<div dir="ltr">Dear Steve,<div>just to be clear, I was not suggesting dwc:establishmentMeans should be deprecated nor its name changed, just that the controlled vocabulary fits the definition.</div><div>I understand your point regarding filtering, but it doesn't work due to the conflation of concepts and the need to accommodate observations and checklists. The solution I propose would still allow filtering, but would avoid them being mixed up if they were a planted native species, for example.</div><div><br></div><div>Two data elements that the invasive species researchers want, and are not provided currently, are the pathway of introduction and the nativeness (unconflated). If we don't do this using dwc:establishmentMeans, what else do you propose?<br></div><div>The third elements "occurrenceStatus" is needed for conservation assessments and for invasive species researchers. There is currently no way in a checklist to say something is extinct. No one has yet questioned this suggested change, presumably because dwc:occurrenceStatus has been rather orphaned by dwc:individualCount. I'm a little surprised that no one has mentioned this, but dwc:occurrenceStatus currently can be used for occurrences (present or absent). However, this proposal would only make it suitable for checklists (e.g. extinct).</div><div><br></div><div>Much of the controversy of these proposals comes down to the use of DwC for checklists verses observations. I think I've said it before, but it would help is the DwC definitions would distinguish between terms used in these different contexts.</div><div><br></div><div>Before the TDWG meeting in December I hope to find the time to analyse the current usage of dwc:establishmentMeans and dwc:occurrenceStatus. That should make interesting reading.<br></div><div><br></div><div>Regards</div><div>Quentin</div><div> </div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><br></div><div><br></div><div>Dr. Quentin Groom</div><div>(Botany and Information Technology)</div><div><br></div><div>Botanic Garden Meise</div><div>Domein van Bouchout</div><div>B-1860 Meise</div><div>Belgium</div><div><br></div><div><a href="http://orcid.org/0000-0002-0596-5376" target="_blank">ORCID: 0000-0002-0596-5376</a></div><div><br></div><div>Landline; +32 (0) 226 009 20 ext. 364</div><div>FAX: +32 (0) 226 009 45</div><div><br></div><div>E-mail: <a href="mailto:quentin.groom@plantentuinmeise.be" target="_blank">quentin.groom@plantentuinmeise.be</a></div><div>Skype name: qgroom</div><div>Website: <a href="http://www.botanicgarden.be" target="_blank">www.botanicgarden.be</a></div><div><br></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 25 June 2016 at 16:16, Steve Baskauf <span dir="ltr"><<a href="mailto:steve.baskauf@vanderbilt.edu" target="_blank">steve.baskauf@vanderbilt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div bgcolor="#ffffff" text="#000000">
I don't think that dwc:establishmentMeans should be deprecated. It's
possible that the definition or list of recommended values should be
changed, but I think it satisfies an important use case as it is
currently defined (or at least the way that I understand its
definition). My understanding of the use case (based on previous
discussion on this list from years ago) is as a filter for occurrence
records - to allow the searcher to exclude occurrence records based on
the amount of human intervention that was involved in the organism
being established at the particular location where it was found in the
occurrence. There is a sort of gradient of intervention:<br>
<br>
<b>native</b>: no human intervention was ever involved in causing the
organism's species to occur at that location. Example:
<a href="http://bioimages.vanderbilt.edu/ind-baskauf/10897" target="_blank">http://bioimages.vanderbilt.edu/ind-baskauf/10897</a> where an <i>Acer
negundo</i> individual was found in a forest with no apparent human
intervention to cause that individual to be there.<br>
<br>
<b>naturalised:</b> human intervention was involved in causing the
species to occur at that location, but the population persists at that
location without human intervention. Example:
<a href="http://bioimages.vanderbilt.edu/ind-baskauf/12179" target="_blank">http://bioimages.vanderbilt.edu/ind-baskauf/12179</a> where a <i>Taraxacum
officinale</i> individual was found in a lawn. <i>Taraxacum officinale</i>
arrived in Cheatham County, Tennessee as a result of human
intervention, but no human did anything to make that individual be at
that location. In fact, humans are probably trying to get rid of its
population, but it still persists.<br>
<br>
