downloads

Questions and answers about downloads: what they are and where to get them.

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.

How do I access older versions of gene association files?

Here are several options:
  1. old database dumps, requires knowledge of schema and SQL for retrieving info, need to be able to restore the whole db
  2. http://archive.geneontology.org/full/
  3. CVS attic for individual gene_association files
  4. http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/A...
  5. cvs repository for individual gene_association files
  6. For example, SGD file history goes back to 2004

How do I find all annotations for species X that I can't find in AmiGO?

  1. Open the QuickGO web-page http://www.ebi.ac.uk/QuickGO/
  2. Click on the Search and Filter GO annotation sets link located beneath the search box
  3. This will lead you to an Annotation download page where you can click the filter icon (Located to the right hand side of the page)

What is the difference between the filtered and unfiltered versions of the GOA UniProt gene associations files?

The filtered version available on the GO Download's site (gene_association.goa_uniprot_noiea ) does not contain annotations for those species where a different Consortium group is primarily responsible

What is the best way to obtain the GO annotations for a list of UniProt Accession Numbers in batch?

With UniProt accession numbers, you can obtain all GO annotations by parsing a GOA gene association file, which are provided in a simple tab-delimited format. These files are available from the GOA FTP site.