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<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Dear All,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Completely agree with Rich’s
analysis.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>May I coin two new terms? But before, I
think we should separate the definition of occurrences from their use, which
remove many questions evocated in previous messages):<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Occurrence:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>At least a triplet (a taxon name, a
location, a time); whatever the precision of each member of the triplet
is.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>The difference is in only in the use that
we can do of an occurrence depending on the respective precision of each member
of the triplet. Ontologies by definition should reflect the patterns not the
processes (although technically I suppose that processes can be described by
ontologies … but it is an extension of the meaning of the word).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Name:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>From “living organism” (extant
or fossil) down to infrasubspecific rank if needed. Can it be a common name?
Yes, it may decrease the precision or even the accuracy, that is all.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Location:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>From Earth/continent/ocean/catchment down
to precise geocoordinates. Earth is always implicit and by default until we
find life out in space.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Time:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>From 4.5 billion year range / geological
era down to a precise date/time stamp.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Here are the two new terms I propose (and
more could be coined using the same way):<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Geoccurrence: an occurrence with
geocoordinates.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Loccurrence: an occurrence with only a
locality/geographic name.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Should we coin terms for occurrences resulting
from modeling?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Another consideration: species distribution
modeling is a rationalization of the production of distribution maps, just like
cladistics is a rationalization of the production of phylogenies.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>For cladistics, in essence we sample
individuals in the real genealogic tree (= tokogenetic tree of Hennig): but can
we say that actually all characters used in cladistics lead back to a given
individual? Maybe true for molecular data but this statement needs more
thinking; I don’t think it is true for morphology, and it is the same way
for synthetic descriptions and older works, as Rich described as using all imprecise
old records.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Likewise for distribution, we sample individuals,
and also use the best of loccurrences based on imprecise location (cf. Jeremy
Jackson work on historical records and trends).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>As for recording nativeness, I would
suggest that it is a general issue for all controlled vocabularies that try to establish
categories over a continuum: the only way to get rid of all these problematic
definitions, and most probably incl. occurrences, is to express them with fuzzy
logic: we can say that a species is more or less native, especially if the
abundance is gradient from a center to peripheral areas, and then it could
derive from species distribution modeling based on geoccurrences and loccurrences
expressed as fuzzy functions.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>So the next step is to include fuzzy logic
in ontologies ;-). And TDWG becoming a fuzzy think tank ;-).<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>BW<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Nicolas.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'><o:p> </o:p></span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>Richard Pyle<br>
<b><span style='font-weight:bold'>Sent:</span></b> Wednesday 13 October 2010
07:08<br>
<b><span style='font-weight:bold'>To:</span></b> tuco@berkeley.edu<br>
<b><span style='font-weight:bold'>Cc:</span></b> tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [tdwg-content] How to
record "Nativeness"?</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Thanks, John. I agree that there
will be little value in trying to define and name distinct units of space and
time, but there may be value in defining units along the taxonomic axis.
However, we should first come to a community consensus on what the maximum
scope of each axis is.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>My sense is that the maximum scope of
space is "Earth" (at least until we begin
documenting populations of extraterrestrial life).</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>My sense is that the maximum scope of time
is effectively "any window of time during the past 4 billion years or
so".</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>But I don't have a clear
sense for what the maximum scope of "one or more
organisms" ought to be. I'm content with extending it to
"populations" as a unit of "organisms", because I see a
smooth transition from two individual organisms all the way up to a population
of organisms. But should we accept taxonConcept (which can be
thought of as an implied set of populations) as an extension of
"organisms"? If so, then "Animalia Occurred on Earth
sometime during the past 2 billion years" is a legitimate Occurrence
record (pretty damn useless...but still legitimate).</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>I think it matters, and is relevant to
this exchange -- both because of Steve's point about more clearly defining what
an "Occurrence" can be, and because we still don't have a good idea
of how and where to score "nativeness" (for which there is clearly an
expressed need).</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>I agree that fitness-for-use should be
determined from the content of the records, but coming back to Donald's (and
others') point about filtering "non-native" records, there needs to
be a way to include this information in the content of the records in
order to determine fitness-for-use. I believe that a controlled
vocabulary for establishmentMeans will probably be all we have to
do to satisy 95% of the user need. But before we can nail down what
that controlled vocabulary would encompass, I think we need to come to some
sort of consensus on the issues that Steve has articulated.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Aloha,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=blue face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:blue'>Rich</span></font><o:p></o:p></p>
<blockquote style='border:none;border-left:solid blue 1.5pt;padding:0cm 0cm 0cm 4.0pt;
margin-left:3.75pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
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<p class=MsoNormal style='margin-bottom:12.0pt'><b><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
gtuco.btuco@gmail.com [mailto:gtuco.btuco@gmail.com] <b><span style='font-weight:
bold'>On Behalf Of </span></b>John Wieczorek<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, October 12, 2010
11:29 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Richard Pyle<br>
<b><span style='font-weight:bold'>Cc:</span></b> Steve Baskauf; joel sachs;
tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [tdwg-content] How to
record "Nativeness"?</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Occurrence is admittedly a problematic term. Its current definition is
vague following in the grand tradition of Dublin Core term definitions. Rich's
interpretation echoes what Steve wrote and comes closest in my mind to what an
occurrence really is meant to be, namely "evidence of one or more organisms
occurring at a place and time." This leaves open all of the vast continuum
of scales - geographic, temporal, and taxonomic - at which occurrences can be
described. I'm not sure exactly what is solved by trying to make named
distinctions between different scales or levels of detail (on any of the three
axes) of Occurrence. The core of the issue really boils down to fitness-for-use
of records and a potential user's capacity to accurately determine that. These
should be characteristics that can be determined from the content of the
records.<o:p></o:p></span></font></p>
</blockquote>
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