<b>adventitive</b>: human intervention was involved in causing the
species to occur at that location, but no intentional effort was made
to cause that particular individual to be there and the population is
not likely to persist. Example:
<a href="http://bioimages.vanderbilt.edu/ind-baskauf/33559" target="_blank">http://bioimages.vanderbilt.edu/ind-baskauf/33559</a> where a <i>Triticum
aestivum</i> individual was found growing in a construction site. <i>Triticum
aestivum</i> is not native to Cheatham County, Tennessee and as far as
I know, populations of it do not persist in the area without human
intervention. This individual was not managed in an agricultural
field; rather it appeared to have gotten started accidentally from
straw used as mulch to protect planted grass seed. <br>
<br>
<b>managed:</b> human intervention was involved in causing the species
to occur at that location, and intentional efforts cause the organism
to be at that location and to persist there. Example:
<a href="http://bioimages.vanderbilt.edu/vanderbilt/12-43" target="_blank">http://bioimages.vanderbilt.edu/vanderbilt/12-43</a> where an <i>Acer
negundo</i> was present as part of landscaping on a college campus. <br>
<br>
Maintaining a "gradient" of values like this allows a user to perform a
variety of screens on occurrence data. Users may only want native
occurrences, perhaps because they want to collect DNA from native
populations or want to see what the organism looks like when it grows
in its native habitat. Users may search for native+naturalised
occurrences in order to develop a checklist of species that are likely
to be found over a long period of time in natural areas. Users may
search for native+naturalised+adventive occurrences to develop a list
of organisms that might be found in an area, including incidental
occurrences. Users may search for managed occurrences to find
locations (which would include zoos and botanical gardens) where they
might be able to easily obtain samples of the organism from a contact
person.<br>
<br>
Using dwc:establishmentMeans as a value for occurrence records of a
particular organism at a very precise location and a particular time is
a very different use case that using it to assess populations of
organisms in a broader area over a broader time to find out things such
as whether a species is invading an area or not. In the examples
above, <i>Acer negundo</i> is a native species to Tennessee, but
<a href="http://bioimages.vanderbilt.edu/vanderbilt/12-43" target="_blank">http://bioimages.vanderbilt.edu/vanderbilt/12-43</a> is not a native
occurrence of <i>Acer negundo</i> since it was planted and managed by
humans at that location.<br>
<br>
I agree that the two (or more) uses of dwc:establishmentMeans probably
should be separated. My guess would be that using
dwc:establishmentMeans the way that I described it above is more
common, but I may just be biased because that's the way that I use it.
The way I've described its use seems to be very much in keeping with
the definition that is given for the term. If I had my way, I'd get
rid of the value "invasive" and add the value "adventive" to the list
of recommended values. "Invasive" is the value that doesn't really
fit, because it's really difficult to assess that status based on a
single occurrence record. The GBIF Establishment Means controlled
vocabulary at
<a href="http://rs.gbif.org/vocabulary/gbif/establishment_means.xml" target="_blank">http://rs.gbif.org/vocabulary/gbif/establishment_means.xml</a> indicates
that "introduced" is a superclass for naturalised, invasive, and
managed, which I suppose could have some utility if that were made
clear.<br>
<br>
One might make the case that "establishmentMeans" is not a good "name"
for what the term means, and that it should be changed. However, one
should keep in mind that dwc:establishmentMeans is an abbreviation for
the URI <a href="http://rs.tdwg.org/dwc/terms/establishmentMeans" target="_blank">http://rs.tdwg.org/dwc/terms/establishmentMeans</a> and as such,
it's an identifier, not a descriptive label. Changing labels doesn't
"break" anything; changing URIs does. If we don't like the definition
of dwc:establishmentMeans, we should figure out how it is most commonly
used and change the definition to match that use. That would be the
approach that would provide the maximum stability for Darwin Core. I
think that we made a mistake in the past when we changed
dwc:individualID to dwc:organismID. I understand that there's a desire
to make the local name parts of URIs "make sense" with respect to the
meaning of the term, but that's only a convention, not a requirement.
