[tdwg-content] "Wrong" RDF, was Re: What I learned at the TechnoBioBlitz
Steve Baskauf
steve.baskauf at vanderbilt.edu
Thu Oct 14 04:07:52 CEST 2010
I was just ready to leave work when I wrote this and since then I'm
feeling like I should clarify just what I mean by "wrong" ways of using
RDF. I recognize that TDWG encourages flexibility in the ways that
standards such as DwC are used. As such, it doesn't usually define
"right" and "wrong" ways of using the standards. What I mean by calling
some uses "wrong" is not intended to discourage the creative use of DwC
terms in RDF. What I mean is that one must be careful to make sure that
RDF statements mean what is intended. Here is an example. The Dublin
Core term dcterms:language means "the language of the resource". On
multiple occasions, I've seen this term used in RDF as a property of a
resource whose metadata is written in a certain language. This is
"wrong" because the subject of the statement is the resource itself, not
the resource's metadata. The need for this kind of clarity is apparent
in the case of media. For example, if we are providing metadata in
English that describes a nature film which has audio in German, the
correct statement is that [film] dcterms:language "de", NOT [film]
dcterms:language "en". This problem is handled appropriately in the
MRTG schema by creating the (required) term mrtg:metadataLanguage. The
correct statement would be [film] mrtg:metadataLanguage "en" . (I'm
using "[film]" in lieu of a URI identifier for the film.) If, however,
we were writing RDF to describe the metadata itself rather than the
film, then it would be appropriate to say [film's metadata]
dcterms:language "en" . In straight XML, we might get away with
semantic sloppiness if the senders and receivers of the XML "understand"
what the intended subject is of the term dcterms:language. But in RDF,
we have to assume that the receiver of the RDF is a "stupid" computer
which only infers exactly what is said and not what we MEANT to say.
I believe that this is a very important point that all parties need to
keep in mind before we happily march off creating RDF templates for the
general public to use. In particular, I have some serious problems with
the way that people are associating properties with instances of the
dwc:Occurrence class. I believe that these "wrong" ways originate with
the historical roots of Darwin Core as a means to describe specimens. I
will illustrate what I mean. In many cases, a specimen is created by
killing an organism and gluing it to a piece of paper (if it's a plant)
or putting it in a jar (if it's an animal). It is natural to ask the
question "what kind of species is the specimen?". We can look at the
specimen and make a statement like [specimen] dwc:scientificName
"Drosophila melanogaster" and it pretty much makes sense. However, in
the new Darwin Core standard, we have a broader category of "things"
(a.k.a. resources) that we call Occurrences which include specimens but
which also includes observations and probably all kinds of things like
images, DNA samples, and a whole lot of other things. If we try to
apply the same kind of statement to other kinds of Occurrences besides
specimens we immediately run into problems. If we say that [digital
image] dwc:scientificName "Drosophila melanogaster" we are making a
nonsensical statement. The digital image can have properties like its
photographer, its format, its pixel dimensions, etc. but the image
itself does not have a scientific name. The scientific name is a
property of the thing that was photographed. It makes even less sense
if we are talking about observations. An observation is a situation
where somebody observes an organism. The observation can have
properties like the observer, the location, etc. However, if we say
[observation] dwc:scientificName "Drosophila melanogaster" we are saying
that that act of observing has a scientific name. That is an incorrect
statement. So the general statement [Occurrence] dwc:scientificName
"Drosophila melanogaster" does not make sense when applied to all
possible types of Occurrences. Rather, the organism that we are
observing is the thing that has a scientific name.
In all of the examples above, the correct statement is [individual
organism] dwc:scientificName "Drosophila melanogaster". The specimen is
an occurrence of the individual organism. The image is an occurrence of
the individual organism. The observation is an occurrence of the
individual organism. These statements may seem odd because we are used
to thinking of an Occurrence being an occurrence of the "species" but
it's not really. The image is not an image of the Drosophila species
concept nor is it an image of the string "Drosophila melanogaster". The
image is an image of an individual fruit fly. The individual fruit fly
is a representative of the taxon, the image and the observation are not.
This point becomes more clear if we look at a situation where several
types of occurrence records are collected from the same individual.
Let's say that we capture a bird, photograph it, collect a feather from
it, collect a DNA sample and band it and let it go. Later somebody sees
the band and reports that as an observation. How do we connect all of
these things? Do we create an identifier for the specimen (the feather)
and then say that the image and the DNA sample came from it? That would
be wrong. We could take an image of the feather, but that would be a
different thing from an image of the bird. We didn't get the DNA sample
from the feather, we got it via a blood sample from the bird. The band
observation is not an observation of the feather, or the image or the
DNA sample. It's an observation of the bird which was never any kind of
specimen living or dead. The bird is an individual organism and that's
what we need to call it. Right now we don't have anything in Darwin
Core that can be used to rdfs:type the bird, which is why I proposed
Individual as a Darwin Core class.
I could say these things more clearly in RDF, but since because many
members of the audience of this message aren't familiar with RDF/XML
they would probably zone out and the point would be lost. The point is
that we need to have identifiable classes of "resources" (the technical
name for "things" like physical artifacts, concepts, and electronic
representations) for all of the things that that we need to describe and
inter-relate in the Darwin Core world. Right now, we are missing one of
the important pieces that we need, which is a class for the Individual.
If we are satisfied with creating an RDF model that only works for
specimens and one-time observations, then we probably don't need
Individual as a Darwin Core class. On the other hand, if TDWG and GBIF
are really serious about creating a system (Darwin Core and RDF based on
it) that can handle other types of Occurrences like multiple images of
live organisms, observations of the same organism over time, and
multiple types of Occurrences collected from the same organism, then
this capability should be built into the system from the start. When I
got back from the TDWG meeting, I was all excited about trying to use
Darwin Core Archives with my live plant image collection. However, it
quickly became evident that it could not work because Occurrences were
at the center of the diagram rather than Individuals. So unless
something changes, we are already embarking on the process of locking
out these other Occurrence types.
I hate to sound like a broken record (do we have those any more?), but
read my paper on this subject. It explains the rationale better than
this email, has nice diagrams, and gives RDF examples to illustrate
everything (https://journals.ku.edu/index.php/jbi/article/view/3664).
If somebody has a better idea of how to develop an internally consistent
system that can handle the problems I've raised here that DOESN'T
involve Individuals (i.e. other "right"[=semantically accurate] ways to
express properties and relationships among Identifications, Taxa,
diverse types of Occurrences, etc.) I'd like to hear what it is. Or
perhaps as Stan has suggested, there needs to be a task group that can
hash out alternative views. But let's have the discussion before we
post models and suggest people use them.
Steve
Steve Baskauf wrote:
> 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
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> tdwg-content mailing list
>> >>> tdwg-content at lists.tdwg.org
>> >>>
>> >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>> >>>
>> >>> _______________________________________________
>> >>> tdwg-content mailing list
>> >>> tdwg-content at lists.tdwg.org
>> >>>
>> >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ________________________________
>> >>>
>> >>> Please consider the environment before
>> printing this email
>> >>> Warning: This electronic message together
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>> >>> you must not read, use, disclose, copy or retain
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>> >>> The views expressed in this email may not
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>> >>> http://www.landcareresearch.co.nz
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>> >>
>> >> _______________________________________________
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>>
>>
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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
>
--
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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