[ensembl-dev] question on variation API

[Fiona Cunningham]

Dear Nathalie,

We agree that it would help to have an ontology. This is something we plan to do. 

Many thanks for your feedback. 

Fiona

> Le 3 Oct 2013 à 16:52, nconte at ebi.ac.uk a écrit :
> 
> HI Laurent,
> 
> I understand this depends on the source of the data and in some databases
> phenotype traits are more or less meaningful.
> It would be really great to have  a ontology system to get with one term
> all variation corresponding to certain diseases for example.
> Best,
> Nathalie
> 
>> 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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> 
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