BioPortal 2.3 Release Notes - Revision history

Cyoun: /* New features */

2010-02-24T21:04:59Z

New features

Cyoun: /* New features */

2010-02-10T23:25:04Z

New features

Mdorf: /* New features */

2010-02-10T17:30:38Z

New features

Mdorf: /* New features */

2010-02-05T21:23:29Z

New features

Palexand: /* BioPortal UI Internal Features and Bugfixes */

2010-02-04T20:05:26Z

BioPortal UI Internal Features and Bugfixes

Palexand: /* Other features and bug fixes */

2010-02-04T20:05:09Z

Other features and bug fixes

Palexand: /* New features */

2010-02-04T02:31:51Z

New features

Palexand: /* New features */

2010-02-04T02:23:46Z

New features

Noy: /* New features */

2010-02-03T01:41:04Z

New features

Noy: /* Known issues */

2010-02-03T01:39:45Z

Known issues

@@ Line 8: / Line 8: @@
 * Users can now exclude the annotations created with synonym terms.
 * Users can now exclude the annotations less than a certain length.
-* There is a change in the XML returned by the Annotator service. Please note that the <semanticTypeBean> information is presented differently in <concept>. The Get all terms REST service is also affected.
+* There is a change in the concept XML returned by the Annotator service. Please note that the <semanticTypeBean> information is presented differently in <concept>. The Get all terms REST service is also affected.
 <pre>
 <concept>
@@ Line 34: / Line 34: @@
          </semanticTypes>
 </concept>
 </pre>

@@ Line 8: / Line 8: @@
 * Users can now exclude the annotations created with synonym terms.
 * Users can now exclude the annotations less than a certain length.
-* There is a change in the XML returned by the Annotator service. The <sematicTypeBean> information is presented differently. The Get all terms REST service is also affected.
+* There is a change in the XML returned by the Annotator service. Please note that the <semanticTypeBean> information is presented differently in <concept>. The Get all terms REST service is also affected.
 * There is a change in the XML returned by the /obs/ontologies service. The ontologyBean now includes the following output:

@@ Line 22: / Line 22: @@
 	<format>OWL</format>
 </ontologyBean>
 </pre>

@@ Line 9: / Line 9: @@
 * Users can now exclude the annotations less than a certain length.
 * There is a change in the XML returned by the Annotator service. The <sematicTypeBean> information is presented differently. The Get all terms REST service is also affected.
 * Users can now define target terminologies for RRF ontologies via the BioPortal UI.
 * Referencing the tabs on ontology visualization pages in the BioPortal UI is now done using the tab name:

@@ Line 35: / Line 35: @@
 * New lexbig JAR intended to fix the problem with the graph not focused properly when there are 2 ontologies with the same uri.(Bioportal bug #1783)
-=== BioPortal UI Internal Features and Bugfixes ===
+== BioPortal UI Internal Features and Bugfixes ==
 * Fixed bug in autocomplete drop-downs where they could not distinguish between two ontologies or concepts with the same name.
 * New functionality to display messages on the front page with a close button that remembers that users closed the message. Set $FRONT_NOTICE in environment.rb to your desired message in order to display a message.

