[Taxacom] Global biodiversity databases

Tue Aug 7 20:35:27 CDT 2012

Thanks, Paddy...

For anyone interested, I prepared and presented a quick status report on IRMNG and its philosophy/design principles (some of which are very pertinent to this thread) to the aforementioned GN meeting in Hawaii in March (by Skype, unfortunately!) and have just uploaded the slides to slideshare here:

http://www.slideshare.net/tony1212/irmng-presentation-march-2012

Paddy/Rich, I note a report from this meeting was a planned output but have yet to see one. Any chance of the latter appearing? It would also maybe advance and inform some of the discussions / issues arising in this thread.

Regards - Tony

From: dpatterson.mbl at gmail.com [mailto:dpatterson.mbl at gmail.com] On Behalf Of David Patterson
Sent: Wednesday, 8 August 2012 7:25 AM
To: Rees, Tony (CMAR, Hobart)
Cc: deepreef at bishopmuseum.org; Robert.Guralnick at colorado.edu; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Global biodiversity databases

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<mailto: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<mailto:taxacom-bounces at mailman.nhm.ku.edu> [taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of Richard Pyle [deepreef at bishopmuseum.org<mailto: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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