[tdwg-content] What I learned at the TechnoBioBlitz
Steve Baskauf
steve.baskauf at vanderbilt.edu
Wed Oct 13 22:06:57 CEST 2010
Stan,
Thanks for the clarification. My concern here is that standard or not,
if examples are posted on the Google Darwin Code site, they will have an
implied "stamp of approval" and will be used by others as a template
(despite that site being labeled as "for discussion and development" not
everyone can post to it and that implies some authority). In the case
of straight XML, that isn't really that big of an issue. XML can mean
whatever one wants as long as there is an agreement between the sender
and the receiver (perhaps in the form of a formal XML schema) as to what
the elements represent. I believe that RDF is a different beast. When
one exposes RDF, the receiver is unknown. Therefore, the RDF has to
actually "mean" something to the receiver without a pre-arranged
agreement. In a generic XML document, the elements can simply be a list
of string values of terms with no implied "meaning" except what might be
inferred by grouping them in a container element. In RDF, the elements
represent properties of particular resources. I believe strongly that
although there may be several "right" ways to express properties of
members of DwC classes, there are many more "wrong" ways that should not
be used. By "right" I mean that they make sense semantically in that
the properties logically are ones that should actually belong to the
described resource. I do not believe that the discussion of these
issues has progressed to the point where there is a consensus on the
"right" use of DwC terms for some types of resources and therefore I am
opposed to the posting of RDF examples on any official Darwin Core sites
without a lot more discussion UNLESS the examples are clearly labeled as
examples intended for discussion and not for use as templates. If you
want such examples, I can provide
http://bioimages.vanderbilt.edu/vanderbilt/4-145.rdf as an example for
an Individual
http://bioimages.vanderbilt.edu/baskauf/79695.rdf as am example of an
Occurrence that is a live plant image and
http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0138.rdf as an
example of an Occurrence that is an herbarium specimen
I would be happy to discuss the reasons why I structured the RDF as I
did (although mostly those examples are already rationalized in
https://journals.ku.edu/index.php/jbi/article/view/3664), but I would
not go so far as to say that they are "right" without some discussion.
What I intended when I suggested that I might write some kind of guide
for Darwin Core represented in RDF/XML was really a document that
explained to beginners what the point was of RDF, the basics of how one
can structure properties in RDF using examples that are Darwin Core
terms, and options for creating URIs that refer to resources that are
described in separate files or within the same file. I wasn't really
suggesting that it be a full-blown recommendation with specific
guidelines for the use of particular terms or structuring of files for
particular classes of resources, although that would be a good thing
ultimately. I guess I was seeing some kind of a beginner's guide as a
way to involve more people (who aren't up on RDF) in the discussion. I
don't think that it should be necessary to complete full "standards"
process before such a document were made available. It would probably
be better to have some kind of road map where that document would be the
first segment but would later be followed by guidelines for specific
classes of resources with examples. I think that such a modular
approach would be the most beneficial because pieces of it could
actually get done in a timely fashion rather than requiring the whole
thing to be complete before any of it would be accepted.
I do think a task group for Darwin Core RDF would be a good idea. If
nobody is in a huge hurry, I don't mind trying to charter such a group,
although I'd be just as happy if somebody else wanted to do it and I
would just try be an active participant. I will look at the links you
suggested, thanks.
Steve
Blum, Stan wrote:
> Steve,
>
> The TDWG process for creating standards is here:
> http://www.tdwg.org/about-tdwg/process/ This is worth reading if
> you haven’t done so already.
>
> Another document worth reading is the standards format specifiation
> http://www.tdwg.org/standards/147/ I never pushed this “standard”
> through public review, but it still functions a guideline for
> formatting and our view of what is isn’t within scope of a “standard”.
> In other words, we are doing our best to follow the basic ideas laid
> out there about the kinds of specifications:
>
> Type 1 -- normative specification, versioned;
> Type 2 -- versioned, supplementary documentation;
> Type 3 — uncontrolled supplementary documentation.
>
> The page of examples John and others have put up on the DarwinCore
> site is non-normative, uncontrolled documentation.
>
> The thing you were proposing sounded like an applicability statement —
> offering guidance about how another standard, RDF, should be used in
> biodiversity informatics. These can also be treated as standards, and
> get TDWG ratification as standard, but don’t create a de-novo standard.
>
> Interest groups and task groups are explained in the Process. If you
> want to create an applicability statement for RDF and DarwinCore, you
> could prepare a task group charter and submit it to the executive for
> approval. Approval would make it a formal Task Group. See other task
> group charters for examples.
>
> -Stan
>
>
>
>
> On 10/13/10 6:33 AM, "Steve Baskauf" <steve.baskauf at vanderbilt.edu> wrote:
>
> OK, because of a momentary heavy work load I'm still in the
> process of getting caught up on this thread, but this is moving so
> fast I feel like I'm being left in the dust. Last week I offered
> to help facilitate creating some guidelines and examples for
> RDF/XML in Darwin Core. I was told that we should follow the
> community process of forming an interest group, getting
> participants, etc. and have been waiting for some guidelines on
> how that process is supposed to work. Now we are surging ahead
> with examples and help pages again. Are we following a process or
> not and if so, what is it?
> Steve
>
> Tim Robertson (GBIF) wrote:
>
> I will also help with examples. If we are doing XML / RDF
> formats, lets get an example record conforming to the Text
> guidelines in there as well for completeness (most useful when
> dealing with checklists).
>
>
>
>
>
> On Oct 12, 2010, at 10:31 PM, John Wieczorek wrote:
>
>
>
> I am interested in helping with an examples page. The page
> could have XML and RDF examples illustrating particular
> use cases, as you have recommended. Create an "Examples"
> page on the Table of Contents and then have all of the
> examples on one page with an index of links to specific
> examples at the top? I made a straw man page to show what
> I am thinking at
> http://code.google.com/p/darwincore/wiki/Examples.
>
>
> On Tue, Oct 12, 2010 at 11:41 AM, "Markus Döring (GBIF)"
> <mdoering at gbif.org> wrote:
>
>
> 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 at lists.tdwg.org
> [tdwg-content-bounces at lists.tdwg.org] On Behalf Of
> Richard Pyle [deepreef at bishopmuseum.org]
> >> Sent: Tuesday, 12 October 2010 5:41 p.m.
> >> To: Jerry Cooper; tdwg-content at lists.tdwg.org;
> tdwg-bioblitz at 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 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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> >>>
> >>>
> >>>
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--
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
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