[ensembl-dev] Regarding annotation to genes

Will McLaren wm2 at ebi.ac.uk
Wed Aug 17 14:37:41 BST 2011


Hello Gaurav,

On 17 August 2011 11:31, gaurav thareja <gaurav4thareja at gmail.com> wrote:
> Hi,
>
> I am querying ensembl genome browser for human with search term "drug
> response + diabetes". I am getting 10 genes as hits.
>
> 1) What is the source of this information?

Most of the evidence will be from MIM annotations attached to the
genes themselves; you can see an example of this for the first hit in
your search here:

http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000106331;r=7:127250346-127255982

> 2) How can i get the source of this information using Perl API ?(As in case
> of variation database, we can use variationannotation)

Something like the following code would work:

my $ga = $reg->get_adaptor("human","core","gene");
my $g = $ga->fetch_by_stable_id("ENSG00000106331");

foreach my $dbentry(grep {$_->dbname =~ /mim/i} @{$g->get_all_DBEntries}) {
  # do stuff
}

See http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBEntry.html
for detail on DBEntry objects

> 3) How can I get all variations associated with a single gene using Perl
> API?

We don't yet have a call in the Variation API to do this. This is
tricky, since the variation associations we have come from external
databases, and hence the associated genes are provided by external
sources and do not correspond reliably to Ensembl genes.

We will take a look at doing something like this if there is a demand
for doing so.

Thanks

Will McLaren
Ensembl Variation

>
> Regards
>
> Gaurav Thareja
>
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