Hello, I'm developing an Ontology with a large set of individuals too, and i've the same problem.The solution i found is use one tool that transforms the ontology in a relational database and makes the reasoning over this db. I'm actually using the Stardog RDF Database (http://stardog.com).
I dont know if its actually the best solution for this problem (reasoning over ontologies with large ABox), but i hope it helps.Best Regards.PS.: I read about large ABOX reasoning problems in http://eelab.sjtu.edu.cn/jxcg/images/student/41%20Minerva%20A%20Scalable%20OWL%20Ontology%20Storage%20and%20Inference%20System.pdf
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