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Thanks for the information, Pete. I was very interested to try doing a
SPARQL query using the urnburner interface (as I have already confessed
to lack of experience with that). One thing I was curious about was
how OpenLink/uriburner knew what metadata to run the query on. I was
going to redo the process to see if there was an option to point to
some particular triple store, but the site seems to be down at the
moment. Or do they run the query on data that they have "discovered"
through links on the cloud or on data that people have asked them to
scrape/crawl?<br>
<br>
As cool as the SPARQL querying thing is, I still think that I have a
general issue with the approach that you are suggesting, i.e. that each
"species concept" has a set of classes defined as "partOf" the general
species concept class for that species. For the sake of argument,
let's say that you manage to describe a species concept for each of the
approximately 1.7 million described species. That means that you will
have 1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Image">http://lod.taxonconcept.org/ses/XXXXX#Image</a> classes,
1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Occurrence">http://lod.taxonconcept.org/ses/XXXXX#Occurrence</a> classes,
1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Indivdual">http://lod.taxonconcept.org/ses/XXXXX#Indivdual</a> classes,
1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Taxonomy">http://lod.taxonconcept.org/ses/XXXXX#Taxonomy</a> classes, 1.7
million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#NCBI_Taxonomy">http://lod.taxonconcept.org/ses/XXXXX#NCBI_Taxonomy</a> classes,
1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#OriginalDescription">http://lod.taxonconcept.org/ses/XXXXX#OriginalDescription</a>
classes, and 1.7 million
<a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Population">http://lod.taxonconcept.org/ses/XXXXX#Population</a> classes in addition to
the 1.7 million <a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/XXXXX#Species">http://lod.taxonconcept.org/ses/XXXXX#Species</a> classes
that describe the species concept itself. That is a total of 13.6
million separate classes in your model that are needed to describe
biodiversity records of life on earth. In contrast, we defined or
imported a total of seven classes to do the same thing in Darwin-SW
(not counting foaf:Person which is somewhat tangential to the ontology)
and those seven classes should be capable of describing biodiversity
records of life on earth. My point here is that the structure of the
taxonconcept.org ontology seems to be designed around making queries
easy (by creating a class for anything that somebody may want to ask
about), but not around describing classes that reflect the structure of
databases that people in the TDWG community are likely to use. In
contrast, simple queries would (it seems to me) be difficult to
construct based on Darwin-SW, but it would be relatively easy to adopt
the class structure to the primary types of things that people keep
track of in databases (even "flattened" databases that only explicitly
recognize fewer than the seven classes in Darwin-SW). So it's a
trade-off, but it seems like it would be more productive to put the
burden on the few software developers (i.e. people who would be
creating clients that could search RDF databases/triple stores) than on
the many data providers. <br>
<br>
I also still do not see how you get around the problem that I mentioned
in my May 1 email
(<a class="moz-txt-link-freetext" href="http://lists.tdwg.org/pipermail/tdwg-content/2011-May/002385.html">http://lists.tdwg.org/pipermail/tdwg-content/2011-May/002385.html</a>).
In a nutshell, let's say that a tree in an arboretum has its HTTP URI
GUID on a label nailed to its trunk. If I take a picture of that tree
(recording evidence of an Occurrence) and assign that tree to a Taxon
through an Identification, and somebody else collects a specimen from
that tree and assigns that same tree to a different Taxon through their
own Identification, how could a query on a txn: species occurrence tag
ever show me both the occurrence record associated with the image and
the one associated with the specimen? I am going to query for <br>
<br>
describe ?s where { ?s a
<a class="moz-txt-link-rfc2396E" href="http://lod.taxonconcept.org/ses/[myTaxon]#Occurrence"><http://lod.taxonconcept.org/ses/[myTaxon]#Occurrence></a> }<br>
<br>
which will pick up the occurrence documented by my image, but it would
not pick up the occurrence documented by the specimen, which would
require the search<br>
<br>
describe ?s where { ?s a
<a class="moz-txt-link-rfc2396E" href="http://lod.taxonconcept.org/ses/[theOtherPersonsTaxon]#Occurrence"><http://lod.taxonconcept.org/ses/[theOtherPersonsTaxon]#Occurrence></a>
}<br>
<br>
In other words, the approach that you are suggesting requires me to
know in advance what other Identifications somebody else may apply to
the tree and either: <br>
type my occurrence record with those other taxa tags or <br>
know to run a separate query for each of those taxa<br>
<br>
Either of these involves mind-reading on my part. This is different
than the way one would find this out using Darwin-SW. In Darwin-SW,
one would first query for Identifications that specified [myTaxon] and
then find the dsw:Individuals associated with those Identifications.
