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REATING A DISTRIBUTED BIOGEOGRAPHY DATA MANAGEMENT SYSTEM FOR AFRICA

Biodiversity is very much the order of the day, especially after the 'Rio Conference' (United Nations Conference on Environment and Development, Rio de Janeiro, 1992). While this recent attention to biodiversity is very welcome, it is all too often forgotten that a very old branch of the biological sciences, taxonomy, is a sine qua non for any work on biodiversity, or informed decision-making in conservation. Taxonomy is the science of naming living organisms, and classifying them in groups of common descent. Hence taxonomy provides the 'vocabulary' of the biodiversity language: it provides a standard way of referring to species, the basic building blocks of biodiversity.

Naming of species is governed by three different codes for taxonomic nomenclature: one for zoology, one for botany, and one for bacteria. These codes lay down rules on what constitutes a valid publication, how names should be formed, and how to take earlier descriptions into account. A very useful introduction on these codes has been written by Jeffrey ( Biological Nomenclature , Edward Arnold: 1989).

Unfortunately, things are never as simple as they look. Naming and classifying all living organisms in a way that satisfies all taxonomists proves to be a daunting task. The number of species is enormous: some recent estimates put the number at 30,000,000 species of higher organisms, of which less than 1,500,000 have been described. No one really can even make an estimate of the number of bacteria species: every scoop of soil or bucket of water seems to yield new species.

Another set of problems stems from the historical nature of taxonomy: for every new species that is described, all earlier descriptions have to be taken into account. There are strict rules of priority, and a vague description in a 100-year old obscure publication might take precedence over a brand new one in a widely distributed international journal. Hence the need to build comprehensive databases of all species descriptions, so that a prospective author of a species description can stay clear of these pitfalls.

Taxonomists are human (usually), and humans tend to sometimes disagree, sometimes change their mind. When taxonomists do this, other users of the taxonomic nomenclature (like ecologists, physiologists…) suffer: species change name, and often the validity of a name depends on the taxonomist you are talking to. Hence, again, the need to create taxonomic databases, and to record, in those databases, the source of information used, and the need to keep track of synonyms or invalid names.

Taxonomic databases

In spite of the importance of standardised species lists for taxonomic nomenclature, no such lists presently exist for the Western Indian Ocean. In the light of recent interest in biodiversity this lack becomes even more glaring, especially as it is one of the factors to be taken into account when planning Integrated Coastal Zone Management.

Several global initiatives exist to inventorise all published taxonomic names. Botanists are fortunate in having started this exercise early enough. Index Kewensis has been published on paper for many years, keeping a record of all plant names. Since some years now, all information in the hard copy volumes is available on a single CD ROM, which can be obtained from the Royal Botanic Gardens in Kew. Note, however, that this is just a list of published names; there is no information on which name is the currently valid one in a set of synonyms, and there is no distribution information.

Zoologists are not that lucky, and face problems that might seem insurmountable. First of all, the number of animals is at least an order of magnitude higher than the number of plants, possibly even two. Another set of problems is the zoologists' own making: many of the species descriptions are published in languages that are not widely spoken (botanists stick to Latin), and the rules and regulations for the nomenclature are somewhat more lax than for botany. Two global programmes dealing with botany and zoology are Species 2000, and ETI.

Some databasing efforts are directed specifically at gathering information on marine organisms; some examples are

• Veron's global list of Corals, which is in preparation

• Sheppard's Corals of the Indian Ocean, which will be distributed on a CD ROM

• FishBase, a CD ROM produced at ICLARM, Manilla, giving global information on fish

• ETI's series of CD ROM products, which includes one on Sea Cucumbers of Northern  Australia, and one on Marine Mammals

• The WDC-A's NODC Taxonomic Codes. While this database does not include distribution information, it is a useful for checking spelling and higher taxonomy

• The Marine Species Registry of UNESCO developed in collaboration with ETI.

In spite of the above list, we felt that there was still a lack of information for the Western Indian Ocean region. With the exception of Sheppard's data, all of the above have a world-wide scope, which makes progress for this (or for any particular) region frustratingly slow. And, with the exception of the coral databases, and of FishBase, most are far from completion. Even FishBase, whose approach being comprehensive in its taxonomic covering, still has ways to go to exhaust all possible sources for species distribution.

ODINAFRICA

The Ocean Data and Information Network for Africa (ODINAFRICA) brings together marine institutions from twenty-five Member States of the Intergovernmental Oceanographic Commission of UNESCO from Africa (Algeria, Angola, Benin, Cameroon, Comoros, Congo, Cote d'Ivoire, Egypt, Gabon, Ghana, Guinea, Kenya, Madagascar, Mauritania, Mauritius, Morocco, Mozambique, Namibia, Nigeria, Senegal, Seychelles, South Africa, United Republic of Tanzania, Togo, and Tunisia).

