1. GLOBAL BIODIVERSITY INFORMATION FACILITY ECAT Programme Update David Remsen & Markus Döring

2. ECAT Goals l GBIF provides a simple and extensible solution for publishing taxonomic checklists l Published data used to improve access and data interoperability within the portal l Published data supports taxonomic name services l Name services support development of tools that meet national and regional needs.

3. SCOPE of ECAT publishing l Taxonomic Catalogues l Monographs/Flora/Fauna l Annotated Species Checklists l Regional l Thematic l Nomenclators l Name Dictionaries l No taxonomy

4. Darwin Core Archive Format

5. Vocabularies.gbif.org l Community-driven l Internationalised l Vocabularies l Extensions l Tested l Ready for release See Spanish PageSpanish Page

6. Extensions l Extend the DwC l For Occurrence-level l For Species-level l Draft l Add relevant vocabs. l Review l Publish!

7. Terms of Bionomenclature l Taxonomic Std Reference l Print Publication l Online Reference l Semantic l Supports vocabulary building l April Go to websiteto website

8. Publishing Checklists to GBIF l Integrated Publishing Toolkit (next version) l Full & “lite” l Direct DWC Output from Sources l HIT Adapters for existing sources l Spreadsheets l Desktop Applications l Refactoring existing online Tools (ITIS, EDIT)

9. HIT Adapters

10. DatabaseClassificationSynonymsVernacularDistrib. Catalogue of Life 2009Yes ITISYes Tree of LifeYes--- USDA PlantsYes GRIN GermPlasm TaxonomyYes - NCBI TaxonomyYes Palaeobiology DatabaseYes -- See Example DWC Archive Output View the Project Wiki page with links to all source ScriptsProject Wiki page source Scripts

11. Publishing by Spreadsheet l Simple l Validated l Developing countries l Conforms to existing workflow

12. Publishing by Spreadsheet l Forms and auto-complete l Metadata and data l Occurrence data l Species Checklists l Embedded vocabularies

13. Desktop Application l Desktop Application l Publishes DwCA l Currently used GBIFS l ~100 sources l 600,000 records l 90 languages l Could be deployed

14. DwCA Validating Tool View the DwCA ValidatorDwCA Validator

15. Published DWC Archive files l Current Status l Manually Curated l 82 ECAT sources l 14Taxonomic authority files l 64 Vernacular Name Lists l 2 Nomenclatural Lists l 2 Thematic Lists l 5,800 occurrence classifications l 15M different usages l 11,454,896 unique names assigned to 4.8M name groups l 4,612,444 canonical names

16. Importing Data

17. ChecklistBank Command Line Tool l Bundles many tasks into 1 executable jar l adding/deleting/exporting resources, (pre)importing, lexical grouping, nub build l * to be used by HIT module l * importing in 3 steps: l 1) preimport terms l 2) import into isolated db schema l 3) accepting import into public schema

18. Checklist Data Qualities 1. Highly relational taxonomic data, almost all records linked in a tree hierarchy + basionym 2. Wrong or missing records destroy dataset integrity, not just a single record! 3. Different to flat, unrelated occurrence records Syntactically damaged sources wrong mappings wrong character encodings end of line breaks or tabs within data Data Quality broken referential integrity bad names (e.g. «Unallocated Family») missing or unused controlled vcabularies, e.g. «art» for rank species Names can be published in several ways ScientificName ScientificName + Authorship Genus + Authorship Genus + SpeciesEpitheton (+ Rank + InfraspecificEpitheton)+ Authorship Classifications can be published in several ways Normalised via parentNameUsageID Normalised via parentNameUsage Denormalised via Kingdom,Phylum,Class,Order,Family,Genus

19. Checklist Bank Model l Lexical Group l Gerardia paupercula var. borealis (Pennell) Deam l Gerardia paupercula (Gray) Britt. var. borealis (Pennell) Deam l Gerardia paupercula (A.Gray) Britton var. borealis (Pennell) Deam l Gerardia paupercula borealis l Gerardia paupercula borealis (Pennell) Deam l Nomenclatural Group l Gerardia paupercula var. borealis (Pennell) Deam l Agalinis paupercula var. borealis Pennell

20. Taxonomic Backbone (Nub) What it is How it is built

21. Composite Taxonomic Backbone l Largest integrated taxonomy in the world l 200 million occurrences l One taxonomic hierarchy

22. Nub Relevance l Nub Management Classification is used for l provide hierarchy of names l crosswalking between taxonomies l All biodiversity data is aligned via names l Considerable variation in higher taxa l => Maps & Statistics l External linkages, e.g. EOL maps l More details: http://livelink.gbif.org/gbif/livelink/overview/3233870 Cronquist classification Mimosaceae: 3,200 species Caesalpiniaceae: 2,000 species Fabaceae: 14,000 species “Modern” classification Fabaceae: 19,200 species Mimosoideae: 3,200 species Cæsalpinioideae: 2,000 species Faboideae: 14,000 species

23. Nub Components

24. Nub Building l Regular Checklist Resource l Lexical Grouping l Canonical homonyms l Authorship matching difficult l => canonical names + kingdom l Ignore noisy occurrence derived only names? l Nub Assembling l 8 CoL kingdoms l Each LexGroup becomes a nub usage l Contradicting classifications l Intermediate rank synonyms l Select preferred, wellformed name l Stable IDs l Rated sources, nomenclatural resources for names, taxonomic for classification Subphylum in ANIMALIA Vertebrata Vertebrate Vertebrata Cuvier, 1812 Algae genus in PLANTAE Vertebrata Vertebrata Gray Vertebrata S.F. Gray, 1821

25. Nub Building

26. Admin Console View the Admin ConsoleAdmin Console

27. Discovery: Portal and Services

28. Checklist Bank Portal l 82 ECAT Resources l 14 Taxonomic Catalogues l 64 Vernacular Name lists l 2 Thematic Lists l 2 Nomenclators Go to PortalPortal

29. Checklist Bank Web Services l Checklist Service l Name Usage Resolver l Name Usage Service l Name Usage Navigation Service l Name String Service l Image Service Go to API PagePage

30. Name Parser l Uses l Comparing l Matching l GBIF Backbone l “Did you mean” Try GBIF Name ParserName Parser

31. Name Recognition Services View GBIF Name Recognition Tools l Updated Service l March 2010 l DWC API l Uses l IAIA parsing l Adding names to metadata l Checklists from documents

32. “TaxonTagger” tools View TaxonTaggerTaxonTaggerSample document (Butterfly list)document

33. Using Name Services: Data Entry Google Docs: Live ExampleLive Example

34. Taxonomic Indexing l Mining names from publishing RSS feeds l IAIA reports l KNB Knowledge network l Mapping to Species lists l “Any red-listed species in this set of IAIA reports.” Name Parser API TaxonFinder API Checklist Bank API

35. Other 2010/11 l Mapping Services l Linking a data collection to a specific taxonomic authority l Taxonomic Validation and Annotation of Occurrence data. l Linking to Community Species Pages