Then one would look for all of the dwc:Occurrences that were associated
with the dsw:Individuals. The fact that somebody else assigned the
tree to a different taxon is irrelevant to me finding the occurrences
of the tree. This is messy and I don't see how you could do it with
SPARQL, but I don't think it would require complex programming to write
software that could do it. Since the taxonconcept.org ontology also
has properties to relate occurrences to individuals and individuals to
identifications and taxa, one could do the same kind of complex
search. But that leaves me wondering what purpose the "lightweight
tags" have if they can't be used reliably to search for all of the
metadata that others have put out on the cloud. They allow me to find
out about things that I already know but restrict my ability to
discover unknown things. <br>
<br>
Steve<br>
<br>
Peter DeVries wrote:
<blockquote
cite="mid:BANLkTik2R3Ec4Dyr64Fm5Q4fkX8Pu5AsXA@mail.gmail.com"
type="cite">Hi Steve,
<div><br>
</div>
<div>I try to take some time to think about your notes, sorry for the
delay.</div>
<div><br>
</div>
<div>There are many different contexts that can be used when thinking
about species and related data.</div>
<div><br>
</div>
<div>It is often useful to separate these contexts into different
kinds of related entities.</div>
<div><br>
</div>
<div>Here are some contexts that I think are useful to separate</div>
<div><br>
</div>
<div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Image">http://lod.taxonconcept.org/ses/mCcSp#Image</a>
- An image of a Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Occurrence">http://lod.taxonconcept.org/ses/mCcSp#Occurrence</a>
- An occurrence of a Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Individual">http://lod.taxonconcept.org/ses/mCcSp#Individual</a>
- An individual Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Taxonomy">http://lod.taxonconcept.org/ses/mCcSp#Taxonomy</a>
- A Basic Taxonomy for the Cougar, one alternative among many
potential classifications</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy">http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy</a>
- The NCBI Taxonomy for Cougar, or starting at the lowest available
clade</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription">http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription</a>
- The Original Description of the Cougar, ideally with links to the PDF
or BHL URI.</div>
<div><br>
</div>
<div>* Note that in this model a species can have several Taxonomies
or classifications. This reflects the reality that the same species has
one hierarchy in NCBI and a different one in CoL.</div>
<div><br>
</div>
<div>You can find all the tagged images of the Cougar by finding all
those that are of the type <<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Image">http://lod.taxonconcept.org/ses/mCcSp#Image</a>></div>
<meta charset="utf-8">
<div><br>
</div>
<div>Here is one example of an image that is tagged in this way.
(From <a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.html">http://lod.taxonconcept.org/ses/v6n7p.html</a> )</div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<foaf:Image rdf:about="<a moz-do-not-send="true"
href="http://assets.taxonconcept.org/seuuids/603bebac-cc44-4168-bbf7-b11b976f9d79/Puma_concolor_480x320.jpg">http://assets.taxonconcept.org/seuuids/603bebac-cc44-4168-bbf7-b11b976f9d79/Puma_concolor_480x320.jpg</a>"></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<rdf:type rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Image">http://lod.taxonconcept.org/ses/v6n7p#Image</a>"/></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<dcterms:isPartOf rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Species">http://lod.taxonconcept.org/ses/v6n7p#Species</a>"/></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<dcterms:source rdf:resource="<a moz-do-not-send="true"
href="http://commons.wikimedia.org/wiki/File:Mountain_lion.jpg">http://commons.wikimedia.org/wiki/File:Mountain_lion.jpg</a>"/></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<dcterms:contributor>United States Department of
Agriculture</dcterms:contributor></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<cc:license rdf:resource="<a moz-do-not-send="true"
href="http://creativecommons.org/publicdomain/">http://creativecommons.org/publicdomain/</a>"/></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<wdrs:describedby rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.rdf">http://lod.taxonconcept.org/ses/v6n7p.rdf</a>"/></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
