[BioC] annotation data packages in BioC1.9

[Nianhua Li]

Hi,

I would like to briefly summarize the changes of annotation data
packages in release 1.9.
==================
Package Statistics
==================
    genome annotation packages: 8    CDF packages: 301   
    probe data packages: 279    annotation packages: 330   
  Among the above 918 packages, 206 CDF, 206 probe and 206 annotation
packages are provided by Molecular and Behavioral Neuroscience Institute
of University of Michigan.
============
New Packages
============
   Annotation data for codelink chips from GE healthcare, contributed by
Diego Diez
    adme16cod       ADME Rat 16-Assay Bioarray Annotation Data
    h10kcod         CodeLink UniSet Human I Bioarray (~10 000 human
genes) Annotation Data
    h20kcod         CodeLink UniSet Human 20k I Bioarray Annotation Data
    hi16cod         CodeLink Human Inflammation 16 Bioarray Annotation Data
    hwgcod          CodeLink Human Whole Genome Bioarray (~55 000 human
genes) Annotation Data
    m10kcod         CodeLink UniSet Mouse I Bioarray (~10 000 mouse gene
targets) Annotation Data
    m20kcod         CodeLink UniSet Mouse 20k I Bioarray Annotation Data
    mi16cod         CodeLink Mouse Inflammation 16 Bioarray Annotation Data
    mwgcod          CodeLink Mouse Whole Genome Bioarray (~36 000 mouse
gene targets) Annotation Data
    r10kcod         CodeLink UniSet Rat I Bioarray (~10 000 rat gene
targets) Annotation Data
    ri16cod         CodeLink Rat Inflammation 16 Bioarray Annotation Data
    rwgcod          CodeLink Rat Whole Genome Bioarray (~34 000 rat gene
targets) Annotation Data
   Annotation data for chips from RNA/MRC, contributed by Simon de Bernard
    hs25kresogen    RNG_MRC Human Pangenomic 25k Set Annotation Data
(hs25kresogen)
    mm24kresogen    RNG_MRC Mouse Pangenomic 24k Set Annotation Data
(mm24kresogen)
====================
Deprecated  Packages
====================
    prt440acdf and prt440scdf
================================
Major Changes in Annotation Data
================================
    All the LOCUSID environments (e.g. hgu95av2LOCUSID, GOLOCUSID2GO) in
annotation packages are deprecated, and  ENTREZID environments (e.g.
hgu95av2ENTREZID, GOENTREZID2GO) are provided as replacements.
==========================================
Bug Fix and Minor Changes in Annotation Data
==========================================
    ** Fixed data parsing problem in GENENAME environments in annotation
packages.
       (bug report:
http://article.gmane.org/gmane.science.biology.informatics.conductor/10076)
    ** Fixed data parsing problem in MAP environments in annotation
packages. Here is an example:
        > get("40653_at", hgu95av2MAP)
        in older version:
            [1] "1q43|1q23.1 according to Sierra (Genomics 79"
            [2] " 177"
            [3] " 2002) [AFS]"
        now: 
            [1] "1q43"
            [2] "1q23.1 according to Sierra (Genomics 79, 177, 2002) [AFS]"
    ** Update on ath1121501 and ag:
       ** add ENTREZID environment for compatible with GoHyperG
         (bug report:
http://article.gmane.org/gmane.science.biology.informatics.conductor/9715)
       ** add GENENAME environment
         (feature request:
http://article.gmane.org/gmane.science.biology.informatics.conductor/8984
           and
http://article.gmane.org/gmane.science.biology.informatics.conductor/4793)
       ** change data source of PubMed annotation
         (feature request:
http://article.gmane.org/gmane.science.biology.informatics.conductor/7945)
       ** add KEGG pathway annotation to PATH environment, move AraCyc
pathway annotation to ARACYC environment
       ** change source of probe to gene mapping, now use TAIR
       ** add MULTIHIT environment when one probe maps to multiple genes

cheers

nianhua