uBio & Free taxonomic information

[Ken Kinman]

Dear All,
      The Prometheus project sounds very interesting and promising, and not
surprisingly (to me at least) it comes from the botanical community.  If
they should need a test case from zoology, I would highly recommend Kent
Carpenter's revision of Family Caesionidae which he summarized (from earlier
papers) and systematically analyzed in Systematic Biology (Vol. 42:142-154).
      (1) I hope I am assuming correctly that Prometheus could explicitly
present Carpenter's recognition of two paraphyletic genera (and of
paraphyletic groups in general).
      (2) I am wondering how high up the taxonomic hierarchy the Prometheus
system will attempt to go.  Would it even attempt to deal with taxon names
above the ranks regulated by the Codes of Nomenclature?  And how would it
handle the name of a broad Order Poales (which is not the earliest name) as
in the classification of the Angiosperm Phylogeny Group?
         ----- Thanks,
                    Ken Kinman

*****************************************
>From: MARTIN PULLAN <M.Pullan at RBGE.ORG.UK>
>Reply-To: MARTIN PULLAN <M.Pullan at RBGE.ORG.UK>
>To: TAXACOM at USOBI.ORG
>Subject: Re: uBio & Free taxonomic information
>Date: Thu, 22 May 2003 10:18:29 BST
>
>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

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