Bio4j Thanksgiving treats!

Hi all!

Thanksgiving is almost here and we got just in time a lot of special treats for you:

New github organization

All bio4j related repositories are now under the organization bio4j in github.

New wiki(s)

The old wiki hosted at has been moved to the corresponding Bio4j repository wiki. More information has been added as well as structuring the previous data. Besides that, new wikis are being created for each bio4j related tools repositories.

NCBI taxonomy

We’re happy to announce the official incorporation of NCBI taxonomy data into Bio4j DB, as well as an index for retrieving NCBI taxons from gene identifiers (GI); so there’s no need anymore to parse that huge gi_taxid_nucl NCBI table in order to achieve that. There’re no changes made to Uniprot taxonomy but you can now navigate to the equivalent NCBI taxon using the relationship NCBITaxonRel.

Reactome terms

We’ve included Reactome terms references included in Uniprot files, so from now on you can retrieve both all terms associated to a specific protein as well as all proteins associated to an specific term.

New EBS snapshot for this release

For those using AWS (or willing to…) there’s a new public EBS snapshot containing the last version of Bio4j DB. The snapshot details are the following:

  • Snapshot id: snap-aa5cd3c2
  • Snapshot region: EU West (Ireland)
  • Snapshot size: 100 GB

Bio4j DB is under the folder bio4jdb. In order to use it, just create a Bio4jManager instance and start navigating the graph!

UP 2011 Bio4j presentation

We’re really pleased to announce our presence in this year’s UP 2011 Cloud Computing Conference. The presentation will be held on day 4 Thursday, December 8 2011. Check the agenda for the conference here.


and happy Thanksgiving! ;)