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[Gofriends] [Obo-discuss] file format: OBO to table convertion

Chris Mungall cjm at berkeleybop.org
Wed Dec 9 14:49:34 PST 2009


Hi Zhiliang

You can use go-perl to convert obo files into flat denormalized tables.

There are a number of different relational schemas that support  
ontologies encoded in obo format, including the GO database schema.  
You can use go-db-perl to create a MySQL database with any obo file  
loaded.

http://www.geneontology.org/GO.tools.software-libraries.shtml#go-perl
http://www.geneontology.org/GO.tools.software-libraries.shtml#go-db-perl
http://www.geneontology.org/GO.database.shtml

On Dec 9, 2009, at 1:00 PM, Zhiliang wrote:

> I searched but failed to find -- is there a tool to convert OBO  
> files into
> a table-based (better yet, ready to load into MySQL in a GO  
> structure)?
>
> Thanks,
> Zhiliang
>
>
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