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

John Deck jdeck at berkeley.edu
Sun May 26 05:55:09 CEST 2013


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.   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/ in
> conjunction with the MIxS developers).****
>
> ** **
>
> Modification to proposed terms:****
>
> ** **
>
> Term Name: MaterialSample****
>
> Identifier: http://rs.tdwg.org/dwc/dwctype/MaterialSample<http://rs.tdwg.org/dwc/terms/MaterialSample>
> ****
>
> Namespace: http:/rs.tdwg.org/dwctype/ <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.****
>
> 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_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/MaterialSampleID<http://rs.tdwg.org/dwc/terms/MaterialSample>
> ****
>
> Namespace: http://rs.tdwg.org/dwc/terms/<http://rs.tdwg.org/dwc/terms/MaterialSample>
> ****
>
> 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: 2013-05-25****
>
> 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&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,  fax: (615) 322-4942****
>
> If you fax, please phone or email so that I will know to look for it.****
>
> http://bioimages.vanderbilt.edu****
>
>     ****
>
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content****
>
>
>
> ****
>
> ** **
>
> --
> John Deck
> (541) 321-0689****
>
>
>
> ****
>
> -- ****
>
> 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,  fax: (615) 322-4942****
>
> 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
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