that has less than 2 N&S conditions. |
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GForge number |
Brief description of item |
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(make configurable) Default search parameters for Advanced Search are not default for search w/in search |
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Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work |
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Change of Focus after Retire |
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Protege incorrectly exporting names with quotes |
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Single quote mark around multi-word parents |
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Hierarchy is not refreshing the D when retire concept |
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Incorrect unretire functionality |
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Tool Tab compression and disappearance |
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search string appears empty when invoked from restriction dialog box |
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Convert project to format seems to run twice |
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Create a restriction with retired individual in premerge only |
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lucene search option falls off pull down list not sure of the trigger |
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Explanation server syncronization issue with retire action |
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protege:readOnly=true behavior is unexpected |
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Inconsistant reject button availablility |
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PROMPT Tree View reject gave null pointer exception |
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Legacy_Concept_Name is ReadOnly but will be replicated in copy/split actions |
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Legacy_Concept_Name should not transfer during merge |
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User's Guide goes to Protege 2000 page |
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Cannot change case of PT and PN |
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inheritance of role restrictions is no longer working correctly |
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Strange behavior on Preferred Name change |
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Failure of Lucene to index at runtime |
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LQT nested query causes error dialog |
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Edit of Preferred_Name does not always sync the NCI PT |
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Search using contains is very slow |
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Rejection of changes to Retired Concept branch caused deletion of newly retired classes |
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Selection of display slot for individuals is not scrollable |
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Properties that have spaces cannot be edited in the Edit tab |
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identificable? |
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SPCA contrib source |
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Error Message displays association error, yet performs edit |
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Strange output during Explanation Server restart |
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Duplicate Full Syn atom could not be deleted via NCI Editor Tab |
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unable to find concept |
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Remove hard-coding of LONG_DEFINITION and other deprecated complex properties |
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Cannot add role after editing a parent due to loss of focus in class browser |
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"Increase or Decrease Font Size" causes Edit Tab increment |
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extra prefix string when exporting ALT-DEFINITION and DEFINITION |
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report writer fails to produce output |
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EditTab not persisting complex properties correctly |
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GO_Annotation props not showing in correct panel |
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Allows duplicated roles to be added with batch processing |
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Different “Reviewer Name” is displayed |
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"Delete Parent" is allowed to delete last parent when batch processing. |
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OLD_PARENTS and OLD_ROLEs ought to be added simultaneously |
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batch delete definitions fails |
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“Required field” for FULL_SYN is not enforced when doing Batch Processing. |
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“Required field” for DEFINITION or ALT_DEFINITION is not enforced when doing Batch Processing. |
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deleting a role takes rdfs:label (preferred name) and should take rdfs:ID |
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Trouble with usage of datatype properties |
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Spotty Synchronization of NCIEditor Hierarchy with Explanation and OWLClasses Tabs |
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Enable the use of rdfs:comment |
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New strange behavior on PT change |
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Preretire fails if redirect or remove two of the same restrictions pointing to the preretiree |
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Generate Report with attributes does not display Definition or FULL_SYN |
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AQP export needs to escape comma everywhere |
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rename a class and rename it back leads to loss of type information. |
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Tabs in Edit Tab Preferences can't be removed. (Tabs in Edit Tab Preferences can't be added). |
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"Delete FULL_SYN" in batch processing doesn't work |
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Batch delete of Semantic_Type fails |
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Need to be able to configure Property Value Query in the LQP |
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Performance Issues |
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New concept with existing rdf:ID fails to be created, insufficient error message. |
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Can only shutdown protege server through the Administer Server GUI |
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There is error message when batch processing special characters "& and <" fails. |
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Classification Optimization |
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Reasoner Error While Classifying in Standalone Mode |
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New scenarios that have strange behavior on PT change |
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Performance testing |
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Preretire causes multiplication of OLD_SOURCE_ROLEs from referencing classes |
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Figure out if LQP result display timing is okay for a number of search scenarios. |
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LastUsageInvocationHandler being called with a high frequency |
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Restrictions drop off when toggling from primitive to defined related to concurrency |
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Split and Copy don't work in protege ByCode 1.4.2.174. |
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Typo in Batch Load parent causes infinitely repeating exception |
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Qualifiers of Complex Properties don't display (ByCode) |
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Legacy_Concept_Name ReadOnly works but it is passed to new concepts |
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Retired concept is not listed under Retired Concepts |
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Changing Preferred name makes 2nd rdfs:label be added. (NCIt - ByCode) |
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There is no check-box next to Retire in the "Edit Tab Preferences" |
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Cannot Edit Concept assigned in NCI Workflow (NPO) |
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java.lang.NullPointerException is displayed in console windows after check /uncheck Copy, Split, Merge, or Retire in Preference. |
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Association Edit/Delete failed. |
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Does not retain assignment of workflow task from creation dialog |
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report writer fails to produce correct output for no attributes |
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The record number in the batch log may not match with the "line number" of the input file. |
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An invalid value is able to be added into the protperty Contributing_Source by the batch processing |
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Need to use Display slot in Explanation tab panel |
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After merge, redirected filler values are not updated by the Explanation Server |
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A user was able to premerge two classes into a third class during concurrent editing |
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Duplicate restrictions after merge with restriction pointing to surviving concept |
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Invalid messagebox/warning to user when modify a concept with N&S restrictions |
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Review panel from LQT pane displays class name as "foo" |
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Exceptions are thrown when closing "Select a property" dialog-box nested in "Edit an Object-Valued Property" dialog-box. |
The defects in the following list were not reproducible, or were fixed as a by-product of refactoring, or were related to configuration setup.
GForge number |
Brief description of item |
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IndexOutOfBoundsException in Mac OS X |
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Red Widget Appears after Loading Thesaurus OWL File to Protege Database |
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Variability in Batch Loading Times |
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Notes on behavior of logins to the Annotation project |
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Hierarchy scrolls out of control |
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embedded XML is converting XMLLiterals to strings |
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Changing the value of property "protege:readOnly" doesn't work. |
The defects in the following list were not reproducible, or were fixed as a by-product of refactoring, or were related to configuration setup.
GForge number |
Brief description of item |
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search string appears empty when invoked from restriction dialog box |
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refactoring namespaces |
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Need a fail-safe for creating codes for properties |
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Edit tab does not handle & or < properly |
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role groups not handled when toggling prim/defined |
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(NPO) Association Edit/Delete failed. |
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Improved formatting of batch load with error |
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When invalid format is provided on a clone it doesn't retain previously entered Definition |
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"Create Workflow Task" doesn't work" in 1.4.2.223 ByCode. |
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PreMerge "two concepts" after renaming them is not allowed. |
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Generate Reports shows undesirable internal values |
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Extra box character shows in generated report |
No caCORE dependencies. This software is used for editing and maintaining NCI Thesaurus and BiomedGT
Release |
Date |
---|---|
1.0 |
Jun 07 |
1.1 |
Sept 07 |
1.2.0 |
Dec 07 |
1.2.1 |
Feb 08 |
1.2.2 |
May 08 |
1.2.3 |
Jul 08 |
1.2.3 Patch |
Aug 08 |
1.3.0 |
Mar 09 |
1.4.0 |
Sep 09 |
1.4.1 |
Jan 10 |
1.4.2 |
Sep 10 |