>From an application or machine perspective, dwc:t03958 is just as good
of an identifier as dwc:establishmentMeans. Get the human-readable
label and definition right, but don't change or deprecate the URI
unless absolutely necessary.<span class="HOEnZb"><font color="#888888"><br>
<br>
Steve</font></span><div><div class="h5"><br>
<br>
Quentin Groom wrote:
<blockquote type="cite">
<div dir="ltr">Dear Rich,
<div>Thanks for taking a look at the proposal!</div>
<div><br>
<div>perhaps you could clarify your comment regarding the upper limit
of "population". Is this what I would call the use of Darwin Core for
observations verses checklists?</div>
<div><br>
</div>
<div>You can only tell if an organism is invasive if you monitor it
over time therefore this term in inappropriate for a single
observation. Also, whether something is invasive is a different concept
to whether something is native or alien, both can be invasive. I seems
to me that the currently suggested vocabulary for
dwc:establishmentMeans is conflating two concepts. Also, none of these
terms have much to do with how the organism became established.</div>
<div><br>
</div>
<div>Currently, there are no fields where nativeness can be properly
described and all we need is 1. This is needed for calculating
essential biodiversity variables, for horizon scanning and invasive
species monitoring. This is in contrast to occurrenceStatus where we
currently have three ways to declare absence.</div>
<div><br>
</div>
<div>I would have preferred to deprecate the term
dwc:establishmentMeans, because its definition doesn't match its
suggested vocabulary. However, I chose to retain it for the sake of
stability. It has already been suggested that a better term would be
introductionMeans.</div>
<div><br>
</div>
<div>I don't understand your way of indicating nativeness or how it
would work. For many species nativeness is a concept based upon limited
available evidence. It isn't something that can be pinned down to a
particular event or location. If Darwin Core was only ever used for
single observations I would agree that we don't need a term for
nativeness, but as it is also used for checklists and we have to
accommodate terms that relate to a taxon over a large area.</div>
<div><br>
</div>
<div>Regards</div>
<div>Quentin</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><br>
</div>
<div><br>
</div>
<div>Dr. Quentin Groom</div>
<div>(Botany and Information Technology)</div>
<div><br>
</div>
<div>Botanic Garden Meise</div>
<div>Domein van Bouchout</div>
<div>B-1860 Meise</div>
<div>Belgium</div>
<div><br>
</div>
<div><a href="http://orcid.org/0000-0002-0596-5376" target="_blank">ORCID:
0000-0002-0596-5376</a></div>
<div><br>
</div>
<div>Landline; +32 (0) 226 009 20 ext. 364</div>
<div>FAX: +32 (0) 226 009 45</div>
<div><br>
</div>
<div>E-mail: <a href="mailto:quentin.groom@plantentuinmeise.be" target="_blank">quentin.groom@plantentuinmeise.be</a></div>
<div>Skype name: qgroom</div>
<div>Website: <a href="http://www.botanicgarden.be" target="_blank">www.botanicgarden.be</a></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On 25 June 2016 at 08:13, Richard Pyle <span dir="ltr"><<a href="mailto:deepreef@bishopmuseum.org" target="_blank">deepreef@bishopmuseum.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204,204,204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
<div bgcolor="white" link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Hi
All,</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">When
we discussed the scope of the class “Organism”, I believe we considered
the upper limit of “population” – but I can’t remember whether we
accepted that upper limit. If so, then the “Organism” instance
participating in an particular Occurrence instance could logically be
qualified as “invasive” or “native” (or whatever), in which case it
seems more appropriate to apply terms such as “native”, “introduced”,
“invasive”, etc. to dwc:establishmentMeans</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">I
realize this is squishy, but we don’t really have another class within
DwC-space to which the property of “native”, “introduced”, “invasive”,
etc. can be applied. Moreover, I don’t think there SHOULD be such a
class, because it short-circuits the basis for the presence of Taxon X
at Location Y (i.e., this should be established via
Taxon-->Identification-->Organism-->Occurrence-->Event-->Location).</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">I
realize this is an extraordinarily convoluted way of saying “Taxon X is
native to Location Y”; but ultimately that’s what we want…. Right?</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Aloha,</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)">Rich</span></p>
<p class="MsoNormal"><span style="font-size:11pt;font-family:"Calibri","sans-serif";color:rgb(31,73,125)"> </span></p>
<div style="border-style:none none none solid;border-color:-moz-use-text-color -moz-use-text-color -moz-use-text-color blue;border-width:medium medium medium 1.5pt;padding:0in 0in 0in 4pt">
<div>
<div style="border-style:solid none none;border-color:rgb(181,196,223) -moz-use-text-color -moz-use-text-color;border-width:1pt medium medium;padding:3pt 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10pt;font-family:"Tahoma","sans-serif";color:windowtext">
