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

[Hilmar Lapp]

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.

  -hilmar


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

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