[BioC] o

[John Zhang]

You probably need to parse two files to get the mappings you want. One of the 
file (ftp://ftp.ncbi.nih.gov/refseq/locuslink/LL_tmpl.gz) from LocusLink 
contains mappings from GenBank Accession numbers to GO ids. Another is the file 
from GO (ftp://ftp.geneontology.org/pub/go/xml/go_200211_termdb.xml.gz) that 
contains GO terminologies. 

I would suggest that you create a ";" separated text file with one column for 
GenBank names and another for GenBank Accession Numbers. Then, write a segment 
of Perl script and parse LL_tmpl.gz using AnnBuilder (following the examples in 
the vignette - Basic functions of AnnBuilder). That will give you the mappings 
from GenBank names to GO ids. AnnBuilder already have a parser (GOMXLParser) to 
parser the GO file (Code examples in the vignette - Source specific functions of 
AnnBuilder). What you need to do then is just to map the GO ids to GO terms. 


>To: bioconductor@stat.math.ethz.ch
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>Date: Thu, 19 Dec 2002 09:38:13 +0100
>
>Hello!
>I don't know how
>to associate  ontology  to a long list of GeneBank Name (a txt-tab file or
>an XML file given
>by cDNA Agilent Scanner& Sw), i.e.
>I would as output a formatted file with 4 columns (1:GeneBank Name
>2,3,4:ontology).
>I know that I have to perform a mapping of genes, I got  a  look on
>AnnBuilder pkg and annotate pkg,
>but I 've not idea from where to start.
>Some suggestion? Thanks in advance!
>
>A. S.
>
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