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VESPER V isual E xploration of Spe cies- R eferenced Repositories

Explore data quality issues in Darwin Core Archives (DWCA) through web-based visualizations, leveraging HTML5, SVG, CSS3, and D3 toolkit.

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VESPER V isual E xploration of Spe cies- R eferenced Repositories

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  1. VESPERVisual Exploration of Species-Referenced Repositories Martin Graham & Jessie Kennedy Edinburgh Napier University

  2. Introduction • VESPER – an exploration into data quality issues for Darwin Core Archives (DWCA) • DWCA’s are files for storing detailed species-based data sets • How does a user know which data sets are useful and complete?

  3. Valid vs. Useful • GBIF has tools to test DWCA validity • This work is about visualising data we assume is “valid” but are unsure of “usefulness” • Taxonomy is broken • Dates are wrong • Lions in the sea • In many cases the usefulness of such data is only seen when visualised in context

  4. Approach • Web-based visualisation of DWCAs • Uses HTML5 • SVG, CSS3, FileWriters, ArrayBuffers • D3 toolkit • Client side only • Visualise basic dimensions of data • Taxonomy • Geography • Time • & Miscellaneous Stats

  5. Darwin Core Archives Data Files (CSV) Exactly one Zero or more Meta Files (XML) Core Taxa/Occurrence Data Eml.xml Extension ID == Core ID Extension Describes Meta.xml Extension

  6. Zapped by Zip • Zip files make things smaller • Good for network transport • But analysing the data means we have to make things big again Expand even more (String copying, UTF-16 etc) Expand a lot

  7. Zip Zapped • Partial Unzip • Analyse fields listed in meta file • Disregard verbose fields • Find combinations of fields that can be used to generate a visualisation • List choice of available visualisations for a meta.xml and just extract chosen fields

  8. Taxonomy • Sunburst / Icicle plot • Some difficulties with high fan-out taxa • Though a lot of these are data quality issues

  9. Taxonomy • Sunburst / Icicle plot • Some difficulties with high fan-out taxa • Though a lot of these are data quality issues

  10. Geography • Based on popular leaflet.js library • And Markercluster plugin • Some adaptations to show selected items

  11. Temporal • Simple bar chart • With rangeslider • Zoom in and see yearly patterns (i.e not much at xmas)

  12. Miscellaneous • Sanity check - Empty data count

  13. Miscellaneous • Taxonomic fan-out for hollow curve anomalies • Export selected IDs • These can be saved or sent somewhere else

  14. Selection • Selections in one view are reflected in the other views for the same data • Multiple views, linking

  15. Conclusion • Javascript visualisations for DWCA archives • Quickly shows areas of quality issue • Can handle large archives if only key fields are analysed

  16. Fin • http://www.soc.napier.ac.uk/~cs22/vesperDemo/vesper/demoNew.html • Feedback welcome • Thanks to GBIF, Canadensys, EMBL for data • Funded by BBSRC • Ask for a demo

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