SIV813: Applications of Computers in Medicinebhalla/SIV813Lect1and2.pdfSIV813: Applications of Computers in Medicine 1. EHRs – Standardized Electronic Health Records Databases 2.

SIV813: Applications of Computers in Medicine

1. EHRs – Standardized Electronic Health Records Databases

2. Medical Information Repositories- e.g., MedlinePlus 3. Web Services- e.g., Medline Connect

Subhash Bhalla

Department of Computer Science and Engineering, July-Sept. 2013

Applications of Computers in Medicine

• Title =

• Applications of Computers +

• Data

( from Medical Applications )

1. For these Applications

a) Study – Database Systems, Data Warehouses, Temporal Databases, Information Retrieval, query language for web users, knowledge representation.


• Domain Experts: Doctors, Nurses, Medical researchers, Community service persons Skilled users and semi-skilled users

• Domain: Patient’s Records +

Knowledge repositories

Web user level skills for development and programming


• 1. Knowledge XML, Relatinal model, JSON,

• 2. User Interfaces Query-by-example (QBE), XQBE (XML Query-by-example)

• 3 Tools XML (Berkeley dbxml, Zorba, IBM DB2) – all are free software

• 4 Data Sources

a) Web Repositories (Study data model- MedlinePlus), Electronic Health Records

b) Web Services (Medline Connect) http://www.nlm.nih.gov/medlineplus/connect/service.html


• 1. Biology

• 2. Medicine Vs Healthcare OUR FOCUS

• 3. Hospital OUR FOCUS

• Bio-medical – Human (genes, protiens, drugs, chemicals, systems biology, anatomy) OUR FOCUS

• 4. Chemistry

• 5. Plants, agriculture, Ayurvedic, Unani, Homeopathy, ……..

• 6. Zoology - experiments on rats / mice

DOT (graph description language) • example script that describes the bonding structure of an

ethane molecule. This is an undirected graph and contains

node attributes.

• graph ethane {

• C_0 -- H_0 [type=s];

• C_0 -- H_1 [type=s];

• C_0 -- H_2 [type=s];

• C_0 -- C_1 [type=s];

• C_1 -- H_3 [type=s];

• C_1 -- H_4 [type=s];

• C_1 -- H_5 [type=s];

• }

• Many interfaces for graphic visualization and query


• 1. Interoperability

Data representation and sharing –

Hospitals sharing patient data ? – ADL ? (KML/XML)

• 2. User’s Interactions

Query languages, Forms (Oracle Query Builder), General pupose query languages for skilled and semi-skiiled users


• 3. Web Repositories of data

Exercise 1. – a) Make a list of these for our focus of study, b) all related topics – search on google

• 4. Web Services for data resources

Exercise 2. – Make a list of these for our focus of study – search on google

Exercise 3. – How to connect and use MedlinePlus Connect


• Exercise 4:

• Difference between: Medline and MedlinePlus

• A) what are these used for ?

• B) Who uses these ?

• C) What type of Questions users have ?

• D) Can these be answered without new query tools (drawbacks of existing tools)

Applications of Computers in Medicine • 1. Web Repository of Human Genes http://www.nigms.nih.gov/Research/FeaturedPrograms/HGCR/ 2. Biobank Catalog - Coriell Institute for Medical Research http://www.coriell.org/research-services/biobanking/biobank-catalog 2. Human Protiens - BioGRID | Database of Protein and Genetic Interactions http://thebiogrid.org/ 3. List of biological databases - Wikipedia, the free encyclopedia

http://www.nigms.nih.gov/Research/FeaturedPrograms/HGCR/

http://www.coriell.org/research-services/biobanking/biobank-catalog





http://thebiogrid.org/

Applications of Computers in Medicine • 1. • State of Databases: Web Repositories • A) Raw data • Example: ISRO, NASA, JAXSA sources for lunar dara –

pictures, CO2 readings, altitude readings: read and use FORTRAN IV programs

• B) Semi-prepared data with a access model- • Data for pictures in google MAPs/google earth (i) User can scroll or enlarge; (ii) Data download in HTML, XML, KML, ADL User

can adopt the data in a database and query OUR GOOD FORTUNE in 2013 Most Sources ! OK

Medlineplus

Online Medical Encyclopedia

Made available by

U.S. National Library of Medicine (NLM)

National Institutes of Health

2013/9/18 Wanming Chu 12

Medline Home Page

http://medlineplus.gov/

2013/9/18 Wanming Chu 13

Proposal 2010-11

• 1. Data Form XML

• A) Map data KML; XML

• B) EHRs XML templates

• C) MedlinePlus (HTMLXHTMLXML) XML

• 2) XML (query langauge) xquery/xpath/xslt

• State-of-the-art: Relational-Style XML Query, by- T.L.Sato and Morishita,SIGMOD 2008.

