Appendix A – Glossary

A

ACT Network

Accrual [of Patients] to Clinical Trials; NCATS-funded consortium of CTSA hubs that incorporates SHRINE instances across the USA; precursor to ENACT Network

AMA

American Medical Association; author of CPT and HCPCS coding standards

AMIA

American Medical Informatics Association (amia.org)

Apache

web server software for hosting the i2b2 webclient (user interface) on Linux; may be deployed on the same host as the Wildfly server

C

CDM

Common Data Model; a way of organizing data into standardized structures and observational content to enable alignment of patient data across multiple organizations; also see i2b2/tranSMART CDM and OMOP CDM

CMS

US Center for Medicare and Medicaid Services; authors of SynPUF CDM

coding scheme

a way of coding "concepts" in clinical research informatics; various terminology standards define coding schemes; for instance, the Common Procedural Terminology standard uses the CPT-4 coding scheme, which assigns a 5-digit number to each "procedure" in its taxonomy (e.g., CPT4:42810)

concept

a concept in the i2b2 ontology is an item in the taxonomy or list of terms describing clinical research informatics; a diagnosis of diabetes, a tonsillectomy procedure, a prescription of aspirin, the patient's age, and hemoglobin A1C blood test results are all concepts in the i2b2 ontology

CPT

Current Procedural Terminology; Level 1 of HCPCS coding standard for healthcare procedures; authored by AMA

CRI

Clinical Research Informatics; the realm of healthcare research where i2b2 is employed

CTSA

Clinical and Translational Science Award from the NIH; healthcare research institutions that receive the CTSA grant are prime candidates for inclusion in the ENACT Network

D

de-identified data

over 18 different types of personal data must be removed from patient records to qualify as “de-identified” data; not generally useful for research; NOT the same as "limited-data-set" data

DHHS

US Department of Health and Human Services (Federal); also HHS

Docker

a software program that emulates a virtual machine; a Docker "image" of the i2b2 core server is available for testing and/or exploring i2b2; Docker allows i2b2 to be run in a sheltered environment on a non-production host; it is not recommended for production use

domain

also called "category"; a class of data in clinical research informatics; diagnoses, procedures, medications, lab tests, and demographics are examples of domains in the i2b2 ontology

E

EHR

Electronic Health Records (also EMR)

EMR

Electronic Medical Records (also EHR)

ENACT

Evolve to Next-gen ACT; NCATS-funded consortium of CTSA hubs that incorporates SHRINE instances across the USA; successor to the ACT Network

ETL

extract, transform, load (database conversion); the primary ETL for i2b2 is in the conversion of EHR/EMR to the CRC database (CDM)

F

FDA

US Food and Drug Administration; author of NDC

FHIR

Fast Healthcare Interoperability Resources, interoperability standard from HL7 (say “fire”)

G

GIS

Geographic Information Services

H

HCPCS

Healthcare Common Procedure Coding System; authored by AMA (say "hick-picks")

HIPAA

Health Insurance Portability and Accountability Act, 1996, allows people to transfer their health insurance from one employer to another; includes privacy and security standards (say "hipp-uh")

HHS

US Dept. of Health and Human Services

HL7

Health Level Seven International, an ANSI-accredited standards-developing non-profit organization, since 1987 (www.hl7.org); author of FHIR, and coding standards for Administrative and Clinical concepts

I

i2b2

Informatics for Integrating Biology and the Bedside (i2b2.org)

i2b2/tranSMART CDM

The i2b2/tranSMART common data model is the primary patient data model used in i2b2 and tranSMART. It consists of a "star schema": one table for the multitude of patient-related observations, supported by "dimension" tables for patient demographics, encounter records, provider information, etc.

ICD

International Classification of Diseases; coding standards for diagnoses and procedures; authored by WHO and NCHS

IHTSDO

International Health Terminology Standards Development Organisation; see SNOMED International

IIS

web server software for hosting the i2b2 webclient (user interface) on Windows; may be deployed on the same host as the Wildfly server

image

a copy of the i2b2 core software that is packaged for use in a Docker container

IRB

Institutional Review Board; approval by an IRB is required anytime human subjects are part of the research at an institution

J

JBoss

former name of the Wildfly server software (say "jay-boss")

JDK

Java Development Kit; a version of Java that includes the Java compiler and support libraries; required for i2b2; not the same as the JRE

JRE

Java Runtime Environment; a version of Java that does not include the Java compiler nor related support libraries; not used in i2b2

L

LDS

see limited data set

limited data set

PHI which excludes direct identifiers of the patient, their family, employer, etc. May include city, state, ZIP code, general geographic info, DOB, DOD, age in years, months, days, or hours. Still protected under HIPAA. This is NOT the same as de-identified data; some could say it is only "partially" de-identified. It may NOT include name, address, phone, email, SSN, MRN, insurance ID, account #’s, license #’s, vehicle IDs, device IDs, URLs, IP addresses, biometric IDs, photos, etc.

