[tdwg-content] What I learned at the TechnoBioBlitz
David Remsen (GBIF)
dremsen at gbif.org
Tue Oct 12 04:44:22 CEST 2010
The GBIF vocabulary server has a draft "Nativeness" vocabulary that
contains a list of these and other terms representing a useful
controlled list for dwc:establishmentMeans.
http://vocabularies.gbif.org/vocabularies/nativeness
This might serve as a platform for follow-on development. I could
assist in providing administrative access to this vocabulary. This
vocabulary development platform is under evaluation and we will be
moving forward on vocabulary development and integration within the
GBIF network.
David Remsen
On Oct 12, 2010, at 11:26 AM, 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
> 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 OfDonald.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
> 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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