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

[Steve Baskauf]

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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>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>>     
>
>
>
>   

-- 
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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