[tdwg-content] opposing anything that comes from outside a small click was Re: If you need something for referring to a population, then it is probably best to do it as a related class

Peter DeVries pete.devries at gmail.com
Sun May 1 03:54:43 CEST 2011

Hi Steve,

I was expressing my disappointment about how this process operates, not
disappointment in you or your efforts.

A while back I posted several messages with examples showing that the
current DarwinCore, while good for it's current use, is not well suited for
the Semantic Web.

I proposed that we work on something that might be better suited for that
use while data providers continued to use the DarwinCore.

There seemed to be no consensus that this was the thing to do, or that
anyone else agreed with my proposal.

It is not clear how TDWG decisions are made. There seem to be discussions
and debate, not voting or clear consensus on the email list.

What does seem to happen is some mysterious entity, *that I like to call the
TDWG Illuminati*, seems decide what the "consensus" is.

So apparently there was consensus that we should investigate a more semantic
version of the DarwinCore and the minting a separate set of URI"s was
blessed by the Illuminati.

What I don't understand is this: Is there is any real difference between
examples that start with "txn" are any "dsw"

Haven't I said all along that my stuff could be moved into the DarwinCore?

The reason I created txn was that my efforts at advocating for a markup that
followed Linked Open Data best practices was going nowhere.

I needed URI's that resolved correctly.

The issue relating to my TaxonConcepts are complicated, the specifics will
need to come at a later date.

However, I take issue with the idea that Taxon = name use when you consider
the actual practice of the vast majority of biologists and the actual data
sets that are available.

If NCBI, eBird, BOLD, or any data from of the countless field and lab
observations were tagged with a "sensu" or "secundum" then you might have an

So the consensus in the larger biological community is that this is not how
information about species is tagged.

The goal of my TaxonConcepts is provide machine / human interpretable
species concepts so that different biologists can more reliably and
repeatedly determine which concept is the most appropriate "tag" for the
individual organism they are looking at in a microscope or through

A tag that can remain stable to changes in nomenclature like that seen seen
with Aedes / Ochlerotatus.

A first step in this process is to connect that species to the many name
variants with which it is associated.

A second step is to link the concept to closely related concepts,
identifiers and other existing documentation on the web.

Some of these concepts include links to the original description, etype
pages, BOLD barcodes etc. They have the ability to be linked to the type and
other specimens.

They have been looked at very carefully my leaders in the Linked Open Data
community and the GeoSpecies / TaxonConcept are seen as one of the better
designed LOD data sets.

In general, SPARQL queries on a local or LOD endpoint work as expected.

Are they perfect? No.


- Pete

On Fri, Apr 29, 2011 at 9:46 PM, Steve Baskauf <steve.baskauf at vanderbilt.edu
> wrote:

