[Taxacom] Global biodiversity databases

Tue Aug 7 16:25:01 CDT 2012

My expectation is as Rich's, that knowledge will be distributed among a big
array of hopefully fully open sources.  This applies as much to taxonomies
as to anything else.  Biology is too 'soft', requires too much
interpretation, and is too dynamic to be packaged into a single
world-view.  We need to look beyond the convenience of arbitrary rules. And
where do such arbitrary rules let us down, Tony asks?  Perhaps we might
look at reasons why IRMNG appeared, and why there are a myriad of
taxonomies and phylogenies out there on the web.

1. Not exposing the alternative views as to the concepts for species
2. Not exposing the alternative views as to the relationships among species
3. Not able to express the insights that emerge from new analyses
4. Inconsistent application of  nomenclatural standards
5. Lack of consistent principles underpinning systems
6. Arbitrary cutoffs between extant and extinct
7. Incomplete coverage - despite the information being out there
8. Data not open and freely available
9. Questionable authoritativeness
10. Economics
11. etc.

The task is not to think of a master system as an end point, but as part of
what we might hope to become a very dynamic process in which we can draw
the parts together and display them in a myriad of views.  We can get there
if we focus on the process, rather than on the products.

David Patterson

On Tue, Aug 7, 2012 at 4:41 PM, <Tony.Rees at csiro.au> wrote:

> Dear Rich, Rob, all,
>
> quoting Rob:
> > We've been working on a project
> > called Map of Life (http://mappinglife.org), that is meant to aggregate
> not
> > just point occurrence records but also range maps, area inventories,
> > ecoregion checklists, etc. globally and for all taxa.
>
> Along similar lines are a range of other data integration/mapping projects
> such as GBIF, OBIS, EOL, AquaMaps, LifeMapper, UK National Biodiversity
> Network, Atlas of Living Australia...
>
> However I see these more as clients of the system that is being discussed
> than creators of it; and maybe I have clouded the waters myself by saying
> that I wish for some of these "species attributes" to be available via the
> "master biodiversity database" - I still do, so obviously clarifying the
> boundaries of "who holds what" will become important.
>
> The one thing that projects such as the above all have in common is a need
> for a "taxonomic backbone" i.e. curated master taxonomy (or taxonomies)
> such that the work of assembling one does not have to be repeated every
> time. I believe this is the "enabling" product (or service) which is at the
> heart of this thread and which currently does not exist from any single
> source. It is the space in which the Catalogue of Life aspires to operate
> once complete (hopefully including fossil as well as extant taxa). So one
> could re-cast the questions around (a) is the CoL still the best model or
> vehicle to supply such a service, (b) what are the prospects for completion
> of the CoL (and when), plus mechanisms for keeping the same updated with
> minimum latency, (c) are the data fields, present structures, and services
> presently offered by CoL adequate for user needs, or if not, why not, and
> (d) how will the CoL (or other service in this space) both benefit from,
> and contribute to developments
>   in the GN area.
>
> I say this not because of any desire to criticise the CoL, but because it
> does have a good critical mass and substantial footprint to date (some gaps
> acknowledged) and does offer a very successful model of current
> inter-database collaboration, and by its own admission aspires to be the
> global standard and data/service provider  in this area; also because if it
> did not exist, we would have to invent it (and others have already saved us
> that work).
>
> So maybe (without going into discussions of the type "I looked at the data
> for species X and it was wrong") we can look at questions such as the above
> at the more conceptual level and say, what's currently missing from the CoL
> that users need, and how do we get from where we are today to where we
> would like to be in the future.
>
> (If the answer to this is a resounding silence I will presume either that
> all present users are 100% happy, or wisely they are too polite to
> criticise another's project in a public forum such as this one).
>
> Regards - Tony
>
>
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [
> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard Pyle [
> deepreef at bishopmuseum.org]
> Sent: Wednesday, 8 August 2012 3:21 AM
> To: 'Robert Guralnick'
> Cc: 'TAXACOM'
> Subject: Re: [Taxacom] Global biodiversity databases
>
> >   Rich et al. --- I am just not comfortable with the question: "Do you
> expect a
> > comprehensive and reliable GBD to exist in the foreseeable future (or do
> you
> > think that one or more already exist)?"
>
> Neither am I.  I didn't write the questions; I only took a shot at the
> answers (something I feel like I am going to regret.....)
>
> > We've been working on a project
> > called Map of Life (http://mappinglife.org), that is meant to aggregate
> not
> > just point occurrence records but also range maps, area inventories,
> > ecoregion checklists, etc. globally and for all taxa.
>
> This is exactly the sort of effort I meant when I said that the emphasis
> should be on integration, not building more databases.
>
> >  There is no GBD.  There won't be.  Thank goodness.
>
> It depends on how you define it.  My contention is that there already is a
> GBD (with the "D" sensu lato).  We just need to be better about tying all
> the pieces together.
>
> Aloha,
> Rich
>
>
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-- 
___________________________________
David J Patterson

Senior Scientist, Marine Biological Laboratory
Life Sciences Lead, Data Conservancy
globalnames.org

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