Part 3: Storing, Querying, and Integrating Biomedical Data

Achard, F., et al. "XML, Bioinformatics and Data Integration." Bioinformatics 17, no. 2 (2001): 115-125.

Schweiger, R., et al. "Plug-and-Play XML: A Health Care Perspective." Journal of the American Medical Informatics Association 9, no. 1 (January/February 2002): 37-48.

Stanislaus, R., et al. "An XML Standard for the Dissemination of Annotated 2D Gel Electrophoresis Data Complemented with Mass Spectrometry Results." BMC Bioinformatics 5, no. 9 (2004). (PDF)

Florescu, D., and D. Kossman. "Storing and Querying XML Data using an RDBMS." Bulletin of the IEEE Computer Society Technical Committee on Data Engineering 22 (1999): 27-34. (See pp. 27-34 in (This resource may not render correctly in a screen reader.PDF))

Shanmugasundaram, J., et al. "Relational Databases for Querying XML Documents: Limitations and Opportunities." Proceedings of the 25th VLDB Conference, Edinburgh, Scotland, 1999. (PDF)

Zhang, C., et al. "On Supporting Containment Queries in Relational Database Management Systems." Proceedings of ACM SIGMOD 2001, Santa Barbara, CA. (This resource may not render correctly in a screen reader.PDF)

Tatarinov, I., et al. "Storing and Querying Ordered XML Using a Relational Database System." Proceedings of ACM SIGMOD 2002, Madison, WI.

Lesser, U. "A Query Language for Biological Networks." Bioinformatics 21, suppl. 2 (2005): ii33-ii39.

Krishnamurthy, L., et al. "Pathways Database System: An Integrated System for Biological Pathways." Bioinformatics 19, no. 8 (2003): 930-937.

Cerami, E. G., et al. "cPath: Open Source Software for Collecting, Storing, and Querying Biological Pathways." BMC Bioinformatics 7 (2006): 497. (PDF)

Part 4: Ontology Management in Systems Biology

Horridge, M., et al. "A Practical Guide To Building OWL Ontologies Using The Protégé -OWL Plugin and CO-ODE Tools." Edition 1.0, 1994. (PDF - 2.3 MB)
An excellent introduction to ontologies and the OWL language, in the context of an editing and execution environment called Protégé.

Stein, L. D. "Integrating Biological Databases." Nature Reviews Genetics 4 (May 2003): 337-345.

Searls, D. B. "Data Integration: Challenges for Drug Discovery." Nature Reviews Drug Discovery 4 (January 2005): 45-48.

Davidson, S. B., and L. Wong. "The Kleisli Approach to Data Transformation and Integration." 2001. (Download PDF from CiteSeerx.)

Bhowmick, S. S., P. Cruz, and A. Laud. "XomatiQ: Living With Genomes, Proteomes, Relations and a Little Bit of XML." Proceedings of 19th International Conference on Data Engineering (ICDE'03), 2003.

Broekstra, J., A. Kampman, and F. van Harmelen. "Sesame: A Generic Architecture for Storing and Querying RDF and RDF Schema." Proceedings of the International Semantic Web Conference (ISWC) 2002. (This resource may not render correctly in a screen reader.PDF)

Wilkinson, K., et al. "Efficient RDF Storage and Retrieval in Jena2." Presented at 1st International Workshop on Semantic Web and Databases, September 7, 2003, Berlin, Germany. (This resource may not render correctly in a screen reader.PDF)

Zhou, J., et al. "Minerva: A Scalable OWL Ontology Storage and Inference System." Proceedings of First Asian Semantic Web Conference, 2006, Beijing China.

McGuinness, D. L., and F. van Harmelen, eds. "OWL Web Ontology Language Overview." W3C Recommendation, February 10, 2004. (PDF)

Part 5: Biological Pathways

Lu, J., et al. "SOR: A Practical System for Ontology Storage, Reasoning and Search." Proceedings of VLDB '07, September 23-28, 2007, Vienna, Austria. (This resource may not render correctly in a screen reader.PDF)

Smith, A. K., et al. "LinkHub: A Semantic Web System that Facilitates Cross-database Queries and Information Retrieval in Proteomics." BMC Bioinformatics 8, Suppl. 3 (2007): S5. (PDF)

Lam, H. Y. K., et al. "AlzPharm: Integration of Neurodegeneration Data using RDF." BMC Bioinformatics 8, Suppl 3 (2007): S4. (PDF - 1.1 MB)

Aranguren, M. E., et al. "Understanding and Using the Meaning of Statements in a Bio-ontology: Recasting the Gene Ontology in OWL." BMC Bioinformatics 8 (2007): 57. (PDF)

Kanaris, I., et al. "Building in-silico Pathway SBML Models from Heterogeneous Sources." Proceedings of 8th IEEE International Conference on BioInformatics and BioEngineering (BIBE 2008), Athens Greece, October 8-10, 2008. Paper BI916. doi: 10.1109/BIBE.2008.4696730.

Sharan, R., and T. Ideker. "Modeling Cellular Machinery Through Biological Network Comparison." Nature Biotechnology 24, no. 4 (April 2006): 427-433.

Kelley, Brian P., et al. "Conserved Pathways Within Bacteria and Yeast as Revealed by Global Protein Network Alignment." PNAS 100, no. 20 (September 20, 2003): 11304-11309. doi: 10.1073/pnas.1534710100.

Shlomi, T., et al. "QPath: A Method for Querying Pathways in a Protein-protein Interaction Network." BMC Bioinformatics 7 (2006): 199. (PDF)

Sharan, R., et al. "Conserved Patterns of Protein Interaction in Multiple Species." PNAS 102, no. 6 (February 8, 2005): 1974-1979. doi:10.1073/pnas.0409522102.

Part 6: Biological and Medical Data Integration

Bataller, R., and D. A. Brenner. "Liver Fibrosis." The Journal of Clinical Investigation 115, no. 2 (February 2005): 209-218.

Part 7: Grand Challenges

Fishman, M. C., and J. A. Porter. "A new grammar for drug discovery." Nature 437 (22 September 2005): 491-493.

Butcher, E. C., E. I. Berg and E. J. Kunkel. "Systems biology in drug discovery." Nature Biotechnology 22, no. 10 (October 2004): 1253-1259.

Huang, P. H., and F. M. White. "Phosphoproteomics: Unraveling the Signaling Web." Molecular Cell 31 (September 26, 2008): 777-781.