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>>>
>>>
_______________________________________________
>>>
tdwg-content mailing list
>>>
tdwg-content@lists.tdwg.org>>>
>>>
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>>>
>>>
>>>
>>>
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>>>
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