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

[Richard Holland]

The reason BJX does that is because the Genbank format has no  
indication of where a feature came from. So, all there is to go on is  
that it came from Genbank! This allows us to differentiate between  
features on a sequence that were loaded from an original file, and new  
features that have been added to the sequence in the db after it was  
loaded (e.g. by running blast, blat etc. against some local data).

On 11 Aug 2009, at 09:10, Florian Mittag wrote:

> Hi!
>
> I stumbled upon an old post from Hilmar:
>
> On Tue, 18 Mar 2003, Hilmar Lapp wrote:
>> type_term_id is supposed to reference an SO term. source is  
>> supposed to
>> denote the 'method'  (BLAST, BLAT, sim4, genewise, whatnot), as far  
>> as
>> my understanding goes. In the case of reading the features from a
>> GenBank feature table, assigning 'Genbank/EMBL/Swissprot' as the  
>> source
>> (which is what the genbank, embl, and swissprot parsers do in  
>> bioperl)
>> is maybe stretching the definition, but I don't have something
>> substantially better to offer.
>
> I inspected the database after I imported some Genbank files with  
> BioJava, and
> I found that the source_term_id for the seqfeatures is always set to  
> the ID
> of an automatically inserted term "Genbank" with definition "auto- 
> generated
> by biojavax".
>
> I was wondering if there is anything new to the source_term_id.
>
> - Florian
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--
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/