oboformat / oboformat-tools

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README

ABOUT

This is a wrapper for the Java (OWL-API) implementation of

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

Originally the project was a stand-alone Java project on googlecode.
The main code to load, write and convert OBO to OWL is now part of 
the OWL-API (version 3.5.x and later).

GETTING THE CODE

  git clone https://github.com/oboformat/oboformat-tools.git

BUILDING THE PROJECT

  mvn clean package
  
  This maven command will create/update the required jar files to run the converter.. 

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-tools/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  

ISSUE TRACKER

See github issue tracker for the project

https://github.com/oboformat/oboformat-tools