Hello,

I have a question about the use of hibernate queries for a database intensive bioinformatics application. I am completely new to hibernate, so bear with me (I did look through the hibernate docs, though, and didn't see an answer to my question).

I am facing a situation in which I have to query for several thousand genes from a database of (potentially) several million records. Each gene will have a unique identifier that I can use as a selection criterion, but the sets of genes will change from case to case, and in each case I will have to specify all ~1000-10000 of them.

For example, let’s say for simplicity sake that the gene ID’s are numbers from 1 to 10000. In a real world situation, the numbers would not be continuously incremental like this, so I can’t just select for ID’s that are >0 and <=10000. The sql query might look like:

SELECT Annotation.Value FROM AnnotationTable WHERE Gene.ID IN (1,2,3,4,5 …. 9999, 10000);

Is there a way of performing this kind of query using hibernate objects such that it returns the query results in a reasonable amount of time?

Thanks,

Chris Kingsley
UCSF Cancer Center

For queries like this, where no mapped objects have to be created, then yes, Hibernate is just as fast as using plain old jdbc, and the java code would be much simpler than anything jdbc would let you get away with:

Mapping file:
Java code:This will return a List<String> (assuming that value is a String property).