wiki:References
Last modified 10 years ago Last modified on 08/17/07 13:11:00

B. Background

Semantic Web

Wang X, Gorlitsky R, Almerida JS. From XML to RDF: how semantc web technologies will change the design of 'omic' standards. Nature Biotechnology 2005;23:1099-1103 http://www.nature.com/nbt/journal/v23/n9/pdf/nbt1139.pdf. This is funded by a proteomic initiative at NHLBI. Good overview of why XML alone is not good for data integration.

Reference Ontologies

Rosse, C and Mejino, JLV (2007) The Foundational Model of Anatomy Ontology. In Duncan Davidson and Richard Baldock (editors) Anatomy Ontologies for Bioinformatics: Principles and Practice. New York, In press. Springer. http://sigpubs.biostr.washington.edu/archive/00000204/01/FMA_Chapter_final.pdf

Haendel M, Neuhaus F, Osumi-Sutherland D, Mabee P, Mejino JLV, Mungall C, and Smith B. (2007) CARO- The Common Anatomy Reference Ontology. In Duncan Davidson and Richard Baldock (editors) Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, New York, In press. Springer. http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf

Ceusters W, Smith B, Goldberg L. A terminological and ontological analysis of the NCI thesaurus. Methods of Information in Medicine 2005;44:498-507 http://sig.biostr.washington.edu/share/sigweb/pubs/SmithNCITanalysis.pdf.

Smith B, Kumar A, Ceusters W, Rosse C. On carcinomas and other pathological entities. Comparative and functional genomics. In Press 2005 http://sig.biostr.washington.edu/share/sigweb/pubs/SmithPathology2005.pdf.

Smith B. New desiderata for biomedical terminologies. J. Biomedical Informatics. In Press. 2005 http://sig.biostr.washington.edu/share/sigweb/pubs/SmithDesiderata2005.pdf.

Zhang S, Bodenreider O. Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy. Computers in Biology and Medicine. In Press 2005 http://sig.biostr.washington.edu/share/sigweb/pubs/ZhangOntoPrinciples2005.pdf.

C. Preliminary Results

Gennari, J.H., Silberfein, A., and Wiley, J.C. (2005). Integrating genomic knowledge sources through an anatomy ontology. Proceedings of the Pacific Symposium on Biocomputing 2005, pp. 115 - 126. http://faculty.washington.edu/gennari/papers/gennari-PSB-05.pdf

Halevy AY, Ives ZG, Madhavan J, Mork P, Suciu D, Tatarinov I. 2004. The Piazza peer data management system. IEEE Transactions on Knowledge and Data Engineering 16:787-98 http://sig.biostr.washington.edu/share/sigweb/pubs/HalevyPiazza2004.pdf

Mejino JLV, Martin RF, Detwiler LT, and Brinkley JF. (2007) Challenges in Reconciling Different Views of Neuroanatomy in a Reference Ontology of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, Chicago, IL.

D. Research Design

D.1. Aim 1 Design of VDL

Stanford

Noy NF, Musen MA. Specifying ontology views by traversal. In: McIIraith SA, Plexousakis D, Van Harmelen F, editors. The Semantic Web - IWSC 2004: Third International Semantic Web Conference, Nov 7-11. Lecture Notes in Computer Science. Hiroshima, Japan: Springer-Verlag; 2004. p. 713. http://sig.biostr.washington.edu/share/sigweb/pubs/NoyViews2004.pdf.

Dameron O, Rubin DL, Musen MA. Challenges in converting frame-based ontology into OWL: the Foundational Model of Anatomy case-study. In: Proceeding, American Medical Informatics Association Fall Symposium. Washington, DC; 2005. p. 181-185. http://sig.biostr.washington.edu/share/sigweb/pubs/DameronAMIA2005.pdf.

Noy NF, Rubin DL, Musen MA. Making biomedical ontologies and ontology repositories work. IEEE Intelligent Systems 2004;19(6):78-81 http://smi-web.stanford.edu/people/noy/papers/ontologyLibraries.pdf.