</foaf:Image></font></div>
</div>
<div><br>
</div>
<div>You are correct in noting that an occurrence of a species could
simply be typed in a similar way, and maybe that would be better than
the somewhat awkward.</div>
<div><br>
</div>
<div>txn:occurrenceHasSpeciesOccurrenceTag</div>
<div><br>
</div>
<div>I originally went with this name because I wanted it to be clear
that the subject and objects should be.</div>
<div><br>
</div>
<div>If we use this data set as and example <a moz-do-not-send="true"
href="http://ocs.taxonconcept.org/ocs/index.html">http://ocs.taxonconcept.org/ocs/index.html</a> (Mainly
TDWG BioBlitz 2010)</div>
<div><br>
</div>
<div>We can demonstrate how this is useful for SPARQL Queries.</div>
<div><br>
</div>
<div>We can run a
<meta charset="utf-8">
SPARQL describe query for all the observations of the Honey Bee with
this query.</div>
<div><br>
</div>
<div>
<div><font class="Apple-style-span" face="'courier new', monospace">PREFIX
txn: <<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ontology/txn.owl#">http://lod.taxonconcept.org/ontology/txn.owl#</a>></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">describe
?s where { ?s txn:occurrenceHasSpeciesOccurrenceTag <<a
moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/z9oqP#Occurrence">http://lod.taxonconcept.org/ses/z9oqP#Occurrence</a>>
}</font></div>
</div>
<div><br>
</div>
<div> * It might be simpler to mark these observations up as
having a type of <span class="Apple-style-span"
style="font-family: 'courier new',monospace;"><<a
moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/z9oqP#Occurrence">http://lod.taxonconcept.org/ses/z9oqP#Occurrence</a>>.</span></div>
<div><span class="Apple-style-span"
style="font-family: 'courier new',monospace;"><br>
</span></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
<meta charset="utf-8">
<span class="Apple-style-span" style="font-family: arial;"> In
this case the query would look like this. (You can use "a" as a short
cut meaning (<a moz-do-not-send="true"
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#type">http://www.w3.org/1999/02/22-rdf-syntax-ns#type</a>)</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div>
<meta charset="utf-8">
<div>
<div><font class="Apple-style-span" face="'courier new', monospace">
PREFIX txn: <<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ontology/txn.owl#">http://lod.taxonconcept.org/ontology/txn.owl#</a>></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
describe ?s where { ?s a <<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/z9oqP#Occurrence">http://lod.taxonconcept.org/ses/z9oqP#Occurrence</a>>
}</font></div>
</div>
</div>
<div><font class="Apple-style-span" face="'courier new', monospace"> </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">
</font><font class="Apple-style-span"
face="arial, helvetica, sans-serif">* I would need to redo the
occurrence record RDF for this new query to work</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><br>
</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">We can take that
original query above and paste into the LOD SPARQL Endpoint <a
moz-do-not-send="true" href="http://uriburner.com/isparql/">http://uriburner.com/isparql/</a> (Advanced
Tab)</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">Run the query </span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">This link will
run the query - will probably not go through all email system intact.
See <a moz-do-not-send="true" href="http://bit.ly">bit.ly</a> link
below.</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">< <a
moz-do-not-send="true"
href="http://uriburner.com/isparql/view/?query=PREFIX%20txn%3A%20%20%20%20%20%3Chttp%3A%2F%2Flod.taxonconcept.org%2Fontology%2Ftxn.owl%23%3E%0A%0Adescribe%20%3Fs%20where%20%7B%20%3Fs%20txn%3AoccurrenceHasSpeciesOccurrenceTag%20%3Chttp%3A%2F%2Flod.taxonconcept.org%2Fses%2Fz9oqP%23Occurrence%3E%20%7D%0A%20&endpoint=/sparql&resultview=navigator&maxrows=50&view=1">http://uriburner.com/isparql/view/?query=PREFIX%20txn%3A%20%20%20%20%20%3Chttp%3A%2F%2Flod.taxonconcept.org%2Fontology%2Ftxn.owl%23%3E%0A%0Adescribe%20%3Fs%20where%20{%20%3Fs%20txn%3AoccurrenceHasSpeciesOccurrenceTag%20%3Chttp%3A%2F%2Flod.taxonconcept.org%2Fses%2Fz9oqP%23Occurrence%3E%20}%0A%20&endpoint=/sparql&resultview=navigator&maxrows=50&view=1</a>></span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">Bit.ly version <a