tdwg-content [mailto:<a href="mailto:tdwg-content-bounces@lists.tdwg.org" target="_blank">tdwg-content-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Steve Baskauf<br>
<b>Sent:</b> Sunday, June 19, 2016 1:45 PM<br>
<b>To:</b> Quentin Groom<br>
<b>Cc:</b> <a href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><br>
<b>Subject:</b> Re: [tdwg-content] A proposal to improve Darwin
Core for invasive species data</span></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Getting caught up on this thread after a
holiday. <br>
<br>
Some previous discussion on dwc:establishmentMeans in 2010 was at:<br>
<a href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html" target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html</a><br>
<a href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html" target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html</a><br>
<br>
The opinion expressed in that thread was that dwc:establishmentMeans
was a property of an organism at a particular place and time (i.e. an
Occurrence.): how did a particular organism come to be in that place at
that time. In that view, an organism might be at a location because it
was a representative of a native species, or because it was managed at
that location by humans. In that perspective, it would not make sense
to use the value "invasive" with dwc:establishmentMeans because that is
more of a property of a species at a location rather than an individual
organism at that location and time. <br>
<br>
Steve<br>
<br>
Quentin Groom wrote: </p>
<div>
<div>
<p class="MsoNormal">I've been working on a proposal to improve
Darwin Core for use with invasive species data.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">The proposal is detailed on GitHub at <a href="https://github.com/qgroom/ias-dwc-proposal/blob/master/proposal.md" target="_blank">https://github.com/qgroom/ias-dwc-proposal/blob/master/proposal.md</a>.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">The proposal is for a new term "origin" and
suggested vocabularies for establishmentMeans and occurrenceStatus.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I'd welcome your feedback on the proposal.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">From my perspective it provides some needed
clarity on the establishmentMeans and occurrenceStatus fields, but also
adds the origin that is needed for invasive species research and for
conservation assessments.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I'm not sure of the best way to discuss this,
but if you have concrete proposals for changes you might raise them as
issues on GitHub, as well as mentioning them here.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Regards</p>
</div>
<div>
<p class="MsoNormal">Quentin</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal"><br clear="all">
</p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Dr. Quentin Groom</p>
</div>
<div>
<p class="MsoNormal">(Botany and Information Technology)</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Botanic Garden Meise</p>
</div>
<div>
<p class="MsoNormal">Domein van Bouchout</p>
</div>
<div>
<p class="MsoNormal">B-1860 Meise</p>
</div>
<div>
<p class="MsoNormal">Belgium</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"><a href="http://orcid.org/0000-0002-0596-5376" target="_blank">ORCID:
0000-0002-0596-5376</a></p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Landline; +32 (0) 226 009 20 ext. 364</p>
</div>
<div>
<p class="MsoNormal">FAX: +32 (0) 226 009 45</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">E-mail: <a href="mailto:quentin.groom@plantentuinmeise.be" target="_blank">quentin.groom@plantentuinmeise.be</a></p>
</div>
<div>
<p class="MsoNormal">Skype name: qgroom</p>
</div>
<div>
<p class="MsoNormal">Website: <a href="http://www.botanicgarden.be" target="_blank">www.botanicgarden.be</a></p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><br>
<br>
</p>
<pre>-- </pre>
<pre>Steven J. Baskauf, Ph.D., Senior Lecturer</pre>
<pre>Vanderbilt University Dept. of Biological Sciences</pre>
<pre> </pre>
<pre>postal mail address:</pre>
<pre>PMB 351634</pre>
<pre>Nashville, TN 37235-1634, U.S.A.</pre>
<pre> </pre>
<pre>delivery address:</pre>
<pre>2125 Stevenson Center</pre>
<pre>1161 21st Ave., S.</pre>
<pre>Nashville, TN 37235</pre>
<pre> </pre>
<pre>office: 2128 Stevenson Center</pre>
<pre>phone: (615) 343-4582, fax: (615) 322-4942</pre>
<pre>If you fax, please phone or email so that I will know to look for it.</pre>
<pre><a href="http://bioimages.vanderbilt.edu" target="_blank">http://bioimages.vanderbilt.edu</a></pre>
<pre><a href="http://vanderbilt.edu/trees" target="_blank">http://vanderbilt.edu/trees</a></pre>
<pre> </pre>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<pre cols="72">--
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
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
<a href="http://bioimages.vanderbilt.edu" target="_blank">http://bioimages.vanderbilt.edu</a>
<a href="http://vanderbilt.edu/trees" target="_blank">http://vanderbilt.edu/trees</a>
</pre>
</div></div></div>
</blockquote></div><br></div>