[tdwg-content] New Darwin Core terms proposed relating to material samples
Richard Pyle
deepreef at bishopmuseum.org
Sun May 26 23:25:54 CEST 2013
Thanks John -
Yes, I agree - the description you forwarded definitely fits how we have
been using "Individual". The main reason we selected that term was to stay
in harmony with the existing "individualID" in DWC. Besides, other
candidate terms ( "thing", "stuff", "unit", etc.) all seemed a bit vague.
The match is not perfect, though, because some of the things we represent as
"individuals" (herd, school, etc.) are not "sampled" (unless a visual
observation counts as a sample). So, it would seem that "material sample"
would be a subset/subclass of what we have been using for "Individual".
My main question, though, was more along the lines of what progress (if any)
has been made towards establishing a formal class in DWC for "Individual"
(representing the set of terms applied to attributes of what is intended by
the existing DWC "individualID") - presumably modeled after the Darwin-SW
"IndividualOrganism". And, whether or not there has been any progress,
would there be any value in contemplating both that topic (expansion of
dwc:individualID into a class), and this topic (proposed new
dwc:materialSample) within the same discussion?
Aloha,
Rich
From: jdeck88 at gmail.com [mailto:jdeck88 at gmail.com] On Behalf Of John Deck
Sent: Saturday, May 25, 2013 5:55 PM
To: Richard Pyle
Cc: Steve Baskauf; TDWG Content Mailing List; Robert Whitton
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
material samples
Hi Rich,
I'm on my way home from Copenhagen and leaving very soon so will write just
a quick response to you. The view of those folks who submitted the
MaterialSample ticket
(https://code.google.com/p/darwincore/issues/detail?id=167) is defined well
by the following paragraph:
A "material sample" can pertain to general matter in which organisms may
exist, in whole, in part, or in conjunction with many other organisms. The
"material sample" may exist for a brief period, such as a tissue that is
destructively sampled when it is converted to DNA extract. It may also
represent a collection of multiple taxa, such as a soil or water sample that
is used with the intention of describing the diversity of organisms, whether
the actual organisms are later recovered from such a sample, or whether that
sample is processed (sometimes destructively, which is when the entire
sample is consumed for an analysis process) in order to generate a set of
derivatives directly from organisms (e.g.16S sequences from a metagenomics
run). A "material sample" may also yield connections to other indicators of
biodiversity aside from taxa, such as a transcriptome, indicating which DNA
is actively being expressed at a particular point in time.
In reading your idea of what an individual may be, it is not so different
than what we're proposing. However, MaterialSample makes no assumptions
about what any affiliated names or properties may or may not be, and can be
composed of many possible sub-units. Also, the notion of what you're
describing is a bit of a stretch when the common dictionary definition of
individual is means "single or separate".
John
On Sun, May 26, 2013 at 3:31 AM, Richard Pyle <deepreef at bishopmuseum.org>
wrote:
Hi All,
I'm on my way home from Berlin, and catching up on this thread.
I wanted to take this opportunity to describe what Rob Whitton and I have
been working on over the past year or so, along these lines.
Basically, we've been running with the idea of an "Individual" class - as
originally proposed by Steve and discussed at some length on this list a
while ago. This has been documented for DSW:
https://code.google.com/p/darwin-sw/wiki/ClassIndividual
We have (or intend to) drop the "Organism" part, so it's just an
"Individual" - because in our data model it doesn't need to be limited to an
organism.
Anyway, the reason I mention this here is that we have found it to be a very
powerful tool for tracking our data much more closely to "reality" than is
achieved when force-fitting everything into the Occurrence class. I also
mention it because we are using it for the same function that the proposed
MaterialSample/ID seems to be used for.
