[BioSQL-l] Abstracts and Full Text on References

[Hilmar Lapp]

Yes and no. I was working on one at GNF. I'll have to create this in  
the repository.

	-hilmar

On Jul 18, 2006, at 4:41 PM, mark.schreiber at novartis.com wrote:

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