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Re: [BiONT][BioRDF] Mussels

From: June Kinoshita <junekino@media.mit.edu>
Date: Thu, 4 May 2006 15:03:08 -0400
Message-Id: <794539D4-AC33-4BEB-8532-E3A464A4EE59@media.mit.edu>
Cc: <public-semweb-lifesci@w3.org>
To: Matthias Samwald <samwald@gmx.at>

On May 4, 2006, at 4:47 AM, Matthias Samwald wrote:

>>  One of them is mussels. Q: what should this resolve to?
> It seems that this is a VERY common problem when one has to map  
> existing taxonomies and classification schemes. Many of them do not  
> have a concise class-subclass structure. Two examples I had to deal  
> with already are Entrez Taxonomy and the IUPHAR naming scheme of  
> receptors. The problem is that in such complex taxonomies there are  
> many different levels of granularity (phylum, class, genus, species  
> etc.), but most taxonomies/naming schemes do not cover all of these  
> different levels of granularity. For instance, from the IUPHAR  
> naming scheme we can derive a code for a serotonin receptor  
> ('2.1:5HT:') and codes for serotonin receptors 1A, 2A, 2B etcc  
> ('2.1:5HT:1:5HT1A:' etc.), but there is no code for serotonin  
> receptor 2, or serotonin receptor 4 (including all of its  
> subtypes). This can be very annoying in practice.
> Another problem is that many databases use more general names (e.g.  
> 'frog') when they are in practice referring to a more specific  
> thing (e.g. 'Xenopus sp.').
> kind regards,
> Matthias Samwald
> PS: I would guess that 'bivalvia' would be the common taxonomic  
> term that is semantically closest in meaning to 'mussels'.

We thought about this quite a bit when we developed the controlled  
vocabulary for the Antibody database. The curator was dependent on  
the information supplied by the manufacturer, so if the manufacturer  
indicated "mussel" without specifying the species, that's what we  
used. The only way to find out the exact species would be to contact  
the manufacturer and try to track down the original source. This  
seems impractical, to say the least.

Our scheme is based on what is available in the data. If we had  
picked common term (e.g. bivalvia), we would have lost more specific  
information. On the other hand, if the manufacturer provides a  
nonspecific term (e.g. frog), we can't assume that it is xenopus  
without confirmation. In the end, we figured that the individual  
users would choose the taxonomic level that is important in their  
specific application.

Received on Thursday, 4 May 2006 19:03:56 UTC

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