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I think if I'm understanding what John wrote, he was going to
substitute "taxon" for "species (or lower taxonomic rank if it exists)"
with the understanding that Individual is not intended to be used for
aggregates of different taxa. That would solve this problem, right?<br>
Steve<br>
<br>
Nico Cellinese wrote:
<blockquote
cite="mid:013DC7E8-8368-421C-846F-3565E2BACF1C@flmnh.ufl.edu"
type="cite"><br>
<div>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.</div>
<div><br>
</div>
<div>Nico (the other one)</div>
<div><br>
</div>
<div>
<blockquote type="cite">
<div><br>
On Wed, Nov 3, 2010 at 7:24 AM, Steve Baskauf <<a
moz-do-not-send="true" href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>>
wrote:<br>
<br>
John,<br>
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 <b>Individual
should only include groups of organisms that are reliably known to be
of a single species</b> - <b>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</b>). 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<br>
<br>
iple species.<br>
<br>
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).<br>
<br>
Steve<br>
<br>
<br>
John Wieczorek wrote:<br>
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)."<br>
<br>
<br>
<br>
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.<br>
<br>
Steve argues that Identifications should be applied only to aggregates
of a single taxon.<br>
<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
<br>
<br>
Comment 7 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7</a>>
by baskaufs <<a moz-do-not-send="true"
href="http://code.google.com/u/baskaufs/">http://code.google.com/u/baskaufs/</a>>
, Today (8 hours ago)<br>
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:<br>
<br>
Definition: The category of information pertaining to an individual
organism or<br>
a group of individual organisms that can reliably be known to represent
a single species (or lower taxonomic rank if it exists).<br>
<br>
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.<br>
<br>
Refines: N/A<br>
<br>
Please note that as a precautionary measure, I have removed the
statement that Individual refines <a moz-do-not-send="true"
href="http://purl.org/dc/dcmitype/PhysicalObject">http://purl.org/dc/dcmitype/PhysicalObject</a>
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.<br>
<br>
Steve Baskauf<br>
<br>
<br>
<br>
<br>
Delete comment <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#</a>><br>
<br>
Comment 8 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8</a>>
by <a moz-do-not-send="true" href="mailto:deepreef@hawaii.rr.com">deepreef@hawaii.rr.com</a>
<<a moz-do-not-send="true"
href="http://code.google.com/u/deepreef@hawaii.rr.com/">http://code.google.com/u/deepreef@hawaii.rr.com/</a>>
, Today (8 hours ago)<br>
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.<br>
<br>
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.<br>
<br>
<br>
<br>
Delete comment <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#</a>><br>
<br>
Comment 9 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9</a>>
by baskaufs <<a moz-do-not-send="true"
href="http://code.google.com/u/baskaufs/">http://code.google.com/u/baskaufs/</a>>
, Today (8 hours ago)<br>
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<br>
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.<br>
<br>
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<br>
Message: 2<br>
Date: Wed, 3 Nov 2010 10:38:58 -0700<br>
From: John Wieczorek <<a moz-do-not-send="true"
href="mailto:tuco@berkeley.edu">tuco@berkeley.edu</a>><br>
Subject: Re: [tdwg-content] Request for vote on proposals to add<br>
<span class="Apple-tab-span" style="white-space: pre;"> </span>Individualas
a Darwin Core class and to add the term individualRemarks<br>
<span class="Apple-tab-span" style="white-space: pre;"> </span>as
a termwithin that class<br>
To: "Blum, Stan" <<a moz-do-not-send="true"
href="mailto:SBlum@calacademy.org">SBlum@calacademy.org</a>><br>
Cc: "<a moz-do-not-send="true" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>"
<<a moz-do-not-send="true" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>><br>
Message-ID:<br>
<span class="Apple-tab-span" style="white-space: pre;"> </span><<a
moz-do-not-send="true"
href="mailto:AANLkTikBMK47LN0r7ppgb8MoQtGqzmseppYVKpTcj7FL@mail.gmail.com">AANLkTikBMK47LN0r7ppgb8MoQtGqzmseppYVKpTcj7FL@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
This is what happened to Organism, from the thread?Re: [tdwg-content]<br>
Treatise on Occurrence, tokens, and basisOfRecord [SEC=UNCLASSIFIED].<br>
<br>
John said:<br>
<br>
"I like Organism, but I don't like the inconsistency it would make<br>
with individualID and individualCount on the one hand, or extra work<br>
to change these to organismID and organismCount on the other.<br>
Individual doesn't carry these extra burdens, and could be added<br>
without breaking any existing applications."<br>
<br>
Rich said "OK" so it must be OK. ;-)<br>
<br>
On Wed, Nov 3, 2010 at 10:03 AM, Blum, Stan <<a
