<div dir="ltr"><div>On The Name: <br><br></div>I'd prefer dwc:2357. Oh, wait maybe that's not so opaque...<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 17, 2014 at 1:34 PM, joel sachs <span dir="ltr"><<a href="mailto:jsachs@csee.umbc.edu" target="_blank">jsachs@csee.umbc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Everyone,<br>
<br>
I'd like to comment on the proposed addition to Darwin Core of an<br>
"organism" class<br>
(<a href="https://code.google.com/p/darwincore/issues/detail?id=205" target="_blank">https://code.google.com/p/darwincore/issues/detail?id=205</a>). I am one of the submitters of this proposal, but I have<br>
some reservations/suggestions/questions about both the definition and the<br>
name. Taking them in turn:<br>
<br>
The Definition<br>
The proposed definition is:<br>
"A particular organism or defined group of organisms considered to be<br>
taxonomically homogeneous. An organism in the sense used here is defined<br>
as OBI:0100026 (<a href="http://purl.obolibrary.org/obo/OBI_0100026" target="_blank">http://purl.obolibrary.org/obo/OBI_0100026</a>). Instances of<br>
the Organism class are intended to facilitate linking of one or more<br>
Identification instances to one or more Occurrence instances. Therefore,<br>
things that are typically assigned scientific names (such as viruses,<br>
hybrids, and lichens) and aggregates whose occurrences are typically<br>
recorded (such as packs, clones, and colonies) are included in the scope<br>
of this class."<br>
<br>
There are a few things to note here:<br>
i. The definition of OBI:0100026 is "A material entity that is an<br>
individual living system, such as animal, plant, bacteria or virus, that<br>
is capable of replicating or reproducing, growth and maintenance in the<br>
right environment. An organism may be unicellular or made up, like<br>
humans, of many billions of cells divided into specialized tissues and<br>
organs." This definition is not internally consistent, since it delineates organisms as being either unicellular or<br>
multi-cellular, while at the same time explicitly including viruses, which<br>
are acellular.<br>
<br>
ii. The reference to OBI:0100026 does not add clarity to the<br>
DwC definition, since the DwC definition goes on to include the clarifying aspects of the OBI<br>
definition (viruses and lichens are organsims), while leaving out the<br>
muddying aspects of the OBI definition (organisms are unicellular or<br>
multicellular). The DwC definition also extends the the OBI defintion (to include wolf packs).<br>
<br>
iii. The rdf definition of OBI:organism inherits axioms from the Basic<br>
Formal Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to any particular upper ontology, as there is no consensus upper<br>
ontology. (Some scientific communities use Dolce, some use SUMO, and many<br>
have deliberately chosen to use none at all.) In general, I like the<br>
notion of Darwin Core as a glossary of terms, on top of which various<br>
data models can be built. When we import terms that carry with them an<br>
abundance of ontological commitment, it raises the stakes for those who choose to<br>
use TDWG vocabularies. (In contrast, when Darwin Core imported "Location"<br>
from Dublin Core, it did so at no cost, since Dublin Core is not tied to<br>
any particular upper world-view.)<br>
<br>
<br>
The Name<br>
There have been multiple debates about a good name for this class, and<br>
there was never consensus. (In addition to "Organism",<br>
candidates included "Individual", "OrganismalIndividual",<br>
"TaxonIndividualOrGroup", "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms", "OccurringThing".) I agree that we're unlikely to agree on a consensus name, but I question why we need a name at all. Although TDWG has traditionally used<br>
transparent identifiers for terms, this has been by convention, and is not<br>
a requirement. Is it time to test the "opaque identifier" waters? Are<br>
there potential problems with having a mix of transparent and opaque<br>
identifiers in our vocabularies? If not, could we call this class<br>
dwc:12345? Should we?<br>
<br>
<br>
Thoughts on any of the above?<br>
<br>
Many thanks,<br>
Joel.<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Robert A. Morris<br><br>Emeritus Professor of Computer Science<br>UMASS-Boston<br>100 Morrissey Blvd<br>Boston, MA 02125-3390<br><br><br>Filtered Push Project<br>Harvard University Herbaria<br>Harvard University<br><br>email: <a href="mailto:morris.bob@gmail.com" target="_blank">morris.bob@gmail.com</a><br>web: <a href="http://efg.cs.umb.edu/" target="_blank">http://efg.cs.umb.edu/</a><br>web: <a href="http://wiki.filteredpush.org" target="_blank">http://wiki.filteredpush.org</a><br><a href="http://www.cs.umb.edu/~ram" target="_blank">http://www.cs.umb.edu/~ram</a><br>===<br>The content of this communication is made entirely on my<br>own behalf and in no way should be deemed to express<br>official positions of The University of Massachusetts at Boston or Harvard University.
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