[Bioperl-l] Bioperl and BioSQL status

[William Hsiao]

Hi,
  My lab is interested in adapting BioSQL as the basis
for a functional genomic database that will support
microarray analysis we wish to perform in the near
future.  The types of information we wish to include
in the database include pathway, signal peptide,
transcription factors, binding sites, promotors,
protein domains, signal peptides, subcellular
localization information, etc.  The database will need
to accommodate both eukaryotic and prokaryotic
genomes/genes, and will need to be flexible to
accommodate future analysis results that we may
perform.  I have taken a look at the BioSQL schema,
and from the available documentation, the schema,
theoretically, can accommodate the different types of
information.  However, it might be more reasonable to
extend the current schema to suit the specific types
of information to simplify insertion and update. 
First, I am wondering if anyone has any suggestions on
the best (or good) approach to house the data types I
mentioned above (i.e. the current BioSQL schema design
is not strong typed, is it better to use a strong
typed database (e.g. GUS) for storing such
information)?  More specifically, I am wondering if we
decided to add additional tables to the schema (but
keep the original tables in tact), will that break the
bioperl modules (bioperl-db, etc) that are associated
with BioSQL?  Second, if we add more columns (fields)
to the existing tables, will that break bioperl-db? 
Is BioPerl adaptor for BioSQL designed to accommodate
the possibility that the actual schema might be
expanded?

Thank you

William Hsiao
Brinkman Laboratory, SFU
  

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