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Context

As part of the GCRMN Governance & Implementation Plan and ongoing discussion with the GCRMN Working Group, it has been proposed to form a Task Force on Data Quality and Data Access & Sharing. These two themes touch on aspects of Standards used for taxonomy, functional traits, environmental and socio-economic data.

To assist with the interoperability and comparability of data within and across GCRMN regions, it is important there are similar standards used. As part of the Knowledge Management and FAIR principles, this module will focus on techniques for accessing remote databases and documenting the extraction steps and clearly identified sources that can be modified & updated as required by monitoring programmes.

This wiki page identifies some key components of this standardisation and some R tools that can help with this task.

Key components

  1. Taxonomy. In the compilation of regional and global data sets for coral reef monitoring, there can be different ways for recording taxonomic information, including a mixture of Genus and species data, Families, or functional groups (e.g. “Hard Coral”). Some of these categories are due to the limits of taxonomic resolution in the field or expertise of the monitoring group.
  2. Functional Traits. There is a number of ways to assign functional attributes to taxa that can assist in understanding the status & trends of coral reef ecosystems. Often, these functional traits are assigned by individual investigators or monitoring programmes that vary within and across regions.
  3. Environmental Variables. The characterisation of environmental variation (i.e. oceanographic, climatic, geomorphology) can be important for understanding the results of coral reef monitoring data. As there are a number of different sources of environmental data, which can range from global remote-sensed to locally derived data. These different sources may vary in how they characterise environmental variables and the temporal and spatial resolution of the information.
  4. Socio-economic Information. In GCRMN regional Status & Trends) reports, it is common to include socio-economic information as potential pressures or drivers of change in coral reef ecosystems. Similar to the environmental variables discussed above, these can range in the source of information from globally compiled information to detailed ”on-the-ground”_ survey information. As the collection and calculation of different socio-economic indicators can vary across data sources and purpose of the information, it is important to be able to use comparable data for within and across regions.

As establishing these standards are a work in progress for the GCRMN, for the purposes of this training course, we will focus on general techniques for accessing these different sources and highlight a number of “useful” packages to link with taxonomic, trait and environmental data.

Next steps

There are a number of R packages and tools that can assist with the standardisation of taxonomic, functional trait, socioeconomic and environmental data sources.

In this module, we will explore some of them. One particularly useful package to help standardise taxonomy is taxize. The strategy used for extracting taxonomic information can apply across a number of different remote databases, so the technique used in this exercise has application across a number of dimensions for coral reef monitoring.