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Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

From: Peter DeVries <pete.devries@gmail.com>
Date: Fri, 4 Jun 2010 21:29:51 -0500
Message-ID: <AANLkTiktjqKG06wHfJFyoKd3VG-QYXwnQ6Ms0GUEIRR2@mail.gmail.com>
To: joel sachs <jsachs@csee.umbc.edu>
Cc: public-lod@w3.org, pedantic-web@googlegroups.com
Hi Joel,

Thanks very much :-)  I will fix the foaf.

Yes, besides these not really being the same "kinds" of entities - some are
name like things and some are concept-like things. They often entail
incompatible subclassing. I was thinking that doing it this way leaves the
decision on how to interpret these connections to the data consumer.

For some uses like "topic" they are close enough, but for others they are
not.

skos:closeMatch seemed to be the best choice, although some have suggested
creating a specialized vocabulary.  ??

- Pete

On Fri, Jun 4, 2010 at 9:00 PM, joel sachs <jsachs@csee.umbc.edu> wrote:

> Pete,
>
> I notice that you use skos:closeMatch (instead of owl:sameAs) to assert
> near equivalence amongst species concepts. E.g.,
>
> <owl:Class rdf:about="http://lod.taxonconcept.org/ses/mCcSp#Species">
>        <skos:closeMatch rdf:resource="
> http://dbpedia.org/resource/Monarch_(butterfly)"/>
>
> In an area as tricky as species concepts, I agree that skos:closeMatch has
> advantages over owl:sameAs. (For example, closeMatch is not transitive,
> which makes it harder for errors to propagate.)
>
> You then make a series of foaf:isPrimaryTopicOf statements, such as
>
> <owl:Class rdf:about="http://lod.taxonconcept.org/ses/mCcSp#Species">
>        <foaf:isPrimaryTopicOf rdf:resource="
> http://en.wikipedia.org/wiki/Monarch_(butterfly)"/>
>
> But foaf:isPrimaryTopicOf is an inverse functional property. Since I assume
> you agree with the assertion (from dbpedia) that
>
> <rdf:Description rdf:about="
> http://en.wikipedia.org/wiki/Monarch_(butterfly)">
>        <foaf:primaryTopic rdf:resource="
> http://dbpedia.org/resource/Monarch_(butterfly)"/>
>
> you are, in fact, asserting that your Monarch Butterfly and dbpedia's
> Monarch Butterfly are owl:sameAs each other. (Is there a reason you need
> foaf:primaryTopic, instead of, say, dc:subject?)
>
> I look forward to using this dataset -
> Regards,
> Joel.
>
>
>
>
> On Fri, 4 Jun 2010, Peter DeVries wrote:
>
>  Hi Everyone,
>>
>> I am working on a new model for species concepts at TaxonConcept.org.
>>
>> These are an extension of my work on GeoSpecies, and are also designed to
>> investigate mapping names to concepts as part of the Global Names
>> Initiative<http://gni.globalnames.org/>
>>
>> .
>>
>> The main difference between these and GeoSpecies are that each species
>> concept is a class.
>>
>> This is to address some users who feel that species are best modeled as a
>> class.
>>
>> Other groups would like species modeled as an instance.
>>
>> This is mainly those groups that are dealing with large numbers of species
>> occurrence records.
>>
>> To deal with these different needs I have come up with the following
>> solution.
>>
>> Each species concept has related "Tags" that are instances.
>>
>> For example
>>
>> In this RDF there is a description of the following species concept
>>
>> http://lod.taxonconcept.org/ses/mCcSp.rdf
>>
>> there is a description of the following species concept
>>
>> http://lod.taxonconcept.org/ses/mCcSp#Species
>> URIBurner <
>>
>> http://linkeddata.uriburner.com/about/html/http/lod.taxonconcept.org/ses/mCcSp%01Species
>>
>>>
>>>
>> <txn:speciesConceptHasSpeciesTopicTag rdf:resource="
>> http://lod.taxonconcept.org/ses/mCcSp#Topic"/>
>>
>> <txn:speciesConceptHasSpeciesOccurrenceTag rdf:resource="
>> http://lod.taxonconcept.org/ses/mCcSp#Occurrence"/>
>>
>> <txn:speciesConceptHasSpeciesIndividualTag rdf:resource="
>> http://lod.taxonconcept.org/ses/mCcSp#Individual"/>
>>
>> I created the #Topic tag because I originally was thinking about using
>> that
>> to label those resources that have that species as a topic.
>>
>> Some think this may be unnecessary, but I have left it in for now while I
>> think about it.
>>
>> The "mCcSp#Occurrence" tag is to indicate that the entity is an occurrence
>> of that species.
>>
>> These are instances of the class txn:SpeciesOccurrenceTag, which allows
>> someone to partition the data set into only the information that is about
>> species occurrence records.
>>
>> The "mCcSp#Individual" tag is to represent individuals of that species.
>>
>> Another feature of the species concept RDF is that it maps the species
>> concept to related entities on the LOD and as foreign keys in other data
>> sets.
>>
>> The data set is available via my semantic site map at:
>> http://lod.taxonconcept.org/sitemap.xml.gz
>>
>> And is currently live on the LOD. A SPARQL Endpoint is being setup.
>>
>> The data set contains about 86,000 species concepts.
>>
>> ** We have notice that there maybe some problems with the Fungi section,
>> so
>> I would avoid those for the time being. **
>>
>> I have created a smaller example RDF dump file at:
>> http://lod.taxonconcept.org/taxonconcept_subset.rdf.gz
>>
>> This contains a combination of species concepts and related linked data
>> including Image galleries and a small sample of occurrence records.
>>
>> Here are some examples as viewed through the Sigma service.
>>
>> Monarch Butterfly Danaus plexippus <
>> http://sig.ma/search?pid=5d903f44eb963350b77074b7d9e80ff9 >
>>
>> Eastern Tree Hole Mosquito Ochlerotatus triseriatus  <
>> http://sig.ma/search?pid=5d903f44eb963350b77074b7d9e80ff9 >
>>
>> Additional Examples can be found at:
>>
>> http://www.taxonconcept.org/example-taxa/
>>
>> I also have some example SPARQL Queries that work on the LOD.
>>
>> http://www.taxonconcept.org/example-sparql-queries/
>>
>> I would appreciate feedback on these models and any suggestions for how
>> they
>> could be improved. :-)
>>
>> Thank you for your time and consideration.
>>
>> - Pete
>>
>> Ontology: http://lod.taxonconcept.org/ontology/txn.owl
>>
>> Ontology Doc: http://lod.taxonconcept.org/ontology/doc/index.html
>>
>> ----------------------------------------------------------------
>> 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 <http://about.geospecies.org/>
>> ------------------------------------------------------------
>>
>>


-- 
----------------------------------------------------------------
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 Saturday, 5 June 2010 02:30:25 UTC

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