moz-do-not-send="true" href="mailto:SBlum@calacademy.org">SBlum@calacademy.org</a>>
wrote:<br>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">All:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">What happened to changing the term to
organism? ?I think the word organism, at least strictly speaking, is
closer to our intention than individual.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Compare the definitions you get from:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="http://www.google.com/search?hl=en&q=define:+individual&btnG=Search">http://www.google.com/search?hl=en&q=define:+individual&btnG=Search</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">And<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="http://www.google.com/search?hl=en&q=define:+organism&btnG=Search">http://www.google.com/search?hl=en&q=define:+organism&btnG=Search</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-Stan<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On 11/3/10 9:02 AM, "John Wieczorek" <<a
moz-do-not-send="true" href="mailto:tuco@berkeley.edu">tuco@berkeley.edu</a>>
wrote:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On Wed, Nov 3, 2010 at 7:24 AM, Steve
Baskauf <<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>>
wrote:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">John,<br>
</blockquote>
<blockquote type="cite">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<br>
</blockquote>
<br>
ltiple species.<br>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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).<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Steve<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">John Wieczorek wrote:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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)."<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Steve argues that Identifications should be
applied only to?aggregates?of a single taxon.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">?Comment?7 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c7</a>>
?by?baskaufs <<a moz-do-not-send="true"
href="http://code.google.com/u/baskaufs/">http://code.google.com/u/baskaufs/</a>>
,?Today (8 hours ago)<br>
</blockquote>
<blockquote type="cite">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:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Definition: The category of information
pertaining to an individual organism or<br>
</blockquote>
<blockquote type="cite">a group of individual organisms that can
reliably be known to represent a single species (or lower taxonomic
rank if it exists).<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Refines: N/A<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Please note that as a precautionary
measure, I have removed the statement that Individual refines <a
moz-do-not-send="true"
href="http://purl.org/dc/dcmitype/PhysicalObject">http://purl.org/dc/dcmitype/PhysicalObject</a>
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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Steve Baskauf<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">?Delete comment <<a
moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#</a>><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Comment?8 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c8</a>>
?by?deepreef@hawaii.rr.com <<a moz-do-not-send="true"
href="http://code.google.com/u/deepreef@hawaii.rr.com/">http://code.google.com/u/deepreef@hawaii.rr.com/</a>>
,?Today (8 hours ago)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">?Delete comment <<a
moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#</a>><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Comment?9 <<a moz-do-not-send="true"
href="http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9">http://code.google.com/p/darwincore/issues/detail?id=69&colspec=ID%20Type%20Status%20Priority%20Milestone%20Owner%20Reporter%20Summary%20Opened#c9</a>>
?by?baskaufs <<a moz-do-not-send="true"
href="http://code.google.com/u/baskaufs/">http://code.google.com/u/baskaufs/</a>>
,?Today (8 hours ago)<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">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<br>
</blockquote>
<blockquote type="cite">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.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">_______________________________________________<br>
</blockquote>
<blockquote type="cite">tdwg-content mailing list<br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
</blockquote>
<blockquote type="cite"><a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<br>
<br>
------------------------------<br>
<br>
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End of tdwg-content Digest, Vol 20, Issue 17<br>
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<pre class="moz-signature" cols="72">--
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) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
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