moz-do-not-send="true" href="http://bit.ly/lM6vWB">http://bit.ly/lM6vWB</a></span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">and get a esult
(Not very pretty, or interpretable by humans)</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">We can select
make "Make Pivot" from the top left corner of the Window.</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">This will run the
query and feed the data to MS Pivot which parses and displays the
result.</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">In theory, and I
hope in the future, there will be an open source solution that does
this as easily and does not require MS Silverlight.</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">The result is a
Browsable Pivot View which you can select to view the result by
Observer, Location etc.</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"><br>
</span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">This <a
moz-do-not-send="true" href="http://bit.ly">bit.ly</a> will take you
to a view by observer (the person who made the observation) <a
moz-do-not-send="true" href="http://bit.ly/lacRb1">http://bit.ly/lacRb1</a></span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;"></span></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"><span
class="Apple-style-span" style="font-family: arial;">This <a
moz-do-not-send="true" href="http://biit.ly">biit.ly</a> will take you
to a view by dwcArea <a moz-do-not-send="true"
href="http://t.co/eu55BaG">http://t.co/eu55BaG</a></span></font></div>
<meta charset="utf-8">
<div><br>
</div>
<div>I have bundled all these examples including screenshots into one
<a moz-do-not-send="true" href="http://bit.ly">bit.ly</a> bundle so
you won't need Sliverlight to get an idea on how this works.</div>
<div><br>
</div>
<div><a moz-do-not-send="true" href="http://bit.ly/iXg2y8">http://bit.ly/iXg2y8</a> <-
Link to Bit.ly bundle with screen shots etc.<br>
</div>
<div><br>
</div>
<div>I have included closeups of the Pivot settings in the top right
corner so you can see how to change the attribute that Pivot uses to
create the view.</div>
<div><br>
</div>
<div>Note also that if you go to the Knowledge Base View of the Honey
Bee you can browse to the observations of that species.</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fz9oqP%23Species">http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fz9oqP%23Species</a>
Bit.ly Link <a moz-do-not-send="true" href="http://bit.ly/g1zzJC">http://bit.ly/g1zzJC</a><br>
</div>
<div><br>
</div>
<div>Since I have updated to the latest version of Virtuoso the
strange URI links have been replaced with Human readable text from the
label view for that entity.</div>
<div><br>
</div>
<div>This includes the links to occurrences, gni names strings, and
links to GeoNames.</div>
<div><br>
</div>
<div>Part of the reasoning behind this structure is to make explicit
to computers what context we are talking about.</div>
<div><br>
</div>
<div>The human brain makes these context switches automatically but
computers do not.</div>
<div><br>
</div>
<div>That said there are areas where they could be improved or
simplified.</div>
<div><br>
</div>
<div>Also I think that you will need a class for each species
concept, but they are all instances of txn:SpeciesConcept - something
allowed in OWL2.</div>
<div><br>
</div>
<div>My ontology has probably changed slightly since you last saw it. </div>
<div><br>
</div>
<div>OWL <a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ontology/txn.owl">http://lod.taxonconcept.org/ontology/txn.owl</a></div>
<div><br>
</div>
<div>OWL Doc <a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ontology/doc/index.html">http://lod.taxonconcept.org/ontology/doc/index.html</a></div>
<div><br>
</div>
<div>Respectfully,</div>
<div><br>
</div>
<div>- Pete</div>
<div><br>
</div>
<br>
<div class="gmail_quote">On Mon, May 2, 2011 at 8:16 AM, Steve
Baskauf <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu" target="_blank">steve.baskauf@vanderbilt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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OK, Pete, I'm going to try to write the other email that I mentioned in
the previous one. This email relates to the actual suggestion that you
made in the email, that is to use the URIs of the form like:
<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Occurrence" target="_blank">"http://lod.taxonconcept.org/ses/mCcSp#Occurrence"</a>.
