Acronym Soup GBIF, TDWG & GUIDs

1. Acronym SoupGBIF, TDWG & GUIDs Jerry Cooper

2. Global Biodiversity Information Facility (GBIF) • Established in 2000 through non-binding MOU (25 countries + 31 organizations) • Essentially a global information infrastructure for sharing primary biodiversity data (species occurrences) • GBIF network currently provides access to 120 million records from 1000 ‘collections’ • Infrastructure evolved from existing exemplar networks – Species Analyst/DiGIR (Kansas), BioCISE/BioCASE (EU – Berlin) • Taxonomic Databases Working Group (TDWG) provides a forum for development of GBIF technology

3. Taxonomic Databases Working Group (TDWG) • Now re-badged as ‘TDWG- Biodiversity Information Standards’ • 20 year history with focus of activity at an annual meeting • Initial focus on database design and data dictionaries • Recently evolved towards data exchange standards,ontologies and data sharing protocols • An appropriate forum for developing the Veg-X standard?

4. Taxonomic Databases Working Group (TDWG) • Existing TDWG Standards (existing or actively being developed): • Taxon Concept Schema (TCS) • Access to Biological Collection Data (ABCD) • Darwin Core (DC) • Structured Descriptive Data (SDD) • Collection – Institutional Metadata • Literature (citation and document structures for taxonomic literature) • Images • Geospatial • Observation & Specimens • Alien Invasive Species Profiles • Globally Unique Identifiers (GUIDs) • TAPIR (TDWG Access Protocol for Information Retrieval)

5. TDWG GUIDs • Need for unique, persistent, resolvable identifiers to communicate about objects • TDWG promotes Life Science Identifiers (LSIDs) • LSIDs are of the form: • urn:lsid:indexfungorum.org:names:417119 • They are resolvable • LSIDs are not URLs – resolution requires extra software. • Debate continues about merits of LSID versus HTTP mediated schemes

6. LSIDs in action...

7. Server-side LSID resolver

9. Record Metadata returned as RDF XML Document

10. RDF subject-predicate-object triples for TCS name object

11. X-Standards, RDF & GUIDs • TDWG reformulating existing standards expressed in XML-Schema as part of a generalized ‘TDWG Ontology’ • RDF Metadata are formalized as ‘vocabularies’ derived from the ontology • E.g. Return from IndexFungorum conforms to TDWG TCS Vocabulary • LCR working on DotNet LSID server/resolvers and linking TCS/ABCD (for IndexFungorum and Zoobank)

12. Conclusions • GUIDs essential for cross-referencing in any X-Standard – even if present as generic URI ‘placeholders’ for such things as Taxon Concepts etc. • Merits of LSID/RDF still debated • TDWG Ontologies and LSID RDF vocabularies immature • But ... point the way to components of a Veg-X standard that need to be harmonized across standards • TDWG – appropriate umbrella organisation for development of a Veg-X standard.

14. Taxon Concepts VegBank Vocabulary • Assertions • name/publication intersection • Interpretation • something labelled with an assertion (observation, collection etc) • Correlation • between interpretations as >,<, = • Usage • 3rd party opinion, i.e. party 1 believes that party 2’s interpretation using name X should be labelled with name Y

15. Flavours of Taxon Concepts • Use of names in primary taxonomic literature • Nomenclatural statement (name attached to types, isotypes & protologue description) • Homotypic synonyms (names based on same type, ‘objective’) • Heterotypic synonyms (names based on different types • taxonomic opinion expressed as published list of synonyms. Perhaps with emended description and lists of collections examined • Use of names in secondary taxonomic literature • names within floras/faunas, guide books, keys etc • Use of names attached to ‘events’ • names within species lists, surveys, observation records etc For LCR & NZOR: • 1 & 2 stored in taxonomic database. • 3 stored against ‘events’ database. • Systems need to ‘expand’ names against combined concept stores. • TCS is designed to accommodate 1 & 2, not necessarily 3