[Taxacom] Global biodiversity databases

[Roderic Page]

Hi Paul,

On 8 Aug 2012, at 07:44, Paul Kirk wrote:

> NCBI doesn't aggregate scientific literature - it's certainly discoverable at NCBI via the abstract - but only those in 'ivory towers' have full access to the article in the distributed system of primary publishers. Not sure what to make of 'unified taxonomic classification' but I'll pass on that one.

NCBI aggregates the literature in that it provides consistent identifiers for articles (PubMed ids), and in many cases provides links to full text (in some cases the text is open access, e.g. those articles archived in PubMed Central).

By "unified taxonomic classification" I mean NCBI has one classification around which it organises all the data. in contrast, each taxonomic classification tends to have it's own classification, so users have to translate classifications between databases.

I guess my point is that all the data is available in one place, is internally consistent, can be freely downloaded and repurposed, and the identifiers NCBI uses are the de facto identifiers for numerous other projects (e.g., accession numbers in the literature, NCBI taxon ids in derived databases, PubMed identifiers in bibliographic software such as Mendeley). I'd argue that genomics has benefited greatly from such a centralised resource.

Regards

Rod


> 
> Just my two penn'orth ...
> 
> Paul
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Roderic Page [r.page at bio.gla.ac.uk]
> Sent: 08 August 2012 07:34
> To: TAXACOM
> Subject: Re: [Taxacom] Global biodiversity databases
> 
> 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
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> 
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---------------------------------------------------------
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