I use RAP api for PHP to query my knowledge (RDF, OWL and etc.) but I cannot find the way to apply SWRL that I designed on Protege. Somebody suggests me to use Jena.
In my opinion the easiest way is to use the OWL-API with Java. It is easy to integrate the Pellet or the Hermit reasoner which then does exactly what you want. But, of course, Java != PHP. In this case I would provide a Java Webservice which handles my PHP requests. Afaik it is very tricky to handle SWRL with Jena, because you need additionally the JESS rule engine (http://herzberg.ca.sandia.gov/jess/).
I use owl-api to perform the SWRL rules and use JavaFX for working with web pages in Java Applications.
http://docs.oracle.com/javafx/2/webview/jfxpub-webview.htm
In the near past I've used Jena to integrate a set of SWRL rules (pre-authored in Protege 3.4.4) for artificial intelligent and automated reasoning mechanisms. The programming language was -once more- Java and the only prerequisite was to include the Pellet reasoner. Both Apahe Framework and Pellet (now on GitHub) have extensive tutorials and examples, so give it a try instead of using PHP which has limited, or not at all, support in Semantic Web area...
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