[tdwg-content] Occurrences, Organisms, and CollectionObjects: a review

Steve Baskauf steve.baskauf at vanderbilt.edu
Thu Sep 8 19:47:11 CEST 2011

I see your point here.  There has been some previous discussion on this 
list about classes for describing things like ecosystems and other 
larger scale phenomena involving collections of living things.  But I 
don't think that discussion has been anything close to as extensive as 
the discussion surrounding individuals/organisms and 
tokens/evidence/collectionObjects.  So I think the questions: "who needs 
the superclass?"  and "what do they want to do with it?" (i.e. 
competency questions) need to be asked.  Then somebody needs to create a 
definition and a proposal.  I don't think any of those things have 
happened so far for larger-scale aggregates of living things. 

I think it is possible (actually likely) that other groups may already 
have terms for some aggregates that we might adopt.  Vegetation 
classification schemes come to mind as well as several ecoregions 
classification schemes.


Bob Morris wrote:
> I was perhaps unclear.  I don't mean to suggest a superclass that has
> some other notion of taxonomic organization.  I meant to suggest one
> that simply has \some/ notion of organization. That wouldn't change
> the offered definition of Organism, but rather give people who feel
> they need some notion of an organized set of biological stuff a way to
> define other subclasses  with different organizations.  It would, for
> example, let people use DwC to describe some aspects of ecosystems
> able to do so without having to pretend that an ecosystem is always a
> special kind of Organism, or vice-versa.
> It doesn't look to me like you envision that
> http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity would
> be suitable for describing ecosystems, possibly even for those
> ecologists that think a hierarchy of ecosystem types is as fundamental
> to what the study as are classical taxonomic hierarchies to classical
> taxonomists.
> Bob
> On Thu, Sep 8, 2011 at 10:40 AM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu> wrote:
>> 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:
>> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002690.html
>> 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
>> http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity
>> 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.
>> Steve
>> 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
>> subclass.
>> 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
>> homogeneous.
>> 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).
>> Gregor
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>> --
>> 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.
>> delivery address:
>> 2125 Stevenson Center
>> 1161 21st Ave., S.
>> Nashville, TN 37235
>> office: 2128 Stevenson Center
>> phone: (615) 343-4582,  fax: (615) 343-6707
>> http://bioimages.vanderbilt.edu

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.

delivery address:
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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