[ensembl-dev] variation API mouse phenotype question

[Fiona Cunningham]

Many thanks to both of you for your input. 

Best wishes,

Fiona

Le 20 Jun 2013 à 14:21, Paul Denny <paul.denny3 at gmail.com> a écrit :

> I'd agree with both of those suggestions; I have a mouse genetics / phenotyping background
> Best regards,
> Paul Denny
> 
> 
> 
> On 20 Jun 2013, at 13:50, nconte at ebi.ac.uk wrote:
> 
>> 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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