[Biopython] creating simple genome database

[Joshua Klein]

Hello,

Have you considered BioSQL <http://www.biosql.org/wiki/Main_Page> or Chado
<http://gmod.org/wiki/Chado_-_Getting_Started>? Without a more explicit
list of what you're looking for, I can't say for sure they have all you
need, but they're both a good start.

BioPython has a BioSQL tutorial <http://biopython.org/wiki/BioSQL> on the
wiki, and an implementation
<https://github.com/biopython/biopython/tree/master/BioSQL> in their
codebase. BioSQL is "language neutral" in that its expected all of the big
Bio* projects have an implementation. It is however not being actively
worked on, and its focus is fairly narrow.

Chado is part of the GMOD project, which also supports things like FlyBase,
and it is much broader in scope than BioSQL, but it isn't very well
supported in Python, outside of http://gmod.org/wiki/Chado_Django_HOWTO,
which is tightly coupled with the Django web application framework. A
comparison from Chado's wiki
<http://gmod.org/wiki/Overview#Chado_and_BioSQL> between Chado and BioSQL.

It's unlikely they all have exactly what you need, but they're a good
starting point. If you want to use their schema as a jumping-off point,
consider using sqlalchemy <https://pypi.python.org/pypi/SQLAlchemy/1.0.6>and
sqlacodegen <https://pypi.python.org/pypi/sqlacodegen/1.1.0>to get you 50%
of the way there. The SQLAlchemy project has support for automatic
reflection of database schema so that you can use an existing database
without explicitly writing out its entire schema, and sqlacodegen takes
this a step further and produces Python code describing the schema
reflected for the more expressive object-relational-mapper.


On Fri, Jul 10, 2015 at 4:46 AM, Karin Lagesen <karin.lagesen at medisin.uio.no
> wrote:

> Hi!
>
> I am in need of creating a simple genomics database, basically one that
> contains the information found in a genbank record. However, I need one
> that contains info for multiple genomes, and thus I need several tables, an
> organism table, a feature table, etc. I have been looking around for
> something like this, because I couldn't imagine that this wasn't already a
> solved problem. I imagined that this would be useful for loads of
> researchers out there. However, nothing found yet.
>
> Hence this email. Do any of you know of something like this already
> existing, or if not, do you have any suggestions for how I go about making
> my own?
>
> Thanks a lot in advance,
>
> Karin
>
> --
> Karin Lagesen, PhD
> Institute of Informatics
> University of Oslo
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