[Bioperl-l] ER proteins

[Chris Mungall]

GO also has a fledgling perl API for accessing the GO database or
flatfiles, which bioperlers may be interested in.

GO is a directed acyclic graph with nodes connected by "isa-a" or
"part-of" arcs so it's not just a case of searching for
terms that match ER (GO:0005783).

using the perl modules it's possible to do a query like this:

$apph = GO::AppHandle(-dbname=>"go", -dbhost=>"spitz.lbl.gov");
$assocs = $apph->get_associations({name=>"endoplasmic reticulum"},
                                  {evcodes=>["TAS", "IDA"]});
foreach my $assoc (@$assocs) {
  printf 
    "Gene: %s evidence for association: %s %s",
     $assoc->gene_product->symbol,  
     $assoc->evidence->code(),
     $assoc->evidence->xref->xref_key();
}

this fetches all genes associated with the ER and it's descendants, for
which there is pretty good evidence for location in the ER (TAS =
traceable author statement, IDA=inferred from direct assay)

see
http://www.fruitfly.org/annot/go/database/modules/GO::AppHandle.html
for the API

one thing that would be useful for GO would be a locuslink parser / index
in bioperl, in order to query the human GO associations in genbank.
currently we just have model-organism-database sanctioned associations for
SGD/MGI/Flybase in there right now.

On Fri, 9 Mar 2001, Aaron J Mackey wrote:

> 
> The Gene Ontology consortium has this kind of information:
> 
> www.geneontology.org
> 
> -Aaron
> 
> On Fri, 9 Mar 2001, Xinghua Lu wrote:
> 
> > Dear All,
> >
> > I am wondering if anyone on this mailing list knows a proteome database that I can retrieve all proteins reside in endoplasmic reticulum (ER) or other cellular compartment.  If there is such a database, I would like to develop a module to retrieve the information.  Thanks in advance.
> >
> > Best,
> > Xinghua Lu
> >
> 
> -- 
>  o ~   ~   ~   ~   ~   ~  o
> / Aaron J Mackey           \
> \  Dr. Pearson Laboratory  /
>  \ University of Virginia  \
>  /  (804) 924-2821          \
>  \  amackey@virginia.edu    /
>   o ~   ~   ~   ~   ~   ~  o
> 
> 
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