[ensembl-dev] variation API mouse phenotype question

[Paul Denny]

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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> 
> 
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