[BioSQL-l] _removeSequence

[Hilmar Lapp]

On Jun 20, 2005, at 8:20 AM, Martina wrote:

> Hi,
>
> so I have this new database (still biosqldb-mysql.sqlv 1.40 2004/11/04 
> 01:49:41) and after removing all sequences, I do still have entries in 
> term, term_relationship,term_relationship_term and ontology. And of 
> course, in biodatabase. If I delete the entry in biodatabase too, 
> nothing changes. Is that what is to be expected?

Yes. Deletes cascade through foreign key constraints and nothing else. 
Term has a n:n relationship with bioentry and therefore does not have a 
foreign key to bioentry.

More generally, and provided cascading deletes are enabled, if you 
delete a row in a master table, all corresponding rows in detail tables 
are deleted that stand in a 1:n relationship to the master table (and 
therefore have a foreign key defined pointing to the master table). 
Rows in n:n related tables will not be deleted, but dissociated by 
deleting the corresponding rows from the association table. As 
examples, Comment and Biosequence are 1:n related to bioentry, whereas 
dbxref, reference, and term are n:n related, with bioentry_dbxref, 
bioentry_reference, and bioentry_qualifier_value being the association 
tables.

If this is confusing to you, you should read a general textbook on 
relational databases and normalization which usually will explain this 
a lot better than I do.

> Cause I still have trouble with the dublicate entry key, but that must 
> be my code then.

Yes. When you insert a sequence you must be prepared that when 
inserting its ontology term or tag/value annotation the term may 
already be present because another bioentry uses it too. Similarly for 
Reference and Dbxref (although I believe Biojava doesn't use these - 
yet).

	-hilmar

>
> Thanks
> Martina
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------