[tdwg-tag] Any TCS users with experiences to report?

Richard Pyle deepreef at bishopmuseum.org
Sat Nov 3 06:33:56 CET 2012

I never received Jessie's original post; I only saw it in Tony's reply (I
wonder what other posts are not getting through...).

In any case, thanks to Jessie for sending that -- her description very
closely matches my own recollection of how TCS came to be, and the context
in which it happened.

But I wanted to comment on the same bit that Tony did, but coming from a
different angle:

> > I think it would be great if the major databases that describe taxa
> > (not just list names) described their data as concepts and allowed
> > people to link to their databases when identifying specimens and when
> > sequencing etc, this would be the start of a really useful biodiversity
> network.

I think the fundamental problem that existed during the development of TCS
continues to this day; which is that there is no consensus definition of
what a taxon concept "is" (in an informatics sense).  We throw words like
"circumscription" and such around, and although those words do help clarify
the conversation a bit, they still leave a great deal of "wiggle room" for

Is it a clade?  Is it a class? Is it a set?  In the same way that light is
both a wave and a particle, taxon concepts can be different things at the
same time.

Three things that I think TCS got right (and should not be abandoned or
forgotten with TCS 2.0, or whatever else takes the lead) are:
1) Separation of nomenclature from taxon concepts
2) Flexibility in how to represent the boundaries/definition of taxon
3) Support for 3rd-party concept mapping (i.e., RelationshipAssertions)

But even with these assets, we still have very different ideas about how we
want to define what a concept "is", which we really need to do before we can
come up with a standard data model to represent them.

Pete DeVries has done a lot of work in this area for establishing Taxon
Concepts in LOD space.  I think there is a great deal of overlap between
what he is on about, and what other, more traditional peddlers of taxon
concepts (e.g., CoL), are on about.  However, there is still a rather broad
disconnect in how we might cross-walk these different notions of a concept
to each other.

This is why I have always advocated an approach that focuses on atomized
taxon name usage (TNU) instances.  These are factual in nature, and much
easier to model.  TNUs serve as the foundation for both nomenclatural and
taxon concept domains (the least common denominator, so to speak), and can
serve to bridge not only names to concepts, but concepts to other concepts,
and cross-linking of other information (occurrences, classifications, etc.)
We've focused a lot of our effort these past two years, in part funded by
the BiScCol project and more robustly funded by the Global Names (U.S.)
project, and we're developing some basic web services to leverage the TNU
approach to representing multiple classifications, cross-mapping taxon
concepts, and bridging nomenclature to taxonomy.

But the weakest link for the TNU approach is the lack of robust data
content.  I'm referring to much more than just missing names (which will
total in the low single-digit millions); but also to the missing name-usage
instances (which will number in the hundreds of millions to billions).  The
gears are slowly starting to turn in this area, but there is still a long
way yet to go.

We have another grant pending to further support GNA/GNUB development, and
this time we also have Nico Franz on board to help flesh out a TNU-based
taxon concept model -- which I have tremendous confidence will help guide
the way forward in the long term (I'll leave it to Nico to elaborate).

But as the TDWG TNC person, my current focus is more on the short- and
medium-term needs of the broader community.  For most needs, by most data
providers, TCS, the vocabularies, and DwC/DwCa meet (or exceed) most of the
technical needs (excepting the examples given by Paul).  What I think we
need to do is harmonize those largely overlapping but not-quite-identical
approaches, and integrate the ideas that have come from Pete DeVries' work
(http://www.taxonconcept.org) and from the Darwin-SW efforts.  If we do it
right, we can get rid of the redundancy and expand the functionality at the
same time.


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

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