cgh at MAILSERVER.NHM.AC.UK
Thu Dec 22 10:07:55 CST 1994
From: Charles Hussey, Data Manager, Department of Zoology, The Natural
History Museum, London.
A Research Leader in our Microbiology Section is to begin a Data Modelling
Project and has asked me to circulate TAXACOM Subscribers. If you wish to
respond could you do so direct to Dr. Dave Roberts : dmr at nhm.ac.uk
The text of his message follows:
We have some funding to begin work on a nomenclatural database. The problem
we want to address is how to handle the instability (synonymy and re-
classification) and the tracking of the history of names. Linked to this is
the issue of supporting multiple higher classification systems, which is an
acute problem in fields such as the protista at present.
If a suitable implementation can be designed, we will be able to recover
lists of "what species are in genus X" and "what genera are in Order Y
sensu Jones", including all synonyms and a nomenclatural history. Another
question that can be addressed is whether a name is valid or available.
The database will also be able to provide higher taxonomic structure and
authorities for genus-species names under a chosen system (again, in the
protista there are several systems in current use).
This is important for us in being able to search our collections where
many items are listed under the name by which they were deposited, not the
name which is currently valid; again an acute problem in groups such as
The work we have done to date has led us to believe that an object-
orientated approach (C++) would be most likely to succeed, but it is
possible that languages such as Prolog might be better. The issue that has
led to this conclusion is the recursive nature of a synonymy query. For a
given species, you recover a number of synonyms; for each synonym you must
perform the same enquiry and so on until the list of names does not
recover any new members. Further, the system should check that the original
name itself is still nomenclaturally valid (has not been submerged).
Complications occur when part of a set described under one name are moved
to another name and the original name remains sensu lato or sensu stricto.
The information comprises of comparable volumes of items (names and other
textual data) and links between those data. The links can be stated
explicitly, of course, but the maintenance of such linkage sets could
become unreasonably demanding as the volume of information grows. There are
thought to be some 1.8 million names, with an estimate of 20% synonymy.
The trial group is the Protists (see for example Corliss, 1994. Acta.
Protozoologica 33: 1-51). If we can devise a model capable of handling this
degree of taxonomic instability, it should not prove a major difficulty to
extend it to any other group.
We would like to hear of any work that has been done in this area (e.g.
Beach et al. 1993. pp241-256, in R. Fortuner (ed.) Advances in Computer
Methods for Systematic Biology. John Hopkins University Press). More
importantly, are we trying to re-invent the wheel? If not, is anyone
interested in collaborating on this problem?
Department of Zoology, The Natural History Museum,
Cromwell Road, London SW7 5BD, United Kingdom.
Tel: +44 (0)71 938 8921 [Direct Line]; Fax: +44 (0)71 938 9158
JANET: cgh at uk.ac.nhm
INTERNET: cgh at nhm.ac.uk
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