We define an "Individual" as the physical "something" that underpins an
Occurrence. In the case of organisms, this can be a group (herd, school,
flock, etc.), specimen (either a single specimen, or a lot of multiple
specimens), or any sort of derivative of a specimen (part, tissue sample,
dna extraction, etc.). It corresponds to the intended meaning of
dwc:individualID (http://rs.tdwg.org/dwc/terms/index.htm#individualID), and
also to the meaning of "CollectionObject" from the old ASC/MVZ data model
(see also: https://www.idigbio.org/wiki/images/c/c9/Phase_I_Report.pdf).
So far, it seems to be a very stable and functional unit for tracking myriad
kinds of biodiversity information. It is linked from the Occurrence table,
and is the thing to which taxon determinations are applied. It's also the
thing that represents museum collections objects. The key is that it is
hierarchical. For example, there may be one instance of an "Individual"
that is a school of fish observed on a reef, representing an occurrence.
That Individual instance may have a child "Lot" of, say 5 specimens that
were speared and preserved for a Museum. Each of the five specimens might
then be assigned its own individual instance, as children of the "Lot".
Then, when one or more tissue samples are extracted from one or more of the
specimens, those are represented as additional "Individual" instances that
are children of the respective specimen individual.
What's nice about the way we manage this is that there is inheritance up and
down the hierarchy chain. For example, if the "School" individual is
associated with an Occurrence (observation/collection event), then all of
its children can inherit this information. Likewise, a taxonomic
determination can be applied to any individual in the hierarchy, and that
identification can be inherited up or down the hierarchy as appropriate (the
meaning of "appropriate" is a bit involved, but I'd be happy to elaborate).
I've been out of this discussion for a while, but I guess my main
question/point is to ask whether there has been any progress towards
incorporating the concept of the Darwin-SW concept of "Individual"
(https://code.google.com/p/darwin-sw/wiki/ClassIndividual) into DWC, and if
so, whether this might be a better way of managing materialSample/ID.
Aloha,
Rich
From: tdwg-content-bounces at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Steve Baskauf
Sent: Saturday, May 25, 2013 1:08 AM
To: John Deck
Cc: TDWG Content Mailing List
Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
material samples
John and John,
OK, great! I think this all makes sense to me now. I think that that in
the wiki discussion you might eventually make the comment that although
materialSampleID is conveniently grouped with other terms under the
Occurrence class, a material sample does not have to be a sample from a
living organism which is documented in an Occurrence. It could be something
that may or may not be known to contain one or more living organisms (e.g.
water samples), part of one or more organisms (e.g. tissue samples), or even
no known living organisms (e.g. rock samples). Well anyway, you should say
that if it is true. I think that was the intention when the term was being
discussed. You can confirm whether I have this right or not.
Steve
John Deck wrote:
Steve,
Thanks for your comments. Responding to both of your emails here.
We've removed the class and now have just the MaterialSample dwctype and a
materialSampleID property. dwctype:MaterialSample refines
<http://purl.obolibrary.org/obo/OBI_0000747>
http://purl.obolibrary.org/obo/OBI_0000747. Also, we've updated
materialSampleID to be a new term in the dwc/terms namespace instead of
referencing the MiXS namespace. In our original proposal, we suggested
using the MIxS RDF namespace for this property, however, the GSC did not
make MIxS-as-RDF a standard, as decided recently at GSC15, so we've chosen
not to use that term (by convention) and instead propose creating our own
materialSampleID property in the dwc/terms namespace. (A side note: the
GSC is still very much interested in MIxS as RDF and we'll continue to
maintain and implement <https://code.google.com/p/mixs-as-rdf/>
https://code.google.com/p/mixs-as-rdf/ in conjunction with the MIxS
developers).
Modification to proposed terms:
Term Name: MaterialSample
Identifier: <http://rs.tdwg.org/dwc/terms/MaterialSample>
http://rs.tdwg.org/dwc/dwctype/MaterialSample
Namespace: http:/ <http://rs.tdwg.org/dwc/terms> rs.tdwg.org/dwctype/
Label: Material Sample
Definition: The category of information pertaining to the physical results
of a sampling (or subsampling) event. In biological collections, the
material sample is typically collected, and either preserved or
destructively processed.
