[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review
steve.baskauf at vanderbilt.edu
Thu Sep 8 16:40:13 CEST 2011
Well, I think we've plowed this ground before (actually several times
before). In the first attempt to come up with a consensus definition
for "Individual" (previous name for what we are now calling "Organism"),
we had allowed that an Individual be identified to a single Taxon, but
with no restriction on the level of the taxon. In other words, the
Individual could be taxonomically heterogenous at a lower taxonomic
level as long as its components were part of the same higher-level taxon
(e.g. the infamous marine trawl sample and various jars of samples taken
from it; each jar an "Individual" identified to some higher taxonomic
level that was common to all organisms in the jar). However, there was
a point more recently when someone (I think it was actually you)
requested competency questions for the proposed class. I provided
three, one of which was the ability to track "duplicates" and to infer
that any Identification which applies to one duplicate also applies to
all others. I will say no more here, but simply refer to the email
where I discussed this:
Rich agreed that the ability to draw this kind of inference was valuable
and agreed that requiring that Individuals (now called Organisms) to be
taxonomically heterogeneous was a benefit that outweighted the benefits
that would accrue from allowing them to be taxonomically heterogeneous.
Rich can correct this if I've misrepresented anything he said.
Your suggestion that an Organism be a subclass of something more general
is what Cam and I suggested in an alternate version of darwin-sw. I
will not comment further on this because this approach has already been
outlined in text and diagrams at
I don't have any objection to having a superclass of Organism that
allows taxonomic heterogeneity, but one of the principles of Darwin Core
is that in order for a term to become a part of the vocabulary, at least
several people have to indicate that they want the term and there should
be some reasonable explanation of how people would use the term. That
has happened for Organism. It has NOT happened for
TaxonomicallyHeterogeneousEntity or whatever you want to call it. As I
discuss on the page reference above, allowing taxonomic heterogeneity
introduces some significant complexities in modeling and I for one have
no clue how to deal with them.
Bob Morris wrote:
> What exactly is accomplished by requiring "taxonomically homogenous?"
> Perhaps the problem is that Organism is a subclass of something
> slightly more general, some more general "biologically organized"
> object that has a context dependent organizing principle. For
> example, biologists seem willing to talk about ecosystem instances in
> this way. Also, for some purposes, people seem willing to have
> discourse about an organism in which they include microbes that must
> survive not only on or in the organism, but even a tiny bit away from
> it. So, if one had a slightly more general class, and Organism is
> required to have some enumerated set of specific kinds of organizing
> principles, e.g. those presently on the table, several things happen:
> (a)those who need to have a different organizing principle than the
> current consensus of what organizes an Organism have a place to hang
> their organizing principle, (b) scientific advances about the
> organizing principles of life don't require massive ontological
> disruption(*)...you just move a principle into the appropriate
> Bob Morris
> aka Recovering Algebraist
> (*)well, I suppose the important ones do for the biologists, but I
> suspect they needn't for the formal ontologies, if the upper level
> organizing principle is "organizing principle".
> On Thu, Sep 8, 2011 at 3:56 AM, Gregor Hagedorn <g.m.hagedorn at gmail.com> wrote:
>>> Term Name: Organism
>>> Identifier: http://rs.tdwg.org/dwc/terms/Organism
>>> Namespace: http://rs.tdwg.org/dwc/terms/
>>> Label: Organism
>>> Definition: The category of information pertaining to a specific
>>> instance of an organism (virus, symbiont, individual, colony, group of
>>> individuals, population) reliably be known to taxonomically
>> I see a problem with the "taxonomically homogeneous" since many taxa are not.
>> All obligatory mutualistically symbiontic organisms are excluded (you
>> mention symbiont, but the symbiont is the part of a symbiontic
>> relation, e.g. both the algae taxon and fungus taxon each are a
>> symbiont in a lichen.
>> Contradict if my German biology is at odds with English.
>> The problem is, that individual and set are mixed, so that the
>> "homogeneous" appears to apply also to the individual. Proposal:
>> Definition: The information class pertaining to a specific
>> instance or set of instances of a life form or organism (virus,
>> bacteria, symbiontic life forms, individual, colony, group,
>> population). Sets must reliably be known to taxonomically homogeneous
>> (including obligatory symbiontic associations).
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
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