[tdwg-content] Heretics and illuminati, oh my! [SEC=UNCLASSIFIED]

Steve Baskauf steve.baskauf at vanderbilt.edu
Tue May 10 03:10:25 CEST 2011

Comments inline.

Peter DeVries wrote:
> This may surprise you but on the Linked Open Data Cloud 
> TaxonConcept/GeoSpecies is a well known vocabulary.
> I has been looked at very closely by many in that community and has 
> been revised overtime.
> Other data sets including EUNIS - the European Union Environmental 
> Agency is in part based on it.
I am not knowledgeable enough to dispute this.
> Among the LOD data sets TaxonConcept is one of the few biological 
> datasets that correctly follows the standards.
To which standards are you referring?  W3C?  Generic rules for using RDF 
and OWL?  LOD best-practices?  TDWG?  If TDWG standards, which ones?
> What I don't understand is why your new vocabulary is seen as an 
> official TDWG effort and mine is not.
OK, I think that I said this before, but I'll say it again for clarity:  
DSW is NOT an official TDWG effort!  It is a Cam Webb/Steve Baskauf 
effort.  It is a functioning demonstration of a possible approach to 
describing biodiversity resources in RDF, just as taxonconcept.org is.  
However, it IS based on using terms from Darwin Core, which IS a 
ratified TDWG standard.  It also (for the moment) incorporates the 
sections of the TDWG Ontology which create terms in RDF to describe 
TaxonConcept instances in accordance with another ratified TDWG 
standard: the TSC schema.  So although DSW is NOT an official TDWG 
effort, it is composed of as many pieces of official TDWG efforts as we 
could find to build it from. 
> Also it is not clear to me how you define a taxon. Are /Felis 
> concolor/ and /Puma concolor/ the same thing or different things?
I have already confessed long ago that Cam and I dodged this question by 
not defining the Taxon class ourselves.  We used the relevant sections 
of the TDWG Ontology because it was based on a TDWG standard (TCS) and 
was consistent with other published references discussed on the page 
http://code.google.com/p/darwin-sw/wiki/ClassTaxon.  Ask your question 
to Roger Hyam (who I think wrote most of the TDWG Ontology) and Jessie 
Kennedy (who along with Roger wrote the TCS standard). 
> It is also not clear to me how it is determined what is "accepted" and 
> "consensus" based on the few people that take the time to write to the 
> list.
Well, with regards to Darwin Core, we tried to pay particular attention 
to the comments of John Wieczorek and Markus Döring whose names appear 
on the DwC documentation, and to Rich Pyle who was apparently consulted 
about at least parts of DwC.  I confess that they probably qualify as 
Illuminati, but they did write it.  I would also note that in the 
documentation of DSW we tried to show how the structure of DSW class 
interrelationships was related to earlier models such as the ASC model 
Given that the ASC model has been around since 1992 and formed the basis 
for several later models that were in general use, I think that it has 
some status as "accepted".  In my analysis of the many posts to the list 
over the past couple years 
(http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary), there 
was (in my opinion) general agreement about many of the more 
straightforward classes (such as Event and Identification).  In the 
cases where there was not uniform agreement, we tried to note this in 
the DSW documentation and provide a rationale for why we chose between 
the alternatives viewpoints that were expressed.  I will grant that the 
people who post to the list are probably a minority of the people who 
are receiving the posts.  But that's all we have.
> What do the lurkers think?
> I think for the vast majority of data providers the current DarwinCore 
> works for data submission.
> What could happen in the future is that GBIF takes these records, 
> cleans them and exposes some portion of their data in a a more 
> semantic markup to the LOD cloud.
I tried to express in my last post why I felt that it was consistent 
with the past stated goals of TDWG to prioritize the needs of data 
submission over the needs of semantic interpretation when those two 
goals conflicted.  I took a considerable amount of time to try to 
understand the taxonconcept.org ontology and in a previous message, to 
articulate the questions that I had about the structure of it.  Those 
questions were framed around the basic problem of the tradeoff between 
constructing an ontology that made prioritized semantic querying (the 
subclassing cats by color approach) and constructing an ontology that 
prioritized simplicity in class structure (the single cat type with 
color properties approach).  I don't think that you ever really 
responded to those specific questions/criticisms other than to say that 
your ontology was great and everybody should use it, and to demonstrate 
SPARQL queries with it. 

