[tdwg-content] A proposal to improve Darwin Core for invasive species data

[Quentin Groom]

Dear Steve,
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.
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.

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?
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).

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.

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.

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
Skype name: qgroom
Website:    www.botanicgarden.be


On 25 June 2016 at 16:16, Steve Baskauf <steve.baskauf at vanderbilt.edu>
wrote:

> 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
> Skype name: qgroom
> Website:    www.botanicgarden.be
>
>
> On 25 June 2016 at 08:13, Richard Pyle <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] *On
>> Behalf Of *Steve Baskauf
>> *Sent:* Sunday, June 19, 2016 1:45 PM
>> *To:* Quentin Groom
>> *Cc:* 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
>>
>> Skype name: qgroom
>>
>> Website:    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.eduhttp://vanderbilt.edu/trees
>
>
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