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

[Laurent Gil]

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 
<http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a5692dfaa03010ea9eec3e4a279421496>" 
(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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