ITIS (an explanation of GBIF's data integration activities)

Christopher Lyal chcl at NHM.AC.UK
Wed Jun 30 14:17:00 CDT 2004

Doug Yanega wrote:

Wouldn't it be useful to everyone if every taxonomic publication in
existence could be found on a single website? Wouldn't it be useful
to taxonomists if they no longer had to worry about things like
turnaround times, or page charges, or additional costs if they want
to use high-resolution, full-color digital images in their works?

Now consider the type of system I'm proposing: taxonomist A puts up a
draft manuscript onto the global taxonomy website, and every
subscriber in the world who has flagged that as a taxon of interest
is instantly notified .....


I'm not sure I go for a single website, given the way we are developing
distributed systems.  Nor am I sure that e-journals are necessarily the
only way forwards for publishing taxonomy on the web.  One of the
bottlenecks in getting taxonomy done and out where it can be used is the
necessity of wrapping even a single species description up in a formal
paper with all the bits and pieces that make an editor happy and carry
on selling the journals.  Surely publication on the web can allow us to
break this mould a little?

Anna Weitzman and I have been putting together a schema over the last
year or so that will deal with taxonomic literature - the names
(including synonyms etc), citations, specimen lists, keys, hierarchical
statements etc that are found in pretty well any paper. Basically, it
covers all of the components of taxonomic publications and the taxon
treatments contained within them other than the actual characters, which
are dealt with by other projects. Although taxonomic literature is very
structured there can be an amazing amount of variability, but we hope we
have managed to cover this, (and we are counting on you and others to
point out where we have missed things).  The schema has been written
with a focus on both botanical and zoological taxonomic literature, and
should also accept fungal and paleontological publications, but this has
not been tested. It does not take into account the kinds of data needed
for viral or bacterial publications, and if anyone is interested in
pursuing this in the future we are very open to collaboration.

So what's the point?  Part of it is interoperability - someone mentioned
that it would be good to be able to link straight to the descriptions
from the names; if the descriptions are marked up in the schema we are
developing, this should be possible, since we will ensure that it can be
mapped to the Linnean Core/Napier Schema or whatever standard is
accepted.  Similarly, we have written it to enable mapping to ABCD, so
links can be generated from the relevant description elements to
specimen-level data, for example through GBIF.  Another part is
accessibility.  Given a set of descriptions accessible in this format,
it would be possible to pull up any subset wanted - be that
geographically, taxonomically or temporally defined (or any other
parameter that is accessible).  Moreover, additional descriptions and
taxonomic acts could be added without the need for a full paper being
prepared and going through that particular mill.  Refereeing and making
names formally available/valid according the relevant Code are both
issues that can be dealt with without too much trouble, we think, and in
no sense are we suggesting that the provisions of the various Codes
could be ignored.

We have been developing the schema using the Biologia Centrali-Americana
as a testbed, and we plan, once the schema has gone through a thorough
review, to have the whole 58 biological volumes of the BCA marked up and
put on the web.  This will give a starting point of over 50,000 species.
We have also got several taxonomists to agree to add modern revisions to
the system, thus increasing the complexity through adding multiple
descriptions of taxa in the BCA itself, name changes, and taxa described
since the BCA.

Right now we are at the stage of sending the schema out for comment to
our advisory group.  It will shortly be on the web at If you check out that site
now, you will find more about the project and the full text and images
from the BCA in JPEG format.  If anyone would like to look at the schema
(and give us some feedback) please let either of us know and we'll send
a copy and add you to our mailing list.


Christopher H. C. Lyal,
Beetle Diversity and Evolution Programme,
Department of Entomology,
The Natural History Museum,
Cromwell Road,
London SW7 5BD
tel: +44 (0) 207 942 5113
fax: +44 (0) 207 942 5229
e-mail chcl at
personal page  -

electronic Biologia Centrali-Americana -

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