[Taxacom] Open, Free (was: The economics of biodiversity database initiatives)

Mon Oct 28 17:09:18 CDT 2013

"Free" is also rather oxymoronic in this context, with databases paid for out of public money. It is not so much free as "no choice but to pay"!

________________________________
From: "Tony.Rees at csiro.au" <Tony.Rees at csiro.au>
To: david.j.patterson at asu.edu 
Cc: taxacom at mailman.nhm.ku.edu 
Sent: Tuesday, 29 October 2013 10:59 AM
Subject: [Taxacom] Open, Free (was: The economics of biodiversity database initiatives)

Hi Paddy,

"Open, Free"... dangerous words round these parts...

E.g. "No derivatives" on The Plant List (www.theplantlist.org), also now on the newest version of PaleoDB at www.paleobiodb.org ...

Cheers - Tony

Dr Tony Rees 
Manager | Divisional Data Centre
Marine and Atmospheric Research
CSIRO
E Tony Rees at csiro.au T +61 3 6232 5318
CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, TAS 7001, Australia
www.cmar.csiro.au/datacentre
Manager, OBIS Australia regional Node, http://www.obis.au/
LinkedIn profile: http://www.linkedin.com/pub/tony-rees/18/770/36

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of David Patterson
> Sent: Tuesday, 29 October 2013 8:14 AM
> To: Rafaël Govaerts
> Cc: Taxacom; Paul Kirk
> Subject: Re: [Taxacom] The economics of biodiversity database
> initiatives
> 
> Good to see that it is there.  Sad that I cannot gain access to a
> quality
> image.
> 
> I agree with Alastair on the value of these initiatives, and cannot for
> the
> life of me see any reasonable justification for the 'nay-saying'.  The
> reasons why many biodiversity initiatives don't match up to GenBank
> lies
> partly in the timely origins of GenBank alongside molecular
> technologies,
> whereas the transformation of biodiversity studies to digital has been
> distributed across space and time, hence the heterogeneity.  And the
> information was never conceived as moving into an open and public
> environment, hence the variation in quality.  But if we take collective
> responsibility for gaps and errors and applause, and only if providers
> adopt appropriate annotation technologies, we will have a process for
> continuous quality improvement.
> 
> Federation, Integration, Annotation, Open, Free.
> 
> David Patterson
> 
> 
> 
> 
> On Mon, Oct 28, 2013 at 10:32 PM, Rafaël Govaerts
> <R.Govaerts at kew.org>wrote:
> 
> > Paul, That was merely illustrative. Try a real example like Palmer
> 1070
> > on JSTOR plants http://plants.jstor.org/
> >
> > Rafaël
> >
> > -----Original Message-----
> > From: Paul Kirk
> > Sent: 28 October 2013 11:23
> > To: Rafaël Govaerts; 'Roderic Page'; Taxacom
> > Subject: RE: [Taxacom] The economics of biodiversity database
> initiatives
> >
> > Just tried to find 'Smith 3672' on Jstor ... didn't find it - what
> did I
> > do wrong?
> >
> > Paul
> >
> > ________________________________________
> > From: taxacom-bounces at mailman.nhm.ku.edu [
> > taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Rafaël Govaerts [
> > R.Govaerts at kew.org]
> > Sent: 28 October 2013 11:08
> > To: 'Roderic Page'; Taxacom
> > Subject: Re: [Taxacom] The economics of biodiversity database
> initiatives
> >
> > Dear Rod,
> > The difference is that GenBank provides real objects, namely the
> sequence
> > while GBIF only provides an interpretation of an underlying real
> object
> > (the specimen or observed organism). If images of the specimen or
> observed
> > organism were attached to each record the data would become of real
> use.
> > With types there has been a lot of effort towards that as everyone
> > realised that knowing the type is Smith 3672 is of little use, you
> need an
> > image as now provided by Jstor for many taxa.
> > Rafaël
> >
> >
> > -----Original Message-----
> > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
> > taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
> > Sent: 28 October 2013 10:52
> > To: Taxacom
> > Subject: Re: [Taxacom] The economics of biodiversity database
> initiatives
> >
> > Unusually, perhaps, I find myself agreeing with Stephen, at least as
> far
> > as "understanding/making sense of what is going on".
> >
> > I think there are some tensions in the biodiversity world, perhaps
> because
> > many of the people providing data (either directly or indirectly) are
> not
> > the targeted users of the aggregated data. Many taxonomy databases
> aren't
> > really for taxonomists, they are intended for other people to use
> (e.g.,
> > people doing large-scale biodiversity studies).
> >
> > Databases don't appear to offer much offer in return in terms of
> helping a
> > taxonomist do their own research. The claimed benefits are often
> rather
> > abstract, rather than tangible things that help taxonomic research.
> In
> > particular, databases rarely offer serendipity, the ability to
> discover
> > things that a specialist didn't already know. If a database doesn't
> tell
> > you anything new, there's really not a lot of point (from an
> individual's
> > perspective).
> >
> > Compare this, say, to GenBank. If you work with DNA sequences,
> GenBank is
> > integral to your research. You may find sequences there for your
> organisms
> > that you had no idea existed (e.g., they might be collected for an
> entirely
> > unrelated study in a different discipline). You can discover new
> > information, partly because almost all genomic data goes there, and
> partly
> > because it is easily computable. As an illustration, the phylogenies
> in
> > BioNames (obtained from http://phylota.net/) such as
> > http://bionames.org/trees/phylota/ti106220_cl0_db184are built on
> > sequences from a range of taxonomic, systematic, ecological, and
> > coevolutionary studies. Not only is the tree a synthesis of data from
> > different sources, but if you look at the papers contributing those
> > sequences you have a way into a diverse literature about those
> organisms
> > (as an aside, I suspect GenBank may become the single most important
> > biodiversity database we have, but that's another story).
> >
> > So, one challenge might be to figure out how aggregators can provide
> > tangible value to those providing the data.
> >
> > Regards
> >
> > Rod
> >
> > ---------------------------------------------------------
> > Roderic Page
> > Professor of Taxonomy
> > Institute of Biodiversity, Animal Health and Comparative Medicine
> College
> > of Medical, Veterinary and Life Sciences Graham Kerr Building
> University of
> > Glasgow Glasgow G12 8QQ, UK
> >
> > Email:          r.page at bio.gla.ac.uk
> > Tel:                    +44 141 330 4778
> > Fax:            +44 141 330 2792
> > Skype:          rdmpage
> > Facebook:      http://www.facebook.com/rdmpage
> > LinkedIn:      http://uk.linkedin.com/in/rdmpage
> > Twitter:                http://twitter.com/rdmpage
> > Blog:          http://iphylo.blogspot.com/
> > Home page:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> > Wikipedia:      http://en.wikipedia.org/wiki/Roderic_D._M._Page
> > Citations:
> > http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> > ORCID:          http://orcid.org/0000-0002-7101-9767
> >
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> 
> 
> --
> 
> David J Patterson
> 
> Research Professor, School of Life Sciences, Arizona State University
> Professor (MBL) Brown University, Providence, Rhode Island
> Emeritus Professor, School of Biological Sciences, University of
> Sydney,
> Australia 

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Celebrating 26 years of Taxacom in 2013.