[ensembl-dev] list of SNPs with a phenotype, sql help

[Nathalie Conte]

hi Laurent 
Thanks for this -
I want all SNP associated with a phenotype,not one in particular,  I used diabetes as an example .
is fetch_all the one to use?
public List Bio::EnsEMBL::Variation::DBSQL::PhenotypeFeatureAdaptor::fetch_all

Another question, how do you get the SNPs IDs associated with those phenotypes?
Thanks
Nathalie

On 9 Oct 2014, at 11:44, Laurent Gil <lgil at ebi.ac.uk> wrote:

> Hi Nathalie,
> 
> The database schema is not easy to decipher. We built the following documentation to help to understand the tables/columns:
> http://www.ensembl.org/info/docs/api/variation/variation_schema.html
> At the moment, the variation_attrib table is only used by our colleagues in Ensembl Genomes, so you don't need to use this table to link the variations to the phenotype.
> 
> However, I warmly recommand to use the Variation API: there is a method in the PhenotypeFeatureAdaptor object to retrieve all the data associated with a phenotype: " fetch_all_by_phenotype_description_source_name" (the source name parameter is optional). And from the PhenotypeFeature objects, you can retrieve the variations.
> 
> Best regards,
> Laurent
> On 09/10/2014 11:27, Nathalie Conte wrote:
>> HI, 
>> I am trying to build a sql query in order to select all SNPs (germline and somatic, ie rs1223) associated with a phenotype.(ie diabetes) using sql command.
>> I started building a sql query connecting different tables in homo_sapiens_variation_77_38 database in order to connect the variation table (variation_id, rs1223)and the phenotype table where the description of the phenotype is (ie diabetes).
>> Looking at the schema http://www.ensembl.org/info/docs/api/variation/variation-database-schema.pdf , I am linking variation table through variation, variation_attrib, phenotype_feature_attrib, feanotype_feature, and phenotype.
>> It seems that variation_attri table is empty, so I cannot link the data
>> mysql -hensembldb.ensembl.org -uanonymous -e"SELECT * FROM  variation_attrib   LIMIT 10;" homo_sapiens_variation_77_38 command will return no  result.
>> Could you please help me forward suggestion another path to link variation.variation_id to phenotype.description, or suggest directly a sql command?
>> Thanks in advance
>> Nathalie
>> 
>> 
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