Trait ontology approach Marie-Angélique LAPORTE NCEAS June 7 th 2010

Ontology construction Construction of a functional plant traits ontology Terminological aspects process using SKOS vocabulary Domain knowledge representation using UML class diagram Model transformation : UML → OWL => Formal/explicit representation of a knowledge domain => reasoning on the knowledge => emergence of new knowledge

SKOS Description and sharing of the terms and the relations between these terms, of a knowledge domain, using a simple vocabulary. W3C Recommendation The SKOS vocabulary: Simple Knowledge Organization System  Based on RDF  Data publication on the web  Can be extended by other vocabularies (eg. OWL) or thesauri  Data tagging Advantage : easy way to communicate with the domain experts (no informatics background is needed to understand the notions of definition, preferred label, alternative label, broader relation,narrower relation...)

SKOS Allows to represent “concept schemes” A concept scheme is a set of concepts including relationship between these concepts :  Labels : prefLabel, AtlLabel, HiddenLabel  Semantic relationships : broader, narrower, related,...  Documentaty notes : definition, notes,...

SKOS A concept scheme is not a formal representation => not an ontology Allows mapping between concepts from different concept schemes : exactMatch, closeMatch,broadMatch, narrowMatch, relatedMatch.

SKOS OWL = formal description of a domain SKOS = vocabulary and hierarchical structure SKOS vocabularies are instantiation of OWL Full ontology

SKOS SKOS labeling properties and SKOS note properties are defined as OWL annotation properties. SKOS semantic relations are defined as OWL object properties Future step : enrich SKOS vocabularies as OWL ontologies

UML Modeling the functional plant domain : the semantic relation between the terms are precise Advantage : easy way to interact with the proposed model Exchange with OWL model at the level of metamodel and metametamodel.

Thesauform Web tool dedicated to terminological aspects of a domain: the terms are represented using SKOS vocabulary Domain experts can identify and define rigorously terms of a specific domain. Allows easy management of the conflicts on the terms and the versioning of thesaurii.

Thesauform Technologies used : Tomcat JSP technology to develop a dynamic Web application Jena (Java framework) and SPARQL query language to deal with semantic aspects and manipulate OWL/RDF file SKOS vocabulary specifications to define terms and their organization into thesaurus. DCT, OWL and vocab status vocabularies to manage versioning aspect on terms and scheme aspect.

Plant trait ontology Main purpose: combine the data from the plant trait domain with data from other domain (climate, ecosystem,...) Linkage to OBOE Data integration : TRY, LEDA, Biolflor,... Difficulties : A trait is an vision invented by biologists : modelisation problem to separate the aspects entity, characteristic of an observation