In the RDF that
defines what this URI means, the URI is described as "A lightweight tag
that can be used to label occurrences of this species". What I'm not
sure about is what exactly one is supposed to do with it. From the
example that I was talking about in the previous email
(<a moz-do-not-send="true"
href="http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf"
target="_blank">http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf</a>),
this "tag" is the object of the predicate
txn:occurrenceHasSpeciesOccurrenceTag . So I guess that it is another
way that one could query Occurrence records to find out which ones are
Occurrences of the species having the identifier "ICmLC" (<i>Boloria
selene</i>). But I'm not sure what the advantage of that is. The RDF
for the Occurrence already tells me that the Occurrence has the
txn:occurrenceHasSpeciesConcept property with object URI
<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/ICmLC#Species" target="_blank">http://lod.taxonconcept.org/ses/ICmLC#Species</a>
. I can resolve that URI
and "find out" that the "species concept" (sensu
DeVries) is <i>Boloria selene</i> . But if I used the "lightweight
tag" I'd also have to resolve its URI to find out about it and the RDF
for the tag directs me to the
<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/ICmLC#Species" target="_blank">http://lod.taxonconcept.org/ses/ICmLC#Species</a>
URI anyway via the
dcterms:isPartOf property of the tag. I guess the point is that if one
wants to "find out" about the Occurrence, it takes two steps to get to
the species concept description if I use the tag (first through
txn:occurrenceHasSpeciesOccurrenceTag, then through dcterms:isPartOf)
which is no advantage over just getting there in one step (via
txn:occurrenceHasSpeciesConcept). If the only point is to have
something to put in as a search term, then why not just make the
txn:occurrenceHasSpeciesOccurrenceTag a data property with the literal
object the string "ICmLC"? <br>
<br>
I suppose that one could say that an advantage of the "lightweight tag"
approach would be that one is indicating that the particular Occurrence
is an instance of a class that consists of all Occurrences of the
species <i>Bororia selene</i>. That seems to be what the intention
is. But this seems to be a case of creating many subclasses rather
than having a general class and assigning it properties that help one
to understand the nature of the instance of that class. It requires
the creation of a class for every species on the planet. Instead of
there being a relatively small number of classes that includes the
basic kinds of resources (Occurrence, individual, Identification, taxon
concept) there is a class for occurrences of every kind of taxon
concept.
Actually, there are several classes for every instance of taxon
concept, because you are recommending that the "lightweight tag"
approach be used for other types of things as well, such as individuals
and (in your suggestion below, populations). There isn't anything
intrinsically "wrong" with this approach, but with my bias toward
preferring "well known" types/classes it just seems like a lot to
expect consuming applications to "understand" what amounts to
potentially millions of classes that this method would introduce.<br>
<br>
I also don't quite understand what a txn:SpeciesOccurrenceTag is
exactly. In the RDF that defines the txn:SpeciesOccurrenceTag instance
for <i>Bororia selene</i>
(<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/ICmLC#Occurrence" target="_blank">http://lod.taxonconcept.org/ses/ICmLC#Occurrence</a>)
the
dcterms:description says that it "allow species occurrences to be
modeled as instances of SpeciesOccurrenceTag". But that doesn't seem
to be what is actually occurring. When the Occurrence instance
<a moz-do-not-send="true"
href="http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurrence"
target="_blank">http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurrence</a>
is described, it is not typed as the lightweight tag (which IS a
txn:SpeciesOccurrenceTag because of the implicit typing caused by the
XML container element name). The lightweight tag URI is the object of
the txn:occurrenceHasSpeciesOccurrenceTag property, but that doesn't
make the Occurrence an instance of SpeciesOcurrenceTag as would be the
case (I think) if the lightweight tag URI were the object of a rdf:type
property. Anyway, I'm confused about this.<br>
<br>
The other issue that I would raise with this approach is that it brings
up the same issue that I raised in the other email that I wrote. It
essentially puts a burden of anticipating the results of a query onto
the metadata provider. If one follows the model of allowing multiple
Identifications for an organism, then it is possible that someone
somewhere else might apply their own Identification instance to the
individual represented in the Occurrence. As was the case in my
earlier example, for txn:occurrenceHasSpeciesOccurrenceTag to be useful
as a thing to be queried, the metadata provider would need to somehow
know that this additional Identification had been made, and then create
another txn:occurrenceHasSpeciesOccurrenceTag property for the
Occurrence instance. This seems to somewhat at odds with the benefit
that the Linked Data world has in allowing resources to be created by
people all over the cloud and then linked rather than expecting a
centralized authority to do everything. <br>
<br>
Anyway, maybe you can explain what is going on so that I can understand
it better and maybe explain why this approach is better than just
creating a few classes and describing their instances by descriptive
properties. <br>
<font color="#888888"><br>
Steve</font>
<div>
<div><br>
<br>
Peter DeVries wrote:
<blockquote type="cite">I am still somewhat puzzled why TDWG seems
so opposed to
adopting anything that comes from outside a small click?
