[tdwg-content] Revised Material Sample Proposal
Steve Baskauf
steve.baskauf at vanderbilt.edu
Thu Jun 27 03:34:42 CEST 2013
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
> <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
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