This release fixes a bug in parsing NCBITaxonomy data. The current distributions don't have information about taxonomic (scientific-) names.
Here are the changes in the NCBITaxonomy schema:

• Removed scientificName property; writing real scientific name to the name property instead (it was always empty before)
• Removed comment property; it wasn't used anywhere

See the full list of the closed issues in this release (since v0.11) in the v0.12 milestone.

This is the third release candidate for 0.12, which is going to be the base for 1.0.

• the only change is in the dependency on the bioinfo-utils. It got upgraded to v1.5.0, see the link for more details.

This is the second release candidate for 0.12, which is going to be the base for 1.0. We are in the process of testing a first full data import with this code and the corresponding one in bio4j/bio4j-titan. Everyone should update to this release from 0.12.0-RC1.

Fixes

UniRef related:

• #84 a bug in the UniRef import (the cluster type was checked erroneously)
• #90 id in ImportUniRef logs was wrong
• #88 more null safety in ImportUniRef
• #97 The representant accession of the cluster was not included in the members array property

UniProt:

• #98 proteinGeneName was missing from Protein

We also improved documentation a bit, preparing for what would be done before 1.0. Another mostly cosmetic change is moving from tabs to spaces, as (among other things) the code displays awfully in github.

This is the first release candidate for 0.12, which is going to be the base for 1.0. We are in the process of having a first full data import with this code and the corresponding one in bio4j/bio4j-titan.

This is a first milestone for 0.12.0. In terms of code, it should be pretty close to the final 0.12.0 version; only docs and similar stuff is left. We will have proper release notes for the stable version, for now take a look at

• bio4j 0.12.0 milestone

• Changed package to com.bio4j instead of com.ohnosequences.bio4j;
• Change the name of the abstract node and rel types, move them to the root model package;
• Removed unrelated class CommonData;
• Some general refactoring;

• All obsolete code was removed
• Only the abstract model is left

This release (0.8) has been created from the sources:

• Uniprot KB (both Swiss-prot and Trembl)
• Uniref (50,90,100)
• Gene Ontology termdb full ontology OBO/xml file
• Uniprot isoform sequences fasta file
• RefSeq complete release
• NCBI taxonomy (files nodes.dmp and names.dmp)
• Gene identifier (GI) <--> NCBI taxonomy ID file (gi_taxid_nucl.dmp)
• Enzyme Expasy DB

For this version all sources were downloaded on the date: 09-20-2012
This version was built with Neo4j 1.7 GA

Total size for this release: 105 GB

Here is the list including the snapshot IDs for the different regions:

• eu-west1- --> snap-656efd33

This release (0.7) has been created from the sources:

• Uniprot KB (both Swiss-prot and Trembl)
• Uniref (50,90,100)
• Gene Ontology termdb full ontology OBO/xml file
• Uniprot isoform sequences fasta file
• RefSeq complete release
• NCBI taxonomy (files nodes.dmp and names.dmp)
• Gene identifier (GI) <--> NCBI taxonomy ID file (gi_taxid_nucl.dmp)
• Enzyme Expasy DB

For this version all sources were downloaded on the date: 18-12-2011

Total size for this release: 90 GB

Here is the list including the snapshot IDs for the different regions:

1. eu-west1- --> snap-ca1568a2
2. us-east-1 --> snap-d4a502b0
3. us-west-1 --> snap-5dbe443e
4. us-west-2 --> snap-b6bf0cde
5. ap-southeast-1 --> ------
6. ap-northeast-1 --> snap-f3653399
7. sa-east-1 --> snap-4fc81827