[Taxacom] GBIF: perpetuating probably defunct unpublished names

Sun May 23 17:03:53 CDT 2010

Hi David,

Ken Walker has a good point, but first to clear up a couple of your comments:

>Nothing is free and that includes wikispecies.  It costs money to maintain it's services and to ensure performance and stability.  The costs may not be 
>visible nor at the scale of some of the initiatives you cite,  I really don't know.  But there are costs.  Wikispecies seems to be free in the same way 
>that data published through GBIF is free

As I have said before in this forum, Wikispecies is free to the science community, whereas GBIF etc. are not. Something is free if someone else is paying for it. By this definition Wikispecies is free (since Wikimedia pay for it as a spin off from a larger non-scientific project - Wikipedia) and the others are not. Science money spent on GBIP, EoL, etc. could have been used to document the taxonomy of Gulf of Mexico marsh biota before it is possibly extinguished? As an aside, does anyone know of any probable extinctions resulting from the Gulf War oil spill of 1991? This highly scientifically significant carabid beetle (http://species.wikimedia.org/wiki/Archaeocindis_johnbeckeri) would appear to have been restricted to estuary shores in and near Kuwait. I don't know if it is still with us? Note how my Wikispecies page for this species contains relatively useful and verifiable information and links ...

Geoff Read has just diagreed with Ken and suggests that any blame for bad info on GBIF lies with the data providers! I disagree. The data providers do what they do, not necessarily what GBIF would like them to do! Natural history collections sometimes suffer from being understaffed and other problems which means that their data is very "raw". Let's be honest, the only data you can really hope to rely on is from published taxonomic revisions, but this is only covers a minute fraction of all life on Earth, and the rate of progress is slow. You can't increase the reliability/utility of data just by aggregating it!

If GBIF aren't going to have quality control on raw data, then what real advantage to they have over Google as a data aggregator? Not a lot, IMHO. I would suggest that science resources are better spent:

(1) facilitating and promoting taxonomic revisions;

(2) integrating, rather than just aggregating biodiversity data; and

(3) digitising more of the literature and making it freely available, so sites like Wikispecies can link to it.

>Wikispecies appears to be a web site for people to read, not a standards-based service that integrates itself into distributed validation workflows.  
>If so, this impacts the re-usability of the information you have added to it.    If not,  if someone can show me how we can pass the entire monthly 
>GBIF names index (> 5 million distinct names) through wikispecies to get the useful semantic and syntactic information that would improve the 
>fitness of these data,  I would be happy to work on implementing this.

Yes, another criticism of GBIF is that it is apparently structured in such a way as to be incapable of easily utilising such a valuable and structured source of biodiversity information as Wikispecies!

... just my thoughts, nothing personal ...

Stephen

________________________________
From: David Remsen (GBIF) <dremsen at gbif.org>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Cc: David Remsen (GBIF) <dremsen at gbif.org>; Jim Croft <jim.croft at gmail.com>; taxacom at mailman.nhm.ku.edu
Sent: Sun, 23 May, 2010 9:19:12 PM
Subject: Re: [Taxacom] GBIF: perpetuating probably defunct unpublished names

Stephen,

Asking publishers of collections and observation data to GBIF, BIOCASE, the various taxon-oriented NETs, etc. to validate their names is facilitated by accessible services that make such validation processes possible.    Currently, the source data required for this is either entirely unavailable to these publishers or is scattered in such a wide array of formats and locations that it's simply impractical to build anything from them.  What should the practice be for someone who wants to taxonomically validate their collections data prior to publishing their data via GBIF?

- The data published through GBIF are not qualitatively transformed from the collections where they originate.  GBIF provides infrastructure, standards, capacity, and recommendations on how to publish these data.  Issues of quality and completeness, reside, for the most part, with the original stewards of the data.

- Checking out and validating these data first (pre-publication) is a great idea but it requires an engineered solution that allows an arbitrary data publisher to validate against the equally-arbitrary required source data.  An ad-hoc approach simply won't scale or succeed.

- Wikispecies appears to be a web site for people to read, not a standards-based service that integrates itself into distributed validation workflows.  If so, this impacts the re-usability of the information you have added to it.    If not,  if someone can show me how we can pass the entire monthly GBIF names index (> 5 million distinct names) through wikispecies to get the useful semantic and syntactic information that would improve the fitness of these data,  I would be happy to work on implementing this.

- Nothing is free and that includes wikispecies.  It costs money to maintain it's services and to ensure performance and stability.  The costs may not be visible nor at the scale of some of the initiatives you cite,  I really don't know.  But there are costs.  Wikispecies seems to be free in the same way that data published through GBIF is free.

