On Oct 12, 2010, at 13:14, Roger Hyam wrote:
> 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>>>
>>>
>>>
_______________________________________________
>>>
tdwg-content mailing list
>>>
tdwg-content@lists.tdwg.org>>>
>>>
http://lists.tdwg.org/mailman/listinfo/tdwg-content>>>
>>>
_______________________________________________
>>>
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>>>
tdwg-content@lists.tdwg.org>>>
>>>
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>>>
>>>
>>>
>>>
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>>>
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