[Taxacom] Practical Taxon Concept Software

Anthony Pigott Anthony.Pigott at btinternet.com
Mon Nov 12 04:36:55 CST 2007


Thanks To Gael and Adorian for your help / advice.

Adorian - I think you've very accurately described what I'm looking for and
what many of the issues are.

Regards

Anthony
  -----Original Message-----
  From: Adorian Ardelean [mailto:ardelean at aquaecology.de]
  Sent: 29 October 2007 10:39
  To: Gael Lancelot; Anthony Pigott
  Cc: Taxacom
  Subject: Re: [Taxacom] Practical Taxon Concept Software


  Dear Lancelot,

  From my interpretation, Anthony needs to build/explore several custom and
concurrent (perhaps even ad-hoc) scenarios on what is Dryopteris affinis (in
a neutral fashion). This is highly related with published record (e.g.
monographies, revisional work, in general taxonomic literature) .

  Indeed the results in the search suggested by you may include several
taxonomic concepts, but tracing what taxonomic concept was used when
labeling specimens stops at data source specimen/its label/ or in the best
case its citation in literature. It does not return a whole taxon concept
with lists of related names and relations among them. I guess, for some of
the records the use of LSIDs, RDF and semantic web may be useful for tracing
the applied taxon concept, but I am not sure how much development is
currently put into this.

  As I see things now, there are two directions on how this may be
approached: simple synonymy lists and laborious chresonymy. In first
instance, it would be wonderful if GBIF for example or other similar
projects will produce filters for selecting occurrence data allowing
alternative views (taxon concepts in form of synonym lists) or, why not,
even user suggested views. I guess this is  easily achievable if a standard
is developed and various international resources serve their synonym lists
for further use. However, this may not solve Anthony's issue because
although all labels on specimens say D. affinis behind may be different
taxon concepts (we could have specimens collected in at least 200 years!)
and this can be solved mainly by tracing literature and citation of
specimens in literature (more related to chresonymy). This is a quite
difficult and laborious task that can be actually passed partially to user
side (if we speak about a limited number of records), or to taxon focused
projects. In myNature project (http://mybiosis.org) for example we will ask
users to specify what guide, key, publication was used when ID was given -
this included in metadata of record may help later deciding on what taxon
concept was applied. Aside from this discussion, I see regional biodiversity
focused projects enormously benefiting from such developments.

  All the best,
  Adorian


  At 09:59 29.10.2007, Gael Lancelot wrote:

    This might not be exactly what you're looking for, but GBIF (Global
    Biodiversity Information Facility) connects together a large number of
    specimen and observation databases, and keeps record of the taxonomy
    used in each. You can consult these taxonomies for Dryopteris affinis
    at this link:

http://data.gbif.org/species/search.htm?c[0].s=0&c[0].p=0&c[0].o=Dryopteris%
20affinis&c[1].s=9&c[1].p=0&c[1].o=7000

    More general information to be had at http://data.gbif.org .

    Cheers,

    G. Lancelot

    > Thanks for the responses. I'll try to be a bit more specific. I'd like
to be
    > able to record and organise the various names that taxa have been
given in
    > different treatments so that I can in due course produce a 'preferred
    > taxonomy with synonymy, etc., as traditionally done in a monograph, I
    > suppose, but also to be able to compare and demonstrate alternative
    > treatments in a neutral way.  The immediate target is the Dryopteris
affinis
    > complex in the ferns, which is a  particularly nomenclaturally-tangled
    > asexual species complex in which most taxa have been given a wealth of
names
    > at various levels and with various circumscriptions. I thought it
would be
    > useful way to approach it especially as I'm interested in the idea of
    > databases holding multiple taxonomies (alternative treatments) rather
than
    > the more traditional method of just holding one preferred view with
    > synonymy.
    >
    > Regards
    >
    > Anthony
    >
    >> -----Original Message-----
    >> From: taxacom-bounces at mailman.nhm.ku.edu
    >> [ mailto:taxacom-bounces at mailman.nhm.ku.edu]On Behalf Of Roger Hyam
    >> Sent: 28 October 2007 20:52
    >> To: taxacom at mailman.nhm.ku.edu
    >> Subject: [Taxacom] Practical Taxon Concept Software
    >>
    >>
    >>
    >> Anthony,
    >>
    >> I'd be interested to know your requirements a little better. Why do
    >> you want to track the taxonomies? Are you creating a monograph or
    >> flora/fauna or do you need it to accurately integrate ecological or
    >> other studies?
    >>
    >> The chances are you don't just want Taxon Concept software but want
    >> software to do something "useful" that just happens to handle Taxon
    >> Concepts data correctly.
    >>
    >> Thanks,
    >>
    >> Roger
    >>
    >>
    >>
    >>
    >> On 28 Oct 2007, at 17:00, taxacom-request at mailman.nhm.ku.edu wrote:
    >>
    >> > Date: Sun, 28 Oct 2007 10:03:14 -0000
    >> > From: "Anthony Pigott" <Anthony.Pigott at btinternet.com>
    >> > Subject: [Taxacom] Practical Taxon Concept Software
    >> > To: "Taxacom" <taxacom at mailman.nhm.ku.edu>
    >> > Message-ID:
    >> >     <DCEFIBBAOPBHLHBNBDGHGEKAKAAA.Anthony.Pigott at btinternet.com>
    >> > Content-Type: text/plain; charset="iso-8859-1"
    >> >
    >> > Does anyone have experience of the practical use of software
    >> > supporting the
    >> > creation and use of a database for recording multiple taxonomies,
    >> > i.e. taxon
    >> > concepts, publication-based, etc.?  I've tried a few of the
    >> > examples that
    >> > various people have built and made available for download but so
    >> > far I've
    >> > not found anything that works sufficiently well (or at all,
    >> > sometimes) for
    >> > practical use. Thanks.
    >> >
    >> > Anthony
    >>
    >>
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    >
    >
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    Gaël Lancelot
    Communication Officier
    EDIT - WP1
    (0033)1 40 79 80 19



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  Dr. Adorian Ardelean



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