[BioSQL-l] What should source_term_id in table seqfeature refer to?

[Richard Holland]

On 14 Aug 2009, at 23:56, Hilmar Lapp wrote:

>
> On Aug 11, 2009, at 5:22 AM, Richard Holland wrote:
>
>> Ideally there would be two fields for source_term_id - one for the  
>> algorithm used to generate the data (e.g. BLAST, miRanda), the  
>> other for the source the data came from (e.g. Genbank, miRBase).
>
>
> You mean the source of the data that it was applied to.

Not necessarily. The source of the data that it was applied to (ie.  
the sequence the feature refers to) is a third thing - and that is an  
attribute of the sequence the feature refers to, rather than the  
feature itself.

What I mean is this:

   1. The sequence itself could be downloaded from Genbank, EMBL, or  
elsewhere, or I could have discovered it in-house.
   2. The features on the sequence could have been generated by  
running BLAST, miRBase, etc., or they could be manually annotated.
   3. The features on the sequence could have been downloaded from  
Genbank, EMBL, etc., or they could have been made locally, or by a  
collaborator at another institute.

To my mind these are three distinct things. (1) is sequence-related,  
and (2) and (3) are feature-related.

cheers,
Richard

> I agree though that if you want both you can create a cross-product  
> term and store the decomposition as term_relationship's.
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/