BZN Volume
63, Part 2, 30 June 2006
General
Articles and Nomenclatural Notes
General
Articles and Nomenclatural Notes with the
following titles were published on 30 June
2006 in Volume 63, Part 2 of the Bulletin
of Zoological Nomenclature
Copies
of these General Articles and Nomenclatural Notes
can be obtained free of charge from the Executive
Secretary, The International Commission on Zoological
Nomenclature, c/o The Natural History Museum,
Cromwell Road, London SW7 5BD, U.K. (e-mail: iczn@nhm.ac.uk).
ZooBank: ICZN’s
open-access web-based register of all new animal
names and original descriptions
Andrew Polaszek (Executive
Secretary, ICZN, London, U.K.)
Why do we need ZooBank?
Descriptions of new animal species and associated
nomenclatural acts are currently ‘hidden’ in thousands
of specialised journals and other publications such as monographs
and CDs. This process greatly reduces the ‘visibility’ of
animal names and nomenclatural acts. Establishing ZooBank as
a mandatory register of these names will largely alleviate
this problem. Not only will animal taxonomic data be freely
available, but also an alerting-service targeting taxa of interest
to particular user groups will be provided. Completeness of
the animal species register will be achieved by having registration
of new names as an ICZN requirement for availability, along
with retrospective registration of existing names.
With Code-compliance built into the registration process, an opportunity
to
introduce unprecedented stability into zoological nomenclature
is being provided. The ZooBank interface will provide automatic
checking for Code-compliance, and thus prevent new homonymy,
stabilise spellings, fix genders and stems, and provide stability
in gender agreement. As well as increased stability, the ZooBank
register will provide an opportunity for increased quality
control in animal nomenclature. Current issues such as the
presence or absence of type specimens, accepted categories
of type depositories, the use of offensive names, auctioning
of names and other ethical issues, can be dealt with by amendments
to the present Code. ZooBank will enable the tracking of names
and hence facilitate the correction of many problems prior
to publication and name availability.
As animal taxonomy moves away from its traditional journal or monograph
base towards the internet, the role of a mandatory register increases in importance.
Without such a register, web taxonomy would rapidly become unmanageable, and
thus ZooBank will facilitate ‘true’ web taxonomy – i.e. taxonomy
that exists only on the internet. If web taxonomy is to become a reality, however,
an effective and fair peer-review system still needs to be developed.
A possible additional benefit of ZooBank would be universal availability
of
descriptions. Making the inclusion of original descriptions
mandatory would be very difficult to achieve, partly for reasons
of current copyright laws. However, ZooBank will provide a
voluntary field for original descriptions (e.g. in pdf format),
with no limit on numbers of illustrations. The advantages to
both authors and publishers of having these descriptions freely
available, with links to the original papers, will rapidly
become apparent. Several prominent life sciences publishers
have already agreed to make such information available to ZooBank.
The nature of ZooBank as an (eventually) mandatory name register
clearly separates it from other databasing initiatives such
as Species 2000, ITIS, uBIO, Zoological Record / ION and ECAT.
How will ZooBank work?
Authors or third parties will be provided with the ZooBank online registration
form for the submission of registration information. The usual taxonomic fields
will be included, with additional fields for Code-compliance, type depositories,
gender, stem, type locality details (optional) and, as discussed above, the
description and figures (optional). Registration can be both pre- and post-publication,
and either primary (by the author(s)) or third-party. Registration will be
based on the GUID/DOI (Globally Unique Identifier/Digital Object Identifier)
system. Development of GUIDs for ZooBank will be undertaken in close cooperation
with GBIF (the Global Biodiversity Information Facility) and TDWG (the Taxonomic
Databases Working Group). Assigning GUIDs to animal names and taxonomic acts
will have several parallels with the assignment of accession numbers to gene
sequences in GenBank. Also, as with GenBank, journal editors and publishers
will require authors to register new taxa and nomenclatural acts with ZooBank.
As discussed above, publishers will be encouraged to allow the inclusion in
ZooBank of descriptive/nomenclatural sections of published work.
During the pre-publication phase there will be a holding period during
which as yet unavailable names are not openly accessible. Code-compliance checks
are built into the registration process, and registration will remain free
to all users. ZooBank will be kick-started by making Zoological Record’s
Index of Organism Names data available via a ZooBank portal in mid-2006. Following
this, an initial prototype/proof of concept will be made available as a voluntary
system for a period of nine months to monitor its uptake.
