[ensembl-dev] changes to organisation of bacterial collections in EnsemblGenomes

[PATERSON Trevor]

Whilst testing my JEnsembl Java API against the new release 17 of EnsemblGenomes - I noticed that there has been a major reorganisation of the bacterial collections.

Prior to v17, taxonomically-grouped, stably-named collections of species were used: e.g. 'bacillus', 'escherichia_shigella', 'staphylococcus' etc.

These appear to have been replaced with arbitrarily named collections 'bacteria_1' to 'bacteria_24', and the species contained in these collections do not seem to be grouped in an obviously systematic way.

Previously I had been able to use the stably named collections as part of a mechanism to provide continuity between release versions of the data, by creating a single 'Species' Java object belonging to a stably-named collection, with multiple release versions ( e.g. E.coli K12, part of the 'escherichia_shigella' collections with versions 1 through 16).

The new collection layout breaks this pattern with the main consequence being that this complicates access to different release versions for a given bacterial species (as the actual data will lie in an unpredictably named collection database).

I therefore need to re-design how the JEnsembl API configuration can achieve bacterial  species continuity through releases ( or abandon this feature of JEnsembl for bacteria ...)

Could you please provide some details to help me out?


*        Is this change to collection organization finalized?

*        Is the distribution of species to collections arbitrary?

*        Will the distribution of particular species to particular collections change with each release?

*        Will homologies for bacterial genes (proteins) no longer be curated in neither the 'ensembl_compara_bacteria' nor the 'ensembl_compara_pan_homology' databases?


Thanks for any info
Trevor
Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>
Bioinformatics
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

http://bioinformatics.roslin.ed.ac.uk/

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