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Re: [BiONT][BioRDF] Mussels

From: Steve Chervitz <Steve_Chervitz@affymetrix.com>
Date: Thu, 04 May 2006 16:24:09 -0700
To: Chris Mungall <cjm@fruitfly.org>
CC: Alan Ruttenberg <alanruttenberg@gmail.com>, <public-semweb-lifesci@w3.org>
Message-ID: <C07FDB29.1E339%Steve_Chervitz@affymetrix.com>

Hi Chris,

I thought the wikispecies URL would be an improvement over a wikipedia URL
since it gives you a way to define a resolvable ID using the taxonomic term
itself ('Bivalvia'). Also the content resolved by that URL describes
superclass relations that could be automatically extracted.

But to be sure, the NCBI taxid is a better choice for an identifier since it
more fully describes the taxonomy. In Alan's case, it does seem like he'll
need to create a special class to collect the relevant organisms.

(I actually just stumbled across the wikispecies resource today. It would be
nice if they provided links into the NCBI taxonomy.)


> From: chris mungall <cjm@fruitfly.org>
> Date: Thu, 4 May 2006 15:38:07 -0700
> To: Steve Chervitz <Steve_Chervitz@affymetrix.com>
> Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, <public-semweb-lifesci@w3.org>
> Subject: Re: [BiONT][BioRDF] Mussels
> Hi Steve
> What's the advantage in using a wikispecies URI over an NCBI Taxon ID?
> Of course with the taxon ID we would need a conversion of the NCBI
> taxonomy to OWL classes, which is fairly trivial, and there a number
> of such conversions around (and ideally there would be some kind of
> ontology lifecycle management involved, since species taxonomies are
> not stable)
> Also this doesn't seem to solve the problem that Alan wanted to refer
> to a type that is more specific than Bivalvia, but more general than
> any one taxonomic subclass.
> I favour Alan's solution, which is for him to make his own Mussel
> owl:class, either a stable class or an rdf bnode, and then to
> associate with that class either necessary or preferably necessary
> and sufficient conditions, using stable taxon IDs (and possibly other
> resources) then let the reasoners take care of figuring out
> equivalence or subsumption if queried via these taxon IDs.
> On May 4, 2006, at 3:13 PM, Steve Chervitz wrote:
>> How about using a wikispecies URL, where the taxonomic term appears
>> in the
>> URL:
>> http://species.wikipedia.org/wiki/Bivalvia
>> For mussels you can't currently get much below the Order level, but
>> this is
>> just a matter of fleshing out the wikispecies database.
>> Steve
>>> From: Alan Ruttenberg <alanruttenberg@gmail.com>
>>> Date: Thu, 4 May 2006 01:42:16 -0400
>>> To: <public-semweb-lifesci@w3.org>
>>> Subject: Re: [BiONT][BioRDF] Mussels
>>> Resent-From: <public-semweb-lifesci@w3.org>
>>> Resent-Date: Thu, 04 May 2006 05:42:38 +0000
>>> Another thought is to use  wikipedia URL's as the identifier - there
>>> are often matches at this level of description. The downside is that
>>> you lose the superclass relations that you have in taxonomy, e.g. the
>>> ability to query for mammal, and get back all the primates, mice,
>>> rats, etc.
>>> e.g. http://en.wikipedia.org/wiki/Mussel
>>> -Alan
>>> On May 4, 2006, at 1:29 AM, Alan Ruttenberg wrote:
>>>> I am inclined to create a class which is the union of all these
>>>> classes and then annotate the antibody with that class.
Received on Thursday, 4 May 2006 23:23:56 UTC

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