W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2006

Re: [BiONT][BioRDF] Mussels

From: chris mungall <cjm@fruitfly.org>
Date: Thu, 4 May 2006 15:38:07 -0700
Message-Id: <C07C3571-6DCB-4A38-A122-DF93778CC44B@fruitfly.org>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, <public-semweb-lifesci@w3.org>
To: Steve Chervitz <Steve_Chervitz@affymetrix.com>

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 22:38:06 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:43 GMT