A Semantic Web for Biomedical Informatics

• Lambrix P, `Towards a Semantic Web for Bioinformatics using Ontology-based Annotation', Proceedings of the 14th IEEE International Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises, pp 3-7, 2005. Invited talk.

Biomedical Ontologies and Alignment of Biomedical Ontologies

• slides

• Lambrix P, Tan H, Jakoniene V, Strömbäck L, `Biological Ontologies', chapter 4 in Baker, Cheung, (eds), Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences, pp 85-99, Springer, 2007. ISBN-10: 0-387-48436-1, ISBN-13: 978-0-387-48436-5. publisher's book page.

• Euzenat J, Shvaiko P, Ontology Matching, Springer, 2007.
• Lambrix P, Tan H, `SAMBO - A System for Aligning and Merging Biomedical Ontologies', Journal of Web Semantics, Special issue on Semantic Web for the Life Sciences, 4(3):196-206, 2006. pre-print, journal page.

• List of projects on the Ontology Matching Website, http://ontologymatching.org
• Ontology Alignment Evaluation Initiative
• SAMBO - aligning and merging ontologies
• KitAMO - tookit for evaluating ontology alignment strategies

Standards for Molecular Interaction Data

• slides

• Strömbäck L, Hall D, Lambrix P, A review of standards for data exchange within systems biology, Proteomics, 7(6):857-867, 2007.
• Strömbäck L, Lambrix P, Representations of molecular pathways: An evaluation of SBML, PSI MI and BioPAX, Bioinformatics, 21(24):4401-4407, 2005.
• Juliana Freire, David Koop, Emanuele Santos, and Claudio T. Silva, Provenance for Computational Tasks: A Survey, Computing in Science & Engineering(3), pp. 11-21, 2008.
• Fang Du, Sihem Amer-Yahia and Juliana Freire, ShreX: Managing XML Documents in Relational Databases Proceedings of VLDB Demonstration04.

Probabilistic Graph Models for Gene Regulatory Networks

• slides

• Sachs, K. et al.: Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science 308 (2005) 523-529.
• Friedman, N.: Inferring Cellular Networks Using Probabilistic Graphical Models. Science 303 (2004) 799-805.

Text Mining for Biomedicine

• slides

• Jensen JL, Saric J, Bork P, Literature mining for the biologist: from information retrieval to biological discovery, Nature Reviews Genetics, 7:119-129. 2006.
• Bourne P, Will a Biological Database Be Different from a Biological Journal?, PLoS Comput Biol., 1(3): e34, 2005.
• Phoebe M. Roberts, Mining literature for systems biology, Briefings in Bioinformatics, 7(4):399-406, 2006.
• Russ B Altman, Casey M Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Juhl Jensen, Martin Krallinger, Barend Mons, Seán I O'Donoghue, Manuel C Peitsch, Dietrich Rebholz-Schuhmann, Hagit Shatkay, Alfonso Valencia, Text mining for biology - the way forward: opinions from leading scientists, Genome Biology, 9(Suppl 2):S7, 2008.

• Cohen KB, Hunter L, Natural Language Processing and Systems Biology, Artificial Intelligence and Systems Biology, Springer Series on Computational Biology. Dubitzky W. and Azuaje F. (Eds.). 2005.
• Spasic I, Ananiadou S, McNaught J, Kumar A., Text mining and ontologies in biomedicine: making sense of raw text, Briefings in Bioinformatics, Sep;6(3):239-51, 2005.
• Bodenreider O, Lexical, terminological and ontological for biological text mining, Text mining for biology and biomedicine, Ananiadou S, McNaught J, (Eds.) p 43, 2006.

• Wikiprofessional, http://www.wikiprofessional.org
• GoPubMed - Explore PubMed/Medline with Ontologies, www.gopubmed.com/
• iHOP - Information Hyperlinked over Proteins, www.ihop-net.org/
• PubFinder, www.glycosciences.de/tools/PubFinder