[tdwg-content] Revised Material Sample Proposal

Sat Jun 29 00:16:51 CEST 2013

Great point Steve... i added this modification to our proposal.

On Wed, Jun 26, 2013 at 7:34 PM, Steve Baskauf <steve.baskauf at vanderbilt.edu
> wrote:

> **
> John,
>
> I would like to suggest that somewhere in your revised proposal you state
> explicitly that "MaterialSample" be used as the controlled string value
> when a literal value is given for dwc:basisOfRecord (see
> http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord).  The current
> convention for other type vocabulary values has been to use the last part
> of the URI (e.g. "HumanObservation" for
> http://rs.tdwg.org/dwc/dwctype/HumanObservation and "Event" for
> http://purl.org/dc/dcmitype/Event).  If that pattern were followed, some
> users might provide "OBI_0100051" as the string and based on what you wrote
> below, I don't think that is what you intend.
>
> Steve
>
>
> John Deck wrote:
>
>  NOTE:
>
> Following discussion on the TDWG content list, discussions with OBI
> developers, and discussions with MIxS developers, we have modified the
> original Material Sample Term Proposal in the following document.
>
>  The original document sent to the Darwin Core community for Material
> Sample proposed the OBI term Material Sample (
> http://purl.obolibrary.org/obo/OBI_0000747), which we are now modifying
> to instead reference OBI Specimen (
> http://purl.obolibrary.org/obo/OBI_0100051).  The reason for this change
> is that it came to light that the intention of OBI Material Sample “should
> be representative of the whole from which it is sampled”.  Since this
> definition places an unnecessary constraint on its use we have opted to use
> OBI Specimen instead, which is more closely aligned with our original
> intent. In addition to this change, we have also modified the proposal
> based on the feedback from this list.
>
> -John Deck, Rob Guralnick, Ramona Walls
>
>  ****
>
>  New Term Request: Material Sample
>
>  This is a proposal for two new terms in Darwin Core, relating to the
> addition of the concept, “Material Sample”, described by the identifier
> http://purl.obolibrary.org/obo/OBI_0100051.  The two terms are:
>
>  1) A new BasisOfRecord term MaterialSample with label “Material Sample”
>  that references http://purl.obolibrary.org/obo/OBI_0100051
>
> 2) A new Darwin Core property term, MaterialSampleID.
>
>  Submitters:  John Deck, Rob Guralnick and Ramona Walls
>
>  Justification
>
> The current values in the DwC Type Vocabulary (
> http://rs.tdwg.org/dwc/dwctype/) do well in representing some types of
> biocollections and observations. However, the more general notion of a
> sample is not well represented, because the existing terms are too
> specific.  For example, the DwC terms “Preserved Specimen”, “Fossil
> Specimen”, and “Living Specimen” are appropriate for use in the museum
> community but assume particular properties pertaining to museum
> collections, which “material samples” may or may not have.  Examples of
> “material samples” we are considering (beyond the examples above) are
> surveys that involve soil and water sampling, bulk sampling of specimens
> from, e.g., trawls, microbiological sampling, metagenomics, etc.  These
> sampling approaches often rely on field sub-sampling processes and
> laboratory techniques (e.g., DNA extraction and sequencing) which transform
> the physical material and produce distinct information content and thus
> represent a type of information that is distinct from what DwC has
> typically dealt with. The proposal for adding “Material Sample” as a DwC
> class is to maintain consistency with the way Darwin Core terms are managed
> and organized. This term comes from the Ontology for Biomedical
> Investigations (OBI) class OBI:specimen.  We use the class concept
> definition directly from OBI but provide the more familiar label “Material
> Sample” for use within the biodiversity community and annotate how that
> definition applies in the domain of biological collections.
>
>  A “material sample” can pertain to general matter in which organisms may
> exist, in whole, in part, or in conjunction with many other organisms.  The
> “material sample” may exist for a brief period, such as a tissue that is
> converted to extracted DNA.  It may also represent a collection of multiple
> taxa, such as a soil or water sample that is used with the intention of
> describing the diversity of organisms, whether the actual organisms are
> later recovered from such a sample, or whether that sample is processed in
> order to generate a set of derivatives from organisms (e.g.16S sequences
> from a metagenomics run).  A “material sample” may also yield connections
> to other indicators of biodiversity aside from taxa, such as a
> transcriptome, indicating which DNA is actively being expressed at a
> particular point in time.
>
>  For the purposes of biological collections, we can think of “material
