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Comments inline:<br>
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Hilmar Lapp wrote:
<blockquote cite="mid:3DD7CAA7-3752-4DDE-BAB9-1682E68184DC@nescent.org"
type="cite"><br>
<div>
<div>On May 3, 2011, at 9:00 PM, Steve Baskauf wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium;">But
I was under the impression that one models things by describing classes
and the properties that connect them.</span></blockquote>
<div><br>
</div>
<div>In OWL, properties connect instances, not classes. RDF allows
metaclasses (things that are classes and instances), but doing this
will throw most (all?) reasoners off the track.</div>
</div>
</blockquote>
I knew I would get in trouble talking about this among experts. :-)
Thanks for the correction. I should have said "properties that connect
instances of those classes". I think that is what I meant. My point
was that in creating a model, one doesn't have to enumerate every
particular instance, particularly if there are many of them. One can
describe the class in general and let the users create the instances
that are appropriate for that class. <br>
<blockquote cite="mid:3DD7CAA7-3752-4DDE-BAB9-1682E68184DC@nescent.org"
type="cite">
<div><br>
<blockquote type="cite"><span class="Apple-style-span"
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Classes are (to me) a very different thing than instances of classes.
A model containing more than 13.6 million classes is at least 1.9
million times as complicated as a model with 7 classes.</span></blockquote>
<div><br>
</div>
<div>Yes and no. I can model a taxonomy as a subclass hierarchy of
classes, or as a property-based (memberOf or some such) hierarchy of
individuals that all instantiate a single "Taxon" class. The former
isn't 1 million times more complex than the latter. However, they are
not identical either, and which approach one chooses has significant
consequences for how easy it is to express things about those taxa, and
for inferring new things from those with a DL reasoner. <br>
</div>
</div>
</blockquote>
Well, I guess I was influenced in my thinking about this by
<a class="moz-txt-link-freetext" href="http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot">http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot</a> , particularly
the part about the cats, which I can actually understand pretty well.
To me, the part of that wiki page that is most relevant to this
discussion is: <br>
<p>"Whether the subclassing option is preferable to the tagging
approach depends on the use of the ontology. The TDWG ontology's
principal role is not modeling the entire domain to permit inference
but allowing the mark up of data so that it will flow between
applications as freely as possible. It has to be something that is easy
to map into multiple technologies and something that people can agree
on rapidly.
</p>
<p>This strongly suggests that the tagging approach should be taken
wherever possible. First agree on the basic semantic units and model
the rest of the semantics with tagging. Only subclass when absolutely
necessary."
</p>
The really great thing about this is that I can dodge further
responsibility by just blaming my way of thinking on the people who
posted that page (Roger Hyam modified by Bob Morris, I think). :-) But
seriously, I think that the statement above pretty well summarizes what
may be the difference between what Pete and I are saying. My primary
concern is to allow "the mark up of data so that it will flow between
applications as freely as possible". Pete's point may be to permit
inferencing.<br>
. <br>
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
<a class="moz-txt-link-freetext" href="https://journals.ku.edu/index.php/jbi/article/view/25">https://journals.ku.edu/index.php/jbi/article/view/25</a>) 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.<br>
<blockquote cite="mid:3DD7CAA7-3752-4DDE-BAB9-1682E68184DC@nescent.org"
type="cite">
<div><br>
<blockquote type="cite"><span class="Apple-style-span"
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I would hate to have to draw an RDF graph of that model</span></blockquote>
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<div><br>
</div>
<div>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.</div>
</blockquote>
That was the point I was trying to make (I think).<br>
<br>
Thanks for the clarification, Hilmar.<br>
Steve<br>
<blockquote cite="mid:3DD7CAA7-3752-4DDE-BAB9-1682E68184DC@nescent.org"
type="cite">
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<div><span class="Apple-tab-span" style="white-space: pre;"> </span>-hilmar</div>
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<div> <span class="Apple-style-span"
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<div><font class="Apple-style-span" face="Monaco" size="3"><span
class="Apple-style-span" style="font-size: 11px;">-- </span></font></div>
<div><font class="Apple-style-span" face="Monaco" size="3"><span
class="Apple-style-span" style="font-size: 11px;">===========================================================</span></font></div>
<div><font class="Apple-style-span" face="Monaco" size="3"><span
class="Apple-style-span" style="font-size: 11px;">: Hilmar Lapp -:-
Durham, NC -:- informatics.nescent.org :</span></font></div>
<div><font class="Apple-style-span" face="Monaco" size="3"><span
class="Apple-style-span" style="font-size: 11px;">===========================================================</span></font></div>
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<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>
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