[tdwg-content] Plea for competency questions. Was Re: New terms need resolution: "Evidence"

Peter DeVries pete.devries at gmail.com
Tue Jul 26 21:56:36 CEST 2011

I has thinking it might be best to keep "Individual" as it is and add a new
class called "Sample" or "CollectionObject"

There maybe cases where you want to say that an Occurrence


and also

hasSample (hasCollectionObject)

The Individual

dcterms:hasPart => Leaf_URI
dcterms:hasPart => DNA_Sample_URI


<Leaf_URI> dcterms:isPartOf  <Individual_URI>

in addition you might have the situation where

<Individual_URI> dcterms:isPartOf <Sample_URI>

- Pete

On Tue, Jul 26, 2011 at 1:17 PM, Steve Baskauf <steve.baskauf at vanderbilt.edu
> wrote:

> **
> John Wieczorek has made an additional proposal (
> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002574.html) to
> resolve the issue of "Evidence" by creating a class called
> "CollectionObject".  I believe that his intended meaning for the term is
> exactly what I have intended in the past when I used the term "token".  I
> believe that the proposal for the CollectionObject class is intimately
> related to the question of the definition of Individual/BiologicalEntity
> because I think that the competency questions Rich wants to address through
> the Individual/BiologicalEntity class are a subset of what I would consider
> to be the competency questions for the CollectionObject class.
> Because of TDWG's historical roots in the collections community,
> "occurrences" have been subconsciously or even explicitly linked with the
> evidence that documents them.  For example, PreservedSpecimens have been
> considered a subclass of Occurrence in the Darwin Core type vocabulary.  But
> in the lengthy tdwg-content discussion of 2009-10 (summarized at
> http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary), there
> seemed to be a consensus that an Occurrence is a record of an Individual at
> a particular Time and Location.  That Occurrence is an independent entity
> from the evidence that serves to document it, which could include one (or
> perhaps zero) to many PreservedSpecimens, Images, text files recording
> MachineObservations, etc.  Separating the Occurrence from its documenting
> evidence makes it easier to be explicit about the number and types of
> evidence that document the Occurrence.
> So I would define competency question #1 for the proposed CollectionObject
> class as to:
> 1. document an Occurrence (which I will refer to as the "Occurrence" use of
> evidence).
> However, I would also assert that CollectionObject need not be restricted
> to documenting an Occurrence, but that it may also:
> 2. document the existence of an Individual/BiologicalEntity, aggregates
> that include it, and pieces that came from it (which I will refer to as the
> "Provenance" use of evidence)
> and
> 3. support an Identification to a particular Taxon (the "Identification"
> use of evidence).
> [note: see http://code.google.com/p/darwin-sw/wiki/ClassToken for further
> discussion of this]
> If the CollectionObject is a whole dead organism serving as a museum
> specimen, then it might simultaneously address all three of these
> questions.  The time and place listed on the specimen label provide the
> information about the Occurrence, the dead organism serves as proof of its
> own existence, and determinations typed or written on the label are vouched
> for by the presence of the dead organism.  In this case the need to separate
> these three uses of CollectionObject may not be obvious.
> But consider a more complex situation of the sort that BiSciCol would like
> to be able to handle.  A wildebeest calf is digitally photographed in South
> Africa as it is being captured.  The calf is shipped to a zoo in England
> where a blood sample is taken.  Part of this tissue sample is stored in
> liquid nitrogen, but part is used for a DNA extraction.   The DNA is
> sequenced and used in a molecular phylogeny project.  Here we have 5 pieces
> of evidence (each of which could be assigned GUIDs): the digital StillImage,
> the calf itself in the zoo (a LivingSpecimen), the blood sample, the DNA
> sample, and the DNA sequence in digital text form.  All five of these pieces
> of evidence could potentially reside as CollectionObjects in different
> physical or electronic repositories.
> *Competency question 1 (Occurrence) *
> StillImage: timestamp and embedded GPS metadata associated with the image
> document the time and place where the calf was located at the time of
> capture.
> LivingSpecimen: the collection record that the zoo keeps for the calf
> document the time and place where the calf was located at the time of
> capture.
> (the other three pieces of evidence do not provide information about any
> time and place where the calf was located)
> *Competency question 2 (Provenance)*
> StillImage: a foaf:depiction of the calf (Individual/BiologicalEntity)
