Semantic Web Technologies course

	C. Maria (Marijke) Keet	Home	Research	Other topics

	Semantic Web Technologies course (72010) - 2009/2010 This page contains contact information, schedule, and reading material for the Semantic Web Technologies course taught by Jos de Bruijn and Marijke 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, OWL, and F-Logic (Programming), and the practical use of these languages on the Semantic Web. In addition, the course will focus on important application areas for Semantic Web technology, namely Web Services and Life Sciences. Course location: the lectures will be held in Via Sarnesi 1, Room D003, 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: Marijke 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): 04710 16128 email: {surname}@inf.unibz.it Lectures Schedule and topics (subject to changes): First part (Oct 5 - Nov 10) 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 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 review course contents Note: the material and reading suggestions of the first part by Jos de Bruijn are assumed to be known for this part of the course. 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. 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 OWL Reference OWL Abstract Syntax and Semantics 2. OWL 2 (Nov 17, 2009) This lectures continues with the overview of the OWL languages, and OWL 2 in particular. 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 Recommended 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). 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 also slides of Guarino's OntoLog seminar for a digest of the material. Reference material DOLCE in OWL and in various ultralite versions BFO online 4. Ontology engineering 2: Bottom-up (Nov 24, 2009) Reusing ontologies and extracting ontology-like artifacts from legacy material. 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 summplementary 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) Methodologies and tools, such as OntoClean, Methontology, glassbox reasoning. 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. Recommended 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 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 Semantic Web Best Practices and Deployment Working Group 6. Ontology engineering 4: Parts and temporal aspects (Dec 1, 2009) part-whole relations, LTL/CTL. 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) Fuzzy and rough ontologies Slides - Handouts Basic reading Thomas Lukasiewicz and Umberto Straccia. Managing Uncertainty and Vagueness in Description Logics for the Semantic Web. Journal of Web Semantics, 2008. OR: Umberto Straccia. Managing Uncertainty and Vagueness in Description Logics, Logic Programs and Description Logic Programs. In Reasoning Web, 4th International Summer School, 2008. Recommended reading TBA 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 WWW 8. 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. 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. 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 none 9. 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. 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 content are online (in Bioinformatics and the Bio-ontologies workshop) 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. 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 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" TBA Reference material none 10. SWT for the Life Sciences 3: Text processing (Dec 22, 2009) This lecture focuses on the contributions form natural language processing for minig and using effectively the bio-literaature, and on the feasibility of using NLP to develop and populate ontologies and enhance NLP with ontologies. Slides - Handouts Basic reading 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 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 Recommended reading 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. 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. Reference material none 11. 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. 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 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. Recommended reading Michael DiBernardo, Rachel Pottinger, and Mark Wilkinson. Semi-automatic web service composition for the life sciences using the BioMoby semantic web framework. Journal of Biomedical Informatics, 41(5): 837-847. Reference material none 12. SWT for the Life Sciences 5: Social aspects and review course content (Jan 12, 2009) Wrap up, where we go through social aspects of realising the semantic web for the life sciences and several other topics. Slides - Handouts 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 Recommended reading The Reference Genome Group of the Gene Ontology Consortium. The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Computational Biology, 5(7): e1000431 Life Science IDentifiers, LSID De Roure, D., Jennings, N.R., Shadbolt, N.R. (2005). The semantic grid: past, present, and future. Proceedings of the IEEE, 93(3): 669-681. 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. - If you like this course, you also may be interested in these courses: Non-classical Logics, Computational Logic, Formal Methods, and Knowledge Representation (Description Logics), among others.
	For comments: send an email to keet at inf dot unibz dot it. This page was last updated on September 29, 2009