Occurrence is admittedly a problematic term. Its current definition is vague following in the grand tradition of Dublin Core term definitions. Rich's interpretation echoes what Steve wrote and comes closest in my mind to what an occurrence really is meant to be, namely "evidence of one or more organisms occurring at a place and time." This leaves open all of the vast continuum of scales - geographic, temporal, and taxonomic - at which occurrences can be described. I'm not sure exactly what is solved by trying to make named distinctions between different scales or levels of detail (on any of the three axes) of Occurrence. The core of the issue really boils down to fitness-for-use of records and a potential user's capacity to accurately determine that. These should be characteristics that can be determined from the content of the records.
On Tue, Oct 12, 2010 at 1:11 PM, Richard Pyle deepreef@bishopmuseum.orgwrote:
Damn! I wish I'd read this before writing that massive reply to Roger (note: I'm trying to move this into the new thread with the new subject line).
I agree with most of what Steve wrote, but I still disagree (as I did with Roger) that the distinction between Steve's two meanings of "Occurrence" is so stark. I agree there is a fundamental distinction from the perspective of data management between:
TaxonConcept<-->Location
And
TaxonConcept<-->Occurrence<-->Event<-->Location
My contention, however, is that "TaxonConcept<-->Location" is often (usually? always?) just a short-hand (scant metadata) way of representing "TaxonConcept<-->Occurrence<-->Event<-->Location". Our domain (biodiversity information) is full of these overloaded short-hand terms, and they're often not easy to detect as such (e.g., so many databases simply represent implied taxon concepts as text-string scientific names).
In my mind, the "essence" of an Occurrence is, ultimately, "organism(s) at place and time". The "place and time" part are represented as a dwc:Event class linked to a dcterms:Location class. The tricky part is what do we mean by "organism(s)". I suspect most would agree that an individual bird falls within scope of "organism(s)" in the case of dwc Occurrence. I further suspect that most would agree that a flock of birds also falls within scope.
But what about a population of birds? No? What is a population, other than a set of individual organisms? How is this different from a "flock" (a smaller set of individual organisms)?
And what about a taxon concept? No? What is a taxon concept, other than a (larger) set of individual organisms?
The fact is, there is a smooth continuum spanning:
IndividualOrganism<-->Event GroupOfIndividualOrganisms<-->Event PopulationOfIndividualOrganisms<-->Event TaxonCocnept<-->Event
Each of the four items above has overlapping scope with adjacent items in the list (the overlap between the first two is evident in colonial organisms).
Steve, many thanks for sending the link to your paper. I apologize that I have not read it yet (I often don't have time to stay on top of this list, so I missed your earlier reference to it), but I will. Just be aware that while my contributions to this thread are not in published/peer-reviewd form, they are nevertheless the result of more than two decades of dealing with biodiversity datasets, and very careful thinking and reasoning (i.e., as much as it may seem otherwise, these are much more than spur-of-the-momnent rants).
Aloha, Rich
-----Original Message----- From: tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Steve Baskauf Sent: Tuesday, October 12, 2010 6:37 AM To: joel sachs Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com Subject: Re: [tdwg-content] What I learned at the TechnoBioBlitz
This conversation about values for basisOfRecord, establishmentMeans, and the nature of what actually constitutes a dwc:Occurrence is very important. We have sitting on the table before us several official requests for additions and modifications to Darwin Core: http://code.google.com/p/darwincore/issues/detail?id=68 http://code.google.com/p/darwincore/issues/detail?id=69 http://code.google.com/p/darwincore/issues/detail?id=80 and http://code.google.com/p/darwincore/issues/detail?id=81 that cannot and should not be decided until this discussion occurs. In particular, a discussion of what exactly a dwc:Occurrence is lies at the heart of much of what we are discussing in this thread and is critical to other processes that are moving forward, such as guidelines for how we represent things in RDF. On this list I requested discussion on this suite of topics when I proposed the Darwin Core modifications, and I requested to members of the TAG that this discussion happen at the TDWG meeting. It didn't happen either place, so I'm glad it's happening here now.
Roger has correctly noted that we colloquially talk about Occurrences in two ways that are fundamentally different. We use Occurrence (1) to mean that a species occurs generically at a particular locality (the "checklist" use), and (2) we talk about particular instances of particular individual organisms being noticed at a particular place at a particular time. Based on the clarification that John Wieczorek gave in the thread that surrounds http://lists.tdwg.org/pipermail/tdwg-content/2009-October/000280.html, an Occurrence record simply asserts that an organism was someplace at a certain time (and doesn't imply any fitness of use such as for documenting distributions). This is consistent with meaning (2). I think that the "checklist" use (meaning 1) really should be called something else because it is conceptually something very different.