Comment: For discussion see
<http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary>
http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no
further documentation here until the term is ratified)
Type of Term: <http://www.w3.org/2000/01/rdf-schema#Class>
http://www.w3.org/2000/01/rdf-schema#Class
Refines: <http://purl.obolibrary.org/obo/OBI_0000747>
http://purl.obolibrary.org/obo/OBI_0000747
Status: proposed
Date Issued: 2013-03-28
Date Modified: 2013-05-25
Has Domain:
Has Range:
Refines:
Version: MaterialSample-2013-05-25
Replaces:
IsReplaceBy:
Class:
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
Term Name: materialSampleID
Identifier: <http://rs.tdwg.org/dwc/terms/MaterialSample>
http://rs.tdwg.org/dwc/terms/MaterialSampleID
Namespace: <http://rs.tdwg.org/dwc/terms/MaterialSample>
http://rs.tdwg.org/dwc/terms/
Label: Material Sample ID
Definition: An identifier for the MaterialSample (as opposed to a particular
digital record of the material sample). In the absence of a persistent
global unique identifier, construct one from a combination of identifiers in
the record that will most closely make the materialSampleID globally unique.
Comment: For discussion see
<http://code.google.com/p/darwincore/wiki/MaterialSample>
http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not
exist until the term is ratified).
Type of Term: <http://www.w3.org/1999/02/22-rdf-syntax-ns#Property>
http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines: <http://purl.org/dc/terms/identifier>
http://purl.org/dc/terms/identifier
Status: proposed
Date Issued: 2013-03-28
Date Modified: 2013-05-25
Has Domain:
Has Range:
Version: materialSampleID-2013-05-25
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Occurrence
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
John D. and John W.
On Mon, May 20, 2013 at 7:39 PM, Steve Baskauf
<steve.baskauf at vanderbilt.edu> wrote:
Here is the second question. The proposal proposes a new MaterialSample
class
http://rs.tdwg.org/dwc/terms/MaterialSample
which is in the "main" (dwc:=http://rs.tdwg.org/dwc/terms/ ) namespace. I
guess my question is why we need this class. I can definitely see a
rational for a new class defined as part of the DwC type vocabulary (i.e.
dwctype:MaterialSample). It would be used to type resources that are
material samples. But the class terms in the main (dwc:) namespace are used
as a convenient way to group DwC property terms that might reasonably be
used with instances of that class. However, there really aren't any such
terms.
We already have a convention in which not every type vocabulary class term
has a corresponding class term in the main (dwc:) namespace. There are
dwctype:PreservedSpecimen, dwctype:LivingSpecimen, dwctype:FossilSpecimen,
dwctype:HumanObservation, dwctype:MachineObservation, and
dwctype:NomenclaturalChecklist, none of which have dwc: namespace analogues.
So why does MaterialSample need a dwc: namespace analog?
Steve
John Wieczorek wrote:
Dear all,
TDWG could see a lot of activity in 2013 in anticipation of the meeting in
Florence in October. Much of the activity is related to enabling integration
across multiple parts of our domain. We have the Audubon Core under review
for biodiversity-related media and an impending RDF Guide to supplement the
already extant Text and XML Guides for Darwin Core.
This message is to bring your attention to another integrative initiative,
to introduce terms into Darwin Core that will form a nexus between
Occurrences and the interesting things that happen with physical materials
that result from them, such as, but not limited to, genetic sequencing. A
series of meetings for a little over the past year have inspired our
colleagues in the Genomics Standards Consortium (GSC) to propose to their
constituency to align their terms with Darwin Core, including adopting some
of the Darwin Core terms in place of their own that have the same meaning.
Out of these discussions has come the realization that neither community has
terms to accommodate the concept of an identifiable (objectively, not
taxonomically), trackable material sample. This message constitutes such a
proposal.
This proposal would have no impact on those publishing purely taxonomic
data. It would also have no impact on those publishing occurrence data
unless they want to increase their capacity to distinguish material samples
from organisms more rigorously than is now possible using only the
dwc:preparations term.
