[ensembl-dev] Mouse phenotypes in ensembl API

[Anja Thormann]

Hi Nathalie,

we have phenotype data from EuroPhenome and MGP. You can find more about the sources here: http://www.ensembl.org/info/genome/variation/sources_documentation.html#mus_musculus

We have only gene associated phenotypes for mouse.

Thanks,
Anja
On 24 Jul 2014, at 15:40, Nathalie Conte wrote:

> 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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