This page contains contact information, schedule, and reading material for the Semantic Web Technologies course taught by Jos de Bruijn and Maria Keet.
General Information
Aim: The aim of the course is to make the students familiar with the Semantic Web, with technologies used on the Semantic Web, and with applications using Semantic Web technologies. The course will focus on the theoretical background of various languages on the Semantic Web such as RDF, SPARQL, and OWL, and the practical use of these languages on the Semantic Web. In addition, the course will focus on ontology engineering and important application areas for Semantic Web technology, namely the Life Sciences.
Course location: the lectures will be held in Via Sarnesi 1, Room E412, from 01.10.2007 to 26.01.2008 each Monday 14.00-16.00 and Tuesday 10.30-11.30 (minus holidays; any changes can be found in the RIS calendar).
Contact information: Maria Keet
Office hours: by prior arrangement via e-mail
KRDB Research Centre
Faculty of Computer Science
University of Bozen-Bolzano
via della Mostra 4, 2nd floor
Uni: http://www.inf.unibz.it/krdb
Home: www.meteck.org
Blog: keet blog
tel (office): 0471 016 127
email: {surname}@inf.unibz.it
Lectures
Schedule and topics (subject to changes):
- Oct 5 - Nov 10. First part by Jos de Bruijn
- Lecture 1: Nov 16. Introduction, Web Ontology Language (OWL)
- Lecture 2: Nov 17. OWL 2
- Lecture 3: Nov 23. Ontology engineering 1: Top-down
- Lecture 4: Nov 24. Ontology engineering 2: Bottom-up
- Lecture 5: Nov 30. Ontology engineering 3: Methodologies
- Lecture 6: Dec 1. Ontology engineering 4: Parts and temporal aspects
- Dec 7. No lecture
- Dec 8. No lecture
- Lecture 7: Dec 14. Ontology engineering 5: Dealing with uncertainty and vagueness
- Lecture 8: Dec 15. SWT for the Life Sciences 1: Background and data integration
- Lecture 9: Dec 21. SWT for the Life Sciences 2: Successes and challenges for ontologies
- Lecture 10: Dec 22. SWT for the Life Sciences 3: SWLS and text processing and ontologies
- Jan 4. No lecture
- Jan 5. No lecture
- Lecture 11: Jan 11. SWT for the Life Sciences 4: bioRDF, workflows and services
- Lecture 12: Jan 12. SWT for the Life Sciences 5: Social aspects and recap course contents
- Feb 17. 14.00-16.00 EXAM room E412, Ser-E
1. Introduction, Web Ontology Language (OWL) (Nov 16, 2009)
The first part of the lecture consists of an outline of the rationale and and scope of the topics that will pass the revue. The second part introduces OWL, the family of Web Ontology Languages.Related blog posts: Semantic Web Technologies course part 2: start of an experiment and The Web Ontology Languages
Slides - Handouts
Basic reading
- OWL Guide
- Ian Horrocks, Peter F. Patel-Schneider, and Frank van Harmelen. From SHIQ and RDF to OWL: The making of a web ontology language. Journal of Web Semantics, 1(1):7, 2003.
Recommended reading
- Protege OWL tutorial with the Pizza Ontology
Reference material
2. OWL 2 (Nov 17, 2009)
This lectures continues with the overview of the OWL languages, and OWL 2 in particular.Related blog post: The Web Ontology Languages
Slides - Handouts
Basic reading
- B. Cuenca Grau, I. Horrocks, B. Motik, B. Parsia, P. Patel-Schneider, and U. Sattler. OWL 2: The next step for OWL. Journal of Web Semantics: Science, Services and Agents on the World Wide Web, 6(4):309-322, 2008 (or click here if you are not on the uni network)
Optional reading
- I. Horrocks, O. Kutz, and U. Sattler. The Even More Irresistible SROIQ. In Proc. of the 10th International Conference of Knowledge Representation and Reasoning (KR-2006), Lake District UK, 2006.
