[Taxacom] variants of taxon author names

fautin at ku.edu fautin at ku.edu
Sat Feb 25 11:04:26 CST 2012


The application Syngraph developed by my student Adorian Ardelean does 
precisely this.  It was described in a paper in Zootaxa about five years 
ago.  The download, alas, seems not to be working, but we have relied on 
it for more than a decade to link names used for the same beast.

So it is not only possible, it has been done.  For my database (URL 
below), we enter only published relationships -- not those my students and 
I infer (unless we have published them).  That allows a reader to recover 
the reasoning and decide whether to accept the hypothesis.  So we are 
agnostic about the "truth" of an assertion.  This is simply a record of 
the published literature.  Therefore, a single name may appear in more 
than one synonym list.


Daphne G. Fautin
Professor, Ecology and Evolutionary Biology
Curator, Natural History Museum and Biodiversity Research Center
Haworth Hall
University of Kansas
1200 Sunnyside Avenue
Lawrence, Kansas 66045-7534  USA

telephone 1-785-864-3062
fax 1-785-864-5321
evo user name fautin
skype user name daphne.fautin
website: http://invertebratezoology.biodiversity.ku.edu/home
cv: www.nhm.ku.edu/inverts/daphne.html

       direct to database of hexacorals, including sea anemones
               newest version released 19 August 2011
       http://hercules.kgs.ku.edu/Hexacoral/Anemone2/index.cfm

On Wed, 22 Feb 2012, Peter DeVries wrote:

> 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
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>>>>>>> of these methods:
>>>>>>>
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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
>>>>>> --------------------------------------------------------------------
>>>>>> ------------------
>>> _______________________________________________
>>>>>>
>>>>>> Taxacom Mailing List
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>>>>>>
>>>>>> The Taxacom archive going back to 1992 may be searched with either
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>>>>>>
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>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> Francisco Welter-Schultes
>>>>> Zoologisches Institut, Berliner Str. 28, D-37073 Goettingen Phone +49
>>>>> 551 395536 http://www.animalbase.org
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>>
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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
>>>>
>>>> _______________________________________________
>>>>
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>>>>
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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
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>>> Blog: http://iphylo.blogspot.com
>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>>
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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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>
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