[tdwg-content] What I learned at the TechnoBioBlitz
Richard Pyle
deepreef at bishopmuseum.org
Tue Oct 12 21:30:21 CEST 2010
Hi Arlin,
In principle, I agree with you (at least I desperately want to). But I
would just point out two things:
1) Many, many end-users want to filter results to include only "natural"
occurrences of organisms. For small datasets/analyses, this can easily be
done manually by the end-user. For large datasets and analyses, it would be
very helpful to have this information embedded within the source dataset
(and also the custodian of the dataset will often be in a better position to
make such a judgement).
2) Although I agree that "not uniformly implemented" is a very serious risk
at this point (and hence why I spent so much time writing emails on this
thread), I'm not so sure the solution necessarily needs to be fancy. I'm
still confident it can be resolved with a simple controlled vocabulary. The
hard part will be figuring out the scope of that vocabulary.
Aloha,
Rich
> -----Original Message-----
> From: tdwg-content-bounces at lists.tdwg.org
> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of
> Arlin Stoltzfus
> Sent: Tuesday, October 12, 2010 3:48 AM
> To: tdwg-content at lists.tdwg.org List; tdwg-bioblitz at googlegroups.com
> Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
>
> 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-dat
a-in-2010.html
> > 5.
> > http://tables.googlelabs.com/DataSource?dsrcid=248798
> >
> >
> _______________________________________________
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> >
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> >
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> >
> >
> >
> >
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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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