National Cancer Institute Center for Bioinformatics |
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Product Changes
The objective of this release of Protege 1.4.2 is to provide the remaining feature requests and bugs fixes found in previous Protege 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
* 2948: Object properties available in role construction dialog are restricted according to the domain of the class that the role is being asserted on
* 6082: Forward and Backward navigation buttons have been enabled in the NCIEditTab.
* 16121: Buttons to make a class Defined or Primitive have been added to the NCIEditTab. If the entire list of Necessary conditions is to be made Necessary and Sufficient, the conditions don't need to be made defining one at a time, pressing the appropriate button makes all these conditions N&S. The same applies to making a class primitive starting from a defined class. Individual conditions can still be made either defining or non-defining as necessary.
* 21375: Internal format of complex properties has been modified. An xml schema is now used to specify the format. This affects batch editing jobs that include complex properties. The format to use for DEFINITION and ALT_DEFINITION in a batch edit is:
<ncicp:ComplexDefinition xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#"><ncicp:def-definition>Text of DEFINITION.</ncicp:def-definition><ncicp:def-source>NCI or some other</ncicp:def-source><ncicp:attr>some attribution</ncicp:attr><ncicp:Definition_Reviewer_Name>Someone's name</ncicp:Definition_Reviewer_Name><ncicp:Definition_Review_Date>a date in YYMMDD format</ncicp:Definition_Review_Date></ncicp:ComplexDefinition>
If no attribution is required the entire set of tags can be eliminated from the above. And the format for a FULL_SYN is:
<ncicp:ComplexTerm xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#"><ncicp:term-name>some term</ncicp:term-name><ncicp:term-group>PT or another type</ncicp:term-group><ncicp:term-source>NCI or another source</ncicp:term-source><ncicp:source-code>some code</ncicp:source-code> </ncicp:ComplexTerm>
If no source code is required the entire set of tags can be eliminated from the above.
Behavior To Be Aware Of
A number of GForge items were created that need additional comment.
- GF#22104 - search string appears empty when invoked from restriction dialog box
- GF#23565 - refactoring namespaces
- GF#24510 - Need a fail-safe for creating codes for properties
- GF#26667 - Robustness/QC
- GF#28509 - Edit tab does not handle & or < properly
- GF#28710 - The rejection of the modification failed in Prompt.
- GF#29143 - role groups not handled when toggling prim/defined
- GF#29347 - Cannot complete SMW roundtrip with Protege / NPO SMW
- GF#29513 - Improved formatting of batch load with error
- GF#29517 - When invalid format is provided on a clone it doesn't retain previously entered Definition
- GF#29665 - "Create Workflow Task" doesn't work" in 1.4.2.223 ByCode.
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.
List of New Features
GForge number |
Brief description of item |
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16191 |
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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List of Bug Fixes
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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Other Items Closed
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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CORE Product Dependencies
No caCORE dependencies. This software is used for editing and maintaining NCI Thesaurus and BiomedGT
Release History
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 |