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Re: Is there an NCBI taxonomy in OWL ?

From: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>
Date: Fri, 27 Feb 2009 16:31:36 +0000
Cc: "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
Message-Id: <A146643E-4247-402D-B349-D2525388128D@bbsrc.ac.uk>
To: Chris Mungall <cjm@berkeleybop.org>
Hi, I didn't yet try to read it, but I'm not that worried about its  
size. I was just wondering that these ontologies representation files  
are extremely redundant, so compression would be a natural choice for  
their transfer.
Although it is more of a perspective thinking, I don't think this is a  
big issue at the moment.

I guess extensional subsets are pretty natural in an taxonomy. Is the  
problem only the definition of the subsets of interest, or is there  
something more that I'm missing ?

ciao,
Andrea

Il giorno 26/feb/09, alle ore 04:25, Chris Mungall ha scritto:

>
> 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 Friday, 27 February 2009 16:32:27 GMT

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