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Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

From: Peter DeVries <pete.devries@gmail.com>
Date: Mon, 7 Jun 2010 19:39:05 -0500
Message-ID: <AANLkTik1IlQflK8N3hqjnai0cs0LfS3jf1R2rjdOnu7r@mail.gmail.com>
To: Toby Inkster <tai@g5n.co.uk>, public-lod@w3.org, pedantic-web@googlegroups.com
The new examples of the species concepts are now live via Sindice.

You can find links to them on this page:
http://www.taxonconcept.org/example-taxa/

- Pete

On Mon, Jun 7, 2010 at 2:25 AM, Peter DeVries <pete.devries@gmail.com>wrote:

> I have made the changes they are visible in this RDF.
>
> http://lod.taxonconcept.org/ses/mCcSp.rdf
>
> <http://lod.taxonconcept.org/ses/mCcSp.rdf>I have also updated the
> following:
>
>  http://lod.taxonconcept.org/sitemap.xml.gz (Removed some problematic
> Fungi, now about 66,000 species)
>
>  http://lod.taxonconcept.org/taxonconcept_subset.rdf.gz
>
>  Ontology: http://lod.taxonconcept.org/ontology/txn.owl
>
> Ontology Doc: http://lod.taxonconcept.org/ontology/doc/index.html
>
> The Biol predicates are set as *equivalentproperty*.
>
> Biol Taxonomies are of type Taxonomy, so I created a new Tag <
> http://lod.taxonconcept.org/ses/mCcSp#Taxonomy
>
>   <txn:SpeciesTaxonomyTag rdf:about="
> http://lod.taxonconcept.org/ses/mCcSp#Taxonomy">
>     <skos:prefLabel>A Tag-like resource that is used to label taxonomies of
> the species concept Danaus plexippus se:mCcSp</skos:prefLabel>
>     <txn:speciesTaxonomyTagHasSpeciesConcept rdf:resource="
> http://lod.taxonconcept.org/ses/mCcSp#Species"/>
>     <txn:kingdom>Animalia</txn:kingdom>
>     <txn:phylum>Arthropoda</txn:phylum>
>     <txn:class>Insecta</txn:class>
>     <txn:order>Lepidoptera</txn:order>
>     <txn:family>Nymphalidae</txn:family>
>     <txn:genus>Danaus</txn:genus>
>     <txn:specificEpithet>plexippus</txn:specificEpithet>
>     <txn:scientificNameAuthorship>(Linnaeus,
> 1758)</txn:scientificNameAuthorship>
>     <txn:commonName>Monarch Butterfly</txn:commonName>
>   </txn:SpeciesTaxonomyTag>
>
> I have also added these links to EUNIS, although they maybe somewhat
> problematic since these are the same URI's as the foaf:page.
>
>   <eunis:SpeciesSynonym rdf:about="
> http://eunis.eea.europa.eu/species/90910">
>     <skos:closeMatch rdf:resource="
> http://lod.taxonconcept.org/ses/mCcSp#Species"/>
>     <rdfs:seeAlso rdf:resource="http://eunis.eea.europa.eu/species/90910
> "/>
>   </eunis:SpeciesSynonym>
>
> - Pete
>
> On Sun, Jun 6, 2010 at 4:13 PM, Peter DeVries <pete.devries@gmail.com>wrote:
>
>> Hi Toby,
>>
>> Here is where we seem to have some differences.
>>
>>        txn:species "plexippus" ;
>>        txn:authority "Linnaeus, 1758" ;
>>
>>
>>        txn:epithet "plexippus" ;
>>        txn:author_year "(Linnaeus, 1758)" ;
>>
>>
>> I looked at the latest DarwinCore <
>> http://code.google.com/p/darwincore/wiki/Taxon >
>>
>> Since it would be helpful to allow people to rewrite these easily, or the
>> txn: set equivalent property to.
>>
>> I think it might be best to adopt their set.
>> *
>> *
>> *genus: Carex*
>> *
>> *
>> *specificEpithet: viridula*
>> *
>> *
>> *infraspecificEpithet: elatior*
>> *
>> *
>> *taxonRank: varietas*
>> *
>> *
>> *scientificNameAuthorship: (Schltdl.) Crins*
>> *
>> *
>> *Ideally the scientific name would include the authorship and have three
>> parts to comply with the nomenclatural code (ICBN in this case):*
>> *
>> *
>> *Carex viridula var. elatior (Schltdl.) Crins*
>>
>> I am thinking I should do the following:
>>
>> txn:genus
>> txn:specificEpithet
>> txn:infraspecificEpithet <- am not using these now
>> txn:scientificNameAuthorship
>> txn:taxonRank
>>
>> DarwinCore does not have a dwc:commonName.
>>
>>
>> I can then set your versions for the same thing as equivalent properties
>> in my ontology. I will also cite your ontology in my ontology doc.
>>
>> Does everyone think that this will work? Or is there some side effect I am
>> not thinking off?
>>
>> Should I also set the DarwinCore attributes as equivalent properties.
>>
>> If you look at this page: <http://code.google.com/p/darwincore/wiki/Taxon>
>>
>> You will see what I am talking about in regards to Darwin core literals
>> vs. URI's
>>
>> The taxonRanks should probably be represented as URI's rather than
