[ensembl-dev] variation API mouse phenotype question

Fiona Cunningham fiona at ebi.ac.uk
Wed Jun 19 12:06:22 BST 2013


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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