Protégé 4.0 alpha Plugins
Listed below are a number of plugins already developed for the Protégé 4.0 alpha ontology development framework.
Views can be composed by the user to make up whatever interface they want. Clicking on a plugin in the Views menu puts the user in configure mode, allowing them to drop the view anywhere on the current tab. Views can be stacked, floated, cloned and removed.
One more nice feature of the framework is that most plugins you have installed will tell you when an update is available from the web.
We believe in the "release early" mentality. Please bear in mind that all plugins are prototype alpha software and are under active development.
Please make sure you backup regularly
Documentation
To install the plugins:
- Get the latest release of Protege 4.0 alpha
- Download and unzip plugins into the Protege plugins/ folder
- Next time you start Protege, the plugin will be available
- Accessing the plugin depends on the type - many will be available as additional tabs in the "Tabs" menu or as views in the "View" menu
Guide to writing a simple plugin - this is just to get a flavour of Protégé as a development environment - a "Hello World" if you like. NOW Updated for OWL1.1
Level of Support
As with most new software, things are changing rapidly, so we do not have the resources to actively support the plugins. However, all comments and suggestions/feature request are appreciated!
License
Made available under the GNU Lesser General Public License
Copyright © 2006 The University Of Manchester
Acknowledgements
This work is funded by JISC and the Semantic Mining Network of Excellence.
We work in collaboration with partners from Stanford University and other institutions in the UK.
| Plugin | Description | Protégé release no. |
|---|---|---|
| OWLViz | Graph view of the ontology. | build 57 |
| DL Query | Get sub/superclasses of arbitrary class descriptions. | build 57 |
| Matrix | Tabular views of classes, properties and individuals. | build 57 |
| Sub Ontology Tab | Class hierarchy extraction tool. By Jay Kola (CLEF). | in progress |
| Excel Import | Create class descriptions from excel tables. By Jay Kola (CLEF) | build 61 |
| Cloud Views | Class/Property browsing by various measures of "importance". | build 57 |
| Bookmarks | A list of useful classes/properties, saved with your ontology. | build 57 |
| Cardinality View | Alternative (cardinality focused) restrictions view for OWL classes | build 57 |
| Taxonomy cut+paste | Two example plugins for showing class descendants for pasting into documentation | build 57 |
| Outline/Existential Tree | Views tracing down existential hierarchies for given properties. | build 62 |
| OWLDoc | JavaDoc style HTML export and view for your ontology. | build 57 |
| OPL Support | Ontology transforms with the Ontology Processing Language (OPL). | build 57 |
| The Nerd | The Protégé version of "Clippy" that everyone loves to hate. | build 57 |
| TerMine | Extract candidate terms from a corpus (by Simon Jupp & Matthew Horridge). | build 59 |
| OWL lint | Catch structural problems and likely modelling errors in your ontologies (by Luigi Iannone). | build 59 |
| Annotation Search | Find/filter/text search annotations across all active ontologies. | build 62 |
| Alternative Annotate | An easy to edit metadata set. | build 61 |
| Change View | A useful debugging tool that shows all changes to the model since startup. | build 62 |
OWLViz
The popular OWLViz has been ported over to Protégé 4.0. Implemented as a view, the subsumption graph can now be shown on any tab. In addition, a new imports graph is available to help understand the import dependencies within highly modularised ontologies.
OWLViz requires installation of third party libraries - Graphviz.
Find them under the Tabs and Views-Ontology Views menus respectively
DL Query is part of the standard Protégé 4.0 distribution
Documentation (only slightly out of date) | get source code
DL Query
Quickly test definitions of classes to see that they subsume the appropriate subclasses. Or check for class membership of arbitrary descriptions without having to create named class placeholders.
Find DL Query under the Tabs menu.
OWLViz is part of the standard Protégé 4.0 distribution | get source code
Matrix Tab/Views
Several spreadsheet-style views of an ontology, including existential fillers, individual relationships and an object properties view. Drag and drop to add columns and values.
Find them under the Tabs menu
download plugin | get source code
Sub Ontology Tab (by Jay Kola)
click for more images
Ever wished you could copy/drag and drop a class hierarchy from one ontology into another instead of typing them in? Or ever wished you could extract the class hierarchy from one section of a large ontology like the NCI meta-thesaurus or GO into a separate ontology? If so, the Sub Ontology tab is your answer to these tedious tasks ! What is more, it also lets you copy over the annotations on concepts in the hierarchy being copied/extracted across so the concepts from your ontology can still retain the meta data from the original ontology.
Find it under the Tabs menu as Sub Ontology Tab
Excel Import (by Jay Kola)
Load excel or CSV files and generate classes from the content. Provide rules to create restrictions between columns.
