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

Chuck Miller Chuck.Miller at mobot.org
Thu Sep 8 16:45:33 CEST 2011

"in the many, many, many cases where there will be a 1:1 relationship between an Organism and a CollectionObject..."

Rich has hit on an important point.  The discussion continues to focus on perfecting logic that is all encompassing.  But, is it the best thing to do for the community as a whole to implement solutions that are more complex in order to accommodate the very, very, very few cases (using the counter description to Rich's).

Maybe we should consider keeping the solutions simple (ie current DwC ) for the many, many, many cases and introduce complex extensions only for the very, very, very few.


-----Original Message-----
From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
Sent: Thursday, September 08, 2011 3:52 AM
To: 'Gregor Hagedorn'; tuco at berkeley.edu
Cc: 'TDWG Content Mailing List'
Subject: Re: [tdwg-content] Occurrences, Organisms,and CollectionObjects: a review

> I see a problem with the "taxonomically homogeneous" since many taxa 
> are not.
> All obligatory mutualistically symbiontic organisms are excluded (you
> symbiont, but the symbiont is the part of a symbiontic relation, e.g. 
> both
> algae taxon and fungus taxon each are a symbiont in a lichen.

I don't understand the problem.  Isn't this simply two instances of "Organism" (one symbiont and one host)?

Together, they may comprise a single collectionObject (e.g., specimen); but I see no trouble treating obligatory mutualistic symbionts and their host(s) as distinct instances of "Organism".

> Definition:     The information class pertaining to a specific 
> instance or
set of
> instances of a life form or organism (virus, bacteria, symbiontic life
> individual, colony, group, population). Sets must reliably be known to 
> taxonomically homogeneous (including obligatory symbiontic associations).

I guess it could be defined that way, but I've come around to Steve's view that "taxonomically homogeneous" implies that in cases where more than one individual is involved (colonies, small groups, populations), all such individuals belong to a single species (independently of whether or not we can identify what that species is).  When more than one species is discovered amongst a multi-individual instance of "Organism", then one would create additional instances of Organism to accommodate the heterogeneous taxa.

All of my original examples of things that I would want to be taxonomically heterogeneous (e.g., a single fossil rock with multiple phyla/kingdoms, or a single rock with multiple phyla of invertebrates attached) can be easily aggregated via a single instance of collectionObject, associated with multiple instances of Organism (one for each species[ish] level taxon).

I originally thought that both "Organism" and "collectionObject" would be
redundant, and that only one was really needed.   But I have now been
convinced by Steve (and others) that this would be an unnecessary over-loading of "Organism".  Now that we are contemplating two distinct classes, I have no problem with the more "refined" definition of "Organism".

One concern I do have, however, is in the many, many, many cases where there will be a 1:1 relationship between an Organism and a CollectionObject (i.e., the vast majority of all Museum specimens).  Does that mean that data providers will need to generate two separate Ids (one organismID and one
collectionObjectID) to represent all of these specimens?


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