[tdwg-content] New Darwin Core terms proposed relating to material samples
John Deck
jdeck at berkeley.edu
Wed Jun 12 02:49:16 CEST 2013
On Mon, Jun 10, 2013 at 2:43 PM, joel sachs <jsachs at csee.umbc.edu> wrote:
> Hi Everyone,
>
> I was scared to read this thread, but it turned out to be fun. Despite the
> excellent clarification that occurred, I still have some questions. In
> relation to the proposal below (to introduce the terms MaterialSample, and
> MaterialSampleID):
>
> 1. Given that the decision was made to put MaterialSample in the "dwctype"
> namespace, why is the definition still "The category of information
> pertaining to the physical results of a sampling event …"? Shouldn't the
> definition be "The physical results of a sampling event ..."?
> (Ramona pointed this out in a message that didn't get posted to the list,
> but which Rich responded to [1].)
>
>
yes, I agree with this...
> 2. I believe Steve asked why there needs to be a MaterialSampleID, when
> none of the other dwctype terms (preservedSpecimen, etc.) have IDs. JohnD
> gave a sound defence of MaterialSampleID [2], but his reasoning seems to
> apply equally to preservedSpecimenID, DigitalStilImageID, etc. Did I miss
> the explanation of why MaterialSamples are so different from the other
> dwctype terms? Or is the idea that we will define, e.g.,
>
> dwctype:preservedSpecimen rdfs:subClassOf dwctype:MaterialSample
>
> so that preservedSpecimens will inherit MaterialSampleIDs ?
>
>
MaterialSample doesn't necessarily have to be an occurrence and there could
possibly be multiple occurrences in a sample (or vice versa). Thus we need
the Identifier to track this (especially in the context of DwC represented
as a flat-file)
> 3. In RDF, all resources are identified by URI, and (should be) referenced
> by appropriate predicates (hasIndividual, hasOccurrence, etc.) So my
> understanding is that all the recent discussion about xxxIDs pertains only
> to non-RDF records. Is that correct?
>
Not necessarily.
> Many thanks for the clarification already provided, and for any yet to
> come -
> Joel.
>
> 1. http://lists.tdwg.org/**pipermail/tdwg-content/2013-**May/003008.html<http://lists.tdwg.org/pipermail/tdwg-content/2013-May/003008.html>
> 2. http://lists.tdwg.org/**pipermail/tdwg-content/2013-**May/003006.html<http://lists.tdwg.org/pipermail/tdwg-content/2013-May/003006.html>
>
>
> On Sat, 25 May 2013, 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 <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/<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/dwctype/MaterialSample>
>>
>> Namespace: http:/rs.tdwg.org/dwctype/
>>
>> 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<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<http://www.w3.org/2000/01/rdf-schema#Class>
>>
>> Refines: http://purl.obolibrary.org/**obo/OBI_0000747<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/MaterialSampleID>
>>
>> Namespace: http://rs.tdwg.org/dwc/terms/
>>
>> 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<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<http://www.w3.org/1999/02/22-rdf-syntax-ns#Property>
>>
>> Refines: http://purl.org/dc/terms/**identifier<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://rs.tdwg.org/dwc/terms/Occurrence>
>>
>> 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<http://rs.tdwg.org/dwc/terms/MaterialSample>
>> which is in the "main" (dwc:=http://rs.tdwg.org/dwc/**terms/<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<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<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<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<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<http://rs.tdwg.org/dwc/terms/MaterialSample>
>> Namespace: http://purl.obolibrary.org/**obo/OBI_0000747<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<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<http://www.w3.org/2000/01/rdf-schema#Class>
>> Refines:http://purl.**obolibrary.org/obo/OBI_0100051<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<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<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<http://www.w3.org/1999/02/22-rdf-syntax-ns#Property>
>> Refines: http://purl.org/dc/terms/**identifier<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<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 <http://bioimages.vanderbilt.edu>
>>
>> ______________________________**_________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org
>> http://lists.tdwg.org/mailman/**listinfo/tdwg-content<http://lists.tdwg.org/mailman/listinfo/tdwg-content>
>>
>>
>>
>>
>> --
>> John Deck
>> (541) 321-0689
>>
>>
--
John Deck
(541) 321-0689
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