[tdwg-content] New Darwin Core terms proposed relating to material samples
John Deck
jdeck at berkeley.edu
Mon Jun 24 22:22:11 CEST 2013
>From the clarification email that was sent out in response to the arguments
re: using Individual instead of Material Sample, we indicated the utility
of having distinct ID fields:
"...As was already pointed out, there is no restriction on specifying that
an occurence is associated with more than one type, so any occurrence can
have both an individualID and a materialSampleID."
This allows us to track distinct individuals, occurrences, and material
samples in the same archive. Yes, there are other ways this could be
modelled but this proposal was constructed to be in line with the current
standard.
John
On Mon, Jun 24, 2013 at 3:37 PM, joel sachs <jsachs at csee.umbc.edu> wrote:
> Hi John,
>
> My apologies for the long delay - I wanted to finish reading the draft
> Darwin Core RDF guide, and recent discussion on it, before responding. I
> agree with the assertion made in the guide (section 2.6.1) that there's no
> useful way to use use Darwin Core xxxID terms in RDF. But even were this
> not the case, I struggle to understand the utility of the xxxID terms.
>
> MaterialSampleID, as currently proposed, serves two purposes: it provides
> an identifier for the thing it gets slapped onto, and it also indicates
> that that thing is a MaterialSample. But this second purpose - indicating
> that the thing is a MaterialSample - can be done either by asserting it to
> be
> rdf:type dwctype:MaterialSample
> or by following the convention described in http://rs.tdwg.org/dwc/terms/*
> *guides/text/index.htm<http://rs.tdwg.org/dwc/terms/guides/text/index.htm>.
>
> So all we really need is a mechanism for giving an identifier. Is there a
> reason not to use dc-elements:identifier for this purpose?
>
>
> Best,
> Joel.
>
>
>
>
> On Tue, 11 Jun 2013, John Deck wrote:
>
>
>>
>>
>> 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.o<http://www.ontobee.org/browser/rdf.php?o=OBI&iri=http://purl.obolibrary.o>
>> rg/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
>>
>>
--
John Deck
(541) 321-0689
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