[tdwg-content] A proposal to improve Darwin Core for invasive species data
Steve Baskauf
steve.baskauf at vanderbilt.edu
Sat Jun 25 16:16:55 CEST 2016
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:
*native*: no human intervention was ever involved in causing the
organism's species to occur at that location. Example:
http://bioimages.vanderbilt.edu/ind-baskauf/10897 where an /Acer
negundo/ individual was found in a forest with no apparent human
intervention to cause that individual to be there.
*naturalised:* human intervention was involved in causing the species to
occur at that location, but the population persists at that location
without human intervention. Example:
http://bioimages.vanderbilt.edu/ind-baskauf/12179 where a /Taraxacum
officinale/ individual was found in a lawn. /Taraxacum officinale/
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.
*adventitive*: 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: http://bioimages.vanderbilt.edu/ind-baskauf/33559
where a /Triticum aestivum/ individual was found growing in a
construction site. /Triticum aestivum/ 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.
*managed:* 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:
http://bioimages.vanderbilt.edu/vanderbilt/12-43 where an /Acer negundo/
was present as part of landscaping on a college campus.
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.
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,
/Acer negundo/ is a native species to Tennessee, but
http://bioimages.vanderbilt.edu/vanderbilt/12-43 is not a native
occurrence of /Acer negundo/ since it was planted and managed by humans
at that location.
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 http://rs.gbif.org/vocabulary/gbif/establishment_means.xml indicates
that "introduced" is a superclass for naturalised, invasive, and
managed, which I suppose could have some utility if that were made clear.
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 http://rs.tdwg.org/dwc/terms/establishmentMeans 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.
Steve
Quentin Groom wrote:
> Dear Rich,
> Thanks for taking a look at the proposal!
>
> 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?
>
> 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.
>
> 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.
>
> 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.
>
> 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.
>
> Regards
> Quentin
>
>
>
>
> Dr. Quentin Groom
> (Botany and Information Technology)
>
> Botanic Garden Meise
> Domein van Bouchout
> B-1860 Meise
> Belgium
>
> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>
> Landline; +32 (0) 226 009 20 ext. 364
> FAX: +32 (0) 226 009 45
>
> E-mail: quentin.groom at plantentuinmeise.be
> <mailto:quentin.groom at plantentuinmeise.be>
> Skype name: qgroom
> Website: www.botanicgarden.be <http://www.botanicgarden.be>
>
>
> On 25 June 2016 at 08:13, Richard Pyle <deepreef at bishopmuseum.org
> <mailto:deepreef at bishopmuseum.org>> wrote:
>
> Hi All,
>
>
>
> 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
>
>
>
> 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).
>
>
>
> 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?
>
>
>
> Aloha,
>
> Rich
>
>
>
> *From:* tdwg-content [mailto:tdwg-content-bounces at lists.tdwg.org
> <mailto:tdwg-content-bounces at lists.tdwg.org>] *On Behalf Of *Steve
> Baskauf
> *Sent:* Sunday, June 19, 2016 1:45 PM
> *To:* Quentin Groom
> *Cc:* tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
> *Subject:* Re: [tdwg-content] A proposal to improve Darwin Core
> for invasive species data
>
>
>
> Getting caught up on this thread after a holiday.
>
> Some previous discussion on dwc:establishmentMeans in 2010 was at:
> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001730.html
> http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001731.html
>
> 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.
>
> Steve
>
> Quentin Groom wrote:
>
> I've been working on a proposal to improve Darwin Core for use
> with invasive species data.
>
>
>
> The proposal is detailed on GitHub at
> https://github.com/qgroom/ias-dwc-proposal/blob/master/proposal.md.
>
>
>
> The proposal is for a new term "origin" and suggested vocabularies
> for establishmentMeans and occurrenceStatus.
>
>
>
> I'd welcome your feedback on the proposal.
>
>
>
> 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.
>
>
>
> 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.
>
>
>
> Regards
>
> Quentin
>
>
>
>
>
>
>
>
> Dr. Quentin Groom
>
> (Botany and Information Technology)
>
>
>
> Botanic Garden Meise
>
> Domein van Bouchout
>
> B-1860 Meise
>
> Belgium
>
>
>
> ORCID: 0000-0002-0596-5376 <http://orcid.org/0000-0002-0596-5376>
>
>
>
> Landline; +32 (0) 226 009 20 ext. 364
>
> FAX: +32 (0) 226 009 45
>
>
>
> E-mail: quentin.groom at plantentuinmeise.be
> <mailto:quentin.groom at plantentuinmeise.be>
>
> Skype name: qgroom
>
> Website: www.botanicgarden.be <http://www.botanicgarden.be>
>
>
>
>
>
> --
>
> 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.
>
> http://bioimages.vanderbilt.edu
>
> http://vanderbilt.edu/trees
>
>
>
>
--
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.
http://bioimages.vanderbilt.edu
http://vanderbilt.edu/trees
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