[tdwg-content] What I learned at the TechnoBioBlitz

Tue Oct 12 04:37:41 CEST 2010

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

[cid:image001.png at 01CB6A23.666B0380]

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

[cid:image001.png at 01CB6A23.666B0380]

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> [mailto: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<mailto:tdwg-bioblitz at googlegroups.com>; tdwg-content at lists.tdwg.org<mailto: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-data-in-2010.html
5. http://tables.googlelabs.com/DataSource?dsrcid=248798

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