[tdwg-content] tdwg-content Digest, Vol 20, Issue 17

Wed Nov 3 21:42:12 CET 2010

Hi Nico,

Are you wanting to model things that you think are actually species within a
larger clade or are these more like subspecies?

I think this gets at a bit of what these are to be used for.

Are they for modeling classifications or occurrences and other data about
individuals or sets of individuals which represent instances of species?

- Pete

On Wed, Nov 3, 2010 at 1:19 PM, Nico Cellinese <ncellinese at flmnh.ufl.edu>wrote:

>
> Steve is using Species as ranks in his definition and I think this is the
> wrong approach.  Let's make all this rank agnostic please!  Use the word
> taxon!  What if I have a group of organisms that represents  a polyphyletic
> species and I want to name a lineage (group of organisms) within this
> traditionally recognized species that I am not recognizing as species per se
> (as in rank of species).  In other words, Identifications and ranks are two
> different things, so let's abandon ranks for a more objective discussion on
> taxa. Individuals are definitively not species.
>
> Nico (the other one)
>
>
> On Wed, Nov 3, 2010 at 7:24 AM, Steve Baskauf <
> steve.baskauf at vanderbilt.edu> wrote:
>
> John,
> I'm not sure that I agree with your analysis that the definition prevents
> the possibility of making an Identification at a rank less specific than a
> species.  My revised definition says that the *Individual should only
> include groups of organisms that are reliably known to be of a single
> species* - *it doesn't say that we need to know what that species is (i.e.
> an identification to genus or family can be made with the hope that someone
> down the line would be able to refine the identification to species*).
>  Clarification on this point could be added to the comment or the Google
> Code page, but I don't think there is a problem with the definition per se.
>  However, if there is a consensus that the definition is too restrictive, I
> would not object to changing the wording of the definition from "species (or
> lower taxonomic rank if it exists)" to "taxon" if there were clarification
> added to the comments or Google Code page that Individual was not intended
> to include aggregations of mult
>
> iple species.
>
> I agree that there is a need for a term that represents "collections",
> "bags", "aggregations", or whatever you want to call an aggregation that
> includes multiple species.  But I have never intended that Individual should
> be that term.  If we expand Individual to include aggregates, then it
> becomes unusable for its original intended purpose.  I would prefer for
> someone to propose a different term for aggregates of individuals instead of
> adding that function to Individual.  Then define the relationship of this
> new thing to Individual as a one:many relationship (one aggregation:many
> Individuals).
>
> Steve
>
>
> John Wieczorek wrote:
> Most of you probably do not receive postings from the Google Code site for
> Darwin Core. Steve B. updated the proposal for the new term Individual, and
> then commentary ensued on the Issue tracker. Since there remains an
> unresolved issue, I'm bringing the discussion back here by adding the
> commentary stream below.  The unresolved issue is Steve's amendment is the
> restriction in the definition to "a single species (or lower taxonomic rank
> if it exists)."
>
>
>
> Rich argues that we should not obviate the capability of applying an
> Identification to an aggregate (e.g., fossil), where the aggregate consists
> of multiple taxa.
>
> Steve argues that Identifications should be applied only to aggregates of a
> single taxon.
>
>
>
>
> Steve, aside from the aggregate issue (which should be solved
> satisfactorily), your suggestion is too restrictive, because it would
> obviate the possibility of making an Identification (even for a single
> organism) to any rank less specific than a species. That is a loss of
> capability, and therefore unreasonable.
>
>
>
>
>
> Comment 7 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7>
>  by baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago)
> As a result of the discussion that has taken place on the tdwg-content
> email list during 2010 October and November, I am updating the term
> recommendation for Individual as follows:
>
> Definition: The category of information pertaining to an individual
> organism or
> a group of individual organisms that can reliably be known to represent a
> single species (or lower taxonomic rank if it exists).
>
> Comment: Instances of this class can serve the purpose of connecting one or
> more instances of the Darwin Core class Occurrence to one or more instances
> of the Darwin Core class Identification.
>
> Refines: N/A
>
> Please note that as a precautionary measure, I have removed the statement
> that Individual refines http://purl.org/dc/dcmitype/PhysicalObject because
> the definition of PhysicalObject specifically mentions that the object is
> inanimate.  I am not currently aware of any well-known term that defines
> living things.
>
> Steve Baskauf
>
>
>
>
> Delete comment <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#
> >
>
> Comment 8 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8>
>  by deepreef at hawaii.rr.com <
> http://code.google.com/u/deepreef@hawaii.rr.com/> , Today (8 hours ago)
