May 27, 2008   National Cancer Institute Center for Bioinformatics and Information Technology

1.0 Release History

2.0 New Features and Updates

• This is a minor release, mainly to enable complex properties to be brought into the wiki.  A few additional features were added and bugs fixed. Summary below, for additional details, see:  Release 1.2.2 task table 

Run Time Classification
This new functionality allows editors to classify BiomedGT, or NCIT, in the Protege client-server environment used by the EVS. It depends on an explanation server running independently of the Protege server. The explanation server is initialized with the same data served by the Protege server, and is maintained synchronized with the database as editing occurs by the Protege client. Because of initialization activities, the first classification action by a client will take a number of minutes; subsequent classifications will be faster.
Salient points:

• Enhanced detection of exceptional conditions allowing better error handling and explanation services
• Parallel improvements on the Explanation Tab GUI to make explanations easier to interpret
• Performance increase due to improved memory management and optimizations in the classification and extraction algorithms
  Known issues:
• A side effect of the requirement for synchronization with the explanation server is that batch loads and edits can take longer and throw exceptions. Batch loads and edits need to be conducted under controlled conditions: the recommendation is for the workflow manager to conduct these batch actions in standalone database mode and with the explanation server shut down.
• Limited concurrency. On a classification action by the RTC, there will be a period of time in which the DB is locked for writing. The suggested workaround is for one editor, perhaps the workflow manager, to conduct the classification action and advertise to the editors to cease editing while classification is ongoing. This would still allow browsing of the database by other editors.
• High network communications overhead. The classification time will be significantly increased on classifications by remote editors.

The last two issue will be addressed in a future patch. However, a "remote access" server is being set up that will alleviate communications overhead.

Reporting functionality added to the Advanced Query Plugin
An export function (leveraged from an existing plugin in Protege) has been added to the AQP which allows very detailed reports to be produced in a tabular format. This function doesn't replace the Report Writer.

Increased Configurability
Although written to support editing activities in the EVS, the NCIEditTab plugin has introduced various user interfaces and behaviors that make it an attractive plugin to other editing groups. Hence configurability has been a background refactoring activity as development progressed. This is noted here because with the EVS now editing BiomedGT and NCIT, this aspect becomes very important as the internal format of annotations in BGT is expected to start deviating significantly from NCIT's in the near future. Some features related to display labels remain to be implemented.
Salient points:

• Specifies what properties are qualified and hence need to be edited in one of the complex panels of the NCIEditTab, where qualified properties are properties with multiple xml-delimited subfields as their value.
• Maps xml elements of qualified annotation properties to fields in editing panels.
• Specifies properties and concepts required by the business logic of the various functions in the NCIEditTab (e.g. properties supporting retirement actions).
• Specifies external sources requiring restricted editing privileges.
• Specifies external Semantic Media Wiki servers supporting collaborative development

3.0 Bugs Fixed Since Last Release

• GForge #12797 Warn user user when switching tabs without saving- has been implemented.

• GForge #12781 Refreshing assignment information when multiple Protege sessions are running

• GForge #10766 Strange display of PT in copy tab - pipe delimited full syns should no longer occur
• GForge #12959 Display proposed concept as existing concept - sporadic problem fixed.

4.0 Known Issues

• GForge #8376 Need Review button in Copy tab - not implemented in this version.