Transcript Document

Initiatives to co-ordinate and realise
Southern Africa’s biodiversity heritage
Mervyn W Mansell
Dept of Zoology & Entomology
University of Pretoria
&
Animal and Plant Health Inspection Services
United States Department of Agriculture
c/o U.S. Embassy, Pretoria
CODATA Workshop – CSIR, Pretoria. 5-7 September 2005. Strategies for Permanent Access to Scientific information in Southern
Africa: Focus on Health and Environmental Information for Sustainable Development
The past decade has seen great progress in the development
of biodiversity science, and particularly in taxonomy and
systematics
There have been positive advances in the recognition of
systematics and taxonomy as sciences that are fundamental to
many other disciplines
Also in the funding of biodiversity science, especially
biosystematics
Modern techniques such as molecular and phylogenetic
analyses and biogeography and GIS modelling has taken
systematics into the realms of cutting-edge science
There is also an increasing awareness of the myriad products
that can be derived from, and are dependent upon biodiversity,
which benefit society, science and the environment
The development of bioinformatics and associated software
has placed powerful tools in the hands of biologists for
accumulation and dissemination of biodiversity data, further
enhancing the fundamental position of taxonomy and systematics
Southern Africa is ranked the third-most
biologically diverse region in the world
It contains between 250 000 and 1 million species,
many of which are unique to this area
Because the region’s biota is so diverse, we have yet
to establish the true extent of this diversity
We have a reasonable knowledge of our vertebrate
fauna
Estimates of the plant diversity (22 000 species),
10 % of the world’s flora, is still considered to be an
under-estimation
(Herbert, Smith, Hamer & Scholtz 2001)
The situation for invertebrate animals is poorly known –
with only about one third to half of the species
described (Scholtz & Chown 1995)
Micro-organisms, especially fungi, are even more
neglected (Eicker & Baxter 1999)
This rich resource can neither be conserved nor used to
the benefit of humanity until it is made known and
studied
(Herbert, Smith, Hamer & Scholtz 2001)
Major strides have been made by the plant sciences
community under the leadership of the National
Botanical Institute (NBI) with programmes such as:
SABONET
PRECIS Database
Popular and scientific publications that have raised
awareness of southern Africa’s rich botanical heritage
Excellent infrastructure
The South African National
Biodiversity Institute was
established on 1 September
2004 through the signing into
force of the National
Environmental Management:
Biodiversity Act 10 of 2004 by
President Thabo Mbeki.
The Act expands the mandate
of the National Botanical
Institute to include
responsibilities relating to the
full diversity of South Africa's
fauna and flora, and builds on
the internationally respected
programmes in conservation,
research, education and visitor
services developed over the
past century by the National
Botanical Institute.
Vision: To be the leading institution in biodiversity
science in Africa, facilitating conservation, sustainable
use of living resources, and human wellbeing
Mission: To promote the sustainable use, conservation,
appreciation and enjoyment of the exceptionally rich
biodiversity of South Africa, for the benefit of all people
(SANBI Website)
Many other successful initiatives have also been launched in
South Africa during the past decade to address:
•
Application of biodiversity data to ecological monitoring and
predictive modelling
•
The so-called “taxonomic impediment” – the shortage of
skilled taxonomists and systematics practitioners to
describe, classify and identify the rich fauna
•
Electronic documentation of biodiversity data held in
biological collections locally and abroad
Southern African Loop of
Bionet International
SAFRINET was established in 1996 by the
Southern African Development Community
(SADC) as a technical co-operation network
to promote and sustain realistic self-reliance
in biosystematics services, particularly for
invertebrates and micro-organisms. The
network became operational in 1997
SAEON A DEVELOPING FACILITY OF THE NRF FUNDED BY DST
SAEON is a research facility that establishes and
maintains nodes (environmental observatories, field
stations or sites) linked by an information management
network to serve as research and education platforms for
long-term studies of ecosystems that will provide for
incremental advances in our understanding of ecosystems
and our ability to detect, predict and react to
environmental change. The core research programme will
strive to distinguish between anthropogenic and natural
change as well as to unravel the relations between social
change and ecosystem change.
SA ISIS
SA-ISIS is a research project to develop a framework and methodology for
integrating distributed spatial databases, information and decision support
tools across the Internet.
Within SA-ISIS, components of the previously separate initiatives which are now
included in the project, and funded by the Innovation Fund, are identified as:
* Agriculture.
* Biodiversity and conservation.
* Coastal and marine.
