Report
GBIF Nomenclator
Workshop,
A Workshop was held at the GBIF Secretariat, accommodating
representatives from the main biological nomenclators
(organisations that hold indexes of scientific names applied to organisms –
normally without any assertion of systematics or
inclusion of auxiliary biological information) and a few other organisations
with expertise in storing and communicating taxonomic names.
The main goal of the workshop was to research the possibilities for
incorporating the data held by the Nomenclator organisations into the GBIF
Network.
The nomenclators’ data would serve a number
of functions. In some cases they cover higher taxa that are not so far
available as full catalogues; names or nomenclatural acts may be included that
for some reason were omitted from catalogues or have been published more
recently than the available catalogue.
Incorporation of the nomenclators’ data will
need at least two main topics to be addressed: Issues of Intellectual Property
Rights and issues of protocol and exchange standards to make the arrangement
work.
The meeting was held in a very collaborative and productive atmosphere
and all organisations present did in principle agree to make their data
available to GBIF.
However – as management practices, data storage, and the available
resources vary dramatically among the organisations – bilateral agreements
between GBIF and the individual organisations will need to be put in place.
Agreements – probably in the form of Memoranda of Understanding – will have to
take into account the ways in which GBIF can support the data owners by providing
source recognition for the data used and by providing feedback about the
utilization of the data in the GBIF network. IPR will have to be specified. In
special cases, the Secretariat will probably be able to provide some assistance
with setting up the connections between the nomenclators
and the GBIF Network.
As a baseline for the discussions to lead to such agreements a summary
of the presentations given by the nomenclators and
the discussion about how what would be needed to make them join the GBIF
network is given below, following the agenda of the meeting:
Agenda, Nomenclator Workshop
Venue: GBIF Secretariat, Universitetsparken
15,
Participants:
ECAT Science Subcommittee Chair:
Representing nomenclator organisations:
ICTV Lois Blaine
IF Paul Kirk
ICSP B. J. Tindall
Bergey's
Manual George
Garrity
INA Richard Moe
ZR Nigel Robinson
uBIO
CoLp Mike
Ruggiero, Frank Bisby
IPNI Sally Hinchcliffe
The ECAT Science Committee Chair Chris
Lyal
From the GBIF Secretariat
Director Jim
Edwards
Hours:
Meeting starts at
Topics:
uBio – Universal Biological Indexer and
Organizer (
uBio develops the Taxonomic Names
Server, a catalogue of names and classifications that enable enhanced searches
in literature resources by linking names together, relation. The system is
originally developed for the Library community but has great potential in
scientific use.
Names are stored in a layered model, where
classifications/opinions/taxonomy (in ClassificationBank)
is abstracted from the factual names occurrences together with objective
synonyms (in NameBank). The layers are held together
by a Management System.
Numerous application tools for retrieving
and storing information in the system are developed.
Special emphasis on tools
to match lists of names coming from users with the names already occurring in
the system.
The Online Computer Library Center’s (OCLC) WorldCat
reference catalogue’s (http://www.oclc.org/worldcat/default.htm)
validation procedures were demonstrated as a possible solution for rapidly
getting the system populated with names which then subsequently could become
peer evaluated.
uBio would like to collaborate
with GBIF on developing the NameBank and share this
resource among the organisations.
The Catalogue of Life Partnership – CoLp
(Frank Bisby and Mike Ruggiero)
The CoLp operate a network of Global Species Databases and also some nomenclators are integrated with the system.
CoLp has a MoC
with GBIF, allowing GBIF to use their data in the GBIF Data Portal, provided
that proper source recognition is transmitted with the data.
ICTVdB – The Universal Virus Database International
Committee on Taxonomy of Viruses (Loin
The ICTVdB is the
de facto authority on both nomenclature
and taxonomy of vira and stores a list of approved
virus names.
Virus taxonomy has no kingdom or phyla but
handles strains and isolates. The ICTVdB, however,
handles names only at the species level and above.
The data is considered not complete, missing
the rejected names.
