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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>>>
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>>>
>>>
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>>>
>>>
>>>
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