[tdwg-tag] [tdwg-rdf: 105] Re: Any TCS users with experiences to report?

David Remsen dremsen at mbl.edu
Wed Nov 28 22:20:25 CET 2012

I need to unload some taxonomic bugbears even if I might be fundamentally wrong about some things.

1.   I hate, and have always hated, the term "taxon concept."  It implies that the distinction between a taxon name and a concept is somehow special.  Is it inaccurate to think of names as the "word"s used in taxonomy and concepts are the "definitions".   Geographical names have similar issues.  Don't many regular words themselves suffer this 'concept' problem?  Even the word 'concept' suffers the concept problem. [1]  I personally prefer to use the term 'taxon definition' when describing the issue to anyone who doesn't read this list. It keeps their yes from glazing over.  It's easier for me to digest too.

2. I get very anxious when I get involved in discussions on "sensu" this and "name-usage" that which subsequently link to taxon references that don't actually resolve to anything resembling the actual definition of a taxon!  It seems madness to have nearly any use of a taxon be a distinct concept because someone might have a different thought in their head about what the 'definition' is.

3. My opinion is that only distinct concepts should be distinctly identified.   What distinguishes a distinct taxonomic concept?   One that provides evidence of its circumscription[2] or, more succinctly, a "definition".   

4. ideally the elements used to define a taxon circumscription would be something machine-comparable so you could automagically compare concepts and infer relationships.   It seems most concept-to-concept mappings I've come across, on the other hand, are based on the non-evidence of someone saying A is broader than B and simply recording it that way.  

5. What elements can be used to describe the circumscription of a taxon?  I've come across:
a. specimens - I believe this is what Jessie and Martin Pullen, et al. preferred in the Prometheus work [3].  
b. Types/Original descriptions - I like this way of doing things.  In my opinion it provides the most flexibility for using taxonomy to improve discovery and access to species information.
c.  Morphological characters - Fundamentally I think these must actually be resolved to (a) or (b) above,  don't they?  Seems useful though.
d. Geospatial distribution - iNaturalist does a nice job of distinguishing concepts this way but I don't believe it's actually the definition.   What a pain to make machine-comparable too.
e. Synonymy - This seems to be how some define their taxa but without a clear distinction between taxonomy and nomenclature I don't see how it can work. Adding a nomenclatural synonym changes nothing regarding the circumscription.  So fundamentally this approach has to tie names back to (b) above.  At least if I know that my definition of Gorilla gorilla includes the types for berengei and graueri, and you think they are all distinct than my Gorilla is broader than yours.  
f. DNA - I really don't know anything about that.

6. Lastly, I worry a bit about using the hierarchical ancestry of a taxon as part of its definition.  For species I suppose the parent taxon could be considered an attribute of the concept/definition.  But for higher taxa it makes no sense at all.   

Anyway,  it's off my chest.  I bring it all up for two reasons.  I've rarely come across a term used more ambiguously than the term "taxon concept" and subsequently I've been very nervous about assessing different approaches to modeling them.

best from Woods Hole
Dave Remsen

[1] http://www.thefreedictionary.com/concept
[2] The "word circumscription," itself has at least four senses.  http://www.thefreedictionary.com/circumscription - I prefer circumscription sensu 1.
[3] Raguenaud, C., Pullan, M.R., Watson, M., Kennedy, J., Newman, M., Barclay, P. (2002). Implementation of the Prometheus Taxonomic Model: a comparison of database systems. Taxon, 51(1), 131-142.

On Nov 28, 2012, at 2:28 PM, Richard Pyle wrote:

