pcori methodology standards: academic curriculum · format/syntax of data exchange (i.e., the...

PCORI Methodology Standards:

Academic Curriculum

© 2016 Patient-Centered Outcomes Research Institute. All Rights Reserved.

Prepared by Hadi Kharrazi, MD, PhD

Dan Ford, MD, MPH

Presented by Hadi Kharrazi, MD, PhD

Module 4: Semantic Interoperability

Category 7: Data Networks as Research-Facilitating Structures

DN-1 (requirements for the design and features of data networks) is discussed in

Modules 3, 4, 5, 6, and 7

A. Data Integration Strategy—Module 4

B. Risk Assessment Strategy—Module 6

C. Identity Management and Authentication of Individual Researchers—Module 6

D. Intellectual Property Policies—Module 7

E. Standardized Terminology Encoding of Data Content—Module 4

F. Metadata Annotation of Data Content—Module 4

G. Common Data Model—Module 5

DN-2 (selection and use of data networks) is discussed in Modules 8 and 9

Data Network Methodology Standards Mapping With Content

4

Interoperability is the ability of systems or devices to exchange and use electronic

health information from other systems or devices without special effort on the part of

the user

Interoperability Defined

4

“Foundational” interoperability allows data exchange from one information

technology system to be received by another and does not require the ability for the

receiving information technology system to interpret the data

“Structural” interoperability is an intermediate level that defines the structure or

format/syntax of data exchange (i.e., the message format standards) where there is

uniform movement of healthcare data from one system to another

Need for structure, such as HL7 v2 data exchange

“Semantic” interoperability provides interoperability at the highest level, which is the

ability of two or more systems or elements to exchange information and to use the

information that has been exchanged

Need for an information model, such as RIM in HL7 v3 data exchange

Types of Interoperability

5

Semantic interoperability takes advantage of both the structuring of the data exchange

and the codification of the data, including vocabulary, so that the receiving

information technology systems can interpret the data

This level of interoperability supports the electronic exchange of patient summary

information among caregivers and other authorized parties via potentially disparate

electronic health record (EHR) systems and other systems to improve quality, safety,

efficiency, and efficacy of healthcare delivery

Semantic Interoperability

6

Semantic Interoperability

7

Inter-

operational

maturity

Progress Technical

challenges Semantic interoperability

Variation in

process

Low Now

Reliable, secure

connectivity,

transmission

Shared message syntax

(e.g., HL7 v2)

Varies by

organization

Medium Near

future

Specific shared

standards for

exchange of data

Shared data models (e.g., HL7 v3

RIM); domain-specific standards;

cross-referenced terminologies

Selected

constrained on

common models

High Future Dynamic shared

services

Dynamic data models, ontologies;

shared standards

Collaborative

design; engineered

process

Large number of locally or nationally funded efforts are geared toward ensuring

semantic and/or syntactic interoperability of data for its secondary use for research

and policy decision making

Many of these efforts have established concrete interoperability requirements to which

the institutes participating in the efforts are expected to conform, including specific

data models, vocabulary references for data encoding, and controlled sets of data

elements to use

Promoting specific artifacts, such as curation tools, data models, or interoperability

evaluation criteria developed through a particular initiative, would be less beneficial

because they were developed to meet specific interoperability requirements for their

initiatives

Syntactic interoperability and semantic interoperability are closely intertwined, and

data interoperability requires both aspects

Local and National Efforts

8

Value-based care delivery systems such as accountable care organizations (ACOs) and

patient-centered medical home (PCMHs) require a great deal of interoperability to

integrate disparate systems and harmonize the data in order to acquire the necessary

information about their patient population

Some of the entities involved in the care delivery ecosystem do not use certified

health IT solutions

Mandates

9

Mandates

10

In order for equivalent data elements

from different sources to be

harmonized (treated as equivalent),

processes should be created and

documented that either:

a. Transform and standardize data

elements prior to analysis, or

b. Make transformation logic available

that can be executed when data

are extracted

The selected approach should be based

on an understanding of the research

domain of interest

Data Integration Strategies

11

Data Sources

Data Network (centralized)

