[BioC] Re: Annotation problem

John Zhang jzhang at jimmy.harvard.edu
Thu Dec 4 15:02:03 MET 2003

>I have a few queries in mind, how is the data accessed, annotated and how is 
>the relationship among the data in bioconductor.This I would to know because at 
>the moment we query databases(locally installed) using SRS API interface.If I 
>can get a clear picture of the working of these aspects of bioconductor then I 
>can see if it is feasible for us to use Bioconductor.
>More specifically if I am right I think I would like to have more information 
>on AnnBuilder and ABPrimer .Can you shed more light on it if I am correct.

For a set of target genes that can be mapped to GenBank accession numbers, 
UniGene ids, IMAGE ids, or Locuslink ids, AnnBuilder processes the source data 
from LocusLink, Unigene, Gene Ontology Consortium, UCSC Genome Bioinformatics, 
and KEGG to obtain annotation elements for the target genes and package the 
annotation data so that they can be accessed in R and used directly by other 
packages. The help page for each set of annotation data contained by a pacakge 
has some simple examples on how to access the data. 

The link "MetaData/Annotation Packages" provides some general information about 
the sources used and the procedures involved to build an annotation data package 
using AnnBuilder. A note published in Bioinformatics (Vol. 19, 2003 155 - 156) 
can be another source of reference except that a database is no longer required 
by the latest version of AnnBuilder.

Let me know if you have more specific questions.


>Looking forward to hear from you.
>Yours Sincerely,
>Sunitha Jonnakuty 
>Ph.D Student 
>Dept of Molecular Biophysics 
>German Cancer Research Center ( DKFZ ) 
>TP3, Im Neuenheimer Feld 580 
>D-69120 Heidelberg, Germany 
>Ph    : ++49 (0)6221 422342 (Office) 
>Fax  : ++49 (0)6221 422333 (Office) 

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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