code: public Model convertFromOWL(InputStream in)
  	{
  		init(in);
  
  		//cache the namespaces.
  		namespaces = this.readNameSpaces();
  
  		autodetectBiopaxLevel(); // this may update level, editorMap and factory!
  
  		Model model = factory.createModel();
  
  		model.getNameSpacePrefixMap().putAll(namespaces);
  
  		model.setXmlBase(base);
  
  		boolean fixingPEPS = model.getLevel() == BioPAXLevel.L2 && this.isFixReusedPEPs();
  		if (fixingPEPS)
  		{
  			reusedPEPHelper = new ReusedPEPHelper(model);
  		}
  
  		createAndBind(model);
  
  		if (fixingPEPS)
  		{
  			this.getReusedPEPHelper().copyPEPFields();
  		}
  		
  		reset(in);
  
  		return model;
  	}
docs: Reads a BioPAX model from an OWL file input stream (<em>in</em>) and converts it to a model.
  @param in inputStream from which the model will be read
  @return an empty model in case of invalid input.