> sample” as any type of matter that we can use in order derive further
> evidence needed for identification of taxa, whether it is taxonomically
> homogenous, heterogenous, a single individual, sets of individuals, or
> populations.  However, the definition of the term does not exclude its use
> in broader contexts outside the scope of biological collections.
>
>  How is the term “Material Sample” different from “Individual”?  The
> intent of individualID is fairly clear:  since an Occurrence represents an
> organism at a place and time, the individualID term allows us to assign an
> instance identifier for a particular organism that can be present in at
> multiple events. MaterialSampleID, on the other hand, is intended to allow
> users to say that the basis of an occurence is a material entity (i.e.
> matter) that has been sampled according to some particular method. Whether
> or not this material entity is an individual (sensu individualID in DwC)
> represents an independent axis of classification. 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.
>
>  Adding this term will help align DwC to two other significant projects:
> the Ontology for Biomedical Investigations (OBI), from which we will be
> adapting this term, and the MIxS family of checklists.
>
> The MIxS vocabulary is proposing to adopt MaterialSampleID by clarifying
> the existing term source_mat_id to read:
>
>  “A unique identifier assigned to a material sample (as defined by
> http://rs.tdwg.org/dwc/terms/MaterialSampleID, and as opposed to a
> particular digital record of a material sample) used for extracting nucleic
> acids, and subsequent sequencing. The identifier can refer either to the
> original material collected or to any derived sub-samples. The INSDC
> qualifiers /specimen_voucher, /bio_material, or /culture_collection provide
> additional context and suggested syntax for this identifier for data
> submitted to INSDC databases.”
>
>  The MIxS source_mat_id term clarification proposal is pending based on
> the outcome of this proposal.
>
>  Connecting a DwC Record to a MIxS record would have the advantage of
> aligning DwC terminology (geospatial, taxonomic) with sequencing
> terminology (investigation, environment, nucleic acid sequence source,
> sequencing) and with OBI (investigation, roles, processes), using “Material
> Sample” as the pivot point between the standards.
>
>  Definition:
>
>  From OBI ((http://purl.obolibrary.org/obo/OBI_0100051): “A material
> entity that has the specimen role.”
>
>  A specimen role (http://purl.obolibrary.org/obo/OBI_0000112) in OBI is
> defined as  “a role borne by a material entity that is gained during a
> specimen creation process and that can be realized by use of the specimen
> in an investigation”.  The operative word is “can”.  That is, the specimen
> is not required to be realized by use in an investigation.  However, it
> is worth nothing that deposition into a museum or biobank can fulfill the
> criteria of “use in an investigation”, if necessary (for discussion, see
> http://sourceforge.net/p/obi/obi-terms/677/).
>
>  We have chosen to use the label “Material Sample” instead of using the
> OBI label “Specimen” for this definition. This allows us to distinguish
> this term from other types containing the word “Specimen” currently in use
> in the Darwin Core vocabulary, which have their own meaning, distinct from
> the concept we are proposing.  In the natural history community, biological
> specimens have a colloquial meaning, typically referring to a voucher held
> by a biorepository for research.   We intend a more inclusive definition,
> and thus, when we refer to “DwC Material Sample” here, we are actually
> referring to the class of entities defined by “OBI Specimen”.
>
>  In order to clarify how this definition may be considered in a
> biological collections context, we wish to include a
> http://www.w3.org/2000/01/rdf-schema#comment annotation within the DwC
> vocabulary which would read: “In biological collections, the material
> sample is typically collected, and either preserved, transformed by some
> process, or destructively processed”  Further clarification on the use of
> this term, including this document, would be provided in the supplementary
> documentation and the Darwin Core wiki.
>
>  Comment: N/A
>
>  Refines: N/A
>
>  Has Domain:  N/A
>
>  Has Range: N/A
>
>  Replaces: N/A
>
>  Summary:
>
>  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: A resource describing 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>
> http://purl.obolibrary.org/obo/OBI_0100051<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-2013-06-24
>
> 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>
>
> Namespace: http://rs.tdwg.org/dwc/terms/<http://rs.tdwg.org/dwc/terms/MaterialSample>
>
> 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)
>
>
> --
> 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
>
>

-- 
John Deck
(541) 321-0689
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