| Lec # | Topics | Readings |
|---|---|---|
| 1 | Introduction Objectives and Methodology The Information-driven Scientific Method Ontology and Semantics for Biomedical Information Term Paper Instructions | |
| 2 | The Life Cycle of Scientific Data Hypothesis to be Tested Data Acquisition: Design Data Acquisition: Measurement and Storage Analysis and Modeling Accomodating the Unknown - by Design | Neumann, Eric K., Eric Miller, and John Wilbanks. "What the semantic web could do for the life sciences." Drug Discovery Today 2, no. 6 (2004): 228-236. Advisory Committee to the Director, NIH Working Group on Biomedical Computing. "The Biomedical Information Science and Technology Initiative." Bethesda, MD: National Institutes of Health, U.S. Department of Health and Human Services, 1999. Release 1.0 21, no. 1 (2003): 1-36. (Entire periodical.) |
| Part I: Basic Technologies (3 Weeks) | ||
| 3 | General Principles of Client-Server Architectures Several contemporary papers on client-server architecture will be assigned for reading and discussed under the following topics: The Parts: Client, Server, and "Glue" Dividing the Tasks Re-usable Code Projections of Hardware and Software Trends | Wong, Stephen T. C., and H. K. Huang. "Design Methods and Architectural Issues of Integrated Medical Image Data Base Systems." Computerized Medical Imaging and Graphics 20, no. 4 (1996): 285-299. |
| 4 | Database Technology I Object and Relational Database Technology The Database Schema Accessing Databases: SQL, ODBC, and JDBC Size, Performance, and Other Issues | Covitz, Peter A., et al. "caCORE: A common infrastructure for cancer informatics." Bioinformatics 19, no. 18 (2003): 2404-2412. Gupta, Amarnath, Bertram Ludäscher, and Maryann E. Martone. "Knowledge-Based Integration of Neuroscience Data Sources." 12th Intl. Conference on Scientific and Statistical Database Management (SSDBM), Berlin, Germany, IEEE Computer Society, July, 2000. Hollander, Dave, and C. M. Sperberg-McQueen. "Happy Birthday, XML®!" The World Wide Web Consortium Issues XML® 1.0 as a W3C Recommendation. Development History. |
| 5 | Database Technology II Designing Database Schema Stored Procedures and Similar Mechanisms Local vs. Global Databases Database Federation | Kemp, Graham J. L., Nicos Angelopoulos, and Peter M. D. Gray. "A Schema-based Approach to Building a Bioinformatics Database Federation." Presented at the Proc. IEEE Int. Symp. Bio-Informatics Biomed. Eng. (BIBE), Washington, DC, November 2000. Stonebraker, Michael, and Paul Brown. Object-Relational DBMSs: Tracking the Next Great Wave. 2nd ed. San Francisco, CA: Morgan Kaufmann Publishers, Inc., 1999, pp. 31-34. ISBN: 9781558604520. |
| 6 | Client Technology The Classic Tradeoff: Server-side vs. Client-side Functionality Handling Data Returned From the Server Choice of Client Software: Java or ?? Graphics Capability | Seshadri, Govind. "Understanding JavaServer Pages Model 2 Architecture." JavaWorld, December 29, 1999. Hall, Marty. "Java Integrated Development Environments (IDEs) and Editors." Dichter, Carl, and Chris Tynes. "Which Java visual development environment is best for you?" JavaWorld, June 1, 1997. "Oracle JDeveloper 10g Overview." An Oracle White Paper. March 2004. JCreator - Java IDE. Borland Software. "Borland JBuilder 2005 Technical Overview." (PDF) Gibbs, Charles. "Setting Up a Java Development Environment for Linux." Linux Gazette 45 (September 1999). The Middleware Company Research Team. "Assisted SOA Development: Productivity Comparison of SOA Development Tools." November 2004. (Notice: company discontinued.) |
| 7 | The Umbilical Cord And Alphabet Soup Java Contributions Network Technologies: TCP/IP, Sockets, Threads Encapsulation Layer: XML®, RDF Use of CORBA | Sun Microsystems, Inc. "Java Technology. Java 2 Platform, Enterprise Edition (J2EE) Overview." Sun Developer Network. |
