Acronym SoupGBIF, TDWG & GUIDs

Jerry Cooper

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

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?

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)

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

LSIDs in action...

Server-side LSID resolver

Record Metadata returned as RDF XML Document

RDF subject-predicate-object triples for TCS name object

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)

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.

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

Flavours of Taxon Concepts1. 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

2. Use of names in secondary taxonomic literature• names within floras/faunas, guide books, keys etc

3. 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