Semantic

Transformation

Analytics

Semantic Data

Semantic

Transformation

Standardized patient-identifying attributes should be required in the relevant

exchange transactions

Any changes to patient data attributes in exchange transactions should be coordinated

with organizations working on parallel efforts to standardize healthcare transactions

Certification criteria should be introduced that require certified EHR technology to

capture the data attributes that would be required in the standardized patient-

identifying attributes

The ability of additional, nontraditional data attributes to improve patient matching

should be studied

Certification criteria should not be created for patient matching algorithms or require

organizations to utilize a specific type of algorithm

Data Linkage and Patient Matching

12

CEHRT that performs patient matching, to demonstrate the ability to generate and

provide to end users reports that detail potential duplicate patient records, should be

considered

Work with the industry to develop best practices and policies to encourage consumers

to keep their information current and accurate

Work with healthcare professional associations and the Safety Assurance Factors for

EHR Resilience (SAFER) Guide initiative to develop and disseminate educational and

training materials detailing best practices for accurately capturing and consistently

verifying patient data attributes

Continue collaborating with federal agencies and the industry on improving patient

identification and matching processes


13

More information:

https://www.healthit.gov/sites/default/files/patient_identification_matching_final_

report.pdf


14

Metadata can be envisioned as words in a dictionary—words that describe words

Metadata provide information about another piece of data

Metadata can describe the standards used to create a piece of data or the location on

a computer network where it was created

Metadata can describe data, processes, and systems

They can be technical, business, or operational in nature

They can relate database schemas, data definitions, key performance indicator

definitions, interface specifications, report layouts, and source-to-target mappings

Metadata Annotation

15

Administrative metadata:

Metadata related to the use, management, and encoding processes of digital

objects over a period of time

Descriptive metadata:

Metadata that describe a work for purposes of discovery and identification, such as

creator, title, and subject

Structural metadata:

Metadata that indicate how compound objects are structured, provided to support

use of the objects

Types of Metadata

16

Semantic and administrative aspects of data contents are annotated with a set of

metadata items

Metadata annotation helps to correctly identify the intended meaning of a data

element and automated compatibility check among data elements

Metadata are usually assigned to data items and their values

Standardized terminologies used to encode the data are also a type of metadata

Metadata can be assigned for various levels of granularities

For example, ADaM requires metadata annotation to be applied to data variables,

values, data sets, and data analysis results

Metadata Annotation

17

Metadata capture core semantics (human-readable names, definitions, standardized

concept IDs) and additional administrative information (owner, data element lifecycle,

created date, revision date, and version) of a data element

Sometimes metadata may include provenance information, including processes,

references, or artifacts that helped produce the associated data

Metadata annotation is a labor-intensive process

Metadata Annotation

18

Patient identity metadata

Used to select a particular patient from a population

The proposed standard would require:

• Name

• Date of birth

• Address

• Zip code

• Other patient identifier(s)—unique identifying information, such as the last four

digits of Social Security numbers, driver's license number, the provider's patient

identification number, or some combination thereof

Examples:

• <birthTime value=“19600427”/>

• <effectiveTime value=“20101217093047”/>

Metadata Annotation

19

Provenance metadata

Describe the data set's history and origin, as well as any modifications made to it

since its creation

This would include:

• Tagged data element identifier (i.e., linking other tagged data elements to each

other, such as linking a diagnostic study to the patient encounter that led to the

test)

• Time stamp

• Actor and actor affiliation

More info:

Office of the National Coordinator for Health Information Technology (ONC)

Meaningful Use stage 2 includes certain metadata requirements

Metadata Annotation

20

International Classification of Diseases (ICD):

First published in 1893, it has been revised at roughly 10-year intervals, first by the

Statistical International Institute and later by the World Health Organization

Terminologies / Coding Systems:

International Classification of Diseases (ICD)

21


International Classification of Diseases (ICD)

22

ICD-9

ICD-9-CM

ICD-10

ICD-10-CM

Source: World Health Organization. International Classification of Diseases (ICD).

Available at: http://www.who.int/classifications/icd/en/. Accessed November 18, 2015.

