Figure 3

Example of a visual query. The pattern shown represents the query:

“All the elements of type protein whose name contains the string “P53” that are part of an interaction taking place in the nucleoplasm region”.

This pattern was generated while browsing the Homo sapiens Reactome export in Pathway Commons, by declaring as variable two of the elements. It presents several elements describing the structure of a pathway: these are from the BioPAX ontology (blue in the figure). The object of the CELLULAR-LOCATION property is a term defined in Reactome (in purple). Results of this query on the Reactome Homo sapiens ontology are presented in Table 1. This query can be used both to map its results to an existing Cytoscape network, or to generate a new network from all possible occurrences of the relative pattern in the ontology.