| Lec # | Topics | lectures |
|---|---|---|
| 1 | Introduction Objectives and Methodology The Information-driven Scientific Method Ontology and Semantics for Biomedical Information Term Paper Instructions | (PDF) |
| 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 | (PDF) |
| 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 | (PDF) |
| 4 | Database Technology I Object and Relational Database Technology The Database Schema Accessing Databases: SQL, ODBC, and JDBC Size, Performance, and Other Issues | (PDF) |
| 5 | Database Technology II Designing Database Schema Stored Procedures and Similar Mechanisms Local vs. Global Databases Database Federation | (PDF) |
| 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 | (PDF) |
| 7 | The Umbilical Cord And Alphabet Soup Java Contributions Network Technologies: TCP/IP, Sockets, Threads Encapsulation Layer: XML, RDF Use of CORBA | (PDF) |
| 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 | (PDF) |
| 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 | (PDF) |
| Part II: Selected Examples (3 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 | (PDF) |
| 11 | Medical Imaging Information II Integration of Metadata into the Images Compression Integration of Images into the Healthcare Environment: IHE Beyond Databases: Structured Reporting | (PDF) |
| 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 | (PDF) |
| 14 | Micro Array Information II Methods of Analysis Use Cases for Analysis Storage and Query of Metadata An Example: Pacific Northwest National Laboratory | |
| 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 | (PDF - 1.2 MB) |
| 16 | Swan: Semantic Web Applications in Neuromedicine Guest lecture by Tim Clark, Massachusetts General Hospital and Harvard Medical School | (PDF - 2.6 MB) |
| 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 | (PDF 1) (PDF 2) |
| 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 | (PDF) |
| 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 | (PDF) |
| 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" | |