Please make sure that the file explicitly asserts all rdfs:subClassOf triples. 
When you open files in TBC, the system will add "trivial" inferences to make 
sure that each named class has at least one named superclass. These are then 
inferred triples, which would not be available by default if your file is 
loaded through SPARQLMotion. Also, you may want to import the system triples to 
get the same environment like in TBC.

In your query below I don't understand the use of ?arg2. Furthermore, the use 
of the rather ugly (legacy) function smf:countResults could be replaced with a 
SPIN function such as spl:objectCount.

Regards,
Holger


On Dec 18, 2009, at 2:31 PM, TKC wrote:

>   I have written a SparqlMotion script that imports an ontology, say
> "Main," using the "Import RDF From Workspace" module. (Now, "Main,"
> itself, imports several sub-ontologies.) Following this module, I have
> a Sparql query that attempts to retrieve all subclasses of
> "owl:Thing"--from "Main" and from all ontologies that "Main" imports.
> Why am I getting only a partial listing of subclasses?
> 
>   The query I run after the import looks like this:
> 
> SELECT ?subject ?subClasses
> WHERE {
>    ?subject rdfs:subClassOf ?object .
>    LET (?object := smf:buildURI("{?arg2}")) .
>    LET (?subClasses := smf:countResults("SELECT * WHERE {?x
> rdfs:subClassOf ?subject}")) .
> }
> 
> My SparqlMotion script is intended to be a Web service behind a Flex
> tree that shows classes and their parentage within a federated
> ontology. Rather than build an entire ontology into the tree, I want
> to lessen the load on the client by only fetching sublcasses when a
> user clicks to expand a node.
> 
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