[ensembl-dev] Mouse phenotypes in ensembl API

[Anja Thormann]

Dear Nathalie,

we import data from DGVa for mouse already:
http://www.ensembl.org/info/genome/variation/sources_documentation.html#mus_musculus

I will check the Phenotype and QTL data provided by MGI and let you know if decide to import the data for our next releases.

Thank you for pointing out the data sources. I'll keep you updated.

Kind regards,
Anja

On 24 Jul 2014, at 16:56, nconte at ebi.ac.uk wrote:

> Thanks
> Any plans to get more data in soon like
> dbSNP dGVA MGI?
> BW,
> Nathalie
> 
>> Hi Nathalie,
>> 
>> we have phenotype data from EuroPhenome and MGP. You can find more about
>> the sources here:
>> http://www.ensembl.org/info/genome/variation/sources_documentation.html#mus_musculus
>> 
>> We have only gene associated phenotypes for mouse.
>> 
>> Thanks,
>> Anja
>> On 24 Jul 2014, at 15:40, Nathalie Conte wrote:
>> 
>>> Hi Anja, I have successfully retrieved phenotypes with fetch_all_by
>>> _gene method.
>>> I am retrieving so far data from MGP with KO gene - is there any other
>>> data sources for mouse phenotypes, what about variation phenotypes ?
>>> 
>>> script
>>> my $pfs = $pf_adaptor->fetch_all_by_Gene($gene);
>>> if ( scalar(@$pfs)== 0 ){print "no PHE\n";}else{
>>> foreach my $pm(@{$pfs}){ if ($pm){
>>> print "\t",
>>> $pm->allele_symbol,"\t",$pm->source,"\t",$pm->phenotype->description,
>>> "\n";
>>> }else {next;}
>>> 
>>> Thanks
>>> N
>>> 
>>> On 23 Jul 2014, at 16:52, Anja Thormann <anja at ebi.ac.uk> wrote:
>>> 
>>>> Hello Nathalie,
>>>> 
>>>> we have only genes associated with phenotypes for mouse. You need to
>>>> use fetch_all_by_Gene.
>>>> 
>>>> Kind regards,
>>>> Anja
>>>> 
>>>> 
>>>> On 23 Jul 2014, at 16:46, Nathalie Conte wrote:
>>>> 
>>>>> Hi ,
>>>>> Is there mouse phenotypes available through the ensembl API ?
>>>>> I am trying to retrieve mouse phenotypes from the API using the
>>>>> phenotype feature adaptor =
>>>>> Bio::EnsEMBL::Registry->get_adaptor('mouse', 'variation',
>>>>> 'phenotypefeature'),
>>>>> using fetch_all_by_Variation method, and cannot retrieve any -
>>>>> Please advise,
>>>>> Thanks,
>>>>> Nathalie
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>> 
>>> 
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
> 
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140729/769e876c/attachment.html>