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

John Deck jdeck at berkeley.edu
Fri May 31 19:53:51 CEST 2013

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, "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


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 ****
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content

John Deck
(541) 321-0689
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