[BioSQL-l] a biosql/biojavax localization question

[mark.schreiber at novartis.com]

>Is_Circular is a general attribute that will apply to any sequence 
>(given the fact that many sequences are indeed circular). This, and 
>the fact that one may even want to search for it, would justify 
>inclusion directly as a column in the biosequence table.
>
>Is_Taxon_Hidden is one of those attributes that BioSQL by design 
>handles through attribute/value associations, that is, using ontology 
>term associations that have a value (the term is the attribute name).
>
>However, there is no taxon_qualifier_value table in BioSQL, so in 
>essence you are asking for adding that table.
>
>Does anybody else have ideas for taxon attributes for which this 
>table may be used?

A taxon_qualifier_value table would be potentially useful. One may want to 
have conflicting taxa (taxonomists never agree) that could be 
differentiated by use of a qualifier. The hidden attribute could also be 
one. 

>I don't really favor a proliferation of 'localized' versions of 
>BioSQL - this tends to defeat the purpose both of the rationale 
>behind a standardized persistence interface, as well as the design of 
>the schema for ultimate extensibility through weak typing and the use 
>of controlled vocabularies.
>
>Any thoughts to this end welcome.

I think that the best way to avoid localized versions might be to release 
a BioSQL 1.1 as soon as possible. The is_circular column has been on the 
todo list for a very long time. The above taxon_qualifier_value table 
would also be required to give more complete persistence of genbank data. 
Is there any reason why 1.1 cannot be released promptly?

I also wonder about how likely a standardised persistence interface is 
when there is the possibility of using custom ontologies. Biojavax is much 
better at using the correct tables in BioSQL but we use our own ontology 
terms for all kinds of qualifiers. The way we persist data to BioSQL is 
undoubtably closer to BioPerlDB than the old biojava mapping but whenever 
ontology comes into it there is bound to be breaks. To be truely unified 
the two projects (and all the other bio*s) would need to use a common 
ontology. I gues I am saying what do you mean by standardised persistence?

- Mark