Day 1 - Monday, October 2, 2000

Session 1: 8:30 - 9:00 AM

Faculty

Educational Objectives

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Session 1A: 9:00 - 10:00 AM

Faculty

Educational Objectives

At the completion of the session, participants will:

• Understand the "interagency model" and the government-industry-university approach to the HPCC work.
• Understand the initial opportunities in biomedical applications of the NII.
• Have a beginning set of funding contacts.

Session Outline

1. High Performance Computing and Communications federal program
• Background and Legislation
• Objectives and Organization
• Phase 1
• Accomplishments - Grand Challenges
• Progress on Grand Challenge Problems
• Phase 2
• National Information Infrastructure
• National Challenge Applications
• Non-medical
• Medical
2. NLM Role in the NII
• Intramural Research
• UMLS
• Visible Human
• Extramural Research
• NII medical testbed
• Telemedicine
• Computer-based patient record
• Public Policy Issues
• Medical Data Privacy
• National Security
• Intellectual Property Rights
• Traditional Copyright Demands
• Today's Revolution in Electronic Publishing
• Federal Research Funding Sources for Medical Informatics
• NLM Programs
• Other HHS Programs
• Other federal agency support

Session 2: 10:30 AM - 12:00 N

Faculty

Educational Objectives

• Understand the historical evolution of computerized data handling methods
• Know the relative strengths and weaknesses of hierarchical, relational, information network, and object-oriented database systems
• Understand the process of development of a set-theory-based relational data model, including entity-relationship definitions, principles of fully normalized relational models, state transitions and data flow diagrams.
• Understand the design principles involved in the transformation of a flat file record structure to a normalized relational structure (lab exercise).

Session Outline

• Database definitions and paradigms
• What is a Database?
• Historical Evolution of data management techniques
• General benefits of Database Management Systems (DBMSs)
• DBMS types
• Heirarchical
• Information Network (linked lists and pointers)
• Relational
• Object-oriented
• XML
• Principles of Relational database design
• Representation of real world objects and their attributes
• Relationships between objects
• Table notation formalisms
• Relationships: one-to-one, one-to-many, many-to-many
• System design and building methods
• Entity-relationship diagrams
• State Transition Models
• Data Flow Diagram
• Transforming flat files to tables
• A sample problem in database design

Session 3: 1:30 - 3:00 PM

Faculty

Educational Objectives

• Have received an introduction to the history of the Unified Medical Language System
• Be introduced to the content of the UMLS Knowledge Sources: the  Metathesaurus, the Semantic Network and the SPECIALIST lexicon
• Have viewed a demonstration of the UMLS Knowledge Source Server
• Have viewed a demonstration of the UMLS Metathesaurus browser application in the Internet Grateful Med program, including the introduction of related concepts and co-terms
• Have received an introduction to technologies that are shaping the further development of the Internet and the ways we use it.

• Unified Medical Language System
• History
• The UMLS Metathesaurus
• The UMLS Semantic Network
• The SPECIALIST lexicon
• The UMLS Knowledge Source Server
• The Internet Grateful Med Metathesaurus browser as an example of a UMLS application, with emphasis on related concepts and co-terms
• Internet Futures
• Context
• Internet Protocol (IP)
• IPv6
• Quality of Service (QOS)
• Optical switching
• Virtual Private Networks (VPNs)
• Digital Spread Spectrum
• Bluetooth
• Wireless Access Protocol (WAP)
• Ubiquity (wearable computing)
• Dynamic content
• Standards/open source

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Session 4: 3:30 - 5:00 PM

Faculty

Educational Objectives

Session Outline

1. PubMed Overview
2. Automatic Term Mapping
• Search Formulation and Retrieval
• Search Refinement
• Feature's Bar (Limits, Preview/Index, History and Clipboard)
3. Related Articles
4. LinkOut
5. Cubby
6. NLM's Gateway Overview
7. Searching Multiple Databases
8. Using MeSH
9. Define Your Own Display Format
10. Hands on lab time

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Evening Session

Faculty

Educational Objectives

At the completion of the session, participants will:

• Have created a personal web page with one or more images, and hyperlinks using free HTML editor (Netscape Composer)
• Have a basic understanding of digital image editing software (Photoshop).
• Have created a class resource that enables participants to know one another better

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Day 2 - Tuesday, October 3, 2000

