Preparation
-----------

Install Protege (4.2, but 4.1 may be fine)

  http://protege.stanford.edu

Install Elk (0.3 or higher)

  http://code.google.com/p/elk-reasoner/downloads/list

Install lego plugin

  http://code.google.com/p/owltools/downloads/list

  (note: if you are updating you need to remove the old one)

In Protege menu, select:

  Views/Ontology Views/Lego annotations

  (I place this in my Individuals tab)

OR

  Tabs/Lego annotations

place this where you like. I have it 

Getting started
---------------

  cd examples/
  cp template-worm.owl my-pathway-named.owl

open my-pathway-named.owl in Protege4

You will be spending most of your time in the "Individuals tab"

General tip: work backwards. If you create the node at the end of the
arrow it will "be there waiting for you" when you create the source
node. Ultimately it's up to you.

Click the "+<>" in the top left. Give the activity a name. Make it the
same as in the pathway diagram in the paper, but add
"activity". E.g. "unc-1 activity". If the same gp type has multiple
roles, individuate it. But ultimately these labels are just for you to
help organize.

Under "Types" add (+):

* An MF
* A class expression "enabled_by some <gp>"
* A class expression "occurs_in some <Loc>"

Under "property assertions" add:

* {directly,indirectly}_activates <activity>
* part_of <process>

You might want to make the process individual first