[tdwg-content] Revised Material Sample Proposal

[John Deck]

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)
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