Establish Task Group for MaterialSample #358
Comments
tucotuco
added
Class - MaterialSample
Task Group - Material Sample
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EXCELLENT!!! Thank you, @Jegelewicz !!!! I am happy to volunteer as a charter core member (if others agree, of course). |
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I would like to have a little clearer picture about the scope of this proposed group. It seems to me that the preliminary name of the group (MaterialSample) implies that the scope of the group's task is narrower than what would probably be necessary to actually address all of the issues raised in #314. In my view, what would really be required is essentially working out the data/graph model near the center of the TDWG universe. That would therefore overlap with issues related to that:
There are probably others that are not popping into my head at the moment. That isn't to say that the task isn't important and useful, but if it is really as broad as I'm thinking, then the number of stakeholders who should be involved and the amount of time to finish could potentially be large. This is a topic that I'm interested in, and therefore would like to participate. However, I have a leadership role in two other TDWG interest/task that are trying to wrap up their work on major initiatives in the next 6 months. So my ability to participate would be somewhat limited during that timeframe. |
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Steve, Teresa, John, Rich, et al. --- I was involved in the
original proposal for a MaterialSample term and have been quietly following
the discussions. I agree with Steve about the challenge of the scope of
this group, and whether and how to define narrower, achievable goals.
Still, that is one remit of the Task Group and if it turns out that all
paths require a much deeper dive, that is important information as well.
So, I guess I am "volunteering" to be involved somehow, in whatever way
seems best. I will remind people (see below for the gory details) that the
original intent of the addition of the materialSample terms was to provide
a means to represent samples more broadly than conceived in the context of
Darwin Core in 2013, when the proposal was made. I do think it is high
time to come back to some of these discussions.
Best, Rob
…____________________________________________________________________________________________
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)
On Thu, Jun 10, 2021 at 7:20 AM Steve Baskauf ***@***.***> wrote:
I would like to have a little clearer picture about the scope of this
proposed group. It seems to me that the preliminary name of the group
(MaterialSample) implies that the scope of the group's task is narrower
than what would probably be necessary to actually address all of the issues
raised in #314 <#314>. In my view, what
would really be required is essentially working out the data/graph model
near the center of the TDWG universe. That would therefore overlap with
issues related to that:
1. Dealing with the limitations of the star schema of DwC-A.
2. Other groups who are interested in an overarching model for TDWG
(i.e. ABCD)
3. differing needs/requirements of Linked Data approaches vs.
relational database approaches vs. spreadsheet approaches.
4. Concerns of the museum-centric contingent of TDWG vs. concerns of
the human/machine observation contingent.
There are probably others that are not popping into my head at the moment.
That isn't to say that the task isn't important and useful, but if it is
really as broad as I'm thinking, then the number of stakeholders who should
be involved and the amount of time to finish could potentially be large.
This is a topic that I'm interested in, and therefore would like to
participate. However, I have a leadership role in two other TDWG
interest/task that are trying to wrap up their work on major initiatives in
the next 6 months. So my ability to participate would be somewhat limited
during that timeframe.
