[Taxacom] variants of taxon author names

Peter DeVries pete.devries at gmail.com
Wed Feb 22 15:10:09 CST 2012


Hi Rich,

I have been thinking that one way to do this is with a synonomy document
that is edited by the taxonomic expert.

It would have the following form, and could could be implemented with a
simple spreadsheet that is later processed into RDF.

The species concept  => relationship predicate => "The Name" => GNI ID
                                 => relationship predicate => "The Other
Name" => GNI ID

The GNI ID could be looked up and applied later during the conversion to
RDF.

the top relationship property is *taxonNameID*

all other relationships are subproperties of these

http://lod.taxonconcept.org/ontology/doc/objectproperties/taxonNameID___-25377385.html


For instance here is one of the malaria names http://bit.ly/wWN8rW

(I probably do not need all these name variations but I put in what Paddy
gave me.)

Unless there seems to be another popular alternative I tend to follow the
following pattern.

A taxon name like "Puma concolor" is a *TaxonName* while the URI that
represents that name is *TaxonNameID*

http://gni.globalnames.org/name_strings/6c3dc35f-d901-5cc5-b9c8-ad241069b9f8

A person who has described a taxon is a txn:Taxonomist which is a subclass
of dbpedia:Scientist

- Pete

On Wed, Feb 22, 2012 at 2:51 PM, Richard Pyle <deepreef at bishopmuseum.org>wrote:

