[ensembl-dev] variation API mouse phenotype question

[nconte at ebi.ac.uk]

dear Fiona,
I can think of a couple for example
1-data from MGI seems very relevant- you can search by slice on the genome
and retrieve phenotype annotations
http://www.informatics.jax.org/searches/allele_form.shtml

2- data from IMPC ,
http://www.mousephenotype.org/data/phenotypes/MP:0005293

thanks
Nathalie



 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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