- Diego Calvanese, Giuseppe De Giacomo, Domenico Lembo, Maurizio Lenzerini, Antonella Poggi, Mariano Rodriguez-Muro, and Riccardo Rosati. Ontologies and databases: The DL-Lite approach. In Sergio Tessaris and Enrico Franconi, editors, Semantic Technologies for Informations Systems - 5th Int. Reasoning Web Summer School (RW 2009), volume 5689 of Lecture Notes in Computer Science, pages 255-356. Springer, 2009
- Keet, C.M. and Rodriguez, M. Toward using biomedical ontologies: trade-offs between ontology languages. AAAI 2007 Workshop on Semantic e-Science (SeS'07), 23 July 2007, Vancouver, Canada. AAAI 2007 TR WS-07-11, 65-68.
Reference material
- OWL quick Reference
- OWL 2 Web Ontology Language Structural Specification and Functional-Style Syntax
- OWL 2 Web Ontology Language Profiles
3. Ontology engineering 1: Top-down (Nov 23, 2009)
We look at the "historical" development of ontology engineering since the mid 1990s, and what they are used for. One step of ontology development is the use of foundational ontologies (such as BFO, DOLCE, GFO) and their formalisations (on paper in FOL, in OWL DL, Isabelle).Related blog post: Ontology engineering Top-down and Bottom-up
Slides - Handouts
Basic reading
- Guarino, N. Formal Ontology in Information Systems. Proceedings of FOIS'98, Trento, Italy, June 6-8, 1998. IOS Press, Amsterdam, pp. 3-15
- Barry Smith. Beyond Concepts, or: Ontology as Reality Representation, Achille Varzi and Laure Vieu (eds.), Formal Ontology and Information Systems. Proceedings of the Third International Conference (FOIS 2004), Amsterdam: IOS Press, 2004, 73-84.
Recommended reading
- Masolo, C., Borgo, S., Gangemi, A., Guarino, N., Oltramari, A.: WonderWeb Deliverable D18--Ontology library. WonderWeb. http://wonderweb.semanticweb.org/ (2003). There are also slides of Guarino's OntoLog seminar for a digest of the material.
- Presutti, V., Gangemi, A., David, S., de Cea, G. A., Surez-Figueroa, M. C., Montiel-Ponsoda, E., Poveda, M. A library of ontology design patterns: reusable solutions for collaborative design of networked ontologies. NeOn deliverable D2.5.1, Institute of Cognitive Sciences and Technologies (CNR). 2008.
- An example of combining (linking, integrating, importing) top-level ontologies with domain ontologies: BioTop
Reference material
- DOLCE in OWL and in various ultralite versions
- BFO online
- The owl versions of DOLCE and BFO in DL and Manchester syntax in one pdf
4. Ontology engineering 2: Bottom-up (Nov 24, 2009)
Reusing ontologies and extracting ontology-like artifacts from legacy material.Related blog post: Ontology engineering Top-down and Bottom-up
Slides - Handouts
Basic reading
- L. Lubyte, S. Tessaris. Automatic Extraction of Ontologies Wrapping Relational Data Sources. In Proc. of the 20th International Conference on Database and Expert Systems Applications (DEXA 2009). To appear.
- Keet, C.M. Factors affecting ontology development in ecology. Data Integration in the Life Sciences 2005 (DILS'05), Ludaescher, B, Raschid, L. (eds.). San Diego, USA, 20-22 July 2005. Lecture Notes in Bioinformatics LNBI 3615, Springer Verlag, 2005. pp46-62. and supplementary tables
Recommended reading
- Christine Golbreich and Ian Horrocks. The OBO to OWL mapping, GO to OWL 1.1! In Proc. of the Third OWL Experiences and Directions Workshop, number 258 in CEUR (http://ceur-ws.org/), 2007. See also with wiki page on oboInOwl
- Dagobert Soergel, Boris Lauser, Anita Liang, Frehiwot Fisseha, Johannes Keizer and Stephen Katz. Reengineering thesauri for new applications: the AGROVOC example. Journal of Digital Information 4(4) (2004)
Reference material
- D2R Map: database to RDF mapping
- OMG's Ontology definition metamodel with interactions between UML and OWL & RDF
5. Ontology engineering 3: Methodologies (Nov 30, 2009)
This lecture takes a closer look at parameters for ontology design, methods (such as OntoClean, glassbox reasoning), and more comprehensive methodologies (Methontology, MoKi, NeOn methodology).Related blog post: Methods and methodologies
Slides - Handouts
Basic reading
- Guarino, N. and Welty, C. An Overview of OntoClean. in S. Staab, R. Studer (eds.), Handbook on Ontologies, Springer Verlag 2004, pp. 151-172
- Fernandez, M.; Gomez-Perez, A. Pazos, A.; Pazos, J. Building a Chemical Ontology using METHONTOLOGY and the Ontology Design Environment. IEEE Expert: Special Issue on Uses of Ontologies, January/February 1999, 37-46.