← Older revision		Revision as of 20:05, 4 February 2010
Line 34:		Line 34:
	* Implemented support for OpenID Authentication		* Implemented support for OpenID Authentication
	* New lexbig JAR intended to fix the problem with the graph not focused properly when there are 2 ontologies with the same uri.(Bioportal bug #1783)		* New lexbig JAR intended to fix the problem with the graph not focused properly when there are 2 ontologies with the same uri.(Bioportal bug #1783)
		+
		+	=== BioPortal UI Internal Features and Bugfixes ===
		+	* Fixed bug in autocomplete drop-downs where they could not distinguish between two ontologies or concepts with the same name.
		+	* New functionality to display messages on the front page with a close button that remembers that users closed the message. Set $FRONT_NOTICE in environment.rb to your desired message in order to display a message.
		+	* Updated language on error messages when attempting to browse individuals/properties.
		+	* Fixed a bug where submiting a remote ontology would trigger an exception because the app was looking for an uploaded file.
		+	* Fixed a bug in URI generation for resources where fixnums were being interpreted as strings without conversion.
		+	* Added a custom logging framework to enable logging to the BioPortal Core.
		+	* Added functionality to hide explore and download links using a global array. This fix is temporary until this information is stored in the ontology metadata.
		+	* A custom Google Analytics ID can now be provided via the environment.rb file.
		+	* If metrics don't exist, the UI now checks prior versions (back through 21 versions, three weeks for ontologies that are updated daily). The user is informed that the metrics are from a previous version and given a link to that version.
		+	* When registering a new account, a check is now made to make sure that the username doesn't already exist.
		+	* Before displaying a link for downloading diffs, the UI now makes sure that the diff is between that ontology and the prior existing ontology. This is to handle cases where an ontology may have been deleted but the record of a diff still exists. (Bug #1389)
		+	* Somehow sorting was removed from the resources on the Resource Index tab. This has been re-enabled.
		+	* Extending the slider on the ontology visualization page now works properly in IE (Bug #1500)
		+	* The BioPortal UI is now using the REST service to gather its list of Groups and related ontologies. In addition, Groups have been added to the ontology summary page. (Bug #1607)
		+	* Fixed a bug where visiting the "Submit new ontology" link on the Browse page while logged out didn't redirect properly once a user logged in (Bug #1486).
		+	* Removed extra characters from search fields on the BioPortal index page (Bug #1390)
		+	* Refactored much of the code in the DataAccess class to implement a common method to store/retrieve objects from the cache and make calls to the BioPortal Core when objects aren't in the cache.
		+	* Exception handling for IO errors due to calls to the back-end that could not be completed. Generally these were improper or unknown concept ids being passed by GoogleBot, but there were some genuine errors that weren't being handled. The user is now informed, via a very basic error message, when a concept can't be found in an existing ontology.
		+	* Added a REST_DOMAIN config option so that we could pass this parameter to Flex apps and have them use the appropriate locations for REST services. Prior to this the Flex apps were hard-coded to use production for many parts of their operation.
		+	* Added a FLEX_URL config option to allow for hosting of Flex apps in different locations.

← Older revision		Revision as of 02:31, 4 February 2010
Line 10:		Line 10:
	* There is a change in the XML returned by the Annotator service. The <sematicTypeBean> information is presented differently. The Get all terms REST service is also affected.		* There is a change in the XML returned by the Annotator service. The <sematicTypeBean> information is presented differently. The Get all terms REST service is also affected.
	* Users can now define target terminologies for RRF ontologies via the BioPortal UI.		* Users can now define target terminologies for RRF ontologies via the BioPortal UI.
		+	* Referencing the tabs on ontology visualization pages in the BioPortal UI is now done using the tab name:
		+	** http://bioportal.bioontology.org/visualize/40644#mappings

@@ Line 1: / Line 1: @@
 == New features ==
-* BioPortal will process SKOS labels for preferred names, synonyms, etc.
+* BioPortal will process SKOS labels for preferred names and synonyms:
 * Ontologies used by Annotator & Hierarchy services will now be updated on a regular basis (around every week).
 * The filtering of annotation by semantic types is available only for the ontologies which provide that information

← Older revision		Revision as of 01:39, 3 February 2010
Line 20:		Line 20:
	* ISA closure in the Annotator and Hierarchy services do not work properly for NCIT and Galen. This will be fixed in an upcoming release.		* ISA closure in the Annotator and Hierarchy services do not work properly for NCIT and Galen. This will be fixed in an upcoming release.
	* Some mappings present in BioPortal are not yet available for use with the Annotator.		* Some mappings present in BioPortal are not yet available for use with the Annotator.
		+
		+	== Other features and bug fixes ==
		+
		+	* Implemented updates to Hierarchy (OBS Wrapper) Services to conform to the new OBS output XML structure
		+	* Added case sensitivity check for the root concept (per #1793)
		+	* Upgraded the deprecated Acegi Security to Spring Security
		+	* Implemented support for OpenID Authentication
		+	* New lexbig JAR intended to fix the problem with the graph not focused properly when there are 2 ontologies with the same uri.(Bioportal bug #1783)