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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 |
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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 |
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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 |
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18 |
Firespout: The Launching of an Information Technology Company
Guest Lecture by Ngon Dao, Formerly CEO of Firespout |
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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 |
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23 |
Student Paper Presentations II |
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24 |
Student Paper Presentations III |
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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. |
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26 |
Last Class (Part 2)
Open Discussion in "Relaxed Atmosphere"
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