[Biopython] creating simple genome database

[Karin Lagesen]

Thankyou for good responses. I am trying out BioSQL now, and it looks 
like it might be what I need.

Karin


On 10.07.2015 15:21, Joshua Klein wrote:
> 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 <mailto: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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