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課程單元 lectures
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
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
4 Database Technology I

Object and Relational Database Technology

The Database Schema

Accessing Databases: SQL, ODBC, and JDBC

Size, Performance, and Other Issues
5 Database Technology II

Designing Database Schema

Stored Procedures and Similar Mechanisms

Local vs. Global Databases

Database Federation
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
7 The Umbilical Cord And Alphabet Soup

Java Contributions

Network Technologies: TCP/IP, Sockets, Threads

Encapsulation Layer: XML, RDF

Use of CORBA
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
9 Putting it All Together: Complete Architectures

Component Definition and Documentation

Connecting the Components

Robustness and Maintenance

Performance and Security


Standards for Data Interchange
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
11 Medical Imaging Information II

Integration of Metadata into the Images


Integration of Images into the Healthcare Environment: IHE

Beyond Databases: Structured Reporting
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
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
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
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"