[tdwg-content] "Individual" use case

Richard Pyle deepreef at bishopmuseum.org
Tue Nov 2 09:33:34 CET 2010


Thanks, Dean -- you've reminded me of something that hadn't come up
previously in the "Individual" discussion.  Several times the assertion has
been made (perhaps even by me?) that an Individual is assumed to be a single
taxon.  This assertion always triggered something int he depths of my brain,
but I couldn't figure out what -- but now I remember, the need to deal with
multi-taxon "lots" of organisms, and track them with sspecimen-like (and
hence Individual-like) properties.  I believe Stan Blum dealt with this
extensively in the ASC data model (CollectionObject, I think it was called),
and it needed to accomodate not only multi-taxon lots of the sort that you
describe, but also things like fossil specimens that have multiple phyla, or
even Kingdoms, permanently combined within the same "CollectionObject".
 
But this is only an asterisk, because it doesn't really break the notion of
"same taxon" for an Individual, as long as the scope of "taxon" stretches
all the way up to Domain.  Even the sample with plants, animals, and
bacteria fall within the taxon circumscription of "life".
 
But in any case, I agree with your general approach to "derived"
specimens/samples -- which happens a lot in the DNA tissue sampling world.
We can start with a multi-phylum aggregated lot, then split it out not only
to the individual organism, but all the way into the parts and tissue
samples realm.
 
I don't know how DwC handles this (ResourceRelationship class?), but it's
certainly important (and increasingly so) in the natural history specimens
realm.
 
Rich


  _____  

From: tdwg-content-bounces at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Dean Pentcheff
Sent: Monday, November 01, 2010 10:05 AM
To: tdwg-content at lists.tdwg.org
Subject: [tdwg-content] "Individual" use case


Count me in as another late entry to this discussion, lurking under the
rumbling flight paths of the VLPs (Very Large Postings).

Here's a potential case to consider in the whole "how to file all the parts"
issues that seem to be arising. It's a parent/child scheme that we're
implementing for our marine invertebrate specimen database. We think we are
being reasonable in the way we thought of this. We hope that this concept
could be accomodated by DwC. That's the sum of the contribution for
consideration: we hope DwC can/will cope with this. It may well be that it
happily does so under all of the "Individual" interpretations that are
bouncing around. But hey, we thought we'd toss it in just to make sure.

With marine invertebrates, we very often find ourselves subsampling
collected things (yes, "thing" is deliberately vague to avoid misusing any
heavy-baggage words). It is intrinsic to the nature of the collections.
Things often arrive as unsorted lots (think of a jar full of coral rubble in
95% alcohol, sitting on our shelf). We want to have a record for that jar in
our database, so it gets one, with a recordID. 

Months later, we sort the jar to phylum level, and each of those jars gets a
record, each with a recordID, and those jars go on a shelf. We treat those
records as children of the unsorted-lot-record, and they each have a pointer
back to that unsorted-lot parent record.

Then we later sort one of those phylum-level jars into species jars. Those,
in turn, each get a record with a recordID, and point to their parent
phylum-level-jar record. And so forth down to individuals in jars, and
tissue samples of individuals, and DNA extracts of those tissues. 

To complete the picture: many specimens do, of course, come in simply as an
individual in a jar. Those just get a record, and that's that: no parent, no
child (no child yet... until there's a tissue sample).

Key points: 
1. We never know how many levels of subsorting there will be. That differs
from the "preparation" orientation of many vertebrate collections (for
example), where there's a predefined set of preps that can come from each
collected individual. We very often don't start with individuals. 
2. Each thing, whether it comes in the door directly or is derived from
something that did, gets a first-class catalog record, and the sole unifying
feature that gets us the full information on a thing are the parent-child
relationships of the data records. Information has to continue to reside in
those records and be accessible from the "children" (an example would be a
transfer to a different preservative when pulling one individual into a
specimen jar from a lot jar: you need to know the preservative this thing is
in now, and you also need to know what preservative its parent thing was
in).
3. One field of each record has to document whether the item still exists: a
thing may be completely subdivided into subparts leaving nothing left over
to put back on the shelf. But in that case, we still keep the data record
since it's still the parent of the subsorted things and still holds the
relevant historical information.

So one day when we push these data out into the Wild World in a DwC context,
the thing we'd like to see accomodated is the ability of systems outside our
own walls to resolve back up that chain of subsorting to build the whole
information set for a thing, including the relevant information from its
logical "parents".

OK, now we'll be delighted to hear that this scheme was obviously
accomodated all along, or alternately, that this whole concept is a pretty
dumb way of cataloging our holdings.

-Dean
-- 
Dean Pentcheff
Research Associate, Natural History Museum of LA County
pentcheff at gmail.com
dpentche at nhm.org


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