Really, I can't speak for Cam, but from my perspective, I would guess 
that 5% or less of the time I spent working on DSW was involved in 
actually writing the RDF (that's excluding the time it took to learn how 
to use Protege and Subversion).  At least 95% of the time or more was 
spent puzzling over emails and papers, writing annoying questions to the 
list to try to get people to talk about how they understood things, and 
then writing up the documentation with references.  If you want people 
to accept the taxonconcept.org ontology as a means to markup metadata 
and type resources, then I would encourage you to write up some detailed 
documentation explaining how your approach is similar or different from 
earlier models (and if different, why).  Also, some detailed 
explanations of what you intend the classes to represent would be 
helpful.  For example, I had initially assumed that what you meant by 
"Occurrence" and "SpeciesIndividual" meant the same thing as we had 
described for "Occurrence" and "IndividualOrganism" in the DSW 
documentation.  However, in your email responses it was clear to me that 
you meant something different (although I'm not sure what that was).

You suggested (if I'm understanding you correctly) in a previous email 
that you created taxonconcept.org so that its terms and classes could be 
used as a part of the TDWG infrastructure.  If that is your intention, 
then you need to describe in a detailed document how the mapping from an 
existing data markup standard (i.e. DwC) to taxonconcept.org should be 
accomplised.  As I pointed out in an earlier email, the structure of 
taxonconcept.org is rather complex ("reticulated") and potentially 
utilizes up to millions of classes, some of which have (to me) unclear 
connections to the DwC classes.  The correspondence between DSW classes 
and DwC classes is generally not an issue because DSW classes ARE DwC 
classes (mostly).

> The goal of my species concepts are to create URI's for a species that 
> have a RDF (machine interpretable) and HTML representation.   (the 
> HTML representation is likely to change in the future to something 
> much better) 
> That URI can then be used as a GUID that is relatively stable despite 
> changes in nomenclature and classification hierarchies.
> This allows searches for occurrence records and other data that are 
> tied to the thing most call /Puma concolor/ but is also known by many 
> other names.
> The alternative is for someone to search under all the potential name 
> variants (assuming that they know them all)
As I pointed out before, taxonconcept.org is built around taxa-related 
classes and as such it is good at doing the kinds of taxonomy-related 
queries that you describe above.  However, the TDWG community also 
includes people who are less interested in taxonomy and more interested 
in things like tracking individual whales over space, connecting 
different types of evidence that is located in different institutions, 
collecting data on one organism over time, etc.  That is why I 
questioned constructing a taxon-oriented ontology rather than an 
ontology containing a few general classes of things.

