[Taxacom] Scope of current Biodiversity Informatics initiatives

Wed Feb 17 05:08:32 CST 2010

Hi Stephen

I certainly didn't mean financially involved.  I was just wondering if
wikispecies was in any sense "your baby" (or perhaps your mate's baby,
as it were) rather than just your tool of preference.

I assume not as you would presumably have said so in your previous
reply.

Cheerio, Mike

__________________________

Mike Sadka

Interactive Media

x5462

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: 16 February 2010 20:29
To: Mike Sadka
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Scope of current Biodiversity Informatics
initiatives

Hi Mike,
I'm not quite sure what you are asking, exactly? I have no financial
interest in Wikispecies, nor indeed in anything at all! I'm not sure
quite what you mean by a "user"? I am a contributor (=editor), and an
admin (=trusted editor). Anybody in the world can be either of those
things if they choose to contribute freely to Wikispecies in a manner
that the existing admins approve of...
Cheers,
Stephen

________________________________________
From: Mike Sadka [M.Sadka at nhm.ac.uk]
Sent: Wednesday, 17 February 2010 12:02 a.m.
To: Stephen Thorpe
Cc: taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] Scope of current Biodiversity Informatics
initiatives

Hi Stephen

Forgive me asking, but do you have any connection with wikispecies other
than being a user?

Cheerio, Mike

__________________________

Mike Sadka
Interactive Media
x5462

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: 16 February 2010 03:32
To: Tony.Rees at csiro.au; r.page at bio.gla.ac.uk
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Scope of current Biodiversity Informatics
initiatives

As a quick first reply, let me add to your list info on another global
bioinformatics initiative:

- Wikispecies aspires to provide human users with verifiable,
up-to-the-minute information on the biodiversity/taxonomic state of play
of all taxa at all levels, living or fossil. Additionally, it tries to
provide links to publications and images of taxa whenever these are
available. Distributional, bionomic, and taxonomic comments are also
provided on talk pages, and taxa are cross-referenced with associated
taxa (e.g. parasites and hosts). Nomenclatural issues are also fleshed
out in full. Low level information is integrated into a single
consistent classification (with alternatives indicated). The focus is on
content, and HOW the pages are written (in terms of explicit
referencing), not WHO wrote them. Since Wikispecies does not confine
itself to harvesting names from already existing secondary sources, it
covers many groups for which there is little integrated information
currently available, for example Coleoptera and also Acari.

________________________________________
From: Tony.Rees at csiro.au [Tony.Rees at csiro.au]
Sent: Tuesday, 16 February 2010 4:00 p.m.
To: Stephen Thorpe; r.page at bio.gla.ac.uk
Cc: taxacom at mailman.nhm.ku.edu
Subject: Scope of current Biodiversity Informatics initiatives

Stephen,

OK, I have topped up the coffers with a few new cents (for better or
worse), so here goes.

You write:

<snip>

Whenever I ask a straight question, nobody answers it, but here I go
again:

what does GBIF have to offer that is different to what CoL has to offer
that is different to what EoL has to offer, etc? Is what they offer
worth the cost? In a world of rapidly disappearing biodiversity (in some
parts, anyway), isn't it more sensible to "describe it before it is
gone" as a priority? Wikispecies is there to integrate it all, not
perfectly, but cheaply ...

</snip>

Actually you ask three questions. Here is perhaps the briefest possible
answer to the first one.

- CoL (Catalogue of Life) integrates names data at the species level
from multiple "authoritative" sources into a single catalogue that can
be used by other initiatives, or interrogated by humans over the web (or
also offline via CD-ROM). By its own estimates it is around 60% complete
at this time, for extant taxa only.

- GBIF integrates species occurrence data (in the main) from multiple
providers, and where possible, uses the CoL Catalogue as a means to
organise and navigate through its data where such information is
available in CoL; again its clients include humans over the web, and
machine-level users i.e. other initiatives that can connect remotely to
GBIF data services.

- EOL aspires to provide summary information about species attributes,
again integrated from many sources, including maps/occurrence data from
GBIF but also descriptive information, images, and more, and also uses
the CoL Catalogue as a means to organise and navigate through its data
where possible.

The main aim is to avoid redundant data entry/capture, i.e. "enter once,
use many times", to transfer information between the systems by as
automated means as possible, and for each to concentrate on its
specialist area of interest and expertise.

There are also related, but by no means identical, other major
initiatives such as GNA and ZooBank. GNA aims to handle all published
names (if you like, a mix of "authorized" and "non-authorized but out
there anyway" names), using CoL as one contributory source but by no
means the only one; ZooBank is a prototype registry of newly published
animal names, possibly also covering already published ones
retrospectively, which can once again be used by humans or machine
readable to provide unique identifiers and associated attributes for
names, and the publication instances by which names are made available.

Each is in a varying degree of completeness to date, so of course it is
possible to point to taxa or information that is missing from the
relevant slots in any initiative; however in general these are hoped to
be addressed (by as efficient means as available, or can be devised) as
the activities proceed.

Others will obviously be in a clearer position to elaborate than myself,
should you have further specific questions related to particular
initiatives and the manner of data transfer between them, and either
real or perceived overlap. Of course the interested person can also
discover much relevant information via the home pages of the relevant
initiatives.

Hope this helps,

Regards - Tony

Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities:
http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info:
http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen Thorpe
Sent: Tuesday, 16 February 2010 11:18 AM
To: Roderic Page
Cc: TAXACOM
Subject: Re: [Taxacom] In defense of DOIs

>It's not "bioinformatics people" who drove the adoption of DOIs, it was
publishers looking for a way to increase the value of their content
through linking. Links mean greater traffic (e.g., through citations),
as well as an improved experience for the reader (e.g. links that don't
break)

Well, I don't know the history, but now publishers have a free
alternative for greater traffic through linking - wasn't it you who
pointed out a while ago that Zootaxa has many thousands of citations
(and links) on Wikispecies/-pedia, all at no cost to them? Direct links
to Zootaxa very rarely break.

>Viewing everything in terms of taxonomy runs the risk of missing the
bigger picture
I agree, but it is unclear what the "bigger picture" is? Industries that
manipulate primary information have their place (and Zoological Record
is a particularly useful one IMO), but one could argue that there is
simply far too much of that sort of thing going on in the world today...

Whenever I ask a straight question, nobody answers it, but here I go
again:

what does GBIF have to offer that is different to what CoL has to offer
that is different to what EoL has to offer, etc? Is what they offer
worth the cost? In a world of rapidly disappearing biodiversity (in some
parts, anyway), isn't it more sensible to "describe it before it is
gone" as a priority? Wikispecies is there to integrate it all, not
perfectly, but cheaply ...
_______________________________________________

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
_______________________________________________

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