BioPortal Import Plugin - Revision history

TaniaTudorache at 21:34, June 13, 2014

2014-06-13T21:34:53Z

TaniaTudorache at 23:08, May 9, 2014

2014-05-09T23:08:40Z

TaniaTudorache: /* Download */

2012-09-20T19:39:48Z

‎Download

TaniaTudorache: /* Download */

2012-08-24T18:10:17Z

‎Download

TaniaTudorache: /* Download */

2012-02-06T23:39:49Z

‎Download

TaniaTudorache at 19:37, August 8, 2011

2011-08-08T19:37:09Z

TaniaTudorache at 19:36, August 8, 2011

2011-08-08T19:36:37Z

TaniaTudorache at 01:35, July 16, 2011

2011-07-16T01:35:37Z

TaniaTudorache at 01:08, July 16, 2011

2011-07-16T01:08:34Z

TaniaTudorache: /* Limitations and known issues */

2011-07-16T01:08:10Z

‎Limitations and known issues

@@ Line 23: / Line 23: @@
 '''As of May 2014, the BioPortal Import plugin does not work anymore.'''
-BioPortal has updated its [http://data.bioontology.org/documentation REST APIs] and the plugin has not been ported to the new API, yet.
+BioPortal has updated its [http://data.bioontology.org/documentation REST APIs] and the plugin has not been ported to the new API, yet. We plan to add this functionality to [[WebProtege]]. Follow [https://github.com/protegeproject/webprotege/issues/152 this GitHub issue] for updates.
-As a work around, you may open the BioPortal ontology directly in Protege 4.x, and edit it (for example, extract branch by deleting the rest of the ontology, or by using the Refactor menu -> Copy/move/delete axioms). To open the BioPortal ontology in Protege 4.x, do these simple steps:
+As a work around for now, you may open the BioPortal ontology directly in Protege 5.x, and edit it (for example, extract branch by deleting the rest of the ontology, or by using the Refactor menu -> Copy/move/delete axioms). To open the BioPortal ontology in Protege 5.x, do these simple steps:
 # Copy the download link of the ontology from the ontology summary view in BioPortal (e.g., right-click on the link -> Copy link address)
-# Start Protege 4.x
+# Start Protege 5.x
 # Go to File menu -> Open from URL, and paste the link in the box

← Older revision		Revision as of 23:08, May 9, 2014
Line 16:		Line 16:
	<div style="display:block; float:left; width:100%;">		<div style="display:block; float:left; width:100%;">

−	`	+
	= Overview =		= Overview =
		+
		+	<div style="background: #FDECE7; border: 2px solid #AE5B08; padding: 10px 15px 10px 20px; margin: 30px 430px 0 0; ">
		+
		+	'''As of May 2014, the BioPortal Import plugin does not work anymore.'''
		+
		+	BioPortal has updated its [http://data.bioontology.org/documentation REST APIs] and the plugin has not been ported to the new API, yet.
		+
		+	As a work around, you may open the BioPortal ontology directly in Protege 4.x, and edit it (for example, extract branch by deleting the rest of the ontology, or by using the Refactor menu -> Copy/move/delete axioms). To open the BioPortal ontology in Protege 4.x, do these simple steps:
		+
		+	# Copy the download link of the ontology from the ontology summary view in BioPortal (e.g., right-click on the link -> Copy link address)
		+	# Start Protege 4.x
		+	# Go to File menu -> Open from URL, and paste the link in the box
		+
		+	</div>

	The plugin allows a user to '''import classes from external ontologies and terminologies stored in the [http://bioportal.bioontology.org BioPortal ontology repository]''' into the local ontology.		The plugin allows a user to '''import classes from external ontologies and terminologies stored in the [http://bioportal.bioontology.org BioPortal ontology repository]''' into the local ontology.

@@ Line 178: / Line 178: @@
 Even if the plugin is distributed with Protege 3.x release, we might need to make changes to the plugin to keep in sync with the BioPortal releases and to add enhancements and bug fixes. For this reason, we also provide separate download for the plugin.
-We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/bioportalReference.zip here]. Unzip it into your Protege 3.4.x plugin folder. (Make sure you override the old versions of the plugin.)
+We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/bioportalReference.zip here]. Unzip it into your Protege 3.x plugin folder. (Make sure you override the old versions of the plugin.)
-The plugin is open source and the source code is available in our SVN: http://smi-protege.stanford.edu/svn/bioportal-reference-plugin/trunk/ and it is licensed under Mozilla Public License.
+The plugin is open source and the source code is available in our SVN and it is licensed under Mozilla Public License (MPL).
 = Where to get help and complain =

@@ Line 178: / Line 178: @@
 Even if the plugin is distributed with Protege 3.x release, we might need to make changes to the plugin to keep in sync with the BioPortal releases and to add enhancements and bug fixes. For this reason, we also provide separate download for the plugin.
-We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/tmp/bioportalReference.zip here]. Unzip it into your Protege 3.4.x plugin folder. (Make sure you override the old versions of the plugin.)
+We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/bioportalReference.zip here]. Unzip it into your Protege 3.4.x plugin folder. (Make sure you override the old versions of the plugin.)
 The plugin is open source and the source code is available in our SVN: http://smi-protege.stanford.edu/svn/bioportal-reference-plugin/trunk/ and it is licensed under Mozilla Public License.

