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@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@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@lists.tdwg.org [tdwg-content-bounces@lists.tdwg.org] On Behalf
Of Richard Pyle [deepreef@bishopmuseum.org]
>> Sent:
Tuesday, 12 October 2010 5:41 p.m.
>> To: Jerry Cooper;
tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
>>
Subject: Re: [tdwg-content] What I learned at the
TechnoBioBlitz
>>
>> Hi
Jerry,
>>
>> Before we agree to disagree, let
me try to elaborate a bit more:
>>
>> I think
we both agree that "Nativeness" (to borrow Dave's term) is
a
>> property of a taxon at a geographic locality (it
could also be a property of
>> a taxon in a class of
habitat, but few people actually frame it this
way).
>>
>> The reason I think that
"Nativeness" is best represented as a property of an
>>
Occurrence, rather than of a taxon, is that a taxon is a
circumscribed set
>> of organisms, usually based on
evolutionary relatedness or morphological or
>> genetic
similarity. By contrast, an Occurrence is about the
presence of a
>> member or multiple members of a taxon
concept in space and time (i.e., at a
>> particular
place and time).
>>
>> We often think of
Occurrence records in terms of individual organisms
(e.g.,
>> specimens, or specific observed or
photographed organisms), and I agree,
>> it's weird to
think of "Nativeness" as it applies to an individual
organism.
>> However, my understanding is that
Occurrence instances can also apply to
>> populations
-- which is what terms such as establishmentMeans
and
>> occurrenceStatus fit into this
class.
>>
>> More generally, if we agree that
"Nativeness" is a property of a taxon at a
>>
particular locality, the way that this intersection is usually
manifest in
>> DwC is via Occurrence and Event
instances.
>>
>> How else would you represent
"Nativeness" within DwC?
>>
>>
Aloha,
>> Rich
>>
>>>
-----Original Message-----
>>> From: tdwg-content-bounces@lists.tdwg.org
>>>
[mailto:tdwg-content-bounces@lists.tdwg.org] On
Behalf Of Jerry Cooper
>>> Sent: Monday, October 11,
2010 6:02 PM
>>> To: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
>>>
Subject: Re: [tdwg-content] What I learned at the
TechnoBioBlitz
>>>
>>> We will have to
agree to disagree.
>>>
>>> For me at
least 'Native', 'Invasive' etc are clearly
not
>>> properties associated with a collection
event. They are
>>> collective statements, not
necessarily about properties of
>>> the taxon as a
whole, but about the properties of a taxon in
>>>
some restricted sense - usually geographically
restricted.
>>>
>>> GISIN, like our
model here in NZ, pulls together such
items
>>> under a triplet of taxon/occurrence
statement/geographical
>>> extent linked to a
publication.
>>>
>>>
>>>
Jerry
>>>
>>>
>>>
-----Original Message-----
>>> From: Richard Pyle
[mailto:deepreef@bishopmuseum.org]
>>>
Sent: Tuesday, 12 October 2010 4:23 p.m.
>>> To:
Jerry Cooper
>>> Cc: tdwg-content@lists.tdwg.org; tdwg-bioblitz@googlegroups.com
>>>
Subject: RE: [tdwg-content] What I learned at the
TechnoBioBlitz
>>>
>>> Hi
Jerry,
>>>
>>> Yes, this is a road I've
been down before. Intuitively,
>>> these terms
seem like they should apply to taxon concepts,
>>>
but it turns out that's not the right way to do it.
Things
>>> like "native" and "invasive" are
not properties of taxon
>>> concepts; they're the
property of an occurrence (which, I
>>> suspect, is
why establishmentMeans is included in the
>>>
Occurrence class in DwC; e.g., see the examples
at
>>> http://rs.tdwg.org/dwc/terms/index.htm#establishmentMeans
>>>
>>>
Rich
>>>
>>>
________________________________
>>>
>>>
From: tdwg-content-bounces@lists.tdwg.org
>>>
[mailto:tdwg-content-bounces@lists.tdwg.org] On
Behalf Of Jerry Cooper
>>>
Sent: Monday, October
11, 2010 4:38 PM
>>>
Cc: tdwg-content@lists.tdwg.org;
>>>
tdwg-bioblitz@googlegroups.com
>>>
Subject: Re:
[tdwg-content] What I learned at the
>>>
TechnoBioBlitz
>>>
>>>
>>>
>>>
Rich,
>>>
>>>
>>>
>>>
Let's not confuse
those terms which are best 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@lists.tdwg.org
>>>
[mailto:tdwg-content-bounces@lists.tdwg.org] On
Behalf Of Richard Pyle
>>>
Sent: Tuesday, 12
October 2010 3:27 p.m.
