Pellet + OWLAPI + SWRL

I've found over the last couple of months that there are a LOT of different ways to mess up when trying to use SWRL, Pellet, and OWLAPI. I'll try to list everything I can remember getting stuck on or potentially getting stuck on. Feel free to add your own by comment.

Java Heap Overflow errors:

1. remember that you can add more memory to java in Eclipse for a single project by going to Run -> Open Run Dialog -> Arguments and then adding -Xmx1024M to your VM Arguments (or some other value instead of 1024).
   
   
2. A great solution is to break your data into separated named graphs where you know the information will not be important between the graphs. For me, this fixed everything (especially in FaCT++ where it fixed speed issues as well). I had data about patients that I knew were not the same patient, and I reason about each patient one at a time.
   
   
3. Still not enough? I'm not sure what to say yet, but I have some extremely unthought out guesses: try KAON2 because I heard it scales better (but might only scale for speed), try a database backend with an rdf to sql mapper (such as D2R Server), and try OWL-Lite (if expressive enough for you). None of these guesses might do anything to fix your problem, but they are what I'm going to try next if I hit this problem. Please tell me if these options would or wouldn't help.
   
   
4. If you're using SWRL rules, try the Rete algorithm (if using a version of Pellet pre-1.5.2). Turn Rete algorithm on by writing this line: PelletOptions.USE_CONTINUOUS_RULES = true;
   I've heard there are some specific cases where this algorithm is slower, but it usually isn't.
   
   
5. This probably won't happen to you because you are smarter than me. But make sure when you are trying to write "facts" between individuals you don't refer to classes. Write it like this:
   axioms.add( factory.getOWLObjectPropertyAssertionAxiom( personInd, hasWeightOP, weightInd ) );
   
   and not like this:
   OWLObjectValueRestriction hasWeightTheWeight = factory.getOWLObjectValueRestriction( hasWeightOP, weightInd );
   axioms.add( factory.getOWLClassAssertionAxiom( personInd, hasWeightTheWeight ) );

SWRL rules just won't work:

1. Is your SWRL rule Safe? I saw a few different definitions of "SWRL rule safety" but the one that seems to be right is: Make sure all individuals that are involved are explicitly added! For example, if you have a rule like this:
   Person(?x) ^ drives(?x,?y) ^ Car(?y) -> Driver(?x)
   and you have an instance of person which is also an instance of "drives some Car", but you don't have an the instance of Car that he drives explicitly added, the rule will not return the person instance as a driver instance. For more check this part of the ProtegeWiki: SWRLLanguageFAQ.
   
   
2. Simplify rules as much as possible. Don't use negation (NOT) and don't use disjunction (OR). I've never had a problem with this, or even tried it, but I seem to remember people having problems with this... somewhere.

Reasoning takes too long!

1. I'm still working on this... but reducing expressivity can't hurt. It sounds like OWL-Lite would make a huge difference for speed, but you have to sacrifice so much that personally, it doesn't seem like it's ever worth it unless you want structured tags and don't care about answering queries.
2. Try FaCT++. It was orders of magnitude faster when I used iterative reasoning as explained above.