[Taxacom] The economics of biodiversity database initiatives

[David Campbell]

GenBank is an extremely valuable resource, yet it also has its weaknesses.
Not to pick on it, but rather to hopefully promote improvement and to think
about how to address similar problems in other databases

They do have some taxonomic staff, but not enough to thoroughly check up on
all the data.  Yes, there are many points where classification is not
agreed upon, but there are also several points of general agreement.  It's
not helpful when the same species is listed under several different names.

More prominent and more medically-related publications are generally
followed by GenBank, but more obscure (e.g., a lot of taxonomic journals
and perhaps most publications not in the Latin alphabet) are often missed.
"Unpublished" means "hunt and see if it is available".

The chain of command for correcting an error is often unclear.
Particularly in the case of misidentification, there is reluctance to make
a correction without the author confirming it.  It's good not to
immediately accept all submitted "corrections", either, but sequences that
place with the wrong phylum are fairly definitely in need of correction.

Data retrieval could be more flexible.  It is not fully possible to pick
and choose which data fields you want, for example - you have to take one
of the standard formats.


On Mon, Oct 28, 2013 at 7:08 AM, Rafaël Govaerts <R.Govaerts at kew.org> wrote:

> 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_db184 are 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
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> Home page:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia:      http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations:
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> ORCID:          http://orcid.org/0000-0002-7101-9767
>
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-- 
Dr. David Campbell
Assistant Professor, Geology
Department of Natural Sciences
Gardner-Webb University
Boiling Springs NC 28017