[Biojava-l] Re: [BioSQL-l] _removeSequence

Richard HOLLAND hollandr at gis.a-star.edu.sg
Sun Jun 26 11:11:30 EDT 2005

The revamped BioJava/BioSQL classes will expose the rank to the user for all tables which have ranks.


-----Original Message-----
From:	biosql-l-bounces at portal.open-bio.org on behalf of Simon Foote
Sent:	Wed 6/22/2005 12:15 AM
To:	Martina
Cc:	Hilmar Lapp; biosql-l-bounces at portal.open-bio.org; BioJava; biosql-l at open-bio.org
Subject:	Re: [Biojava-l] Re: [BioSQL-l] _removeSequence

Hi Martina,

In fact you can, as rank is the field that allows this to happen.  In 
Biojava, currently it's just a linearily incremented number such that 
you can have the same type and source IDs for a given bioentry.

For example, adding a Genbank entry with 10 CDS features for 1 bioentry 
will give you identical keys for bioentry_id, type_term_id and 
source_term_id, but will have a rank of 1 - 10 for each.


Martina wrote:

> That means, that I can't have 2 features refering to the same bioentry 
> with the same type (= type_term_id)and source (=source_term_id) but 
> different parent features because of the composite key bioentry_id in 
> the seqfeature table? Or what does "rank" in that table mean (its part 
> of that key), how can I get different ranks?
> Martina
> Hilmar Lapp wrote:
>> The Biojava people will respond to this. Note though that 
>> Term_Relationship is for storing subject-predicate-object triples of 
>> terms, so I'm not sure why you want to use it for storing/associating 
>> annotation. Maybe you meant bioentry_qualifier_value?
>>     -hilmar
>> On Jun 21, 2005, at 3:10 AM, Martina wrote:
>>>> 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.
>>> Ok, the proper way is to catch the SQLException in BIOSQLFeature, 
>>> test if it is a Dublicate key entry, get the identifier of the term 
>>> (would that be the BioSQLfeatureId ?) and insert it in the 
>>> term_relationship table? And there is no nice BioJava method for 
>>> this, I have to do it "manually", like conn.prepareStatement(..) and 
>>> stuff?  BioJava spoiled me so!
>>> Martina
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Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca

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