<div dir="ltr">Hello,<div><br></div><div>Have you considered <a href="http://www.biosql.org/wiki/Main_Page">BioSQL</a> or <a href="http://gmod.org/wiki/Chado_-_Getting_Started">Chado</a>? 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.</div><div><br></div><div>BioPython has a BioSQL <a href="http://biopython.org/wiki/BioSQL">tutorial</a> on the wiki, and an <a href="https://github.com/biopython/biopython/tree/master/BioSQL">implementation</a> 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.</div><div><br></div><div>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 <a href="http://gmod.org/wiki/Chado_Django_HOWTO">http://gmod.org/wiki/Chado_Django_HOWTO</a>, which is tightly coupled with the Django web application framework. <a href="http://gmod.org/wiki/Overview#Chado_and_BioSQL">A comparison from Chado's wiki</a> between Chado and BioSQL.</div><div><br></div><div>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 <a href="https://pypi.python.org/pypi/SQLAlchemy/1.0.6">sqlalchemy </a>and <a href="https://pypi.python.org/pypi/sqlacodegen/1.1.0">sqlacodegen </a>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.</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jul 10, 2015 at 4:46 AM, Karin Lagesen <span dir="ltr"><<a href="mailto:karin.lagesen@medisin.uio.no" target="_blank">karin.lagesen@medisin.uio.no</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi!<br>
<br>
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.<br>
<br>
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?<br>
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Thanks a lot in advance,<br>
<br>
Karin<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
Karin Lagesen, PhD<br>
Institute of Informatics<br>
University of Oslo<br>
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