BIS TDWG Conference, New Orleans 2011

Knowledge Organization Systems Session - Introduction

Éamonn Ó TuamaSenior Programme Officer, Inventory, Discovery, Access (IDA)Global Biodiversity Information Facility (GBIF)

20 October 2011

KOS symposium

1. Introduction: the GBIF context (Éamonn Ó Tuama)

2. GBIF KOS task group report (Bob Morris)

3. The GBIF KOS work programme: prioritised requirements and proposed solutions (Dag Endresen)

4. BioPortal as an ontology management system (Hilmar Lapp)

5. The TDWG Vocabularies (Greg Whitbread)

6. Managing the Darwin Core set of terms (John Wieczorek)

Knowledge Organization Systems

- Term lists: glossaries, dictionaries, gazetteers

- Classifications / categorizations: taxonomies

- Relationships: thesauri, ontologies

... to manage the vocabularies used for sharing biodiversity information.

simple relationships a model of a domain

e.g., Dewey Decimal Classification

Hodge G. 2000. Systems of Knowledge Organization for Digital Libraries: Beyond Traditional Authority Files. http://www.clir.org/pubs/reports/pub91/contents.html

taxonRank

higherClassification

taxonConceptIDcollectionCode

geodeticDatumspecificEpithet

coordinatePosition

Darwin Core – a glossary of terms

collectionCode: The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived. Examples: "Mammals", "Hildebrandt", "eBird".

nt Natural resourcesnt Biological resources

nt Genetic resources

nt Germplasmuf Genetic materialuf Germplasm resourcesrt Protoplasmrt Genesrt Gene poolsrt Biodiversityrt Germplasm collectionsrt Gametes

AgroVoc vocabulary – a thesaurus

bt Resources

bt = broader termnt = narrower termuf = used forrt = related term

http://aims.fao.org/standards/agrovoc/functionalities/hierarchy

SKOSSimple Knowledge Organisation System

Ontology – a model of a domain

ontologies = computable dictionaries

inverseOf

sameAs

transitiveProperty

http://www.ksl.stanford.edu/software/jtp/doc/owl-reasoning.html

The facts:(owl:inverseOf collectorOf hasCollector)(collectorOf Charles_Darwin Galapagos_Finches)Imply the fact:(hasCollector Galapagos_Finches Charles_Darwin)

The facts:(rdf:type hasAncestor owl:TransitiveProperty)(hasAncestor Charles_Darwin Robert_Darwin)(hasAncestor Robert_Darwin Erasmus_Darwin)imply the fact(hasAncestor Charles_Darwin Erasmus_Darwin )

The facts:(owl:sameAs Human Person)(rdf:type Human rdfs:Class)(rdf:type Person rdfs:Class)imply the fact(owl:equivalentClass Human Person)

Need for KOS

- requirement for principles and best practices for developing ontologies (TDWG 2009)

- lack of vocabularies/ontologies (eBiosphere)

- advance the TDWG ontology architecture (TDWG 2009)

- tools for TDWG Interest Groups to support standard development process (TDWG 2009)

- collaboration on ongoing support mechanisms for essential shared vocabularies (GBIF LGTG Report)

- hackathon to merge Darwin Core with existing TDWG ontologies and current GBIF vocabularies work (GBIF LGTG Report)

- recognition that not everyone has to be an ontologist - use of human readable vocabularies + ontology proper (TDWG 2009)

GBIF position paper on KOS Robert A MorrisTerry CatapanoDonald HobernHilmar LappNorman MorrisonNatasha NoyMark SchildhauerDavid Thau

GBIF Vocabularies Service

Mapping tools for a range of community-supported vocabularies and Darwin Core extensions

GBIF Vocabularies Service

Audubon Core extension to Darwin Core

- New dedicated position at GBIF (Dr Dag Endresen) funded through external projects (ViBRANT, i4Life)

KOS activities at GBIF

- Review GBIF Vocabularies Service and related systems -> develop vocabulary management system

- Engage with wider community: - participation in Dublin Core workshop, Sept 2011- KOS symposium at TDWG 2011 Conf, Oct 2011

- Review recommendations in KOS task group report and develop implementation roadmap

Key requirement: a platform to support the development, maintenance and governance of vocabularies for the biodiversity community

DCMI Vocabulary Workshop

- Very keen to collaborate with TDWG and share experience

- No turn-key solution

Den Haag, 21 Sept, 2011

- Managing a forum in which community can focus on issues around management of vocabularies and develop best practices

Key issues

1. Establishing a community site for managing our vocabularies

2. Central role of TDWG TAG

3. Whither the TDWG vocabularies site?

4. Whither the TDWG vocabularies?

5. Relationship of DwC to TDWG vocabularies

6. Separating term definitions from modeling

7. Introducing semantics in DwC: identifying classes – a good idea?

8. Need for a high level conceptual model?