- Keet, C.M. Ontology design parameters for aligning agri-informatics with the Semantic Web. 3rd International Conference on Metadata and Semantics (MTSR'09) -- Special Track on Agriculture, Food & Environment, Oct 1-2 2009 Milan, Italy. F. Sartori, M.A. Sicilia, and N. Manouselis (Eds.), Springer CCIS 46, 239-244.
Optional reading
- Gomez-Perez, A.; Fernandez-Lopez, M.; Corcho, O. Ontological Engineering. Springer Verlag London Ltd. 2004. available in the UniBz library, shelf mark 3 QP 345 G633
- Mari Carmen Suarez-Figueroa, Guadalupe Aguado de Cea, Carlos Buil, Klaas Dellschaft, Mariano Fernandez-Lopez, Andres Garcia, Asuncion Gomez-Perez, German Herrero, Elena Montiel-Ponsoda, Marta Sabou, Boris Villazon-Terrazas, and Zheng Yufei. NeOn Methodology for Building Contextualized Ontology Networks. NeOn Deliverable D5.4.1. 2008.
- Parsia, B., Sirin, E., Kalyanpur, A. Debugging OWL ontologies. World Wide Web Conference (WWW 2005). May 10-14, 2005, Chiba, Japan.
- M. Horridge, B. Parsia, and U. Sattler. Laconic and Precise Justifications in OWL. In Proc. of the 7th International Semantic Web Conference (ISWC 2008), Vol. 5318 of LNCS, Springer, 2008.
Reference material
6. Ontology engineering 4: Parts and temporal aspects (Dec 1, 2009)
This lecture focuses on part-whole relations, which are deemed a core relation in subject domains such as medicine, biology, geographic information systems, and manufacturing. Some basic notions of temporal knowledge (LTL/CTL, time ontology) will also pass the revue.Related blog post: Part-whole relations and time
Slides - Handouts
Basic reading
- Keet, C.M. and Artale, A. Representing and Reasoning over a Taxonomy of Part-Whole Relations. Applied Ontology, IOS Press, 2008, 3(1-2): 91-110.
Recommended reading
- Artale, A., Guarino, N., and Keet, C.M. Formalising temporal constraints on part-whole relations. 11th International Conference on Principles of Knowledge Representation and Reasoning (KR'08). Gerhard Brewka, Jerome Lang (Eds.) AAAI Press, pp 673-683. Sydney, Australia, September 16-19, 2008
- Alessandro Artale, Christine Parent, and Stefano Spaccapietra. Evolving objects in temporal information systems. Annals of Mathematics and Artificial Intelligence (AMAI), 50:5-38, 2007, Springer.
Reference material
- Time ontology in OWL
- Some problems, workarounds, and pitfalls for using part-whole relations are described in the W3C Editor's Draft on Simple part-whole relations in OWL Ontologies
7. Ontology engineering 5: Dealing with uncertainty and vaguenes (Dec 14, 2009)
This lecture covers probabilistic, possibilistic, fuzzy, and rough ontologies.Related blog post: Dealing with uncertainty and vaguenes
Slides - Handouts
Basic reading
- Thomas Lukasiewicz and Umberto Straccia. 2008. Managing Uncertainty and Vagueness in Description Logics for the Semantic Web. Journal of Web Semantics, 6:291-308. OR:
- Umberto Straccia. Managing Uncertainty and Vagueness in Description Logics, Logic Programs and Description Logic Programs. In Reasoning Web, 4th International Summer School, 2008.
