Acronym Soup GBIF, TDWG

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Acronym SoupGBIF, TDWG GUIDs

• Jerry Cooper

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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

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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?

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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)

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TDWG GUIDs

• Need for unique, persistent, resolvable
  identifiers to communicate about objects
• TDWG promotes Life Science Identifiers (LSIDs)
• LSIDs are of the form
• urnlsidindexfungorum.orgnames417119
• They are resolvable
• LSIDs are not URLs resolution requires extra
  software.
• Debate continues about merits of LSID versus HTTP
  mediated schemes

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LSIDs in action...
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Server-side LSID resolver
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Record Metadata returned as RDF XML Document
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RDF subject-predicate-object triples for TCS name
object
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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)

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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.

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Taxon Concepts VegBank Vocabulary

• Assertions
• name/publication intersection
• Interpretation
• something labelled with an assertion
  (observation, collection etc)
• Correlation
• between interpretations as gt,lt,
• Usage
• 3rd party opinion, i.e. party 1 believes that
  party 2s interpretation using name X should be
  labelled with name Y

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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