[tdwg-content] What I learned at the TechnoBioBlitz
Gail Kampmeier
gkamp at illinois.edu
Tue Oct 12 06:27:49 CEST 2010
An earlier version of the draft DwC had a simple flag of ValidDistribution (true/false). This is perhaps the flag that Donald was looking for, which morphed into the more complex establishmentMeans, to give various stakeholders the chance to figure out more precisely as you say "what, exactly are we interested in knowing?" John's current version is more flexible but does suggest a controlled vocabulary, which has not been worked out, but ValidDistribution = false would capture the pandas in DC and the Ross's gull (http://www.allaboutbirds.org/guide/Rosss_Gull/id) in Massachusetts, and for a particular point in time. It would not, however, adequately capture the extensive escapes, accidental and purposeful introductions of non-native species that become established, and are later considered to be ValidDistribution = true (apparently this might also now be the case for Ross's gull, but I remember the big hooha in 1975!). When is this line considered to be crossed? This is likely why John, in his wisdom, decided to deprecate ValidDistribution in favor of something with a broader possible interpretation.
Thanks for your discussion below.
Gail
On Oct 11, 2010, at 11:00 PM, Richard Pyle wrote:
> Hi Gail,
>
> Yes, and this gets back to Donald's original point, and one I've wrestled
> with for a long time -- which boils down to, "what, exactly, are we
> interested in knowing"?
>
> In my experience, most people seem most concerned with whether an organism
> got to where it was
> captured/observed/photographed/surveyed/monitored/whatever with the aid of
> humans, or without. I think the reason for this is that most people
> distinguich between "natural" and "artificial" on the basis of how much
> control humans had in it.
>
> After that, the next most important question tends to be whether it's an
> anomalous occurrence, or a locally reproducing population. This is where we
> get into waifs & vagrants (I see the examples you gave as subcategories of
> "Native", in my hyper-simplified vocabulary in my earlier post); and from
> there, it gets into shades of grey on how "established" the population is
> (e.g., does it achieve the threshold of "naturalized"?)
>
> Unfortunately, these two things (how it got there, vs. whether it's locally
> reproducing) are really different metrics, yet people often try to combine
> them into the same category.
>
> From my read of http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans,
> both metrics are evident. In a sense, the presence of the word "established"
> might seem to restrict it to only locally-reproducing populations. However,
> one could also interpret the word "establish" in the context of individual
> organism (e.g., how did this individual Ross's Gull get established in
> Massachusetts?)
>
> The GBIF vocabulary that Dave sent the link for also seems to mix the two
> metrics.
>
> And there are other considerations I've seen in databases as well (including
> our own): such as the distinction between "adventive" and "intentional"
> introductions. Also, the word "invasive" (one of the examples on the DwC
> page for establishmentMeans) suggests another angle, implying some sort of
> "harm" done to the ecosystems or to human interests such as agriculture.
>
> So again, I ask: "What, exactly, are we interested in knowing?" If I read
> Donald correctly, he simply wants to filter out occurrence records of Pandas
> in Washington DC. But Niche Modellers might come from a different angle,
> and seek evidence of whether or not an organism is capable of sustaining a
> locally reproducing population in some particular place (regardless of
> whether the founders of the pupulation were brought by humans, or got there
> on their own).
>
> If we can answer that question, then the next question will be whether we
> can pack all the answers into a single controlled vocabulary for
> "establishmentMeans", or whether we may need to think about another DwC
> term, with a slightly different meaning.
>
> Aloha,
> Rich
>
>
> ________________________________
>
> From: Gail Kampmeier [mailto:gkamp at illinois.edu]
> Sent: Monday, October 11, 2010 4:41 PM
> To: Richard Pyle
> Cc: tdwg-content at lists.tdwg.org; tdwg-bioblitz at googlegroups.com
> Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
>
>
> Your human-centered distinctions will likely prove to be useful in
> certain contexts (quarantine; invasive species watches), but think of birds
> or insects blown or carried into areas by meteorological events that survive
> and become established for a season or more, or as curiosities of
> observation (Ross's gull in Massachusetts). Range extension is important in
> climate change research and may have nothing to do with direct human
> activities outlined below.
>
> Cheers!
> Gail
>
>
> On Oct 11, 2010, at 9:26 PM, Richard Pyle wrote:
>
>
> 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
>
> <image001.png>
>
> 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
>
> <image001.png>
>
> 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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