>> literals.
>>
>> Also note that it is likely that different groups, Wikipedia, ITIS, NCBI
>> etc. place the taxa in slightly different groups.
>>
>> So we are likely to see things like this in the cloud, note the duplicate
>> genus and epithet names for the same vocab.
>>
>> http://lod.taxonconcept.org/ses/x6gDo#Species
>>
>> txn:genus => Lithobates
>> txn:genus => Rana
>> txn:epithet => catesbeianus
>> txn:epithet => catesbeiana
>>
>> Also Note that it is difficult to tell which genus name goes with which
>> epithet?
>>
>>     <foaf:page rdf:resource="http://en.wikipedia.org/wiki/Bullfrog"/>
>>     <foaf:page rdf:resource="
>> http://species.wikimedia.org/wiki/Rana_catesbeiana"/>
>>     <foaf:page rdf:resource="http://www.eol.org/pages/330963"/>
>>     <foaf:page rdf:resource="http://eunis.eea.europa.eu/species/10586"/>
>>     <foaf:page rdf:resource="
>> http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&amp;search_value=775084<http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=775084>
>> "/>
>>     <txn:hasGBIF>13801188</txn:hasGBIF>
>>     <txn:hasITIS>775084</txn:hasITIS>
>>     <txn:hasEOL>330963</txn:hasEOL>
>>     <txn:hasNCBI>8400</txn:hasNCBI>
>>
>> This is one reason that I have started to think about linking out to
>> several alternative phylogenies. Right now I only have some to class.
>>
>>     <txn:inDBpediaClade rdf:resource="
>> http://dbpedia.org/ontology/Amphibian"/>
>>     <txn:inCoLClass rdf:resource="
>> http://lod.taxonconcept.org/ontology/phylo/CoL/CoL_2010_base.owl#Class_Amphibia
>> "/>
>>
>> On Sun, Jun 6, 2010 at 2:06 PM, Kingsley Idehen <kidehen@openlinksw.com>wrote:
>>
>>> Toby Inkster wrote:
>>>
>>>> On Fri, 4 Jun 2010 18:06:08 -0500
>>>> Peter DeVries <pete.devries@gmail.com> wrote:
>>>>
>>>>
>>>>
>>>>> I would appreciate feedback on these models and any suggestions for
>>>>> how they could be improved. :-)
>>>>>
>>>>>
>>>>
>>>> The following:
>>>>
>>>> @prefix txn: <http://lod.taxonconcept.org/ontology/txn.owl#> .
>>>>
>>>> <http://lod.taxonconcept.org/ses/mCcSp#Species>
>>>>        a owl:Class ;
>>>>        txn:kingdom "Animalia" ;
>>>>        txn:phylum "Arthropoda" ;
>>>>        txn:class "Insecta" ;
>>>>        txn:order "Lepidoptera" ;
>>>>        txn:family "Nymphalidae" ;
>>>>        txn:genus "Danaus" ;
>>>>        txn:epithet "plexippus" ;
>>>>        txn:author_year "(Linnaeus, 1758)" ;
>>>>        txn:commonName "Monarch Butterfly" ;
>>>>        foaf:page <foo> .
>>>>
>>>> Appears to be an almost identical way of representing a species concept
>>>> to the one I came up with a couple of years ago:
>>>>
>>>> @prefix txn: <http://purl.org/NET/biol/ns#> .
>>>>
>>>> <http://lod.taxonconcept.org/ses/mCcSp#Species>
>>>>        a txn:Taxonomy ;
>>>>        # note: txn:Taxonomy rdfs:subClassOf rdfs:Class.
>>>>        txn:kingdom "Animalia" ;
>>>>        txn:phylum "Arthropoda" ;
>>>>        txn:class "Insecta" ;
>>>>        txn:order "Lepidoptera" ;
>>>>        txn:family "Nymphalidae" ;
>>>>        txn:genus "Danaus" ;
>>>>        txn:species "plexippus" ;
>>>>        txn:authority "Linnaeus, 1758" ;
>>>>        txn:commonName "Monarch Butterfly" ;
>>>>        txn:seeAlso <foo> .
>>>>
>>>> I wonder if you could reuse the URIs I minted rather than creating new
>>>> ones?
>>>>
>>>>
>>>
>>> Peter,
>>>
>>> +1
>>>
>>> Re. reuse request from Toby. It early days, so little or no cost ;_
>>>
>>>  If we could stamp out any incompatibilities between the two ontologies,
>>>> then I'd be happy to point the http://purl.org/NET/biol/ns URI at your
>>>> ontology, so we'd just have a single merged ontology.
>>>>
>>>>
>>>
>>> Great!
>>>
>>>
>>> --
>>>
>>> Regards,
>>>
>>> Kingsley Idehen       President & CEO OpenLink Software     Web:
>>> http://www.openlinksw.com
>>> Weblog: http://www.openlinksw.com/blog/~kidehen
>>> Twitter/Identi.ca: kidehen
>>>
>>>
>>>
>>>
>>>
>>
>>
>> --
>> ----------------------------------------------------------------
>> 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
> ------------------------------------------------------------
>



-- 
----------------------------------------------------------------
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 Tuesday, 8 June 2010 00:46:06 UTC

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