[ensembl-dev] Mouse phenotypes in ensembl API

[Nathalie Conte]

Hi Anja, I have successfully retrieved phenotypes with fetch_all_by _gene method.
I am retrieving so far data from MGP with KO gene - is there any other data sources for mouse phenotypes, what about variation phenotypes ?

script
my $pfs = $pf_adaptor->fetch_all_by_Gene($gene);
if ( scalar(@$pfs)== 0 ){print "no PHE\n";}else{
foreach my $pm(@{$pfs}){ if ($pm){
print "\t", $pm->allele_symbol,"\t",$pm->source,"\t",$pm->phenotype->description, "\n";
}else {next;} 

Thanks
N

On 23 Jul 2014, at 16:52, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hello Nathalie,
> 
> we have only genes associated with phenotypes for mouse. You need to use fetch_all_by_Gene.
> 
> Kind regards,
> Anja
> 
> 
> On 23 Jul 2014, at 16:46, Nathalie Conte wrote:
> 
>> Hi , 
>> Is there mouse phenotypes available through the ensembl API ?
>> I am trying to retrieve mouse phenotypes from the API using the phenotype feature adaptor = Bio::EnsEMBL::Registry->get_adaptor('mouse', 'variation', 'phenotypefeature'),
>> using fetch_all_by_Variation method, and cannot retrieve any -
>> Please advise,
>> Thanks,
>> Nathalie
>> 
>> 
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> 
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