What is the best way to obtain the GO annotations for a list of Ensembl IDs in batch?

You can do this using QuickGO (www.ebi.ac.uk/QuickGO).
  1. Click on the 'Search and filter GO annotation sets' link, which will take you to a table of all annotations in the GOA database. You now have to filter this set on your gene IDs.
  2. Click on 'Filter' in the top right toolbar, select the 'Gene Product ID' tab and then paste your Ensembl gene IDs into the text box, line separated.
  3. Then click on submit. It takes a while but the result is a table of annotations for your gene IDs. However, they will have been mapped back to UniProt accessions.
  4. To get the annotations with the Ensembl IDs displayed, click on the 'ID mapping' icon in the top right toolbar and select 'Ensembl gene IDs' and submit. The annotations will now be displayed with the Ensembl IDs.
  5. From the top right toolbar you can download the annotations or look at the statistics of the annotation set.