Method 1   
The simplest way to load an OWL Database project is to load programmatically the project (pprj file), which already contains all database connection information:

Project prj = Project.loadProjectFromFile("/home/pizza_db.pprj",errors);
OWLModel owlModel = (OWLModel) prj.getKnowledgeBase();
...

Method 2
The second method should be used if there is no project file (.pprj) associated with the OWL Database ontology.  

OWLDatabaseKnowledgeBaseFactory factory = new OWLDatabaseKnowledgeBaseFactory();         
Project prj = Project.createNewProject(factory, errors);
OWLDatabaseKnowledgeBaseFactory.setSources(prj.getSources(), "com.mysql.jdbc.Driver", "jdbc:mysql://localhost:3306/protege", "pizza", "user", "password");
prj.createDomainKnowledgeBase(factory, errors, true);

OWLModel owlModel = (OWLModel) prj.getKnowledgeBase();

上面两种方法都需要一个project，难道是protege owl api必须的吗？欢迎讨论。

public class OntoDBUtil {
private OntoDBUtil(){
}
public static OntModelSpec getModelSpec( ModelMaker maker ) {
/*create a spec for the new ont model that will use no inference over models
made by the given maker (which is where we get the persistent models from)*/
OntModelSpec spec = new OntModelSpec( OntModelSpec.OWL_MEM );
spec.setImportModelMaker( maker );
return spec;
}
/* 连接数据库*/
static IDBConnection connectDB(String DB_URL,String DB_USER,String DB_PASSWD,String DB_NAME){
                      return new DBConnection ( DB_URL, DB_USER, DB_PASSWD, DB_NAME);
} /*从文件读取本体并将其存入数据库*/
static OntModel createDBModelFromFile(IDBConnection con,String name,String filePath){
         ModelMaker maker = ModelFactory.createModelRDBMaker(con);
         Model base=maker.createModel(name);
         OntModel newmodel=ModelFactory.createOntologyModel(getModelSpec(maker),base);
         newmodel.read(filePath);
         return newmodel;
}  

/*从数据库中得到已存入本体*/
static OntModel getModelFromDB(IDBConnection con,String name){
         ModelMaker maker = ModelFactory.createModelRDBMaker(con);
         Model base=maker.getModel(name);
         OntModel newmodel=ModelFactory.createOntologyModel(getModelSpec(maker),base);
         return newmodel;
}

}