<div dir="ltr"><div><div>Rich- You might peruse<br><br><a href="http://www.w3.org/DesignIssues/Axioms.html#opaque">http://www.w3.org/DesignIssues/Axioms.html#opaque</a><br><br></div>In truth, I don't know whether Sir Tim has changed his view, but I'll be surprised and disappointed if so.<br><br></div><div>I support removal of the OBI reference. I support an opaque reference. <br></div><div><br></div>Bob<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 17, 2014 at 2:06 PM, Richard Pyle <span dir="ltr"><<a href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Joel,<br>
<br>
As I fellow submitter and strong supporter of the Organism class for DwC, I,<br>
like you, have been uneasy with the cross-reference to OBI:0100026 in the<br>
definition. It may be appropriate to include this in some sort of<br>
qualifying remarks about the class, but it doesn't seem to be appropriate to<br>
include the reference in the definition. Even though it is somewhat<br>
softened by the phrase "in the sense" (as opposed to some sort of "same as"<br>
assertion), I would support the removal of the sentence "An organism in the<br>
<span class="">sense used here is defined as OBI:0100026<br>
</span>(<a href="http://purl.obolibrary.org/obo/OBI_0100026)" target="_blank">http://purl.obolibrary.org/obo/OBI_0100026)</a>." from the definition of<br>
dwc:Organism.<br>
<br>
I still believe that a human-friendly name is very helpful. The barrier is<br>
not the standard or how it's named. The barrier is how humans interpret and<br>
implement the standard. Giving the class an opaque identifier (I would, of<br>
course, vote in favor of a UUID!) would probably create a barrier to<br>
progress through opacity that is greater than the barrier of confusion<br>
through mis-interpretation of an imperfect human-friendly name like<br>
"Organism".<br>
<br>
Of course, you didn't even indicate the term that we have been using for<br>
years, and which I prefer, which is "IndividualOrganism". However, in the<br>
interest of progress, I strongly oppose re-opening the "name" can of worms.<br>
DwC is riddled with mis-applied names of things, and we can still manage to<br>
muddle our way through it (provided the definitions are clear). For<br>
example, the term "Occurrence" has been used to represent "things" that<br>
range from actual occurrence instances (e.g., observations of organisms at a<br>
place and time), to individual organisms (e.g. specimens as a proxy to the<br>
occurrence of an organism at the time it was extracted from nature), to<br>
evidence (e.g. photographs of organisms), to occurrence-evidence instances<br>
(photographs of organism in nature). Yet we still manage to exchange data<br>
(perhaps less efficiently than we could).<br>
<br>
Anyway, I support the removal of the OBI reference in the definition of<br>
"Occurrence", and I oppose re-visiting the issue of the label we apply to<br>
the proposed new dwc class.<br>
<br>
Aloha,<br>
Rich<br>
<div class="HOEnZb"><div class="h5"><br>
<br>
> -----Original Message-----<br>
> From: <a href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [mailto:<a href="mailto:tdwg-content-">tdwg-content-</a><br>
> <a href="mailto:bounces@lists.tdwg.org">bounces@lists.tdwg.org</a>] On Behalf Of joel sachs<br>
> Sent: Wednesday, September 17, 2014 9:34 AM<br>
> To: <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
> Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed<br>
> Organism term)<br>
><br>
> Everyone,<br>
><br>
> I'd like to comment on the proposed addition to Darwin Core of an<br>
"organism"<br>
> class (<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<br>
one of<br>
> the submitters of this proposal, but I have some<br>
> reservations/suggestions/questions about both the definition and the name.<br>
> 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<br>
> 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<br>
> Organism class are intended to facilitate linking of one or more<br>
Identification<br>
> instances to one or more Occurrence instances. Therefore, things that are<br>
> typically assigned scientific names (such as viruses, hybrids, and<br>
lichens) and<br>
> aggregates whose occurrences are typically recorded (such as packs,<br>
clones,<br>
> and colonies) are included in the scope 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<br>
> system, such as animal, plant, bacteria or virus, that is capable of<br>
replicating or<br>
> reproducing, growth and maintenance in the right environment. An organism<br>
> may be unicellular or made up, like humans, of many billions of cells<br>
divided<br>
> into specialized tissues and organs." This definition is not internally<br>
consistent,<br>
> since it delineates organisms as being either unicellular or<br>
multi-cellular, while<br>
> at the same time explicitly including viruses, which are acellular.<br>
><br>
> ii. The reference to OBI:0100026 does not add clarity to the DwC<br>
definition,<br>
> since the DwC definition goes on to include the clarifying aspects of the<br>
OBI<br>
> definition (viruses and lichens are organsims), while leaving out the<br>
muddying<br>
> aspects of the OBI definition (organisms are unicellular or<br>
multicellular). The<br>
> 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<br>
> Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to<br>
any<br>
> particular upper ontology, as there is no consensus upper ontology. (Some<br>
> scientific communities use Dolce, some use SUMO, and many have<br>
deliberately<br>
> chosen to use none at all.) In general, I like the notion of Darwin Core<br>
as a<br>
> glossary of terms, on top of which various data models can be built. When<br>
we<br>
> import terms that carry with them an abundance of ontological commitment,<br>
it<br>
> raises the stakes for those who choose to use TDWG vocabularies. (In<br>
contrast,<br>
> when Darwin Core imported "Location"<br>
> from Dublin Core, it did so at no cost, since Dublin Core is not tied to<br>
any<br>
> 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<br>
> was never consensus. (In addition to "Organism", candidates included<br>
> "Individual", "OrganismalIndividual", "TaxonIndividualOrGroup",<br>
> "OrganismOrTaxonomicallyHomogenousGroupOfOrganisms",<br>
> "OccurringThing".) I agree that we're unlikely to agree on a consensus<br>
name,<br>
> but I question why we need a name at all. Although TDWG has traditionally<br>
> used transparent identifiers for terms, this has been by convention, and<br>
is not a<br>
> requirement. Is it time to test the "opaque identifier" waters? Are there<br>
> potential problems with having a mix of transparent and opaque identifiers<br>
in<br>
> our vocabularies? If not, could we call this class dwc:12345? Should we?<br>
><br>
><br>
> Thoughts on any of the above?<br>
><br>
> Many thanks,<br>
> Joel.<br>
><br>
> _______________________________________________<br>
> tdwg-content mailing list<br>
> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
<br>
_______________________________________________<br>
tdwg-content mailing list<br>
<a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
<a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
</div></div></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.
</div>