COBrA Curation Tool: OBO Explorer
Help Page

Download The OBO Explorer and other OBO Tools can be downloaded from here:
Installation will be easier if you download the OBO Tools file as it bundles the OBO Converter with the OBO Explorer.

Install The OBO tools are Protege plug-ins. If you do not have Protege installed you need to download and install it, see
On all platforms, the plug-ins are installed by expanding the tar archive at the top level of the Protege installation directory, e.g. in /Protege_3.2. The archive will create new directories in the ./plugins directory. Expand the archive using WinZip, StuffIt, or at the commandline: tar -xvf obo-tools.tar. The directory structure should contain these 3 directories (among others)
The OBO Explorer requires no further installation, however, Protege requires Java to run. Java 1.5 should be installed, see: If you are unsure whether you have the correct version of java, try typing 'java -version' at the commandline:
java version "1.5.0_06" on OS X or
java version "1.5.0_04" on Linux.

User Guide

Protege must be configured to show the OBO Explorer tab, and this is done after starting Protege (double-click the Protege icon) and creating a new Project.

1. Creating a Protege Project
If you plan to open an OBO format file (.obo), begin by creating a new Project in Protege (see screenshot immediately below) but do not select Create from Existing Sources (see right), always ensure that OWL/RDF Files is selected, then simply click Finish.

Alternatively, if you want to open an OWL file, proceed as above but select the Create from Existing Sources option, click Next, then select the file (see below) and select the language profile (see right) and click Finish.

2. Configuration: To show the OBO tools, configure Protege as follows:
  • Under the Project menu, select Configure, then in the pop-up dialog select the OBO tools: OboClassesTab, OboConverterTab and OboOntologyTab (see right).
  • Three tabs titled "OBO Explorer", "OBO Converter" and "OBO Ontology Metadata" should appear. These are used to load and edit OBO Ontologies.

3. Loading an OBO format file:
Unless you have loaded an OWL file in step 1:
  • Select the OBO Converter tab
  • Click OBO Input File and select the file
  • Click Start! the interface should look as below
  • Click Close and the interface should appear as shown top right, you can now select the OBO Explorer tab and edit the ontology.
  • In case of an error (bottom right), try creating a new Protege Project and repeating the loading procedure. Errors may occur if you load a new ontology while an ontology is already loaded as the new ontology will be merged with the loaded ontology - which may not be what you intend.
Loading completes successfully:
Loading generates an error:

4. Editing: using the OBO Explorer
The OBO Explorer tab provides access to the definitions and cross-references associated with GO and OBO terms. For more information about the OBO format see
Having created a Protege Project and configured Protege to show the OBO tools, select the OBO Explorer tab. It should appear as below:

Click to enlarge:

The OBO Explorer stores edits to database cross-references (DbXRefs), synonyms and IDs automatically, i.e. without a 'commit' action. Text fields are saved by typing return/newline. Unsaved text is dispayed in blue. Note that most text fields in Protege are saved by typing return.
The interface functions as follows:

5. Creating new classes

6. Properties and Logic
Protege has additional interface components and other powerful features to enable you to create and reason about OWL ontologies, these user guides will help you:

This page can be found at: