[BioSQL-l] Abstracts and Full Text on References

[mark.schreiber at novartis.com]

Hello -

There are no specific plans for biojava although the Reference object 
could easily be modified to contain 

String getAbstract()
void setAbstract(String abs)
etc.

I wonder if the full text of an article should be a byte[] or BLOB or a 
String/ CLOB. Are people more likely to want to store a PDF (usually more 
available) or a parsed String?

- Mark





Hilmar Lapp <hlapp at gmx.net>
07/14/2006 12:59 AM

 
        To:     mark.schreiber at novartis.com
        cc:     biosql-l at open-bio.org
        Subject:        Re: [BioSQL-l] Abstracts and Full Text on References


Sounds reasonable to me. Attribute association wouldn't be desirable 
I think (it would only bloat and overload the value field).

The only thing I'd be concerned about is accumulating stuff that is 
not supported by the language bindings ... i.e., bioperl doesn't 
support this, and so there isn't a way for bioperl-db to do so 
either. What are the plans for Biojava?

Are any Biopython or Bioruby folks on this list? Any comments from 
those fronts?

                 -hilmar

On Jul 13, 2006, at 1:23 AM, mark.schreiber at novartis.com wrote:

> Hi -
>
> As an enhancement for a future version of BioSQL it would be nice 
> to have
> CLOB rows for abstract and full text (Full text might need to be a 
> BLOB
> depending on format). Obviously they could both be null.
>
> Alternatively they could be in another table linked to Reference. I 
> don't
> know if it could be done via the term relationship method??
>
> Any thoughts?
>
> - Mark
>
> Mark Schreiber
> Research Investigator (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
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
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>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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