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NCI Protégé 1.4.1 Release Notes
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National Cancer Institute Center for Bioinformatics
Protege 1.4.1 Release Notes
28 January 2010
Product Changes
The objective of this release of Protege 1.4.1 is
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to provide bugs fixes found in
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previous. Protege releases as well
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as completing a feature request for formatting of the complex properties and improving performance for batch edits.
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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, 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.
- 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.
- 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.
List of New Features
GForge number | Brief description of item |
|---|---|
Protege tab for reasoning server administration (including status information and kb reload) | |
Would like to do 'property present' LQT queries with object properties | |
Domain and Range checks on property restrictions at edit time | |
Not able to have a NOT query in the nested query | |
Restrict access to OWLClasses tab | |
the changes ontology sees changes involving internal protege classification slots (e.g. protege:inferredSuperclassOf) | |
Use of parseType=Literal for complex properties | |
Changes Tab does not reflect items created in Batch Load | |
Need indication of classifier run | |
Button to make a concept defined | |
BACK and FORWARD Buttons |
List of
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Bug Fixes
GForge number | Brief description of item |
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Focus of editor switches while creating restrictions | |
LQT results don't have search criteria appended at the end of the file. |
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Restrictions added flagged as changes to Restriction classes in Prompt | |
LQT nested query causes error dialog | |
fitering inherited restrictions | |
Cannot edit restriction that has an apostrophe in the filler value |
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Add Individual button should only be enabled when hasValue is selected | |
Batch edit to delete associations needs full association rdfs:ID |
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Would like to do 'property present' LQT queries with object properties
Restore nci-specific export function in inferred tree widget |
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Domain and Range checks on property restrictions at edit time
Link which opens when an unstructured proposal is imported, opens an xml. | |
infinite loop in Report Writer | |
Report Writer fails on rerun after a cancel | |
null pointer in Protege OWL layer |
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Can't change tabs unless focus is on a concept | |
After split one of the classes ended up with owl:thing as the only parent | |
In Copy pane, the Preferred_Name and PT are automatically sync'ed with an improper AQ. |
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Editing a role with Cardinality requires reselecting Cardinality | |
Report Writer shows anon class defined by conjunction of NandS | |
Report Writer incapable of generate completed report | |
CompleteableCache throws a nullpointer exception |
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Lucene indexing failure with database data | |
Refresh of screen after classification slow and using up desktop resources | |
BatchEditor gives a false positive | |
Cannot edit the concept from workflow | |
Batch edit takes a long time | |
database accumulates garbage over a period of time | |
NPE when selecting row from PROMPT differences table |
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Use of parseType=Literal for complex properties
During a batch edit a new definition is accepted even without the qualifiers. |
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Changes Tab does not reflect items created in Batch Load
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Need indication of classifier run
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Can the Read-Only view look like the Review pane (have one page with all class info)? |
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Protege 1.4 loads ndf-rt with exceptions, property tab has the ugly widget | |
Inability to reject and/or ignore suggestions from the classifier | |
Expands the first top level node under owl:Thing when add Restriction | |
Slow performance when creating new concepts including split and copy |
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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Legacy_Concept_Name issues | |
ReadCommited Cache throws a nullpointer exception. |
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(duplicate of 24360 ) Runtime errors during batch edit |
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Expands the first top level node under owl:Thing when add Restriction
Imports ontologies through the metadata tab is not working | |
Error editing concepts from workflow with changes in ConceptType | |
rethink and redesign workflow of pre-merge/pre-retire | |
Make Changes tab show login and log out |
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popup windows are inaccessible in Citrix protege |
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Wrong Starting Point for Add/Edit Parent Class -- dup 22786 |
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Other Items Closed
- The defects in the following list were not reproducible, some of these were deemed fixed as a by-product of refactoring.
9298 Prompt - accept and reject icons in 'changed by' panel of 'table' view don't work
The defects in the following list were either considered invalid or did not require a fix
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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 |
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