BioPortal Import Plugin

by Jithun Nair, Tania Tudorache

The BioPortal Import Plugin allows the user to import classes from external ontologies stored in BioPortal. The user can import entire trees of classes with a desired depth and choose which properties to import for each class.

Versions & Compatibility

This section lists available versions of BioPortal Import Plugin.

No version information available.

If you click on the button below to add a new version of BioPortal Import Plugin, you will be asked to define a page title for the new version. Please adhere to the naming convention of BioPortal Import Plugin X.X.X when you define the new page!

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Overview

The BioPortal Reference plugin is added as an action to the OWLClasses tab of the Protege-OWL user interface. The plugin allows a user to import classes from external BioPortal ontologies into a local ontology in Protege-OWL. The basic steps in using the plugin are to: a) browse through all the BioPortal ontologies (except remote ones) and select which one to import classes from; b) select one or more classes to import from the BioPortal ontology, and c) import them as subclasses of the selected class in the local ontology.

The plugin uses the RESTful services provided by BioPortal to allow the user to browse through the latest versions of all BioPortal ontologies. However, remote ontologies (identified by the value of their isRemote property) cannot be explored in the plugin, since BioPortal does not provide the information for these ontologies through its REST services. The user can view the classes of the selected ontology in an expandable tree format, and also view the properties of each class.

The plugin is configurable and works with Protege-OWL. The configurations provide users with the ability to: a) import entire subtrees of classes from BioPortal ontologies; b) save the imported classes as a separate ontology and/or as a file to the local disk, and c) choose which (if any) property values to import for each class and assign an equivalent user property for each imported property, if desired.

What does it look like

Like this:

Under the hood

To store the internal representation of an external reference, the plugin creates by default an instance of a ExternalReference class. The plugin can be configured to create classes instead of instances for the external references. In OWL, the details of the external references are stored as values of predefined annotation properties (e.g., conceptId, ontologyName, url etc.).

An example of an external reference instance to class Country from the Galen ontology in BioPortal is shown below:

To search BioPortal, get the details of a reference, see a graph visualization, etc, the plugin invokes the BioPortal Restful Services.

How does it work

The usage of the plugin should be quite straightforward.

To create a new external reference just click on the link Create a new reference from BioPortal. After that you will see a popup window like this:

By default, the plugin will start a search in BioPortal using the selected class (or property, individual) name; in the case above, Heart. The panel shows the list of search results for the term from BioPortal: You will see the term name and the ontology in which it was found.

If you are not satisfied with the searched term or results, you may type in your own search term.

To import an external reference simply click on the Import link. A new external reference instance (or class, depending on your configuration) has been created for you.

Before importing, you also have the option of looking at the content of the term in BioPortal, by clicking on the little File icon on a row. You will see the details of the term from BioPortal (this will not be imported):

Alternatively, you may click on the little tree icon from a row to see a graph representation of the neighbourhood of the referenced term from BioPortal. A new window will open in your default web browser (e.g. Firefox, Safari, IE, etc.) showing the neighbourhood graph. You will need to have Flash installed to see the graph.

How to use it

The BioPortalReference plugin is just a slot widget, which means that it can be attached to properties at classes (also metaclasses) to be used instances (or classes).

Create a reference property

To use it with OWL projects, first decide on a property that will store as values the instances of external references. You can either choose from existing properties (foaf:topicOf, or others), or you can create your own annotation property, for example, externalReference. You may also use object properties, or just plain RDF properties. If you don't already have this property defined in your ontology, please create it.

Configure the form

Second step is to configure the form of the class where you want to use the plugin. For example, if you would like to add external references to all classes (e.g., Pizza class, Heart class, etc.), then you will have to configure the form of the owl:Class. To configure the form, click on a class in your ontology and click on the little F icon at the top-right hand side of the ClassesTab. You will get a dialog whether to make owl:Class visible, click OK.

Then go to the Forms Tab (you may already be there after closing the dialog), make sure that owl:Class is selected, and double click on an empty spot. You will get a dialog with all properties and their attached widget. For the reference property from step 1 (e.g., externalReference) associate the BioPortalReferenceWidget.

