[ensembl-dev] question on variation API

[Laurent Gil]

Hi Nathalie,

Unfortunately, because we import phenotypes from multiple sources, we 
don't have yet an ontology system for the phenotypes in Ensembl.
We try to merge some terms, but it's quite limited.

Best regards,

Laurent
Ensembl Variation

On 03/10/2013 15:58, nconte at ebi.ac.uk wrote:
> HI Laurent, Thanks for fixing the bug,
> concerning the list, does it work like an ontology or you have to select
> all terms corresponding to a condition?
> example if you want all SNP concerning ADDISON disease you have to select
> all 4 phenotypes below?
> ADDISON DISEASE
>
> Addison disease, susceptibility to
>
> Addison's disease
>
> Addisons disease
>
> thanks
> Nat
>> Hi Nathalie,
>>
>> Concerning the first question, this was a bug and I committed a fix on
>> the branch 73 of the ensembl-variation CVS.
>> You can find the list of phenotype on the Ensembl website, e.g. for
>> human: www.ensembl.org/Homo_sapiens/Phenotype/All
>>
>> Best regards,
>>
>> Laurent
>> Ensembl Variation
>>
>> On 03/10/2013 13:57, Nathalie Conte wrote:
>>> hi, I am trying ot use this method in order to get only the variation
>>> I am interested in using phenotype as a filter:
>>> public Reference
>>> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_with_phenotype_by_Slice
>>> 	(
>>> 	)
>>>
>>>     Arg [1]    : Bio::EnsEMBL:Variation::Slice
>>> <http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Slice.html>
>>>   $slice
>>>     Arg [2]    : $variation_feature_source [optional]
>>>     Arg [3]    : $phenotype_source [optional]
>>>     Arg [4]    : $phenotype_name [optional]
>>>     Example    :
>>>    my @vfs = @{$vfa->fetch_all_with_phenotype_by_Slice($slice)};
>>>     Description: Retrieves all germline variation features associated
>>> with phenotypes for
>>>                  a given slice.
>>>                  The optional $variation_feature_source argument can be
>>> used to
>>>                  retrieve only variation features from a paricular
>>> source.
>>>                  The optional $phenotype source argument can be used to
>>>                  retrieve only variation features with phenotypes
>>> provided by
>>>                  a particular source.
>>>                  The optional $phenotype_name argument can
>>>                  be used to retrieve only variation features associated
>>> with
>>>                  that phenotype - this can also be a phenotype's dbID.
>>>     Returntype : reference to
>>> listBio::EnsEMBL::Variation::VariationFeature
>>> <http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html>
>>>     Exceptions : throw on bad argument
>>>     Caller     : general
>>>     Status     : Stable
>>> I have 2 questions
>>> 1-I first tried to use this without any option
>>> my $vf_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human',
>>> 'variation', 'variationfeature');
>>>   my @vfs =
>>> @{$vf_adaptor->fetch_all_with_phenotype_by_Slice($human_slice)};
>>> this is the output I get, any idea?
>>> DBD::mysql::st execute failed: Unknown column 'pf.seq_region_id' in
>>> 'where clause' at
>>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm
>>> line 446, <> line 2.
>>> DBD::mysql::st execute failed: Unknown column 'pf.seq_region_id' in
>>> 'where clause' at
>>> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm
>>> line 446, <> line 2.
>>>
>>> 2-the optional $phenotype_name argument can be used, where can I find
>>> a lit of all phenotype name please?
>>>
>>> Many thanks
>>> Nathalie
>>>
>>> --
>>>
>>>
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