| Concept
of the provisional checklist
"Potential
Taxa" in the checklist database
System
setup
Source
datasets and their derivation
TDWG geographical scheme
Generic
classification
Diacritics
Sponsor
acknowledgements
The concept of a provisional Checklist was
developed at a meeting of the IOPI Checklist
Committee at the Real Jardín Botánico in Madrid,
Spain, October 2, 1995.
This decision to start an initial preliminary
Checklist with minimal extra funding was made
in light of slow progress with the planned full
Checklist and no likelihood of substantial funding
being found without having some preliminary
product. This initial provisional Checklist
is available on the WorldWide Web via the
IOPI Home Page and serves several functions:
- demonstrate to funding bodies that the Checklist
is a viable project
- enable us to test procedures for entering
and botanically editing data
- enable contributors to the Species Plantarum
project to expeditiously submit data for the
Checklist.
This provisional Checklist includes basic data
for each species (or infraspecific taxon if
present), with three levels of data present:
(i) source datasets (the data shown as provided
by the database owners or custodians), (ii)
partly coordinated /edited entries, and (iii)
fully coordinated entries.Users will access
data by entering the taxon name into a query
form on the screen. The basic data included initially depends on
what is available from each source. The family name is also included
(given as in the published Kew list, at least
initially - that list is continually being refined).
Users can access data by entering the taxon
name (genus or genus* for all entered species
or genus + species for a particular species)
into a query form on the screen.
The preliminary Checklist started with three datasets, namely those for Australia,
Peru and Europe. The Casuarinaceae from the
research of Karen Wilson and Dr Lawrie Johnson
was added as an example of a whole family. Other
datasets have been added since (see source
datasets).
Custodians of existing datasets are invited
to contact Karen Wilson to discuss inclusion
of their data for wide availability. We have
(limited) funding to help with computerising
non-electronic datasets. These datasets are received by Richard Pankhurst
in Edinburgh or Walter Berendsohn in Berlin
and are then hand edited, with funding needed
to hire help to speed up this task. The 'master'
Checklist is currently kept at Berlin for access
via the Home Page.
[Karen Wilson, Convener, IOPI Checklist Committee]
The database stores and maintains source datasets
in their original form. The source datasets
represent a certain view of a taxon at the time
of the publication of the reference cited. This
taxonomic concept, represented by a scientific
name and its source reference ("sec." = secundum,
according to) is called a potential taxon.
The edited or partly edited record in the database
represents a potential taxon which is presently
considered to have a preferred status. The taxonomic
editor can relate other potential taxa (source
records) to that preferred view. It may for
example be stated that the view of the taxon
given in a specified Flora or Monograph is congruent,
included, or only partly included in the preferred
view. This provides a powerful tool to map information
linked to such source records (e.g. descriptive
information, uses, etc.) to the currently preferred
view.
For a discussion of "Potential Taxa" see the
presentation published under Session IV,
Data Structures for Taxonomic Names and Classifications
(http://research.calacademy.org/taf/proceedings/Proceedings.html),
or the articles in Taxon 44:207-212 (1995) and
46:283-309 (1997).
[Walter Berendsohn]
The system in Berlin currently consists of
a database server under Windows 2000 Server,
with the database management system SQL Server
2000. HTML pages are served to the World Wide
Web
using Active Server Pages on an Internet Information
Server (on a separate server). The ASP program
constitute the called BerlinModelViewer v 1.0
that will soon be released under public license.
The first setup of the database, which was
accessible on the WWW until May 31,1997, was
implemented by Mark A. Ziegler, who also programmed
the generic conversion tool for tagged field
format formerly used in data import. This first
GPC database was completely
re-designed (May - July 1997) by Frank Wolfram,
with the aim of closer adherence to the published
IOPI model. The interface between SQL Server
and Internet Information Server is now implemented
using Microsoft Active Server Page technology.
Finally during Oct. 2002 Mar. 2003 the database
was again remodelled and migrated to the Berlin
Model by Javier de la Torre. .
The text on the WWW pages was written (if not
cited otherwise) by Walter Berendsohn and Karen Wilson.
Geographic distributions for fully edited taxon
records in the GPC database are to use the Botanical
Recording Units (BRU's) as published in Hollis,
S. & Brummitt, R. (1992): World Geographical
Scheme for Recording Plant Distributions, Plant
Taxonomic Database Standards No. 2, International
Working Group on Taxonomic Databases for Plant Sciences
(TDWG), Hunt Institute for Botanical Documentation,
Pittsburgh. The data are available in electronic
form under http://www.bgbm.org/TDWG/geo/default.htm.
The second version of the scheme is available
under http://www.tdwg.org/geo2.htm.
However, most of the source datasets provided to
IOPI do not adhere to this standard, so that a "distribution phrase"
is used
to accomodate non-standard (or proprietary
standard)
geographical data. In case that a "proprietary" encoding of the geographical distribution is
used, please provide a text or table (will be included as a URL in the notes field of
checklist output; example: Flora Europaea, Med-Checklist).
Although the Berlin Model database supports alternative
classifications, for the incorporated source
datasets a pragmatic approach was taken to
facilitate access to the data. The classification
provided by the source record is cited ("SourceHigherTaxon")
in unaltered form. However,
assignment of higher taxa for record retrieval purposes
is based on a very simple hierarchical scheme. All
records in
the database are linked to a generic record in a
single source, which in turn provides the
family name.
The data on genera are based
on the publication Vascular Plant Families and Genera
compiled by R.K.Brummitt and published by the Royal
Botanic Gardens, Kew in 1992 (available from Kew's
Mail Order Department). The file currently undergoes
major revision and an updated version will be
provided. However, for the time being the file (and the additions
introduced in the process of importing datasets
for the IOPI database) continues to be used as the
generic backbone of the GPC. It can be downloaded
in delimited text format,
by kind permission of RGB Kew. (Please note that
this is a modified version of the Brummitt data;
genera which have been added in the process of importing
datasets can be identified by their GeneraKew_ID
beeing higher than 100000. These additional records
have not been edited at all, the names have only
been added to allow linking of the imported source
datasets to family names. They may be included in
the revised version of the Kew list under other
ID numbers.)
Assigning a source record to a genus in the table
may be hampered by the presence of generic homonyms.
Since the authors are not cited from the Kew list,
this is only relevant (for the functioning of the
GPC) if the family assignment differs between the
homonyms. The complete table can be provided upon
request.
Diacritics and
other special characters
The GPC database uses the Unicode standard
character set. These characters are converted to
HTML tags during a query when output to the
World Wide Web is generated. During
imports, we can convert any character encoding,
as long as the codes are unique and the
specification is provided with the dataset.
However, source data files which use ANSI or
HTML tags are the least troublesome.Characters
not in the ANSI character set must be
transliterated or encoded by the provider of the
dataset. This information should be included in
the description of the dataset.
(Direct financial contributions.)
Data conversions were supported by grants from
the New Phytologist Trust (US$1 500) and from
an anonymous donor ($ 750). The former has also
sustained IOPI from the start ($2 250 p.a.).
Setting up the initial version of the database
was supported by a grant from the International
Association for Plant Taxonomy ($1 000). The
implementation of the revised database version
was supported by a grant from an anonymous donor
($5 000). CODATA has granted up to $5 000 p.a.
for several years to assist the travel of key
Checklist Committee members. Further
development of the database, particularly the
interface to the Species 2000 project, is
financed by the European Union in the context of
the Species2000 europa project. A number of
projects are using the Berlin Model database and
the IOPI project is using output from those
projects (see Berlin
Model pages).
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