The aim is to make both spatial and nonspatial data and information on the
environment available and accessible to a wide stakeholder group through the
connectivity of the Internet. The SA-ISIS Project is a multicollaboration, integrated
initiative. The principal investigators include RC-ISCW (Agricultural Research Council Institute for Soil, Climate and Water); CSIR Environmentek (Water, Environment and
Forestry Division) and CSIR icomtek (Information and Communications Technology);
and the University of Pretoria, Department of Zoology & Entomology and Centre for
Environmental Studies.
SOUTH AFRICAN SOCIETY OF
SYSTEMATIC BIOLOGISTS
Was formed in 1999 to provide greater cohesion
between the various disciplines involved in
taxonomic and systematics research
One of the major achievements of this society
was the formulation of a document that brought
critical issues relating to taxonomy and
systematics research in South Africa to the
attention of the Dept of Arts, Culture, Science
and Technology (DACST) and the National
Research Foundation (NRF)
Herbert, DG, Smith, GF, Hamer, ML & Scholtz, CH (2001) Taxonomy and
systematics research in South Africa: vital research facing a crisis in
capacity and resources
South Africa’s biological heritage is diverse and unique, but much of it
remains undocumented
It is consequently unavailable for application in all other relevant fields
Taxonomy and systematics research is a fundamental biodiversity science
that has a critical role to play in the implementation of government policy
and in South Africa’s ability to meet its international commitments – such
as the CBD.
Museums and herbaria are priceless and irreplaceable reference facilities
that record our biological heritage – yet very little financial support is
available for biosystematics research
Despite numerous warnings South Africa’s museums and herbaria are
facing crippling financial difficulties and capacity in this sector continues
to decline at an alarming rate
Taxonomic capacity and systematics research is in danger of falling below
critical mass levels, and our ability to contribute in a broader African
context is threatened.
A co-ordinated, national initiative focussing on fundamental biodiversity
research, with the support of stakeholder government departments is an
urgent priority.
(Herbert, Smith, Hamer & Scholtz 2001)
This document received a most positive
response from the National Department
of Science and Technology (DST) and
the National Research Foundation (NRF)
Directly led to the establishment of the
South African Biosystematics Initiative
(SABI)
(Ms Marjorie Pyoos – now Deputy Director General of DST)
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The issues that SABI was to address included:
Breaking down of ivory-towerism – dialogue and
collaboration between various disciplines involved in
taxonomic and systematics research to confront
common issues
The so-called “taxonomic impediment” – the shortage
of skilled taxonomists and systematics practitioners
to describe, classify and identify the rich fauna
Attract new and innovative students to the science
of taxonomy and systematics
Improve the image of taxonomic research
Address a shortage of funding for taxonomic
research
Application of taxonomy and systematics in the
generation of demand-driven products to benefit,
society, science and the environment
Electronic documentation of biodiversity data held in
biological collections locally and abroad
GBIF was established by the OECD (Organization for Economic Cooperation and Development) megascience working group on
biological informatics that was established in January 1996.
In December 2000 an invitation to participate in GBIF was sent to
Science Ministers of all countries and economies.
The opening meeting took place in Montreal, Canada in March
2001
In June 2001 Copenhagen was chosen to host the Secretariat, with
Dr Jim Edwards as Executive Secretary and Director of the
Secretariat
The focus of GBIF is to make the world’s primary
biodiversity data freely available on the internet
GBIF has four main focus areas:
ECAT – Electronic Catalogue of the Names of Known Organisms
DIGIT – Digitization of Natural History Collections
DADI – Data Accessibility and Data Interoperability
OECD – Outreach and Capacity Development
It also operates through a system of NODES where participant
countries and Associates form a network of sites each with its
own portals and data-gathering activities.
