[tdwg-content] New Darwin Core terms proposed relating to material samples
Steve Baskauf
steve.baskauf at vanderbilt.edu
Sat May 25 13:08:00 CEST 2013
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>
> <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 <mailto: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 <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 <tel:%28615%29%20343-4582>, fax: (615) 322-4942 <tel:%28615%29%20322-4942>
> 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
--
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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