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Data visualisation task for pro-iBiosphere
by David King* (Open University), Jeremy Miller (Naturalis), Guido Sautter (Plazi), Serrano Pereira (Naturalis)
Inspired by Pensoft's development in electronic publishing workflows, in combination with marked-up texts generated using GoldenGATE, Jeremy Miller (Naturalis) devised the design for a dashboard to visualise treatment data with the aim of better understanding that data and assisting with its quality control. Ultimately, Jeremy's vision would make it be possible to offer a kind of reverse Biodiversity Data Journal, resurrecting primary data from marked-up legacy literature for aggregation and re-analysis. Our challenge in the recent pro-iBiosphere hackathon, excellently hosted by Naturalis, was to craft a prototype to extract and display the data for Jeremy's dashboard.
Working with GoldenGATE's author, Guido Sautter, enabled us to immediately refine one weakness of the original design: rather than process exported GoldenGATE marked-up text to extract statistical data, we could have GoldenGATE extract it for us and make that data available for export. Hence, GoldenGATE's functionality was extended and a new API service made freely available at for us to use, and for anyone else to use who wishes to explore this statistical data. Some solid visualisation work by Serrano Pereira, a recent recruit to Naturalis, using the established frameworks jQuery, jqPlot and jVectorMap saw the exported data rendered into the form Jeremy envisaged.
A version of the demonstrator produced during the hackathon is currently available at, courtesy of Plazi, a pro-iBiosphere partner. We look forward to refining and enhancing the existing demonstrator in-line with feedback from Jeremy and other users, and from its presentation at pro-iBiosphere's final event in June.
Jeremy's original concept for the dashboard is available from
The code for GoldenGATE can be downloaded from
The documentation for GoldenGATE's statistical export service is available from
The code for the demonstrator dashboard can be downloaded from

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This project has received funding from the European Union’s Seventh Programme for research, technological development and demonstration under grant agreement No 312848