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@bishopmuseum.org] Sent: Tuesday, 12 October 2010 4:23 p.m. To: Jerry Cooper Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@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@lists.tdwg.org[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Jerry Cooper Sent: Monday, October 11, 2010 4:38 PM Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@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 taxonconcept rather than a specific collection/observation of a taxon at a location.
There are existing vocabularies for taxon-relatedprovenance, like those in GISIN, or the vocabulary Roger mentioned in his PESI talk at TDWG.
However, against a specific collection you can only recordwhat 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 theobvious 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@lists.tdwg.org[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: Tuesday, 12 October 2010 3:27 p.m. To: Donald.Hobern@csiro.au; tuco@berkeley.edu Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
I certainly agree it's important! I was just saying that asimple 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 isinhabiting the natural environment)
Captive (brought by humans and still maintained in captivity) You might also throw in "Cryptogenic", which is an assertionthat 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 themore 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 (toolate?); I just wanted to steer more towards controlled vocabulary, than simple flag field.
Aloha, Rich ________________________________ From: Donald.Hobern@csiro.au[mailto:Donald.Hobern@csiro.au] Sent: Monday, October 11, 2010 3:44 PM To: Richard Pyle; tuco@berkeley.edu Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com Subject: RE: [tdwg-content] What I learned at the TechnoBioBlitz
Hi Rich. I recognise this (and could probably define manydifferent 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 LivingAustralia
CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT2601
Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern@csiro.auWeb: http://www.ala.org.au/ From: Richard Pyle [mailto:deepreef@bishopmuseum.org] Sent: Tuesday, 12 October 2010 12:33 PM To: Hobern, Donald (CES, Black Mountain); tuco@berkeley.edu Cc: tdwg-content@lists.tdwg.org;tdwg-bioblitz@googlegroups.com Subject: RE: [tdwg-content] What I learned at the TechnoBioBlitz
I'm not so sure a simple flag will do it. We haveexamples 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@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Donald.Hobern@csiro.au Sent: Monday, October 11, 2010 2:59 PM To: tuco@berkeley.edu Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@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 ofLiving Australia
CSIRO Ecosystem Sciences, GPO Box 1700,Canberra, ACT 2601
Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern@csiro.auWeb: http://www.ala.org.au/ From: gtuco.btuco@gmail.com[mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Tuesday, 12 October 2010 11:34 AM To: Hobern, Donald (CES, Black Mountain) Cc: jsachs@csee.umbc.edu; tdwg-bioblitz@googlegroups.com; tdwg-content@lists.tdwg.org Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
Natural occurrence is meant to be capturedthrough the term dwc:establishmentMeans (http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans).
On Mon, Oct 11, 2010 at 5:16 PM,Donald.Hobern@csiro.au wrote:
Thanks, Joel. Nice summary. One addition which we do need toresolve (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 LivingAustralia CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern@csiro.au Web: http://www.ala.org.au/
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org[mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of joel sachs Sent: Monday, 11 October 2010 10:47 PM To: tdwg-bioblitz@googlegroups.com; tdwg-content@lists.tdwg.org Subject: [tdwg-content] What I learned at the TechnoBioBlitz
One of the goals of the recent bioblitz wasto 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 forcitizen 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 ordiverged from DwC in the bioblitz:
i. We added obs:observedBy [2], since thereis 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] insteadof 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 toexpress 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 userfriendly 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 ofthe 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 theoriginal 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 anotherfield 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@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