At the time of writing, Pathway Commons integrates seven pathway and interaction databases. Information on network neighbours of any given entity can be accessed as a BioPAX document, written in OWL-DL. As such, no additional syntactic ontology needs to be created: the populated BioPAX ontology returned from nearest neighbour query is the syntactic ontology. A portion of the BioPAX ontology is shown in Figure 5. The BioPAX document used in this work is available for download with this supplementary material.
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Pathway Commons provides binary interaction data without also providing the direction of the reaction. BioPAX can store information about which species are reactants, products or modifiers, but the data coming from Pathway Commons does not provide this information.