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

Richard Pyle deepreef at bishopmuseum.org
Wed Nov 28 20:28:26 CET 2012

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.

. 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:


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

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.


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

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.



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

More information about the tdwg-tag mailing list