[tdwg-content] 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
Wed May 4 15:15:30 CEST 2011

Hi Steve, Bob and Hilmar,

It might be helpful to think of it this way.

This species concept http://lod.taxonconcept.org/ses/mCcSp#Species

is *both* an instance of txn:SpeciesConcept and an owl:Class

The occurrence record

*both* an instance of txn:Occurrence and an instance of

This identification record has links back to the species concept, occurrence
and individual

bit.ly http://bit.ly/jtLgNu

My reasoning behind the current structure is that you want to be able to
easily query for:

*Occurrences at at the TDWG BioBlitz*

PREFIX txn:     <http://lod.taxonconcept.org/ontology/txn.owl#>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf:    <http://xmlns.com/foaf/0.1/>

select distinct ?s, ?o as ?image,  ?kingdom, ?phylum, ?class, ?order,
?family, ?genus, ?sciname, ?cname where {
 ?s rdf:type txn:Occurrence.
 ?s dcterms:isPartOf <
 ?s txn:kingdom ?kingdom.
 ?s txn:phylum  ?phylum.
 ?s txn:class   ?class.
 ?s txn:order   ?order.
 ?s txn:family  ?family.
 ?s txn:genus   ?genus.
 ?s txn:hasScientificName   ?sciname.
 optional {?s  foaf:depiction ?o.
           ?s  txn:commonName ?cname}.

Run This Query:  bit.ly/kZ8C1Q

*Species expected in Massachusetts*
PREFIX txn:     <http://lod.taxonconcept.org/ontology/txn.owl#>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX massachusetts: <http://sws.geonames.org/6254926/>

select distinct ?s,  ?sciname, ?cname,  ?concept where {
  ?s rdf:type txn:SpeciesConcept.
  ?s txn:isExpectedIn massachusetts:.
  ?s txn:hasScientificName   ?sciname.
  ?s dcterms:identifier ?concept.
  optional {?s  txn:commonName ?cname}.

Run This Query  http://bit.ly/mt3Tsx

And get results free of all inappropriate identifications.

Do you want the misidentifications showing up in these species lists?

How would a general user correctly determine which of these identifications
are correct?

Those that are interested in looking at the identification history of a
particular specimen can do so,

It would also be possible to create your own identification RDF file and
apply that to the data set.

As to what vocabulary to use, I think it is best to use what exists as long
as it works properly.

With weighting based on how many other data sets use those same URI's

I use Geonames for locations and DBpedia for Taxonomic Authors.  (I also
link to a lot of similar related data sets either through URI's or their ID
like ITIS.)

I wish the BHL would expose URI's for publications and GBIF would expose
URI's for specimens - especially type specimens.

There are efforts to document the well known LOD vocabularies and work out
interoperability issues. Here is a sample.

http://www4.wiwiss.fu-berlin.de/lodcloud/state/  <= Lists best practices and
what data sets seem to be following them. GeoSpecies ~ TaxonConcept


I am still thinking about how to handle multiple classifications.

The current thinking has been to markup the different hierarchies with
things like #Taxonomy and #NCBI_Taxonomy.

If someone then chooses to tie their version of the TaxonConcept Species
concepts to a specific hierarchy they can create a sameAs mapping file that

ID#Taxonomy owl:sameAs ID#Species

I would also like to use URI's for the different clades like I have with
GeoSpecies but that will take some work.

Another option would be to do something like this.

txn_kingdom: Animalia or URI_To_Animailia
txn_phylum:  Chordata or URI_To_Chordata

ncbi_kingdom: URI_To_UniProt_Animalia
ncbi_phylum: : URI_To_UniProt_Chordata

That is have different predicates to allow one species concept to have
several different taxonomic hierarchies.

These operate as tags, not as subclasses.

One issue with Uniprot and Bio2RDF is that the clades are subclassed, so you
don't want to do owl:SameAs unless you want to entail that subclassing.

Here is an example of a Uniprot taxon

In regards to missing potential identifications or occurrences, I don't know
how much a problem this would actually be since they should show up in the

However, it might be interesting to creating a listener that watches for
?:Occurrences and ?:Identifications and harvests them.

Or make a PingTheSemanticWeb type service for them.


