Queries to Pharmacoracle can be are performed in the Manchester syntax. In order to do queries we need to know the names of the elements in the OWL ontologies. In addition we need expressions of cardinality that are used to connect OWL Properties and OWL Classes{| class="wikitable"|-! Cardinality word !! Cardinality !! Explanation|-| some || || Connects a property to at least one class |-| exactly || number || Connects a property to an exact number of classes|-| min || number || Connects a property to a minimum number of classes|}  For each query we add a code word to indicate the relationship between our query and the desired answer (cf. the DL Query tab in the desktop version of Stanford's Protégé)

| SubClasses || Get elements that contain the query (but not equivalentto the query)