Optional reading
- Jiang, Y., Wang, J., Tang, S., and Xiao, B. 2009. Reasoning with rough description logics: An approximate conceptsapproach. Information Sciences, 179:600-612.
- Extensive AAAI'07 tutorial slides by Umberto Straccia
Reference material
none yet, but there are some tools you might want to try out and there was a W3C incubator group for Uncertainty Reasoning on the WWW8. SWT for the Life Sciences 1: Background and data integration (Dec 15, 2009)
We fist look at the kick-off by the Gene Ontology Consortium and then more recent advances that aim for data integration and the use of Semantic Web Technologies in one way or another.Related blog post: SWT for HCLS: background and data integration
Slides - Handouts
Basic reading
- The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nature Genetics, May 2000;25(1):25-9.
- Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L. Whetzel, Suzanna Lewis. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25, 1251-1255 (2007).
- Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Scott Marshall M, Ogbuji C, Rees J, Stephens S, Wong GT, Elizabeth Wu, Zaccagnini D, Hongsermeier T, Neumann E, Herman I, Cheung KH. Advancing translational research with the Semantic Web, BMC Bioinformatics, 8, 2007.
Recommended reading
- Joshua S. Madin, Shawn Bowers, Mark P. Schildhauer and Matthew B. Jones. (2008). Advancing ecological research with ontologies. Trends in Ecology & Evolution, 23(3): 159-168.
- Erhard Rahm. Data Integration in Bioinformatics and Life Sciences. EDBT Summer School, Bolzano, Sep. 2007.
- OBO Foundry
Reference material
none9. SWT for the Life Sciences 2: Successes and challenges for ontologies (Dec 21, 2009)
Successes and challenges for using OWL ontologies in the life sciences, with two success stories and an overview of challenges as viewed from the ontologist's perspective.Related blog post: Successes and challenges for ontologies in the life sciences
Slides - Handouts
Basic reading
- Wolstencroft, K., Stevens, R., Haarslev, V. Applying OWL reasoning to genomic data. In: Semantic Web: revolutionizing knowledge discovery in the life sciences, Baker, C.J.O., Cheung, H. (eds), Springer: New York, 2007, 225-248. book at disposal from Marijke Keet and papers with similar message/content are online (in Bioinformatics here and the Bio-ontologies workshop)
- Stefan Schulz, Holger Stenzhorn, Martin Boekers and Barry Smith. Strengths and Limitations of Formal Ontologies in the Biomedical Domain. Electronic Journal of Communication, Information and Innovation in Health (Special Issue on Ontologies, Semantic Web and Health), 2009.
Recommended reading
- Calvanese, D., Keet, C.M., Nutt, W., Rodriguez-Muro, M., Stefanoni, G. Web-based Graphical Querying of Databases through an Ontology: the WONDER System. ACM Symposium on Applied Computing (ACM SAC'10), March 22-26 2010, Sierre, Switzerland.
- Keet, C.M., Roos, M. and Marshall, M.S. A survey of requirements for automated reasoning services for bio-ontologies in OWL. Third international Workshop OWL: Experiences and Directions (OWLED 2007), 6-7 June 2007, Innsbruck, Austria. CEUR-WS Vol-258. And its follow-up "Reasoning requirements for bio-ontologies: the harvest from OWLED & DL 2007"
- Zhang S, Bodenreider O, Golbreich C. Experience in reasoning with the Foundational Model of Anatomy in OWL-DL. In: Pacific Symposium on Biocomputing 2006, Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE, (Eds.). World Scientific, 2006, 200-211.
Reference material
none10. SWT for the Life Sciences 3: Text processing and ontologies (Dec 22, 2009)
This lecture focuses on the contributions from natural language processing to SWT and bio-ontologies, in particular regarding the efforts in NLP-driven ontology learning, ontology population, and sorting search results.Related blog post: SWLS and text processing and ontologies
Slides - Handouts
Basic reading
- Witte, R. Kappler, T. And Baker, C.J.O. Ontology design for biomedical text mining. In: Semantic Web: revolutionizing knowledge discovery in the life sciences, Baker, C.J.O., Cheung, H. (eds), Springer: New York, 2007, pp 281-313.
