ABOUT

This is a java implementation of

• A parser for OBOF1.4 syntax
• An implementation of the OBOF1.4 mapping to OWL (uses the OWLAPI)

GETTING THE CODE

For now there are no releases; get the code via svn:

svn checkout http://oboformat.googlecode.com/svn/trunk/ oboformat-read-only

RUNNING THE CONVERTER ON THE COMMAND LINE:

You may find it helpful to add the bin dir to your path:

export PATH="$PATH:$HOME/oboformat-read-only/bin"

Convert a file like this:

obolib-obo2owl cell.obo [--to owlxml|manchester] -o FILE-PATH

You have to specify the file path as a URL; e.g

obolib-obo2owl cell.obo -o file:///Users/me/cell.owl

You may find it convenient to do this:

obolib-obo2owl cell.obo -o file://pwd/cell.owl

Alternative syntaxes like this:

obolib-obo2owl cell.obo --to manchester -o file://pwd/cell.owl

Windows users can run the obo2owl as:

bin\obolib-obo2owl.bat -o test_resources\caro.owl test_resources\caro.obo  

LIMITATIONS

See

http://code.google.com/p/oboformat/issues/list