[Taxacom] BHL & GBIF data vetted

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Tue Jan 18 14:18:19 CST 2011

Hi again Wolfgang,

>In the paper-print era, taxonomy was progressing largely in time-stamped 
>*finished* worksteps with clear authorship, which could be summarized/ 
>interpreted from a current point of view

I guess I still think that there may be some confusion here between "primary 
taxonomy" (=taxonomy), and "secondary taxonomy" (="bioinformatics"), and that 
your point quoted above applies to the former, but less clearly the latter, so 
we might be talking about different things??

At any rate, the new site Species-ID, from my point of view, has the advantage 
over Wikispecies/Wikipedia of allowing me to post some unpublished "background 
information" concerning the presence or absence of certain taxa on published New 
Zealand faunal lists, which serves to lessen the gap between what is published 
and the reality of what is actually out there in the field and where it is 
distributed. For example, 

there is a certain amount of confusion in the published literature concerning 
the identity and distribution of this species. It is actually quite common on 
the New Zealand mainland, but nowhere is this fact published. There is only a 
single published specimen record from the N.Z. mainland, but this is just 
because I only sent *one* of my specimens to Michael Balke. Going only by the 
published information, one could doubt that the species is actually established 
on the N.Z. mainland, and suspect the single specimen to be a vagrant or a case 
of mislabelling, but I know this not to be the case. Species-ID is a useful 
vehicle for providing this sort of "background info" to clarify something which 
is unclear from the published literature. But I don't really see that Species-ID 
has any advantages over Wikispecies in providing "time-stamped *finished* 
worksteps with clear authorship, which could be summarized/ interpreted from a 
current point of view", it is rather just that Wikispecies has an 
NOR restriction that Species-ID does not have ...

So, I'm not sure that we need to continue to develop new infrastructures, but I 
*am sure* that we do need to enter a great deal more data into the existing 
infrastructures like Wikispecies and Species-ID ...



From: Wolfgang Lorenz <faunaplan at googlemail.com>
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Cc: "taxacom at mailman.nhm.ku.edu" <Taxacom at mailman.nhm.ku.edu>; 
Coleoptera-ZSM at zsm.mwn.de
Sent: Wed, 19 January, 2011 4:39:46 AM
Subject: Re: [Taxacom] BHL & GBIF data vetted

Hi Stephen & All,

I will certainly agree when you point to some fantastic advantages of the 
permanent *manuscript stage* that is in the wiki system and other dynamic online 
projects, but the flux in e-published taxonomic information is not without 
certain problems. 

In the paper-print era, taxonomy was progressing largely in time-stamped 
*finished* worksteps with clear authorship, which could be summarized/ 
interpreted from a current point of view. 

In the electronic media, we now have an increasing number of work-in-progress 
with unclear, often changing authorships. This does have consequences on our 
ability to manage information tied to taxonomic names, - and probably it was 
this situation that led to projects like "Global Names Architecture" where 
biodiversity informaticians are trying to make sense out of *naked* namestrings 
that are more or less stripped from usage context, - names that are no longer 
interpretable "chresonyms". 

My impression is, biodiversity informatics could proceed much more 
straightforward if we had a better distinction between online information that 
is in manuscript stage and *finished* (preferrably reviewed) worksteps that are 
intended for permanent, public, scientific record.
We have been discussing similar things with e-publication of Code-relevant acts. 
I think there's a wider issue: E.g., what counts as "usage" in the sense of  the 
Code, e.g., in context with "prevailing usage"...? 


2011/1/17 Stephen Thorpe <stephen_thorpe at yahoo.co.nz>

following on with more comments ...
>one crucial aspect to any good system for presenting biodiversity informatics 
>data is that it allows *anyone* who notices an error to easily flag it or 
>preferably fix it. It is clear how the wiki system facilitates this, but not 
>clear to me how your "finished PDFs" handle it???
>to make the more general point once again: the problem for biodiversity 
>informatics in the world today is that there are too many independent 
>initiatives, all wanting to "do it their way", and aften trading on their own 
>supposed "authority". We *must* develop better ways to make info verifiable to 
>the end user if they need to, and recognise that many people have a part to play 
>in making available good biodiversity data, so there is no point claiming 
>authority and excluding others from being able to contribute, for the inevitable 
>result will be a global biodiversity informatics data quality crisis ... if 
>indeed we don't have that already ...
From: Wolfgang Lorenz <faunaplan at googlemail.com>
>To: "taxacom at mailman.nhm.ku.edu" <Taxacom at mailman.nhm.ku.edu>
>Cc: Coleoptera-ZSM at zsm.mwn.de
>Sent: Tue, 18 January, 2011 12:18:58 AM
>Subject: [Taxacom] BHL & GBIF data vetted
>Dear All,
>putting together the legacy data from the literature for a taxon can still
>be an immense challenge. Even getting the complete picture of the known
>distribution range of a single species - past and extant -  is one of the
>most time-consuming tasks I can think of. A task that has been performed
>reliably for only a tiny fraction of our known species, - despite the fact
>that such data are the basic units of biogeography and are indispensable for
>biodiversity conservation.
>In light of such a background, we cannot value high enough all the efforts
>that have been made and are being made through initiatives like BHL and
>However, only taxon experts can easily recognize the errors in the output of
>these largely automated data portals. Not so the average user  - most
>biologists, students, conservationists, journalists, politicians .... The
>risk of being misinformed with data from GBIF or BHL is very high for
>someone who is not a taxon expert who is able to vet the data.
>So I'd like to ask: What can the friendly expert do to share his vetting
>results with a wider user community?
>Maybe we do not need more than what we already have with the existing tools
>in BHL (e.g., the name search tool in BHL!) and GBIF (e.g., its excellent
>download-options). In addition to the important  wiki ideas (with more great
>things here: http://www.species-id.net), don't we also have the option to
>create open-access PDFs for our vetting results?
>Maybe it's possible to have a central place for such "catalogue-style" PDFs
>with a manuscript-stage quarantine, maybe closely allied with ZooBank? (not
>directly as a topic within ZooBank, but don't we need to know the usage
>history of names for a number of nomenclatural reasons, too?)
>Let me just illustrate this with the following example (test version only,
>still incomplete and, of course, access to a bibliography for understanding
>the micro-citations is needed but it is still a work in progress):
>In contrast to the wiki system, where publications are more or less in a
>permanent manuscript stage, such PDFs would be citable, *finished*, and
>time-stamped documents with clear authorship.
>As you can see in the example: it has its own accepted name for the taxon
>(=current chresonymy with synonymy), and the full "legacy chresonymy", i.e.,
>the accepted names used in previous publications. It also has embedded
>hyperlinks to BHL (still incomplete), - an expert-created/-filtered
>counterpart to what you get with the BHL name search (which cannot
>distinguish homonyms, for example). The map display can be directly compared
>with what you get as overview map through the GBIF data portal (see link
>below the map), etc....
>Maybe an optimistic dream: but in the early stages of this "official decade
>of biodiversity", it shouldn't be impossible to organize more substantial
>funding for fundamental things...
>Best regards,
>Wolfgang Lorenz, Tutzing, Germany
>Taxacom Mailing List
>Taxacom at mailman.nhm.ku.edu
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>(1) http://taxacom.markmail.org
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