[Biojava-dev] BioSQL Implementation

[Simon Foote]

Hi Thomas & Mathew,

I think my first attempt at sending this failed due to the attachment.

I've been following the development of the BioSQL schema and I noticed 
in an email from Hilmar last week on the BioSQL list that a release was 
imminent.  And as of today May 23, he said mostly next week.

Thus, I've been modifying the biojava code to get it working with the 
latest schema within MySQL.  The main changes have been the following:

1) Ontology_term table to term table with applicable id name changes.

2) Seqfeature_location table to location table with applicable id name 
changes

3) Seqfeature_relationship table --> parent and child changes to object 
and subject

4) Changes to generate unique rank numbers within several tables as the 
schema has unique indexes on several of them. (bioentry_qualifier_value, 
seqfeature, etc) - some were already there but commented, others I added 
& commented the code

5) Also, changed the thrown exceptions to conform to the non-deprecated 
constructors.

6) A bunch of little things that I have commented in the code

7) The only part I haven't touched is the Assembly parts as I couldn't 
figure out how they are incorporated with the latest schema.

8) Alas, the special case keys comment in BioSQLSequenceAnnotation looks 
like reference and dbxref didn't get nuked, so should I attempt to 
incorporate those keys into the system. And I guess dbxref in 
BioSQLFeatureAnnotation as well.

I've been testing the various methods (addSequence, removeSequence, 
getSequence, etc) with a bacterial genomes from genbank and I think I 
have everything working correctly.

I don't have CVS access to biojava, so if you let me know where to send 
it, I will email the modified code to you, for your perusal.

Regards,
Simon Foote



-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca