A boon for biodiversity data management at SANParks
Funding from the JRS Biodiversity Foundation is going to boost bioinformatics at SANParks by providing skilled staff and access to technology to standardise, collate, store and share SANParks’ biodiversity data.
The JRS Biodiversity Foundation has awarded SANParks a grant extension of US$ 498,100 (~R 7,500,000) to expand existing bioinformatics work. This grant builds on good biodiversity data foundations in SANParks, enabling a transition to the digital data commons. It will allow access to the latest software and interfaces to improve knowledge collation and data sharing on key taxa and ecosystems, including estuaries, freshwater systems, pollinators and invertebrates, ultimately aiding applied research activities and enabling more responsive management.
Five contract staff positions will be advertised, including a Bioinformatics Manager, based at the Cape Research Centre in Cape Town, a Bioinformatics Scientist, based at the Arid and Central Research Unit in Kimberley, a scientist to collate knowledge on freshwater and estuarine systems, based at the Rondevlei office in the Garden Route, a scientist to collate knowledge on pollinators and invertebrates, based in Skukuza, and a Visual Data Scientist, based either in Cape Town or the Garden Route. Additionally, a specialised consultancy will develop biodiversity information management tools to help SANParks collate, standardise, store and share species data for national parks. The project also aims to digitise and curate species data for all national parks and develop state of knowledge reports on estuaries, freshwater systems, pollinators and invertebrates to inform management and policy.
The data management system will enable parks to continually update species lists and distribution maps from diverse data sources as inputs to various assessments and decision making. Additionally, curated visual datasets with clear guidelines for capturing and storing future datasets should facilitate improved availability and use of SANParks’ extensive collection of visual data, including photographs from camera traps and baited remote underwater videos. The Visual Data Scientist will also assist in conducting and developing protocols for automated analysis of visual data.
Substantial progress has been made globally in the past decade on bioinformatics, which is “an interdisciplinary field that develops methods and software tools for understanding biological data” (Wikipedia). Collating and sharing SANParks species data requires conversion into standardised formats and upholding certain data standards going forward. To improve data synchronization within SANParks and with external biodiversity data custodians and managers, a group working on plant data across SANParks’ four research nodes met in Skukuza at the end of March 2022 to workshop the management of SANParks’ herbarium data. Understanding data requirements for inputting herbarium and other plant data into BRAHMS database software and interrogating SANParks’ plant data highlighted that substantial data cleaning is required to convert data into an appropriate format for collation in a database. This is not unusual for biodiversity data as Kiara Ricketts, a BRAHMS software guru from SANBI, assured participants.
Plant data management workshop participants in the Skukuza herbarium. Back row (Left to Right): Nicola van Wilgen Bredenkamp (Global Change Scientist), Kiara Ricketts (SANBI), Dian Spear (Bioinformatics Officer), Johan Baard (GIS & Vegetation Ecology Scientist), Hugo Bezhuidenhout (Vegetation Ecologist); Middle row: Nikisha Singh (Curator: Skukuza Biological Reference Collection), Letlhogonolo Mokopelo (Environmental Monitor); Front row: Judith Botha (Senior Science Manager) (Image credit: Chenay Simms)
Some of the shared data problems across SANParks’ research nodes include a lack of metadata to describe the data and how it was collated, plant naming that does not correspond to the scientific names on the annually-updated South African National Plant Checklist, and inconsistencies of dates, coordinates, measurements and formats.
The new grant from the JRS Biodiversity Foundation will help resolve some of SANParks’ existing data management challenges by providing human resources and funding dedicated to data management, which is a vital but often overlooked aspect of conservation management. By the end of the two-year project, a substantial amount of knowledge and species data will be easily accessible to both SANParks staff and the public. This will facilitate conservation research and improved conservation management.
When starting a project, it is vital to build personal relationships, especially when the team is geographically dispersed. (Left to Right): Johan Baard (Knysna), Danny Govender (Skukuza), Nicola van Wilgen Bredenkamp (Cape Town), Dian Spear (Cape Town), Letlhogonolo Mokopelo (Kimberley) at Mathekenyane Hill near Skukuza.
