When using ensembl, database entries are linked to GO terms at the transcript level. According to the documentation in the Perl api, the GO terms listed are those associated with the Swiss Prot entry for the transcript. These GO terms are then linked directly to the transcript as xrefs via the appropriate tables in the database (object-xref and ontology_xref). However, as far as I can see, there is no method (using the database directly) of determining the category of a GO term(biological process/cellular component/ molecular function). There do not seem to be any fields in the database schema that capture this information
Please can you advise if there is a method of determining the GO term category.
EDIT: In response to the second answer, this code resides in the perl api for retrieving ontology terms
SELECT DISTINCT term.term_id, term.accession, term.name, term.definition, term.subsets, ontology.namespace FROM ontology JOIN term USING (ontology_id) JOIN synonym USING (term_id) WHERE ( term.name LIKE ? OR synonym.name LIKE ? ));
but where are these tables (term/ontology/synonym). They are not in the main databases and they are not in the ontology_mart database either on the biomart server
Thank-you for your time