Diagnosis-Related Group (DRG):

The coding system is an abstraction of an abstraction

It is applied to lists of ICD-9-CM codes, which are themselves derived from medical

records

The principal bases for the groupings are factors that affect cost and length of stay


Diagnosis-Related Group (DRG)

23


Diagnosis-Related Group (DRG)

24 Source: Centers for Medicare and Medicaid Services. List of Diagnosis Related Groups (DRGS), FY2008. Available at: https://www.cms.gov/Research-Statistics-Data-

and-Systems/Statistics-Trends-and-Reports/MedicareFeeforSvcPartsAB/downloads/DRGdesc08.pdf. Accessed November 18, 2015.

MS-DRG MDC TYPE MS-DRG Title

177 04 MED Respiratory infections & inflammations w MCC

178 04 MED Respiratory infections & inflammations w CC

179 04 MED Respiratory infections & inflammations w/o CC/MCC

180 04 MED Respiratory neoplasms w MCC

181 04 MED Respiratory neoplasms w CC

182 04 MED Respiratory neoplasms w/o CC/MCC

183 04 MED Major chest trauma w MCC

184 04 MED Major chest trauma w CC

185 04 MED Major chest trauma w/o CC/MCC

186 04 MED Pleural effusion w MCC

187 04 MED Pleural effusion w CC

188 04 MED Pleural effusion w/o CC/MCC

Current Procedural Terminology (CPT):

Developed by AMA in 1966 to provide a pre-coordinated coding scheme for

diagnostic and therapeutic procedures, which has since been adopted in the United

States for billing and reimbursement


Current Procedural Terminology (CPT)

25

CPT Codes for evaluation and management: 99201–99499

CPT Code Range Description

(99201–99216) Office/other outpatient services

(99217–99220) Hospital observation services

(99221–99239) Hospital inpatient services

(99241–99255) Consultations

(99281–99288) Emergency department services

(99291–99292) Critical care services

(99304–99318) Nursing facility services

(99324–99337) Domiciliary, rest home (boarding home) or custodial care services

(99339–99340) Domiciliary, rest home (assisted living facility), or home care plan oversight

(99341–99350) Home health services

(99354–99360) Prolonged services

(99363–99368) Case management services


Current Procedural Terminology (CPT)

26 Source: CPT & ICD-9 Coding. Available at: https://en.wikipedia.org/wiki/Current_Procedural_Terminology. Accessed December 7, 2015.

Systematized Nomenclature of Medicine (SNOMED):

Developed by the College of American Pathologists

Offers a multi-axial system for describing pathologic findings through post-

coordination of topographic (anatomic), morphologic, etiologic, and functional

terms


Systematized Nomenclature of Medicine (SNOMED)

27

Terminologies /

Coding Systems:

Systematized

Nomenclature of

Medicine

(SNOMED)

Source: The IHTSDO SNOMED CT Browser. Available

at: http://browser.ihtsdotools.org/. Accessed

December 28, 2015. 28

Logical/Laboratory Observations, Identifiers, Names and Codes (LOINC):

Originally developed for lab results, but the system has been extended to include

nonlaboratory observations (vital signs, electrocardiograms), so “Logical” has

replaced “Laboratory” to reflect the change


Logical/Laboratory Observations, Identifiers, Names and Codes (LOINC)

29

Sample LOINC Codes (sample segments)

LOINC Component Short Name System Units

15026-8 Androstanediol Androstanediol SerPl-sCnc Ser/Plas nmol/L

1850-7 Androstanediol Androstanediol Ur-mCnc Urine ng/mL

23815-4 Androstanediol Androstanediol 24h Ur-mRate Urine mg/24 H

9640-4 Androstanediol Androstanediol SerPl-mCnc Ser/Plas ng/dL

11127-8 Erythrocytes RBC Mar Bone mar mL

11273-0 Erythrocytes RBC Bld Auto Bld -

13627-5 Erythrocytes RBC Smn Ql Micro Semen -

13945-1 Erythrocytes RBC #/area UrnS HPF Urine sed /HPF

12628-4 Glucose Glucose DiafP-mCnc Dial fld prt mg/dL

12629-2 Glucose Glucose 24h DiafP-mCnc Dial fld prt mg/dL

14386-7 Glucose Glucose Gast-mCnc Gast fld mg/dL

14743-9 Glucose Glucose BldC Glucomtr-sCnc BldC mmol/L

Terminologies / Coding Systems: Logical/

Laboratory Observations, Identifiers, Names and Codes (LOINC)

