[tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)

[Bob Morris]

Rich-  You might peruse

http://www.w3.org/DesignIssues/Axioms.html#opaque

In truth, I don't know whether Sir Tim has changed his view, but I'll be
surprised and disappointed if so.

I support removal of the OBI reference. I support an opaque reference.

Bob

On Wed, Sep 17, 2014 at 2:06 PM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:

> Hi Joel,
>
> As I fellow submitter and strong supporter of the Organism class for DwC,
> I,
> like you, have been uneasy with the cross-reference to OBI:0100026 in the
> definition.  It may be appropriate to include this in some sort of
> qualifying remarks about the class, but it doesn't seem to be appropriate
> to
> include the reference in the definition.  Even though it is somewhat
> softened by the phrase "in the sense" (as opposed to some sort of "same as"
> assertion), I would support the removal of the sentence "An organism in the
> sense used here is defined as OBI:0100026
> (http://purl.obolibrary.org/obo/OBI_0100026)." from the definition of
> dwc:Organism.
>
> I still believe that a human-friendly name is very helpful.  The barrier is
> not the standard or how it's named.  The barrier is how humans interpret
> and
> implement the standard.  Giving the class an opaque identifier (I would, of
> course, vote in favor of a UUID!) would probably create a barrier to
> progress through opacity that is greater than the barrier of confusion
> through mis-interpretation of an imperfect human-friendly name like
> "Organism".
>
> Of course, you didn't even indicate the term that we have been using for
> years, and which I prefer, which is "IndividualOrganism".  However, in the
> interest of progress, I strongly oppose re-opening the "name" can of worms.
> DwC is riddled with mis-applied names of things, and we can still manage to
> muddle our way through it (provided the definitions are clear).  For
> example, the term "Occurrence" has been used to represent "things" that
> range from actual occurrence instances (e.g., observations of organisms at
> a
> place and time), to individual organisms (e.g. specimens as a proxy to the
> occurrence of an organism at the time it was extracted from nature), to
> evidence (e.g. photographs of organisms), to occurrence-evidence instances
> (photographs of organism in nature).  Yet we still manage to exchange data
> (perhaps less efficiently than we could).
>
> Anyway, I support the removal of the OBI reference in the definition of
> "Occurrence", and I oppose re-visiting the issue of the label we apply to
> the proposed new dwc class.
>
> Aloha,
> Rich
>
>
> > -----Original Message-----
> > From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-
> > bounces at lists.tdwg.org] On Behalf Of joel sachs
> > Sent: Wednesday, September 17, 2014 9:34 AM
> > To: tdwg-content at lists.tdwg.org
> > Subject: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed
> > Organism term)
> >
> > Everyone,
> >
> > I'd like to comment on the proposed addition to Darwin Core of an
> "organism"
> > class (https://code.google.com/p/darwincore/issues/detail?id=205). I am
> one of
> > the submitters of this proposal, but I have some
> > reservations/suggestions/questions about both the definition and the
> name.
> > Taking them in turn:
> >
> > The Definition
> > The proposed definition is:
> > "A particular organism or defined group of organisms considered to be
> > taxonomically homogeneous.  An organism in the sense used here is defined
> as
> > OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026).  Instances of
> the
> > Organism class are intended to facilitate linking of one or more
> Identification
> > instances to one or more Occurrence instances.  Therefore, things that
> are
> > typically assigned scientific names (such as viruses, hybrids, and
> lichens) and
> > aggregates whose occurrences are typically recorded (such as packs,
> clones,
> > and colonies) are included in the scope of this class."
> >
> > There are a few things to note here:
> > i. The definition of OBI:0100026 is "A material entity that is an
> individual living
> > system, such as animal, plant, bacteria or virus, that is capable of
> replicating or
> > reproducing, growth and maintenance in the right environment. An organism
> > may be unicellular or made up, like humans, of many billions of cells
> divided
> > into specialized tissues and organs." This definition is not internally
> consistent,
> > since it delineates organisms as being either unicellular or
> multi-cellular, while
> > at the same time explicitly including viruses, which are acellular.
> >
> > ii. The reference to OBI:0100026 does not add clarity to the DwC
> definition,
> > since the DwC definition goes on to include the clarifying aspects of the
> OBI
> > definition (viruses and lichens are organsims), while leaving out the
> muddying
> > aspects of the OBI definition (organisms are unicellular or
> multicellular). The
> > DwC definition also extends the the OBI defintion (to include wolf
> packs).
> >
> > iii. The rdf definition of OBI:organism inherits axioms from the Basic
> 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 ontology. (Some
> > scientific communities use Dolce, some use SUMO, and many have
> deliberately
> > chosen to use none at all.) In general, I like the notion of Darwin Core
> as a
> > glossary of terms, on top of which various data models can be built. When
> we
> > import terms that carry with them an abundance of ontological commitment,
> it
> > raises the stakes for those who choose to use TDWG vocabularies. (In
> contrast,
> > when Darwin Core imported "Location"
> > from Dublin Core, it did so at no cost, since Dublin Core is not tied to
> any
> > particular upper world-view.)
> >
> >
> > The Name
> > There have been multiple debates about a good name for this class, and
> there
> > was never consensus. (In addition to "Organism", candidates included
> > "Individual", "OrganismalIndividual", "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 transparent identifiers for terms, this has been by convention, and
> is not a
> > requirement. Is it time to test the "opaque identifier" waters? Are there
> > potential problems with having a mix of transparent and opaque
> identifiers
> in
> > our vocabularies? If not, could we call this class dwc:12345? Should we?
> >
> >
> > Thoughts on any of the above?
> >
> > Many thanks,
> > Joel.
> >
> > _______________________________________________
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> > tdwg-content at lists.tdwg.org
> > http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
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-- 
Robert A. Morris

Emeritus Professor  of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390


Filtered Push Project
Harvard University Herbaria
Harvard University

email: morris.bob at gmail.com
web: http://efg.cs.umb.edu/
web: http://wiki.filteredpush.org
http://www.cs.umb.edu/~ram
===
The content of this communication is made entirely on my
own behalf and in no way should be deemed to express
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