[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

Steve Baskauf steve.baskauf at vanderbilt.edu
Sat Apr 30 04:46:33 CEST 2011

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 
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.org is, 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.


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

More information about the tdwg-content mailing list