Note: The new widget will be created under the top widget (it's a bug), so just drag the top widget to right a little bit, and drag from underneath the BioPortalReference widget to a place of your choice in the UI.

Configure the widget

Normally, you would not change the default configuration of the widget, but in case you need to customize it for your own project please read this section. Otherwise, you may just skip it.

You may configure the widget in the Forms Tab by double clicking on the BioPortalReference widget. In the 'Columns Tab, you may configure what columns and the width of each column that should show up:

For example, you may remove the url slot and this will be removed from the display of the BioPortalReferenceWidget, or you may add other column, or switch the order.

In the Search Tab, you may configure the search parameters for BioPortal:

The result

Below is a screenshot that shows the OWLClasses tab, for which we have configured using the steps above, the BioPortalReference widget:

Download

The plugin is distributed with the Protege 3.4.2 release and newer. However, we might need to make changes to the plugin to keep in sync with the BioPortal releases. For this reason, we also provide separate downloads for the plugin.

We have a patch version of the plugin for Protege 3.4.3, that can be downloaded from 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.

Developer's Guide

This plugin is very easy to extend.

Configure the classpath and Eclipse setup

First, you should get the sources of the plugin from the SVN repository, as explained in the above section. The plugin depends on:

• standard-extensions (get the one in the zip from here)
• protege-owl
• xstream libs (get the binary version from here, Libs needed in the classpath: xpp3_min_xyz.jar and xstream-xyz.jar)

If you would like to use Eclipse development environment, we have a guide of how to set it up for plugin development here.

Explanation of classes

The plugin is very simple. It has classes for UI and classes for accessing BioPortal through rest services.

The slot plugin class (main UI) is: edu.stanford.bmir.protegex.bp.ref.BioPortalReferenceWidget

The panel in which you can search and import from BioPortal is: edu.stanford.bmir.protegex.bp.ref.SearchPanel

The reference model class that creates the reference instances and makes the actual import is: edu.stanford.bmir.protegex.bp.ref.ReferenceModel

If you would like to change the way that references are imported, change the method (or create your own):

public Instance createReference(String bpBaseUrl, String conceptId, String ontologyVersionId, String preferredName, String ontologyName)

The package org.ncbo.stanford contains the classes that can can invoke a rest service to BioPortal and that can read in the results. All you need to invoke the services is in the org.ncbo.stanford.util package.

Invoke BioPortal Rest services

The BioPortal Rest services are documented here.

For example, to invoke a search in BioPortal, you can use the utility class:

BioportalSearch sd = new BioportalSearch();
String urlStr = "http://rest.bioontology.org/bioportal/search/Myocardial%20Infarct?pagesize=20&pagenum=1";
try {			
   Page p = sd.getSearchResults(new URL(urlStr));
   SearchResultListBean data = p.getContents();
   for (SearchBean searchBean : data.getSearchResultList()) {
       System.out.println(searchBean.getPreferredName() + "\t" + searchBean.getOntologyDisplayLabel());
   }
 } catch (MalformedURLException e) {
    e.printStackTrace();
 } catch (IOException e) {			
    e.printStackTrace();
 }

For an example implementation see: edu.stanford.bmir.protegex.bp.ref.SearchPanel.getSearchResultsHtml()

To get all details of a concept, you can use the following code:

BioportalConcept c = new BioportalConcept();		
String urlStr = "http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource";		
try {			
   ClassBean cb = c.getConceptProperties(new URL(urlStr));
   System.out.println(cb.getFullId() + " " + cb.getId() + " " + cb.getLabel());
   Map<Object, Object> relationsMap = cb.getRelations();
   for (Map.Entry<Object, Object> e : relationsMap.entrySet()) {
        System.out.println(e.getKey() + ": " + e.getValue());				
   }			
 } catch (MalformedURLException e) {
       e.printStackTrace();
 }

Where to get help and complain

If you have any problems with the plugin, please post a message on the protege mailing list (protege-owl for OWL ontologies, and protege-discussion for Protege frames ontologies). Instructions for posting on the lists are here:

http://protege.stanford.edu/community/lists.html

Before posting, please check the email list archives, whether the question has already been answered:

http://protege.stanford.edu/community/archives.html