Download the file, and unzip it into a folder. Check the requirements
Launch the mapping shell using the command:

./pyontomap

Inside the shell, you can try to map a random group of terms from one ontology to another using the command:

mapsome ontoname1 ontoname2

The ontologies must be in the folder ontologies/, and their name must include the extension.
You can map two full ontologies using the command:

mapall ontoname1 ontoname2

You can search the mapping for one term from one ontology to another term in another ontology using the command:

map term@ontoname1 ontoname2

You can check what are the results of the matchers for a pair of terms using the command:

compare term1@ontoname1 term2@ontoname2