I am really tired of working around with these methods. I could only get the immediate super class of the given search string input. even listHierarchyRootClasses() method returns all blank nodes, it is not returning any named classes that I see in protege editor. Like I said, this ontology is an external one, i have no control over this owl file. but it's is very important that my search technique works for external ontologies also (as a test condition). for example the "Neuron" class is up in the hierarchy. my search term "Gamma_motor_neuron" is mapped exactly to the "Gamma_motor_neuron" ( a trivial case where search string is an exact match with the ontology term). But my validation routine wants to make sure that the mapped ontology class "Gamma_motor_neuron" is indeed a subclass of "Neuron". But I could only retrieve Superclasses only upto the immediate parent node "spinal_motor_neuron". But in the actual scenario the list should go in this fashion: "Gamma_motor_neuron" is_a "spinal_motor_neuron" is_a "motor_neuron" is_a "neuron".

However, the same routine works for my own ontology. I could retrieve the top level nodes and satisfy my validation criteria.

OntClass tmpcls = cls; while(!suprcls.equalsIgnoreCase("Axonal_terminal")&&!suprcls.equalsIgnoreCase("Interneuron")&&!suprcls.equalsIgnoreCase("Principal_cell")&&!suprcls.equalsIgnoreCase("Neuron")){
            tmpcls=tmpcls.getSuperClass();
            out.println(tmpcls);
            suprcls=tmpcls.getLocalName();
            out.println(suprcls);
}

so this is a clear example of problems for trying to create a integrative approach. Ironically, the gist of ontologies is to share the domains. I want to achieve this by hook or crook

On a different note. On my other post, the stupidity that I am talking about is, the way i am trying to map with the ontology terms with a string matching like below. this obviously is not going to be a solution. there are definitely more valid terms than these four.

while(!suprcls.equalsIgnoreCase("Axonal_terminal")&&!suprcls.equalsIgnoreCase("Interneuron")&&!suprcls.equalsIgnoreCase("Principal_cell")&&!suprcls.equalsIgnoreCase("Neuron")){

-Thanks
Sri