The earlier phases of ODINAFRICA enabled the participating member states to get access to data available in other data centres worldwide, develop skills for manipulation of data and preparation of data and information products, and develop infrastructure for archival, analysis and dissemination of the data and information products.

The goal of the current phase of ODINAFRICA will be to improve the management of coastal and marine resources and the environment in participating countries by: enhancing data flows into the national oceanographic data and information centres in the participating countries, strengthening the capacity of these centres to analyse and interpret the data so as to develop products required for integrated management of the coastal areas of Africa, and increase the delivery of services to end users.

The focus will be on preparing data and information products to enable the Member States to address the key issues identified in the African Process:

1. Coastal erosion,
2. Management of key ecosystems and habitats,
3. Pollution,
4. Sustainable use of living resources, and
5. Tourism.

The government of Flanders, Belgium has provided US$2.5 million to support the implementation of ODINAFRICA-III. The following thematic work packages will be implemented to achieve the objectives of ODINAFRICA-III: Coastal Ocean Observing System: will focus on upgrading and expanding African network for in-situ measurements and monitoring of ocean variables (e.g. sea-level, temperature, salinity, currents, winds, etc), provision of near real-time observations of ocean variables, and building adequate capacity for collection, analysis and management of sea-state variables. About 15 tide stations will be installed or up-graded and some of them equipped with sensors for other meteorological and oceanographic parameters.

Data and Information Management : will focus on further development and strengthening of National Oceanographic Data Centres (NODC) to manage data streams from the coastal ocean observing network, upgrading infrastructure in the NODC's (including internet access and computer systems), Integrating biogeographic and hydrological data steams into NODC systems, Building capacity for data and information managers for new NODC's established as part of this project, and Rescue historical data (especially sea level data).

Development of Marine Biodiversity Databases

Participants in the Marine Biodiversity Data management courses held in Oostende, Belgium (April 2005), and Mauritius (August 2005) emphasized the need to immediately commence preparation of inventories of experts, datasets, institutions, and species lists. This information can be extracted from existing databases such as AFRILIB, MEDI Africa, and AFRIDIR. The MEDI Africa database should also be updated with the biodiversity information collected. Five workshops, each lasting 2-weeks will be organized to compile input for the OBIS system on taxonomic groups of particular importance [data entry]. Data sources (databases, publications) should be identified on beforehand, and made available during the workshop. The priority groups, identified on the basis of commercial importance, were: mollusks, polychaetes, echinoderms, sponges, stony corals.  The first workshop (on molluscs) was held from 13-23 March 2006, at the IODE Project Office. A second workshop Asha Poonyth (Mauritius) and Malika Bel Hassen (Tunisia) were nominated as coordinators for Eastern/Southern Africa and Western/Northern Africa respectively. The Committee further recommended that the databases developed be included in the ODINAFRICA Marine Atlases, and that the data be re-organised in terms of LMEs for publication.

  Objectives

1. Identifying a suitable metadata format to capture the relevant information on who holds which data, in which formats and populate the meta database,
2. Creating a list of available species lists,
3. Integrating species lists in a single reference list,
4. Adding and mainstreaming of bio geographical records,
5. Setting up of OBIS (Ocean Bio geographical Information system) node: AfrOBIS and a DiGIR provider, in the National Oceanographic Data Centres.

  Meta-data activities

T he general idea of starting with the metadata, in order to create an inventory and decide on priorities on the basis of this inventory was supported. Several mechanisms to capture and distribute metadata are in place in the framework of IODE, and should be used for this project.

relevant institutes and experts were contacted and requested to add or update their records in AfriDIR. This is done in close collaboration with the local NODC, and with the national ODINAfrica Information Manager. Directory for marine & freshwater professionals (AFRIDIR) format improved 160 entries available from Kenyan scientists and uploaded onto Ocean Expert. http://www.oceanexpert.net

Relevant datasets are not only databases sensu strictu , but also lists of species that are often published in project reports, theses and other grey literature. It is expected that the country reports, produced for the Country Study for the Convention on Biological Diversity, will be a rich source of information.

