The document discusses ontology design patterns (ODPs), which are reusable solutions to common modeling problems when building ontologies. It provides an overview of the history and use of ODPs, including in the domain of bio-ontologies. Various types of ODPs are described, such as extensional patterns and content patterns. The advantages of using ODPs in ontology engineering are improved modularity, reusability, communication and more. Guidelines for documenting and applying ODPs are also presented.

1. 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 Damjanovic
Salzburg Research Forschungsgesellschaft m.b.H.
Jakob Haringer Straße 5/3 | 5020 Salzburg, Austria
T +43.662.2288-427 | F +43.662.2288-222
violeta.damjanovic@salzburgresearch.at
www.salzburgresearch.at

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

3. Outline
| Ontology Engineering
| History of Using Patterns in Ontology Engineering
| ODP: General Remarks
| Bio-Ontology Engineering
| Classification of ODP for Bio-Ontologies
Adapted SET Triple in Action
|
| The Advantages of Using ODP in Bio-Ontology Engineering
| ODP Initiative: Classification of Ontology Patterns
| Content ODP
| Description Template of SDP Applied to ODP
| Conclusions
| Literature
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 3

4. 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
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 4

5. 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 Ontologies
Using 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.
| …
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 5

6. 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]:
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 6

7. 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.
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 7

8. 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)
|
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 8

9. 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
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 9

10. Adapted SEP Triple in Action
[Seidenberg & Rector, 2006]
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 10

11. The Advantages of Using ODP in Bio-Ontology Engineering
| Design
Rich and granular modelling
|
Semantic encapsulation
|
Robustness and modularity
|
Reasoning
|
Alignment
|
| Implementation
Focused development
|
Rapid prototyping
|
Reengineering
|
| Communication
Good communication
|
Documented modelling
|
Comprehension of advances in KR
|
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 11

12. ODP Initiative: Classification of Ontology Design Patterns
[Presutti et al., 2008]
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 12

13. 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
|
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 13

14. 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
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 14

15. Description Template of SDP Applied to ODP [Aranguren et al., 2008]
http://martinfowler.com/articles/writingPatterns.html#CommonPatternForms
| Name and classification
| Intent
| Also known as
| Motivation
| Applicability
| Structure
| Participants
Elements (in ODP)
|
| Collaboration
Relationships (in ODP)
|
| Consequences
| Implementation
| Sample code
OWL DL ontology with the whole ODP
|
The important parts of the ODP described using DL notation (or Manchester
|
abstract OWL syntax)
| Known uses
| Related patterns
| References (possible publications or web pages where can it be founded)
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 15

16. 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/
|
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 16

17. 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.
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 17

18. Contribute to the ODP efforts
• http://www.ontologydesignpatterns.org
• http://www.w3.org/2001/sw/BestPractices/
01.04.2009 © Salzburg Research Forschungsgesellschaft 2008. No reproduction without written permission. 18