[Taxacom] The economics of biodiversity database initiatives
Stephen Thorpe
stephen_thorpe at yahoo.co.nz
Mon Oct 28 16:42:24 CDT 2013
>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<
Back to community curation again! Wouldn't it be nice if volunteers would correct all one's mistakes, and/or add content to one's skeletal infrastructure?
From: David Patterson <david.j.patterson at asu.edu>
To: Rafaël Govaerts <R.Govaerts at kew.org>
Cc: Taxacom <taxacom at mailman.nhm.ku.edu>; Paul Kirk <P.Kirk at kew.org>
Sent: Tuesday, 29 October 2013 10:13 AM
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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