[tdwg-content] Test Example of Beetle Occurrence in DarwinCore

Peter DeVries pete.devries at gmail.com
Thu Dec 24 08:33:28 CET 2009

Hi Kevin,

- the uri burner link didn't work first off (it seemed to strip off one of
the / after the http:// ?? - I entered it manually, then it worked)

Weird it works for me, here it is again.


- why is there a capital B in your url (I'm sure it doesn’t matter, just
curious) ?

Just a fluke of copying and pasting a made up uuid. (it should have been all
lowercase, but works as an example.)

The top part describes the RDF file itself, the description of the
observation data follows. The idea behind this is that the metadata
about the file itself should be have a different URI than the thing it
describes. The metadata about the file has a foaf:primaryTopic
of the #dataset. The #dataset part should have had a foaf:isPrimaryTopicOf
that points back to the .rdf file description. It has
it now and you can see within uriburner that you can click back between the
two in that interface.

This also allows one to make statements about the file itself that are
separate from those about the #dataset.

- I like how you have done the hasPart and isPartOf thing to aggregate the
> components - is this a standard way to do things?  I hadn't seen it before
> I don't know about "standard" but it is part of good practices. It links
the different parts of the dataset together. Without something like that
there is no
way to know that a particular resource like the #observation (when floating
in the data cloud) is part of something else

> - should the dwc namespace be http://rs.tdwg.org/dwc/terms/#, rather than
> http://rs.tdwg.org/dwc/terms/index.htm# ?
I followed the documentation page in googlecode, but after your note I
looked at the example and changed it to


> - I see you have linked the
> http://rs.tdwg.org/dwc/terms/index.htm#nameAccordingToID<http://linkeddata.uriburner.com/about/html/http/rs.tdwg.org/dwc/terms/index.htm%01nameAccordingToID>to a taxon concept.  I think the idea is to link it to a literature
> reference, where the taxon was circumscribed.  but for some people this may
> be the same thing???
This issue has gone back and forth a few times. I was originally thinking
that having a TaxonConceptID would allow someone to tag their specimens
and observations to a easily accessible clear concept. If you look at the
original description of *Ochlerotatus triseriatus* (*Culex triseriatus*) it
a little over a paragraph and, as described, could be up to 10 different
species of mosquito. I don't think most mosquitoes are identified with an
particular formal taxonomic description in mind unless you consider one of
the widely used keys a formal description. Also unless there is a global
unique identifier for each of these descriptions it will be difficult to
automatically determine if the literature reference is actually the same. In
other words, as it currently is structured linking to a literature reference
simply perpetuates the "are these the same or are these different?"
confusion into the digital realm.

Think about it this way; of the millions" of observation records in GBIF,
how many of the specimens were assigned names after identifier consulted a
formal species description?

Some mosquito workers use their own unpublished keys, I use the latest
Darsie. Doesn't this mean that we are not tagging specimens to the same
species description? How will this limit the ways in which this data can be

I suspect there will be similar problems with records of frogs and birds.

I feel I am in the middle of the road on this. There are a very large number
of people who feel that the NCBI number is the species concept.

As diagrammed:

<Publication is Species Concept>                                    <Pete>
          <BarCode is Species Concept >      <NCBI TaxonID is the Concept>

> - it might be better to have your "has close match" links in the dwc:Taxon,
> that links to the geospecies object, and other objects such as IT IS
> concepts?

Yes, if NameAccordingToID is supposed to point to formal description then I
will need to do something else.

sorry to be pedantic, but it is probably more for my benefit, than yours -
> ie to help me understand how I should do such a thing myself.
No, I did not think you were being pedantic. How else are we supposed to
figure out how these should look and work? Someone else showed me how to
do the foaf:primaryTopic etc. with the understanding that will explain it to
other people. I am still not clear on how to produce correct dwc, so the
only way to get it right is to mark up some examples, fail and then keep
trying until we have something that works as people expect.

I would eventually like to get my observation records to work in a way that
does not break what I do have working.

Also I think that people are thinking of me and my not exactly TDWG'y
examples as a problem when they really should be more worried about
the large number of very influential people that think that the NCBI taxon
id is the species concept. Their is a small window of time in which we can
design something that will be adopted and used by non-taxonomists, after
which every described species will have a NCBI taxon id that is "close
enough" to satisfy most potential users.

Thanks and Happy Holidays!

- Pete

> Looks really good though.
> Kevin
> *From:* tdwg-content-bounces at lists.tdwg.org [mailto:
> tdwg-content-bounces at lists.tdwg.org] *On Behalf Of *Peter DeVries
> *Sent:* Thursday, 24 December 2009 1:08 a.m.
> *To:* tdwg-content at lists.tdwg.org; young at entomology.wisc.edu
> *Subject:* [tdwg-content] Test Example of Beetle Occurrence in DarwinCore
> Hi TDWG'ers,
> After Gail's ECN email I made up a demo/trial DarwinCore Occurrence Record
> of one of Dan's beetle records.
> Here is my example
> http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf
> You can click through the various parts via uriburner
> http://linkeddata.uriburner.com/about/html/http://rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf<http://linkeddata.uriburner.com/about/html/http:/rdf.geospecies.org/datasets/Bcb50c3c-13f5-4c0c-A6de-5f422e2b88c7.rdf>
> Happy Holidays!
> - Pete
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
GeoSpecies Knowledge Base
About the GeoSpecies Knowledge Base
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