Wow - what a thread to come back to.

I saw my name mentioned so I ought to chip in. I also think we are conflating two distinct things under the name "occurrence". 

This point is largely just expanding on what Kevin just said. Going down the road he was wise enough not to go down!

The vocabulary I briefly presented at TDWG was aimed at occurrence of taxa in regions but the general thrust of my talk was intended to pose the questions: Why should we score taxa to regions at all? Shouldn't this always be the results of a query on occurrence records? The answer will always depend on the question asked.

Take two examples.

A tiger roaming "free" in London living off a diet of squirrels and tourists. Occurrence records for this organism are just occurrence records. Why the tiger is in London (climate change, introduction, invasion, escape) is not a quality of it being there. They are value judgements added later.

A tiger sitting in a cage a London Zoo is "managed" in that it is being maintained there by a human effort. We are recording the fact that someone has placed it there and held it in that position for our edification.

As Kevin says, when I observe an individual (or flock of individuals) I do not observe their "introducedness" or their "nativeness" this is something that is derived from combining multiple observations of occurrence of individuals.

I would therefore advocate that we just have a flag on an occurrence record that says "intended for distribution" i.e. this is not maintained here in a garden/zoo/farm etc. To say any more on a occurrence record is misleading and there are occasions when even this flag will be ignored in analysis. I think we already have this field.

There are of course grey areas (biology always has grey areas). A Scots Pine growing in the highlands may be part of a 150 year old naturalistic plantation. It is therefore native to the region, possibly of local genetic stock but has been planted in that position. For some applications this could be considered managed and for others not.

The status of taxa in regions is a completely different thing. As soon as we talk about aggregating multiple observations (or lack of them) then we are talking about the results of analysis instead of primary observations.  Only at this point should we be talking about the status of the "occurrence" in terms of native/invasive/naturalised etc. This may not even be based on extant records. For example, a taxon can be invasive in an area without actually occurring there. i.e. it used to be there but is presumed to be irradiated.

Does the problem occur because we are using the same term "occurrence" to mean both a primary unit of data gathering and the result of an analysis (possibly even just a hypothesis if it is the result of niche modelling)? How could we differentiate between these two? The discussion probably comes back to 'basisOfRecord' again and our fundamental classes of object. 

Sorry to be long winded. 

Roger


On 12 Oct 2010, at 09:36, Kevin Richards wrote:

I also have always felt that "nativeness" should apply more to an occurrence than a taxon, but have swayed from one opinion to the other on a regular basis.  So my conclusion is that "nativeness" is a propety of both, and require both, in a way - and that these different perspectives are actually the same thing.

Eg, if we describe (in a basic way) :
Ocurrence = Taxon at Location

then if we say that Nativeness is a property of a Taxon that is restricted by Location  (jerry's view)
then this is equivalent to saying that Nativeness is a property of an Ocurrence ! (Rich's view)

As Rich points out, it doesnt make a whole lot of sense to apply Nativeness to a single occurrence, but I'm not sure this is what is meant by stating that "this specimen of Poa anceps that I collected from Christchurch is 'Native'" - but more that "I have found a specimen of Poa anceps in Christchurch and from knowledge of other previously recorded ocurrences, I know that this occurence/taxon is Native in this area"

Also I tend to feel that a lot of biodiversity properties are properties of ocurrences  - EVEN taxon names are a property of an occurrence and not of this 'concept' of a species - but I wont go down that road right now   :-)

Also, we discussed this topic a while ago on the tdwg content list, having worked out that "nativeness" or what we call "biostatus" is a fairly complicated topic, involving taxon names, locations, time, and aspects like 'origin' and 'presence', ...

Kevin

________________________________________
From: tdwg-content-bounces@lists.tdwg.org [tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle [deepreef@bishopmuseum.org]
Sent: Tuesday, 12 October 2010 5:41 p.m.
To: Jerry Cooper; tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz

Hi Jerry,

Before we agree to disagree, let me try to elaborate a bit more:

I think we both agree that "Nativeness" (to borrow Dave's term) is a
property of a taxon at a geographic locality (it could also be a property of
a taxon in a class of habitat, but few people actually frame it this way).

