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Re: Is there an NCBI taxonomy in OWL ?

From: Chris Mungall <cjm@berkeleybop.org>
Date: Fri, 27 Feb 2009 09:11:50 -0800
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, "andrea splendiani (RRes-Roth)" <andrea.splendiani@bbsrc.ac.uk>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, Maryann Martone <maryann@ncmir.ucsd.edu>
Message-Id: <96CC384E-F597-4A75-9B78-94CBDC9070DF@berkeleybop.org>
To: Kei Cheung <kei.cheung@yale.edu>

On Feb 26, 2009, at 7:03 PM, Kei Cheung wrote:

> I gave the following neuroscience URI examples in my biordf talk at  
> C-SHALS yesterday.
>
> http://dbpedia.org/resource/Dopamine_receptor
> http://purl.org/ycmi/senselab/ 
> neuron_ontology.owl#Dopaminergic_Receptor
> http://purl.org/nif/ontology/NIF-Molecule.owl#nifext_5832
>
> I pointed out that the last one might be a possible solution. There  
> might be hope. :-)

Actually, I think the last one is changing to
http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#nifext_5832

There is also FMA:61811 "Dopamine receptor", and it's various  
translations to URIs, including http://purl.org/obo/owl/FMA#FMA_61811

PRO has various classes such as DR(1)-like, but PRO is a structural  
classification, whereas dopanine receptor is a functional  
classification. GO:0004952 "dopamine receptor activity" is the  
relevant functional classification. So I would suggest all the various  
URIs for DR state an equivalence to PRO:000000001 [protein] that  
has_function some GO:0004952, which will allow reasoners to determine  
equivalence between them all, plus you get the cognate representations  
of all the UniProt records for DRs for free.

>
> -Kei
>
>
> Alan Ruttenberg wrote:
>
>> So I count three different sets of URIs for NCBI taxonomy so far. :(
>> -Alan
>>
>> On Fri, Feb 27, 2009 at 11:37 AM, Chris Mungall  
>> <cjm@berkeleybop.org> wrote:
>>
>>> also..
>>>
>>> part of the NCBI taxonomy is in NIF Organism:
>>>
>>> http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Organism.owl
>>>
>>> See also:
>>>
>>> https://wiki.neuinfo.org/xwiki/bin/view/Main/NIFSTDoverview
>>> http://neuinfo.org
>>>
>>>
>>> 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...
>>>>
>>>> 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 17:12:51 GMT

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