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 .
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@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
2.
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.
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
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
(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
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
(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
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@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
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.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
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
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office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
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know to look for it.
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John Deck
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