[BioSQL-l] circular

[Hilmar Lapp]

Interesting question.

I'd argue that the root question is whether the boolean property of 
circularity is best considered as an annotation of a bioentry with 
sequence, or as a core property of a biosequence.

Annotation generally is something that's applicable to some but not to 
other entries. A core property is something that can be well defined 
for (almost) all rows, and/or is necessary to define uniqueness or 
operations on the object.

Is_circular can certainly be defined for all biosequence rows. Also, in 
order to define operations like taking a subsequence of length 100 
starting 50bp before the end, knowing whether the sequence is circular 
makes a critical difference.

So, short-term you can store it as annotation (tag/value) on the 
bioentry, but long-term I think this needs to be added to the 
biosequence table as a column.

	-hilmar

On Jun 20, 2005, at 3:01 AM, mark.schreiber at novartis.com wrote:

> So 'is_circular' should be the blessed term. It really needs to be a
> convention so that reading and writing is consistent between bio*
> projects.
>
> Would it be a good idea for the sequence table of BioSQL 1.1 to have a
> circular column?
>
> - Mark
>
>
>
>
>
> "Marc Logghe" <Marc.Logghe at devgen.com>
> 06/20/2005 05:33 PM
>
>
>         To:     Mark Schreiber/GP/Novartis at PH, <biosql-l at open-bio.org>
>         cc:
>         Subject:        RE: [BioSQL-l] circular
>
>
> Hi Mark,
> As far as I am aware of, there is currently no field available in the
> bioentry table to store that kind of flag.
> It is parsed out from genbank files by BioPerl, though.
> It is taken from the genbank Locus line, eg.
> "LOCUS       BBPLAS                  2687 bp    DNA     circular BCT
> 12-MAR-1999"
> You can check the resulting Bio::Seq::RichSeq object by running the
> is_circular() method from Bio::PrimarySeq.
> A solution would be to make a Bio::Factory::SequenceProcessorI 
> compliant
> processor and pass that as an option to your load_seqdatabase.pl 
> script.
> In the procesor itself, you can for instance do the following:
> 1) check for circularity using the is_circular() method
> 2) if circular, add a term to your sequence object (eg. annotation 
> term,
> gene ontology term 'is_circular') indicating it is circular
>
> My 0.02$
>
> Cheers,
> Marc
>
>
>> -----Original Message-----
>> From: biosql-l-bounces at portal.open-bio.org
>> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of
>> mark.schreiber at novartis.com
>> Sent: Monday, June 20, 2005 7:34 AM
>> To: biosql-l at open-bio.org
>> Subject: [BioSQL-l] circular
>>
>> Hello -
>>
>> When circular sequences (plasmids, bacterial genomes etc) are
>> stored in BioSQL how is their circularity indicated? Or, what
>> should the convention be?
>>
>> - Mark
>>
>> Mark Schreiber
>> Principal Scientist (Bioinformatics)
>>
>> Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road
>> #05-01 Chromos
>> Singapore 138670
>> www.nitd.novartis.com
>>
>> phone +65 6722 2973
>> fax  +65 6722 2910
>>
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>
>
>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------