<div><br>
</div>
<div>
<div>I was thinking that it would be best to create a separate
class
that can be used for populations of a species.</div>
<div><br>
</div>
<div>This would require adding an additional tag to the
TaxonConcept
Species Concept Model, which currently includes several tags like
entities</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Species" target="_blank">http://lod.taxonconcept.org/ses/mCcSp#Species</a>
<- The Species Concept for the Cougar</div>
<div><br>
</div>
<div>
<div>See <a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.htm" target="_blank">http://lod.taxonconcept.org/ses/v6n7p.htm</a>l
HTML</div>
<div> <a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.rdf" target="_blank">http://lod.taxonconcept.org/ses/v6n7p.rdf</a>
RDF</div>
<div> <a moz-do-not-send="true"
href="http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23Species"
target="_blank">http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23Species</a>
Knowledge Base View (<a moz-do-not-send="true"
href="http://bit.ly%20bit.ly/gMFqR1" target="_blank">http://bit.ly
bit.ly/gMFqR1</a></div>
<div> </div>
</div>
<div>The model mints URI's for the following related entities.
See
RDF. or KB View</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Image" target="_blank">http://lod.taxonconcept.org/ses/mCcSp#Image</a>
- An image of a Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Occurrence" target="_blank">http://lod.taxonconcept.org/ses/mCcSp#Occurrence</a>
- An occurrence of a Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Individual" target="_blank">http://lod.taxonconcept.org/ses/mCcSp#Individual</a>
- An individual Cougar</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#Taxonomy" target="_blank">http://lod.taxonconcept.org/ses/mCcSp#Taxonomy</a>
- A Basic Taxonomy for the Cougar, one alternative among many
potential classifications</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy"
target="_blank">http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy</a>
- The NCBI Taxonomy for Cougar, or starting at the lowest available
clade</div>
<div><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription"
target="_blank">http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription</a>
- The Original Description of the Cougar, ideally with links to the PDF
or BHL URI.</div>
<div> </div>
<div> </div>
<div>Here is how a subset of these would relate to the new
#Population Tag and related semantic entities.</div>
<div><br>
</div>
<div><br>
</div>
<div>This tag is used an individual organism that that is an
instance
of the species concept pecies concept RDF.</div>
</div>
<div>
<div>This allows you to refer to a individual cougar in a way
that is
separate from the concept of cougar and retains links to other data
relating to that species concept.</div>
<div><br>
</div>
<div><br>
</div>
<div><font face="tahoma, sans-serif">
<txn:SpeciesIndividualTag rdf:about="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Individual" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Individual</a>"></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:title>A Tag for individuals of the species concept Puma
concolor se:v6n7p</dcterms:title></font></div>
<div><font face="tahoma, sans-serif">
<skos:prefLabel>A Tag-like resource that is used to label
individuals of the species concept Puma concolor
se:v6n7p</skos:prefLabel></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:identifier><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Individual" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Individual</a></dcterms:identifier></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:description>A lightweight tag that can be used to label
individuals of this species. These allow individual organisms to be
modeled as instances of SpeciesIndividualTag</dcterms:description></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:isPartOf rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Species" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Species</a>"/></font></div>
<div><font face="tahoma, sans-serif">
<wdrs:describedby rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.rdf" target="_blank">http://lod.taxonconcept.org/ses/v6n7p.rdf</a>"/></font></div>
<div><font face="tahoma, sans-serif">
</txn:SpeciesIndividualTag></font></div>
<div><br>
</div>
<div>Add a tag for a species population to the species concept
RDF.</div>
<div>This allows you to refer to a population of cougars in a way
that is separate for an individual cougar and retains links to other
data relating to that species concept.</div>
<div><br>
</div>
<div><font face="tahoma, sans-serif">
<txn:SpeciesPopulationTag rdf:about="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Population" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Population</a>"></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:title>A Tag for populations of the species concept Puma
concolor se:v6n7p</dcterms:title></font></div>
<div><font face="tahoma, sans-serif">
<skos:prefLabel>A Tag-like resource that is used to label
populations of the species concept Puma concolor
