Initiatives to co-ordinate and Initiatives to co-ordinate and realise Southern Africa’s realise Southern Africa’s

biodiversity heritagebiodiversity heritage

Initiatives to co-ordinate and Initiatives to co-ordinate and realise Southern Africa’s realise Southern Africa’s

biodiversity heritagebiodiversity heritage

Mervyn W MansellMervyn W MansellDept of Zoology & EntomologyDept of Zoology & Entomology

University of PretoriaUniversity of Pretoria&&

Animal and Plant Health Inspection ServicesAnimal and Plant Health Inspection ServicesUnited States Department of AgricultureUnited States Department of Agriculture

c/o U.S. Embassy, Pretoriac/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

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

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.

(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 Southern African Loop of Bionet Bionet InternationalInternational

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 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.

SAEON A DEVELOPING FACILITY OF THE NRF FUNDED BY DST

SA ISISSA-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)

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 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 world’s primary biodiversity data freely available on

the internet

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 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

TO CONTRIBUTE TO SOUTH AFRICA'S SUSTAINABLE DEVELOPMENT BY FACILITATING ACCESS TO

BIODIVERSITY AND RELATED INFORMATION ON THE INTERNET

WITH THE VISION

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

Managed under the auspices of the NRF – Project Manager: Ms Renee le Roux

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 mathematically-based system

Subsaharan Africa Subsaharan Africa PointsPoints

Green – native rangeBlue – invaded range within Africa

Predictive modeling by Townsend Petersen

University of Kansas, Lawrence

Predictive modeling by Townsend Petersen

University of Kansas, Lawrence

Take Native Range Points Take Native Range Points OnlyOnly

Build Ecological Niche Build Ecological Niche ModelModel

Overlay African Invaded Range Points as Overlay African Invaded Range Points as TestTest

Project to Entire World – (Potential Distribution)Project to Entire World – (Potential Distribution)

“Time is fun when you are having flies”

Global Biodiversity Information Facility

GBIFCame 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

Global Biodiversity Information Facility

GBIFCame 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

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

Network GoalsNetwork Goals

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 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.