Ontology Engineering

This page provides some structure to the blog posts that have to do with ontology engineering. They provide gentle introductions to some of the sub-topics and contain links to relevant background material.

NOTE of caution: The list is far from a complete and/or balanced overview—it merely reflects what I bothered to write about in a blog post (which reflect my publications only partially). In due time, more posts will be added, but I do not aim for a neat coverage here (I try during the course, but my blog is not a course). Thus, they are pertinently not a substitute for a book, nor does it cover all core and elective topics of an ontology training session, and nor does it give a balanced overview of current research trends in ontology engineering. Nevertheless, I hope the overview is helpful in some way.

Posts starting with 72010 SemWebTech served as introductory notes to the lectures of that course and are better integrated, updated, and extended in the lecture notes for COMp718, but additional topics are covered here as well.

1. Informal introduction to ontologies

• 1.a Any semantic search for insects
• 1. b 72010 SemWebTech lecture 8: SWT for HCLS—background and data integration
• 1.c 72010 SemWebTech lecture 9: successes and challenges for ontologies in the life sciences
• 1.d Ontologies for better communication
• 1.e (n)ontologies and the thorny issue of their definitions
• 1.f A strike against the ‘realism-based approach’ to ontology development
• 1.g Ontological realism, methodologies, and mud slinging: a few notes on the AO trilogy

 

2. Ontology languages and automated reasoning

• 2.a 72010 SemWebTech lecture 1+2: the Web Ontology Languages
• 2.b Reasoning requirements for bio-ontologies: the harvest from OWLED & DL07
• 2.c From the Description Logics Workshop 2010, Waterloo
• 2.d Automating approximations in DL-lite ontologies
• 2.e The rough ontology language rOWL and basic rough subsumption reasoning

 

3. Top-down ontology development

•  3.a Foundational ontologies
•  3.a.i 72010 SemWebTech lectures 3+4: Ontology engineering top-down and bottom-up
• 3.a.ii African Wildlife Ontology tutorial ontologies
• 3.a.iii Outcome of the empirical assessment on the use of foundational ontologies in ontology development
• 3.a.iv First release of the foundational ONtology SElection Tool ONSET
• 3.a.v Refining constraints on RO’s transformation_of relation and Transformation, again with the link to the published paper
• 3.b Part-Whole relations
• 3.b.i 72010 SemWebTech lecture 6: parts and temporal aspects
• 3.b.ii Nontransitive vs. intransitive direct part-whole relations in OWL
• 3.b.iii Representing the difference between mandatory and essential parts and wholes
• 3.b.iv Part-whole relations, mereotopology, and the OntoPartS tool

 

4. Bottom-up ontology development

• 4.a Overview: 72010 SemWebTech lectures 3+4: Ontology engineering top-down and bottom-up
• 4.b Databases and conceptual data models
• 4.b.i Working towards WONDER data
• 4.b.ii Object-Role Modeling and Description Logics for conceptual data modeling
• 4.b.iii A note on improving the quality of conceptual data models with a reasoner
• 4.c Natural language and ontologies
• 4.c.i 72010 SemWebTech lecture 10: SWLS and text processing and ontologies
• 4.c.ii Every American is a NamedPizza
• 4.d Other approaches
• 4.d.i Bottom-up ontology development using bio-diagrams

 

5. Methods and methodologies

• 5.a Overview: 72010 SemWebTech lecture 5: methods and methodologies
• 5.b Parameters
• 5.b.i A collection of parameters for ontology design (short version, tailored to agricultural domain)
• 5.b.ii More ontology design parameters and dependencies between them and the post with the link to the IJMSO paper
• 5.c On methodologies and realism
• 5.c.i Ontological realism, methodologies, and mud slinging: a few notes on the AO trilogy
• 5.c.ii Outcome of the empirical assessment on the use of foundational ontologies in ontology development
• 5.d Tools
• 5.d.i First release of the foundational ONtology SElection Tool ONSET

 

6. Bio-ontologies

• 6.a 72010 SemWebTech lecture 8: SWT for HCLS—background and data integration
• 6.b 72010 SemWebTech lecture 9: successes and challenges for ontologies in the life sciences
• 6.c 72010 SemWebTech lecture 10: SWLS and text processing and ontologies
• 6.d Bottom-up ontology development using bio-diagrams
• 6.e Ontologies in ecology: putting the lessons-learned to good use and moving forward
• 6.f Metadata and semantics conference MTSR’09 and semantics for the agricultural domain
• 6.g Upcoming Dagstuhl seminar on the development of a environment ontology and Progress on the EnvO at the Dagstuhl workshop

 

7. Applications

• 7.a Successful applications
• 7.a.i 72010 SemWebTech lecture 9: successes and challenges for ontologies in the life sciences
• 7.b Ontology-based Data Access
• 7.b.i Tools to access data through an ontology
• 7.b.ii Case studies of ontology interoperation with OBDA and OBDI
• 7.b.iii The WONDER system for ontology browsing and graphical query formulation

 

8. Specialised topics

• 8.a 72010 SemWebTech lecture 6: parts and temporal aspects
• 8.b Uncertainty and vagueness
• 8.b.i 72010 SemWebTech lecture 7: dealing with uncertainty and vagueness
• 8.b.ii Rough ontologies from an ontology engineering perspective
• 8.b.iii The rough ontology language rOWL and basic rough subsumption reasoning
• 8.c 72010 SemWebTech lecture 11: BioRDF and workflows
• 8.d Ontology-driven conceptual data modeling
• 8.d.i Identification and keys in UML class diagrams
• 8.d.ii Book chapter on conceptual data modelling for biological data
• 8.d.iii Object-Role Modeling and Description Logics for conceptual data modeling
• 8.d.iv A note on improving the quality of conceptual data models with a reasoner