I'm using the same sparql statement using two different clients but both are not returning the same results. The owl file is in rdf syntax and can be accessed here. This is the sparql statement:

PREFIX wo:<http://purl.org/ontology/wo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> select ?individual where { ?individual rdf:type wo:Class }

I'm using it using top braid and the following python program:

>>> import rdflib
>>> import rdfextras
>>> rdfextras.registerplugins()
>>> g=rdflib.Graph()
>>> g.parse("index.owl")
<Graph identifier=N39ccd52985014f15b2fea90c3ffaedca (<class 'rdflib.graph.Graph'>)>
>>> PREFIX = "PREFIX wo:<http://purl.org/ontology/wo/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
>>> query = "select ?individual where { ?individual rdf:type wo:Class }"
>>> query = PREFIX + query
>>> result_set = g.query(query)
>>> len(result_set)
0

Which is returning 0

This query constructs a graph containing all the triples in which wo:Class is used as a subject, predicate, or object:

PREFIX wo: <http://purl.org/ontology/wo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
construct { ?s ?p ?o } 
where { { ?s ?p wo:Class . bind( wo:Class as ?o ) } union{ ?s wo:Class ?o . bind( wo:Class as ?p ) } union{ wo:Class ?p ?o . bind( wo:Class as ?s ) }
}

I made a local copy of your data and the results I get are (in Turtle):

@prefix vs:    <http://www.w3.org/2003/06/sw-vocab-status/ns#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix wo:    <http://purl.org/ontology/wo/> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .wo:Class  a              owl:Class ;rdfs:comment     "A class is a scientific way to group related organisms together, some examples of classes being jellyfish, reptiles and sea urchins. Classes are big groups and contain within them smaller groupings called orders, families, genera and species."@en ;rdfs:label       "Class"@en ;rdfs:seeAlso     <http://www.bbc.co.uk/nature/class> , <http://en.wikipedia.org/wiki/Class_%28biology%29> ;rdfs:subClassOf  wo:TaxonRank ;vs:term_status   "testing" .wo:class  rdfs:range  wo:Class .

There are no individuals of type wo:Class in your data. The result set ought to be empty.