30 Source: https://loinc.org.

National Drug Codes (NDC) and RxNorm:

NDC, produced by the Food and Drug Administration (FDA), is applied to all drug

packages

RxNorm is the result of a collaboration between the FDA, the National Library of

Medicine (NLM), the Veterans Administration (VA), and the pharmacy knowledge

base vendors

European countries use other classification systems, such as the Anatomical-

Therapeutic-Chemical (ATC) classification


National Drug Codes (NDC) and RxNorm

31


National Drug Codes (NDC) and RxNorm

32

Unified Medical Language System (UMLS):

Started by NLM in 1986 to construct a resource that would bring together and

disseminate controlled medical terminologies

Its principal component is the Metathesaurus, which contains over one million terms

collected from over 100 different sources and attempts to relate synonymous and

similar terms from across the different sources


Unified Medical Language System (UMLS)

33

Terminologies /

Coding Systems:

Unified Medical

Language System

(UMLS)

34

Health Level 7 (HL7)

The purpose of a data-interchange standard is to permit one system, the sender, to

transmit to another system, the receiver, all the data required to accomplish a

specific communication, or transaction set, in a precise, unambiguous fashion

Open Systems Interconnection (OSI) reference model describes seven levels of

requirements or specifications for a communications exchange:

• Physical, data link, network, transport, session, presentation, and application

Level 7, the application level, deals primarily with the semantics or data-content

specification of the transaction set or message

• Reflected in HL7 name

HL7 is the most widely implemented healthcare data-messaging standard and is in

use at more than 1,500 healthcare facilities

Data Exchange Standards

35

Health Level 7 (HL7)

Version 1.0 served mainly to define

the scope and format of standards

Version 2.0 was the basis for several

data-interchange demonstrations

involving more than 10 vendors

Version 2.2 was approved by ANSI as

the first healthcare data-

interchange American National

Standard

Version 3.0 is object oriented and

based on a Reference Information

Model (RIM)


36

An example of an HL7 v2.3 ADT

transaction message


An example of an

HL7 v3 CCDA

(Consolidated

Clinical Document

Architecture)

formatted discharge

summary

37

Digital Imaging and Communications in Medicine (DICOM):

The purposes of the ACR/NEMA standard were to promote a generic digital-image

communication format, to facilitate the development and expansion of picture-

archiving and communication systems

ASTM E1238:

Standard specification for transferring clinical observations between independent

systems

Used in commercial and reference clinical laboratories

IEEE 1073:

Standard for Medical Device Communications

Has produced a family of documents that defines the entire seven-layer

communications requirements for the Medical Information Bus (MIB)

Other Data Exchange Standards

38

ASC X12:

An independent organization accredited by ANSI

Has developed message standards for purchase-order data, invoice data, and other

commonly used business documents

UCC:

An ANSI-approved organization

Defines the universal product code

Standards include specifications for the printing of machine-readable

representations (bar codes)

Other Data Exchange Standards

39

Health Level 7 (HL7) http://www.hl7.org

International Health Terminology Standards

Development Organization (IHTSDO)

http://www.ihtsdo.org

World Health Organization (WHO) http://www.who.int/peh-emf/standards/en

Clinical Information Modeling Initiative (CIMI) http://www.opencimi.org

International Organization for Standardization

(ISO13606)

http://www.iso.org/iso/iso_technical_committe

e?commid=54960

Open Electronic Health Record (OpenEHR) http://www.openehr.org

Clinical Data Interchange Standards

Consortium (CDISC)

http://www.cdisc.org

Standards and Interoperability (S&I) Framework http://www.siframework.org

Standards Organizations / Collaborations for Health IT

40

HIMSS Interoperability Definition and

Background

http://s3.amazonaws.com/rdcms-

himss/files/production/public/HIMSSorg/Conten

t/files/AUXILIOHIMSSInteroperabilityDefined.pdf

ONC Interoperability Roadmap http://www.healthit.gov/sites/default/files/na

tionwide-interoperability-roadmap-draft-

version-1.0.pdf

Data for Individual Health (JASON report) https://healthit.ahrq.gov/sites/default/files/d

ocs/publication/2014-jason-data-for-individual-

health.pdf

Additional Information

41

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