Five more years of upscaling SA's environmental observation and information infrastructure and outputs

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"It ... took almost a decade to move from the original ideas of SAEON science to the current status of having published the Core Science Framework. If anything, this reflects the amount of conceptualisation and deliberation required to establish a solid base for a comprehensive organisation expected to deliver sound scientific products relevant to environmental governance and sustainable development in South Africa."

Fast forward five years and it is clear that SAEON has indeed been delivering on all three core principles entrenched in its mandate - observation science, information management and science education outreach. Significantly, the organisation is transcending national boundaries to contribute to global knowledge and networks; its long-term environmental observation platforms have played a significant role in garnering international recognition for South African environmental science.

SAEON reviewed its performance over the past five years as part of the National Research Foundation’s five-year review by an international team during the month of July 2015. Below is a summary of SAEON’s performance in two of the three core tenets of its mandate:

ENVIRONMENTAL OBSERVATION SYSTEMS AND RESEARCH

By Johan Pauw and William Bond

Competitive research - from savanna to Antarctica

To ensure a continuing flow of research information on environmental change, SAEON scientists identified projects with short, medium and longer term reporting cycles using existing data sets, where possible. South Africa has among the longest running field experiments in the southern hemisphere and some are the longest running in the world. They include mountain catchment experiments exploring the effects of land cover change on streamflow, fire manipulations, herbivore exclusions and stocking rate studies.

SAEON has placed considerable emphasis on finding the data, quality checking, converting data to useable modern formats, and, in several major cases, analysing and publishing the results. These long-term studies represent a unique national advantage and have contributed significantly to international recognition of South African environmental science.

As regards the provision of research infrastructure, in the past few years SAEON has become increasingly important in providing cutting-edge technology, logistical support and scientific advice to local researchers. Whether in Algoa Bay or in the depths of the Karoo, SAEON was able to provide logistical support to researchers, accessing research sites, using sophisticated equipment and harnessing technical skills to maintain its sophisticated equipment and, in some cases, to build equipment.

Publication output is one measure of competitive research output. Table 1 shows a healthy output of research papers in ISI-accredited journals. The number of published items using a SAEON address has grown by more than 300% from 2009 to 2014 as listed in Google Scholar's 'My citations'.

Table 1: Publications in ISI-accredited journals. Counts for 2015 are papers published online up to March 2015.

SAEON science is very well-connected internationally, as reflected in research publications with authors from diverse countries and institutions, as well as in its scientists who serve on 20 international science committees. With sponsorship from, among others, 17 international institutions, SAEON was able to send its postdoctoral and doctoral students to 10 labs and meetings abroad during the past year, and, by so doing, invested in future research of global significance. In a collaborative cruise by eight countries, SAEON even participated in the first quantitative under-ice diving trip to study krill in the Antarctic winter.

SAEON participated in the first quantitative under-ice diving trip to study krill in the Antarctic winter

SAEON has been effective at using South Africa's unique geographic advantages to develop international engagements. Examples include oceanographic collaborations for exploring the Agulhas current, analyses of how complex mountain climate will influence climate change responses of our rich, endemic mountain floras, and world-class savanna research which has attracted collaborators from around the world; as evidenced by the 15 international institutions that were hosted by SAEON in the 2014-15 financial year.

Establishing and maintaining research infrastructure and platforms

SAEON has succeeded in setting up key environmental research infrastructure in both its terrestrial and marine nodes. In the terrestrial nodes, the focus has been on meteorological equipment at selected sites and restoring and upgrading infrastructure and hydrological equipment in mountain catchment areas in KwaZulu-Natal and Western Cape nodes.

The ASCA programme is establishing deep ocean moorings to measure the Agulhas current, thought to have widespread influences on our climate

The meteorological stations are located in remote areas, especially mountainous terrain, where they add critical coverage to the existing network of stations run by the South African Weather Service and the Agricultural Research Council. Some of the stations transmit their observations via cell phone connections and the data is made available in near-real time on the Internet. The Cathedral Peak weather data, for example, can be found here.

Table Mountain serves as another example: here a network of 25 stations was set up to explore local topographic variation in mountain terrain. The network revealed major differences in temperature within a few tens of metres, a complexity of climate that has been overlooked in macro-climate analyses of climate change responses of the biota.

Fog collectors are revealing patterns of fog deposition in the Cape mountains that are likely critical for some mountain ecosystems and the plants they contain. New funding has enabled the acquisition of new equipment that will provide a network of flux towers and hydro-meteorological equipment  representative of most of South Africa's land surface.

The Arid Lands Node has renovated the existing infrastructure of the Tierberg LTER site, of which SAEON is now the legal owner

In the ocean, analogous equipment has been acquired for measuring physical properties of the sea, with a major focus on Algoa Bay as a sentinel site. Direct observation of marine organisms, including fish species and their stocks, has been made possible using underwater cameras mounted on remotely-operated underwater vehicles. The technology is among the best available for this purpose.

In the open ocean, Argo floats measure key physical variables. Through collaborative agreements between the USA, the Netherlands, the Department of Environmental Affairs and the Department of Science and Technology (DST), the ASCA  (Agulhas System Climate Array) programme is establishing deep ocean moorings to measure the extraordinarily fast-flowing Agulhas current, thought to have widespread influences not only on our climate, but also that of other parts of the world.