> The example queries are to show that the system seems to work in the 
> way people expect.
> To do this correctly and allow the functionality that people seen to 
> want it will need to be a little complex.
> Respectfully,
> - Pete
> On Mon, May 9, 2011 at 3:53 PM, Steve Baskauf 
> <steve.baskauf at vanderbilt.edu <mailto:steve.baskauf at vanderbilt.edu>> 
> wrote:
>     Being either fearless or a fool (is there actually a difference?),
>     I shall tread into this subject area at which I am a mere novice. 
>     So be kind...
>     I think that there may be several "solutions" to this problem. 
>     The one that is "correct" probably depends on what one is trying
>     to accomplish.  So I will try to describe in the most succinct way
>     what Cam and I were trying to accomplish with DSW, and how that
>     fits in with this thread.  Cam and I basically wanted to do two
>     things:
>     1. Make it possible to use GUIDs RIGHT NOW (not five years from
>     now). 
>     2. Create an extremely stripped down ontology that would be
>     non-controversial enough that people might actually use it, but
>     which wouldn't do anything so bad that it would inhibit future
>     development in the Semantic Web context (i.e. it could be extended
>     in the future by clever people to do clever Semantic Web stuff). 
>     Amazingly, the GUID Applicability Statement has achieved the
>     status of Standard-hood! (http://www.tdwg.org/standards/150/) 
>     Hooray!  I sort of missed the announcement, but ran across the
>     fact the other day when I was surfing through the TDWG website. 
>     Since the GUID A.S. is now a TDWG Standard, I would say it would
>     now officially be a best-practice to follow it.  In particular,
>     Recommendation 11 states "Objects in the biodiversity domain that
>     are identified by a GUID should be typed using the TDWG ontology
>     or other well-known vocabularies in accordance with the TDWG
>     common architecture."  This is somewhat problematic, given that
>     the TDWG ontology (with the possible exception of the
>     Taxon/TaxonConcept part) is effectively ("socially"?) deprecated. 
>     What is the alternative "other well-known vocabulary"?  There is
>     none, at least none having any kind of official status with TDWG. 
>     I recently discovered (or maybe re-discovered) the Technical
>     Architecture Group (TAG) Technical Roadmaps from 2006-2008:
>     http://www.tdwg.org/uploads/media/TAG_Roadmap_01.doc
>     http://www.tdwg.org/fileadmin/subgroups/tag/TAG_Roadmap_2007_final.pdf
>     http://www.tdwg.org/fileadmin/subgroups/tag/TAG_Roadmap_2008.pdf
>     I might have seen them before, but if so it was at the point where
>     I was really not knowledgeable enough to comprehend them.  I found
>     it very instructive to read about what the TAG had in mind when it
>     set out to create the TDWG Ontology.  In particular (from the 2007
>     Roadmap):
>     "From the point of view of exchanging data - such as in the
>     federation of a number of natural history collections - there is
>     no need for a standards architecture.  The federation is a closed
>     system where a single exchange format can be agreed on. ... This
>     model has worked well in the past but it does not meet the primary
>     use case that is emerging.  Biodiversity research is typically
>     carried out by combining data of different kinds from multiple
>     sources. The providers of data do not know who will use their data
>     or how it will be combined with data from other sources. The
>     consumer needs some level of commonality across all the data
>     received so that it can be combined for analysis without the need
>     to write computer software for every new combination." [This
>     brings to mind the very "different kinds" of resources Cam is
>     documenting in Borneo and the "multiple sources" that will be
>     handling the metadata once those resources are sent off to
>     herbaria, labs, and arboreta.]
>     and from the 2008 Roadmap:
>     "If GUIDs are used to uniquely identify 'pieces' of data we need
>     to have a shared understanding of what we mean by a 'piece of
>     data' i.e. what kind of thing is it that a particular id applies
>     to, a specimen, a person, an observation, a complete data set. We
>     also need to have a shared understanding of at least some of the
>     properties we use to describe these things."
>     Having been barely aware of TDWG's existence in 2008, I am
>     blissfully ignorant of whatever disagreements may have occurred
>     regarding LSIDs, reification, or whatever, and really don't want
>     to know about them.  All I can say as an outside observer is that
>     it appears that the failure of the initial efforts to get GUIDs
>     and the TDWG Ontology off the ground was because the system
>     envisioned was too complicated to maintain, too complicated to
>     gain a consensus, and to complicated to actually explain to
>     anybody.  Now that GUIDs seem to have a new lease on life, it
>     seems like the greatest chance of successfully implementing them
>     is to start by keeping things absolutely as simple as possible. 
>     To Cam and me, Darwin Core seemed to be the only candidate for
>     something relatively simple and relatively universally accepted on
>     which one could base an ontology that could be used to type GUIDs
>     and to use to express "a shared understanding of at least some of
>     the properties used to describe" biodiversity resources.  Although
>     I was somewhat skeptical that there was a "community consensus"
