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

Richard Pyle deepreef at bishopmuseum.org
Thu Sep 18 07:00:56 CEST 2014

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.




(confessed mental self-fornicator)


From: Bob Morris [mailto:morris.bob at gmail.com] 
Sent: Wednesday, September 17, 2014 10:20 AM
To: Richard Pyle
Cc: joel sachs; tdwg-content at lists.tdwg.org
Subject: Re: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)


Rich-  You might peruse


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. 




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

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

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.


> -----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
> 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
> OBI:0100026 (http://purl.obolibrary.org/obo/OBI_0100026).  Instances of
> Organism class are intended to facilitate linking of one or more
> 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,
> 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
> into specialized tissues and organs." This definition is not internally
> 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
> since the DwC definition goes on to include the clarifying aspects of the
> definition (viruses and lichens are organsims), while leaving out the
> 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
> Ontology (BFO). I've long argued that it's a mistake for TDWG to commit to
> particular upper ontology, as there is no consensus upper ontology. (Some
> scientific communities use Dolce, some use SUMO, and many have
> 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
> import terms that carry with them an abundance of ontological commitment,
> raises the stakes for those who choose to use TDWG vocabularies. (In
> when Darwin Core imported "Location"
> from Dublin Core, it did so at no cost, since Dublin Core is not tied to
> particular upper world-view.)
> The Name
> There have been multiple debates about a good name for this class, and
> 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
> 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
> 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
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Robert A. Morris

Emeritus Professor  of Computer Science
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Filtered Push Project
Harvard University Herbaria
Harvard University

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