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Re: Lightweight RDF to Map Various Semantic Representations of Species

From: Antoine Isaac <aisaac@few.vu.nl>
Date: Wed, 02 Dec 2009 08:40:03 +0100
Message-ID: <4B1619D3.6080906@few.vu.nl>
To: Peter DeVries <pete.devries@gmail.com>
CC: public-lod@w3.org, SKOS <public-esw-thes@w3.org>
Hi Pete,

One can indeed understand that you prefer to have closeMatch between things that are indeed much more similar.
I guess that in the first Linnaeus classification, pumas were considered to be some form of cats, and then the name of the class was changed. Even if the beast itself remains, its understanding by biologists has changed, making it quite a different concept, arguably.

I don't really understand when you say that LSID "will" change with each yearly update, though. I would have hoped that once "felis concolor" has been given an ID once, it keeps it, at least until the next time that name itself is changed.

Cheers,

Antoine

PS: By the way, this CoL classification is a great use case for those interested in concept versioning and changes. Looking at [1] I would have thought that "Felis concolor Linnaeus, 1771" and "Puma concolor (Linnaeus, 1771)" are two labels (possibly represented using the more complex skos-xl:Label class [2]) of one same concept. But their respective pages show that different hierarchical links are being maintained for those two classes, making them indeed different skos:Concepts. I knew of course that this happens, but it's nice to have all data published, and in RDF :-)

[1] http://www.ubio.org/browser/details.php?namebankID=105509
[2] http://www.w3.org/TR/skos-reference/skos-xl.html


> Hi Antoine,
> 
> The ubio LSID's are more of a "name-like" thing, there are different 
> LSID's for the entities:
> 
> Puma concolor (Linnaeus, 1771) urn:lsid:ubio.org:namebank:2478181
> Felis concolor Linnaeus, 1771 urn:lsid:ubio.org:namebank:110521
> 
> The Catalog of Life LSID seems to be an identifier for the species, 
> however, the LSID will change with each new yearly update to the Catalog 
> of Life.
> So the 2010 CoL LSID for the Cougar will be different than the 2009 CoL 
> LSID.
> 
> It is for this reason that I made the ubioLSID a skos:relatedMatch while 
> having the CoL LSID a skos:closeMatch.
> 
> Does that seem to make sense?
> 
> Thanks for your interest :-)
> 
> - Pete
> 
> 
> On Tue, Dec 1, 2009 at 10:09 AM, Antoine Isaac <aisaac@few.vu.nl 
> <mailto:aisaac@few.vu.nl>> wrote:
> 
>     Hi Peter (ccing the SKOS list, as this is a SKOS implementation,
>     after all :-)
> 
>     I also think that's really a cool effort, with a great potential!
> 
>     My question would be about your choices wrt. the use of relatedMatch
>     and closeMatch: why do we have
>     http://rdf.taxonconcept.org/ses/v6n7p skos:relatedMatch
>     urn:lsid:ubio.org:namebank:105509 and
>     http://rdf.taxonconcept.org/ses/v6n7p skos:closeMatch
>     http://purl.uniprot.org/taxonomy/9696
>     ?
>     All three seem to be about the same beast, namely the one at [1].
>     I'd be very much interested in hearing about your decision criterion!
> 
>     Cheers,
> 
>     Antoine
> 
>     [1] http://www.ubio.org/browser/details.php?namebankID=105509
> 
> 
>         Hi LOD'ers :-)
> 
>         I am trying to work out some way to map the various semantic
>         representations for a species, in conjunction with a friendly
>         three letter organization.
> 
>         The goal of these documents is in part to improve "findability"
>         of information about species.
>         The hope is that they will also help serve as a bridge from the
>         LOD to species information from the three letter organization
>         and it's partners.
> 
>         The resources are mapped using skos:closeMatch.
> 
>         This should allow consumers to choose those attributes of each
>         species resource that they think are appropriate.
> 
>         It has been suggested to me that more comprehensive documents
>         describing species should be in the form of OWL documents, so I
>         have included nonfunctional links to these hypothetical resources.
> 
>         I have the following examples, and am looking for comments and
>         suggestions.
> 
>         RDF Example  http://rdf.taxonconcept.org/ses/v6n7p.rdf
> 
>         <http://rdf.taxonconcept.org/ses/v6n7p.rdf>Ontology      
>          http://rdf.taxonconcept.org/ont/txn.owl
> 
>         <http://rdf.taxonconcept.org/ont/txn.owl>Ontology Doc
>          http://rdf.taxonconcept.org/ont/txn_doc/index.html
> 
>         VOID              http://rdf.taxonconcept.org/ont/void.rdf
> 
>         <http://rdf.taxonconcept.org/ont/txn_doc/index.html>I look
>         forward to your comments and suggestions, :-)
> 
> 
>         - Pete
>         ----------------------------------------------------------------
>         Pete DeVries
>         Department of Entomology
>         University of Wisconsin - Madison
>         445 Russell Laboratories
>         1630 Linden Drive
>         Madison, WI 53706
>         GeoSpecies Knowledge Base
>         About the GeoSpecies Knowledge Base
>         ------------------------------------------------------------
> 
> 
> 
> 
> 
> -- 
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
> ------------------------------------------------------------
Received on Wednesday, 2 December 2009 07:40:32 UTC

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