Hi Protege, can multiple ontologies be handled? That is;
1) Can I load two ontologies A and B and have one ontology with duplicates merged/removed?
I’m not sure I fully understand the question. By duplicates do you mean entities that have the same name, but a different (full) IRI? Two (or more) ontologies can be loaded in the same Protege workspace window. Note that OWL has an imports mechanism that you can use to create dependencies between ontologies.
Can I run reasoners on a limit subset of an ontology?
2) Say I have a list of classes, individuals, object properties, data properties can I run the reasoner considering only the part of the ontology on the list?
This would certainly be nice. Currently, in Protege, you’d have to extract that subset as an ontology and reason over that. Since you seem interested in preserving entailments over the input list of entities, I would recommend logic-based modules. See http://owl.cs.manchester.ac.uk/research/modularity/ for further information on this type of modularity, and pointers to module extractors as well as OWL API support.
Chainsaw could do what you require (if it doesn’t already), seeing as it decomposes input ontologies and as a result it practically has modules ready to be served for any given set of entities.
3) Can I then load a second list and run on that subset?
Same as above. You could build a reasoner wrapper that takes a selection of entities, computes one or more modules for one or more input lists, and dispatches to a reasoner of choice, or even multiple reasoners…