- Pete

On Wed, May 4, 2011 at 6:04 AM, Steve Baskauf
<steve.baskauf at vanderbilt.edu>wrote:

>  Thanks, Bob, for the examples.  I will try to dig my way through them.
> I don't want to give the impression that Darwin-SW was not intended to
> facilitate any reasoning.  That is, after all why it is called "Darwin-SW"
> instead of "Darwin-data-markup".  I know that Cam is quite interested in the
> "semantic" end of it, and when he has Internet again I hope he will chime in
> on this.  I'm simply confessing what my primary concern is (data markup).
> When we started working on the ontology, we decided to make it as simple as
> possible while still trying to permit every (or almost every) kind of class
> and relationship that was discussed in the Oct/Nov discussion.  The result
> was to have a single class Occurrence whose instances are described by
> properties, not 1.7 million classes N#occurrence and so on for the other six
> classes in the model.  The intention was that DSW 1.0 would be constructed
> in such a way that it could support the addition of more complex components
> (Cam has actually marked the posted version at version 0.2 which means that
> it is certainly subject to improvement) and possibly more complex
> reasoning.  But the more complex stuff was not put into the model at the
> start because we wanted something that (hopefully) most people could agree
> represents reality reasonably well (at least a TDWG form of reality since it
> uses the structure of DwC as its basis) and hence it would actually have the
> possibility of being used by more than two people.
> I hope that people realize that I'm not making these comments to give Pete
> a hard time or anything.  I really am trying to understand the relative
> benefits and problems of modeling on class of cat with many properties vs.
> creating a class of cats for every property we care about.  Clearly Pete's
> interest is in Taxon Concepts in the sense that he has defined them.  OK,
> just to set up a straw man, let's say that I am interested in geography more
> than taxonomy.  So I define a class and URI for every state and province in
> the world.  I have no idea how many of those there are, but I'll guess 400.
> Now I want to describe other things in the biodiversity informatics world.
> So I mint classes http://baskaufgeo.org/lod/ohio#occurrence for
> occurrences that happen in Ohio,
> http://baskaufgeo.org/lod/swaziland#occurrence for occurrences that happen
> in Swaziland, http://baskaufgeo.org/lod/tennessee#occurrence,
> http://baskaufgeo.org/lod/ohio#taxon,
> http://baskaufgeo.org/lod/swaziland#taxon,
> http://baskaufgeo.org/lod/tennessee#taxon, etc. etc. for all 400
> state/provinces and all seven basic types of things in the biodiversity
> domain.  I can now do cool queries that involve geography.
> OK, maybe I'm somebody else and I love thinking about temporal
> relationships.  So I create http://baskauf-time.org/lod/1959may#occurrencefor occurrences that happen in May of 1959,
> http://baskauf-time.org/lod/2005may#occurrence for occurrences that
> happened in May of 2005, etc.  Given a billion or so years of life on earth,
> that would give me about 12 billion classes for each of the six other basic
> kinds of things I want to model.  I could do all kinds of cool queries that
> involve time now.
> So which one of these three ontologies are we going to adopt?  The taxon
> based one?  The time based one?  The geography based one?  Now we are not
> just having to chose whether to model things as a single class of cats whose
> instance have many color and reproductiveMethod properties vs. many classes
> of cats each defined on the basis of its color.  We must decide whether it's
> better to have many classes of colors each defined by the kind of animal
> that has that color, or many kinds of reproductive systems, each with
> different kinds of animals, etc.  Where is it going to end and how could we
> agree on which system to use?  It seems to me that it would be better to
> have a class of cats, a class of reproductive systems, etc. and connect
> their instances with properties.
> Am I somehow thinking about this incorrectly?
> Steve
> Bob Morris wrote:
> See, for example,
> Mungall et al., “Integrating phenotype ontologies across multiple
> species”, Genome
> Biology 2010, 11:R2 doi:10.1186/gb-2010-11-1-r2)
> Ward Blondé et al.  "Reasoning with bio-ontologies: using relational
> closure rules to enable practical querying", Bioinformatics (2011)
> doi: 10.1093/bioinformatics/btr164
> Calder, et al. "Machine Reasoning about Anomalous Sensor Data"http://dx.doi.org/10.1016/j.ecoinf.2009.08.007 or in manuscript form
> at http://efg.cs.umb.edu/pubs/SensorDataReasoning.pdf
> ...
> OK, so  maybe these knowledge domains are all hypothesis-driven
> sciences (i.e.,  sciences), and <whatever dsw is modelling> is not.
> But that would be sad.
> Bob
> p.s. I had almost finished something else on this thread when Hilmar
> beat me to the punch. But here's a slightly different expression of
> his point:
> It turns out that the differences between instances and classes is
> mainly important in contexts in which you have declaimed interest,
> namely reasoning.  In the RDF/RDFS/OWL stack, enforcing a distinction