> LivingSpecimen: owl:sameAs the calf (Individual/BiologicalEntity)
> blood sample: dcterms:isPartOf the calf (Individual/BiologicalEntity)
> DNA sample: dcterms:isPartOf the blood sample which dcterms:isPartOf the
> calf (Individual/BiologicalEntity)
> DNA sequence: [sequencedFrom] the DNA sample which dcterms:isPartOf the
> blood sample which dcterms:isPartOf the calf (Individual/BiologicalEntity)
> (all five pieces of evidence support the existence of the calf, and the
> provenance of each piece of evidence can be traced back to the calf)
> *Competency question 3 (Identification)*
> As part of the phylogenetic analysis, the DNA sequence could serve as
> evidence for assigning the calf to a particular taxon.
> A mammal expert in Australia might examine the digital StillImage via the
> web and assert that the calf is a wildebeest.
> Another mammal expert in England might examine the calf at the zoo and
> assert that the calf is a wildebeest (or perhaps look at the calf in the zoo
> when it is full grown and also look at the StillImage taken at the time it
> was captured and make the assertion based on two forms of Evidence).
> (the DNA sample itself apart from the sequence probably wouldn't be used as
> evidence for an Identification; the blood sample might if the cytology were
> distinctive)
> -----------
> I would assert that the bottom line here is that an entity that falls
> within the proposed CollectionObject class would need to address at least
> one of these three competency questions.  It would not be necessary for it
> to address all three.  The properties of instances of the CollectionObject
> class would be that they could be connected through object properties to
> Occurrences, Individuals/BiologicalEntities, or Identifications; and that
> they could have data properties that we typically assign to collected items
> such as catalogNumber, collectionCode, preparation, etc.  John has suggested
> moving DwC terms for such properties from under Occurrence to the proposed
> CollectionObject class (
> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002574.html).  As
> John has noted, this is a significant change, but I believe that it is an
> important one if one is to accept the distinction between Occurrences and
> the evidence that documents them - an imperative in more complex cases such
> as I outlined above.
> ----------
> I want to end this email by returning to Rich's outlook on the "Individual"
> issue.  In his various posts, it seems to me that much of what he wants to
> accomplish through the "Individual" class falls within what I've defined
> here as competency question 2 (tracking provenance of resources, in
> particular physical things that are, include, or are taken from living
> organisms).  It seems like the CollectionObject class is fully capable of
> doing much of what he wants to accomplish.  Just get rid of the term
> "Individual" - as Paul Murray has noted (
> http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002615.html) it
> already has a different meaning.  Use "CollectionObject" to address Rich's
> provenance competency questions (tracking and connecting collected objects)
> and "BiologicalEntity" to address mine (joining zero-to-many Occurrences to
> zero-to-many forms of evidence to zero-to-many Identifications).  So then
> what IS an actual individual organism like the wildebeest calf?  It is a
> BiologicalEntity if it has been documented as an Occurrence or assigned an
> Identification.  It is a CollectionObject if it was collected for a zoo, or
> shot and mounted in a museum.  Or it can be both simultaneously if it is
> both documented and collected.  If none of these things were done, then it's
> neither a BiologicalEntity nor a CollectionObject - it's simply a wildebeest
> calf.  Define the class/type of the thing by the properties that you wish to
> assert for it (or the competency questions that you can answer for it).
> With regard to the issue of taxonomically heterogeneous entities: tracking
> the provenance of taxonomically heterogeneous CollectionObjects and
> CollectionObjects that are pieces of organisms is not really a big deal.  A
> fish fin isPartOf an individual fish isPartOf a jar of a mixed fish isPart
> of a marine trawl.  However, tracking and reconciling Identifications of
> taxonomically heterogeneous collections of things and their subsamples (the
> second part of what Rich wanted to accomplish) is more complex task that I
> cannot at this point wrap my head around (see the "Additional Comments" at
> http://code.google.com/p/darwin-sw/wiki/TaxonomicHeterogeneity for more
> commentary on this).
> Steve
> --
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
> postal mail address:
> VU Station B 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) 343-6707http://bioimages.vanderbilt.edu
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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