Will ZooBank be accepted?
A registration system for plants was introduced
into the Botanical Code at the time of the Tokyo Botanical
Congress (1993) but was not ratified at the following St Louis
Congress (1999), although a voluntary registration system ran
for several years. Several reasons have been put forward to
explain why plant and fungal taxonomists failed to adopt mandatory
registration. Firstly, botanists have far fewer names to deal
with, about one tenth, compared with zoologists. Secondly,
there is already a very effective universal checklist of plant
names in the form of the International Plant Name Index (IPNI).
Finally, a section of the botanical community was unhappy about
the way in which the registration clause had been introduced
into the Tokyo Code. For bacteria, a mandatory registration
system has been in place since 1980. Bacterial names are considered
to be validly published only if published in the International
Journal of Systematic and Evolutionary Microbiology (formerly International
Journal of Systematic Bacteriology). Mycologists have
recently introduced MycoBank, a voluntary registration system.
In order to gauge acceptance by the zoological community, a dedicated
discussion list for ZooBank has been established at http://list.afriherp.org/mailman/listinfo/zoobank-list.
It has been suggested that mandatory registration of organismal names is authoritarian,
and/or imperialistic, as well as requiring extra work for taxonomists. For
this reason, the development and implementation of ZooBank need to be done
in as user-friendly a manner as possible, and registration needs to be made
straightforward. We need to be able to demonstrate that the benefits of ZooBank
far outweigh any additional effort and resources required to create it. With
the cooperation of Zoological Record staff, at least in the initial stages
of development, and provision for third party registration, much of the burden
is potentially lifted from authors. However, extra resources for the development
of ZooBank are clearly necessary, and a business plan is therefore being developed
which will be available in mid-2006. Funding will be sought from a variety
of sources, including charitable trusts, foundations, and national and international
donors.
To a certain extent, the establishment and acceptance of ZooBank will
depend upon the adherence of zoologists to the ICZN Code rather than adoption
of any other proposed nomenclatural systems such as the Phylocode or Biocode.
The experience of the last few years suggests such adoption of alternative
codes extremely unlikely.
The advent of web-based taxonomy seems inevitable, and thus many of the
aspects of ZooBank and the ICZN Code that are affected by traditional journal
or monograph-based publication will cease to be relevant. A scenario whereby
the act of registration would effectively constitute publication is clearly
a strong possibility in the near future. Before that can happen, a rigorous
and democratic peer-review system needs to be in place to enable solely web-based
taxonomy.
Finally, the year 2008 represents 250 years – a quarter of a millennium – of
Linnaean zoological nomenclature. It would be extremely timely if the ZooBank
register were to be complete for retrospective registration, and up to date
for new animal names, by that date.
ZooBank and Zoological
Record: a partnership for success
Nigel J. Robinson (Director,
Operations & Development, Thomson Zoological Ltd, York,
U.K.)
Having served the zoological
research community for almost 150 years, Zoological Record
(ZR) is now the oldest continuing index to the life science
literature and contains the most complete and up to date record
of animal taxonomy in the World. Initiated by a group of scientists
associated with the British Museum in 1864, ZR was supported
by the Zoological Society of London until 1980 when BIOSIS
undertook production operations as joint publisher. In 2004,
BIOSIS was acquired by the Thomson Corporation. Now backed
by a global organization, and despite the many changes, highs
and lows, over the years, ZR still continues where many others
have failed, and still has its original mission to provide
a service to the scientific community, with particular reference
to biodiversity and taxonomy.
Today, ZR is produced by a team of 32 staff based in York, U.K. Taxonomic
indexing is carried out by graduate zoologists using highly sophisticated systems
and data capture procedures developed in-house specifically for ZR. These systems
produce accurate output quickly, with articles generally being processed within
2–11 days of receipt; they use form-based validation and data entry with
over 100 integrated checks to ensure data quality, and have allowed ZR to build
publisher relations so that comprehensive coverage can be obtained in a timely
fashion. ZR has never been more accurate, complete or up to date.