>>>
To: Donald.Hobern@csiro.au; tuco@berkeley.edu
>>>
Cc: tdwg-content@lists.tdwg.org;
>>>
tdwg-bioblitz@googlegroups.com
>>>
Subject: Re:
[tdwg-content] What I learned at the
>>>
TechnoBioBlitz
>>>
>>>
>>>
>>>
I certainly agree it's
important! I was just 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@csiro.au
>>> [mailto:Donald.Hobern@csiro.au]
>>>
Sent:
Monday, October 11, 2010 3:44 PM
>>>
To:
Richard Pyle; tuco@berkeley.edu
>>>
Cc:
tdwg-content@lists.tdwg.org;
>>>
tdwg-bioblitz@googlegroups.com
>>>
Subject:
RE: [tdwg-content] What I learned at
>>> the
TechnoBioBlitz
>>>
>>>
Hi
Rich.
>>>
>>>
>>>
>>>
I
recognise this (and could probably 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@csiro.au
>>> <mailto:Donald.Hobern@csiro.au>
>>>
>>>
Web:
http://www.ala.org.au/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
From:
Richard Pyle [mailto:deepreef@bishopmuseum.org]
>>>
Sent:
Tuesday, 12 October 2010 12:33 PM
>>>
To:
Hobern, Donald (CES, Black Mountain);
>>> tuco@berkeley.edu
>>>
Cc:
tdwg-content@lists.tdwg.org;
>>>
tdwg-bioblitz@googlegroups.com
>>>
Subject:
RE: [tdwg-content] What I learned at
>>> the
TechnoBioBlitz
>>>
>>>
>>>
>>>
I'm
not so sure a simple flag will do it. 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@lists.tdwg.org
>>>
[mailto:tdwg-content-bounces@lists.tdwg.org] On
Behalf Of
>>> Donald.Hobern@csiro.au
>>>
Sent:
Monday, October 11, 2010 2:59 PM
>>>
To:
tuco@berkeley.edu
>>>
Cc:
tdwg-content@lists.tdwg.org;
>>>
tdwg-bioblitz@googlegroups.com
>>>
Subject:
Re: [tdwg-content] What I
>>> learned at the
TechnoBioBlitz
>>>
>>>
Thanks,
John.
>>>
>>>
>>>
>>>
This
is useful, but 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@csiro.au
>>> <mailto:Donald.Hobern@csiro.au>
>>>
>>>
Web:
http://www.ala.org.au/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
From:
gtuco.btuco@gmail.com
>>> [mailto:gtuco.btuco@gmail.com] On Behalf Of
John Wieczorek
>>>
Sent:
Tuesday, 12 October 2010 11:34 AM
>>>
To:
Hobern, Donald (CES, Black Mountain)
>>>
Cc:
jsachs@csee.umbc.edu;
>>> tdwg-bioblitz@googlegroups.com; tdwg-content@lists.tdwg.org
>>>
Subject:
Re: [tdwg-content] What I
>>> learned at the
TechnoBioBlitz
>>>
>>>
>>>
>>>
Natural
occurrence is meant to 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@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@csiro.au
>>>
Web:
http://www.ala.org.au/
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
-----Original
Message-----
>>>
From:
tdwg-content-bounces@lists.tdwg.org
>>>
[mailto:tdwg-content-bounces@lists.tdwg.org] On
Behalf Of joel sachs
>>>
Sent:
Monday, 11 October 2010 10:47 PM
>>>
To:
tdwg-bioblitz@googlegroups.com;
>>>
tdwg-content@lists.tdwg.org
>>>
Subject:
[tdwg-content] What I
>>> learned at the
TechnoBioBlitz
>>>
>>>
One
of the goals of the 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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mailing list
>>>
tdwg-content@lists.tdwg.org
>>>
>>>
http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>>
>>>
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>>>
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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