[Taxacom] ICZN and Wikispecies (was Re: "nude" Coccinellid genera?)

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Mon Mar 11 01:28:02 CDT 2013

Hi Rich,
I bet you paint bright and colourful pictures in your spare time? Or have a side line in manufacturing spinning tops, with only positive spin, of course!! :)
The truth, as always, is somewhere in between. Actually, I don't see the issue as "my way is best", or at least it is not me who is saying that!
Ultimately, *some* structured database type questions will be able to be answered using Wikispecies, but not all. On the other hand, if we are not careful, the rival structured databases will be able to answer the questions alright, except that they could very easily do so using poor quality data, so either way "we have a problem Houston"! As far as data quality goes, the whole only adds up to more than the some of its parts *if* the parts are all pointing in more or less the same direction, if not, then they cancel out! I suggest that a way to go might be to make sure that each individual part does something slightly different. The problem with "willy nilly linking" the parts together is that many data conflicts might result, and apparent consensus may merely be due to data being harvested from the same source by several of the parts (so, for example, having CoL and EoL both saying the same thing can add spurious credibility until you realise that their
 data is from the same source). At any rate, the issues involved in this enterprise are extremely complex and inherently messy, not to mention somewhat "political" ...

From: Richard Pyle <deepreef at bishopmuseum.org>
To: 'Stephen Thorpe' <stephen_thorpe at yahoo.co.nz>; 'Lyubomir Penev' <lyubo.penev at gmail.com> 
Cc: "'TAXACOM at MAILMAN.NHM.KU.EDU'" <TAXACOM at mailman.nhm.ku.edu> 
Sent: Monday, 11 March 2013 6:24 PM
Subject: RE: [Taxacom] ICZN and Wikispecies (was Re: "nude" Coccinellid genera?)

No doubt! But Wikispecies is not a structured database, and as such, has some limitations.  For example, can you quickly tell me how many species were described from 1850-1900 using only Wikispecies?  How about generate a checklist of all the fishes of Fiji?  Can you do an analysis over time of how certain names have been treated as valid or as synonyms?  These are the kinds of queries (and many, many, many, many more) that are extremely easy to do with a structured database.
Don’t get me wrong – I think Wikispecies is an extremely valuable component to the whole picture (the only reason I didn’t include it in the list on my email, is I didn’t want you to challenge me in lumping it in with the “alphabet soup”).
The days of “may way of organizing information is better than your way” should be long behind us by now.  All of the things that currently exist server a valuable purpose; otherwise they wouldn’t exist (OK, that’s not necessarily true – but it probably true in the vast majority of cases).  So let’s please move beyond the simpleton perspective of “this way is better”, and move more towards finding ways to increase the value of *ALL* of these systems by connecting them together.
As for page histories – the data are definitely there (we have a robust edit log system).  It’s just a matter of adding it to the public pages.  One of the many features that is on the “to do” list.
But I agree – ZooBank is not in the business of taxonomy.  However, many other database systems are (CoL, WoRMS, ALA, EoL, etc., etc.), so by connecting them all together (including Wikispecies), the whole adds up to much more than the sum of the parts.
From:Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz] 
Sent: Sunday, March 10, 2013 6:35 PM
To: Richard Pyle; 'Lyubomir Penev'
Subject: Re: [Taxacom] ICZN and Wikispecies (was Re: "nude" Coccinellid genera?)
Hi Rich,
You can possibly guess what I am going to say in response to that! Wikispecies offers a currently far more complete "name finding" facility than ZooBank does, and it includes both strictly nomenclatural (eg. http://species.wikimedia.org/wiki/Template:Larochelle_%26_Larivi%C3%A8re,_2013) and taxonomic approaches (eg. http://species.wikimedia.org/wiki/Moriomorphini).  I contribute to ZooBank as somewhat of a backup. Both are now more or less on a par in terms of open edit, though ZooBank does not make public page histories. I believe that users will prefer the added taxonomic perspective, in addition to purely nomenclatural, and it will be a very long time indeed before any rival to Wikispecies can catch up on the mix of these two elements that Wikispecies currently offers...
From:Richard Pyle <deepreef at bishopmuseum.org>
To: 'Stephen Thorpe' <stephen_thorpe at yahoo.co.nz>; 'Lyubomir Penev' <lyubo.penev at gmail.com> 
Cc: "'TAXACOM at MAILMAN.NHM.KU.EDU'" <TAXACOM at mailman.nhm.ku.edu> 
Sent: Monday, 11 March 2013 5:22 PM
Subject: RE: [Taxacom] ICZN and Wikispecies (was Re: "nude" Coccinellid genera?)

Hi Stephen,

> Well, publishers are the main users of ZooBank who gain anything tangible
> from the "services" of ZooBank. They use it to facilitate e-only
> which is nevertheless Code compliant. ZooBank doesn't really offer any
> "services" to anyone!

Actually, that's not really true.  From the perspective of many publishers,
it's just one more pain-in-the-backside hurdle that they need to deal with
during their publication workflow.  Frankly I see no reason why ZooBank
benefits them.  Yes, ZooBank is one of the requirements for e-only
publication, but that's not a "service" provided by ZooBank.  E-only
publication would be a lot easier for most publishers if it didn't include
the registration requirement.

THANKFULLY, many publishers and journal editors have been extremely
cooperative and supportive of the concept of ZooBank -- not so much because
of the e-publication thing, but because they recognize the importance of a
stable nomenclature upon which all of biology ultimately depends (at least
in the current paradigm, which has been maintained for the past two and a
half centuries).  In particular, Pensoft, PLoS ONE, Zootaxa, and several
others have been very supportive of ZooBank -- even well before the
e-publication Amendment was passed.

The value of ZooBank to everyone else will come as two things start to
1) ZooBank gets populated with historical content (Sherborn, Hymenoptera
Name Server, plus many other zoological databases that have expressed
willingness to contribute);

2) The Global Names Architecture services start to ramp up (already

As for #2, the analogy I always give people for GNA is the DNS system of the
internet.  Everyone on the planet uses it all day long, but without
realizing it.  This is why I see GNA as different from the "alphabet soup".
Most of the big players (CoL, EOL, GBIF, WoRMS, ALA, IPNI, Tropicos, Index
Fungorum, ZooBank, and many, many others) provide valuable services to end
users.  The purpose of GNA is to build a low-level *infrastructure* to allow
all of those existing services interoperate more effectively.  I explained
this in some detail here:

See the slides starting at about 5:20, through 6:35, and again from 8:40
through 10:20.

If we can make both of those things happen, then ZooBank will play one of
the key roles (along with IPNI, IF, MycoBank, and the registry of Bacteria
-- when it goes digital) for anchoring text-string names to metadata-rich,
usage-based data "objects" (Protonyms and other Code-governed actions
involving nomenclature), which themselves serve as keystone records for all
taxon-name-usages (including all taxon concept definitions).

Paddy Patterson has been make the strong and compelling point that we need
to shift our framing of biodiversity informatics away from the realm of
research tools, and more towards universal, foundational, information
infrastructure.  When we start to achieve that vision, a great deal or order
will emerge from the disconnected morass of biodiversity data that we used
to spend hours and hours in the library tracking down, and now spend fewer
hours -- but still many hours -- surfing the web to track down.

As long as we can find a common pathway to bring some sense of cohesion to
all this biodiversity data, I'm confident the money will be there to support
each of the core components and services (including ICZN & ZooBank).  If we
keep to the "data silo" structure, I'll be much less optimistic.


Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
Associate Zoologist in Ichthyology
Dive Safety Officer
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org

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