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

Peter DeVries pete.devries at gmail.com
Mon May 9 23:43:22 CEST 2011

Hi Steve,

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.

Among the LOD data sets TaxonConcept is one of the few biological datasets
that correctly follows the standards.

What I don't understand is why your new vocabulary is seen as an official
TDWG effort and mine is not.

Also it is not clear to me how you define a taxon. Are *Felis concolor* and
*Puma concolor* the same thing or different things?

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.

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.

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)

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.


- Pete

On Mon, May 9, 2011 at 3:53 PM, Steve Baskauf
<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 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.
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> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
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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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