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I agree with this sentiment as well as:
Given that, perhaps a good path to take would be to task ourselves with proposing a DwC schema that addresses the limitations of the star schema of DwC-A while keeping in mind the differing needs/requirements of Linked Data approaches vs. relational database approaches vs. spreadsheet approaches and the concerns of the museum-centric contingent of TDWG vs. concerns of the human/machine observation contingent. Is this doable or are we setting ourselves up for endless discussion and debate? Is there some smaller task we could take on that would start the ball rolling in the desired direction or should we ask for wholesale upheaval? In part, I think this would create a revision to the definition of Darwin Core which includes:
Because I think a lot of what was discussed in #314 operates under a different understanding. Maybe more like Darwin Core is primarily based on evidence for taxa, as documented by observations, samples, and related information. Thoughts? |
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I'd very much like to be included also. |
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I would also like to be included in this MaterialSample Task Group. |
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Thanks to @Jegelewicz |
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Hi @Jegelewicz, |
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Hi Teresa, I'd like, on behalf of DINA, where we have identified similar issues as were raised in #314 and in related issues, offer to participate in the proposed task group. We agree with @baskaufs that the issue may have implications that extend well beyond dwc:MaterialSample itself and that therefore scope and deliverables of the group need to be concretized. |
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Since it looks like this is going to happen, you can put me down on the core member list. Also, @Jegelewicz, I would be happy to advise you on the technical details of task group formation, requirements, etc. since I've been involved in chartering/running a number of them. Just ping me off list at steve.baskauf@vanderbilt.edu if you want to set up a call to talk about what it would involve. |
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I'd like to be included on behalf of GGBN and CD. |
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I hope this come under the Observations & Specimens Interest Group, though as has been said, the scope needs further definition. |
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It seems like this would also be part of #302 |
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@baskaufs has drawn my attention to this proposal. I'm not a regular member of this community, but I was a primary designer of related work in OGC (O&M) and W3C (SSN/SOSA) and also have some vision of what is going on in IGSN (originally geology samples, now being used a bit in some adjacent disciplines). So I think I could contribute here. |
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Let's get this party started! I have started a draft charter for this group as a Google Document and sent everyone who expressed an interest an email sharing the folder. If you don't get an invitation, please let me know. |
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@afuchs1 just sent an invite to the draft charter and a poll for meeting days/times. Welcome! |
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@Jegelewicz - I too would very much like to participate in this working group. |
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@datadavev can I get your email so that I can share the draft charter with you? |
Yes of course - dave.vieglais@gmail.com |
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I am interested to take part in this MaterialSample task group (dag.endresen@gmail.com) |
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@dagendresen just sent an invite to the draft charter and a poll for meeting days/times. Welcome! |
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@Jegelewicz Following @baskaufs logic I would also like to join, at least until the direction is clear. |
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Looking at the poll results, we can get @albenson-usgs, @datadavev , @ghwhitbread and @dr-shorthair together at 4PM MDT. I would be happy to meet up with you all then and try to drag in at least one other person who attends the first meeting. Would this work? |
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I can be at both if that helps. |
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As can I.
…On Fri, Jun 25, 2021 at 11:52 AM Sharon Grant ***@***.***> wrote:
I can be at both if that helps.
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Assuming that's 22:00 UTC, that certainly works for me. |
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See here for time zone comparison of the last proposal. While I'd be generally not available after 7 pm Berlin time, for the first meeting I would be able to meet up until 4 pm MDT (end of meeting), corresponding to 12 pm Berlin time, if that helps. |
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@cboelling I understand, but the second time is meant for those who cannot make the first time. There would be two meetings. |
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Also - sorry about all of the changes to the second invite - I think it should be correct now. |
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I intend to attend both. Thanks for setting these up. |
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So... I got three invites this morning for the following dates/times: I'm assuming the first of these was in error, but the calendar invite said that both of the latter two were "changed", so I just wanted to confirm. I am available to attend all three days/times, but want to make sure I've got all the correct dates/times in my calendar. |
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@deepreef Sorry for that. The final day/time is July 21 @ 2200 UTC |
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Sorry if this is a very dumb question, but can someone please explain the difference between DarwinCore and https://github.com/DiSSCo/openDS ? |
You will surely get different answers to this, but here is one part of the answer. Darwin Core is a vocabulary of terms, grouped into categories (e.g. Occurrence) which allow us to build things. openDS is an idea being built around the Digital Object Architecture. My understanding is that DOA has been around for about 20yrs and was opened up in around 2015 and put into the newly founded Dona Foundation. |
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Thank you! That's all gonna take me a while to process. |
