[ensembl-dev] Clinical/LSDB SNPs

[Pontus Larsson]

Hi Chris,

It's not entirely clear to me exactly what kind of annotations you're after
but for human, we have grouped these variations together into a variation
set called 'Clinical/LSDB variations from dbSNP' and you can retrieve these
via the VariationSet module. You can for example get phenotype annotation
data when available for these variations via the VariationAnnotation module.
I've included a short sample script below:

use Bio::EnsEMBL::Registry;

my $reg = "Bio::EnsEMBL::Registry";
$reg->load_registry_from_db("ensembldb.ensembl.org", 5306, "anonymous");

# Get a VariationSetAdaptor and the LSDB set
my $vsa = $reg->get_adaptor("human","variation","variationset");
my $vs = $vsa->fetch_by_name("Clinical/LSDB variations from dbSNP");

# Get a VariationAnnotationAdaptor
my $vaa = $reg->get_adaptor("human","variation","variationannotation");

# Get an iterator for the variations in this set
my $it = $vs->get_Variation_Iterator();

# Iterate over the variations and get annotations if available
my $v;
my $vas;
my $count = 0;
while ($it->has_next()) {
  $v = $it->next();
  $vas = $vaa->fetch_all_by_Variation($v);
  print $v->name() . " has " . (scalar(@{$vas}) ? "" : "no ") . "phenotype
annotations\n";
  foreach my $va (@{$vas}) {
    print "\t" .
join("\t",($va->source_name(),$va->phenotype_description())) . "\n";
  }
  $count++;
  last if ($count > 100);
}

Hope this helps
/Pontus





2011/3/2 <cj5 at sanger.ac.uk>

> Hi,
> Could anybody please advise how the Variations API might be use to
> retrieve the Clinical/LSDB Submissions annotation for a SNP, as available
> on the dbSNP website?
> Thanks
> Chris
>
>
>
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> http://lists.ensembl.org/mailman/listinfo/dev
>
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