While ZooBank should clearly be driven and organised by ICZN, as a partner
ZR can help by contributing data and back-end processing to enable the project
to become reality much earlier, with greater ongoing efficiency, and with more
complete data than would otherwise be possible. Many of the requirements of
ZooBank are already in place in ZR data capture and processing, or are contained
within the newly enhanced and freely accessible Index to Organism Names service
(www.organismnames.com). These features include alerts to new names, ability
for authors to submit names and publications for inclusion, original description
references, links to recent articles containing the name, links to ZR and on
to full text publications, links to web resources for the name, etc. So, ZR
is in an ideal position to support the ZooBank names registry project.
Given the existing coverage of ZR, and the processing already in place,
it is
proposed that new names published in the scientific literature
are captured and indexed by ZR, validated for Code-compliance,
and registered in ZooBank as part of the routine ZR processing.
Working with ICZN, it would be relatively easy to check Code-compliance
based on ZR data capture. Much of the information required
to perform these checks is already gathered as part of normal
indexing operations. Any published articles submitted by authors
and publishers could be routed the same way ensuring registration
and inclusion of associated biology and nomenclatural acts
in ZR with minimal costs and overheads for authors, publishers
and ICZN. In addition, as all years of ZR will be made available
electronically during 2006, the ZR data can be used to assist
in retrospective registration of existing names linking to
the most comprehensive set of animal names data in the world.
As a sign of commitment to the project, Thomson plans to continue working
with such organizations as the Global Biodiversity Information Facility (GBIF)
and Species 2000 (the Species 2000 webservers are hosted and maintained by
Thomson), and will provide support to ICZN, assisting in the development of
a prototype ZooBank over the coming months. The involvement of a commercial
company as a partner brings the advantage of advanced, ready built technology,
and stability/longevity going forward. With links to the published literature,
much as full text articles, ZR is an ideal partner to accelerate, assist and
participate in the ZooBank project and we look forward to a fruitful partnership.
ZooBank and GBIF
Per de Place Bjørn
(GBIF, Copenhagen, Denmark)
The Global Biodiversity
Information Facility is a megascience facility aimed at making
the world’s biodiversity data freely and universally
available via the internet,and sharing primary scientific biodiversity
data to benefit society, science and a sustainable future.
GBIF participants currently comprise 47 country members and
31 international organisations (including ICZN). There are
currently 149 GBIF data providers, serving data from 517 collections.
To date, these have contributed more than 73 million specimen
and observation records, and more than 500,000 species records
(more than a million names), most of these from the Species
2000/ITIS Catalogue of Life project. The data include, however,
a large number of unregulated
names from labels and field observations, and GBIF plans to
develop tools to directly serve taxonomic data to GBIF from
providers.
How can GBIF collaborate with ZooBank and thereby enhance taxonomy? GBIF
and TDWG are setting out to form a community around GUIDs for biodiversity
data. A workshop is scheduled for early February 2006 to explore infrastructure,
with the possible adoption of Life Science IDentifiers (LSIDs) or Digital Object
Identifiers (DOIs). LSID’s take the following format: urn:lsid:<domainName>:<namespace>:<objectId>[:<revisionId>];
so an LSID referring to a specimen record in the GBIF network (with identifiers
assigned centrally) could take the form: urn:lsid:gbif.net:Specimen:2706712
while a record from IPNI might be in the form: urn:lsid:ipni.org: TaxonName:82090–3:1.1.
Clearly the ZooBank project needs will be incorporated in this process. A GBIF-hosted
discussion list on GUIDs is available at: http://wiki.gbif.org/guidwiki/.
Other multi-disciplinary fields where GBIF is planning to have a role – and
where ZooBank data will be pivotal – are the development of standards
for web-wide integration of taxonomical working methods (Web-enabled taxonomy)
as well as standards for web-representation of broad biological information – Species
Pages.
The availability of ZooBank data will also be heightened by dissemination
through the GBIF portal as GBIF will form a link between taxonomically related
databases and databases about animal distribution and ecology, including data
related to conservation and genomics. Naturally, new entries can be immediately
available through the GBIF portal and network.
For instance, the linkage between specimens and observations and the
unique ZooBank entries will largely reduce ambiguity in biodiversity science.
The integration of existing, well-curated and reviewed Global Species Databases
as available through the Catalogue of Life Partnership may form a future structure
to enable retrospective capture and registration of animal names.
Implementing the digital
taxonomic revolution: alternative strategies for a web-based
registry of taxonomic names
Richard Pyle (Bishop Museum,
Honolulu, Hawaii, U.S.A.)