> Oi Vey!
> OK, I’m not sure whether it’s best to respond to the email list, or comment
> on the post, so I’ll do both.
> First…. There technically isn’t  a “ZooBank data model”.  ZooBank isn’t a
> database, it’s a service build on the Global Names Usage Bank (GNUB)
> database.  The GNUB database is MUCH broader in scope than ZooBank.  ZooBank
> is only concerned with the specific subset of TNUs that involve
> nomenclatural acts as governed by the ICZN Code.  There are many, many, many
> more TNUs that are not nomenclatural acts, and/or involve names outside the
> scope of Zoology.  
> Second, like many other database projects, we’ve focused our available time
> much more on “doing”, rather than documenting.  However, it’s becoming
> increasingly clear that we need much more documentation about the GNUB data
> model, and I’ll try to bump that task up the priority list for the coming
> weeks. For now, I’ve uploaded four images to the ZooBank server showing the
> table relationships:
> http://zoobank.org/images/TaxonNameUsageCluster.jpg
> http://zoobank.org/images/ReferenceCluster.jpg
> http://zoobank.org/images/AgentCluster.jpg
> http://zoobank.org/images/CoreTables.jpg
> The first of these will be the most helpful to this discussion; but the
> others are of potential interest.  Also, this is the data model as it now
> stands.  Following a very productive meeting last April, there is a draft
> new data model that is mostly the same, but adds more capability to capture
> specific details about name usages.  But the general data model remains the
> same.
> Now, on to Rod’s post:
> 1) Nice choice of the example species!
> 2) The graph looks mostly right, but it’s hard in some cases to figure out
> what labels go with what arrows.  For example, the “protonym” in the
> upper-left corner of the image seems to apply to the vertical solid line
> connecting the top-left oval (which should be labeled "Belonoperca Fowler &
> Bean, 1930 sensu Eschmeyer 2004 "), and the other "protonym" applies to the
> recursive link for the protonym itself.  Similarly, the parentusageuuid off
> to the left applies to the vertical arrow from Belonoperca F&B to Serranidae
> sensu F&B.  It took me a while to figure out what was going on with the
> labeling of arrows.
> 3) Another issue with the graph is that the dotted lines from the three
> "sensu" TNUs to the respective original description publications are not
> links that actually exist in the data model, so it seems inappropriate to
> represent them in the graph.
> 4) While it's fair to say that the graph may look "to look a tad
> complicated" -- is it any more complicated than it needs to be?  After you
> get rid of the superfluous dashed lines from the "sensu" usages to the
> original publications, what specific pieces of information represented do
> you feel are not necessary to reflect taxonomic information? Taxonomy is,
> after all, a tad complicated in how it has worked over the past 250 years.
> I think part of the reason why many of the myriad existing databases don't
> quite fulfill the overall needs is that they aren't quite complicated
> enough.  In other words, too many databases take too many shortcuts in
> representing information, thereby reducing the overall utility.
> I have a major report due on Friday, so I can't respond in more detail now;
> but I will be glad to address any points of confusion or elaborate more
> completely on how the GNUB data model is structured (and why it is
> structured the way it is) next week.
> Aloha,
> Rich
> Richard L. Pyle, PhD
> Database Coordinator for Natural Sciences
> Associate Zoologist in Ichthyology
> Dive Safety Officer
> Department of Natural Sciences, Bishop Museum
> 1525 Bernice St., Honolulu, HI 96817
> Ph: (808)848-4115, Fax: (808)847-8252
> email: deepreef at bishopmuseum.org
> http://hbs.bishopmuseum.org/staff/pylerichard.html
> Note: This disclaimer formally apologizes for the disclaimer below, over
> which I have no control.
> From: Roderic Page [mailto:r.page at bio.gla.ac.uk] 
> Sent: Wednesday, November 28, 2012 1:04 AM
> To: Richard Pyle
> Cc: 'Steve Baskauf'; tdwg-rdf at googlegroups.com; Tony.Rees at csiro.au;
> pmurray at anbg.gov.au; Simon.Pigot at csiro.au; J.Kennedy at napier.ac.uk;
> eotuama at gbif.org; tdwg-tag at lists.tdwg.org; 'David Patterson'
> Subject: Re: [tdwg-rdf: 105] Re: [tdwg-tag] Any TCS users with experiences
> to report?
> To try and get my head around the various models of taxon names, usages, and
> concepts being discussed I've created a graph of my understanding of the
> data model underlying
> ZooBank http://iphylo.blogspot.co.uk/2012/11/zoobank-data-model.html . This
> may or may not reflect the actual situation, I'll leave that to Rich to
> comment on.
> Regards
> Rod
> ---------------------------------------------------------
> 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
> Skype: rdmpage
> Facebook: http://www.facebook.com/rdmpage
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
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