[Biopython-dev] [BioSQL-l] SwissProt DE lines and bioentry.description field in BioSQL

Hilmar Lapp hlapp at gmx.net
Sat May 16 23:37:14 UTC 2009

On May 16, 2009, at 7:28 PM, Peter wrote:

>> That could be changed to an XML string:
>> <?xml version="1.0" encoding="UTF-8"?>
>> <gene_names>
>>  <gene_name>
>>    <Name>GC1QBP</Name>
>>    <Synonyms>HABP1</Synonyms>
>>    <Synonyms>SF2P32</Synonyms>
>>    <Synonyms>C1QBP</Synonyms>
>>  </gene_name>
>> </gene_names>
>> Thinking about this we should attempt to coalesce around a standard  
>> instead
>> of forcing the other Bio*  to a specific format.
> How would you record this in BioSQL?  As an XML string for an  
> annotation value?

Yes. A TagTree object can be serialized to XML, and the XML can be  
stored as the annotation value in BioSQL. As the XML can be read back  
in, it allows full round-tripping.

> Brad has suggested JSON might be useful for this kind of thing (see
> also per-letter-annotation discussion).

JSON could be another serialization format, but XML is equally or  
better supported in all languages except JavaScript. Furthermore, you  
could just send the XML to the browser and have an XSLT (either  
directly, or indirectly through JavaScript doing the transformation)  
do the rendering.

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

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