[tdwg-content] What I learned at the TechnoBioBlitz

Tue Oct 12 05:23:27 CEST 2010

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 at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Jerry Cooper
	Sent: Monday, October 11, 2010 4:38 PM
	Cc: tdwg-content at lists.tdwg.org; tdwg-bioblitz at 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 at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
	Sent: Tuesday, 12 October 2010 3:27 p.m.
	To: Donald.Hobern at csiro.au; tuco at berkeley.edu
	Cc: tdwg-content at lists.tdwg.org; tdwg-bioblitz at 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 at csiro.au
[mailto:Donald.Hobern at csiro.au] 
		Sent: Monday, October 11, 2010 3:44 PM
		To: Richard Pyle; tuco at berkeley.edu
		Cc: tdwg-content at lists.tdwg.org;
tdwg-bioblitz at 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 at csiro.au
<mailto:Donald.Hobern at csiro.au> 

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

		From: Richard Pyle [mailto:deepreef at bishopmuseum.org] 
		Sent: Tuesday, 12 October 2010 12:33 PM
		To: Hobern, Donald (CES, Black Mountain); tuco at berkeley.edu
		Cc: tdwg-content at lists.tdwg.org;
tdwg-bioblitz at 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 at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of
Donald.Hobern at csiro.au
			Sent: Monday, October 11, 2010 2:59 PM
			To: tuco at berkeley.edu
			Cc: tdwg-content at lists.tdwg.org;
tdwg-bioblitz at 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 at csiro.au
<mailto:Donald.Hobern at csiro.au> 

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

			From: gtuco.btuco at gmail.com
[mailto:gtuco.btuco at gmail.com] On Behalf Of John Wieczorek
			Sent: Tuesday, 12 October 2010 11:34 AM
			To: Hobern, Donald (CES, Black Mountain)
			Cc: jsachs at csee.umbc.edu;
tdwg-bioblitz at googlegroups.com; tdwg-content at 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 at 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 at csiro.au
			Web: http://www.ala.org.au/

			-----Original Message-----
			From: tdwg-content-bounces at lists.tdwg.org
[mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of joel sachs
			Sent: Monday, 11 October 2010 10:47 PM
			To: tdwg-bioblitz at googlegroups.com;
tdwg-content at 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-data-in-2010.html
			5.
http://tables.googlelabs.com/DataSource?dsrcid=248798

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