[tdwg-content] What I learned at the TechnoBioBlitz
David Remsen (GBIF)
dremsen at gbif.org
Tue Oct 12 07:20:15 CEST 2010
Our approach within the DarwinCore Archive context has been to add
dwc:establishmentMeans to the Distribution extension (see http://rs.gbif.org/extension/gbif/1.0/distribution.xml)
that would support the publishing of specific and multiple
geospatial areas with distinct establishmentMean values. This would
makes sense primarily where the basis of record is a taxon and not an
occurrence. The term "Nativeness" as a label for the vocabulary is
arbitrary in the sense that there is no specific linkage to the
dwc:establishmentMeans concept. But we could reference it
specifically in an extensions definition as a recommended vocabulary
for use with that concept.
Best, David
On Oct 12, 2010, at 1:41 PM, Richard Pyle wrote:
>
> 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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