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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks, Bob. Of course, Identifiers > URIs. URIs fail my own Opacity Axiom, in that most of them start with “http://”, which temps people into inferring that they can be dereferenced via the HTTP protocol.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Aloha,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Rich<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>(confessed mental self-fornicator)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Bob Morris [mailto:morris.bob@gmail.com] <br><b>Sent:</b> Wednesday, September 17, 2014 10:20 AM<br><b>To:</b> Richard Pyle<br><b>Cc:</b> joel sachs; tdwg-content@lists.tdwg.org<br><b>Subject:</b> Re: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'>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><o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'>In truth, I don't know whether Sir Tim has changed his view, but I'll be surprised and disappointed if so.<o:p></o:p></p></div><div><p class=MsoNormal>I support removal of the OBI reference. I support an opaque reference. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>Bob<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Wed, Sep 17, 2014 at 2:06 PM, Richard Pyle <<a href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>> wrote:<o:p></o:p></p><p class=MsoNormal>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>sense used here is defined as OBI:0100026<br>(<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<o:p></o:p></p><div><div><p class=MsoNormal><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><o:p></o:p></p></div></div></div><p class=MsoNormal><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. <o:p></o:p></p></div></div></div></body></html>