ProtegeTips

To load the humancyc biopax.owl file into protege 3.1, on Mac OS X, without having it run out of memory, edit the file /Applications/Protege_3.1/Protege.app/Contents/Info.plist. Change the lines reading VMOptions -Xms9M -Xmx95M

to

VMOptions -Xms250 -Xmx512

This causes protege to launch with a minimum of 250M of memory, and a maximum of 512M, which is adequate to load the file.

To read in a biopax owl file in Protege 3.1: If you are starting up Protege, then choose "Create New Project...". From the list, choose OWL files. Check off the box at the top that says "Create from Existing Sources". Click next. Enter the name of the file in the text box, or click the icon in the top left corner (box with little plus sign) to get a file system browser and then choose the file. Click next. Select language profile "OWL DL", then click the finish button.

If you are already in the application, from the menu choose "File" "New Project" and follow the above steps.

If you are running under Mac OS X, you might want to choose, from the menu, Window->Look and Feel->Mac OS X Aqua, which will e.g. put the menu bar where you are used to seeing it (in the menu bar, rather than in the document window).

bader notes: BTW, Mike pointed out to me today that Protege has a feature that automatically makes the instance to class conversion as I showed. When viewing instances under the individuals tab, right-click on an instance and select "Convert individual to class"

However this isn't necessarily available in all protege projects. It appears to be available for an owl project, but when I tried it on the project Imre created the menu isn't offered.

Ugh. If you try to convert Imre's project to an OWL project you get inconsistent behavior depending on what you do. You can export to format OWL using File > Export to Format, and then create a new project from the owl file. You can convert the project to OWL using File > Convert Project To Format..., which modified the project and also creates an OWL file. You can create a new project from the OWL file of the previous step. In all cases the instance view looks different from the original - you no longer see the slots of the instances, e.g. Stoichiometry of the participant. You can only get the create class from individual menu when you create a new project from an OWL file (not from the in place converted to OWL project). If you do create a class from an individual then you once again see the slots.

Creating an class from an individual does not create recursive restrictions on the values of the slots. Rather it creates a hasValue restriction on the class, creating a copy of the (recursively expanded) value of the slot on the individual.