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

joel sachs jsachs at csee.umbc.edu
Wed Sep 17 22:34:10 CEST 2014


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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