> The answer, to me, is obvious:
>
> Build an infrastructure that cross-links ALL of the identifiers (and makes
> it exceedingly easy to do so).  The reality is that we have a plethora of
> identifiers now, and there is no easy way to predict which ones will be
> persistently actionable  5, 10, 50, 100 years from now.  What we want is a
> mechanism to cross-reference ("SameAs") these different identifiers (and
> tools to make this easy and delightful), so that when a given identifier
> dies, a call to that identifier can be re-directed to a comparable one.  It
> would also be an extremely valuable resource for reconciliation across
> overlapping datasets, and aggregation/reconciliation of metadata tied to
> different identifiers.
>
> Building the infrastructure is the easy part.  The hard part is
> understanding how the identifiers map.  For example, if one database
> defines
> each record in a table of Agents as a "person", and another defines each
> record as a "name of a person", then we have a logical mis-match, and
> "SameAs" direct mappings would be a mistake.
>
> I am increasingly of the belief that one of the greatest impediments our
> community has towards achieving the data-integrated utopia we have been
> discussing recently, is that we define our data objects in subtly different
> ways.  Nowhere is this more problematic than in the realm of scientific
> names of organisms.  I think this problems accounts for a large percentage
> of the explanation for the disparity between "Where we should be" with data
> integration in our community, and "Where we are".
>
> Aloha,
> Rich
>
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> > bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
> > Sent: Wednesday, February 22, 2012 7:56 AM
> > To: taxacom
> > Cc: Peter DeVries
> > Subject: Re: [Taxacom] variants of taxon author names
> >
> > Yes, but the issue is "who else uses that identifier?" It's no good
> minting an
> > identifier if it's not used elsewhere, ideally as widely as possible. So
> a
> linked
> > data advocate would say that Dbpedia ids are more widely used and
> > therefore enable you to potentially pull in a much bigger set of data.
> >
> > But I take your point. In my experience we either have no digital
> identifiers
> > (e.g., a lot of specimens, a lot of literature) or too many (e.g.,
> taxonomic
> > names).
> >
> > Regards
> >
> > Rod
> >
> > On 22 Feb 2012, at 17:42, Paul Kirk wrote:
> >
> > > a single identifier like what is already available for Linnaeus ...
> > http://www.ipni.org/ipni/idAuthorSearch.do?id=12653-1 ... :-) ... and
> has
> > been for a couple of decades.
> > >
> > > In haste,
> > >
> > > Paul
> > > ________________________________________
> > > From: taxacom-bounces at mailman.nhm.ku.edu
> > > [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Roderic Page
> > > [r.page at bio.gla.ac.uk]
> > > Sent: 22 February 2012 16:53
> > > To: taxacom
> > > Cc: Peter DeVries
> > > Subject: Re: [Taxacom] variants of taxon author names
> > >
> > > Dear Francisco,
> > >
> > > The DBpedia entry is based on Wikipedia as it was in July 2011. It's a
> > consequence of the way it is built that it won't be as current as
> Wikipedia
> > (there is a somewhat experimental "live" version).
> > >
> > > But I don't think Pete is necessarily advocating using Dbpedia to get
> all the
> > alternative names for a person - rather it provides a single identifier
> we
> can
> > hang all those names on. An analogy might be all the alternative names
> for
> a
> > journal (abbreviations, etc.). If the journal has an ISSN then we can use
> that
> > to unambiguously refer to that journal.
> > >
> > > If two data sets both identify Linnaeus using
> > http://dbpedia.org/page/Carl_Linnaeus then it becomes trivial to link
> the
> > data sets together. Otherwise we are left to match strings that may or
> may
> > not refer to the same thing.
> > >
> > > Regards
> > >
> > > Rod
> > >
> > >
> > > On 22 Feb 2012, at 16:05, Francisco Welter-Schultes wrote:
> > >
> > >>> Here is the DBpedia entry for Carl Linnaeus
> > >>> http://dbpedia.org/page/Carl_Linnaeus
> > >>>
> > >>> The various names used for him shows up under rdfs:label
> > >>
> > >> Does not really convince me. The content entries were taken at some
> > >> time a few years ago from Wikipedia but not updated afterwards, and
> > >> the labels show only an arbitrary selection of name variants
> > >> (obviously the ones selected as the name for the headlines by various
> WP
> > language sections).
> > >> The result is that the researcher's Swedish original name Linnæus
> > >> does not show up in the list.
> > >>
> > >> Francisco
> > >>
> > >>
> > >>> I have been working to link the original species descriptions to
> > >>> their authors using Linked Open Data methods.
> > >>>
> > >>> Many taxonomic authors have entries in Wikipedia which means that
> > >>> they exist in DBpedia
> > >>>
> > >>> The example below shows how the identifier for the original species
> > >>> description of the mosquito Ochlerotatus triseriatus links to the
> > >>> author Thomas Say in DBpedia.
> > >>>
> > >>> Original Description of Ochlerotatus triseriatus
> > >>> http://bit.ly/yWV3Tg
> > >>>
> > >>> I have notice that changes in the titles of the Wikipedia pages
> > >>> changes the URI (identifier).
> > >>>