14

Web Sites for Searching Medical Encyclopedia

1. MedlinePlus: Medical Encyclopedia

2. Middle Georgia Orthopaedic: Medical Ency…

3. UT Medical Center - A.D.A.M. Health Illu...

4. Medical Encyclopedia from Drugs.com

5. Multi Media Medical Encyclopedia- University of Maryland Medical Center

15

1. MedlinPlus - Medical Encyclopedia

Search by Alphabetic A-Z index

Search by keyword

16

MedlinPlus - medical encyclopedia

search methods • Search by keyword

– Phrase, e.g. “health services research”

– Case insensitive

– Boolean

• OR, e.g. Flu OR bird

• NOT/-, e.g. flu NOT bird

• +(exact word) e.g +mammogram, only find mammgram

• *, e.g mammo*, find mammogram, mammography, etc

• Search by alphabetic A-Z index

17

2.Middle Georgia Orthopaedic

• Embed a MedlinePlus search box

18

Embedded medlineplus Search box

3.UT Medical Center - A.D.A.M. Health

19

Category search

Search by Alphabetic A-Z index

UT Medical Center - A.D.A.M. Health

Search methods

• Search by alphabetic A-Z index

• Category search – Diseases and Conditions

– Special Topics

– Injuries

– Surgeries

– Nutrition

– Symptoms

– Poisons

– Tests

20

http://www.mgo.md/encyclopedia.cfm

4.Drugs.com

21

Category search

Search by keyword

Drugs.com

Search methods

• Search by keyword

• Category search – Disease

– Injury

– Nutrition

– Poison

– Special Topic

– Surgery

– Symptoms

– Test

22

5.University of Maryland Medical Center

23

Mobile version

Category search

Alphabetic A-Z index

Search keywor

d

University of Maryland Medical Center

Search method • Search keyword

• Link search by alphabetic A-Z index • Category search

– Research a disease or condition – Lookup a symptom – Learn about a test – Prepare for a surgery or a procedure – Learn what to do after being discharged – Self-Care Instructions – Questions to Ask Your Doctor – Nutrition, Vitamins & Special Diets – Injuries – Poisons

• Mobile version

24

Common Search Methods for Web Resources

• Search by keyword

– Keyword search operators:AND, OR, NOT

– Plus/Minus: +

– Phrases：words enclosed within double quote

– Stemming[*]: sing* will search sings, singer, etc

– Case sensitive/insensitive

• Alphabetic index navigation

• Category navigation

25

A.D.A.M Medical Encyclopedia

• About 4000 articles

• Categories of diseases, tests, symptoms, injuries, and surgeries

• Each Article includes title, subtitle, image, and update date,read more, etc.

26

How to search the contents of the subtitles

• Database for web resources

• SQL or Xquery

• Web-based Query Interface

27

Why search the contents of the subtitles

• Keyword search may return large numbers of irrelevant articles

• Navigation only get single article

• To get closely related articles

• To do incremental search

• Based on user requirements

28

CHF-Connected Health Framework

• Microsoft

• (Connected Health Framework). http://www.microsoft.com/industry/healthcare/technology/HealthFramework.mspx

• Chapter 1

http://www.microsoft.com/industry/healthcare/technology/HealthFramework.mspx

http://www.microsoft.com/industry/healthcare/technology/HealthFramework.mspx

CHF (ch1-p40)

• Integration and Interoperability

• Terms:

• 1. Medical Record – Hospital, clinic – 1 treatment, Improved integration – 2nd visit ? (Hospital level);

• 2. Health Record – Job medical care (health checks of employees)(Employment level)

• 3. Social care Records – Insurance , Pension – duration life-time, Cost vs. expenses- Coutry level (social Security Number in US)


• Integration Trends

• EHR EMR + Healthcare + Social Care

• Integration Interoperability

• Medical Health Social






• Health and Social Care Directions

• various economic, government, and environmental factors

- influence and regulate e-Health and e-Care,

- influence the development of solutions.

CHF-Connected Health Framework • Mandates and Directives • European Union, as part of the eEurope 2005 Action Plan14, - member states should develop health information networks - between points of care (hospitals, laboratories, and homes) - with broadband connectivity - by the end of 2005, required to ensure online health services were provided to citizens (such as information on healthy living and illness prevention, electronic health records, tele-consultation, and e-

reimbursement). - support a common approach a) patient identifiers; b) electronic health record architecture

through standardization and c) to support the exchange of good practices on possible additional functionalities, such as medical emergency data and secure access to personal health information.


