I've been using DAVID for gene ontology IDs for years but this -> https://www.biostars.org/p/245/ says it hasn't been updated in like 6 years.  Is there anything else that's useful and up-to-date?  I usually use Uniprot, KEGG, and GO IDs for everything.  http://geneontology.org/ wants me to input a species but the species I deal with aren't really model organisms.  I have a lot of random microbes. 

**What can I use instead of DAVID? Preferably accessible through Python or web interface**.  If there is some REALLY good that's for R I'm open but that's a last resort for me (It takes me a while to do anything in R). 
The Gene Ontology consortium has created their own enrichment tool through AmiGO 2 http://amigo.geneontology.org/amigo (and/or with Panther http://pantherdb.org/webservices/go/overrep.jsp). This will be *the* most up-to-date tool you can use.

Intermine provides up-to-date enrichment tools (web interfaces or accessible by API) for a lot of species here: http://intermine.org/ 
Choose the closest species mine if you can, it doesn't need to be a perfect match - especially for GO which is species-neutral; though some of the other functions they index can (or should) be species-aware. For microbes, YeastMine/Saccharomyces cerevisiae database might be the best? InterMine/MODs get updated GO annotations as they come out, or very soon after (~ up to 3 month delay depending on production cycles).