MASDEA, the Marine Species Database for Eastern Africa, was taken as the initial species list to serve as the taxonomic reference for the project. MASDEA has to be expanded with Mediterranean and Atlantic species lists; in an initial phase this will be done by combining MASDEA with information in the European Register of Marine Species (ERMS, for Northern Atlantic and Mediterranean taxa) and the Register for Antarctic Marine Species  (RAMS, for Southern Atlantic/Antarctic). This work will be undertaken in close collaboration with OBIS, and also specifically with the OBIS node for the Indian Ocean, IndOBIS. The software for the database is developed in Access.

Making content visible

Biogeographical records will be made visible through several portals:

• All records will be contributed to the international OBIS portal, and through there to the Global Biodiversity Information Facility GBIF
• Records for Eastern and Western Africa will be made visible also through AfrOBIS, run by SADCO
• Records for Eastern Africa will be offered to IndOBIS, the Indian node for the OBIS network
• Records for Northern Africa will be made visible through EurOBIS, run by VLIZ
• All records generated within the framework of ODINAfrica will be made visible through a separate portal on the ODINAfrica web site

Organisation

The ‘regions' for the purpose of the biodiversity activities of ODINAfrica are defined as follows: 

• Northern Africa: Mauritania east to and including Egypt
• Western Africa: Senegal south to and including South Africa
• Eastern Africa: Kenya south to and including South Africa, Madagascar and the island states

No ODINAfrica activities take place in Sudan south to and including Somalia.

The DiGIR project is a collaborative effort

DiGIR is currently established as an open source project on Source Forge ( http://sourceforge.net ).

Specified in an XML Schema (.xsd)

The Ocean Biogeographic Information System (OBIS)

The Ocean Biogeographic Information System (OBIS) is the information component of the Census of Marine Life ( CoML ), and a Marine component of ‘Global Biodiversity Information Facility (GBIF). It is a growing network of researchers in more than 45 nations Canada, Europe  US, South America, Africa, Indian Ocean, Australia, New Zealand engaged in a 10-year initiative to assess and explain the diversity, distribution, and abundance of life in the oceans - past, present, and future.

OBIS is a web-based provider of global geo-referenced information on marine species. It contains expert species level and habitat level databases and provide a variety of spatial query tools for visualizing relationships among species and their environment. OBIS strives to assess and integrate biological, physical, and chemical oceanographic data from multiple sources. Users of OBIS, including researchers, students, and environmental managers, will gain a dynamic view of the multi-dimensional oceanic world. You can explore this constantly expanding and developing facility through the OBIS Portal '

The OBIS Portal accesses data content, information infrastructure, and informatics tools - maps, visualizations, and models – to provide a dynamic, global facility in four dimensions (the three dimensions of space plus time). Potential uses are to reveal new spatial/temporal patterns; to generate new hypotheses about the global marine ecosystem; and to guide future field expeditions. The scope of OBIS offers new challenges in data management, scientific cooperation and organization, and innovative approaches to data analysis. Maintaining the principle of open access, the digital atlas developed by OBIS is expected to provide a fundamental basis for societal and governmental decisions on how to harvest and conserve marine life. The November 2000 (Vol.13 No.3) issue of Oceanography, the official magazine of The Oceanography Society, was dedicated to OBIS, and reports of meetings and workshops, together with other publications, can be found at the Publications page.

Background

Life on Earth is made up of interrelated populations of distinct plant and animal species. Over evolutionary time, natural selection through physical and biological processes has produced the set of chemical blueprints – the unique genomes -- that define these species, maintain their integrity over successive generations, and permit favorable adaptations to flourish over time. These species-specific genomes are thus the fundamental units of life on this planet. The myriad populations of diverse species characterized by these genomes interact with the physical environment and among themselves to produce the complex spatial and temporal patterns of ecosystem function that provide the goods and services necessary for human survival. As burgeoning human societies place ever-greater demands on these natural systems, it becomes more vital to assess the current state of ecosystems on a species-specific level, to discern the changes that are taking place, and to predict future impacts of changes.

Because of their area, volume, and diversity of life, the world's oceans are the dominant component of the biosphere. Thus, an assessment of life on Earth must in major part be an assessment of life in the world's oceans –hence the Census of Marine Life and OBIS. The complexity of the marine ecosystem, and its interactions with social and political systems, demand an interdisciplinary and integrated approach. Traditional discipline-centered research methodologies yield a wealth of snapshots of the complex and ever-changing marine world. The challenges are to fill the gaps in these insights, to synthesize coherent patterns of marine life in space and time, and to develop testable hypotheses and predictive models of the origin and maintenance of these patterns.