• US Govt.

healthcare reform aim to provide coverage and access to care, for all citizens.

Improving the exchange of health information and interoperability between different providers

Interoperability

1. Semantic Integration – Data Integration

-meaning of Data (What is “Patient”) ? Different

a) Standardize it; or b) understand it

2. Application Integration – Systems Integration

- exchange and use information over organizational boundaries

3. Infrastructure Interoperability – Technical Interoperability

- ensure the uniform movement and presentation of data + protect the its security and reliability

Interoperability

• Semantic Interoperability Assume patient means – the same thing

[System 1] [System 2] (must be ensured)

• Semantic Disintegratity (James Martin)

Confusion or errors due to non-standard definitions, or not understood data.

Communication of Data

• 1. Definitions

• 2. Standards to encode

• Example – Identity data

• 1. Hospital – use Patient Id for treatment

• 2. UK – NHS number (used in all patient related transactions) UK and Scotland (different Id);CANADA (each province has different Id);EU Countries ? patient record is at many places

Communication of Data

• 1. Social Care Agencies Many agencies

Use their own IDs.

• To access data from different sources:

[Make Domain Level Index] Allow only

authorized users

• (Name, Address, DoB) Hash Key

• 2. PROBLEM Privacy and Confidentiality

Communication of Data 1. List in an Indexing service (register)

Keys Secondary Agencies

2. Patient can decide to link or not enlist with some agencies (alcohol reform list ?).

3. Data at any source can be accessed using Key

USA Medical Id Healthcare Id Soc.Sec.No.

Coding of Data • Many systems and standards:

1. Systematized Nomenclature of Medicine-Clinical Terms(Snomed-CT),

2. Reed Clinical Classification (RCC),

3. American Medical Association Current Procedural Terminology (CPT),

4. WHO - International Classification of Diseases (ICD-10),

5. others

all have specific purposes.

issues of translation (when one standard is used in one system and another standard is used in a second)

(there is no 1:1 mapping between terms).

• Almost universal agreement XML offers an appropriate vehicle for information exchange

Coding of Data

• “Translation engines”

available from Health Language (http://www.healthlanguage.com)

offer conversion from one code to another

include free-format text parsers.

[ Such parsers can be used to assemble data from diverse sources and using diverse coding systems, perhaps accessed using a multi-agency index, into a lifelong, longitudinal electronic Patient/clinical Records]

Health Level Seven • Health Level Seven HL-7 - American National Standards Institute (ANSI)-accredited Standards Developing Organization

(SDO) in healthcare ; - Domain Clinical and administrative data - Agency not-for-profit volunteer organization. - Since 1996 new generation of standards known as Version 3 (V3) (Old generation V2 ) under V3 : (A) Has HL7 Development Framework (HDF). (B) HDF Reference Information Model (RIM), Aim of V3: produce consistency in the definition of different information objects and their

representation in messages, Covers: (a) Messages; (b) Forms; (c ) Decision-support Mechanisms; and (d) electronic patient record structures.

HL7 V3 standards are developed as models independent from the actual implementation.

Preferred implementation technology XML. [difficulty] many existing systems do not use HL7 V3, often using HL7 V2 or other formats for

their external communications. Conversion modules have to be written to compose HL7 V3 messages.

Questions

• 1. Standards – tags ? / DTD ? / Schema ?

• 2. Old Systems use HL7 (V2) and other formats Conversion modules Legacy Migration ?

OpenEHR

• 1. Open Standard

• 2. Management Storage

• 3. Information Retrieval (IR)

• 4. Exchange of Health Data in EHRs

• 5. Single ‘Life-time’, Vendor independent , and person centric EHR

• 6. Primary focus is not exchange of Data between EHRs; Message standards do that-

(i) ISO 13606;

(ii) HL7

OpenEHR

• 7. Excludes all specifications of clinical information Out (of Information Model).

• 8. Creates powerful means to express clinical and patient needs

• (i) Use formal ways Archetypes

• (ii) Archetypes are Computable

• (iii) Core of Health Information Archetypes

Archetypes • 1. Medical concepts Represented

Information is reusable

• 2. Uses Templates for Aggregation of Archetypes,

• to support

• (i) Forms;

• (ii) Documents; and

• (iii) Mesages

IHE-Integrated Healthcare Enterprise

• Since 1997: provides integration profiles

• Formed by a consortium of radiologists and IT experts

• Aims to create a process through which interoperability can be implemented.

• The group gathers use case requirements, identifies available standards, and develops technical guidelines that manufacturers can implement.