> > >>> At this point I think the value that the DBpedia entries bring
> > >>> offset the occasional changes in the URI.
> > >>>
> > >>> It might be helpful if everyone added a Wikipedia entry for those
> > >>> authors they are familiar with.
> > >>>
> > >>> We can then create a list of the variants of taxon author names for
> > >>> each author.
> > >>>
> > >>> Here is the DBpedia entry for Carl Linnaeus
> > >>> http://dbpedia.org/page/Carl_Linnaeus
> > >>>
> > >>> The various names used for him shows up under rdfs:label
> > >>>
> > >>> Respectfully,
> > >>>
> > >>> - Pete
> > >>>
> > >>> On Wed, Feb 22, 2012 at 3:24 AM, Armand Turpel
> > >>> <armand.turpel.mnhn at gmail.com
> > >>>> wrote:
> > >>>
> > >>>> Does someone know where to find a source which lists all variants
> > >>>> of taxon author names?
> > >>>>
> > >>>> Example:
> > >>>>
> > >>>> Linnaeus, L., Linne, Linné
> > >>>> which swedish original name is Carl Nilsson Linnæus
> > >>>>
> > >>>> _______________________________________________
> > >>>>
> > >>>> Taxacom Mailing List
> > >>>> Taxacom at mailman.nhm.ku.edu
> > >>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > >>>>
> > >>>> The Taxacom archive going back to 1992 may be searched with either
> > >>>> of these methods:
> > >>>>
> > >>>> (1) by visiting http://taxacom.markmail.org
> > >>>>
> > >>>> (2) a Google search specified as:  site:
> > >>>> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> > >>>>
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> --------------------------------------------------------------------
> > >>> ----------------
> > >>> Pete DeVries
> > >>> Department of Entomology
> > >>> University of Wisconsin - Madison
> > >>> 445 Russell Laboratories
> > >>> 1630 Linden Drive
> > >>> Madison, WI 53706
> > >>> Email: pdevries at wisc.edu
> > >>> TaxonConcept <http://www.taxonconcept.org/>  &
> > >>> GeoSpecies<http://about.geospecies.org/> Knowledge Bases A
> > Semantic
> > >>> Web, Linked Open Data <http://linkeddata.org/>  Project
> > >>> --------------------------------------------------------------------
> > >>> ------------------
> > _______________________________________________
> > >>>
> > >>> Taxacom Mailing List
> > >>> Taxacom at mailman.nhm.ku.edu
> > >>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > >>>
> > >>> The Taxacom archive going back to 1992 may be searched with either
> > >>> of these methods:
> > >>>
> > >>> (1) by visiting http://taxacom.markmail.org
> > >>>
> > >>> (2) a Google search specified as:
> > >>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> > >>>
> > >>
> > >>
> > >> Francisco Welter-Schultes
> > >> Zoologisches Institut, Berliner Str. 28, D-37073 Goettingen Phone +49
> > >> 551 395536 http://www.animalbase.org
> > >>
> > >>
> > >> _______________________________________________
> > >>
> > >> Taxacom Mailing List
> > >> Taxacom at mailman.nhm.ku.edu
> > >> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > >>
> > >> The Taxacom archive going back to 1992 may be searched with either of
> > these methods:
> > >>
> > >> (1) by visiting http://taxacom.markmail.org
> > >>
> > >> (2) a Google search specified as:
> > >> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> > >>
> > >
> > > ---------------------------------------------------------
> > > Roderic Page
> > > Professor of Taxonomy
> > > Institute of Biodiversity, Animal Health and Comparative Medicine
> > > College of Medical, Veterinary and Life Sciences Graham Kerr Building
> > > University of Glasgow Glasgow G12 8QQ, UK
> > >
> > > Email: r.page at bio.gla.ac.uk
> > > Tel: +44 141 330 4778
> > > Fax: +44 141 330 2792
> > > AIM: rodpage1962 at aim.com
> > > Facebook: http://www.facebook.com/profile.php?id=1112517192
> > > Twitter: http://twitter.com/rdmpage
> > > Blog: http://iphylo.blogspot.com
> > > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> > >
> > > _______________________________________________
> > >
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> > >
> > > The Taxacom archive going back to 1992 may be searched with either of
> > these methods:
> > >
> > > (1) by visiting http://taxacom.markmail.org
> > >
> > > (2) a Google search specified as:
> > > site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> > >
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> > >
> >
> > ---------------------------------------------------------
> > Roderic Page
> > Professor of Taxonomy
> > Institute of Biodiversity, Animal Health and Comparative Medicine College
> of
> > Medical, Veterinary and Life Sciences Graham Kerr Building University of
> > Glasgow Glasgow G12 8QQ, UK
> >
> > Email: r.page at bio.gla.ac.uk
> > Tel: +44 141 330 4778
> > Fax: +44 141 330 2792
> > AIM: rodpage1962 at aim.com
> > Facebook: http://www.facebook.com/profile.php?id=1112517192
> > Twitter: http://twitter.com/rdmpage
> > Blog: http://iphylo.blogspot.com
> > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The Taxacom archive going back to 1992 may be searched with either of
> > these methods:
> >
> > (1) by visiting http://taxacom.markmail.org
> >
> > (2) a Google search specified as:
> > site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
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-- 
------------------------------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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