Getting OBO-Edit Started

1) Install Java 1.4 or higher

On Macs, Java 1.4 can be installed automatically by doing a system software update. On any other platform, download the appropriate binaries from http://java.sun.com/j2se/1.4.2/download.html. To run Java applications, all you need is the JRE (Java Runtime Environment). If you need all the tools to run and create Java applications, download the J2SE SDK (Software Development Kit).

What version of Java do I have?

Most new computers come with some version of Java already installed. To figure out what version you have, open up a command prompt, or console, or terminal, or whatever you use on your platform to type commands onto a command-line. Then type:

java -version

and press enter. You should get a response like:

java version "1.5.0_06"

Java(TM) 2 Runtime Environment, Standard 
Edition (build 1.5.0_06-b05)

Java HotSpot(TM) Client VM (build 1.5.0_06-b05, 
mixed mode, sharing)

The very first line tells you which version of Java is installed.

If you get a response like:

'java' is not recognized as an internal or external command, operable program or batch file.

bash: java: command not found

Check that you typed a space after "java" and before "-version". If you entered the command correctly but still do not get a response indicating a specific version of Java, then Java is not installed, and you need to follow the installation instructions above.

2) Get OBO-Edit

Download the latest version of OBO-Edit from our Sourceforge project at http://sourceforge.net/projects/geneontology

There will be several downloads to choose from.

If you are a Windows user: Always download the Windows installer
If you are a Mac user: You can either use the Mac installer or the platform independent installation. The Mac installer is easy to use, and will create a shortcut in the Mac OS dock for you. However, the installer software we use seems to introduce a lot of memory overhead. Many Mac users have reported better performance from the platform independent release.
If you are a Linux user: Choose between the platform independent release, the Linux release, or the general Unix release. OBO-Edit is developed and tested using the platform independent release on a Suse Linux machine, so the platform independent release is probably your most reliable choice.

3) Install and Launch OBO-Edit

If you are using a platform-specific installer: Run the installer program and follow the onscreen prompts. It's simple. Icons for running/uninstalling the program will be created on your start menu (or dock, or whatever).
If you are using the platform independent version: Unzip the .tar.gz archive you downloaded (on unix platforms, run "tar zxvf <filename>") into the directory of your choice. On unix platforms (including Mac OS), run the "oboedit" shell script to start the program (to do this on most Unix platforms, change to the OBO-Edit directory and type "./oboedit"). On other platforms, launch the oboedit.jar file in the OBO-Edit installation directory. This can be done either by double-clicking, or by running the command "java -jar oboedit.jar" at a command prompt.

4) Get an ontology

Download an ontology from the Open Biological Ontologies site at http://obo.sourceforge.net/

5) Open the ontology

Go to the "File" menu and choose "Load...". A box will appear that looks like this...

Choose "OBO Flat File Adapter" from the "Data adapter" dropdown list. Click the browse button and find your ontology file on the disk, or type the path to the file you want to load into the "Load files" field. Click the "Ok" button.

Your file is loaded! Tinker away.