Registration, publication,
and availability can be defined for our present purposes as
follows: Registration is the process of entering a complete
record in the ZooBank registry. Publication refers to Code-compliant
published works, as defined in Chapter 3 (Articles 7–9)
of the 4th Edition of the ICZN Code. An available name is a
scientific name applied to an animal taxon that conforms to
the provisions of the Code. Below I will present the following
three scenarios relating to registration and publication, and
how they affect, and are affected by, the current Code: 1.
(Publication + Registration) = Availability (Polaszek et al.,
2005; ZooBank Technical Article, pp. 3–5); 2. Registration
= Availability (Polaszek et al., 2005; ZooBank Technical Article,
pp. 5–9); 3. Registration = Publication = Availability
(Doug Yanega post to ZooBank List, 22 Sep 2005).
1. Publication + Registration = Availability. To be available,
names and acts must be published in accordance with existing
Code rules, and be registered. Registration can take place
either before publication, or after publication. If before
or within two years after publication, the date of availability
is the publication date (figs. 1 & 2). If more than two
years after publication, the date of availability is the registration
date (fig. 3). The advantages of this scenario include relatively
small changes to existing taxonomic practice, rapid implementation
via an amendment to the 4th edition of the Code, the maintenance
of implicit quality control via traditional publication venues,
and consequently, perhaps, broader acceptance by the taxonomic
community. Possible disadvantages include a somewhat complex
procedure involving asynchronous publication and registration
events, arbitrary time periods affecting dates of availability,
and petitions to the Commission in certain special circumstances.
However, given the existing complexities of the ICZN Code these
procedures can hardly be considered as particularly complex.
Another possible perceived disadvantage would be an ambiguous ‘grey
zone’ between publication and registration when names
and acts are ‘assumed’ to be available, even though
technically not available until registered. Again, the probability
is that most authors will register new names prior to publication,
eliminating this problem entirely. While this scenario still
suffers from all the complexities and ambiguities associated
with traditional paperpublication entangled with nomenclatural
availability, it would hardly differ from current practice,
so would not really add up to an increase in complexity. Finally,
scenario 1 would require a (possibly extensive) increase in
the active role of ICZN Secretariat staff (and associated costs)
to process registration requests and verify Code-compliance
before issuing GUIDs and exposing registration details to the
public.
ق. Registration = Availability.
With this procedure, the process of registration itself is
all that is required for availability of new names and acts.
Prior or subsequent publication through traditional venues
is encouraged, but is not integral to nomenclatural availability
(fig. 4). Some advantages of this system would be that the
legalities of nomenclatural availability and the science of
taxonomy are disentangled from each other; there would be no
ambiguity about dates of availability; existing complexities
of nomenclatural availability of published works are moot,
and only minor increases to the active role of ICZN staff (and
associated costs) are envisaged. Possible disadvantages include
a fundamental change to the way taxonomic names and acts are
established (eliminating the publication process from the act
of nomenclatural availability). However, this would not necessarily
be a problem from the perspective of the taxonomists (i.e.
virtually the same as scenario 1), and in fact would only require
a change to the technical legality of nomenclatural availability,
not necessarily any change to taxonomic practice. To implement
this system, more extensive changes are also needed in the
Code, such that these could probably only be implemented in
a 5th Edition of the Code (perhaps 5–10 years away).
However, it will probably anyway take several years to work
out the details and demonstrate the feasibility via a working
voluntary registration system. Another possible objection is
that taxonomists would lose their primary benchmark for establishing
professional status, i.e. their CVs would have fewer publications
listed. Taxonomists’ professional status is established
by publishing articles on scientific taxonomy and classification,
which would continue exactly as before; only the legalities
of nomenclature would be dissociated from publications – not
the science of taxonomy. While it is possible that some journals
might not want to publish taxonomic descriptions if articles
no longer carry the ‘prestige’ of establishing
new names and acts in accordance with ICZN rules, it is also
true that prestige in scientific publicationscomes from the
quality of the science content of the published articles, and
not from fulfilling a legalistic technicality for nomenclatural
availability. Elimination of quality control/peer review from
the process of establishing new names and nomenclatural acts
could also be perceived as a disadvantage, but since the Code
requires neither peer review nor quality control, the scenario
would be no different from the current situation. It could
also be argued that the ICZN requirement for publication de-facto
forces most names and acts through peer review anyway. The
possibility that bad taxonomists (and non-taxonomists) might
abuse the system by registering hundreds of bogus and unneeded
names, perhaps for unscrupulous reasons (e.g. selling names
for money) is also unaffected by the choice of possible scenarios – i.e.
it always remains possible. The same goes for those taxonomists
who might never get around
to publishing the full description after the name is registered,
potentially creating many names without robust taxonomic definitions.
