[ensembl-dev] Mouse phenotypes in ensembl API

[nconte at ebi.ac.uk]

Thanks
Any plans to get more data in soon like
dbSNP dGVA MGI?
BW,
Nathalie

> 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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