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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., 1998, pp. 31-34. ISBN: 1558604529.
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


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


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: 0970136900. (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
- 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"