[tdwg-content] New Darwin Core terms proposed relating to material samples

John Deck jdeck at berkeley.edu
Wed Jun 12 02:50:17 CEST 2013

On Mon, Jun 10, 2013 at 2:51 PM, joel sachs <jsachs at csee.umbc.edu> wrote:

> Hi Markus,
> You mention below "an exercise to actually map a large number of use cases
> to darwin core records with real values", which sounds like a potentially
> illuminating activity. Can you share the results of the exercise?
That will be shared soon --- the group is writing up a report...


> Best,
> Joel.
> On Mon, 27 May 2013, "Markus Döring (GBIF)" wrote:
>  Hi all,
>> I just returned from a DwC workshop in Copenhagen, but we haven't
>> completed the report yet. Until it is available I wanted to throw into this
>> discussion some main ideas which I think are very relevant:
>> First of all I see an essential difference in character between the
>> current dwc idea of Individual(ID) and a MaterialSample, Occurrence,
>> Evidence or alike: The Individual has no notion of time and space, whereas
>> the others all have. IndividualID was primarily added to Darwin Core to
>> group occurrence records about the same "Individual", e.g. when dealing
>> with bird ringing, whale tracking or tree tagging. It could also provide
>> useful to track herbarium duplicates. The actual Individual class does not
>> hold any direct dwc term as they are all dependent on time or locality
>> (think about occurrence classics such as life stage, sex, behavior etc). So
>> in this light MaterialSample and Individual are very different concepts
>> which we should keep distinct I believe.
>> Another surprising outcome of an exercise to actually map a large number
>> of use cases to darwin core records with real values (using the text
>> guidelines) was that we ended up preferring a dynamically typed Occurrence
>> class via the basisOfRecord property and mostly did away with any class
>> terms. This actually draws on Steves proposal to only add a new dwc type
>> term to basisOfRecord instead of creating a new MaterialSample class term.
>> Along with a much richer, hierarchical and probably ontology controlled
>> definition of such basisOfRecord terms we felt we can go a long, long way.
>> best,
>> Markus
>> On 26.05.2013, at 23:34, Richard Pyle wrote:
>>  Thanks for the *EXCELLENT* post -- this gets to the heart of what I was
>>> trying to ask. I don’t have time to respond in detail, but will come back
>>> to this in a bit.
>>> Rich
>>> From: tdwg-content-bounces at lists.**tdwg.org<tdwg-content-bounces at lists.tdwg.org>[mailto:
>>> tdwg-content-bounces@**lists.tdwg.org<tdwg-content-bounces at lists.tdwg.org>]
>>> On Behalf Of Steve Baskauf
>>> Sent: Sunday, May 26, 2013 3:09 AM
>>> To: Robert Guralnick
>>> Cc: TDWG Content Mailing List; Robert Whitton; John Deck;
>>> rlwalls2008 at gmail.com
>>> Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to
>>> material samples
>>> I suppose that Rich and Rob W. have already looked at
>>> http://code.google.com/p/**darwin-sw/wiki/**TaxonomicHeterogeneity<http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity>.  I think it pretty much encapsulates what they are talking about.  I
>>> should note that the way DSW defines dsw:IndividualOrganism does not
>>> require it to be a single organism.  It can be a collection of organisms
>>> (herd, colony, school) or part of an organism (tissue).  The basic
>>> requirement is that it is a "taxonomically homogeneous entity".  In a
>>> variant form of DSW (dsw_alt.owl) we included "taxonomically heterogeneous
>>> entity" (THeE) which would basically include what Rich and Rob W. are
>>> talking about (lots of organisms which are seperatable and aren't
>>> necessarily from the same lowest taxonomic level).  It should be no
>>> surprise that THeE does what Rich wants because we included it in DSW
>>> because during the preceding discussion Rich said he wanted something like
>>> it.  In dsw_alt.owl, properties like "hasPart" and "isPartOf" are used to
>>> connect physical entities whose properties can be inferred by inheritance.
>>>  What this diagram includes that Rich did not mention are "tokens"
>>> (evidence).  We defined a class for evidence, but we also considered not
>>> having evidence being an explicit class.  Not defining an explicit Token
>>> class would have simplified the diagram at the bottom of the page - one
>>> could just say that there should be evidence and it should be linked to the
>>> resource it documents.  Token and THeE/IndividualOrganism are not disjoint
>>> classes - the physical entity can be the evidence if somebody "owns" it and
>>> makes it available for people to examine.  However, in DSW, Token and THeE
>>> are not synonymous because we allow evidence to include things that are not
>>> physically derived from the entity (e.g. images, sounds, string data
>>> records) in addition to physical specimens.
>>> I think that we have to be careful when we say "we don't need X", "there
>>> is pressing value for X but not for Y", "X is too vaguely defined", etc.
>>>  MaterialSample does exactly what the metagenomics people need because they
>>> invented it to serve the purposes they want it to serve (handle material
>>> samples in which one may or may not ever know what all organisms are
>>> included or even if there are organisms in it).  Individual (sensu
>>> Pyle/Whitton)/THeH is just vague enough to do what Rich and Rob W. want it
>>> to do with their lots and specimens, but is too vague for Rob G.
>>>  IndividualOrganism (sensu DSW) and Token does exactly what Cam Webb and I
>>> want it to do with our images, specimens, DNA samples, and data records,
>>> and the requirement that IndividualOrganism be taxonomically homogeneous
>>> allows us to infer that a determination applied to one resource also
>>> applies to other resources which are derived from the same
>>> IndividualOrganism (a requirement not stated by the others) but it's too