> Hi Pete,
> I want to respond to your message in two parts.  It may take me some time
> to write a response to the second part (i.e. questions about your
> suggestion) so it may not come right away.  But I also wanted to comment
> about the first part, that is:
> Peter DeVries wrote:
>> I am still somewhat puzzled why TDWG seems so opposed to adopting anything
>> that comes from outside a small click?
>>  I'm not exactly sure if this is directed at Cam and me (in the context of
> darwin-sw), or to others.  If it is directed at me, then you can read my
> response.  If not, then you can ignore it.
> First of all, I'd like to say that I greatly respect the work that you've
> done on trying to promote the use of LOD in the TDWG community.  I have read
> every one of your posts and have tried to understand all of them to the
> extent that I'm able.  I think we referenced your posts over 20 times at
> http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary, cited
> your taxon concept examples at
> http://code.google.com/p/darwin-sw/wiki/ClassTaxon and included your model
> in the analysis of previous models at
> http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels.
>  Your suggestion of using the geo: scheme was included in the discussion of
> the Location class at
> http://code.google.com/p/darwin-sw/wiki/ClassLocation .  I would say that
> at least half of what I know about RDF comes from looking at your examples
> and trying to understand what you have done.  I am therefore very grateful
> for the work that you have done and your enthusiasm for bringing creative
> ideas into the community.
> So why did Cam and I create Darwin-SW instead of just using your ontologies
> at taxonconcept.org ?  There are several reasons, some of which are
> alluded to at
> http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels .
>  But to be succinct (OK, maybe not that succinct), I'll state them here:
> 1. Darwin Core is a ratified TDWG standard.  It therefore qualifies as a
> "well-known" vocabulary.  If I refer to dwc:recordedBy as a property, people
> in the biodiversity informatics community will know what it means.  If I
> refer to dwc:Identification, it will also be known in our community.  For
> this reason, Cam and I wanted as much as possible to build Darwin-SW on
> Darwin Core rather than using terms that we or any other individual minted.
> 2. Cam and I wanted the Darwin-SW ontology to (as much as possible) reflect
> the community consensus on what classes meant and and how they were related
> to each other.  Of course, the problem is knowing what that consensus was.
>  After the hundreds of emails that were posted on the tdwg-content list from
> September 2010 to the present, I feel like I have a much better
> understanding of what the consensus is than I did before (where there IS a
> consensus, of course).  I have spent more hours than I care to remember
> trying to read, re-read, and understand the various emails that were sent
> and then asking annoying questions until somebody was patient enough to
> explain things to me.  Most of those explanations are referenced on the
> class wiki pages.  So I don't consider the ideas embodied in Darwin-SW to be
> "our" ideas - they are the ideas we absorbed from the community, including
> you.  (If you want to see "my" actual ideas, look at the examples in my
> Biodiversity Informatics article.  I don't really think that they are really
> that good any more.)  The outlook of DSW also recognizes historical
> precedents such as the ACS model.  As cool and clever as taxonconcept.orgis, it fundamentally represents Pete DeVries' ideas.  That means that it
> will readily be accepted by you, but the community may be less apt to buy
> into it if it doesn't embody community concepts.  It may turn out that
> Darwin-SW does NOT actually represent the community consensus (as we hope it
> does), or is stupid, or doesn't work.  In those cases, it will get shot down
> and somebody else will pick up the task of trying to figure out what the
> community consensus is about how things should be represented in RDF.  I
> should note that I don't think the discussion last Oct/Nov was limited to a
> clique of TDWG architects.  I was an active participant and I certainly
> don't qualify as a TDWG insider, having only been to one TDWG meeting for
> less than 24 hours and knowing almost no other TDWG contributors personally.
> 3.  There are a couple of structural things about taxonconcept.org terms
> and classes that I have questions about and I'll raise them in my second
> email to come after this one.  But I think that one of the most problematic
> things about taxonconcept.org for me is the way that you describe taxon
> concepts.  I hate to even bring up the subject because it's taken me months
> just to try to understand what people mean when they are talking about a
> taxon concept and I don't want to unleash another hundred emails about the
> minutae of taxon concepts, which people on this list love to talk about.  So
> suffice it to say that the sense that I've gotten from the many posts on the
> subject is that most people see a Taxon Concept (= = Taxon and similar to a
> "taxon name use") as the combination of a taxon name and a "sensu" or
> "secundum" (accordingTo) reference.  That's how it is modeled in the TCS
> model, which is another ratified TDWG standard.  That's also how it's
> modeled in the unfinished TDWG ontology, which despite its unfinished state
> is nonetheless is actually being used by some people to describe taxon
> concepts (see http://code.google.com/p/darwin-sw/wiki/ClassTaxon for links
> to some examples).  When I look at how you model taxon concepts such as in
> http://lod.taxonconcept.org/ses/v6n7p.rdf which describes the species
> concept http://lod.taxonconcept.org/ses/v6n7p#Species , there are a lot of
> metadata about the scientific name, related name strings, URIs that
> represent similar resources, connections to the original description, etc.
>  But I don't see any sensu/secundum reference or a property that links to
> one.  So although http://lod.taxonconcept.org/ses/v6n7p#Species is a cool
> thing that links to a lot of useful information about Puma concolor, it
> doesn't seem to be the same thing as what everybody else is calling a taxon
> concept.  If I were to link to your "species concepts", you and I might know
> what that meant, but nobody else would.  That is in contrast to a tc:Taxon
> (= = tc:TaxonConcept) instance which is defined by reference to the TCS
> model and I would therefore consider "well known" (and is what we DO
> reference in DSW).
> So I think that in some sense, my reluctance to adopt individually "minted"
> classes and properties comes from the reason why I'm interested in RDF in
> the first place.  I'm actually NOT very interested in using RDF to do
> reasoning in the "Semantic Web" sense - I guess I'm still a bit of a skeptic
> about how likely it is that anybody will be able to find out anything useful
> by doing reasoning on RDF that they suck in from the cloud, particularly if
> lots of people are using their own minted properties and if different people
> intend for the classes they use to rdf:type things to mean different things
> and have different properties.  What I AM interested in is figuring out a
> way to make it possible for people to have a consistent understanding of the
> meaning of metadata that they discover when they resolve GUIDs.  I think
> that will be increasingly important when projects like BiSciCol get rolling.
>  The only way that I see this as possible is to base properties primarily on
> vocabularies that a lot of institutions already "understand" and are using,
> like Darwin Core.
> That doesn't mean that people will ONLY use Darwin Core.  I have already
> heard plenty of talk on this list about using other vocabularies such as
> geo:, skos:, and foaf: (with some cautions from Bob).  John Wieczorek, the
> architect of the Darwin Core standard, proposed adding geo: terms to DwC
> (see http://code.google.com/p/darwincore/issues/detail?id=82).  There are
> also at least four people on this list that I know are interested in trying
> to make sure that DwC can interface with the OBOE ontology. So I don't think
> it is fair to say that "TDWG" is opposed to adopting things outside its
> clique.  I just think that people are cautious about supporting things that
> they are not familiar with (or perhaps don't understand) and in a lot of
> cases just don't have the time (or aren't willing to take the time) to
> figure out something new.
> So I hope that you aren't discouraged that people are slow to jump on the
> LOD bandwagon.  I think that more people will be interested in supporting it
> when they start seeing tangible applications within our community and that's
> already starting to happen.  Unfortunately, since you are so far ahead of
> the rest of us in your understanding of how the LOD world works, I think
> that you are probably doomed to be one of the ones pulling the wagon! :-)  I
> look forward (as I have in the past) to hearing more of your innovative
> ideas.
> Steve
> --
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
> postal mail address:
> VU Station B 351634
> Nashville, TN  37235-1634,  U.S.A.
> delivery address:
> 2125 Stevenson Center
> 1161 21st Ave., S.
> Nashville, TN 37235
> office: 2128 Stevenson Center
> phone: (615) 343-4582,  fax: (615) 343-6707
> http://bioimages.vanderbilt.edu

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
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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