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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 02:25:52 -0500
Message-ID: <AANLkTikQTE0jZRg3J5x6MRL6cYcQzAgAgZshpYi9bLVm@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>
Cc: Toby Inkster <tai@g5n.co.uk>, public-lod@w3.org, pedantic-web@googlegroups.com
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
------------------------------------------------------------
Received on Monday, 7 June 2010 07:26:29 UTC

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