Bio4j 0.8 is here!

Hi everyone!

I’m glad to announce the release of Bio4j 0.8 including more than 5.488.000 new proteins and 3.233.000 genes among others, plus the following improvements and features:

Pfam families

Bio4j includes now all Pfam families included in Uniprot KB (both Swiss-Prot and TrEMBL). For that, both a new node type and relationship type have been created:

  • PfamNode

  • ProteinPfamRel (this relationship connects a protein and the respective Pfam families associated to it)

The following properties have been added to the Pfam node including:

  • ID
  • Name

Besides, an exact index for the Pfam family ID property has also been created ( pfam_id_index ).

NCBI taxonomy tree GI index improved

Old merged node IDs have been incorporated to the Gene Identifier <–> Taxonomy units index. That means that now all the pairs GI-TaxID which included old merged Tax-ID are also part of the index, resulting on a higher rate of hits when using the index. For that we used the file meged.dmp provided in the official tax dump file provided by the NCBI.

Bio4j and Bio4jModel projects unification

Bio4j project has absorbed Bio4jModel project from this release on.

Until now, Bio4jModel library included the core classes for the manipulation and traversal of the graph while Bio4j project only included the importing programs. I’ve been thinking for a while that this could be confusing and, since there was no real need to keep them as independent projects, I decided to put it all under Bio4j (you just need one jar file now ;) ).

New script for the importing process

You don’t have to worry anymore about manually downloading/decompressing/etc… the sources for the DB in case you want to import Bio4j in your own cluster/machine. Just run the script and it will do it all for you.

Bug fixes

  1. MetalIonBindingSiteFeature This feature relationship had an erroneous name assigned and it’s been fixed.

Well, that’s all for now, I’ll be posting more information about this new release soon ;)