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Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

From: Peter DeVries <pete.devries@gmail.com>
Date: Sun, 6 Jun 2010 16:13:38 -0500
Message-ID: <AANLkTinresm6nZ8ta7GAX1w42LhgP6IxbgP7nDXf9LpZ@mail.gmail.com>
To: Kingsley Idehen <kidehen@openlinksw.com>
Cc: Toby Inkster <tai@g5n.co.uk>, public-lod@w3.org, pedantic-web@googlegroups.com
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
"/>
    <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
------------------------------------------------------------
Received on Sunday, 6 June 2010 21:14:19 UTC

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