[Bioperl-l] bioperl-db revival

[Ewan Birney]

I have decided to revive bioperl-db for "simple" sequence storage.

[note to Hilmar/Jason - this is definitely the right place to put this now
I have written some of the SQL/code. It is completely bioperl dependent at
the moment. Our discussion about wider ranging infrastructure is
definitely worth keeping alive but this project is so dependent on bioperl
there's not much point in pretending otherwise]


The aim is a pretty vanilla set of SQL tables, quite normalised, nothing
fancy. The only sticking point are the dreaded feature locations, which,
if we go the full fuzzy modelling (aaaaarh not the fuzzies again) I
will need help (jason - can you face the fuzzies again?). 

At the moment I am going to have a cheeky "unparsed_location" string table
for the fuzzies.


To bind to the SQL tables I will have a series of pretty vanilla
"adaptors" talking Ensembl or FlyBase, equivalent I believe to Java Bean
singleton objects talking java (? java experts to correct me) which
mediate persistence of Bio::Seq objects.

The only wrinkle here is how to deal/detect nicely one-instance style
objects, such as Species (homo sapiens). I will I hope glean some wisdom
from Arne Stabenau on this tomorrow but if anyone has some helpful ideas,
just put them down here.


For output, it will definitely support appropiate Bio::DB:: *I interfaces
and probably extend it for simple field orientated queries that can be
easily mapped to SQL (nothing fancy)


For input it will have a loader script that can load a SeqIO stream into
the database.


It will be able to support mutliple logical "databases" (eg, swissprot and
genbank) in the same db instance and handle multiple versions of
sequences. It will not currently handle true entry-granualarity
mutability, but if anyone has any must-do-now aspects please shout.


I want to put code in the Bio::DBSQL:: namespace. Is this ok?


Code will go into the bioperl-db cvs module


I have a tight-ish deadline on this, so please shout if you feel you want
to add anything.





ewan




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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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