se:v6n7p</skos:prefLabel></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:identifier><a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Population" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Population</a></dcterms:identifier></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:description>A lightweight tag that can be used to label
populations of this species. These allow populations of a species to be
modeled as instances of SpeciesIndividualTag</dcterms:description></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:isPartOf rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Species" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Species</a>"/></font></div>
<div><font face="tahoma, sans-serif">
<wdrs:describedby rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p.rdf" target="_blank">http://lod.taxonconcept.org/ses/v6n7p.rdf</a>"/></font></div>
<div><font face="tahoma, sans-serif">
</txn:SpeciesPopulationTag></font></div>
<div><br>
</div>
<div><br>
</div>
<div>This is the RDF for a population, it has as one of it's
parts an
individual organism.</div>
<div>It is typed to indicate that it refers to a population of
Cougars.</div>
<div><br>
</div>
<div><font face="tahoma, sans-serif">
<owl:Class rdf:about="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation"
target="_blank">http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation</a>"></font></div>
<div><font face="tahoma, sans-serif">
<rdf:type rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/ses/v6n7p#Population" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Population</a>"/></font></div>
<div><font face="tahoma, sans-serif">
<skos:prefLabel>The population of North American Cougars Puma
concolor se:v6n7 </skos:prefLabel></font></div>
<div><font face="tahoma, sans-serif">
<dcterms:hasPart rdf:resource="<a moz-do-not-send="true"
href="http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Individual"
target="_blank">http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Individual</a>"/></font></div>
<div><font face="tahoma, sans-serif">
<wdrs:describedby rdf:resource="<a moz-do-not-send="true"
href="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf"
target="_blank">http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf</a>"/></font></div>
<div><font face="tahoma, sans-serif">
</owl:Class></font></div>
<div><br>
</div>
<div>Respectfully,</div>
<div><br>
</div>
<div>- Pete</div>
<p><font face="tahoma, sans-serif">-------------------------------------------------------------------------------------</font></p>
<p><font face="tahoma, sans-serif">Pete DeVries</font></p>
<p><font face="tahoma, sans-serif">Department of Entomology</font></p>
<p><font face="tahoma, sans-serif">University of Wisconsin -
Madison</font></p>
<p><font face="tahoma, sans-serif">445 Russell Laboratories</font></p>
<p><font face="tahoma, sans-serif">1630 Linden Drive</font></p>
<p><font face="tahoma, sans-serif">Madison, WI 53706</font></p>
<p><font face="tahoma, sans-serif">Email: <a
moz-do-not-send="true" href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a></font></p>
<p><font face="tahoma, sans-serif"><span><a moz-do-not-send="true"
href="http://www.taxonconcept.org/" target="_blank">TaxonConcept </a></span><span> &
<a moz-do-not-send="true" href="http://lod.geospecies.org/"
target="_blank"><span>GeoSpecies</span></a> Knowledge Bases</span></font></p>
<p><font face="tahoma, sans-serif">A Semantic Web, <a
moz-do-not-send="true" href="http://linkeddata.org/" target="_blank"><span>Linked
Open Data </span></a> Project</font></p>
<p><font face="tahoma, sans-serif">---------------------------------------------------------------------------------------</font></p>
<br>
</div>
</blockquote>
<br>
</div>
</div>
<div>
<pre cols="72">--
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: <a moz-do-not-send="true" href="tel:%28615%29%20343-4582"
value="+16153434582" target="_blank">(615) 343-4582</a>, fax: <a
moz-do-not-send="true" href="tel:%28615%29%20343-6707"
value="+16153436707" target="_blank">(615) 343-6707</a>
<a moz-do-not-send="true" href="http://bioimages.vanderbilt.edu"
target="_blank">http://bioimages.vanderbilt.edu</a>
</pre>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
------------------------------------------------------------------------------------<br>
Pete DeVries<br>
Department of Entomology<br>
University of Wisconsin - Madison<br>
445 Russell Laboratories<br>
1630 Linden Drive<br>
Madison, WI 53706<br>
Email: <a moz-do-not-send="true" href="mailto:pdevries@wisc.edu"
target="_blank">pdevries@wisc.edu</a><br>
<a moz-do-not-send="true" href="http://www.taxonconcept.org/"
target="_blank">TaxonConcept</a> & <a moz-do-not-send="true"
href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge
Bases<br>
A Semantic Web, <a moz-do-not-send="true" href="http://linkeddata.org/"
target="_blank">Linked Open Data</a> Project<br>
--------------------------------------------------------------------------------------<br>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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