Assuming that when we talk about a dwc:Occurrence we intend meaning (2), it is important to clarify what aspect of an organism occurring somewhere at some time we intend for dwc:Occurrence to mean. When people talk about Occurrences, the conversation often goes awry because people are considering an Occurrence to include more or fewer conceptual entities. I don't know if images can be embedded in messages sent to the list, so look at this image: http://bioimages.vanderbilt.edu/pages/resource-diagram.gif before reading further. In that diagram, I'm trying to be as generic as possible. I think it is the intention of both TDWG and GBIF to go beyond thinking that Occurrences can only be specimens. So consider that this generic Occurrence could be a PreservedSpecimen, but could also be an image of an organism, DNA sample, or any other token of the presence of the Organism at a particular time and place (or a HumanObservation that has no token at all). I have heard people say that an Occurrence is a dctype:Event. That recognizes the arrow on the left side of the diagram which represents the time and place of the Occurrence. I have heard people say that if we photograph an organism, that is an "observation" with associated media. That recognizes the collected metadata (i.e. the "observation") part and the representation of the organism part (the photograph). When we talk about a PreservedSpecimen being an Occurrence, we probably intend the metadata as well as the physical thing in a jar or glued to a sheet of paper (the representation of the organism) and may or may not include the arrow on the left. I have taken the position that an Occurrence includes all of the components shown in the diagram. I'm not saying that this is the correct or only view on this subject, but if somebody intends for an Occurrence to mean something else, then they need to be clear about which component(s) of the diagram they are talking about.
Being conceptually clear about these things is important because that clarity informs the decision-making process about the pending issues that I mentioned, such as whether DigitalStillImage should be added as a DwC type (and hence have a URI and be an accepted value for dwc:basisOfRecord) and how we should structure RDF when we try to describe the properties of an Occurrence. If by "basisOfRecord" we mean a representation or token on which the Occurrence is based (or lack of token in the case of observations), then we should add as DwC types any type of physical or digital artifact that will be used by several people to document that an Occurrence existed at some point. It would not make logical sense to say that sometimes the basisOfRecord can be an artifact like a specimen, but other supporting artifacts such as digital images cannot and must be relegated to being associatedMedia.
I am not going to say more on this topic right now, partly because I have mid-semester progress reports to finish by the end of the day, but mostly because I wrote a paper discussing these issues and it lays out the conceptual framework I'm talking about better than I can in an email. I have cited that paper both in my requests for the Darwin Core changes and in previous emails to this list. However, based on the various emails that have been flying around, I don't think many people on the list have read it. That paper isn't a spur of the moment rant. I spent over a year writing it, solicited and received comments about it from a number of people including several people on the TAG, and went through the peer review process for several months before it was finally published this spring. It does not necessarily represent "the correct" view on the topics that we are discussing, but I believe that it does represent a logically consistent way of conceptualizing Occurrences and how a broad range of types of Occurrences can be described and related to other resources. If others can present clear and consistent alternatives to the framework that I've suggested, I would like to hear what they are. The article, Biodiversity Informatics 7:14-44 can be accessed at https://journals.ku.edu/index.php/jbi/article/view/3664 . In particular, take note of the discussion on p.27-28 regarding the criterion for determining whether an Occurrence documents a species' distribution, p. 28 where I discuss the difference between the use of dwc:recordedBy and dcterms:created, and p. 29 where I suggest controlled values for dwc:establishmentMeans that can be used for differentiating the extent to which an individual documented by an Occurrence occurs "naturally" at its location (native, naturalized, adventive, or cultivated - intended to apply to either plants or animals; a farm or zoo animal would be considered "cultivated"-I would be happy to define and propose these as a controlled vocabulary). These are all things that have come up in this thread. I also should note that I have been successfully applying this framework to live plant images at http://bioimages.vanderbilt.edu where I serve RDF that is consistent with the design discussed in the paper.
I would like to say more about the relationship between LivingSpecimens, Individuals, establishmentMeans, and indicating whether an Occurrence document's a species' distribution, but that will have to wait until later.
Steve Baskauf
joel sachs wrote:
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:
- 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.
- 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.
- 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].
- 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.
- 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.
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-201
0.html 5. http://tables.googlelabs.com/DataSource?dsrcid=248798
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content .
-- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences
postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A.
delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235
office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content
tdwg-content mailing list tdwg-content@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content