SABIF – the South African Node of GBIF came into being in
April 2003 when Minister Valli Moosa signed a MoU with GBIF
South African Biodiversity Information Facility
Managed under the auspices of the NRF – Project Manager: Ms Renee le Roux
In signing the MoU South Africa has agreed that a co-ordinated
international scientific effort is needed to enable users throughout
the world to discover and use the vast quantities of biodiversity
data available
WITH THE VISION
TO CONTRIBUTE TO SOUTH AFRICA'S SUSTAINABLE
DEVELOPMENT BY FACILITATING ACCESS TO BIODIVERSITY
AND RELATED INFORMATION ON THE INTERNET
The missions of SABIF are to:
Promote the sharing of data and information under a common set of
standards by:
Developing and maintaining metadatabases
Establishing and maintaining a web portal
Providing funding for data digitisation
Providing funding for data provider interface
Facilitating the development of application tools for data use
Encouraging networking and co-ordination of activities
Contribute to education, training and capacity development for
promoting national access to data
Facilitate marketing and awareness raising of the benefits and
applications for end users
Advise on national and international initiatives
SABIF Portal was formally launched on 7 June 2005
and can be viewed at:
www.sabif.ac.za
Already four data providers:
Albany Museum, Grahamstown
South African Institute for Aquatic Biodiversity,
Grahamstown
Iziko Museums, Cape Town
Avian Demography Unit, University of Cape Town
DATABASES
Comprise the core element in the digitization of both specimen
(collection) and species (taxonomic) data
Vast amounts of specimen-associated data are incarcerated in
biological collections throughout the world. These data are an
untapped source of immense value to many fields of human endeavour,
ranging from agriculture to biodiversity, medicine, sustainable use,
tourism, botanical and zoological research and conservation
The only way to liberate and employ collections and taxonomic data is
through electronic databasing, and the dissemination of these data
via the internet in the form of PORTALS such as those of GBIF and
SABIF, WEB PAGES, CDs and even HARDCOPY PUBLICATIONS
For a comprehensive overview of the applications of biological specimen data,
consult the paper: Uses of Primary Species-Occurrence Data by Arthur Chapman
on the GBIF website
Modern and burgeoning database technology is placing
very powerful tools into the hands of biologists and
large amounts of integrated data are now becoming
instantly available
Databases also provide “virtual collections” for
research and as insurance against disaster
Emphasize the relevance and justification for
centuries of museum-based research and accumulation
of collections
Museums and institutions will continue to hold
custodianship (Not ownership) of their collections and
associated data
These data can be provided to portals such as those
of GBIF and SABIF or other users, subject to agreed
principles
The database formats will differ depending on
organism type, and GBIF has produced tools, including
the Darwin and Linnaean Cores and the DIGIR interface
protocols that deal with disparities between databases
Databases should conform to the RELATIONAL
DATABASE philosophy and model because of the
numerous advantages inherent in this mathematicallybased system
Subsaharan Africa Points
Green – native range
Blue – invaded range within Africa
Predictive modeling by Townsend
Petersen
University of Kansas, Lawrence
Take Native Range Points Only
Build Ecological Niche Model
Overlay African Invaded Range Points as Test
Project to Entire World – (Potential Distribution)
“Time is fun when you are having flies”
Global Biodiversity Information Facility
GBIF
Came into existence as a megascience project
under the auspices of the OECD (Organization for
Economic Co-operation and Development
Was formally constituted in 1999 with a Secretariat
being housed in Copenhagen Denmark.
The focus of GBIF is to make the world’s primary
biodiversity data freely available on the internet
Major strides have, however, been made by
the plant sciences community under the
leadership of the National Botanical Institute
(NBI) with programmes such as:
SABONET
PRECIS Database
Popular and scientific publications that have
raised awareness of southern Africa’s rich
botanical heritage
Excellent infrastructure
Network Goals
To support national and sub-regional programmes for sustainable agricultural
development, and the conservation and sustainable use of the environment and
biodiversity.
To assist SADC member governments to meet their commitments to Agenda 21 of
UNCED, and their obligations as signatories to the Convention on Biological
Diversity.
To serve as an effective enabling activity under-pinning the broader interventions
needed to assist SADC member governments to achieve full implementation of the
Convention.
To provide SADC and individual member governments, and international
organizations, NGOs, IGOs, and donors with biological programmes within the
subregion, with the best possible advice on biosystematic matters, and the best
possible services in support of these programmes
Integrated solution
GMS's technological innovation goal for SA-ISIS was to integrate resources from
various parties, without having to move all the resources to a central place. This
would mean that resources would be available centrally, but with the added
advantage that the resource is still residing at the custodian's site. This means that
the custodian still has control over his data in terms of availability and maintenance.
One of the main technical challenges was to create a GIS map that is composed from
multiple, geographically separated ArcIMS machines. Although this technology is
available by using vector streaming, this is not viable over slow Internet connections.
GMS could not find technology anywhere in the world that would enable them to
serve maps from multiple ArcIMS servers without using vector streaming.
As a result, GMS had to create this new technology themselves. A new HTML viewer
was created from scratch. This communicated with a central map server, which was
also written by GMS. This map server in turn decided which layers would be rendered
by which ArcIMS machines and instructs them to do so. It then retrieves all the
separately rendered layers and combines them into one map, which is passed back to
the client HTML viewer.
This means that ArcIMS machines sitting at the University of Pretoria, the University
of Stellenbosch and in central Pretoria could render the map the client is seeing
without him even knowing this. The map server keeps track of the state of the
combined map project for each client, including layer visibilities, current extent, etc