[BioSQL-l] a biosql/biojavax localization question

David Scott david at autohandle.com
Mon Jul 3 17:55:58 UTC 2006

sure hilmar-

in the genbank taxonomy file - nodes.dmp:
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-

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 :
> ===========================================================

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