The reason I think that "Nativeness" is best represented as a property of an
Occurrence, rather than of a taxon, is that a taxon is a circumscribed set
of organisms, usually based on evolutionary relatedness or morphological or
genetic similarity.  By contrast, an Occurrence is about the presence of a
member or multiple members of a taxon concept in space and time (i.e., at a
particular place and time).

We often think of Occurrence records in terms of individual organisms (e.g.,
specimens, or specific observed or photographed organisms), and I agree,
it's weird to think of "Nativeness" as it applies to an individual organism.
However, my understanding is that Occurrence instances can also apply to
populations -- which is what terms such as establishmentMeans and
occurrenceStatus fit into this class.

More generally, if we agree that "Nativeness" is a property of a taxon at a
particular locality, the way that this intersection is usually manifest in
DwC is via Occurrence and Event instances.

How else would you represent "Nativeness" within DwC?

Aloha,
Rich

-----Original Message-----
From: tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Jerry Cooper
Sent: Monday, October 11, 2010 6:02 PM
To: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz

We will have to agree to disagree.

For me at least 'Native',  'Invasive' etc are clearly not
properties associated with a collection event. They are
collective statements, not necessarily about properties of
the taxon as a whole, but about the properties of a taxon in
some restricted sense - usually geographically restricted.

GISIN, like our model here in  NZ, pulls together such items
under a triplet of taxon/occurrence statement/geographical
extent linked to a publication.


Jerry


-----Original Message-----
From: Richard Pyle [mailto:deepreef@bishopmuseum.org]
Sent: Tuesday, 12 October 2010 4:23 p.m.
To: Jerry Cooper
Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
Subject: RE: [tdwg-content] What I learned at the TechnoBioBlitz

Hi Jerry,

Yes, this is a road I've been down before.  Intuitively,
these terms seem like they should apply to taxon concepts,
but it turns out that's not the right way to do it.  Things
like "native" and "invasive" are not properties of taxon
concepts; they're the property of an occurrence (which, I
suspect, is why establishmentMeans is included in the
Occurrence class in DwC; e.g., see the examples at
http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans

Rich

________________________________

       From: tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Jerry Cooper
       Sent: Monday, October 11, 2010 4:38 PM
       Cc: tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com
       Subject: Re: [tdwg-content] What I learned at the
TechnoBioBlitz



       Rich,



       Let's not confuse those terms which are best applied
to a taxon concept rather than a  specific
collection/observation of a taxon at a location.



        There are existing vocabularies for taxon-related
provenance, like those in GISIN, or the vocabulary Roger
mentioned in his PESI talk at TDWG.



       However, against a specific collection you can only
record what the recorder actually knows at that location for
that specific collected taxon, and not to infer a status like
'introduced' etc.



       So, to me, the vocabulary reduces even further - and
the obvious ones are 'in cultivation', 'in captivity',
'border intercept' . Our botanical collection management
system would hold more data on provenance of a specific
collection and linkages between events - from the wild at t=1,
x=1 to cultivation in botanic garden Y at t=2, X=2 etc. But
then we often have that data because we are generating it.



       Jerry





       From: tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle
       Sent: Tuesday, 12 October 2010 3:27 p.m.
       To: Donald.Hobern@csiro.au; tuco@berkeley.edu
       Cc: tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com
       Subject: Re: [tdwg-content] What I learned at the
TechnoBioBlitz



       I certainly agree it's important!  I was just saying
that a simple flag probably wouldn't be enough.  I like the
idea of a controlled vocabulary (as you and John both allude
to), and I can imagine about a half-dozen terms that our
community will no-doubt adopt with almost no debate.....  :-)



       In my mind, the broadest categories (and likely most
useful) would be something like:



       Native (was there without any assistance from humans)

       Introduced (got there with the assistance of humans,
but is inhabiting the natural environment)

       Captive (brought by humans and still maintained in captivity)



       You might also throw in "Cryptogenic", which is an
assertion that we do not know which of these categories a
particular organism falls (not the same as null, which means
we don't know whether or not we know)



       Of course, each of these can be further subdivded,
but the more we subdivide, the greater the ratio of
fuzzy:clean distinctions. I would say that the terms should
be established in consultation with those most likely to use
them (e.g., as you suggest, distribution analysis, niche modellers,
etc.)  For example, it might be useful to distinguish between
an organism that was itself introduced, compared to the
progeny (or a well-established
population) of an intoduced organism. This information can be
useful for separating things likely to become established in
new localities, vs. things that do not seem to "take" in a
novel environment.