- Dimitra Alexopoulou, Thomas Waechter, Laura Pickersgill, Cecilia Eyre, and Michael Schroeder. Terminologies for text-mining: an experiment in the lipoprotein metabolism domain. BMC Bioinformatics, 9(Suppl4):S2, 2008
Optional reading (recommended for the EMLCT students)
- Hirschman, L., Hayes, W.S., and Valencia, A. Knowledge acquisition from the biomedical literature. In: Semantic Web: revolutionizing knowledge discovery in the life sciences, Baker, C.J.O., Cheung, H. (eds), Springer: New York, 2007, pp 53-81.
- Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Joerg Hakenberg, Jan Moennich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Waechter, Matthias Zschunke, and Michael Schroeder. GoPubMed: Exploring PubMed with Ontological Background Knowledge. In Stephen A. Krawetz, editor, Bioinformatics for Systems Biology. Humana Press, 2008. online: Gopubmed
- Allen H. Renear and Carole L. Palmer. Strategic Reading, Ontologies, and the Future of Scientific Publishing. Science 325 (5942), 828. [DOI: 10.1126/science.1157784] (but see also some comments on the paper)
Reference material
none11. SWT for the Life Sciences 4: bioRDF, workflows and services (Jan 11, 2009)
There are several other topics in the SWLS arena, such as bioRDF, scientific workflows, and Semantic Web services.Related blog post: BioRDF and Workflows
Slides - Handouts
Basic reading
- Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J. Bio2RDF: Towards A Mashup To Build Bioinformatics Knowledge System. Journal of Biomedical Informatics. 2008 Oct;41(5):706-16. online interface: bio2RDF
- Tom Oinn, Matthew Addis, Justin Ferris, Darren Marvin, Martin Senger, Mark Greenwood, Tim Carver, Kevin Glover, Matthew R. Pocock, Anil Wipat and Peter Li. (2004). Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20 (17): 3045-3055. The Taverna website
Optional reading
- Michael DiBernardo, Rachel Pottinger, and Mark Wilkinson. (2008). Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. Journal of Biomedical Informatics, 41(5): 837-847.
- Sahoo., S.S., Shet, A. Hunter, B., and York, W.S. SEMbrowser--semantic biological web services registry. In: Semantic Web: revolutionizing knowledge discovery in the life sciences, Baker, C.J.O., Cheung, H. (eds), Springer: New York, 2007, pp 317-340.
Reference material
- W3C's RDF and SPARQL
- W3C Web Services Activity, with links to the WSDL and SAOP recommendations
12. SWT for the Life Sciences 5: Social aspects and recap course content (Jan 12, 2009)
Wrap up, where we go through social aspects of realising the semantic web for the life sciences and summarise the contents of the previous lectures (part 2 of the course, that is--the recap of part 1 is on 19-1).Related blog post: Social Aspects
Basic reading
- Good BM and Wilkinson MD. The Life Science Semantic Web is Full of Creeps! Briefings in Bioinformatics, 2006 7(3):275-286.
- see basic readings of the previous lectures
Optional reading
- Carole Goble and Chris Wroe. The Montagues and the Capulets. Comparative and Functional Genomics, 5(8):623-632, 2004. doi:10.1002/cfg.442
- see recommended readings of the previous lectures
Reference material
- see reference material of the previous lectures
Supplementary material
- Other resources you might find of use:- Pascal Hitzler, Markus Kroetzsch, Sebastian Rudolph. Foundations of Semantic Web Technologies. Chapman & Hall/CRC, 2009, 455p. shelf mark: 126.3 ST 252 H676 (at disposal from Calvanese)
- Steffen Staab, Rudi Studer (eds.). Handbook on ontologies. Berlin : Springer, 2004. shelf mark: 13 QP 345 S77.
- Frank van Harmelen, Vladimir Lifschitz and Bruce Porter (Eds.). Handbook of Knowledge Representation. Elsevier, 2008, 1034p. shelf mark 126.4 ST 304 H287 (at disposal from Franconi)
- other books in the library (do a keyword search on "semantic web"), which has books on ontology matching, real world applications from industry, ontology management, services, ontology learning and population from text, reasoning & rules, etc.