[Taxacom] Chameleons, GBIF, and the Red List

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Sun Aug 24 17:30:53 CDT 2014

And worse, GBIF pretends to be providing data for *all species*, but the only data it has for most (95+%) of all species is a name!


On Mon, 25/8/14, Michael Heads <m.j.heads at gmail.com> wrote:

 Subject: Re: [Taxacom] Chameleons, GBIF, and the Red List
 To: "Richard Pyle" <deepreef at bishopmuseum.org>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Monday, 25 August, 2014, 10:26 AM
 Richard wrote:
 As Donat has already
 explained, we're not talking about "GBIF
 data", we're
 talking about data
 managed by hundreds (thousands?) of institutions in
 thousands of databases around the planet. 
 GBIF is doing us the
 (tremendously valuable)
 service of aggregating those data in on place, to
 make it incredibly easy for us to locate it.
 But it's not getting any
 data from many of the most important collections
 in US, UK etc. or any from the largest country
 in the world, the one with
 the largest
 expanse of forest etc. That data (in the collections of
 etc) is incorporated in works such as
 'Birds of Russia" and from there into
 sites such as IUCN, but it's not in GBIF.
 So GBIF is not really a *global*
 biodiversity information facility - in practice
 it doesn't supply reliable
 on global distributions, even in the best-known groups. IUCN
 much more useful.
 On Mon, Aug 25, 2014 at 10:05
 AM, Richard Pyle <deepreef at bishopmuseum.org>
 > What you
 describe is EXACTLY what GBIF and others in the
 > informatics world are
 hoping to achieve.
 My previous post (reply to Stephen) covered these parts of
 the process:
 > 1) Data exist in thousands
 of databases around the world
 > 2)
 Aggregators like GBIF make our lives MUCH easier in helping
 us to
 > discover those data
 > 3) We, the experts of the world, spend
 hours "cleaning" data after GBIF
 > has so helpfully allowed us to locate
 > What
 you're talking about is the next step:
 > 4) After we, the
 experts of the world, have spent hours "cleaning"
 > data, how do we allow those efforts
 to propagate back to the sources, so
 that the NEXT person who encounters those records through
 GBIF can benefit
 > from the toils of us
 > There are
 two basic roadblocks to achieving this final step.
 > First, as has been
 made ABUNDANTLY clear in this thread, the data do NOT
 > belong to GBIF.  They belong to the
 hundreds (thousands?) of institutions
 around the world that manage those thousands of databases. 
 > those corrections have to
 find their way back to the source databases, so
 > that GBIF can re-index them with the
 corrections included.  And believe me,
 GBIF and others have tried to do this EXTENSIVELY -- for
 many years.  A lot
 > of the mechanisms
 are being developed (e.g., FilteredPush), but so far
 > there has been slow adoption of those
 mechanisms by the thousands of source
 databases.  There are many reasons for this, but I suspect
 the main reason
 > is that institutions
 are barely keeping up day-to-day activities with
 > ever-shrinking budgets, and simply do not
 have time or IT expertise to
 > implement
 the corrections to the datasets that they manage. Thus,
 > the source data remain
 "unclean", the aggregated data in GBIF remains
 > unclean.
 > The second major roadblock is the lack of
 "proper" identifiers (globally
 > unique, persistent, actionable) for these
 occurrence records.  The only way
 > that
 corrections that you make in your downloaded copy of GBIF
 data is if
 > you can report back on
 exactly which records need cleaning (along with the
 > corrected information).  GBIF does assign
 its own locally unique identifier
 (integer), which could be used for this purpose -- but only
 for piping the
 > data back to GBIF. 
 GBIF can relay the corrections back to the source
 > databases, but that will only be helpful
 to the rest of us if the source
 incorporates the fixes.
 > There is actually a third roadblock, which
 has the potential to become a
 > major
 roadblock, but we haven't bumped into it yet so much
 because we still