Session 1: 8:30 - 10:00 AM

Faculty

Educational Objectives

Session Outline

1. The Primary Data Available
• Sequence data
• DNA data from GenBank, DDBJ, and EMBL submissions
• Protein data from GenBank CDS translations and other databases
• Structure data derived from the PDB
• Supplementary data: literature, mapping, expression, genotypic, phenotypic, sequence alignments

 
2. Ways to Retrieve Sequence Data
• Entrez: A versatile text-based sequence retrieval system
• FTP: Brute-force sequence retrieval
• Retrieval of representative data types
• DNA sequences
• Sequences of individual genes
• Chromosomal sequences
• Complete Genome sequences
• Other DNA sequences (ESTs, GSSs, STSs, HTG sequences)
• Sequence alignments
• Protein sequences
• Sequences of individual proteins
• Proteome sequence sets
3. Higher Level Organizations of Sequence Data
• Links between data records
• Sequence neighbors
• Structure neighbors
• Specialized NCBI resources
• NCBI Taxonomy: A taxonomy of over 70,000 species represented in GenBank
• Genome views: Organized presentations of complete genomes
• Views of Bacterial Genomes
• Views of Eukaryotic Genomes: The Genome Map Viewer
• RefSeq: A database of reference sequences
• LocusLink: A single query interface to curated sequence and descriptive information about genetic loci
• GeneMap'99: A radiation hybrid gene map of the human genome
• COGs: Clusters of Orthologous Groups of proteins from 21 model organisms
• Unigene: Gene anchored clusters of ESTs
• Homologene: Clusters of clusters
• dbSNP: A database of Single Nucleotide Polymorphisms and short insertions or deletions
4. Tools for the Analysis of Sequence Data
• BLAST (Basic Local Alignment Search Tool)
• Basic BLAST
• PSI-BLAST: A BLAST search using a protein profile
• PHI_BLAST: A BLAST search using a amino acid pattern as a seed
• BLAST2Sequences: A BLAST of one sequence against another
• BLAST against microbial genomes
• BLAST against human genomic contigs
• OrfFinder: Locates Open Reading Frames in DNA sequences
• Genotyping Tools
• General Genotyping
• HIV Genotyping
• Electronic PCR: Locates STSs within nucleic acid sequences
• VecScreen: Detecting contamination in nucleotide submissions

 
5. Structure Data: Retrieval and Analysis
• The NCBI Molecular Modeling Database (MMDB)
• Creation of the MMDB from the PDB (Protein Data Bank)
• Viewing MMDB structures with Cn3D
• Superimposing a protein sequence onto a structure using Cn3D
• The Vector Alignment Search Tool (VAST)
• Viewing pre-computed VAST structural alignments
• Submitting a novel structure for a VAST search
6. Data on Gene Expression, Genotypes and Phenotype
• SAGEMap: A resource for the visualization and analysis of SAGE data
• CGAP: The cancer genome anatomy project
• OMIM: A catalog of human genes and genetic disorders

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Session 2: 10:30 - 12:00 N

Faculty

Educational Objectives

At the completion of the session, participants will:

• Know the issues facing the US regarding copyright and database protection world-wide
• Know if they support or do not support federal privacy legislation, and its features
• Understand the basis for current data encryption methods.
• Will have tested at least two Security Token Authentication devices.
• Know if they prefer to operate Challenge Response or Time Synchronous security devices.

Session Outline

1. Intellectual Property Rights
• WIPO Treaty proposals
• Pub Med Plans
2. Encryption
• Basic concepts
• DES Public-Private Key
• Implementation and Devices
a) Data Encryption Technology
• Private Key Encryption
• Digital Encryption Standard
• Kerberos
• Public-Private Key Encryption
b) System Considerations
• Length of Cipher Keys
• Security Token Authentication
c) Devices
• Challenge - Response
• Time Synchronous
3. Medical Data Privacy
• Requirements
• Legislation
• Overview
• Status of Federal Privacy Legislation
• Contentious Issues
• Initial Practical Experience with Medical Data Privacy Assurance

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Session 3: 1:30 - 3:00 PM

Faculty

Educational Objectives

• Understand the basic principles that underlie the design, implementation, and maintenance of a successful digital library.
• Have an understanding of digital library research issues.
• Have pointers to useful resources in digital library research.

