Would we have the energy to compile example dwc records on how to use darwin core for certain use cases? The lack of guidance on how to use darwin core was mentioned earlier. An additional example webpage for the dwc website would surely be really helpful for not only newbies. A dwc record for bird watching, vegetation plot surveys, insect specimen collection, herbarium sheets, zoological garden visits, tissue sample, dna sequence, marine fishing net catches, etc
Id volunteer to do the html page if Im given example records with a short use case description...
Markus
On Oct 12, 2010, at 13:14, Roger Hyam wrote:
Wow - what a thread to come back to.
I saw my name mentioned so I ought to chip in. I also think we are conflating two distinct things under the name "occurrence".
This point is largely just expanding on what Kevin just said. Going down the road he was wise enough not to go down!
The vocabulary I briefly presented at TDWG was aimed at occurrence of taxa in regions but the general thrust of my talk was intended to pose the questions: Why should we score taxa to regions at all? Shouldn't this always be the results of a query on occurrence records? The answer will always depend on the question asked.
Take two examples.
A tiger roaming "free" in London living off a diet of squirrels and tourists. Occurrence records for this organism are just occurrence records. Why the tiger is in London (climate change, introduction, invasion, escape) is not a quality of it being there. They are value judgements added later.
A tiger sitting in a cage a London Zoo is "managed" in that it is being maintained there by a human effort. We are recording the fact that someone has placed it there and held it in that position for our edification.
As Kevin says, when I observe an individual (or flock of individuals) I do not observe their "introducedness" or their "nativeness" this is something that is derived from combining multiple observations of occurrence of individuals.
I would therefore advocate that we just have a flag on an occurrence record that says "intended for distribution" i.e. this is not maintained here in a garden/zoo/farm etc. To say any more on a occurrence record is misleading and there are occasions when even this flag will be ignored in analysis. I think we already have this field.
There are of course grey areas (biology always has grey areas). A Scots Pine growing in the highlands may be part of a 150 year old naturalistic plantation. It is therefore native to the region, possibly of local genetic stock but has been planted in that position. For some applications this could be considered managed and for others not.
The status of taxa in regions is a completely different thing. As soon as we talk about aggregating multiple observations (or lack of them) then we are talking about the results of analysis instead of primary observations. Only at this point should we be talking about the status of the "occurrence" in terms of native/invasive/naturalised etc. This may not even be based on extant records. For example, a taxon can be invasive in an area without actually occurring there. i.e. it used to be there but is presumed to be irradiated.
Does the problem occur because we are using the same term "occurrence" to mean both a primary unit of data gathering and the result of an analysis (possibly even just a hypothesis if it is the result of niche modelling)? How could we differentiate between these two? The discussion probably comes back to 'basisOfRecord' again and our fundamental classes of object.
Sorry to be long winded.
Roger
On 12 Oct 2010, at 09:36, Kevin Richards wrote:
I also have always felt that "nativeness" should apply more to an occurrence than a taxon, but have swayed from one opinion to the other on a regular basis. So my conclusion is that "nativeness" is a propety of both, and require both, in a way - and that these different perspectives are actually the same thing.
Eg, if we describe (in a basic way) : Ocurrence = Taxon at Location
then if we say that Nativeness is a property of a Taxon that is restricted by Location (jerry's view) then this is equivalent to saying that Nativeness is a property of an Ocurrence ! (Rich's view)
As Rich points out, it doesnt make a whole lot of sense to apply Nativeness to a single occurrence, but I'm not sure this is what is meant by stating that "this specimen of Poa anceps that I collected from Christchurch is 'Native'" - but more that "I have found a specimen of Poa anceps in Christchurch and from knowledge of other previously recorded ocurrences, I know that this occurence/taxon is Native in this area"
Also I tend to feel that a lot of biodiversity properties are properties of ocurrences - EVEN taxon names are a property of an occurrence and not of this 'concept' of a species - but I wont go down that road right now :-)
Also, we discussed this topic a while ago on the tdwg content list, having worked out that "nativeness" or what we call "biostatus" is a fairly complicated topic, involving taxon names, locations, time, and aspects like 'origin' and 'presence', ...
Kevin
From: tdwg-content-bounces@lists.tdwg.org [tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle [deepreef@bishopmuseum.org] Sent: Tuesday, 12 October 2010 5:41 p.m. To: Jerry Cooper; tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
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@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Jerry Cooper Sent: Monday, October 11, 2010 6:02 PM To: tdwg-content@lists.tdwg.org; tdwg-bioblitz@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@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 appliedto a taxon concept 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 onlyrecord 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 - andthe 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@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 sayingthat 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 mostuseful) 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 anassertion 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@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 definemany 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 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: 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. Wehave 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@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 completelyuncontrolled - 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 Box1700, 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 becaptured 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@csiro.au wrote:
Thanks, Joel. Nice summary. One addition which wedo 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 ofLiving Australia 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 recentbioblitz 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 exactlyright 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 DwCrecords (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], sincethere 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 bekosher 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 moreuser 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 importantpart 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 foranother 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 oldobservation 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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