[ensembl-dev] question on variation API

nconte at ebi.ac.uk nconte at ebi.ac.uk
Thu Oct 3 16:52:04 BST 2013


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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