[BioC] Re: MetaData 1.6.0

John Zhang jzhang at jimmy.harvard.edu
Fri May 21 17:45:11 CEST 2004

Hi, all,

The developmental version of annotation packages (1.6.0) is now available and 
can be accessed by doing (using hgu95av2 as an example):

> library(reposTools)
> install.packages2("hgu95av2", develOK = TRUE)  

The following changes/additions have been made:

     a. Environments pkgNameNM and pkgNameNP (e. g. hgu95av2NM) no
        longer exist in the platform specific packages
        (e. g. hgu95av2) but are replaced by a new environment
        pkgNameREFSEQ that contains the annotation data for all the
        RefSeq accession records. 
        The environment pkgNameHGID has been droped. Mappings between 
        probe ids to HGID can be obtained through the mappings to LocusLink ids  
        to HGIDs in the homology data package.  

     b. GO package contains new environments ANCESTOR and OFFSPRING
        that maps GO ids to all the ancestor and offspring along the
        GO tree. GOTERM no longer exists and is replaced by GOTERMS
        that maps GO ids to GOTerms objects with a GOId, Ontology
        (originally in GOTERM), Synonym, Secondary, Definition, and 
        Category slots.

     c. homology package now maps internal HomoloGeneIds to homoData
        objects that has slots for organism name, LocusLink ids, 
        internal HomoloGeneIds, GenBack Accession numbers, type of
        similarities, percent of identity, and urls for homologous 
        genes in other organism. Environment LL2HGID maps LocusLink
        ids to internal HomoloGeneIds.

     d. New annotation data packages for non-Affymetrix chips have
        been added. These packages include hguMWG30kA, hguMWG30kB,
        mguAtlas5k mguG4104A, mguG4120A, mguG4121A, mguMWG30kA,
        mguMWG30kB, rguAtlas5k, rguG4105A, rguG4130A, rguMWG10k,
        rguMWG5k. Pakckages with Atlas as part of the names are for BD
        Biosciences microarrays, MWG for MWGAG BIOTECH microarrays, and G
        for Agilent microarrays.
Due to the changes in data structure and contents,  some environments of the 
data packages in 1.6.0 may not be compatible with the libraries in Bioconductor 
release 1.4.0.  

Comments/bug reports are welcome.



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