the loreley of ontology design patterns

The Loreley of the Ontology Design Patterns

Double vocal projection:

http://ontologydesignpatterns.org

http://www.gong.manchester.ac.uk/odp/html/index.html

Dr. Violeta DamjanovicSalzburg Research Forschungsgesellschaft m.b.H.Jakob Haringer Straße 5/3 | 5020 Salzburg, AustriaT +43.662.2288-427 | F +43.662.2288-222violeta.damjanovic@salzburgresearch.atwww.salzburgresearch.at

01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 2

Preamble

| Ontology Design Pattern -> ODP

| ODP: a new testament to known problems in ontology engineering

| ODP: a practical solution to semantic interoperability of different knowledge configurations (components and approaches)


Ontology Engineering

| Ontologies are engineering artefacts that can formally represent the

concepts and their relationships within a given knowledge domain

| Ontologies are implemented in different KR (Knowledge

Representation) languages differing in properties that can be

described along the following axes:

| Syntax

| Semantics

| Expressiveness

| Reasoning

| Ontologies provide shared and common understanding of a domain


History of Using Patterns in Ontology Engineering: Selected papers

| J.R. Reich, 1999: Ontological Design Patterns for the Integration of Molecular Biological Information. GCB’99, Germany.

| introduces the notion of ODP for a particular problem domain in Biology

| S. Staab, M. Erdmann, A. Maedche, 2001: Engineering OntologiesUsing Semantic Patterns. IJCAI '01, USA.

| language independent description of a certain concepts, relation or axiom

| V. Devedzic, 2002: Understanding Ontological Engineering.Communications of the ACM, Vol.45, No.4, 2002, pp. 136-144.

| similarities between traditional SDP and ontologies

| P. Clark, J. Thompson, B. Porter, 2003: Knowledge Patterns. Springer. International Handbooks on Information Systems.

| conceptual patterns that are “morphed” into a given knowledge base by a set of mapping axioms

| V. Svatek, 2004: Design Patterns for Semantic Web Ontologies: Motivation and Discussion. 7th Conf.on Business Inform.Systems.

| A. Gangemi, 2005: Ontology Design Patterns for Semantic Web Content. LNCS 1729 ISWC 2005, 262-276.

| …


Ontology Design Patterns in General (1)

| ODP: abstract, formalized and documented solutions to the frequent

and typical modelling problems

| SDP < --- > ODP

| The UML notation to OWL axioms mapping proposed in [Brockmans

et al., 2004]:


Ontology Design Patterns in General (2)

| ODP: “cookbook recipes” [Aranguren et al., 2008]

| ODPs are abstract and implementation independent

| Applying a particular ODP, e.g.:

| Competency questions help in choosing an appropriate ODP

| Ontology Processing Language (OPL) can be used to create ODP in a

new ontology

| OPL plugin: http://www.co-ode.org/downloads/protege-x/opl/

| ODPs can be classified according to their complexity, granularity,

usability, popularity, etc.


Bio-Ontology Engineering

| GENE (GEne ontology NExt generation) project

| “ODP for the formalization of biological ontologies”, Thesis by Mikel

Egaña Aranguren. 2005. Available @

http://www.gong.manchester.ac.uk/doc/MPhil_thesis.pdf.gz)

| The ODP Catalog can be explored @ http://odps.sourceforge.net/

| ODPs are classified according to the way they are used:

| Extensional ODPs (Exception ODP, N-ary Relationship ODP)

| Good practice ODPs (Normalization ODP, Value Partition ODP, Upper

Level ODP)

| Domain Modelling ODPs (List ODP, Adapted SEP Triples ODP)


