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

Background  Discussion within the community about semantic web technologies as potentially being a good platform for the biodiversity community.  Proposal to TDWG/G&B 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

Ontology Structure Base Ontology Core Ontology Domain Ontology Application Ontologies BaseThing BaseActor CoreTaxonNameCoreInstitution TaxonName NomencalturalType NomeclaturalNote Herbarium ABCDDarwinCore???

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?

Process  Modularise the existing standards  Subgroups contributed possible reusable concepts based on existing standards  TDWG TAG Wiki – Ontology page:   Meeting of subgroup members to draft core ontology  16-18th e-Science Institute, Edinburgh  J Kennedy, R Gales, R Hyam, R Kukla, J Wieczorek  G Hagedorn, M Döering, D Hobern, D Vieglais, S Perry

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 

Ontology Structure Application Ontologies Base Ontology BaseThing BaseActor Core Ontology CoreTaxonNameCoreInstitution Domain Ontology TaxonName NomenclaturalType NomeclaturalNote Specimen ABCD DarwinCore ??? Adapted Roger Hyam (TDWG TAG) TaxonName Specimen Identification

Process  Wiki/ feedback  Re-draft of core ontology  New draft presented at meeting on 8th 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…

Ontology Structure Application Ontologies Base Ontology BaseThing BaseActor Core Ontology CoreNameCoreInstitution Domain Ontology TaxonName NomenclaturalType NomeclaturalNote Specimen ABCD DarwinCore ??? Adapted from TDWG TAG, Roger Hyam TaxonName Specimen Identification BDI_Core Ontology CoreTaxonName CoreBioSpecimen CoreSpecimen

Base layer

Core Layer

BDI Core Taxon Name

BDI Core Taxon Concept

BDI Core BioSpecimen

BDI Core BioObservation

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…

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

Acknowledgements  TDWG/Gordon Betty Moore Foundation