3. Registration = Publication
= Availability. Under scenario 3, the registration website,
ZooBank, would host a comprehensive, edited and peer-reviewed
online journal (such as Zootaxa) in which all names and acts
must be published. The science of taxonomy becomes part of
the nomenclatural process (by changes to the Code), and submitted
manuscripts are open to non-anonymous review by any interested
or concerned taxonomist (fig. 5). Major advantages of this
procedure include zootaxonomic publications appearing in a
single venue (as is now done for Bacteria), instead of scattered
across thousands of journals, and the prevention of unscrupulous
authors ‘stealing’ by trying to submit plagiarised
work to a journal that has a faster turnaround time. All manuscripts
would be examined by a large contingent of reviewers, instead
of just a handful, greatly improving the reviews as well as
democratizing the process. The reviews are also public, instead
of anonymous, so personal grudges or biases of the reviewers
are exposed to scrutiny by the whole community. Furthermore,
a dedicated nomenclatural journal would mean that the review
criteria will explicitly address all necessary aspects of Code-compliance
and proper nomenclature. Other advantages of an online review
process include speed
and openness to feedback. Above all, copyright issues would
cease to be a problem. This scenario would, of course, represent
a major and fundamental change to the way taxonomy is done,
both in terms of legalities of nomenclature as well as for
the science of taxonomy. With such major changes come particular
difficulties, but the trade-off may well be worthwhile. With
respect to online peer-review, it must be borne in mind that
many taxonomic groups do not have many (or even any) experts
who might serve as reviewers, and thus submitted manuscripts
may never receive peer-review. This problem is equally true
for traditional publication venues as well, but with only one ‘official’ taxonomic
journal with potentially thousands of regular contributors
and readers, there is a much better chance of finding someone
who is qualified to review the manuscript. As with scenario
2, above, more extensive changes to the Code would be required,
such that it could probably only be implemented in the 5th
edition, perhaps 5–10 years in the future. In any case,
it will probably take several years to work out the details
and demonstrate the feasibility via a working
voluntary registration system. It could be argued that such
a system would impose a huge burden on the taxonomic community
to provide peer reviews to 20,000+ new names each year, but
in fact the burden would be no more than already exists. For
every manuscript submitted and reviewed through the official
ZooBank online journal, one fewer manuscript would be submitted
to a traditional journal, so there would be no net increase
in the total number of manuscripts to review. A common argument
against such a scenario is that existing journals that depend
on taxonomic descriptions and nomenclatural acts to fill their
pages and maintain a subscriber base may be driven out of business.
Since when is it the job of scientists to keep journal
publishers in business? Journals exist to serve scientists,
not the other way around. Criteria for determining when a submitted
manuscript should be deemed ‘accepted’, and when
(and by whom) will always be a subjective and contentious issue.
This problem could be largely solved by having each manuscript
assigned to an impartial ‘referee’ whose speciality
is outside the particular taxon involved, and who is fully
familiar with the code – serving the same role as a journal
editor. Finally, the legalities of nomenclatural availability,
and the subjective science of taxonomy, would, for the first
time, be formally coupled under Code rules. Controversial as
this sounds, it may be that a significant proportion of zoologists
feel that quality control and peer review should be part of
the Code’s requirements for nomenclaturalavailability.
Copyright: the new
taxonomic impediment
Donat Agosti* & Norman
F. Johnson** (*American Museum of Natural History, New
York, U.S.A. and Naturmuseum der Burgergemeinde, Bern, Switzerland;
**Ohio State University, U.S.A.)
Copyright is a set
of exclusive rights granted by government for a limited time
to regulate the use of a particular form, way or manner in
which an idea or information is expressed. In law, an exclusive
right is the power or right to perform an action in relation
to an object or other thing which others cannot perform. The
law may require that a person seeks such rights through application,
or it may automatically grant such rights. Exclusive rights
may be granted in intellectual property law. Most governments
recognize a bundle of exclusive rights in relation to creative
and scientific works and property under the umbrella term ‘intellectual
property’. An example is copyright (Source: Wikipedia).
