Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

TDWG 2013 Vesper


Published on

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

Published in: Data & Analytics
  • Be the first to comment

  • Be the first to like this

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 • per/demoNew.html – Feedback welcome • Thanks to GBIF, Canadensys, EMBL for data • Funded by BBSRC • Ask for a demo