1. Training course on biodiversity data publishing and fitness-for-use in the GBIF Network, 2011 edition Tools and Resources to Assess and Enhance Fitness-For-Use Meherzad Romer (mromer@natureserve.ca) Senior Data Manager NatureServe Canada www.natureserve-canada.ca ) September 30, 2011

2. Overview 1.Tools that help: o Metadata o Spatial Data o Tabular Data 2.Other resources o Data sources o Documents

3. Tools - Metadata

4. Tools - Metadata Metadata Capabilities of IPT http://code.google.com/p/gbif-providertoolkit http://code.google.com/p/gbif-providertoolkit

5. Tools- Metadata Metadata Capabilities of the IPT http://code.google.com/p/gbif-providertoolkit/ http://code.google.com/p/gbif-providertoolkit/ Geographic coverage metadata in IPT

6. Tools - Metadata Darwin Core Archive Validator http://tools.gbif.org/dwca-validator/ http://tools.gbif.org/dwca-validator/

7. Tools - Metadata Darwin Core Archive Validator http://tools.gbif.org/dwca-validator/ http://tools.gbif.org/dwca-validator/

8. Tools - Spatial Data

9. Tools – Spatial Data BioGeomancer http://bg.berkeley.edu/latest http://bg.berkeley.edu/latest Convert text into coordinates Assign radius of uncertainty Single or Batch process

10. Tools – Spatial Data BioGeomancer http://bg.berkeley.edu/latest http://bg.berkeley.edu/latest Web based only Shows all possibilities

11. Tools – Spatial Data GeoLocate http://www.museum.tulane.edu/geolocate/ http://www.museum.tulane.edu/geolocate/ Convert text to coordinates Assign radius of uncertainty Single or batch process Correct by moving location place mark or drawing polygon Online, stand alone and collaborative versions

12. Tools – Spatial Data InfoXY http://splink.cria.org.br/infoxy?criaLANG=en http://splink.cria.org.br/infoxy?criaLANG=en Coordinates entered in lat/long Can batch process Results precise to the administrative boundaries Output: html or MS Excel spreadsheet

13. Tools – Spatial Data SpOutlier http://splink.cria.org.br/outlier?&setlang=en http://splink.cria.org.br/outlier?&setlang=en Enter lat/long (altitude) Map Better with more locations Uses weighted centre Checks on water/land

14. Tools – Spatial Data SpOutlier http://splink.cria.org.br/outlier?&setlang=en http://splink.cria.org.br/outlier?&setlang=en

15. Tools – Spatial Data Georeferencing Calculator http://manisnet.org/gci2.html http://manisnet.org/gci2.html Input: Coordinates, offsets and headings, uncertainty sources Output: Final coordinates Estimate of error

16. Tools – Spatial Data Diva-GIS http://www.diva-gis.org/ http://www.diva-gis.org/ Basic GIS software Free Biologically oriented Vector/Raster Compatible with many formats

17. Tools – Spatial Data Quantum GIS http://www.qgis.org http://www.qgis.org More complex Free Compatible with Spatial Geodatabases and geographical web services Vector/Raster Community development

18. Tools – Spatial Data The R-project http://www.r-project.org http://www.r-project.org Environment and language for statistical computing. Allows analysis and drawing. Plays nicely with others: GIS, scripting languages

19. Tools – Tabular Data

20. Tools – Tabular Data Name Parser http://tools.gbif.org/nameparser/ http://tools.gbif.org/nameparser/ Atomize Sci. Names 3 parted name Ignores varieties for subspecies

21. Tools – Tabular Data Name Parser http://tools.gbif.org/nameparser/ http://tools.gbif.org/nameparser/

22. Tools – Tabular Data Name Finder http://tools.gbif.org/namefinder/ http://tools.gbif.org/namefinder/ Find scientific names Inputs: File Url Free text

23. Tools – Tabular Data Name Finder http://tools.gbif.org/namefinder/ http://tools.gbif.org/namefinder/ Returns: Count Names as found Recognized form

24. Tools – Tabular Data Taxon Tagger http://tools.gbif.org/taxontagger/ http://tools.gbif.org/taxontagger/ Input: Url PDF file

25. Tools – Tabular Data Taxon Tagger http://tools.gbif.org/taxontagger/ http://tools.gbif.org/taxontagger/ Output: Scientific Names Higher Taxonomy Hightlights names

26. Tools – Tabular Data Checklist Bank (Development Prototype) http://ecat-dev.gbif.org/api/clb http://ecat-dev.gbif.org/api/clb Input: Scientific Names Output: Higher taxonomy

27. Tools – Tabular Data Darwin Test http://www.gbif.es/darwin_test/Darwin_test_in.php http://www.gbif.es/darwin_test/Darwin_test_in.php GBIF France Validate and check records Darwin Core Archive format Coordinate conversions Check names against databases Detect encoding issues Generalize sensitive data (coords) Access based

28. Tools – Tabular Data Scripting/dynamic languages This is geocoding With 10 more lines, you can achieve very specific, complex and custom results

29. Tools – Tabular Data Google Refine http://code.google.com/p/google-refine/ http://code.google.com/p/google-refine/ DEMO

30. Other Resources - Data Sources

31. Data sources OpenStreetMap http://www.openstreetmap.org/ http://www.openstreetmap.org/ Data quality? Free Editable Downloadable Community based

32. Data sources Thesauri Thematic checklists: o Fish : FishbaseFishbase o Animals in general: Index to Organism Name (ION)Index to Organism Name (ION) o Mammals: Mammal Species of the World (MSW)Mammal Species of the World (MSW) o Bacteria: List of Bacteria with Standing in Nomenclature (LBSN)List of Bacteria with Standing in Nomenclature (LBSN) Country codes o ISO 3166-1 or ISO3166-2, available for example in Access format ( http://www.gbif.es/BDQ.php) http://www.gbif.es/BDQ.php

33. Other Resources - Documents

34. Documents GBIF Position Paper http://www.gbif.org/orc/?doc_id=2777 http://www.gbif.org/orc/?doc_id=2777 on Future Directions and Recommendations for Enhancing Fitness-for-Use Across the GBIF Network

35. Documents GBIF Spain BDQ Inventory http://www.gbif.es/BDQ.php http://www.gbif.es/BDQ.php

36. Documents GBIF Online Resource Centre http://www.gbif.org/orc/ http://www.gbif.org/orc/ Browse and download Fitness for use Best practices Training Manuals

37. Thank you. Questions?