[tdwg-content] What I learned at the TechnoBioBlitz

Richard Pyle deepreef at bishopmuseum.org
Tue Oct 12 04:26:38 CEST 2010


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:  <mailto:Donald.Hobern at csiro.au> 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:  <mailto:Donald.Hobern at csiro.au> 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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