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Initiatives to co-ordinate and realise Southern Africa

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Title: Initiatives to co-ordinate and realise Southern Africa


1
SAFRINET to SABIF
Initiatives to co-ordinate and realise Southern
Africas 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
2
  • 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

3
  • 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 regions 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 worlds flora, is still
    considered to be an under-estimation
  • (Herbert, Smith, Hamer Scholtz 2001)

4
  • 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)

5
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 Africas
rich botanical heritage Excellent infrastructure
6
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.
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.
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)
7
  • 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

8
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
9
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.
10
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.
11
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
12
  • South Africas 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 Africas 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 Africas 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)

13
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)
14
  • 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

15
  • GBIF was established by the OECD (Organization
    for Economic Co-operation 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 worlds primary
    biodiversity data freely available on the
    internet

16
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
17
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
18
  • 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

19
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
20
  • 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

21
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
22
  • 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
    mathematically-based system

23
Subsaharan Africa Points
Predictive modeling by Townsend
Petersen University of Kansas, Lawrence
Green native range Blue invaded range within
Africa
24
Take Native Range Points Only
25
Build Ecological Niche Model
26
Overlay African Invaded Range Points as Test
27
Project to Entire World (Potential Distribution)
28
Time is fun when you are having flies
29
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
worlds primary biodiversity data freely
available on the internet
30
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 Africas rich
botanical heritage Excellent infrastructure
31
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

32
Integrated solutionGMS'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 without having
to store state information on the client browser.
All this was accomplished without streaming
vector data, thus enabling the geographically
separated servers to be connected to the central
map server with only an Internet-type link and
still give reasonable response times.The
involved parties' data is now available from a
central server without having to actually reside
on the central server. This leaves the custodians
of the data free to decide which layers they want
to be available for the SA-ISIS portal and also
to set up and maintain the layers at their own
premises on their own hardware.
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