The names are stored in a DELTA based
system which is scheduled to move into XML.
Names are freely available through website
ICTVdB is already incorporated in
the
IPNI - The International Plant Names Index (Sally Hinchcliffe)
IPNI is a collaboration
between The Royal Botanic Gardens,
The data sits in a highly integrated
database system which provides a contributing mechanism and is machine
reachable in a number of formats. The system can deliver query results as XML –
there is a 5000 names limit per request.
A condition for utilizing the data is that
corrections are provided back into the system.
APNI has a larger amount of data associated
with the names than the other sources.
IPNI has at present limited programming
hours and need funding for additional work. However, great interest in
collaboration is expressed.
Bergey’s Manual Trust
Bergey’s Manual can be seen as a
Global Species Database (GSD) of all bacteria, containing 6466 prokaryote
species and an authored taxonomy. The Manual is a commercial product, published
by Springer-Verlag, the content forming base for
income for the Trust.
The data is – however – available free of
charge in the form of pdf-files. The bacterial genera
can be downloaded form the Trust’s homepage, the
species can be acquired by contacting the Trust.
Data is stored in a highly advanced system,
stream-lined for publishing. The format is a specialized SGML.
The taxonomy has links to GenBank
In order to establish machine access to the
system, a mutual benefit statement will have to be developed.
International Committee on Systematics of
Prokaryotes – ICSP (Brian Tindall)
Modern prokaryote nomenclature has its
starting point at January 1. 1980. The ICSP (then the International Committee
on Systematics of Bacteria – ICSB) was involved in
publishing the Approved Lists of Bacterial Names (ALBN) containing the
bacterial names and combinations considered to have standing in nomenclature as
of that date. Names in use previously, but not appearing on that list lost
standing in nomenclature.
The International Journal of Systematic and
Evolutionary Microbiology (IJSEM) (formerly International Journal of Systematic
Bacteriology) is the official organ of the ICSP, and is published for IUMS by
the Society for General Microbiology (UK)
– the journal in
which a new prokaryote name or new combination must appear in order to be
validly published.
Hereby the name is also registered/indexed,
which means that the ICSP officially publishes a complete nomenclatoral
resource of prokaryotes. This comprises
original publications in the IJSEM as well as the “Validation Lists”, in which
new names or new combinations published outside of the IJSEM may be validly
published (and registered/indexed). In addition, the “Notification Lists” in
the IJSEM summarises formal nomenclatural changes which have appeared in
articles in the IJSEM. Both the Validation Lists and the Notifications Lists
are edited by the “List Editor” of the IJSEM, Jean P. Euzéby.
The List of Bacterial Names with
Standing in Nomenclature (LBSN) – a combination of the ALBN and the names
appearing in the IJSB/IJSEM, is, compiled by J.P. Euzéby. The LBSN can be accessed at the LBSN website in HTML
format.
Index Fungorum – IF (Paul Kirk)
IF is the
nomenclator of Fungi. Fungal names are available on-line through the
IF web-site and as a web-service. For IPR reasons, detailed data concerning
newly added names are not served.
The IF
web-service could relatively easily be integrated with GBIF. Data from the
last five years will be provided with limited record contents.
Index to Organism Names – ION (Nigel Robinson)
The animal names appearing in
Zoological Record are being integrated into the ION which is searchable on the
web. The issues dating back to 1970 have been scanned and incorporated. A CGI
interface is available, possibilities for a Web-service
Through the 2003 Seed Money
award to BIOSIS it is already established that GBIF will receive a package of
all names appearing in ZR from 1970 to present. The access to earlier data will
be topic of negotiation.
Index Nominum Algarum
– INA (Richard Moe)
The INA stores image files of
a card file for all published algal names. The card files are in the process of
being digitized into a database. The data include the basionym
along with type information, locality and to some extend new combinations. INA’s web-site gives access to all images and all digitized
names. No machine reachable data available.
INA is in principle interested
in providing data to GBIF, but infrastructure and resources will have to be
worked out in order to make it happen.