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

Richard Pyle deepreef at bishopmuseum.org
Thu Sep 8 10:52:15 CEST 2011

> 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

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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