Session Outline

1. Basic Principles in the Design and Implementation of a Digital Library
• System Design Principles and Practices
• Standards
• Modularity
• Extensibility
• New technologies
• Content and Collection-based Principles and Practices
• Data acquisition and selection
• Metadata
• Intellectual property
• Permanence and persistence of digital objects
• Human Factors Principles and Practices
• Accessibility, usability
• Automation of manual tasks
2. Informatics Research Agenda for Digital Libraries
3. Case Study and Hands-on Exercise
• Profiles in Science
• Assigning metadata tags

Session 4: 3:30 - 5:00 PM

Faculty

Educational Objectives

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Evening Session

Faculty

Educational Objectives

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Day 3 - Wednesday, October 4, 2000

Sessions 1, 2 and 3:  8:30 a.m. - 3:30 p.m.

Faculty

Session Outline

Within medical informatics, there is increasing interest in evaluation and empirical studies.  From an administrative perspective, as institutions invest in new technology, it is critical for them to know how these systems can contribute to health care, education, and research so they can set develop plans and set priorities.  From a more academic perspective, research projects in informatics, including doctoral dissertations and masters theses, now often include an evaluation or empirical study component.  Much of the funded research in informatics is required to have such a component.

This day-long session on evaluation will provide participants with an understanding of the range of evaluation methods that are used in informatics and will address how studies are designed as well as how data for these studies are collected, analyzed, and reported.  We will address during the day many of the challenges that make evaluation difficult, emphasizing those challenges that are particular to medical informatics, and we will discuss methods that have been developed for addressing many of these challenges.

Educational Objectives:

At the completion of the session, participants will be able to:

1. Describe the purposes of evaluation in medical informatics.
2. List several factors that can make it difficult to do evaluation in medical informatics effectively, as well as strategies that can be employed to address these difficulties.
3. Distinguish objectivist (quantitative) and subjectivist (qualitative) approaches, describe the assumptions that underlie them, and explain why both methods are used.
4. Identify the major steps in the process of conducting objectivist and subjectivist studies.
5. Identify the individuals or groups comprising the “audience” for an evaluation study.
6. Describe how the methods and purposes of a study can be matched the level of maturity of an information resource.
7. Frame many of the recurring difficulties of evaluation in medical informatics as problems of measurement.
8. Distinguish between measurement errors that are issues of reliability from those that are issues of validity.  Distinguish between different types of validity.
9. Explain how “measurement studies” can be conducted to identify the sources of error in any measurement process, and to estimate the magnitude of these errors.
10. Explain what is meant by a “gold standard” in the framework of a measurement study.

Identify measurement methods and features of measurement instruments that can be employed to reduce measurement errors.
11. Identify some specific evaluation questions or issues that lend themselves particularly well to subjectivist approaches.
12. Explain how the questions and key issues of a study arise through the process of immersion.
13. Describe the major data collection strategies in subjectivist research, how these are used in a complementary way within a study, and how the data generated by each are analyzed.
14. Explain the steps a researcher can take to ensure the veracity of the findings of a subjectivist study.
15. Describe some of  the barriers to combining objectivist and subjectivist methods within a single study.

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Session 4: 3:30 a.m. - 5:00 p.m.

Faculty

Session Outline

• What is special about medical data?
Large number of entities
Complex naming
Degrees of granularity
Temporal nature
Perspectives for classification
Nesting of modifiers
• Clinical vocabularies
Goals: coding, translation, decision support
Methods
Maintenance issues
• Established vocabularies

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Day 4- Thursday, October 5, 2000

Sessions 1 and 2: 8:30 - 12:00 N

Faculty

Suzanne Bakken, RN, DNSc

Educational Objectives

At the conclusion of the workshop, the learner will be able to do the following:

1. Define evidence-based practice.
2. Describe the foundation for evidence-based practice.
3. Access and interact with Web-based systematic review resources. 
4. Analyze a patient case using a Web-based diagnostic decision support system.
5. Identify the components of expected value decision making.
6. Construct and solve a decision tree using a decision analysis software package.

1. Definitions of Evidence-based Practice
2. Foundation for Evidence-based Practice
1. Standardized terminologies
2. Outcome measurements sensitive to health care interventions
3. Techniques for routinely capturing and analyzing relevant data
4. Electronic networks and standards supporting interoperability
5. Informatics competencies
1. Information retrieval
2. Critical analysis
1. Trial Bank
2. Cochrane Collaboration
6. Tools and techniques for applying domain knowledge to patient-specific situations
1. Issues related to clinical decision making
2. Diagnostic decision support
1. DXplain
3. Expected value decision making
1. Building and solving a decision tree using DATA

Utility assessment

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Sessions 3 and 4: 1:30 PM  - 5:00 PM

Faculty

Douglas Perednia, M.D.
 

