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owl-filter is a preprocessor for SPARQL queries. It parses embedded OWL class expressions and replaces them with FILTER(IN(...)) statements containing the URIs of subclasses of the given class expression (or superclasses, equivalent classes, or instances).

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>`
PREFIX ao: <http://purl.obolibrary.org/obo/my-anatomy-ontology/>
PREFIX of: <http://purl.org/phenoscape/owl-filter/syntax#>
SELECT * 
WHERE 
{
?gene expressed_in ?structure .
?structure rdf:type ?structure_class .
?structure_class rdfs:subClassOf "ao:muscle and (ao:part_of some ao:head)"^^of:omn
}

owl-filter can use any OWLAPI-based OWL reasoner to perform its query expansion.