LOINC

Logical Observation Identifiers Names and Codes (say "loink"); coding standard for healthcare measurements, such as laboratory test values and vital signs; authored by the Regenstrief Institute

N

NCATS

US National Center for Advancing Translational Sciences, part of the NIH (say "en-cats")

NCBC

US National Center for Biomedical Computing

NCHS

US National Center for Health Statistics; author of ICD coding standards

NDC

US National Drug Code; coding standard for medications; authored by FDA

NIH

US National Institutes of Health, under DHHS

NLM

US National Library of Medicine; author of RxNorm and UMLS coding standards

NPO

non-profit organization

O

OCR

HHS Office for Civil Rights, investigates HIPAA violations

OHDSI

Observational Health Data Science and Informatics (ohdsi.org) (say “odyssey”), successor to OMOP (est. 2014)

OMOP

Observational Medical Outcomes Partnership (2009–2014) (omop.org), succeeded by OHDSI (say “oh-mop”)

OMOP CDM

The OMOP common data model is used by many institutions for research. It can be used in the i2b2 CRC database for recording patient data. Many institutions prefer this format over the i2b2 CDM because it more readily supports research outside of i2b2. This CDM can also be joined with the i2b2 CDM to allow the patient data to remain in the OMOP CDM tables, while the i2b2 software accesses the patient data through database views.

Oracle

relational database management system supported by i2b2

P

PHI

protected health information

Postgres / PostgreSQL

relational database management system supported by i2b2 (say "post-gress")

project

an i2b2 project is a specific pairing of a patient database with a metadata database; each i2b2 instance can support multiple projects; a patient database may be paired with multiple metadata databases, but each metadata database may be paired with only one patient database

R

REDCap

Research Electronic Data Capture (projectredcap.org), provided by Vanderbilt University free to NPO’s for conducting research (say "red-cap")

Regenstrief Institute

author of LOINC coding standard

RxNorm

coding standard for medications, part of the UMLS; authored by NLM (say "r-x-norm")

S

SHRINE

Shared Health Research Information NEtwork. (catalyst.harvard.edu/services/shrine/). Application/webapp for querying patient data, a client of i2b2; returns results from multiple institutions (e.g., the ENACT Network). Consists of 3 web apps: Data Steward, Webclient, and Dashboard.

SNOMED

Systematized Nomenclature of Medicine; SNOMED Clinical Terms (SNOMED CT) is a coding standard for all categories of clinical research informatics (say "snow-med")

SNOMED International

same as IHTSDO; author of SNOMED coding standards

SQL

Structured Query Language; used in the relational databases supported by i2b2; example test queries are written in SQL (say "sequel" or "ess-cue-ell")

SQL Server

relational database management system supported by i2b2 (say "sequel server")

SynPUF CDM

Synthetic Public Use Files; a demonstration/development/test patient database consisting of Medicare claim information; not for research use (say "sin-puff")

T

taxonomy

hierarchical arrangement of concepts such that each concept is a "child" of a more inclusive "parent" concept

terminology

a glossary or collection of terms to describe a category or domain; the concepts in the Common Procedural Terminology (CPT) define a terminology for clinical procedures

Tomcat

web server software for hosting Java-based applications; in the world of i2b2, Tomcat is used to host SHRINE applications

tranSMART

software related to i2b2, used for translational studies; incorporates i2b2 CDM, but includes additional databases for genomics, etc. (i2b2.org)

TriNetX

multi-institution research network, similar to i2b2+SHRINE (say "try-net-ex")

U

UMLS

Unified Medical Language System; coding system for all categories of clinical research informatics; authored by NLM

V

VA

US Veterans Administration; author of VA Classes coding standard for medications

vocabulary

similar to terminology; each coding standard periodically publishes a revision of its vocabulary, which defines all the terms which should be in current use in the i2b2 ontology

W

Wildfly

web server software for hosting Java-based applications; in the world of i2b2, Wildfly is used to host the i2b2 core software

WHO

World Health Organization (say "w-h-o", not "who"); author of ICD coding standards