[BioSQL-l] a biosql/biojavax localization question

[Richard Holland]

Personally I'd like to see *_qualifier_value tables for all BioSQL
tables that represents an entity of any kind, be it term, feature,
location, sequence, taxon, or anything else. 

In the case of is_taxon_hidden, this is specific to an individual taxon,
and I can see cases where it would be appropriate to search by it (for
instance, pulling out all ancestors of a given taxon that are visible).
So I think this should be an additional column.

By the way, is there a document somewhere detailing all the changes that
are planned for 1.1?

cheers,
Richard


On Mon, 2006-07-03 at 14:07 -0400, Hilmar Lapp wrote:
> Hi David, I wish I were in the south of France soaking up sun ...  
> although there is no shortage of sun (or heat for that matter, and  
> throw humidity in there too) where I am.
> 
> 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?
> 
> 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.
> 
> 	-hilmar
> 
> On Jul 3, 2006, at 1:55 PM, David Scott wrote:
> 
> > sure hilmar-
> >
> > in the genbank taxonomy file - nodes.dmp:
> > ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt
> > there is a field:
> >
> > GenBank hidden flag (1 or 0)            -- 1 if name is suppressed  
> > in GenBank entry lineage
> >
> > this field controls whether the level is included in the taxonomy  
> > hierarchy when the genbank ORGANISM section is generated - but the  
> > more general problem trying to be solved is:
> > o parse genbank entries
> > o store parsed entry in biosql
> > o pull parsed entry from biosql
> > o (re)create the genbank entry
> > o compare the recreated entry with the source document for  
> > identity. well - ok - almost identical.
> >
> > there are several parameters missing from biosql to make this  
> > possible. the general approach to a solution has been:
> > o alter the biosql table to add a new column (a sql ddl file)
> > o add a private get/set for the column in the biojavax object (a  
> > java file)
> > o add the column to the biojavax hibernate o/r mapping (an xml file)
> >
> > to help others that might have the same objective, and to  
> > accomodate those that don't wish these nonstandard columns  - it is  
> > planned to release the o/r mapping files with the additional  
> > columns/fields commented out - these xml files along with the java  
> > files are checked out with cvs. it was not clear what to do with  
> > the ddl files - and it would be helpful to have them reviewed - no  
> > matter what is done with them.
> >
> > thanks for helping me - i just assumed you were late in responding  
> > because it is summer - and, well - you were in the the south of  
> > france soaking up the sun.
> >
> > looking to you for suggestions-
> > david
> >
> >
> > Hilmar Lapp wrote:
> >> Hi David, sorry for dropping (or rather, not ever picking up) the  
> >> ball on this ... got lost in inbox stack.
> >>
> >> The earlier consensus was if I recall correctly to include  
> >> is_circular as a biosequence attribute in the 1.1 version.
> >>
> >> isTaxonHidden is new to me and I don't even understand what it  
> >> would mean. Can you elaborate?
> >>
> >>     -hilmar
> >>
> >> On Jun 21, 2006, at 11:19 AM, David Scott wrote:
> >>
> >>> biojavax is using hibernate to o/r map the biosql database to  
> >>> biojavax
> >>> objects. biojavax is planning support in the biojavax objects for  
> >>> fields
> >>> not directly supported in the biosql database (e.g. isCircular,
> >>> isTaxonHidden). in order to conform to the current biosql  
> >>> database, the
> >>> default mapping file from biosql to biojavax will comment out the
> >>> unsupported fields (so the object fields will not be initialized)  
> >>> and
> >>> the objects will default an appropriate conforming value (e.g.  
> >>> false for
> >>> isCircular and isTaxonHidden). for users wishing to localize  
> >>> biojavax:
> >>> the user would uncomment the mapping file and alter the database  
> >>> tables.
> >>> altering the database would require running ddl on the existing  
> >>> database
> >>> to create the new table columns. what is the best way to review  
> >>> and then
> >>> distribute the alter/create ddl for users to localize their  
> >>> database?
> >>> _______________________________________________
> >>> BioSQL-l mailing list
> >>> BioSQL-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/biosql-l
> >>>
> >>
> >> --===========================================================
> >> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> >> ===========================================================
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> 
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416