[ensembl-dev] variation API mouse phenotype question

[Fiona Cunningham]

 Dear Nathalie,

We are still finalising our plans for this. Could you tell me what
data will be most useful to you?

Best wishes,
Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612


On 19 June 2013 13:00,  <nconte at ebi.ac.uk> wrote:
> Dear Fiona,
> thanks for your answer. About future plans, do you know already when you
> plan to release mouse phenotypic data  and what kind of data will it be?
> thanks
> Nathalie
>
>> Dear Natalie,
>>
>> At present we do not have phenotype data for mouse, stored in Ensembl.
>> This is something that we will look into in the future. There is data
>> for human and farm animals.
>>
>> Best wishes,
>>
>> Fiona
>>
>> -----------------------------------------------------------------------------------
>> Fiona Cunningham
>> Ensembl Coordinator, Ensembl Variation Project Leader.
>> EMBL-EBI, Genome Campus, Hinxton, UK
>> www.ensembl.org || www.lrg-sequence.org
>> fiona at ebi.ac.uk   || t: +44 1223 494612
>>
>>
>> On 19 June 2013 10:41,  <nconte at ebi.ac.uk> wrote:
>>>> General question,
>>>>
>>>>  I have used the fetch by all variation method on my mouse variations
>>>> with
>>>> the phenotype feature adaptor to retrieve data from mouse variation
>>>> objects and didn't retrieve any phenotype feature so far.(I use the
>>>> same
>>>> method for human variation and it retrieve pheno data).
>>>> This is what I use to fetch phenotype data for Mouse using variation
>>>> objects:
>>>>
>>>> my $mpf_adaptor = Bio::EnsEMBL::Registry->get_adaptor('mouse',
>>>> 'variation', 'phenotypefeature');
>>>> my $pfh = $mpf_adaptor->fetch_all_by_Variation($var);
>>>> ... then print annotation about these $pfh..
>>>>
>>>>
>>>> So I was wondering what kind of Mouse phenotype data can be accessed in
>>>> variation API using phenotype feature object?
>>>>  Is there phenotypic information from SNP, copy number variation, if
>>>> yes
>>>> coming form what source??thanks
>>>> Nathalie
>>>>
>>>>
>>>
>>>
>>>
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>
>
>
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