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

[John Wieczorek]

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)
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