David Remsen
(GBIF)

On May 22, 2010, at 8:04 AM, Stephen Thorpe wrote:

>> but they are still only indicative
> 
> I agree absolutely with you (as always!), but that's probably not how they (i.e., the likes of GBIF, EOL, etc.) advertise themselves - if barrels of leaking oil per day are analogous to levels of uncertainty, they are still claiming only 5000! Do the "math": Wikispecies is "only indicative", but free, so if the "non-frees" are also only indicative, well ...
> 
> Stephen
> 
> 
> 
> 
> ________________________________
> From: Jim Croft <jim.croft at gmail.com>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Cc: taxacom at mailman.nhm.ku.edu
> Sent: Sat, 22 May, 2010 5:48:51 PM
> Subject: Re: [Taxacom] GBIF: perpetuating probably defunct unpublished names
> 
> hoping they read taxacom... just waiting for the funds transfer to
> come through... :)
> 
> as a reasonably bioinfo savvy kind of person, I do not expect anything
> from a data aggregator, or a data provider, to be truthful, complete,
> reliable, precise or accurate.  GBIF, EoL, ALA, AVH, Google, Bing,
> Wolfram Alpha, Guardian, New York Times, Fox News, hey, even
> WikiSpecies - they are all the same: indicative.  OK, some might point
> and some may just wave in the general direction, but they are still
> only indicative.
> 
> find a dataset, any dataset, and I am sure we will be able to find
> something to fault and something to argue about.  It is such a
> demoralising waste of time when, with a bit of duct tape and fencing
> wire and a few chosen expletives we could just fix the damn thing...
> 
> jim
> 
> On Sat, May 22, 2010 at 2:40 PM, Stephen Thorpe
> <stephen_thorpe at yahoo.co.nz> wrote:
>> Jim: you should be BP's (Bigfoot-Print's) new PR guy! :)
>> 
>> perhaps the tone of my email came across a tad too strong, but I do think
>> that in the rare cases where the likes of GBIF do have content on their
>> pages, it isn't so unreasonable to expect it to have been thoroughly checked
>> out and validated FIRST ...
>> 
>> Stephen
>> 
>> ________________________________
>> From: Jim Croft <jim.croft at gmail.com>
>> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
>> Cc: taxacom at mailman.nhm.ku.edu
>> Sent: Sat, 22 May, 2010 4:29:14 PM
>> Subject: Re: [Taxacom] GBIF: perpetuating probably defunct unpublished names
>> 
>> isn't finding, accounting for and correcting these sorts of things
>> what the business of nomenclature and taxonomy is all about?  no harm
>> no foul?
>> 
>> it is probably a bit unreasonable to expect everyone to get everything
>> right every time, and it is no one person's (provider's)
>> responsibility - we are all on the same side, and we all try to
>> address the broken bits we see...
>> 
>> in our collection we work hard to avoid focussing fault.  if there's a
>> problem, it's everyone's problem, and everyone (which in reality
>> usually means someone!) gets to fix it... taxonomy is a bit like
>> that... :)
>> 
>> jim
>> 
>> On Sat, May 22, 2010 at 1:41 PM, Stephen Thorpe
>> <stephen_thorpe at yahoo.co.nz> wrote:
>>> this isn't very helpful:
>>> http://species.wikimedia.org/wiki/Agalba_lawrencei
>>> http://species.wikimedia.org/wiki/Agalba_storeyi
>>> 
>>> at least my Wikispecies pages clearly indicate that they are unpublished
>>> names
>>> 
>>> they will probably never be published as the types were probably labelled
>>> as such before Muona realised that Arisocephalus was a synonym of Agalba, so
>>> these species probably already have names
>>> 
>>> perhaps GBIF should ask its data providers to verify that the names have
>>> been published???
>>> 
>>> Stephen
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 
>>> Taxacom Mailing List
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>> 
>>> The Taxacom archive going back to 1992 may be searched with either of
>>> these methods:
>>> 
>>> (1) http://taxacom.markmail.org
>>> 
>>> Or (2) a Google search specified as:
>>>  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>>> 
>> 
>> 
>> 
>> --
>> _________________
>> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
>> http://www.google.com/profiles/jim.croft
>> 'A civilized society is one which tolerates eccentricity to the point
>> of doubtful sanity.'
>> - Robert Frost, poet (1874-1963)
>> 
>> 
> 
> 
> 
> --_________________
> Jim Croft ~ jim.croft at gmail.com ~ +61-2-62509499 ~
> http://www.google.com/profiles/jim.croft
> 'A civilized society is one which tolerates eccentricity to the point
> of doubtful sanity.'
> - Robert Frost, poet (1874-1963)
> 
> 
> 
> 
> _______________________________________________
> 
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom archive going back to 1992 may be searched with either of these methods:
> 
> (1) http://taxacom.markmail.org
> 
> Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 