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.
Aloha,
Rich
(confessed mental self-fornicator)
From: Bob Morris [mailto:morris.bob@gmail.com] Sent: Wednesday, September 17, 2014 10:20 AM To: Richard Pyle Cc: joel sachs; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] Comments on Darwin Core Issue 205 (the proposed Organism term)
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@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@lists.tdwg.org [mailto:tdwg-content- bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Wednesday, September 17, 2014 9:34 AM To: tdwg-content@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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