Re: [Obo-discuss] (no subject)

[Aaron G. <agu...@ti...>]

I believe ncbi_taxonomy is what you're looking for:
http://www.fruitfly.org/~cjm/obo-download/

As a heads up, in contains many empty synonym lines of the form:
synonym: "" []
which, depending on the robustness of your parser, may cause it to freak 
out.

I've been removing them with:
grep -v 'synonym: "" \[\]' ncbi_taxonomy.obo > cleaned.ncbi_taxonomy.obo

Cheers,
Aaron

mat...@sy... wrote:
> Hello,
> 
> Are you aware of anyone converting or writing a conversion of the NCBI 
> taxonomy into OBO file format. I'm loading several ontologies into a 
> local copy of the ArrayExpress database. Since many of them are OBO file 
> format I was going to write a script to put OBO filesinto AE's Oracle db.
> 
> I was hoping to save a step and find a script to convert the NCBI 
> taxonomy *.dat file into an OBO file.
> 
> Thanks
> Matt Lawrence
> Syngena Biotech Inc, RTP, NC
> 
> 
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-- 
Aaron Gussman - Bioinformatics Engineer I
The Institute for Genomic Research
agu...@ti...
(301) 795-7698