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

[John Deck]

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><http://gensc.org/ns/mixs/materialSampleID>

Namespace: http://rs.tdwg.org/dwc/terms/<http://rs.tdwg.org/dwc/terms/MaterialSample><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: 2013-05-25

Has Domain:

Has Range:

Version: materialSampleID-2013-05-25

Replaces:

IsReplaceBy:

Class: http://rs.tdwg.org/dwc/terms/Occurrence<http://purl.obolibrary.org/obo/OBI_0000747>

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
>
>
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>


-- 
John Deck
(541) 321-0689
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