> I think the definition should be "...represent a single taxon".  We
> shouldn't restrict it to members of the same species (or lower), because
> then we technically can't include things that may represent more than one
> species, yet would best be treated within the scope of an Individual.
>
> Also, I'm slightly partial to the term "Organism" for this class, rather
> than "Individual", because it's more clearly tied to the biology domain, and
> less likely to collide with the word "Individual" in other domains.  I know
> such collision is not a technical problem, but it might lead to some
> confusion.
>
>
>
> Delete comment <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#
> >
>
> Comment 9 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9>
>  by baskaufs <http://code.google.com/u/baskaufs/> , Today (8 hours ago)
> Well, the reason that I defined it to be members of the same species is to
> ensure that the term Individual can serve the primary function that I
> perceived was needed: to make the connection from occurrences to
> identifications.  When I said one or more identifications, I meant one or
> more opinions about what that single species (or lower) was, not that there
> could be multiple identifications of several different species that happened
> to be in the same "bag" such as the contents of a pitfall trap containing
> multiple species, an image that contained several species, or a specimen
> that contained parasites of a different species.  I think that there is a
> need for a term for this other kind of thing, (a heterogeneous "lot",
> "batch", or something), but I think that including this in definition of
> Individual defeats the purpose for which I proposed it.  If there were
> several different species in the "Individual", then
> one would have to specify which identification went with which biological
> individual within the "lot", which would result in actually breaking down
> the "lot" into single species "Individuals" anyway.
>
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> ------------------------------
>
> Message: 2
> Date: Wed, 3 Nov 2010 10:38:58 -0700
> From: John Wieczorek <tuco at berkeley.edu>
> Subject: Re: [tdwg-content] Request for vote on proposals to add
> Individualas a Darwin Core class and to add the term individualRemarks
> as a termwithin that class
> To: "Blum, Stan" <SBlum at calacademy.org>
> Cc: "tdwg-content at lists.tdwg.org" <tdwg-content at lists.tdwg.org>
> Message-ID:
> <AANLkTikBMK47LN0r7ppgb8MoQtGqzmseppYVKpTcj7FL at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> This is what happened to Organism, from the thread?Re: [tdwg-content]
> Treatise on Occurrence, tokens, and basisOfRecord [SEC=UNCLASSIFIED].
>
> John said:
>
> "I like Organism, but I don't like the inconsistency it would make
> with individualID and individualCount on the one hand, or extra work
> to change these to organismID and organismCount on the other.
> Individual doesn't carry these extra burdens, and could be added
> without breaking any existing applications."
>
> Rich said "OK" so it must be OK. ;-)
>
> On Wed, Nov 3, 2010 at 10:03 AM, Blum, Stan <SBlum at calacademy.org> wrote:
>
>
> All:
>
>
> What happened to changing the term to organism? ?I think the word organism,
> at least strictly speaking, is closer to our intention than individual.
>
>
> Compare the definitions you get from:
>
>
> http://www.google.com/search?hl=en&q=define:+individual&btnG=Search
>
>
> And
>
>
> http://www.google.com/search?hl=en&q=define:+organism&btnG=Search
>
>
>
> -Stan
>
>
>
>
> On 11/3/10 9:02 AM, "John Wieczorek" <tuco at berkeley.edu> wrote:
>
>
> I have no further objection if the wording is changed as you propose here.
> If no one else has any objections, this one seems ready to be prepared for
> the TAG following the voting mechanism proposed at TDWG this year. I'll take
> the responsibility to see that through as soon as I can.
>
>
> On Wed, Nov 3, 2010 at 7:24 AM, Steve Baskauf <
> steve.baskauf at vanderbilt.edu> wrote:
>
>
>
> John,
>
> I'm not sure that I agree with your analysis that the definition prevents
> the possibility of making an Identification at a rank less specific than a
> species.? My revised definition says that the Individual should only include
> groups of organisms that are reliably known to be of a single species - it
> doesn't say that we need to know what that species is (i.e. an
> identification to genus or family can be made with the hope that someone
> down the line would be able to refine the identification to species).?
> Clarification on this point could be added to the comment or the Google Code
> page, but I don't think there is a problem with the definition per se.?
> However, if there is a consensus that the definition is too restrictive, I
> would not object to changing the wording of the definition from "species (or
> lower taxonomic rank if it exists)" to "taxon" if there were clarification
> added to the comments or Google Code page that Individual was not intended
> to include aggregations of mu
>
>
> ltiple species.
>
>
> I agree that there is a need for a term that represents "collections",
> "bags", "aggregations", or whatever you want to call an aggregation that
> includes multiple species.? But I have never intended that Individual should
> be that term.? If we expand Individual to include aggregates, then it
> becomes unusable for its original intended purpose.? I would prefer for
