[BioSQL-l] Abstracts and Full Text on References

[mark.schreiber at novartis.com]

Another table is probably best.

Is there a working version of BioSQL 1.1 this can be added to?

- Mark





Hilmar Lapp <hlapp at gmx.net>
07/14/2006 07:24 PM

 
        To:     Richard Holland <richard.holland at ebi.ac.uk>
        cc:     Mark Schreiber <mark.schreiber at novartis.com>, biosql-l at open-bio.org
        Subject:        Re: [BioSQL-l] Abstracts and Full Text on References


Right. I like this. However, it also suggests to have an additional 
table. Who knows what other fields one will want to know for an 
abstract. Also, plenty of references will never have an abstract, 
e.g. automatic submissions, ontology term references etc.

                 -hilmar

On Jul 14, 2006, at 4:10 AM, Richard Holland wrote:

> 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
>

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