• IHE organizes “interoperability showcases” ;

(many vendors assemble to demonstrate the interoperability of their products).

• IHE is an international organization focuses on the development of global standards (and on regional deployment of interoperable products).

• Describe a clinical information need or workflow scenario

• Document how to use established standards (such as HL7, DICOM, and LOINC)

• A group of systems that implement the same Integration Profile address the need/scenario in a mutually compatible way.

2. Application Integration

• Application Integration System Integration

• between two organizations Agencies

• Clinically controlled EHRs are critical but not enough;

• [Example] Patients must be enabled to add missing information (medicines actually taken);

• PHRs (Personal Health Records) EHRs

• (i) Identify person and ensure privacy;

• (ii) Common terminology

2. Application Integration

• Countries (i) National Ids

• (ii) Schemes for data

• (iii) Rules for authentication and authorization

• (iv) Different standards for data coding

• (v) XML, HL7 (V3) standard; and broadly supported healthcare industry standards

Summary - 1

• BUSINESS Healthcare + Social care

[Combine with Medical care]

1. Construct life-long personal health records

2. Allow a citizen to access his/her record

3. Provide portals and gateways to healthcare information and advice

4. Make new role based interfaces Data from underlying current applications

5. Preserve person, subject and time-context across services

Summary – 2 6. Maintain citizen’s confidebtiality

(i) Anonymization

(ii) pseudonymisation

Of data when used outside

7. Comply with national laws and Government standards

8. Use XML, HL7 (V3), IHE, OpenEHR and encoding standards for clinical data

9. Management of person/profession legitimate relationship

10. Construct personal care pathways (workflows)

Summary – 3

• 11. Definition and Management of clinical and Administrative processes

• 12. Delegation of Authority and group authorization to view personal data

• 13. Interfacing and service enablement of legacy applications

• 14. Bio-surveillance and population health

Application Integration needs

• [New / evolving] Application portfolios Service-oriented architecture

• Current applications Service enabled

• Applications offer data and functionality

• in a pre-defined way to external consumers

• Requests and responses are subject to “Contract” availability, accuracy, rules of engagement (authorization and confidentiality rules)

Service-oriented Architecture (SOA)

• SOA means of building Distributed Systems

• SOA maps capabilities and interfaces, (these) can be used in processes

• Focus 1. Course-grained business services

2. Fine-grained Technical services

SOA Technical requirements • Aim --> creating the computing platform

• 1. Open Standards including SOA Web services.

• 2. Security-Enhanced Operations a) providing authentication and authorization

b) business continuity and data management facilities.

• 3. Interoperability across diverse platforms

a) Diverse systems and data sources a coherent, and

controlled environment.

• 4. Reliable and security-enhanced Messaging

a) enabling flexible and agile orchestration of business processes ;

b) linking of disparate islands of automation

SOA Technical requirements • 5. Legacy Integration using open standards

a) Systems in multiple domains, on multiple platforms,.

• 6. Privacy and Confidentiality a) provide patient control over his or her medical data,

b) use by healthcare professionals.

• 7. Managed Computing Environments a) self-monitoring , b) fault-tolerant

providing high levels of robustness and reliability.

• 8. Performance response and ease of use.

• 9. Robust 24/7 Availability a) hardware configuration, b) rigorous software testing, c) system design.

• 10. Hot back-up and Disaster Recovery to cut service interruptions due to external factors.

Conclusions • 1. Construct, maintain, and disseminate a longitudinal,

lifelong record of a person’s health and personal care.

• 2. The record has to be stringently safeguarded

would be the property of the subject,

would have the means of controlling its use and distribution.

• 3. The Microsoft Vision – “Seamless” Health and Social Care:

enable the transformation of Health and Social Care delivery through innovative technology

partnerships with public health programs by connected citizen care,

reducing the Health and Social Care cost burden.

SIV813: Application of Computers

• 1. EHRs and Medical Repositories in India

• 2. EHRs and Medical Repositories : State of the Art

• 3. Example Bio-Medical information Applications-

• a) Standardized EHRs Databases

• b) Modeling Instances of Medical Information Repositories

62


• Directory:

• /misc/buffer/Courses/CSV888/EHRIndia

• FILES:

• Technologies for Healthcare in India

• Need for interoperability standards for healthcare in India

• Recommendations on EMRs April 2013

• Recommendations Committee in India 2010

• Developing a Distributed Electronic Health-Record Store for India

• Healthcare in India – IBM viewpoint 63


• Gentle Reminder:

• Exercises 1 – 4 ( slides 8,9 )

• Please complete and submit

64