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Re: Is there an NCBI taxonomy in OWL ?

From: Chris Mungall <cjm@berkeleybop.org>
Date: Wed, 25 Feb 2009 20:25:43 -0800
Cc: "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
Message-Id: <F8B37477-65E8-4B8A-B6B6-A9779C3E84B0@berkeleybop.org>
To: "andrea splendiani (RRes-Roth)" <andrea.splendiani@bbsrc.ac.uk>

On Feb 25, 2009, at 4:17 PM, andrea splendiani (RRes-Roth) wrote:

> Thanks!
>
> It'2 240M, but compressed is only 9.
> I wonder whether there is some architecture to transparently transfer
> compressed ontologies...

well the obo file is a bit more compact, and the source NCBI file is  
even more compact. The OWLAPI should be able to read the obo (probably  
takes a bit of memory), or you could run the conversion at your end.

Alternatively you could define a subset of interest (aka GO slim),  
either extensionally or intensionally, and we could set something up  
to import only that slim. I know others who would be interested in a  
similar resource.

>
> Ciao,
> Andrea
>
> -----Original Message-----
> From: Chris Mungall [mailto:cjm@berkeleybop.org]
> Sent: 25 February 2009 20:53
> To: andrea splendiani (RRes-Roth)
> Cc: public-semweb-lifesci hcls
> Subject: Re: Is there an NCBI taxonomy in OWL ?
>
>
> On Feb 25, 2009, at 11:58 AM, Andrea Splendiani wrote:
>
>> Hi,
>>
>> I was looking for an NCBI Taxnomoy in OWL, but I didn't find it (or
>> better, could find fragment from other projects...)
>>
>> What is strange though, is that on the obo foundry website
>> (berkeleybop.org/ontologies) there are notes on the ncbi taxonomy
>> representation in owl... but not the representation itself.
>
> Temporarily dropped from the summary page but still available at the
> usual URL
> http://purl.org/obo/owl/NCBITaxon
>
> (warning: large..)
>
>> Does anybody have some hint about where I can fin an OWL version ?
>> Or even an RDF version ? Even better would a sparql endpoint
>> containing it...
>>
>> best,
>> Andrea Splendiani
>>
>>
>>
>
>
Received on Thursday, 26 February 2009 04:26:31 GMT

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