[tdwg-content] What I learned at the TechnoBioBlitz
Richard Pyle
deepreef at bishopmuseum.org
Tue Oct 12 06:41:58 CEST 2010
Hi Jerry,
Before we agree to disagree, let me try to elaborate a bit more:
I think we both agree that "Nativeness" (to borrow Dave's term) is a
property of a taxon at a geographic locality (it could also be a property of
a taxon in a class of habitat, but few people actually frame it this way).
The reason I think that "Nativeness" is best represented as a property of an
Occurrence, rather than of a taxon, is that a taxon is a circumscribed set
of organisms, usually based on evolutionary relatedness or morphological or
genetic similarity. By contrast, an Occurrence is about the presence of a
member or multiple members of a taxon concept in space and time (i.e., at a
particular place and time).
We often think of Occurrence records in terms of individual organisms (e.g.,
specimens, or specific observed or photographed organisms), and I agree,
it's weird to think of "Nativeness" as it applies to an individual organism.
However, my understanding is that Occurrence instances can also apply to
populations -- which is what terms such as establishmentMeans and
occurrenceStatus fit into this class.
More generally, if we agree that "Nativeness" is a property of a taxon at a
particular locality, the way that this intersection is usually manifest in
DwC is via Occurrence and Event instances.
How else would you represent "Nativeness" within DwC?
Aloha,
Rich
> -----Original Message-----
> 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 6:02 PM
> To: tdwg-content at lists.tdwg.org; tdwg-bioblitz at googlegroups.com
> Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
>
> We will have to agree to disagree.
>
> 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.
>
> 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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