The initial request for new terms can be found in the Darwin Core Issue
tracker as http://code.google.com/p/darwincore/issues/detail?id=167. Below I
have elaborated nad formalized the request into the three distinct terms
under consideration, initiating the 30 day minimum public review process to
seek consensus on their inclusion in the Darwin Core standard. Your job,
should you choose to accept it, is to discuss the merits or any perceived
problems in the inclusion of these three terms in Darwin Core.
Below I will give the proposed properties of three terms as they would
appear in the Darwin Core Quick Reference Guide, though these properties
would be included in the RDF of the normative form of the documentation.
A new MaterialSample class: This is for the purpose of organizing
properties, just as the existing classes (Occurrence, Event, Location,
GeologicalContext, Identification, Taxon, etc.) do, without having any terms
declare this class as their domain.
Term Name: MaterialSample
Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http:/rs.tdwg.org/dwc/terms
Label: Material Sample
Definition: The category of information pertaining to the physical results
of a sampling (or subsampling) event. In biological collections, the
material sample is typically collected, and either preserved or
destructively processed, with the intention of being representative of a
greater whole.
Comment: For discussion see
http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not
exist until the term is ratified).
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-03-28
Date Modified: 2013-04-08
Has Domain:
Has Range:
Version: MaterialSample-2013-03-28
Replaces:
IsReplaceBy:
Class:
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
A Darwin Core Type Vocabulary value for basisOfRecord is needed to represent
this new class of information. Luckily, a term already exists in the
Ontology for Biomedical Investigations
(http://www.ontobee.org/browser/rdf.php?o=OBI
<http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.org
/obo/OBI_0000747> &iri=http://purl.obolibrary.org/obo/OBI_0000747). We and
the GSC both propose to reuse this class within Darwin Core as below, making
it the cross-ver point between the two domains.
Term Name: MaterialSample
Identifier: http://rs.tdwg.org/dwc/terms/MaterialSample
Namespace: http://purl.obolibrary.org/obo/OBI_0000747
Label: material sample
Definition: A material entity that has the material sample role
Comment: For discussion see
http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary (there will be no
further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:http://purl.obolibrary.org/obo/OBI_0100051
Status: recommended
Date Issued: 2013-03-28
Date Modified: 2013-03-28
Has Domain:
Has Range:
Version: MaterialSample-2013-03-28
Replaces:
IsReplaceBy:
Class:
ABCD 2.0.6: not in ABCD
In keeping with all other classes in Darwin Core, the Material Sample class
would have a corresponding identifier property. The Genomics Standards
Consortium (GSC) is in the process of proposing this term. If it is
accepted, we propose to use it, and its properties would be as below,
otherwise, the properties would be the same, but have the Darwin Core
namespace and identifier URI.
Term Name: materialSampleID
Identifier: http://gensc.org/ns/mixs/materialSampleID
Namespace: http://gensc.org/ns/mixs
Label: Material Sample ID
Definition: An identifier for the MaterialSample (as opposed to a particular
digital record of the material sample). In the absence of a persistent
global unique identifier, construct one from a combination of identifiers in
the record that will most closely make the materialSampleID globally unique.
Comment: For discussion see
http://code.google.com/p/darwincore/wiki/MaterialSample (this page will not
exist until the term is ratified).
Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines: http://purl.org/dc/terms/identifier
Status: proposed
Date Issued: 2013-03-28
Date Modified: 2013-04-08
Has Domain:
Has Range:
Version: materialSampleID-2013-03-28
Replaces:
IsReplaceBy:
Class: http://purl.obolibrary.org/obo/OBI_0000747
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582 <tel:%28615%29%20343-4582> , fax: (615) 322-4942
<tel:%28615%29%20322-4942>
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
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--
John Deck
(541) 321-0689 <tel:%28541%29%20321-0689>
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582 <tel:%28615%29%20343-4582> , fax: (615) 322-4942
<tel:%28615%29%20322-4942>
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
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