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Although it's been more than 30 days since John opened the public
comment on this proposal, there hasn't been much discussion and no
notification that the comment period has been closed. So I'm going to
make a comment requesting some clarification about this proposal,
stimulated by a comment about namespaces made by Dag Endresen in a
different context. <br>
<br>
I re-read the Issue Tracker posting:<br>
<a class="moz-txt-link-freetext" href="http://code.google.com/p/darwincore/issues/detail?id=167">http://code.google.com/p/darwincore/issues/detail?id=167</a><br>
and the email below. I think that the proposal was to "import" the ID
term mixs:materialSampleID if GSC adopts it (I don't know if they did
or not). That is pretty straightforward. <br>
<br>
With regards to the type vocabulary term, I'm really confused. My
understanding of the current precedent is that for applications which
provide a literal value for basisOfRecord, the pattern would call for
the string "MaterialSample" to be given (for consistency with
"PreservedSpecimen", "MachineObservation", etc.). The URIs for
existing DwC-defined DwC type vocabulary terms follow the pattern: <br>
<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/dwctype/">http://rs.tdwg.org/dwc/dwctype/</a>[LocalName]<br>
where [LocalName] is the controlled text value. Following that
pattern, the type vocabulary term URI would be <br>
<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/dwctype/MaterialSample">http://rs.tdwg.org/dwc/dwctype/MaterialSample</a> <br>
or dwctype:MaterialSample where dwctype: is the abbreviation for the
namespace <a class="moz-txt-link-rfc2396E" href="http://rs.tdwg.org/dwc/dwctype/">"http://rs.tdwg.org/dwc/dwctype/"</a>. <br>
<br>
However, in the email below, the proposed type vocabulary term is given
the URI<br>
<a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/MaterialSample">http://rs.tdwg.org/dwc/terms/MaterialSample</a> which uses the "main" DwC
namespace (dwc: = <a class="moz-txt-link-freetext" href="http://rs.tdwg.org/dwc/terms/">http://rs.tdwg.org/dwc/terms/</a> ) rather than the
dwctype: namespace, while the "namespace" in the proposal is listed as
<a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/OBI_0000747">http://purl.obolibrary.org/obo/OBI_0000747</a> . But that's not a
namespace, its a term. <br>
<br>
If the intention is to import the OBO term, then the URI for the type
vocabulary term would be <a class="moz-txt-link-freetext" href="http://purl.obolibrary.org/obo/OBI_0000747">http://purl.obolibrary.org/obo/OBI_0000747</a>
(namespace: <a class="moz-txt-link-rfc2396E" href="http://purl.obolibrary.org/obo/">"http://purl.obolibrary.org/obo/"</a>). Under the proposal,
I'm not sure if the controlled text value would be "MaterialSample"
(following the existing convention using words and capitalization) or
"OBI_0000747" (following the existing convention that the local name
from the URI is used as the text controlled value. <br>
<br>
I have another question, but I think it would be better to have a
separate email for it.<br>
Steve<br>
<br>
John Wieczorek wrote:
<blockquote
cite="mid:CAHwKGGd_3EoYOsSQFg7N72UTDmViB=ckXczWYfEDaOkm=ktsnA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; ">
<div dir="ltr">Dear all,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
The initial request for new terms can be found in the Darwin Core Issue
tracker as <a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=167">http://code.google.com/p/darwincore/issues/detail?id=167</a>.
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.<br>
<br>
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.<br>
<br>
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. <br>
<br>
Term Name: MaterialSample<br>
Identifier: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/MaterialSample">http://rs.tdwg.org/dwc/terms/MaterialSample</a><br>
Namespace: <a class="moz-txt-link-freetext" href="http:/">http:/</a><a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms">rs.tdwg.org/dwc/terms</a><br>
Label: Material Sample<br>
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.<br>
Comment: For discussion see <a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/wiki/MaterialSample">http://code.google.com/p/darwincore/wiki/MaterialSample</a>
(this page will not exist until the term is ratified).<br>
Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/2000/01/rdf-schema#Class">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<br>
Status: proposed<br>
Date Issued: 2013-03-28<br>
Date Modified: 2013-04-08<br>
Has Domain:<br>
Has Range:<br>
Version: MaterialSample-2013-03-28<br>
Replaces:<br>
IsReplaceBy:<br>
Class:<br>
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)<br>
<br>
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 (<a moz-do-not-send="true"
href="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</a>).
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.<br>
<br>
Term Name: MaterialSample<br>
Identifier: <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/MaterialSample">http://rs.tdwg.org/dwc/terms/MaterialSample</a><br>
Namespace: <a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/OBI_0000747">http://purl.obolibrary.org/obo/OBI_0000747</a><br>
Label: material sample<br>
Definition: A material entity that has the material sample role<br>
Comment: For discussion see <a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary">http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary</a>
(there will be no further documentation here until the term is ratified)<br>
Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/2000/01/rdf-schema#Class">http://www.w3.org/2000/01/rdf-schema#Class</a><br>
Refines:<a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/OBI_0100051">http://purl.obolibrary.org/obo/OBI_0100051</a><br>
Status: recommended<br>
Date Issued: 2013-03-28<br>
Date Modified: 2013-03-28<br>
Has Domain:<br>
Has Range:<br>
Version: MaterialSample-2013-03-28<br>
Replaces:<br>
IsReplaceBy:<br>
Class:<br>
ABCD 2.0.6: not in ABCD<br>
<br>
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.<br>
<br>
Term Name: materialSampleID<br>
Identifier: <a moz-do-not-send="true"
href="http://gensc.org/ns/mixs/materialSampleID">http://gensc.org/ns/mixs/materialSampleID</a><br>
Namespace: <a moz-do-not-send="true" href="http://gensc.org/ns/mixs">http://gensc.org/ns/mixs</a><br>
Label: Material Sample ID<br>
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.<br>
Comment: For discussion see <a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/wiki/MaterialSample">http://code.google.com/p/darwincore/wiki/MaterialSample</a>
(this page will not exist until the term is ratified).<br>
Type of Term: <a moz-do-not-send="true"
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property">http://www.w3.org/1999/02/22-rdf-syntax-ns#Property</a><br>
Refines: <a moz-do-not-send="true"
href="http://purl.org/dc/terms/identifier">http://purl.org/dc/terms/identifier</a><br>
Status: proposed<br>
Date Issued: 2013-03-28<br>
Date Modified: 2013-04-08<br>
Has Domain:<br>
Has Range:<br>
Version: materialSampleID-2013-03-28<br>
Replaces:<br>
IsReplaceBy:<br>
Class: <a moz-do-not-send="true"
href="http://purl.obolibrary.org/obo/OBI_0000747">http://purl.obolibrary.org/obo/OBI_0000747</a><br>
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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