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

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.

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

Darwin Core Archive Format

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

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

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

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)

HIT Adapters

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

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

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

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

DwCA Validating Tool View the DwCA ValidatorDwCA Validator

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

Importing Data

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

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

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

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

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

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: 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

Nub Components

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

Nub Building

Admin Console View the Admin ConsoleAdmin Console

Discovery: Portal and Services

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

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

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

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

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

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

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

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