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@Jegelewicz Would you add me (jutta.buschbom@statistical-genetics.de) as member to the task group, too? This will be the first time that I will be active in DwC, thus, I will need to find out what is involved in being a task group member. My path to the question of MaterialSample starts in SPNHC's Biodiversity Crisis Response Committee and its Regional Diversity subgroup working towards a campaign for expanding a Global Collections Network based on GBIF's GRSciColl, collaborating with GBIF's Data Products group. Working on the input options for GRSciColl and reviewing the data currently recorded in GRSciColl for "a couple" of fields with predefined vocabularies, I proposed a potential solution for some of the fields (tdwg/cd#255 (comment)) to one of the open issues of TDWG's Collections Descriptions Interest Group. In a subsequent email exchange Matt Woodburn from the IG pointed me to the forming MaterialSample-Task Group. In addition, earlier this week as a small ad hoc-subgroup of people active in the Alliance for Biodiversity Knowledge and the Consultation for the Digital Extended Specimen (DES) concept Phase 2 we were looking into finding a good visualization (and description) for the DES and ended up integrating into our discussion the concepts of "evidence" and "token" from #314. My interest in the DES is for it contributing to the implementation of the Convention on Biological Diversity's post-2020 Global Biodiversity Framework and its monitoring. All kinds of (ecosystem, ecology,) species and genetic diversity data are part of that context and will need to be integrated. With both backgrounds, it seems to make sense to join the task group and I would be happy to be able to do so. |
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@jbstatgen I just sent an invite to the draft charter and a poll for meeting days/times. Welcome! I also sent invites to two meetings - you only need to attend one. |
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@Jegelewicz Thanks! |
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For anyone who hasn't already seen this, I think it may help if we have all watched @timrobertson100 GBIF Nodes talk "Looking ahead: GBIF data model - https://vimeo.com/564600741 |
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Another document/organization that might prove useful. |
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Thank you to everyone who attended our first round of MaterialSample task group meetings! Invites have been sent for our scheduled meetings, the third Wednesday of each month (for some of you that will be Thursday!). Note the new meeting room and thank you to @rondlg for providing that! A few assignments: @stanblum The task group would like to open a separate repo in the TDWG GitHub organization so that we can better monitor our discussion and individual issues. Possible? TDWG/material_sample Finally, I am not sure who would set up our community url, but https://www.tdwg.org/community/osr/material-sample/ has been suggested for that. There are still some unresolved comments on the draft charter. @cboelling @gdadade @albenson-usgs your comments are still open and there have been some responses. Please review and if you feel that the comment is resolved, close it, if not, perhaps we should bring it here for discussion. I'd like to have a clean draft that we can approve at our next meeting. Thanks again to everyone! |
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Update on Repo for our Task Group:
-Stan |
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Second notice: There are still some unresolved comments on the draft charter. @cboelling @gdadade @albenson-usgs your comments are still open and there have been some responses. Please review and if you feel that the comment is resolved, close it, if not, perhaps we should bring it here for discussion. I'd like to have a clean draft that we can approve at our next meeting. |
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Thanks @Jegelewicz - I made a change to the document in suggestion mode to try to address my comment but I don't want to resolve my comment until I get feedback from you and others that the change I made is accepted and makes sense. |
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@albenson-usgs right - we will review at the meetings. Thanks! |
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Done! One of my comments has a long discussion, maybe we can save it somewhere before removing the comment? I think we will also need a summary paragraph for the website. That's the text that is shown right below the title, see e.g. https://www.tdwg.org/community/bdq/tg-2/ |
No need - the resolved comments can still be viewed on the document.
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I reviewed the Google Doc and made some suggestions. |
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I believe that this can be closed since the Task Group is chartered and operational: https://www.tdwg.org/community/osr/material-sample/ |
@Jegelewicz has tentatively agreed to convene a task group around the subject matter of MaterialSample as a result of discussions in issue #314. One of the first orders of business is to figure out who will be the charter core members of the task group. These should all be people who are willing to contribute effort to establishing and achieving the goals of the task group. This message can serve as a call for such help. I will certainly participate.
Somewhat hand-in-hand with core membership is establishing a reasonable draft of the scope of the task group. This will help people to decide their level of interest and whether they can commit to providing effort. It will also help in determining the Interest Group under which the Task Group should be chartered. The Executive Committee with the guidance of the Technical Architecture Group can help determine this definitively when the charter is presented or before. Ideas for the scope and tasks can be mined from issue #314 and other issues referenced there and under the Task Group - MaterialSample label. This message also serves as a call for help to define the scope.
The Task Group is an ephemeral entity. It's existence and duration are meant to accomplish something tangible. The scope can adapt over time as necessary, but should be established with a reasonably achievable set of goals and deliverables for which a timeline can at least be estimated.
I would recommend that one ingredient of a successful task group is to delegate known tasks among core members from the outset. That way people who are responsible, for example, for reporting, can have their objective in mind from the outset and keep on top of it rather than having to scramble with the onerous task of trying to pull together information post-facto.
The details of task groups from the standards perspective can be found in the TDWG Process By-laws.
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