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TDWG 2013 Vesper

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Presentation given at TDWG 2013 conference on our visual tool to spot data quality issues in Darwin Core Archives

http://www.vesper.org.uk

Published in: Data & Analytics
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TDWG 2013 Vesper

  1. 1. VESPER Visual Exploration of Species-Referenced Repositories Martin Graham & Jessie Kennedy Edinburgh Napier University
  2. 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. 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. 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. 5. Darwin Core Archives Eml.xml Meta.xml Core Taxa/Occurrence Data Extension Extension Meta Files (XML) Data Files (CSV) Describes Exactly one Zero or more Extension ID == Core ID
  6. 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 a lot Expand even more (String copying, UTF-16 etc)
  7. 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 Implicit Taxonomy acceptedNameUsageID, parentNameUsageID Explicit Taxonomy Any of Kingdom, order, family, genus etc Map decimalLongitude, decimalLatitude Timeline eventDate • List choice of available visualisations for a meta.xml and just extract chosen fields
  8. 8. Taxonomy • Sunburst / Icicle plot – Some difficulties with high fan-out taxa – Though a lot of these are data quality issues
  9. 9. Taxonomy • Sunburst / Icicle plot – Some difficulties with high fan-out taxa – Though a lot of these are data quality issues
  10. 10. Geography • Based on popular leaflet.js library – And Markercluster plugin – Some adaptations to show selected items
  11. 11. Temporal • Simple bar chart – With rangeslider – Zoom in and see yearly patterns (i.e not much at xmas)
  12. 12. Miscellaneous • Sanity check - Empty data count
  13. 13. Miscellaneous • Taxonomic fan-out for hollow curve anomalies • Export selected IDs – These can be saved or sent somewhere else
  14. 14. Selection • Selections in one view are reflected in the other views for the same data – Multiple views, linking
  15. 15. Conclusion • Javascript visualisations for DWCA archives • Quickly shows areas of quality issue • Can handle large archives if only key fields are analysed
  16. 16. Fin • http://www.soc.napier.ac.uk/~cs22/vesperDemo/ves per/demoNew.html – Feedback welcome • Thanks to GBIF, Canadensys, EMBL for data • Funded by BBSRC • Ask for a demo

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