       Anyway...I didn't want to say a lot on this topic
(too late?); I just wanted to steer more towards controlled
vocabulary, than simple flag field.



       Aloha,

       Rich



               ________________________________

                               From: Donald.Hobern@csiro.au
[mailto:Donald.Hobern@csiro.au]
               Sent: Monday, October 11, 2010 3:44 PM
               To: Richard Pyle; tuco@berkeley.edu
               Cc: tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com
               Subject: RE: [tdwg-content] What I learned at
the TechnoBioBlitz

               Hi Rich.



               I recognise this (and could probably define
many different useful flags).  The bottom line is really
whether or not the location is one which should be used for
distribution analysis, niche modelling and similar
activities.  There will certainly be many grey areas, but it
would be good if software could weed out captive occurrences.



               Donald





               untitled



                       Donald Hobern, Director, Atlas of
Living Australia

               CSIRO Ecosystem Sciences, GPO Box 1700,
Canberra, ACT 2601

               Phone: (02) 62464352 Mobile: 0437990208

               Email: Donald.Hobern@csiro.au
<mailto:Donald.Hobern@csiro.au>

               Web: http://www.ala.org.au/

















               From: Richard Pyle [mailto:deepreef@bishopmuseum.org]
               Sent: Tuesday, 12 October 2010 12:33 PM
               To: Hobern, Donald (CES, Black Mountain);
tuco@berkeley.edu
               Cc: tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com
               Subject: RE: [tdwg-content] What I learned at
the TechnoBioBlitz



               I'm not so sure a simple flag will do it.  We
have examples ranging from animals in zoos, to escaped
animals, to intentionally and unintentionally introduced
populations, to naturalized populations -- and just about
everything in-between.  Where on this spectrum would you draw
the line for flagging something as "naturally occurring"?



               Rich



                       ________________________________

                                               From:
tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of
Donald.Hobern@csiro.au
                       Sent: Monday, October 11, 2010 2:59 PM
                       To: tuco@berkeley.edu
                       Cc: tdwg-content@lists.tdwg.org;
tdwg-bioblitz@googlegroups.com
                       Subject: Re: [tdwg-content] What I
learned at the TechnoBioBlitz

                       Thanks, John.



                       This is useful, but completely
uncontrolled - effectively a verbatimEstablishmentMeans.
Having a more controlled version or a simple flag which could
be machine-processible in those cases where providers can
supply it would be useful.



                       Donald





                       untitled



                               Donald Hobern, Director,
Atlas of Living Australia

                       CSIRO Ecosystem Sciences, GPO Box
1700, Canberra, ACT 2601

                       Phone: (02) 62464352 Mobile: 0437990208

                       Email: Donald.Hobern@csiro.au
<mailto:Donald.Hobern@csiro.au>

                       Web: http://www.ala.org.au/

















                       From: gtuco.btuco@gmail.com
[mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek
                       Sent: Tuesday, 12 October 2010 11:34 AM
                       To: Hobern, Donald (CES, Black Mountain)
                       Cc: jsachs@csee.umbc.edu;
tdwg-bioblitz@googlegroups.com; tdwg-content@lists.tdwg.org
                       Subject: Re: [tdwg-content] What I
learned at the TechnoBioBlitz



                       Natural occurrence is meant to be
captured through the term dwc:establishmentMeans
(http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans).

                       On Mon, Oct 11, 2010 at 5:16 PM,
<Donald.Hobern@csiro.au> wrote:

                       Thanks, Joel.

                       Nice summary.  One addition which we
do need to resolve (and which has been suggested in recent
months) is to have a flag to indicate whether a record should
be considered to show a "natural"
occurrence (in distinction from cultivation, botanic gardens,
zoos, etc.).
This is not so much an issue in a BioBlitz, but is certainly
a factor with citizen science recording in general - see the
number of zoo animals in the Flickr EOL group.

