[Biojava-l] field names in term_synonym

Richard HOLLAND hollandr at gis.a-star.edu.sg
Tue Jul 5 23:11:34 EDT 2005

Hi - thanks for pointing that out. The field is also called 'name' in
the Oracle schema as well as HSQLDB. Basically in Oracle you can't call
a field 'synonym' because it is a reserved keyword.

I'm thinking this might need to be a special-case where the SQL
statement should be moved to the database-specific DBHelper class
(HypersonicDBHelper, MySQLDBHelper, OracleDBHelper, etc.), as is done
with references to the 'seq' column of the 'biosequence' table for

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> bradford powell
> Sent: Wednesday, July 06, 2005 3:33 AM
> To: biojava-l at biojava.org
> Subject: [Biojava-l] field names in term_synonym
> org.biojava.bio.seq.db.biosql.OntologySQL refers to the 'name' field
> of the table 'term_synonym'. The field is only called 'name' in the
> hsqldb schema; it is called 'synonym' in the other schemas
> (postgresql, mysql, oracle).
> It seems that the references to 'name' should be changed to 'synonym'
> in lines 305 and 577 of OntologySQL, and that the hsqldb schema be
> corrected to follow the naming schema of the others.
> -- Bradford Powell
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