An example of copyright law impeding progress in taxonomy is revealed
if we examine the number of publications dealing with ant species in 2003,
when fewer than 5% were open-access and the remainder copyrighted.
In 2001 UNESCO produced the Universal Declaration on Cultural Diversity
which reads: ‘While ensuring the free flow of ideas by word and image,
care should be exercised that all cultures can express themselves and make
themselves known. Freedom of expression, media pluralism, multilingualism,
equal access to art and to scientific and technological knowledge, including
in digital form, and the possibility for all cultures to have access to the
means of expression and dissemination are the guarantees of cultural diversity’.
Recent years have seen an unprecedented rise in the number of scientific
and other documents being scanned, and in many cases made freely available
via the internet. However, we feel that the copyright issue is still far from
being addressed. In our opinion, taxonomic publications are ‘legal documents’,
they must conform to the Codes to make the nomenclatural decisions presented
valid. Thus everybody should have access to these legally binding documents.
Taxonomic descriptions are also factual knowledge, that is knowledge based
on direct observations. Thus, taxonomic publications, at least their descriptive
parts, cannot be copyrighted, and should be open access. Species (or taxa in
case of higher level revisions) descriptions can be considered the building
blocks or basic data elements of taxonomic publications. They are very rich
in detail. All the other elements of a publications are inferred from the analysis
and synthesis of taxon descriptions. The descriptions are also the ‘legal’ element
of the publication in compliance with the ICZN Code. Species descriptions can
be further resolved into the basic units, characters in the description sensu
stricto, and the specimen records, which are a species at a given time at a
given locality, i.e. a collecting event. They could be enhanced by shared ontologies
and gazetteers.
The deconstruction of text documents to, for example, XML format would
be a means of placing descriptions in the public domain while circumnavigating
copyright issues. Several initiatives for data domains and standards are currently
being developed, including the Taxonomic Concept Schema, ABCD, DarwinCore,
TaxonX and TaXMLit. Such document deconstruction projects could finally put
species descriptions where they belong: firmly in the public domain, and allow
third parties to build applications to mine, extract and integrate the very
data-rich content of most descriptions.
Name Registration:
One fewer impediment to taxonomy
James B. Woolley (Texas
A&M University, U.S.A.)
We are currently witnessing
a renaissance in systematics. Traditional approaches to collecting,
specimen preparation and study, and the production of, and
access to, published work, have been revolutionized through
new technologies available to taxonomists. Digital technologies
have changed all the rules, and taxonomic collections, literature,
expertise, digital libraries and virtual monographs need to
become distributed, virtual research tools and education resources.
The new taxonomy needs to be web-based, providing a single,
global point of access; distributed—for example, there
are currently more than 350 web sites just for Lepidoptera;
authoritative—we need an electronic catalogue of life;
accessible to multiple audiences and relevant to societal concerns
such as natural resource management, invasive species, agriculture
and medicine. Taxonomic publications should not be end points,
but ‘version control’ devices.
However, there are currently several impediments to the implementation
of this new taxonomy, including lack of funding (most funding for systematics
is devoted to constructing molecular phylogenies, not taxonomy), a dearth of
taxonomists, difficulties inherent in the science itself, and scattered resources
in terms of both specimens and literature. Funding issues have been recognized
by the USA’s National Science Foundation, with their implementation of
Planetary Biodiversity Inventories, revisionary syntheses in systematics and
the PEET (Partnerships for Enhanced Expertise in Taxonomy) programme. The establishment
of ZooBank will go a long way towards providing centralized sources of zoological
taxonomic information.
The overarching finding of the recently published ‘Atkins Report’ (Atkins
et al., 2003), by authors from both academia and industry, is that a new age
has dawned in scientific and engineering research, pushed by continuing progress
in computing, information, and communication technology, and pulled by the
expanding complexity, scope and scale of today’s challenges. The capacity
of this technology has crossed thresholds that now make possible a comprehensive ‘cyberinfrastructure’ on
which to build new types of scientific and engineering knowledge environments
and organizations, and to pursue research in new ways and with increased efficiency.
This cyberinfrastructure will be used to build more ubiquitous, comprehensive
digital environments that are interactive and functionally complete for research
communities in terms of people, data, information, tools, and instruments.