                       Donald




                       Donald Hobern, Director, Atlas of
Living Australia
                       CSIRO Ecosystem Sciences, GPO Box
1700, Canberra, ACT 2601
                       Phone: (02) 62464352 Mobile: 0437990208
                       Email: Donald.Hobern@csiro.au
                       Web: http://www.ala.org.au/









                       -----Original Message-----
                       From: tdwg-content-bounces@lists.tdwg.org
[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of joel sachs
                       Sent: Monday, 11 October 2010 10:47 PM
                       To: tdwg-bioblitz@googlegroups.com;
tdwg-content@lists.tdwg.org
                       Subject: [tdwg-content] What I
learned at the TechnoBioBlitz

                       One of the goals of the recent
bioblitz was to think about the suitability and
appropriatness of TDWG standards for citizen science. Robert
Stevenson has volunteered to take the lead on preparing a
technobioblitz lessons learned document, and though the scope
of this document is not yet determined, I think the audience
will include bioblitz organizers, software developers, and
TDWG as a whole. I hope no one is shy about sharing lessons
they think they learned, or suggestions that they have. We
can use the bioblitz google group for this discussion, and
copy in tdwg-content when our discussion is standards-specific.

                       Here are some of my immediate observations:

                       1. Darwin Core is almost exactly
right for citizen science. However, there is a desperate need
for examples and templates of its use. To illustrate this
need: one of the developers spoke of the design choice
between "a simple csv file and a Darwin Core record". But a
simple csv file is a legitimate representation of Darwin
Core! To be fair to the developer, such a sentence might not
have struck me as absurd a year ago, before Remsen said
"let's use DwC for the bioblitz".

                       We provided a couple of example DwC
records (text and rdf) in the bioblitz data profile [1]. I
think the lessons learned document should include an on-line
catalog of cut-and-pasteable examples covering a variety of
use cases, together with a dead simple desciption of DwC,
something like "Darwin Core is a collection of terms,
together with definitions."

                       Here are areas where we augemented or
diverged from DwC in the bioblitz:

                       i. We added obs:observedBy [2], since
there is no equivalent property in DwC, and it's important in
Citizen Science (though often not available).

                       ii. We used geo:lat and geo:long [3]
instead of DwC terms for latitude and longitude. The geo
namespace is a well used and supported standard, and records
with geo coordinates are automatically mapped by several
applications. Since everyone was using GPS  to retrieve their
coordinates, we were able to assume WGS-84 as the datum.

                       If someone had used another Datum,
say XYZ, we would have added columns to the Fusion table so
that they could have expressed their coordiantes in DwC, as, e.g.:
                       DwC:decimalLatitude=41.5
                       DwC:decimalLongitude=-70.7
                       DwC:geodeticDatum=XYZ

                       (I would argue that it should be
kosher DwC to express the above as simply XYZ:lat and
XYZ:long. DwC already incorporates terms from other
namespaces, such as Dublin Core, so there is precedent for this.

                       2. DwC:scientificName might be more
user friendly than taxonomy:binomial and the other taxonomy
machine tags EOL uses for flickr images.  If
DwC:scientificName isn't self-explanatory enough, a user can
look it up, and see that any scientific name is acceptable,
at any taxonomic rank, or not having any rank. And once we
have a scientific name, higher ranks can be inferred.

                       3. Catalogue of Life was an important
part of the workflow, but we had some problems with it.
Future bioblitzes might consider using something like a CoL
fork, as recently described by Rod Page [4].

                       4. We didn't include "basisOfRecord"
in the original data profile, and so it wasn't a column in
the Fusion Table [5]. But when a transcriber felt it was
necessary to include in order to capture data in a particular
field sheet, she just added the column to the table. This
flexibility of schema is important, and is in harmony with
the semantic web.

                       5. There seemed to be enthusiasm for
another field event at next year's TDWG. This could be an
opportunity to gather other types of data (eg.
                       character data) and thereby
                       i) expose meeting particpants to
another set of everyday problems from the world of
biodiversity workflows, and ii) try other TDWG technology on
for size, e.g. the observation exchange format, annotation
framework, etc.


                       Happy Thanksgiving to all in Canada -
                       Joel.
                       ----


                       1.
http://groups.google.com/group/tdwg-bioblitz/web/tdwg-bioblitz
-profile-v1-1
                       2. Slightly bastardizing our old
observation ontology -
http://spire.umbc.edu/ontologies/Observation.owl
                       3. http://www.w3.org/2003/01/geo/
                       4.
http://iphylo.blogspot.com/2010/10/replicating-and-forking-dat
a-in-2010.html
                       5.
http://tables.googlelabs.com/DataSource?dsrcid=248798


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