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Day 5 - Friday, October 6, 2000

Session 1 - 8:30 AM - 10:00 AM

Faculty

Educational Objectives

1. Be able to list the various techniques and types of entities involved in data acquisition 
2. Describe the different types of data in clinical information systems 
3. Contrast structured from unstructured data acquisition 
4. Describe the basic ASR approaches and the challenges in implementing them 
5. Describe the justification for NLP and the basic challenges.

• Data Acquisition Entities 
• Acquisition Techniques 
• Signal Acquisition 
• Image Acquisition 
• Image Storage 
• Picture Archiving and Communications Systems (PACS) 
• Image Acquisition Challenges 
• Collecting Data from People 
• Text versus codes 
• Structured Data Entry 
• Automated Speech Recognition (ASR) 
• Types of ASR Techniques 
• Types of ASR Systems 
• Economic Issues in ASR 
• HCI Issues 
• Implementation Issues 
• Natural Language Processing 
• Linguistic Layers 
• The Languages in Medicine 
• What are Sublanguages? 
• Challenges for Language Analysis 
• Natural Language Processing Techniques 
• Language Analyzer 
• Lexicon 
• Syntactic Grammar 
• Semantic Grammar 
ASR Demonstration

Session 2 - 10:30 AM - 12:00 N

Faculty

This session will discuss the principles behind inter-system communication in heathcare computing. The current de-facto standard, HL7 will be described. Current development in XML will be discussed. An exercise will involve the use of the Medlee NLP system and and XML parser.

Educational Objectives

1. Describe the requirement for intersystem communication 
2. Discuss the basic principles behind the development of HL7 
3. Discuss the major changes and challenges of HL7 version 3 
4. Define "markup language" and contrast XML to other markup languages 
5. Understand the relation between XML, DTDs and XSLT

Outline 

• Need for Inter-system communication. 
• ISO Open System Interconnection (OSI) level 
• Health Level 7 
• History 
• Current Version 
• Upcomming Version 3 
• Reference Information Model 
• Integrating the Healthcare Enterprise (IHE) 
• HL7 and HIPAA 
• XML 
• What is Markup 
• XML Basics 
• DTD 
• XML and HL7 history 
• Extensible Style Sheets (XSL) 
• XML Architectures 
• Why XML? 
• What XML is not 
• XML Heuristics 
• Exercises 
• NLP 

XML 

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Session 3: 1:30 - 3:00 PM

Faculty

Christopher Cimino, M.D.

Educational Objectives

1. have an understanding of the basic building blocks of the educational interaction: communication, assessment, role-modeling, skills development, and dialogue. 
2. be exposed to several types of educational technology and understand how each complements or complicates each type of interaction 
3. be exposed to several examples of Medical Informatics objectives with a focus on distinguishing skills, knowledge and attitudes. 
4. understand how Informatics skills, knowledge, and attitudes relate to different educational interactions; particularly role-modeling and skill development. 
5. understand how specific Medical Informatics objectives relate to specfic types of educational technology 
6. understand how Informatics teaching can be integrated with other medical education.

Outline

• How Does Education Occur? 
• How does education occur? 
• How do we choose what to teach? 
• What is the educational environment? 
• How does teaching occur? 
• Where does teaching occur? 
• What passes between teacher and student (revisted) 
• Where does technology fit in? 
• Benefits of Integrated Education 
• Obstacles to Integrated Education 
• How do we decide what to teach? 
• Objectives 
• Knowledge 
• Skills 
• Attitudes 
• Mission
• Needs 
• Goals 
• Solutions 
• Evaluation 
• Student Evaluation 
• Program Evaluation 
• Medical Informatics Objectives 
• AAMC Informatics Objectives 
• Organizing principles 
• Required vs. Suggested 
• Teaching and assessing knowledge 
• Teaching and assessing skills 
• Teaching and assessing attitudes 
• Educational technology revisited 
• Education Informatics 
• Technology as a teaching tool 
• Infrastructure needed to teach skills 
• Role models needed for teaching attitude 
• Integration into work-flow needed to develop role models 
• Evaluation of educational technology 
• Education success as measured by science 
• Cost 
• Satisfaction 
• Looking at the environment 
• What kind of institution are you at? 
• Setting determines stakeholders 
• Stakeholders 
• Who determines educational approach? 
• Who determines educational content? 
• Who supports technology? 
• Instigating Change 
• Innovation 
• Long term growth 
• "Willing" but cautious participants 
• Implementing Change 
•  Make use of power of iteration 
•  Conserve support effort 
•  Shape user expectations to be reasonable 
•  Making use of early failure 
• Institutional Problem Solving 

Session 4: 3:30 - 5:00 PM

Education Informatics - Faculty Development 

Faculty

Christopher Cimino, M.D.