Such a cyberinfrastructure will include grids of computational centres, some
with computing power second to none; comprehensive libraries of digital objects
including programmes and literature; multidisciplinary, well-curated, federated
collections of scientific data; thousands of on-line instruments and sensor
arrays; convenient software toolkits for resource, discovery, modelling and
interactive visualization and the ability to collaborate with physically distributed
teams of people using all of these capabilities. Again, according to the Atkins
Report, many contemporary projects require effective federations, distributed
resources (data and facilities) and distributed, multidisciplinary expertise.
Examples of ‘Virtual Science Communities’ include: National Ecological
Observatory Network (NEON), National Virtual Observatory (NVO), Space Physics
and Aeronomy Research Collaboratory (SPARC), Grid Physics Network (GriPhyN),
Biomedical Informatics Research Network (BIRN) and National Science Digital
Library (NSDL). During the last three years NSF has sponsored workshops on
taxonomy, systematics, imaging and databasing. These workshops have called
for a national framework for taxonomic research and natural history collections.
One vision of this framework is the LINNÉ project (Legacy Infrastructure
Network for Natural Environments). LINNÉ would be a distributed, virtual
taxonomic cyberlaboratory, of which each collection or taxonomic research facility
is potentially a node.
Implementation of LINNÉ will modernize the national infrastructure
for taxonomic research with high resolution two- and three-dimensional surface
and internal scanning using computer tomography, remote-controlled digital
microscopy, comprehensive digital libraries, modern collection facilities,
the provision of comprehensive access to taxonomic and collections information
worldwide, and new tools for education and outreach. This ‘virtual research
platform’ will address the so-called ‘big questions’: What
are earth’s species, and how do they vary? How are species distributed
in geographical and ecological space? What is the history of life on Earth,
and how are species interrelated? How has biological diversity changed through
space and time? What is the history of character transformations? What factors
lead to speciation, dispersal and extinction?
Virtually all of the necessary technology is already in place or will
be in the next few years in order to implement this vision. Many national and
international activities are already underway, and initiatives such as the
National Biological Information Infrastructure (NBII) are linking databases,
informatics products and analytical tools for data sharing among governmental
agencies, NGOs, academic institutions and industry. Similarly, GBIF, operating
at the intersection of science, policy and applications, currently comprises
47 member countries, and is especially concerned with access, diversity of
data, setting taxonomic standards (including the development of ECAT, the Electronic
Catalogue of Life), data quality, data cleaning tools, interoperability (including
GUIDs – global identifiers for specimens and collections) and collaboration.
GBIF can provide critical components of cyberframework for LINNEu, and in exchange,
LINNEu will provide data to GBIF. The SYNTHESYS initiative includes 20 European
natural history museums and botanic gardens and is funded through the FPVI
Integrated Infrastructure Initiative Grant. Starting in 2004, the objective
of this 5-year project is to create an integrated European infrastructure for
researchers in the natural sciences. 20 institutions and 11 national taxonomic
facilities are involved in a two part plan comprising access and networking
activities. Other initiatives include the European Network for Biodiversity
Information (ENBI), the European contribution to GBIF, the CHRONOS project
for the earth sciences community, the National Ecological
Observatory Network (NEON) and the Natural Sciences Collections
Alliance. Thus the foundations are already demonstrably in
place, and the challenge is not to invent all of the necessary
components de novo, but rather to identify what is already
there, to implement the new cyberinfrastructure and integrate
these components into an operational system. To do this will
require that we establish a common vision and research agenda,
and that we work as a community, worldwide to achieve it. This
will require a change in our scientific culture necessitating
an integrated, ‘big-science’ approach, and we need
to identify common goals and work together. Other communities
have done this, but there were some tough transitions. For
example, particle physicists had terrible problems with career
recognition and rewards with the switch to a big science paradigm.
Other challenges include the fact that it will cost billions
of dollars; will require Congressional and State action; it
will require a unified user community, will take many years
and will not be easy. However, if successfully achieved, LINNÉ will
preserve our heritage, revitalize taxonomy, and will be the
most important new tool available to biologists in the 21st
century.
Reference
Atkins, D.E., Droegemeier,
K.K., Feldman, S.I., Garcia-Molina, H., Klein, M.L., Messerschmitt,
M.L., Messina, P., Ostriker, J.P. and Wright, M.H. (2003).
Revolutionizing science and engineering through cyberinfrastructure.
Report of the National Science Foundation Blue-Ribbon Advisory
Panel on Cyberinfrastructure, 1–52. NSF, Washington,
D.C.