@@ Line 180: / Line 180: @@
 We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/tmp/bioportalReference.zip here]. Unzip it into your Protege 3.4.x plugin folder. (Make sure you override the old versions of the plugin.)
-The source code of the plugin is available in our SVN: http://smi-protege.stanford.edu/svn/bioportal-reference-plugin/trunk/ and it is licensed under Mozilla Public License.
+The plugin is open source and the source code is available in our SVN: http://smi-protege.stanford.edu/svn/bioportal-reference-plugin/trunk/ and it is licensed under Mozilla Public License.
 = Where to get help and complain =

@@ Line 21: / Line 21: @@
 The plugin allows a user to '''import classes from external ontologies and terminologies stored in the [http://bioportal.bioontology.org BioPortal ontology repository]''' into the local ontology.
-'''This plugin works with the Protege 3.x releases, not Protege 4.x releases'''. We plan to have an implementation of this plugin also in Protege 4 as part of the future work. If you are using Protege 4 to develop your ontology, you can still use this plugin by opening the OWL file in Protege 3.x, make the import, save, and the continue to develop the ontology in Protege 4.
+'''This plugin works with the Protege 3.x releases, not Protege 4.x releases'''. We plan to have an implementation of this plugin also in Protege 4 as part of the future work. If you are using Protege 4 to develop your ontology, you can still use this plugin by opening the OWL file in Protege 3.x, make the import, save, and then continue to develop the ontology in Protege 4.
 The basic '''steps''' in using the plugin are to:

@@ Line 1: / Line 1: @@
 {{Plugin
-|Description=The BioPortal Import Plugin allows users to import classes from external ontologies stored in the BioPortal ontology repository. The user can import entire trees of classes with a desired depth and choose which properties to import for each class.
+|Description=The BioPortal Import Plugin allows users to import classes from external ontologies stored in the BioPortal ontology repository. The user can import entire trees of classes with a desired depth and choose which properties to import for each class. This plugin works with Protege 3.x releases, not Protege 4.x.
 |PluginType=Project
 |ForApplication1=Protege-OWL
@@ Line 20: / Line 20: @@
 The plugin allows a user to '''import classes from external ontologies and terminologies stored in the [http://bioportal.bioontology.org BioPortal ontology repository]''' into the local ontology.
 The basic '''steps''' in using the plugin are to:
@@ Line 172: / Line 174: @@
 = Download =
-The plugin is distributed with the Protege 3.4.7 release and newer. However, we might need to make changes to the plugin to keep in sync with the BioPortal releases and to add enhancements and bug fixes. For this reason, we also provide separate download for the plugin.
+The plugin is distributed with the Protege 3.4.7 release and newer Protege 3.x releases. This plugin does not work with Protege 4.x releases. We plan to support this in the future.
 We have a patch version of the plugin that can be downloaded from [http://smi-protege.stanford.edu/collab-protege/tmp/bioportalReference.zip here]. Unzip it into your Protege 3.4.x plugin folder. (Make sure you override the old versions of the plugin.)

← Older revision		Revision as of 01:35, July 16, 2011
Line 153:		Line 153:

	The plugin creates instances of the <code>OWLNamedClass</code> class to store all the imported classes from BioPortal. If the user chooses to import any property of the imported classes, it is assigned to one of the <code>OWLAnnotationProperties</code> of the current <code>OWLModel</code>, as configured by the user.		The plugin creates instances of the <code>OWLNamedClass</code> class to store all the imported classes from BioPortal. If the user chooses to import any property of the imported classes, it is assigned to one of the <code>OWLAnnotationProperties</code> of the current <code>OWLModel</code>, as configured by the user.
		+
		+	The import metadata properties are defined in the ''provenance.owl'' ontology that is available from [http://protege.stanford.edu/ontologies/metadata/provenance.owl here]. The metadata properties defined in this ontology might change in future versions of the plugin based on the community feedback.

	To display the list of ontologies in BioPortal, get the details of the classes and their properties etc., the plugin invokes the [http://www.bioontology.org/wiki/index.php/NCBO_REST_services BioPortal Restful Services].		To display the list of ontologies in BioPortal, get the details of the classes and their properties etc., the plugin invokes the [http://www.bioontology.org/wiki/index.php/NCBO_REST_services BioPortal Restful Services].

@@ Line 166: / Line 166: @@
 * It is not possible to persist an import configuration into a file to reuse for other ontologies. (future enhancements)
 * The plugin only works with Protege-OWL, and not with Protege Frames ontologies. If there is enough interest in the community, we will also support Frames.
 = Download =

@@ Line 163: / Line 163: @@
 Some of the limitations and known issues are:
 * It is only possible to import the label, definition and synonym properties for a class. Future versions will allow the selection of arbitrary properties to import.
-* While an import is going on, the user interface is blocked, and it is not possible to cancel a long running import (future enhancement).
+* While an import is going on, the user interface is blocked, and it is not possible to cancel a long running import. (future enhancement)
+* It is not possible to persist an import configuration into a file to reuse for other ontologies. (future enhancements)
 = Download =