Whereas SAEON never planned to acquire land for research, a special case was made in order to safeguard a 20-year research site in the Karoo. The 100-ha site had always been in private hands and a succession of landowners allowed it to be used for long-term ecological research. When the resident scientists had to move on, problems arose with regard to access. The owner graciously offered to donate the property to SAEON, which was gratefully accepted. The Arid Lands Node has renovated the existing infrastructure, took over the long-term research and SAEON is now the legal owner of the Tierberg LTER site on behalf of the research community.

SAEON has advanced in leaps and bounds in its ability to manage sophisticated research infrastructure in support of environmental research. These systems need regular checking and maintenance by trained personnel. As they are placed in remote wildlife areas and in the ocean, they are subject to theft, vandalism and damage from natural causes. Current constraints are skilled technical personnel and security.

The Grasslands-Forests-Wetlands Node is in the process of cleaning and publishing long-term historical records for the St Lucia area

DATA SYSTEMS AND PRODUCTS

By Wim Hugo and Johan Pauw

A comprehensive information management system

In 2010, SAEON was contracted by DST to provide platforms for SAEOSS (South African Earth Observation System of Systems) and SARVA (South African Risk and Vulnerability Atlas). This opportunity was used to create a ‘Shared Platform’, combining the meta-data aggregation and management functions, discovery functions, and visualisation/download functions required by these two gateways as well as by SAEON portal users.

As a result, a suite of components was developed to fit into an existing framework in order to support more sophisticated requirements. Simultaneously, the Shared Platform was converted over a period of two to three years to a Service-Oriented Architecture, which allows any standards compliant client component (e.g. for discovery or data visualisation) to use the SAEON Shared Platform services, and likewise for the SAEON Shared Platform User Interfaces to connect to any standardised service globally.

SAEON's fog collectors are revealing patterns of fog deposition in the Cape mountains that are likely critical for some mountain ecosystems and the plants they contain

The conversion to service-oriented architecture had three benefits that were realised during the period under review. It firstly allows any broker or harvesting service to access the metadata records aggregated by SAEON across its contributing systems and stakeholders, and in a SAEOSS context this is being done by the GEOSS (Global Earth Observation System of Systems) Broker, exposing South African environmental and Earth observation data to an international user base.

Secondly, it allows stakeholders to make use of the Shared Platform in innovative ways, either by embedding stand-alone client components into their own web environments, or by calling services and processing the service outputs in their own systems. Thirdly, it allows the rapid deployment of parallel portals and gateways based on the Shared Platform. As such it was used to develop a number of prototypes and operational implementations (BioEnergy Atlas, Network Centre for Socio-Economic Data in Africa, and community collaboration sites, among others).

Starting in 2014, SAEON became the first African member of DataCITE, allowing the creation (‘minting’) of Digital Object Identifiers (DOIs). Work has just been completed on automating this process, so that users who commit metadata to SAEON’s Shared Platform are automatically able to obtain a DOI if desired. This capability is in support of an expected increase in demand for data publication and citation, not least because of the NRF’s movement to Open Access publication for all grant-funded research.

SAEON's shared platform now hosts in the order of 23 000 metadata records, of which 2 300 data sets are available publicly. Of these, only about 1 000 are available as a public, open, standardised service.

SAEON plays an increasingly active role in national and international forums that promote access to scientific and research data. Internationally, SAEON is currently a member of, or has made contributions to:

• ICSU World Data System: Member of the Scientific Committee
• ILTER:  Member and Public Policy Committee chair
• GEO (Group on Earth Observation) and GEOSS: Member of EuroGEOSS Steering Committee, participation in Architecture
• GEO BON (GEO Biodiversity Observation Network): Co-chair of Workgroup 8
• Research Data Alliance: Member of program committee for Plenary 4, membership and/or chair in several working groups
• CoDATA: Session organiser for SciDataCon 2014, member of the Task Group for Preservation of Data in Developing Countries
• Belmont Forum: Working Group contributions
• Eye on Earth Summit, 2012: Participated in development of White Paper
  

Design, development, packaging and promotion of different data products

The SAEON databases hold accessible formatted data that are useful to researchers and policy makers. SAEON personnel developed a number of data products during the period under review, which include two releases of the South African Estuaries Information System; a system for monitoring of ‘Birds at Sea’ observations; and a disk-based version of the South African Risk and Vulnerability Atlas.

The Ndlovu Node's world-class savanna research has attracted collaborators from around the world

The Egagasini Node supports the South African Data Centre for Oceanography (SADCO) and the African Ocean Biodiversity Information System (AfrOBIS). The Elwandle Node has been involved in the development of the national lifeline bibliography database, as well as the national coastal water quality monitoring database.

The Fynbos Node has developed and contributed to the Observations Database through catchment data in South Africa, with its associated climate data, and making these available for further analysis. The Ndlovu Node has acquired, digitised and archived 18 historical data sets on biodiversity from private and provincial game reserves in Limpopo, and has subsequently made these available to the research community.

The National Office, on behalf of the Arid Lands Node, has commissioned the cleaning of the Tierberg Long-Term Research Programme’s data and the cataloguing of its metadata, as well as the metadata for several other long-term projects. The Grasslands-Forests-Wetlands Node is in the process of cleaning and publishing long-term historical records for the Cathedral Peak and St Lucia areas, and driving the development of collaborative project-based websites.

Read more about SAEON’s science education outreach and public engagement initiatives in the next edition of SAEON eNews.