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

Steve Baskauf steve.baskauf at vanderbilt.edu
Mon May 20 19:30:31 CEST 2013

Although it's been more than 30 days since John opened the public 
comment on this proposal, there hasn't been much discussion and no 
notification that the comment period has been closed.  So I'm going to 
make a comment requesting some clarification about this proposal, 
stimulated by a comment about namespaces made by Dag Endresen in a 
different context. 

I re-read the Issue Tracker posting:
and the email below.  I think that the proposal was to "import" the ID 
term mixs:materialSampleID if GSC adopts it (I don't know if they did or 
not).  That is pretty straightforward. 

With regards to the type vocabulary term, I'm really confused.  My 
understanding of the current precedent is that for applications which 
provide a literal value for basisOfRecord, the pattern would call for 
the string "MaterialSample" to be given (for consistency with 
"PreservedSpecimen", "MachineObservation", etc.).  The URIs for existing 
DwC-defined DwC type vocabulary terms follow the pattern:
where [LocalName] is the controlled text value.  Following that pattern, 
the type vocabulary term URI would be
or dwctype:MaterialSample where dwctype: is the abbreviation for the 
namespace "http://rs.tdwg.org/dwc/dwctype/". 

However, in the email below, the proposed type vocabulary term is given 
the URI
http://rs.tdwg.org/dwc/terms/MaterialSample which uses the "main" DwC 
namespace (dwc: = http://rs.tdwg.org/dwc/terms/ ) rather than the 
dwctype: namespace, while the "namespace" in the proposal is listed as 
http://purl.obolibrary.org/obo/OBI_0000747 .  But that's not a 
namespace, its a term. 

If the intention is to import the OBO term, then the URI for the type 
vocabulary term would be http://purl.obolibrary.org/obo/OBI_0000747 
(namespace: "http://purl.obolibrary.org/obo/").  Under the proposal, I'm 
not sure if the controlled text value would be "MaterialSample" 
(following the existing convention using words and capitalization) or 
"OBI_0000747" (following the existing convention that the local name 
from the URI is used as the text controlled value. 

I have another question, but I think it would be better to have a 
separate email for it.

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 <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 
> <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

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