| 8 | Metadata And The Support of Data Analysis Getting the Data Creating Storable Results Storage Options: Keeping the Object Connection (UIDs) Querying and Manipulating the Metadata Implementing Database Federation and Complex Queries | McGuinness, Deborah L., and Frank van Harmelen, eds. "OWL Web Ontology Language Overview." February 10, 2004. |
| 9 | Putting it All Together: Complete Architectures Component Definition and Documentation Connecting the Components Robustness and Maintenance Performance and Security Interoperability Standards for Data Interchange | W3C. "Session V: Life Science Indentifiers - Use Cases, Future Directions." Presented to the Broad Institute, 2004. Quan, Dennis. "BioHaystack: Gateway to the Biological Semantic Web." IBM, 2004. (PPT) Liefeld, Ted. "Session V: Life Science Indentifiers – Use Cases, Future Directions." Presented at the W3C 2004 conference. Broad Institute, Cambridge, MA, 2004. (PDF) (Courtesy of Ted Liefeld. Used with permission.) |
| Part II: Selected Examples (4 Weeks) | ||
| 10 | Medical Imaging Information I The DICOM International Standard The Patient-study-series-image Hierarchy Design of an Object-oriented Database for DICOM Images | Bray, Tim, et al, eds. "Namespaces in XML® 1.1." December 18, 2002. W3C Communications Team. "XML® in 10 points." November 13, 2001. "Life Science Identifier (LSID) Resolution Protocol Project." |
| 11 | Medical Imaging Information II Integration of Metadata into the Images Compression Integration of Images into the Healthcare Environment: IHE Beyond Databases: Structured Reporting | Skodras, A. N., C. A. Christopoulos, and T. Ebrahimi. "JPEG2000: The Upcoming Still Image Compression Standard." Proceedings of the 11th Portugese Conference on Pattern Recognition (RECPA00D). Porto, Portugal, May 11-12, 2000, pp. 359-366. Cimino, J. J. "Review Paper: Coding Systems in Health Care." Methods of Information in Medicine 35 (1996): 273-84. Clunie, David A. "DICOM Structured Reporting: An object model as an implementation boundary." SPIE Medical Imaging (2001). (PDF) Bidgood Jr., W. D., et al. "The Role of Digital Imaging and Communications in Medicine in an Evolving Healthcare Computing Environment: The Model is The Message." Journal of Digital Imaging 11, no. 1 (1998): 1-9. Clunie, David A. "Structured Reporting Concepts." Chapter 1 in DICOM Structured Reporting. Bangor, PA: PixelMed Publishing, 2000. ISBN: 9780970136909. (Out of print.)Maojo, Victor, and Casimir A. Kulikowski. "Bioinformatics and Medical Informatics: Collaborations on the Road to Genomic Medicine?" Journal of the American Medical Informatics Association 10, no. 6 (2003): 515-520. |
| 12 | No Formal Class Meeting Use this week to complete three-page proposals for term paper. Schedule individual guidance sessions with the instructor. Critique will be returned by email prior to Lecture 13 | |
| 13 | Micro Array Information I Raw Data and Experiment Information Existing Information Standards: MAGE-OM, MIAME Existing Database Schema: Array Express, MIAMExpress Integration of Micro Array and Gel Electrophoresis Schema | Stoeckert Jr., Christian J., Helen C. Causton, and Catherine A. Ball. "Microarray databases: standards and ontologies." Nature Genetics Supplement 32 (2002): 469-473. Namprempre, Chanathip. "A Proposed DICOM Format for Electrocardiograms." International Consortium for Medical Imaging Technology (ICMIT). Booch, Grady. "Software Architecture." IBM, 2004. (PPT - 4 MB) |
| 14 | Micro Array Information II Methods of Analysis Use Cases for Analysis Storage and Query of Metadata An Example: Pacific Northwest National Laboratory | Saal, Lao H., Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg and Carsten Peterson. "BioArray Software Environment: A Platform for Comprehensive Management and Analysis of Microarray Data." Genome Biology 3, no. 8 (2002): software0003.1-0003.6. |