Today, as never before, the tools are at hand to meet this challenge – to conduct quantitative, geographically- and temporally-explicit observations and analyses of the living ocean. Taxonomists have new tools to define and identify species through combinations of genomic and morphological analyses, greatly aided by access to worldwide knowledge resources through the Internet. Remotely sensed and in situ observations are increasingly being made available through the Global Ocean Observing System ( GOOS ), creating an unprecedented amount of geo-referenced environmental and ecosystem data. Computer and communications capabilities permit rapid assembly, and meaningful analysis of immense volumes of diverse data. Moreover, earth and life scientists have developed highly capable systems for planning, coordinating, and executing coherent and effective programs on a global scale. OBIS aims to harness these tools in playing its part in the quantum increase in knowledge about the distribution and abundance of life in the oceans that we can expect over the next ten years.

OBIS History and Federation

The initial idea for OBIS developed from a CoML -sponsored Benthic Census Meeting held in October 1997. Recommendations from this meeting led to the establishment of a prototype OBIS Web site at Rutgers in 1998 to demonstrate the initial OBIS concept. The first OBIS International Workshop was held in November 1999 in Washington, D.C. In 2000, the National Oceanographic Partnership Program ( NOPP )- requested proposals for OBIS projects and funded eight through support from the Alfred P. Sloan Foundation , Office of Naval Research, ( ONR ) and National Science Foundation ( NSF ). A more restricted NOPP competition in 2002 resulted in an additional OBIS project on Marine Mammals, Turtles, and Birds . An NSF Postdoctoral Fellowship to Karen Stocks at the San Diego Supercomputing Center resulted in a further OBIS project on Seamounts . These projects, the History of Marine Animal Populations ( HMAP ) project, and the NSF-sponsored OBIS Portal at Rutgers University, NJ, were the initial Members of the OBIS Federation. Subsequently joining are the seven Census of Marine Life Initial Projects , the long-term Chesapeake Bay database of the Trophic Interactions in Estuarine Systems ( TIES ) program, and the Smithsonian Institution's National Marine and Estuarine Invasion Database . Listings of these and of tool contributors can be found at the Contributors, Partners & Links page.

In June 2001, OBIS joined 8 international organizations and 27 countries on the Governing Board of the Global Biodiversity Information Facility ( GBIF ) as an Associate Participant. GBIF is a data system for worldwide biological data, developed under the sponsorship of the Organization for Economic Co-operation and Development ( OECD ) (OECD). OBIS will grow in concert with GBIF to become the major component for ocean biogeography and systematics. A broad range of other affiliations has been formed which include: Intergovernmental Oceanographic Commission ( IOC ), Scientific Committee on Ocean Research ( SCOR ), DIVERSITAS , International Council for the Exploration of the Seas ( ICES ), International Association of Biological Oceanographers (IABO), the International Union of Biological Sciences ( IUBS ), United Nations Environmental Program ( UNEP ), World Conservation Monitoring Centre ( WCMC ), UNESCO Man-And-the-Biosphere ( MAB ), and Global Ocean Observing System ( GOOS ).

Governance and Organization

OBIS is structured as a federation of organizations and people sharing a vision to make marine biogeographic data, from all over the world, freely available over the World Wide Web through the OBIS Portal. OBIS elements agree to develop and promote standards and interoperability in concert with the standards and protocols being developed for other environmental data systems around the world. It is not a project or program, and is not limited to data from CoML -related projects. OBIS is not incorporated, it does not employ staff, own equipment, or apply for funding. Organizations involved in OBIS take on these responsibilities. Any organization, consortium, project or individual may contribute to OBIS (see FAQ and Technical Resources pages to find out how). OBIS is managed by an International Committee with advice from the CoML Steering Committee (see International Committee page for details).

Regional OBIS Node

AfrOBIS
The sub-Saharan Africa OBIS node (AfrOBIS) will collate marine biodiversity information from many sub-Saharan African countries. Data will be reformatted, loaded onto AfrOBIS and uploaded to the international OBIS portal at Rutgers

Host Organization

Southern African Data Centre for Oceanography (SADCO)
SADCO is hosted by the CSIR , a South African parastatal organization delivering a wide range of scientific and technological services to industry and government departments. The SADCO stakeholders and sponsors are the CSIR , the South African Department of Environmental Affairs and Tourism (DEAT) , the South African Navy , the South African National Research Foundation and the Namibian Ministry for Fisheries and Marine Resources . These organizations provide SADCO with funding as well as advice and data, and as such contribute directly to the success of the Data Centre.

Dr Marten Gründlingh
E-mail: mgrundli@csir.co.za

Technical Manager:
Ursula von St Ange
E-mail: uvstange@csir.co.za