Classification of ODP for Bio-Ontologies

| Extensional ODPs:

| N-ary Relationships: to model complex phenomena that have

relationships linking more than one element

| Exception: to model classes that break canonical classifications

| Good practice ODPs:

| Normalization: to build modular and reusable ontologies

| Value Partition: to model attributes of objects that can only have certain

already known values

| Upper Level Ontology: to create an ontology than can integrate different

ontologies in itself

| Domain Modelling ODPs:

| List: to model ordered groups of elements

| Adapted SEP Triples: propagation of properties along the partonomy

relation


Adapted SEP Triple in Action [Seidenberg & Rector, 2006]


ODP Initiative: Classification of Ontology Design Patterns[Presutti et al., 2008]


Content Ontology Design Pattern [Gangemi, 2005]

| Content ODP shows certain characteristics:| Computational components

| Small, autonomous components

| Hierarchical components

| Inference-enabling components

| Cognitively relevant components

| Linguistically relevant components

| Best practice components

| Content ODP ways of creation [Presutti & Gangemi, 2008]| Reengineering from other data models

| Specialization/Composition of other Content ODP

| Extraction from reference ontologies

| Creation by combining the above techniques

| Set of operation for creation of Content ODP| Covering: connects Content ODP and requirements | Clone: copies an ontology element from an existing ontology | Composition: relates two Content ODPs and results into a new ontology | Specialization & Generalization: defines a partial ordering between Content ODPs| Expansion: relation between CODPs and either ontology elements or axioms


Catalog of Content Ontology Design Pattern [Presutti et al., 2008]

| General: types of entities; description; situation; classification; n-ary

classification; object role;

| Parts and collections: part of; time indexed part of; composition; constituency;

collection entity;

| Semiotics: intension extension; information realization;

| Quantities and dimensions: region; region overlap; parameter; parameter

region;

| Participation: participation; co-participation; n-ary participation;

| Organization, management, and scheduling: precedence (sequence); agent

role; task role; time-indexed person role; basic plan description; basic plan

execution; basic plan;

| Business: price; sales and purchase order contracts;

| Time: time interval;

| Space: move;

| Life science: linnean taxonomy;

| Multimedia: multimedia data segment decomposition


Conclusion

| ODP are ready-made solutions for tackling complex modelling issues when creating and maintaining ontologies

| ODP improve ontology engineering in different ways [Brockmans et al., 2004]

| ODPs are abstractions: faster ontology creation; easy way of dealing with the complexity of e.g. OWL-DL

| ODPs produce more modular and robust ontologies: the entities and the structure of ontologies can be explicitly separated

| ODPs improve communication between ontology developers

| ODP life-cycle:

| Identifying ODP

| Testing ODP

| ODP becomes a part of the system (language)

| Protégé plugin for applying ODPs ?

| http://www.co-ode.org/downloads/protege-x/patterns/


Literature

| S. Brockmans, R. Volz, A. Eberhart, P. Löffler, 2004: Visual Modelling of

OWL DL Ontologies Using UML. Proc. ISWC 2004, 198-213.

| M.E. Aranguren, E. Antezana, M. Kuiper, R. Stevens, 2008. Ontology

Design Patterns for Bio-Ontologies: A Case Study on the Cell Cycle

Ontology. BMC bioinformatics 2008, 9(Suppl 5):S1. [BMC Bioinformatics]

| J. Seidenberg, A. Rector, ´2006. Representing Transitive Propagation in

OWL, ER2006.

| V. Presutti, A. Gangemi, 2008. Content Ontology Design Patterns as

Practical Building Blocks for Web Ontologies, In Proceedings of the 27th

International Conference on Conceptual Modeling (ER 2008)

| V. Presutti, et al., 2008. NeOn D2.5.1: A Library of Ontology Design

Patterns: Reusable Solutions for Collaborative Design of Networked

Ontologies.

| A. Gangemi, 2005. Ontology Design Patterns for Semantic Web Content.

LNCS 1729 ISWC 2005, 262-276.


Contribute to the ODP efforts

• http://www.ontologydesignpatterns.org

• http://www.w3.org/2001/sw/BestPractices/

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