>>> restrictive for both Rob G and Rich.  If we start in on the game of saying
>>> "WE need the features that I think are important but not the features that
>>> YOU think are important" then we are in for another month of massive email
>>> traffic on this list and will end up no better off than we were when we
>>> started.
>>> I think that it is clear from this and preceding discussions that there
>>> is a need for some system of tracking things that are like
>>> individuals/organisms/samples/**lots.  It is my believe that what needs
>>> to happen is:
>>> 1. define clearly what the various stakeholders want to accomplish by
>>> their version of individuals/organisms/samples/**lots (i.e. use
>>> cases/competency questions)
>>> 2. use set theory or some other kind of logical system to describe
>>> clearly how the various versions of individuals/organisms/samples/**lots
>>> are related to each other
>>> 3. examine alternative mechanisms for defining the relationships among
>>> the variously defined individuals/organisms/samples/**lots terms and
>>> determine how each approach can or cannot satisfy the use cases/competency
>>> questions.
>>> 4. use one or more mechanisms which pass test #3 to define the terms
>>> that are deemed necessary and include them in some TDWG standard which may
>>> or may not be Darwin Core.
>>> In September 2011, John Wieczorek had packaged several of the proposed
>>> class additions to Darwin Core into a concrete proposal:
>>> http://lists.tdwg.**org/pipermail/tdwg-content/**
>>> 2011-September/002727.html<http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html>.  This proposal was deferred by the Executive Committee (see the last
>>> comment at http://code.google.com/p/**darwincore/issues/detail?id=**117<http://code.google.com/p/darwincore/issues/detail?id=117>) "... until we can further examine broader changes including the new
>>> classes and any insights that might come out of the RDF Interest Group."
>>>  So the RDF Task Group has specifically been charged with the task of
>>> examining the addition of additional classes to Darwin Core and their
>>> implications.  The RDF TG has assembled competency questionshttp://
>>> code.google.**com/p/tdwg-rdf/wiki/**CompetencyQuestions<http://code.google.com/p/tdwg-rdf/wiki/CompetencyQuestions>and use cases
>>> http://code.google.com/p/tdwg-**rdf/wiki/UseCases<http://code.google.com/p/tdwg-rdf/wiki/UseCases>but has not moved beyond that.  So that's a start on Item #1 in the list
>>> above.  However, the process has not moved beyond that.  I recently made an
>>> appeal to the TG for someone to take up work on delivering some concrete
>>> progress on deliverables, but got no responses.  I cannot be the person to
>>> move this forward for two reasons.  One is that I already have my hands
>>> full with the DwC RDF guide (which doesn't address these issues) and the
>>> other is that I have reached the limits of my technical skills and am not
>>> able to take leadership on items #2-#4.  Who will champion this?
>>> At the risk of making this email too long, I will add one more comment.
>>>  There seems to be a developing consensus that an OWL ontology structured
>>> according to the OBO Foundry (http://www.obofoundry.org/) principles is
>>> the answer to #2 and #3 above.  However, I have yet to see the evidence
>>> that the complexity introduced by a formal OWL ontology is necessary or any
>>> actual concrete examples of how an OBO-style ontology would be used to
>>> satisfy the use cases.  We have shown with DSW that some use cases can be
>>> met using only simple RDF and SPARQL (i.e. no actual reasoner involved).  I
>>> presume that Rich and Rob W. have in hand a technical solution to their use
>>> cases that doesn't involve RDF at all.  So I think that there need to be
>>> some iterations of defining and testing before we adopt a technology by
>>> acclimation.  We've been down that road before with the TDWG Ontology and
>>> look how that turned out.
>>> Steve
>>> Robert Guralnick wrote:
>>> I agree with John and Gregor.  The term "individual" doesn't quite seem
>>> to capture the concept or usage.  However, I think there is more general
>>> agreement that there is a pressing need - and immediate value - for a term
>>> to represent "material sample" and derivaties.  It seems that the proposal
>>> on the table serves that need with the right definition, that is explicit,
>>> and that provides necessary linkages to other related domains.
>>> Best, Rob
>>> On Sun, May 26, 2013 at 1:47 AM, Gregor Hagedorn <g.m.hagedorn at gmail.com>
>>> wrote:
>>>> Basically, we’ve been running with the idea of an “Individual” class –
>>>> as
>>>> originally proposed by Steve and discussed at some length on this list a
>>>> while ago.  This has been documented for DSW:
>>>> https://code.google.com/p/**darwin-sw/wiki/ClassIndividual<https://code.google.com/p/darwin-sw/wiki/ClassIndividual>
>>>  We define an “Individual” as the physical “something” that underpins an
>>>> Occurrence.  In the case of organisms, this can be a group (herd,
>>>> school,
>>>> flock, etc.), specimen (either a single specimen, or a lot of multiple
>>>> specimens), or any sort of derivative of a specimen (part, tissue
>>>> sample,
>>>> dna extraction, etc.).  It corresponds to the intended meaning of
>>> I disagree with using "Individual" for sets of objects. It is
>>> surprising, and lacking any clear definition when to stop, that means
>>> a taxon is an individual, a collection is an individual, etc.
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>>> --
>>> 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
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>>> Nashville, TN 37235
>>> office: 2128 Stevenson Center
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John Deck
(541) 321-0689
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