UW

Other

Toivonen, S. Using RDF(S) to provide multiple views into a single ontology. Semantic Web Workshop 2001 HongKong?, China. http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS//Vol-40/Toivonen.pdf

Zoltan Miklos, Gustaf Neumann, Uwe Zdun, Michael Sintek: Querying Semantic Web Resources Using TRIPLE Views, Second International Semantic Web Conference (ISWC), Sanibel Island, Florida, USA, 2003. http://www.dbai.tuwien.ac.at/staff/miklos/p179.pdf

Magkanaraki A, Tannen V, Christophides V, Plexousakis D. Viewing the semantic web through RVL lenses. In: Second International Semantic Web Conference. Sanibel Island, Florida: Springer-Verlag; 2003. p. 96-112. http://sig.biostr.washington.edu/share/sigweb/pubs/MagkanarakiLense2004.pdf.

Volz R, Oberle D, Studer R. Implementing views for light-weight web ontologies. In: IEEE Database Engineering and Application Symposium (IDEAS). Hong Kong, China; 2003. http://sig.biostr.washington.edu/share/sigweb/pubs/VolzViews2003.pdf.

Rosario Uceda-Sosa, Cindy X. Chen, Kajal T. Claypool: CLOVE: A Framework to Design Ontology Views. ER 2004: 844-849. http://www.cs.uml.edu/~cchen/ontology/er_04.pdf

Containment and Minimization of RDF/S Query Patterns, G. Serfiotis, I. Koffina, V. Christophides and V. Tannen, Fourth International Semantic Web Conference (ISWC'05), Galway, Ireland, November, 2005. http://139.91.183.30:9090/RDF/publications/SQOFinal.pdf

Fikes R, Hayes P, Horrocks I. OWL-QL - A Language for Deductive Query Answering on the Semantic Web. Knowledge Systems Laboratory, Stanford University, Stanford, CA, 2003. ftp://ftp.ksl.stanford.edu/pub/KSL_Reports/KSL-03-14.pdf.gz

Haase P, Broekstra J, Eberhart A, Volz R. A Comparison of RDF Query Languages. World Wide Web, http://www.aifb.uni-karlsruhe.de/WBS/pha/rdf-query/rdfquery.pdf, 2004.

Steffen Staab, Rudi Studer (Eds.): Handbook on Ontologies. International Handbooks on Information Systems Springer 2004.

D.2 Aim 2 Implementation of VDL

Stanford

Dameron O, Noy NF, Knublauch H, Musen MA. Accessing and manipulating ontologies using web services. In: McIIraith SA, Plexousakis D, Van Harmelen F, editors. The Semantic Web - IWSC 2004: Third International Semantic Web Conference, Nov 7-11. Lecture Notes in Computer Science. Hiroshima, Japan: Springer-Verlag; 2004. http://smi-web.stanford.edu/people/noy/papers/dameron2004iswc.pdf.

UW

Other

The ICS-FORTH SWIM: A Powerful Semantic Web Integration Middleware, V. Christophides, G. Karvounarakis, I. Koffina, G. Kokkinidis, A. Magkanaraki, D. Plexousakis, G. Serfiotis, and V. Tannen, First International Workshop on Semantic Web and Databases, Co-located with VLDB 2003, Humboldt-Universitat, Berlin, Germany, September 7-8, 2003. http://139.91.183.30:9090/RDF/publications/swdb2003.pdf

Integrating XML data sources using RDF/S Schemas: The ICS-FORTH Semantic Web Integration Middleware (SWIM), I. Koffina, Master's Thesis, Univ. of Crete (2005). http://139.91.183.30:9090/RDF/publications/koffina.pdf

Views and Structured Querying in Self e-Learning Networks, A. Magkanaraki, G. Kokkinidis, V. Christophides, G. Karvounarakis, and D. Plexousakis, WP2 Deliverable 4.3. http://www.dcs.bbk.ac.uk/selene/reports/Del4.3-2.0.pdf

D.3 Aim 3 GUI

University of Victoria

Other

Generating On the Fly Queries for the Semantic Web: The ICS-FORTH Graphical RQL Interface (GRQL), N. Athanasis, V. Christophides and D. Kotzinos, Third International Semantic Web Conference (ISWC'04), Hiroshima, Japan, November, 2004. http://139.91.183.30:9090/RDF/publications/grql-final.pdf