>     about what the DwC classes meant and how they were related to each
>     other, the exhaustive discussion on this list in Oct/Nov convinced
>     me that maybe there WAS a consensus, or at least enough of a
>     consensus to move forward.  Although some people may at the
>     present time be interested in figuring out how to do things like
>     "define 'Fish' as an owl class as well as as a Taxon object", I
>     would assert that is outside the core mission of TDWG as stated:
>     to "develop, adopt and promote standards and guidelines for the
>     recording and exchange of data about organisms evidenced by the
>     historical record".  It is fun to talk about, but to me not the
>     primary consideration in designing a community data exchange
>     model.  This outlook explains to some extent why I asked questions
>     about the complexity of taxonconcept.org <http://taxonconcept.org>
>     and its orientation toward facilitating semantic queries.  There
>     is nothing wrong with that, but it doesn't seem to be the
>     direction that TDWG has said it wants to go.  Perhaps when we have
>     "gotten there" (i.e. have a functioning system using GUIDs for
>     clearly typed resources), we might want to embark further down the
>     road to the Semantic Web.
>     Aside from just importing the DwC classes into the DSW ontology
>     and connecting them with object properties, Cam and I did a little
>     nasty thing with them.  It has been said that declaring ranges and
>     domains for terms doesn't prevent people from using the terms to
>     express relationships among the "wrong" types of things.  Rather,
>     it simply asserts that those things are instances of the classes
>     used in the range and domain declarations for the term.  That is
>     sort of true, but by declaring many of the core DwC classes to be
>     disjoint, we actually ARE preventing people from using the wrong
>     object properties with instances of the wrong classes.  If  Joe
>     Curator rdf:type's a determination as a dwc:Identification, but
>     then uses dsw:atEvent (which has the domain dwc:Occurrence) as a
>     property of the determination, then a reasoner will infer that the
>     determination is a type dwc:Occurrence as well as the explicitly
>     declared type dwc:Identification.  Because dwc:Identification and
>     dwc:Occurrence are disjoint classes, the reasoner will have a
>     fit.  Cam and I are being Naughty (sensu Bob Morris) because we
>     are inhibiting the extensibility of dsw:atEvent, but Joe Curator
>     is being Naughty (sensu Baskauf and Webb) because Cam and I
>     believe in the statement from the 2007 Roadmap: "The consumer
>     needs some level of commonality across all the data received...". 
>     Joe Curator is not being consistent with the "shared understanding
>     of at least some of the properties" to the extent that DSW
>     reflects the "shared understanding" of the TDWG community.  We are
>     basically trying to enforce a sort of orthodoxy on the use of DwC
>     classes as rdf:types and on the connections between the
>     dwc:classes so that people can have some reasonable expectation
>     that they are talking the same language as their partners whose
>     data are also being aggregated in the same federated database. 
>     It seems to me that this "enforcement of orthodoxy" may be very
>     much at odds with the free-wheeling spirit of the Semantic Web
>     community where Anybody Can Say Anything About Anything.  But when
>     I look over those old TAG roadmaps, I see little having to do with
>     clever Semantic inferencing.  I see a lot about providers and
>     consumers understanding what each other are talking about.  To
>     some extent, Darwin Core can provide most of the necessary
>     commonality between providers and consumers.  There were (in our
>     opinion) three areas where it could not.  One was the lack of a
>     class to link repeated sampling events and determinations
>     (dwc:IndividualOrganism or TaxonomicallyHomogeneousEntity if you
>     prefer) and another was a class that allowed for the separation of
>     evidence from the Occurrence documented by it (called by us the
>     dsw:Token class).  The other area was the dwc:Taxon class which
>     did not seem clear enough in its definition nor to possess enough
>     complexity to express the kinds of relationships commonly
>     discussed on this list.  dwc:Taxon needs to be "fixed" before it
>     is Ready For Prime Time (i.e. usable in rdf:type declarations)
>     So I guess having read the various responses to my query and
>     thinking about the history of the TDWG Ontology, I would say that
>     it may not really be important how dwc:Taxon could be tied to
>     tc:Taxon because the two classes probably don't need to be tied
>     together anyway.  As it currently stands, dwc:Taxon (outside of
>     DSW) has no semantic meaning other than what people want to
>     believe that it means because it's not tied to any other classes
>     by object properties of its instances.   The mish-mash of terms
>     describing names and taxa listed under dwc:Taxon add to the
>     confusion - since the DwC vocabulary purposefully does not declare
>     domains for the terms listed under a class they really could be
>     used as properties for an instance of any class anywhere.  In
>     contract, tc:Taxon does have properties that are described clearly
>     in the TDWG Ontology.  The only reason that we declared the two
