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

Steve Baskauf steve.baskauf at vanderbilt.edu
Mon May 20 19:39:19 CEST 2013


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 <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

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20130520/0e43f90c/attachment.html 


More information about the tdwg-content mailing list