Hello everyone,

I am trying to get in touch with GO and/or Ensemble. First of all, I want to get alls GO Terms related to Gen. Here is an example for querieng PTEN in the GO DB:

SELECT
acc, gene_product.symbol
FROM
gene_product
INNER JOIN dbxref ON (gene_product.dbxref_id=dbxref.id)
INNER JOIN species ON (gene_product.species_id=species.id)
INNER JOIN association ON gene_product.id=association.gene_product_id)
INNER JOIN evidence ON association.id=evidence.association_id)
INNER JOIN term ON (association.term_id=term.id)
WHERE
gene_product.symbol = 'PTEN'
and species.genus='Homo'
and species.species='Sapiens'
and term.term_type = 'biological_process'
group by acc;

The Results are 56 Terms, perfectly equivalent to the amigo web interface. But when I query the Ensemble DB like this, for the PTEN protein:

select
*
from
translation
INNER JOIN object_xref ox ON (translation.translation_id = ox.ensembl_id AND ox.ensembl_object_type = "Translation")
INNER JOIN xref USING (xref_id)
INNER JOIN external_db ON (xref.external_db_id = external_db.external_db_id)
INNER JOIN ensembl_ontology_66.term ot on (dbprimary_acc=ot.accession)
where
db_display_name = 'GO' and stable_id = "ENSP00000361021"
and ot.ontology_id=1
group by dbprimary_acc;

I get 42 GO Terms for biological process.

May one of you has a hint for me.

Thanks,

Mario

//EDIT:

I got a bit deeper into it and did 5 things:

1. Use Amigo, searching PTEN
2. Use SQL Query searching PTEN
3. Use BioMart: Search for ENSP00000361021
4. Use Ensemble v66 with query for ENSP00000361021
5. Use Ensemble v66 with query for PTEN

1 and 2 are identical 3,4 and 5 are identical

the 42 GO terms are a subset of the 56. Is amigo may linking to other species?