LSIDs and RDF in TDWG

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LSIDs and RDF in TDWG
Roger Hyam, TDWG, RBGE Donald Hobern, GBIF
June 7-9, 2006 - Edinburgh, UK
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Paradigm

• Starting assumption is that standards are about
  sharing data.
• Sharing data also implies sharing data through
  time.

Archive
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What is Shared?

• Sharing raw literals isnt much use.
• They need to be gathered together into semantic
  units or objects.

perennis
1234
Bellis
TaxonName1234 Bellis perennis
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Semantics of Objects

• Objects need to be based on some shared
  semantics.
• There needs to be somewhere to look up what they
  mean an ontology.

Ontology
TaxonName Bellis perennis
TaxonName?
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Identity of Objects

• How do I refer to this object?
• Who should I credit?
• Who should I send corrections to?
• Is it the same record as I already have or is it
  a new one?
• What is the official version of this data - has
  some one altered it before I received it?

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TDWG TAG-1 Meeting

• There was consensus on-
• Architecture is concerned with shared data
• Biodiversity data will be modeled as a graph of
  identifiable objects
• The semantics of these objects will be encoded in
  a series of shared ontologies
• Ontologies will be related to each other on the
  basis of a shared Base and Core ontologies as a
  minimum
• Discussion continues on how this is done

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Implications

• We need a ontology to define and relate the
  objects we exchange.
• Ontology governance/management is paramount.
• We need a system of GUIDs to identify the
  objects.
• We need a roadmap for the protocols to exchange
  these objects.

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Structure of the Ontology
Base Ontology
BaseThing
BaseActor
Core Ontology
CoreTaxonName
CoreInstitution
Domain Ontology
TaxonName
Herbarium
NomencalturalType
NomeclaturalNote
Application Ontologies
ABCD
DarwinCore
???
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Ontology Governance

• Allow people to create Domain sub-ontologies
  easily prevent alienation.
• Each ontology construct (concept) has a status.
• Status is increased by passing through explicit
  gates defined by actual usage.

Experimental
Shared
Recommend
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What about RDF?

• The need to share identifiable objects has been
  established without reference to a technology.
• We are interested in objects not triples.
• Typical use case involves a client consuming
  semantically heterogeneous data from multiple
  sources.
• Semantic Web technologies would be ideal but
  arent part of the TDWG culture and there are
  unbelievers.

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Current Standards

• DarwinCore DiGIR
• Based on Z39.50
• HTTP based XML message / response
• Simple flat application schemas (RDF-like)
• ABCD BioCASe
• Based on DarwinCore DiGIR
• Complex document structure.
• TAPIR
• Unification of BioCASe and DiGIR
• No RDF, Objects or GUIDs here yet!

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Combing Data

• GBIF data portal is the only application that
  does data integration between these formats.
• No standard way to include XML fragments from
  other XSD other than xsany.
• There is overlap between the different schemas
  and no easy way to merge them.

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What about LSIDs

• GUID-1 meeting considered several GUID
  technologies including (LSID, DOI Handle).
• Life Science Identifiers are being assessed.
• I3C OMG URNs
• urnlsidncbi.nlm.nih.govpubmed12571434
• getData()
• getMetadata()

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LSID Permanence

• LSIDs should not be recycled i.e. Used for more
  that one object.
• LSIDs should always resolve but it is OK for them
  to resolve to a 404 (Gone) error.
• No central authority to control these things.
• Even DOIs go away if there isnt institutional
  backing!

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LSIDs for Everything?

• Are there some things for which LSIDs are
  inappropriate?
• ltlogo rdfresourceurnlsidexample.combranding
  logo.gif /gt
• xsischemaLocationurnlsidexample.comxsdtaxon
  .xsd
• xmlnstnurnlsidexample.comontologytaxon/
• Definitely places where we will use something
  else.
• Other people will use their own identifiers e.g.
  DOI, Handle etc.

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So whats cooking?
Recognised Need For GUIDS
Different GUID Technologies
XSD Based Conceptual Schemas
A TDWG Ontology
XML Based Exchange Protocols
Emergent Semantic Web
OGC Standards (GML)
Other!
200 Data Providers 50 Million Anonymous
Records
BioMOBY
Clients?
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Possible Roadmap

• Build the ontology as a focus for semantics.
• Resolution and Harvest protocols should be
  relatively easy to plug into or wrap round
  existing service providers so approach these
  first.
• Search/Query More problematic BioCASe, DiGIR,
  TAPIR, SPARQL, other?

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Thank You

• Gordon and Betty Moore Foundation
• Global Biodiversity Information Facility
• NESC
• TDWG Members