bio4j v0.12.0

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.

bio4j v0.12.0-RC3

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.

bio4j v0.12.0-RC2

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.

bio4j v0.12.0-RC1

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.

bio4j v0.12.0-M1

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

bio4j v0.11.0

• 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;

bio4j/bio4j v0.10.0

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

bio4j/bio4j v0.8.0

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

bio4j/bio4j v0.7.0

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