>     classes to be equivalent was to signal that we felt that some of
>     the DwC terms listed under dwc:Taxon in the DwC vocabulary could
>     be used as data properties for the things in the tc:Taxon class
>     that people like Paul were describing with properties from the
>     TDWG Ontology.  Tying them together doesn't (at the moment) mess
>     up anything that anybody is doing with dwc:Taxon because (outside
>     of DSW) there isn't anything to actually DO with dwc:Taxon in
>     RDF.  However, the point is well taken that if someone in the
>     future did decide to define properties specifically intended for
>     use with dwc:Taxon, those properties would be hopelessly tangled
>     with tc:Taxon properties. 
>     It seems to me like the real road forward (if one believes as I do
>     that DwC is the only practical alternative to use for typing
>     GUIDs) would be to:
>     1. decide that the TDWG Ontology in its dead form adequately
>     describes taxa, names, and their properties (use it as-is).  OR
>     2. decide that although the TDWG Ontology doesn't do everything
>     that people want it to do at the present time, it could
>     resurrected and modified to do what people want (use it and hope
>     for the future).  OR
>     3. decide to just create the additional classes, e.g. dwc:Name (or
>     dsw:Name if you prefer not to adulterate the "pure" Darwin Core),
>     and object properties for dwc:Taxon and dwc:Name that are needed
>     to get the job done (i.e. just dump the TDWG Ontology as unfixable
>     and make up new stuff). 
>     In any of these three alternatives, there isn't actually any
>     reason to tie the two classes together that I can see.  Of these
>     three, I think the third option would probably be preferable,
>     although it might put Paul (and any others currently using the
>     TDWG Ontology to describe Taxon instances) in the unpleasant
>     position of having to redo their RDF.
>     Steve
>     Paul Murray wrote:
>>     On 09/05/2011, at 2:07 PM, Kevin Richards wrote:
>>>     Paul
>>>     I had the same thought (ie the x is of type dwc:Taxon, y is of type tc:Taxon, we know dwc:Taxon and tc:Taxon are equivalent, so we can reasonably compare x and y).
>>>     And this is built into standard semantic web reasoners - which is a bonus.
>>>     But this was debated (taking into account Bob Morris' issue) with respect to DwC and it was decided the benefits weren't significantly better than having a "dwc:isInCategory" sort of property that could then be "equivalent to" another class property and therefore giving you a similar advantage (admittedly not as good, but similar).
>>>     Do you think this is reasonable or are we just losing too much semantic web benefits by not specifying the domain constraint?
>>     A thing to watch out for is that in OWL DL, you cannot apply
>>     ordinary data and object properties to vocabulary objects
>>     (classes, predicates) - you can only apply annotation properties.
>>     If you apply an ordinary data property to a class, OWL DL treats
>>     this as what it calls "punning": it decides that there is a class
>>     named X and also a named individual named X, and that these have
>>     nothing to do with one another. The individual has properties,
>>     the class has members, and the annotation properties, well:
>>     whatever. Reasoners do not reason over annotation properties:
>>     indeed - that's the entire point. Attempting to put properties on
>>     properties and having classes being instances of classes results
>>     in things that are mathematically undecidable ("this statement
>>     cannot be proven to be true"). (another reason is that is allows
>>     you to put dc:comments and labels on classes, and even if you
>>     declare those classes to be equivalent nevertheless the comment
>>     only applies to the particular thing you put it on) This all
>>     means that dwc:isInCategory, if you want to apply it to dwc:taxon
>>     or other classes, will never have any meaning that semweb
>>     "engines" can get at. The underlying thing is that
>>     dwc:isInCategory is actually a meta-syntactic construct: rather
>>     than using owl to define a vocabulary, you are effectively
>>     attempting to extend OWL itself. But ... maybe that's ok. Maybe
>>     what is attempting to be done here only ever needs to be
>>     understood by humans. Now ... if what you are trying to do is to
>>     define "Fish" as an owl class as well as as a Taxon object - that
>>     is do-able, even to the point of being able to get inheritance
>>     working, using reflexive properties. At least ... I think it is.
>>     I should write a test case. If you have received this
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>>     .
>     -- 
>     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 <tel:%28615%29%20343-4582>,  fax: (615) 343-6707 <tel:%28615%29%20343-6707>
>     http://bioimages.vanderbilt.edu
>     _______________________________________________
>     tdwg-content mailing list
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>     http://lists.tdwg.org/mailman/listinfo/tdwg-content
> -- 
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries at wisc.edu <mailto:pdevries at wisc.edu>
> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies 
> <http://about.geospecies.org/> Knowledge Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
> --------------------------------------------------------------------------------------

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

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