What you are asking for simply is still in development or has not started yet. Please see https://www.wikidata.org/wiki/Wikidata:Development_plan for the development plan. Also CC yourself to https://bugzilla.wikimedia.org/show_bug.cgi?id=52385 and https://bugzilla.wikimedia.org/show_bug.cgi?id=65626 if you want to be kept up-to-date on those specific features.
I've added myself to the CC list for both of those bugs.
I just need to be able to do something like:
SELECT `qid` FROM Wikibase WHERE `Instance Of` = 'Elephant';
Using that list and the Wikibase API, I can do processing on my own of the returned data and take it from there.
That is not possible until simple query functionality is finished.
I knew complex queries were not done yet, but I though simple might be. Its of no worry though. I can run a nightly job to iterate through all of the items to build an index of them that is good enough for what I need.
Though, that does take some of the excitement out of it, even still I think Wikibase would be better than the sort of adhoc system we have now.
If I can figure out how to get everything installed and running, I'd be more than happy to write up a how-to so that other third party reusers will have an easier time in the future.
http://wikiba.se and https://www.mediawiki.org/wiki/Wikibase is what we have. We're in the process of cleaning those up.
Awesome. Thank you for your help. If I run into any problems I'll ask here.
Thank you, Derric Atzrott