[Bioc-devel] Bioconductor 3.3 release: annotation summary

[Obenchain, Valerie]

Hi,

This is a heads up about a few changes we've made to the production of
in-house annotations for Bioconductor 3.3.

# Microarray packages:
 
We will propagate but no longer rebuild the ChipDb, probe and cdf
packages. These data have been static for some time. The packages will
continue to be available in future releases as the same version they are
in the current devel branch.


# KEGG.db

KEGG.db will be propagated at the same version and not rebuilt. KEGG
went commercial several years ago and the alternative is the REST
interface in KEGGREST.


# Inparanoid

The Inparanoid packages will be propagated at the same version and not
rebuilt:

http://www.bioconductor.org/packages/release/BiocViews.html#___InparanoidDb

The last data release was 2007. Is there interest in using homologene
(http://www.ncbi.nlm.nih.gov/homologene) as a replacement? Those data
are 'new' as of May 2014.


# db0, OrgDb, PFAM.db and GO.db

Nothing special here, just rebuilt them.


# TxDb

The only track modified since last release was
TxDb.Rnorvegicus.UCSC.rn5.refGene so that was updated. We've added a few
new TxDbs (refGene track) in the interest of supplying compatible cross
coverage of BSgenome, TxDb and OrgDb packages. These are the building
blocks of the OrganismDb packages and we plan to make use of them after
the release.

Bioconductor 3.3 will host compatible BSgenome, TxDb and OrgDb packages
for these organisms:
human: hg38
chimp: panTro4
cow: bostau8
worm: ce11
dog: canFam3
fly: dm6
zebrafish: danRer10
chicken: galGal4
rhesus: rheMac3
mouse: mm10
rat: rn6
yeast: sacCer3
pig: susScr3


# BSgenome, SNPlocs, XSNPlocs

Herve added BSgenome packages for danRer10, taeGut2 and ce11. He also
added these two contributed by Timothée Flutre:

BSgenome.Vvinifera.URGI.IGGP12Xv0
BSgenome.Vvinifera.URGI.IGGP12Xv2


# OrganismDb

We currently host 3 of these for human, mouse and rat. The packages
don't contain data but instead point to GO.db and a compatible
TxDb/OrgDb pair and for this reason don't need to be updated. We plan on
actively developing this family after the release so no new packages of
this type were generated fro Bioconductor 3.3.

This is my first go-round at producing the annotation packages and they
are now in the devel branch. If you see anything strange or inconsistent
please let me know asap so I can fix before the release.

Thanks.
Valerie



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