[BioSQL-l] Abstracts and Full Text on References

[Richard Holland]

Make it a BLOB and add another column indicating the MIME type of the
BLOB.

	BLOB abstract
	VARCHAR abstract_mime_type

Then if you stored a PDF in it you could set abstract_mime_type to
'application/x-pdf', or if it was plain text, you could set the
abstract_mime_type to 'text/plain'.

cheers,
Richard

On Fri, 2006-07-14 at 09:56 +0800, mark.schreiber at novartis.com wrote:
> 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
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
> >
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416