| 15 | Gel Electrophoresis Statement of the Experimental Problem Defining Experimental Information Objects The Case for Keeping Raw Image Data Creating Individual Tables and Functions Design of a Database Schema for Gel Electrophoresis Interacting with External Analysis Programs Storing and Retrieving Metadata Generalization of Results to Other Experimental Methods | Brazma, Alvis, et al. "Minimum information about a microarray experiment (MIAME)-toward standards for microarray data." Nature Genetics 29 (2001): 365-366. Mitchell, Peter. "A perspective on protein microarrays." Nature Biotechnology 20 (2002): 225-229. Taylor, Chris F., et al. "A systematic approach to modeling, capturing, and disseminating proteomics experimental data." Nature Biotechnology 21 (2003): 247-254. |
| 16 | Swan: Semantic Web Applications in Neuromedicine Guest lecture by Tim Clark, Massachusetts General Hospital and Harvard Medical School | Berners-Lee, Tim, James Hendler, and Ora Lassila. "The Semantic Web." Scientific American (May 2001): 36-43. Hausser, Roland. "The four basic ontologies of semantic interpretation." Keller, Richard M., et al. "SemanticOrganizer: A Customizable Semantic Repository for Distributed NASA Project Teams." International Semantic Web Conference (ISWC) 2004, LNCS 3298, 2004, pp. 767-781. Clark, Tim, Sean Martin, and Ted Liefeld. "Globally distributed object identification for biological knowledgebases." Briefings in Bioinformatics 5, no. 1 (2004): 59-70. Hendler, James. "Science and the Semantic Web." Science 299 (2003): 520-521. Li, Gangmin, et al. "ClaiMaker: Weaving a Semantic Web of Research Papers." Research Paper at International Semantic Web Conference (ISWC) 2002, June 9-12th, 2002 Sardinia, Italia. |
| 17 | Firespout ETL: THE Extract/Transform/Load Engine for Stored Data Guest Lecture by Ngon Dao, Formerly CEO of Firespout | |
| 18 | Firespout: The Launching of an Information Technology Company Guest Lecture by Ngon Dao, Formerly CEO of Firespout | |
| 19 | Biological Image Information SEM, TEM, and Cryo-EM Fluorescent Images Analysis Requirements for Different Imaging Modalities Compression and Other Strategies for Minimizing Storage Similarities with Other Experimental Data Types OME - The Open Microscopy Environment | Swedlow, Jason R. "Informatics and Quantitative Analysis in Biological Imaging." Science 300 (2003): 100-102. DICOM Standards Committee, Working Group 13. "Supplement 15: Visible Light Image for Endoscopy, Microscopy, and Photography." Digital Imaging and Communications in Medicine (DICOM) (July 2, 1999). |
| Part III: Data Integration and Analysis (1 Week) | ||
| 20 | Data Integration and Analysis I Integration in the Hospital Environment - Imaging and Information Flow - Use of the DICOM Standard - The Personal Healthcare Record (EMR) - HL-7: The Hospital Standard for Information Exchange - IHE: Integrated Healthcare Environment The Importance of Use Cases: York Hospital Adding Metadata to Images and Other Records - DICOM Structure Reporting (SR) Diagnostic Coding Systems: SNOMED | |
| 21 | Data Integration and Analysis II Integration in the Biological Environment - New Standards are Required - The Role of the W3C - XML® and RDF as the "Medium and the Message" (i) XML®/RDF for Schema Representation (ii) XML®/RDF for Neutral Transport (iii) RDF/OWL for Semantic Packages Database Considerations - Strengths of Relational Databases - Weaknesses of the Relational Model Solutions - Database Federation Adding Metadata to Images and Other Records | "Standards Man." Health IT World. "Ontology Management System." IBM, October 30, 2003. |
| Part IV: Student Presentations and Summary (2 Weeks) | ||
| 22 | Student Paper Presentations I | |
| 23 | Student Paper Presentations II | |
| 24 | Student Paper Presentations III | |
| 25 | Capstone Roundtable Discussion Session with leading IT professionals from the pharmaceutical and medical community in Boston. Discussion will include current state of IT for dealing with large medical and biological data sources, future challenges, and future opportunities | |
| 26 | Last Class (Part 2) Open Discussion in "Relaxed Atmosphere" | |
Table of Contents
Study Materials
Readings
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