[tdwg-content] What I learned at the TechnoBioBlitz
Arlin Stoltzfus
arlin at umd.edu
Tue Oct 12 15:47:55 CEST 2010
On Oct 12, 2010, at 12:02 AM, Jerry Cooper wrote:
> 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.
And furthermore they are judgments or inferences about things that are
not observed.
Can someone please explain what is the issue here? We can't stop
people from noticing that pandas live in Washington, DC. Why should
we? If an organism is observed in a location, its observed there.
That's reality. Why go further and speculate about the significance
of this observation? What exactly are people afraid of? A fancy
scheme for encoding inferences about "native", "introduced", etc. is
not going to prevent organisms from popping up in unexpected places,
due both to errors and to real events. Data consumers will find ways
to deal with that, but probably not by using a fancy scheme of
judgments that is not uniformly implemented (which, at this point,
seems likely to me).
Arlin
> 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 at bishopmuseum.org]
> Sent: Tuesday, 12 October 2010 4:23 p.m.
> To: Jerry Cooper
> Cc: tdwg-content at lists.tdwg.org; tdwg-bioblitz at 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 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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-------
Arlin Stoltzfus (arlin at umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org
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