[tdwg-content] New Darwin Core terms proposed relating to material samples

[Richard Pyle]

Thanks, John – this is REALLY helpful!

 

A couple questions – can you expand a bit on the differences between
JohnDeckOccurrence123, 124,and 125?  I’m assuming that JohnDeckOccurrence123
is associated with the Event representing the time & place when
JohnDeckTissueSample1 was removed from JohnDeck.  I’m guessing that
JohnDeckOccurrence124 is associated with the Event representing the time &
place when JohnDeckGutSample1 was removed from JohnDeck.  What I don’t
understand is why there needs to be a JohnDeckOccurrence125.  What
Occurrence does that represent?  Later you suggest that JohnDeck
(WholeOrganism) was extracted from nature. Is the extraction-from-nature
Occurrence one of these three Occurrences?

 

What you describe below is consistent with our approach to treating
materialSample as a subclass of Individual (assuming a hierarchical
Individual, which means that ParentIndividualID of both
JohnDeckTissueSample1 and JohnDeckGutSample1 is IndividualID=JohnDeck).  The
nice thing about the hierarchical approach is that deals with the problem
you describe in the last paragraph.

 

Rich

 

 

From: jdeck88 at gmail.com [mailto:jdeck88 at gmail.com] On Behalf Of John Deck
Sent: Friday, May 31, 2013 7:54 AM
To: Richard Pyle
Cc: Markus Döring; Jason Holmberg; TDWG Content Mailing List; Robert
Whitton; Ramona Walls
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
material samples

 

Yep--- that reference point for aggregation can be really powerful:  To
provide a working example of how these identifiers would work, and how they
can act to aggregate data elements, consider the following:



IndividualID = JohnDeck

MaterialSampleID = JohnDeckTissueSample1

OccurrenceID = JohnDeckOccurrence123

Taxon = "Homo sapiens"

 

IndividualID = JohnDeck

MaterialSampleID = JohnDeckGutSample1

OccurrenceID = JohnDeckOccurrence124

Taxon = "Bacteria500"

 

IndividualID = JohnDeck

MaterialSampleID = JohnDeckGutSample1

OccurrenceID = JohnDeckOccurrence125

Taxon = "Bacteria501"

 

JohnDeckTissueSample1 is representative of the Individual itself, while
JohnDeckGutSample1 is still associated with the same Individual but notice
the taxon has changed and it is a new Occurrence as well.  This approach
allows for some sense to be constructed using a flat file approach if
desired.  Providing a Material Sample BoR for OccurrenceID's 124 and 125
provides further context.  Meanwhile, we can consider the implications of,
for example, habitat descriptions (... for JohnDeckOccurrence123 maybe i'd
put http://purl.obolibrary.org/obo/ENVO_01000193, "temperate grassland
biome")  but the distinct occurrence records for the gut samples could be
listed as ( <http://purl.obolibrary.org/obo/ENVO_01000162>
http://purl.obolibrary.org/obo/ENVO_01000162, "organ").

 

Another use for the identifier MaterialSampleID -- lets assume we've
expressed an equivalent identifier for a genbank sample using
MIxS:source_mat_id, a term which references the same OBI:MaterialSample
we're referencing, which allows.  If they're URIs we can model this in RDF
using the MaterialSampleID's as either subjects or objects... this gets us a
step closer for representing contextual information in genbank and DwC
without duplicating metadata across systems (genbank for sequencing metada;
DwC for environmental context)



There are some issues with this approach of course, for example, if we
provide a lat/lng for an occurrence that is a gutsample are we taking the
lat/lng where the gutsample was removed from the organism (may be different
than where a parent organism was isolated from nature).  In this case, we
need to assume that we're referring to where the parent organism was
isolated from nature to be consistent with DwC and implementations in use.
However, the notion of habitat should vary with the occurrence of the actual
organism (e.g. "organ" vs. "temperate grassland biome").  Thus, we can still
aggregate properties around MaterialSample BoR's that are useful but we need
to think carefully about what exactly the properties mean that we assign to
these things.... but this is no different than issues we've encountered
between other BoR's (Fossil, PreservedSpecimen, or
Human/MachineObservation).  

 

John

 

On Thu, May 30, 2013 at 11:48 PM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:

Yes, that’s a fair point!  In a sense, the ID has intrinsic value on its own
if for no other reason than to represent a reference point for aggregation.

 

Nevertheless, I still maintain that if it fulfills that purpose, then it
implies a “thing” (around which other “things” are aggregated), and I can’t
imagine such a “thing” that we would care about for aggregating purposes,
about which we would not associate other property values. 

 

I say all this quite deliberately in reference to “dwc:individualID”, of
course
. J

 

Aloha,

Rich

 

 

From: Markus Döring [mailto:m.doering at mac.com] 
Sent: Thursday, May 30, 2013 7:56 PM
To: Jason Holmberg
Cc: Richard Pyle; TDWG Content Mailing List; Robert Whitton; John Deck;
Ramona Walls


Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
material samples

 

The id value is actually very useful and the only trustworthy way of
grouping records, e.g. all occurrences of the same whale.

Markus 


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-- 
John Deck
(541) 321-0689

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