uBio & Free taxonomic information

[MARTIN PULLAN]

We have been following this thread with some interest and following
Una's comments relating the databasing of circumscriptions using
a specimen oriented approach we feel we have to stick our heads
above the parapet and mention our work on Prometheus.
Prometheus is a data base model (and prototype system based on
the model) designed specifically to address this issue. In part the
model derives from the specimen-based capabilities in Pandora but
goes much further.

The Prometheus project was in fact inspired by the very issues that
Una has raised - specifically the cryptic (i.e. not reflected through
an examination of nomenclature and synonymy) differences in
taxon circumscription. The model has been published in Taxon 49:
55-75. Reprints of this document are available from the project web
site www.prometheusdb.org. In Prometheus we separated the
representation of names from taxa, allowing multiple
representations of the circumscription for each name in the system.

Attention should also be drawn to other projects that are currently
researching this area of taxonomic databases such as
Nomencurator (http://www.nomencurator.org/),
Seek(http://seek.ecoinformatics.org), MoReTax
(http://www.bgbm.org/BioDivInf/Projects/MoreTax), and work on the
Potential Taxon concept by Walter Berendsohn et al.(
http://www.bgbm.org/IOPI/IOPIModel73/7304ptax.htm).

Systems based on names alone make the erroneous assumption
that there is a one-to-one relationship between names and taxa. A
quick examination of the taxonomic process soon reveals that this
is not so. Systems that are intending to provide services that
involve the amalgamation of data from disparate sources that ignore
this fact are in danger of making some serious mistakes. We
would particularly point readers to the MoReTax site where they
have used set theory to study the possible relationships that can
exist between taxon concepts and the validity of amalgamating
data associated with taxon concepts within multiple classifications
and with various degrees of similarity. It is our opinion that the
difficulties associated with this issue have been severely
underestimated. We can see that this is partly a political issue in
that with a large amount of extant taxonomic information it is not
clear which circumscription was in action at the time a data set
was constructed. It would, therefore, be difficult to determine
whether or not data from such sources could be validly
amalgamated. This does not however mean that these issues
should be swept under the carpet, quite the converse the
taxonomic community as a whole should be actively seeking to
resolve these problems so as to ensure that a more enduring
legacy is created.

>The only database tool I know of that even begins to support
>this task in an adequate manner is Richard J. Pankhurst's
>PANDORA.  It does so by allowing the user to record data and
>publications linked to *individual specimens*.

Martin Pullan & Mark Watson


Dr.Martin Pullan
Taxonomic Computing
Royal Botanic Garden Edinburgh
20a Inverleith Row
Edinburgh
Scotland
EH3 5LR

Tel (+44) (0)131 248 2908
Fax (+44) (0)131 248 2901
http://www.rbge.org.uk