[Taxacom] Global biodiversity databases

David Patterson dpatterson at mbl.edu
Wed Aug 8 07:26:03 CDT 2012

I think that is a very wise comment, and points to the need for BOTH
distributed and 'centralized'.  The sdeocnd word does not seem entirely
right. Pinnacle organizations like GenBank and GBIF are like keystone
species, they define the landscape.  They can only do so when they provide
outstanding (= usable) services (vide my earlier posting).  But, they are
not sole players (GenBank is one of a triumvirate, and is accompanied by
other molecular repositories such as aligned sequences databases or
environmental sequence environments).  Nor can they do everything - in the
taxonomy area we are all aware of errors in identification, the very large
number of entries without identifiers, and hierarchical systems that cause
peptic ulcers.

That is, we need to keep thinking about a matrix, and not about a pyramid.
But, not all members of the matrix are equal.

David Patterson

On Wed, Aug 8, 2012 at 2:34 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:

> Reading this thread I fear we are failing to learn from the experience of
> others. The notion that distributed systems will somehow magically provide
> the kinds of services people need seems to me to be fatally flawed. There's
> a great interview that makes this point:
> http://blogs.plos.org/mfenner/2009/02/17/interview_with_geoffrey_bilder/
> In that interview Geoffrey Bilder of CrossRef says:
> "...my personal and unfashionable observation is that “distributed” begets
> “centralized.” For every distributed service created, we’ve then had to
> create a centralized service to make it useable again (ICANN, Google,
> Pirate Bay, CrossRef, DOAJ, ticTocs, WorldCat, etc.)."
> The key phrase here is "usable". Much of the taxonomic databasing has been
> focussed on the needs of providers, not end users. Distributed may met the
> needs of providers (they get to control "their" data) but it does nothing
> for users (who have to search across multiple, often incompatible resources
> to find what they need).
> If you want further evidence, consider the success of NCBI where primary
> data (sequences), a unified taxonomic classification, and the scientific
> literature are aggregated in one place. Anybody want to argue that a
> distributed model would work better? That genomics would be better if NCBI
> didn't exist?
> I suspect the unsatisfactory state of taxonomic (and other biodiversity)
> databases will persist until we switch from trying to keep providers happy
> to trying to giving users with the data and services they need.
> 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
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
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David J Patterson

Senior Scientist, Marine Biological Laboratory
Life Sciences Lead, Data Conservancy

7 MBL Street, Woods Hole, MASS 02543, USA.

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