Educational Objectives 

This session will look at the adaption of clinical faculty to teaching medical informatics. Using specific examples on the internet, participants will face and overcome some of the common obstacles. At the completion of this session 
participants will have 

1. gained practical skills in finding informatics information geared to education. 
2. understand the obstacles to motivating faculty to integrate informatics teaching into other disciplines 
3. know the types of behaviors that promote positive attitudes amoung collegues and students 

Each exercise will be followed by a group discussion of the results of the exercise and concrete lessons learned. 

    Exercise 1: 
        Internet resources to enhance the teaching of a skill objective 
        Examining learning curve obstacles. 

    Exercise 2: 
        Internet resources to enhance the teaching of a knowledge objective 
        Examining quality obstacles 

    Exercise 3: 
        Internet resources to enhance the teaching of a attitude objective 
        Examining reliability obstacles 

    Other obstacles: 
        Social obstacles 
        Work flow obstacles 
        Resource obstacles 
 

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Evening Workshop: 7:00 - 9:00 PM

Faculty

Educational Objectives

Session Outline

1. Present an overview of a generic database web serving system. This overview will consist of identifying and defining the function of the the different elements that compose a database server.
2. A brief introduction to a few of the different database solutions to show how different vendors address the model described in 1.
3. Create an interactive web database using Filemaker Pro 4.0 with a sample database which will address the following:  Querying the database using FORM and embedded URLS
4. Editing a Record via the web
5. Adding/Deleting Records
6. Processing results with format files.
7. Understanding how HTML and database meta tags can interact by:

a. Listing multiple records

b. Formatting a single record

c. Using conditionals to selectively format records

d. Using color and graphics with numeric content

Creating embedded links to Entrez, PubMed, others

Day 6 - Saturday, October 7, 2000

Clinical Data Systems Architecture and Organization

Faculty

Robert Jenders, M.D., M.S.

Educational Objectives
 

1. Learn the major components of health care information system architecture, including various types of data, controlled/structured vocabulary, a data model, a data repository and communication standards.
2. Be able to describe both centralized and distributed architecture models for such systems.
3. Delineate the important components that allow coordination of components in a distributed system.
4. Know the principal forms of knowledge representation for a clinical decision support system, including specialized representations such as Arden Syntax and GLIF, as one component of an overall health care system architecture.
5. Describe the historical evolution of such systems.
6. Identify successful examples of such systems.
7. Learn the major issues in evaluating such systems.

1. System Architecture

a.  Generations of systems
b.  Goals of architecture 
c.  Main types of architecture
d.  Data architecture
    1.  Traditional
    2.  Contemporary
    3.  Types of data
    4.  Encoding data
         a.  Role of vocabulary
         b.  Role of natural language processing
    5.  Data repository
e.  Technical architecture
    1.  Integration models
    2.  Networks
    3.  Distributed vs centralized approaches
    4.  HL7
    5.  IAIMS
    6.  CCOW
    7.  Actual implementation:  Build vs buy?
f.  Case study of integration:  CPMC
    1.  Results review
    2.  Immunization registry
    3.  EMR
2. Clinical Decision Support:  One component of health care system architecture

 a.  Knowledge representation
    1.  Role of KR
    2.  Formalisms:
         a.  Probabilistic
         b.  Procedural
         c.  Production rules
         d.  Case-based reasoning
         e.  Domain ontologies
         f.  Decision tables
         g.  Artificial neural networks
b.  Clinical decision support systems:  Applying knowledge representation
     1.  Historical development
     2.  Specialized types of knowledge representation
          a.  Arden Syntax
          b.  Guideline Interchange Format (GLIF)
3. Examples of successful applications
4. Issues in evaluating systems

Session 3: 1:30 - 3:00 PM

Faculty

Educational Objectives

Session Outline

3:00 PM

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