[Taxacom] ZooBank reality check [ Scanned for viruses ]

Thu Sep 7 02:45:52 CDT 2006

I can only agree with Paul's working taxonomist statement.

At antbase.org we have about the same amount of pages scanned in of little
more than 4,000 publications as the mycologists. All are stored as bound pdf
and single page pdf, linked to a bibliography server and the respective
citation. We had the luck that Smithsonians Atherton Seidall Foundation
supported part of the scanning, and thus some of this burden has been taken
of our shoulders.

This allows us now to venture into the next step, that is to OCR and mark at
least the relevant publications up in taxonx, a mark up standard we
developed to mark up systematics publications (taxonx at sourceforge:
http://sourceforge.net/projects/taxonx; our Wiki
http://wiki.cs.umb.edu/twiki/bin/view/Ants/WebHome, or a brief introduction
(http://antbase.org/databases/xml_publications.htm). The advantage of this
step is, that machines could read the descriptions and reuse them in
mashups, other webpages, and in fact allows to extract names. Probably the
most important element of the mark up are the treatment (description)
boundaries, which associate each bit of a text with a particular species,
defined in a specific nomenclature section. Of course, this could be used to
build up (semi-)automatically list of names needed for such an enterprise as
ZooBank.

The value of simple pdf holdings of systematics literature is nicely
illustrated by a tool called Clustrmaps. We installed this on antbase.org at
the bottom, and it shows the geographic distribution of users of this
library. And the map is only the activity of a little bit more than a week.
Ant people no longer depend on few research libraries.

As Paul points out, if we all move our copies into pdfs, we might all pay
back some of our saved time by building up Zoobank, which then is another
globally available data repository.

The advantage of marking the publications up has also another advantage:
Elimination of copyright. Descriptions are factual knowledge, and thus can
not be copyrighted. If we mark up the publications and serve only the
treatments, we can make them accessible. Such examples are given at Examples
are given at http://antbase.org/databases/xml_docs.html in the right column
under 'xslt'. Again, if people help to read in their documents, OCR them and
mark them up, we could have the best of the world (see
http://wiki.cs.umb.edu/twiki/bin/view/Ants/WorkFlow for a possible work
flow).

This leads to a suggestion to Zoobank: To build up tools allowing the
communities to build up and edit their name databases they now best.

Besides all that, we MUST create Zoobank, and ICZNs initiative deserves
support.

Donat

Dr. Donat Agosti
Science Consultant
Research Associate, American Museum of Natural History and Naturmuseum der
Burgergemeinde Bern
Email: agosti at amnh.org
Web: http://antbase.org
Blog: http://biodivcontext.blogspot.com/
Skype: agostileu
CV
Current Location
Dalmaziquai 45
3005 Bern
Switzerland
+41-31-351 7152

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Paul Kirk
Sent: Thursday, September 07, 2006 12:32 AM
To: TAXACOM
Subject: Re: [Taxacom] ZooBank reality check [ Scanned for viruses ]

I agree with Bobs assessment that some of the comments thus far have been
slightly unfair and definitely misguided. Perhaps more could have been done
to road test the dataset before the vehicle was launched .. or perhaps some
detailed explanation of it's limitations provided.

What I would like to pick up on is the 'working taxonomist' continuing to
take the trouble to check the original literature. This somewhat 'sterile'
but often justified exercise would have been reduced in botany if NCU's had
been accepted, at least as far as uncertainty over reference details was
concerened, amongst other things. But who has access to ALL the relevant
original literature ... outside north america and western europe? Working
taxonomists in much of the rest of the world do not have these luxuries so
one of the 'other enterprises' Bob referred to must be digitizing - just
photographing and NOT in the first instance OCR'ing, parsing, XML'ing etc -
the critical literature for each speciality group to create virual Libraries
for our colleagues in Africa, South America, eastern Europe, Asia ... And
the linking of these images of validating protologues to the names in the
relevant nomenclators - free to all.

And the proof of how easy it is can be found in the world of Mycology for in
a little under two years with just two 'drivers' and a couple of dozen
collaborators we have almost 80,000 page images available with 11,300 of
these relating to an admitedily small proportion of the 380,000 names in the
Index Fungorum database. So you search for your name, click on a link and
read the original description, see the illustrations and find out where the
type is. This is not rocket science, doesn't have nice brand images but it
is all free to the end user. If I hadn't been typing this email I could have
scanned a couple of dozen more pages it's that easy. Perhaps Thompson could
influence some of the on-line but 'closed' image repositories to release
into the public domain the relevant page images of this primary systematic
literature?

Paul

Dr Paul M. Kirk
Biosystematist
CABI UK Centre (Egham)
Bakeham Lane
Egham
Surrey
TW20 9TY
United Kingdom
Telephone: +44 (0) 1491 829023
Fax: +44 (0) 1491 829100
Email: p.kirk at cabi.org
Visit us at www.cabi.org; www.indexfungorum.org; www.librifungorum.org
CABI improves people's lives worldwide by providing
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________________________________

From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Bob Mesibov
Sent: Wed 06/09/2006 22:46
To: TAXACOM
Subject: [Taxacom] ZooBank reality check [ Scanned for viruses ]

Interesting that other ZooBank testers haven't had the (so far) satisfactory
results I've had with taxon names per se. Another question is lurking here,
though: who will use ZooBank as an all-purpose name reference, and why?

I'd personally like to believe that working taxonomists will continue to
take the trouble to check the original literature in their specialty group.
They will only go to compilations prepared by the painstaking nit-pickers
who preceded them in their specialty, and even then will be skeptical.
"Taxonomic librarians" compiling vast databases of nomenclatural information
cannot be expected to do this, whether they work for Thomson or the uBio
effort or any other enetrprise.

The original "prospectus" for ZooBank argued that we needed a name registry
for _current_ taxonomic effort. We also (in zoology) need an online Neave,
simply so that we can try to avoid homonymy.

The idea that ZooBank would be an authoritative source for _past_ taxonomy
was something for the future, yet this seems to be what some site visitors
are expecting _now_, which is not only unfair, but misguided.
---
Dr Robert Mesibov
Honorary Research Associate, Queen Victoria Museum and Art Gallery
and School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 64371195; 61 3 64371195

Tasmanian Multipedes
http://www.qvmag.tas.gov.au/zoology/multipedes/mulintro.html
Spatial data basics for Tasmania
http://www.utas.edu.au/spatial/locations/index.html
---

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