> between classes and instances only occurs pretty high up in the stack,
> when one desires an OWL variant that will offer guarantees that
> reasoners will finish any inference they are asked to verify,
> preferably in less than exponential time . I guess, but am not
> certain, that even in an LOD context, if data are described with an
> OWL ontology that is known to be intractable, e.g. not in OWL DL, that
> it is possible to design SPARQL queries that will never complete. In
> fact, I believe that even with tractable ontologies, there are SPARQL
> queries that are fundamentally exponential in the number of variables.
> p.p.s. Irrelevant, but equivalent, aside about mathematics. At the
> turn of the 20th century, Whitehead and Russell tried (and failed) to
> show that everything about numbers could be logically derived from an
> axiomatic description of the natural numbers (i.e. non-negative
> integers). It was later shown to be the case that you must include in
> your logical foundations something deeper, namely the ability to have
> sets that are elements of other sets (roughly, classes that are
> individuals in other classes.).  Without this, and starting only with
> the natural numbers, you can logically derive all rational numbers
> (fractions) and their arithmetic properties, and even all the
> irrational numbers that are are the solutions of polynomial equations
> with integer coefficients ("algebraic numbers") such as sqrt(2), and
> even solutions of the polynomials that have coefficients that are
> algebraic numbers.  But without introducing the notion of the set of
> subsets of a set, you cannot logically derive the all the interesting
> transcendental numbers (i.e. those which are not the roots of
> polynomials), such as e and pi.  So if you love calculus, you better
> not insist on  distinguishing instances from classes. But if you are
> content with polynomials, you can probably be ontologically sloppy.
> Or, if you don't care about logical foundations of your science, you
> can forget about the whole thing. :-)
> On Tue, May 3, 2011 at 11:51 PM, Steve Baskauf<steve.baskauf at vanderbilt.edu> <steve.baskauf at vanderbilt.edu> wrote:
>  [snip]
> OK, so let's imagine that we mark up several million records of specimens,
> tissue samples, and images as RDF.  (We don't have to imagine very hard, I
> think the BiSciCol group is planning to actually do this within the next
> several months.)  I would really like to hear from some of the people who
> actually use "DL reasoners" (a group which certainly does not include me) to
> know what it is that we could actually find out that would be useful about
> that big data blob using reasoners.  I have already confessed that my
> primary concern is enabling data discovery, transfer, and aggregation using
> GUIDs and RDF.  I'm still somewhat of a "semantic web" skeptic as far as the
> whole inferencing thing is concerned.  Aside from inferring "duplicates",
> I'm really wanting to know what else there is useful that could be reasoned
> outside of the Taxon/TaxonConcept class.  (I can imaging useful reasoning
> being done about things in that class like the relationships among names,
> concepts, parent taxa, etc. e.g. Rod Page's Biodiversity Informatics 3:1-15
> article https://journals.ku.edu/index.php/jbi/article/view/25)  I think this
> (data markup priority vs. inferencing priority) is an important discussion
> to have before the tdwg community can settle on some kind of consensus way
> of turning database records into RDF, particularly if it is going to have a
> big influence on the way the RDF model is set up.  To me, there is a clear
> and immediate need to be able to mark data up in a straightforward way.  If
> we can get the semantic part, too, that would be great but not at the
> expense of data markup.  I just was at a meeting of a bunch of herbarium
> curators.  They desperately need a way to implement GUIDs and aggregate data
> and they need it now.  I really don't think they care one whit about
> inferencing.  If we coalesce on a model that is great for doing cool things
> with 10 records but which can't handle hundreds of thousands of records
> easily and simply, then we are wasting our time.  I don't think we need to
> dither about this for another five years.
>   I would hate to have to draw an RDF graph of that model
> I would as much hate to have to draw an RDF graph of 1.7 million instances.
> The point being, in order to draw a graph of how someone models a domain you
> don't draw a graph of the entire RDF triple store.
> That was the point I was trying to make (I think).
> Thanks for the clarification, Hilmar.
> Steve
> -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
> --
> 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) 343-6707http://bioimages.vanderbilt.edu
> _______________________________________________
> tdwg-content mailing listtdwg-content at lists.tdwg.orghttp://lists.tdwg.org/mailman/listinfo/tdwg-content
> --
> 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) 343-6707http://bioimages.vanderbilt.edu
> _______________________________________________
> tdwg-content mailing list
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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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