A java library for converting obo format documents to OWL, and for converting (a subset of) OWL to obo format. This project is also the current home of the macro expansion library described here.

See the README

See also From OBO to OWL and back: Building Scalable Ontologies from OBO to OWL and back

OBO Format Specification

• obof1.4 spec
• current version
• obof1.4 guide (in progress)
• obof1.2 guide

Instructions for Java Programmers

You can use oboformat.jar within your applications.

• See The API Guide
• See Example Code
• Consult the javadocs for:
• org.obolibrary.obo2owl.Obo2Owl
• org.obolibrary.obo2owl.Owl2Obo
• MacroExpansionVisitor

See also OWLTools, which provides "OBO-format friendly" methods on top of the OWL API, and transparent access to the converter.

Command Line Usage

A simple command line interface is available. First obtain the code and set up your PATH to point to the oboformat directory. For example:

cd
svn checkout http://oboformat.googlecode.com/svn/trunk/ oboformat-read-only
export PATH="$PATH:$HOME/oboformat-read-only"

Type the following for instructions:

obolib-obo2owl -h

Converting from obo to owl:

obolib-obo2owl myont.obo -o myont.owl

The -o argument can be ommitted, in which case it will save a file myont.obo.owl

Converting from owl2obo:

obolib-owl2obo myont.owl -o myont.obo

Graphical User Interface

A graphical user interface is available via the Oort. Oort provides obo2owl and owl2obo capabilities via this codebase. It also provides simple access to more powerful capabilities.

See Graphical User Interface Documentation

Installation Instructions

1. Download the Oort installer for your platform from the OWLTools download site
2. Double click on the installer and follow the instructions
3. You should now have an application called "obo-owl-converter". This provides a GUI for bidirectional conversion

Note that you should also have the full Oort application as well. This extends the capabilities of the basic converter. See the documentation

Mail List

The mailing list "obo-format" is for users and those involved in the specification and development of the code. It is hosted on sourceforge and mirrored on google. You can subscribe to / post from either:

• subscribe via sourceforge
• subscribe via google groups

For oboformat developers, the https://groups.google.com/group/oboformat-issue-tracker list contains notifications from the issue tracker