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

Cellinese,Nico ncellinese at flmnh.ufl.edu
Wed Sep 17 23:34:58 CEST 2014

Hope you are actively working on our paper in addition to this mental masturbation. Tree-thinking is way more orgasmic than organismic terms. I see you have not touched the draft I sent you a week ago :-)


On Sep 17, 2014, at 5:18 PM, Hilmar Lapp <hlapp at nescent.org<mailto:hlapp at nescent.org>> wrote:

Three comments:

OBI class definitions are not carved in stone. If you have issues with the definition (and the ones you express are well taken), why wouldn't you take them to OBI but to DwC? I.e., do you want to suggest that the OBI term definition won't improve in the foreseeable future such that your criticisms are addressed?

As for the BFO, I know that's been brought up repeatedly, but to me that's entirely a red herring. By having a reference to the OBI class, DwC makes no commitment whatsoever to BFO axioms; only users who assert a subclass axiom and expressly import OBI as well as BFO do. I would argue that those who do so make an explicit choice. (Also, that horse has already left the barn by reference to material sample. So even if it wasn't a red herring before, it is one now.)

As for the name, although using opaque identifiers in DwC is something I would wholeheartedly welcome, in this case all it accomplishes is buying time rather than a solution. Opaquely identified terms still need a human-readable label that's succinct, precise, and accurate, and arguably more so, not less, if the identifier is opaque.


On Wed, Sep 17, 2014 at 4:34 PM, joel sachs <jsachs at csee.umbc.edu<mailto:jsachs at csee.umbc.edu>> wrote:

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,

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Hilmar Lapp -:- informatics.nescent.org/wiki<http://informatics.nescent.org/wiki> -:- lappland.io<http://lappland.io/>

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Nico Cellinese, Ph.D.
Associate Curator, Botany & Informatics
Joint Associate Professor, Department of Biology

Florida Museum of Natural History
University of Florida
354 Dickinson Hall, PO Box 117800
Gainesville, FL 32611-7800, U.S.A.
Tel. 352-273-1979
Fax 352-846-1861

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