 > can't get past the
 first two roadblocks. And that is, institutions will not
 > automatically assume that every
 "correction" that is sent to them is
 > actually "correct".  Managers
 of those data will in almost all cases want
 > to review the changes to ensure that they
 are appropriate for updating in
 > the
 source database. And this process, of course, requires time
 > resources that most institutions
 simply do not have.
 > There may be another solution, however,
 which is for GBIF to cache
 > corrections
 submitted by people like you and other experts, such that
 > annotations/corrections can be
 made visible to all users of GBIF data; not
 > just the source datasets.  Perhaps this
 feature already exists.  Perhaps
 > the
 politics of implementing such a feature are too daunting to
 > But the
 bottom line is that we really do need to address this fourth
 > so that we can more effectively
 benefit from the work of others, and
 (conversely), so that our own efforts will benefit more than
 just ourselves.
 > Rich
 > > -----Original
 > > From: Taxacom
 [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf
 > > Of Bob Mesibov
 > > Sent: Sunday, August 24, 2014 11:28
 > > To: Donat Agosti
 > > Cc: TAXACOM; quentin groom
 > > Subject: Re: [Taxacom] Chameleons,
 GBIF, and the Red List
 > >
 > > Donat Agosti wrote:
 > >
 > > "I
 feel, the discussion is too much centered on data that has
 not the
 > > information content
 needed, like studying a Landsat image at 30 meter
 > > resolution and discussing what tree
 species is shown"
 > >
 > > Excellent metaphor! For most
 scientific uses, you need much more data
 > than
 > > is provided
 by any available database. Can you get everything you
 > > online? No. Do existing
 aggregators like GBIF offer a helpful starting
 > point?
 > > For some
 people and some uses, yes.
 > >
 > > But now the important question: when
 you have all the information you
 > >
 need, and clean it and enrich it, do you publish it online
 in a usable
 > form? I
 > > don't know what Quentin
 Groom's project was about, nor do I know if he
 > > published his final data.
 > >
 > > In my own
 case, every one of my 12123 locality records for
 > > Millipedes is freely
 available in CSV format (and in abbreviated form in
 > KML)
 > > from the
 'Millipedes of Australia' website. This store is
 larger and
 > more up to
 > > date and contains fewer errors than
 any aggregator store, or even, the
 > >
 combined data providers' stores (because certain
 providers have been slow
 > > to add my
 edits to particular records, or to upload them to their own
 > > aggregator stores).
 > >
 > > But if
 people like me and Quentin publish data freely to the Web
 > > aggregators don't use this
 improved/extended data, aggregation looks less
 > > and less useful.
 > --
 > > Dr Robert Mesibov
 > > Honorary Research Associate
 > > Queen Victoria Museum and Art
 Gallery, and School of Land and Food,
 > University of Tasmania Home contact:
 > > PO Box 101, Penguin, Tasmania,
 Australia 7316
 > > (03) 64371195; 61 3
 > >
 > > Taxacom Mailing List
 > > Taxacom at mailman.nhm.ku.edu
 > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 > > The Taxacom Archive back to 1992 may
 be searched at:
 > > http://taxacom.markmail.org
 > >
 > > Celebrating
 27 years of Taxacom in 2014.
 > Taxacom Mailing List
 Taxacom at mailman.nhm.ku.edu
 > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
 > The Taxacom Archive back to 1992 may be
 searched at:
 > http://taxacom.markmail.org
 > Celebrating 27 years
 of Taxacom in 2014.
 Dunedin, New Zealand.
 My recent books:
 *Molecular panbiogeography of the tropics.*
 2012. University of California
 Berkeley. www.ucpress.edu/book.php?isbn=9780520271968
 *Biogeography of
 Australasia:  A molecular analysis*. 2014. Cambridge
 University Press, Cambridge.
 Taxacom Mailing List
 Taxacom at mailman.nhm.ku.edu
 The Taxacom Archive back to 1992 may be
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 Celebrating 27 years of
 Taxacom in 2014.

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