Find it under the Tabs menu
Cloud Views
Wondering about the "shape" of your ontology? Several implementations of the popular TagCloud can give you insight into different aspects of your ontology - ratings are based on different criteria (eg class usage, depth in hierarchy etc). The bigger the name, the higher the rating. Sort alphabetically or by rating, and filter out low ranking entities easilly.
Find them under the View-Cloud views menu
download plugin | get source code
Bookmarks
Forever getting lost in large ontologies? Or, want to keep a set of classes/properties handy for a demo? Drag classes/properties into this view and they are accessable anytime to click on. They will also be saved along with your ontology annotations for future reference.
Press Command-B or find it under the Tools menu
download plugin | get source code
Cardinality View
An experimental alternative to the conditions widget that shows restrictions in relation to their cardinality. If several different restrictions are along the same property with the same filler, it "merges" them into a single line to aid readability. It also provides hints as to whether a given set of restrictions are closed.
Find it under the View-Class views menu
download plugin | get source code
Taxonomy cut+paste
Sometimes, all you need is a quick extract of a part of your hierarchy for a paper or presentation. These 2 very simple views provide a quick way to extract parts of your hierarchy into text form. The Tabbed Subclasses view just shows a tab-indented list of your asserted class hierarchy from the currently selected class. The Decendant Names view does the same without indentation. Just cut and paste into your favourite applications.
Find them under the View-Class views menu
download plugin | get source code
Outline/Existential Tree
The subsumption hierarchy is not the only "axis" on which an ontology relies. Many other axis (such as partOf) can be useful for navigation.
The Outline View follows existential (and appropriate cardinality) restrictions to build up a view of the current class by its structure.
The Existential Tree view is a simplified version that shows the tree along a specified property.
Find them under the View | Class views menu
download plugin | get source code
Browser (OWLDoc)
The first rewrite of the popular OWLDoc tool that now has both an export to HTML and a dynamic view that allows you to browse from within Protégé. OWL1.1 is supported and full use is made of the highly optimised OWLAPI Usage model. All links navigate to the appropriate resource. Further features (including a server version with search/query support) are under development.
Find the OWLDoc View (above) under the View-Misc views menu. An HTML presentation of the last selected class, property or individual will be displayed as you browse. Updates to the ontology are reflected immediately.
OWLDoc export (below) is in the Tools menu - just provide a directory to export to and a browser will open when it finishes. OWLDoc will create a bundle of (mostly) static HTML pages for publishing to the web or distributing to colleagues (a small amount of javascript is used to create a fragment of the class hierarchy on each class summary page).
download plugin | get source code
The browser is also implemented as a standalone web ontology browser.
The Protégé Nerd
For all of those die-hard Protégé users who love to reminisce - the Nerd returns - practice your view duplication and create a whole nerd tab - excellent Kitsch value especially made for Olivier Dameron.
Find it under the View-Misc views menu
TerMine Plugin (by Simon Jupp & Matthew Horridge)
The Protégé TerMine plugin uses text mining tools to extract candidate terms from a corpus of text and provides an interface for rapidly bringing these terms into an OWL ontology. It currently uses the TerMine term extraction tool provided by NaCTeM to extract concepts from text. The plugin accesses TerMine via a Web Service over the Internet.
Find it under the Tools menu
full documentation |
download plugin |
get source code
OWL lint Plugin (by Luigi Iannone)
The OWL lint framework is designed to be a flexible way to define and run tests against a set of OWL ontologies for quality control, debugging, best practice and many other purposes. The plugin provides a tab in which lints can be loaded and a report can be generated for the active ontologies.
Find it under the Tabs menu
full documentation | download plugin
Annotation Search View
A view for searching entity annotations for a string or regular expression match. Can also be used with no string specified, just the annotation URI, for finding deprecated entities, or TODO items. The entity name at the start of each result is a link that can be clicked for easy navigation.
Find the view under View | Misc views | Search Annotations
download plugin | get source code
Alternative Annotation View
A view that can be configured to show a set of standard annotation fields for every class/property/individual. This makes it quicker to annotate as they are always in the same order, editable inline and easy to navigate through (Ctrl-Tab/Shift-Ctrl-Tab). Useful when developing in a consortium and some standard metadata set should always be entered.
Configure the view and import/export shared configurations in File | Preferences | Annotate Preferences.
Find the view under View | Misc views | Annotate View
download plugin | get source code
Change View (for debugging)
When writing plugins, particularly those that perform refactoring, it is useful to be able to verify the changes that have been applied to the model. This view provides a very straightforward list of changesets and the axioms that have been added and removed.
Find it under the View | Misc views | Changes menu
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