TDWG Core Ontology

1
TDWG Core Ontology

• J Kennedy
• R Gales, R Hyam, R Kukla,
• J Wieczorek, G Hagedorn, M Döering
• D Vieglais, S Perry , D Hobern

2
Background

• Discussion within the community about semantic
  web technologies as potentially being a good
  platform for the biodiversity community.
• Proposal to TDWG/GB Moore Foundation grant to
  draft a core ontology
• Based on existing TDWG standards
• TCS, ABCD, SDD, DwC
• Take into account TAG developments
• TDWG Technical Architecture Group outcomes
• Biodiversity data will be modelled 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 shared Base and Core ontologies as a
  minimum.
• Group to coordinate development on non-normative
  first pass ontology from existing schemas and
  make recommendation for base and core ontologies

3
Ontology Structure
Base Ontology
BaseThing
BaseActor
Core Ontology
CoreTaxonName
CoreInstitution
Domain Ontology
TaxonName
Herbarium
NomencalturalType
NomeclaturalNote
Application Ontologies
ABCD
DarwinCore
???
4
TDWG Standards

• ABCD
• Specimens, taxon names, institutions, people,
  publications
• DwC
• Specimens, taxon names, institutions, people,
  publications
• TCS
• taxon concepts, specimens, taxon names,
  publications
• SDD
• Descriptions, measurements, specimens, taxon
  names
• Observations
• Locations, specimens, people
• Same concept being defined in many places in many
  ways..
• How can we reuse/share the definitions
  effectively?

5
Process

• Modularise the existing standards
• Subgroups contributed possible reusable concepts
  based on existing standards
• TDWG TAG Wiki Ontology page
• http//wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntolo
  gy
• Meeting of subgroup members to draft core
  ontology
• 16-18th May _at_ e-Science Institute, Edinburgh
• J Kennedy, R Gales, R Hyam, R Kukla, J Wieczorek
• G Hagedorn, M Döering, D Hobern, D Vieglais, S
  Perry

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Process

• The likely core ontology classes identified
• Classes were give textual definitions based on
  Oxford English dictionary where possible
• to aid in the general understanding of what was
  intended by the class.
• The properties for the classes in the core
  ontology were restricted to properties of type
  other core ontology class
• Further definition is left to the domain classes.
• Support concrete representations of the classes
• Needs reviewing by group
• Report on outcome of meeting
• http//www.nesc.ac.uk/talks/687/coremeetingreport.
  pdf

7
Ontology Structure
Domain Ontology
TaxonName
Specimen
NomenclaturalType
NomeclaturalNote
Application Ontologies
ABCD
Specimen
???
DarwinCore
TaxonName
Identification
Adapted Roger Hyam (TDWG TAG)
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Process

• Wiki/email feedback
• Re-draft of core ontology
• New draft presented at meeting on 8th June _at_ eSI
• J Kennedy, R Gales, R Hyam, M Döering, D
  Vieglais, S Perry
• UML model on Wiki
• Presented at GUID-2 meeting
• Few small suggested changes incorporated
• e.g. specimens might not all be biological
• Use core ontology to produce a domain ontology
• Implement a demo to look at issues of using
  ontology
• Next talk

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Ontology Structure
Base Ontology
BaseThing
BaseActor
Core Ontology
CoreName
CoreInstitution
CoreSpecimen
BDI_Core Ontology
CoreTaxonName
CoreBioSpecimen
Domain Ontology
TaxonName
Specimen
NomenclaturalType
NomeclaturalNote
Application Ontologies
ABCD
Specimen
???
DarwinCore
TaxonName
Identification
Adapted from TDWG TAG, Roger Hyam
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Base layer
11
Core Layer
12
BDI Core Taxon Name
13
BDI Core Taxon Concept
14
BDI Core BioSpecimen
15
BDI Core BioObservation
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Implementation

• Ontology specified in OWL
• OWL Lite
• No simple diagrammatic views of OWL ontologies
• Extended it to a domain ontology with literal
  properties for classes
• Used the domain ontology to generate RDF triples
  of an existing data set with little extra effort.
• Next talk

17
Future

• Set up formal TDWG Ontology group?
• Or a task group of TAG?
• Need independent user to test in application
  development
• Need to have group review of ontology
• Meetings this week to discuss the ontology
• Please attend if you are interested

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Acknowledgements

• TDWG/Gordon Betty Moore Foundation