BioPAX Level 1, version 1.2 README File


README TABLE OF CONTENTS

1. File Descriptions
2. BioPAX Group Contact Info

____________________________________________________________________________________

1.  File Descriptions

The following files are included in this distribution of BioPAX:

biopax-level1.owl
-----------------
This is the main definition file for the BioPAX format.  It contains the BioPAX
ontology, encoded in the Web Ontology Language (OWL) format.  This file is also
located here: http://www.biopax.org/release/biopax-level1.owl


biopax-level1-documentation.pdf
-------------------------------
This document provides an overview of BioPAX Level 1, Version 1.2. This includes 
descriptions of the BioPAX ontology classes, sample use cases and best practice
recommendations.


biopax-level1-diagram.pdf
-------------------------
This diagram shows the classes and slots of the BioPAX ontology.  The diagram was
generated using the ezOWL plug-in in the Protege ontology editor.


biopax-level1.html
------------------
This file displays the class and slot comments from BioPAX level 1. It was autogenerated
using GKB Editor.


biopax-short-demo-pathway.owl
-----------------------------
This file contains a short demo pathway - the first two steps of glycolysis.  It is
intended as a simple illustration of how various classes and slots should be used.


biopax-short-demo-pathway.pprj
------------------------------
This is the Protege project file for the short demo pathway.  Loading this file into
Protege, rather than building (or "importing", depending on the Protege version) the
biopax-short-demo-pathway.owl file, will preserve a number of Protege settings that
allow easier viewing of the file.  To load the demo pathway file in this manner both
the biopax-short-demo-pathway.pprj file and the biopax-short-demo.pathway.owl file
must be in the same directory.

Note: This file was created with Protege version 2.1 build 237, OWL plug-in version 1.1
build 135; it may not load properly into other versions.


biopax-example-ecocyc-glycolysis.owl
------------------------------------
This file contains the glycolysis pathway from the EcoCyc database, translated into
BioPAX format.  It is intended to show what a pathway from an existing database
might look like after being translated into BioPAX format.


biopax-example-ecocyc-glycolysis.pprj
-------------------------------------
This is the Protege project file for the EcoCyc glycolysis pathway.  Loading this file
into Protege, rather than building (or "importing", depending on the Protege version) the
biopax-example-ecocyc-glycolysis.owl file, will preserve a number of Protege settings that
allow easier viewing of the file.  To load the EcoCyc glycolysis example file in this
manner both the biopax-example-ecocyc-glycolysis.pprj file and the
biopax-example-ecocyc-glycolysis.owl file must be in the same directory.

Note: This file was created with Protege version 2.1 build 237, OWL plug-in version 1.1
build 135; it may not load properly into other versions.


2. BioPAX Group Contact Info

If you have a question that is not answered in the BioPAX, OWL, or Protege documentation,
please feel free to submit it to the BioPAX-discuss email list (biopax-discuss@biopax.org).
The email list is open to all but you must first join the list in order to post to it.  To
join, go here: http://www.biopax.org/mailman/listinfo/biopax-discuss