> someone to propose a different term for aggregates of individuals instead of
> adding that function to Individual.? Then define the relationship of this
> new thing to Individual as a one:many relationship (one aggregation:many
> Individuals).
>
>
> Steve
>
>
>
> John Wieczorek wrote:
>
>
> Most of you probably do not receive postings from the Google Code site for
> Darwin Core. Steve B. updated the proposal for the new term Individual, and
> then commentary ensued on the Issue tracker. Since there remains an
> unresolved issue, I'm bringing the discussion back here by adding the
> commentary stream below. ?The unresolved issue is Steve's amendment is the
> restriction in the definition to "a single species (or lower taxonomic rank
> if it exists)."
>
>
>
>
> Rich argues that we should not obviate the capability of applying an
> Identification to an aggregate (e.g., fossil), where the aggregate consists
> of multiple taxa.
>
>
> Steve argues that Identifications should be applied only to?aggregates?of a
> single taxon.
>
>
>
>
>
> Steve, aside from the aggregate issue (which should be solved
> satisfactorily), your suggestion is too restrictive, because it would
> obviate the possibility of making an Identification (even for a single
> organism) to any rank less specific than a species. That is a loss of
> capability, and therefore unreasonable.
>
>
>
>
>
>
> ?Comment?7 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7>
> ?by?baskaufs <http://code.google.com/u/baskaufs/> ,?Today (8 hours ago)
>
> As a result of the discussion that has taken place on the tdwg-content
> email list during 2010 October and November, I am updating the term
> recommendation for Individual as follows:
>
>
> Definition: The category of information pertaining to an individual
> organism or
>
> a group of individual organisms that can reliably be known to represent a
> single species (or lower taxonomic rank if it exists).
>
>
> Comment: Instances of this class can serve the purpose of connecting one or
> more instances of the Darwin Core class Occurrence to one or more instances
> of the Darwin Core class Identification.
>
>
> Refines: N/A
>
>
> Please note that as a precautionary measure, I have removed the statement
> that Individual refines http://purl.org/dc/dcmitype/PhysicalObject because
> the definition of PhysicalObject specifically mentions that the object is
> inanimate. ?I am not currently aware of any well-known term that defines
> living things.
>
>
> Steve Baskauf
>
>
>
>
>
> ?Delete comment <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#
> >
>
>
> Comment?8 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8>
> ?by?deepreef at hawaii.rr.com <
> http://code.google.com/u/deepreef@hawaii.rr.com/> ,?Today (8 hours ago)
>
>
> I think the definition should be "...represent a single taxon". ?We
> shouldn't restrict it to members of the same species (or lower), because
> then we technically can't include things that may represent more than one
> species, yet would best be treated within the scope of an Individual.
>
>
> Also, I'm slightly partial to the term "Organism" for this class, rather
> than "Individual", because it's more clearly tied to the biology domain, and
> less likely to collide with the word "Individual" in other domains. ?I know
> such collision is not a technical problem, but it might lead to some
> confusion.
>
>
>
>
> ?Delete comment <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#
> >
>
>
> Comment?9 <
> http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9>
> ?by?baskaufs <http://code.google.com/u/baskaufs/> ,?Today (8 hours ago)
>
>
> Well, the reason that I defined it to be members of the same species is to
> ensure that the term Individual can serve the primary function that I
> perceived was needed: to make the connection from occurrences to
> identifications. ?When I said one or more identifications, I meant one or
> more opinions about what that single species (or lower) was, not that there
> could be multiple identifications of several different species that happened
> to be in the same "bag" such as the contents of a pitfall trap containing
> multiple species, an image that contained several species, or a specimen
> that contained parasites of a different species. ?I think that there is a
> need for a term for this other kind of thing, (a heterogeneous "lot",
> "batch", or something), but I think that including this in definition of
> Individual defeats the purpose for which I proposed it. ?If there were
> several different species in the "Individual", then
>
> one would have to specify which identification went with which biological
> individual within the "lot", which would result in actually breaking down
> the "lot" into single species "Individuals" anyway.
>
>
>
> _______________________________________________
>
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>
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>
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>
>
>
>
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>
> End of tdwg-content Digest, Vol 20, Issue 17
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-- 
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies
Knowledge Base <http://lod.geospecies.org/>
About the GeoSpecies Knowledge Base <http://about.geospecies.org/>
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