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A
ACT Network
Accrual [of Patients] to Clinical Trials (formerly at actnetwork.us); NCATS-funded consortium of CTSA hubs that incorporates SHRINE instances across the USA; precursor to superseded by the ENACT Network
AMA
American Medical Association (ama-assn.org); 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
ANSI
American National Standards Institute (ansi.org)
B
BioPortal
comprehensive repository of biomedical ontologies (bioportal.bioontology.org); managed by NCBO
C
category
also called "domain"; a class of data in clinical research informatics; diagnoses, procedures, medications, lab tests, and demographics are examples of categories in the i2b2 ontology
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 (cms.gov); 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 (CPT) 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 NCATS at NIH (ncats.nih.gov/research/research-activities/ctsa); healthcare research institutions that receive the CTSA grant are prime candidates for inclusion in the ENACT Network
D
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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) (hhs.gov); 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 Network
Evolve to Next-gen ACT (enact-network.org); NCATS-funded consortium of CTSA hubs that incorporates SHRINE instances across the USA; successor to the ACT Network
ETL
extract, transform, and 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 (fda.gov); author of NDC
FHIR
Fast Healthcare Interoperability Resources (fhir.org) (say “fire”), an 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 (hhs.gov)
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 (i2b2i2b2transmart.org)
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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 datarecords, provider datainformation, etc.
ICD
International Classification of Diseases; coding standards for diagnoses and procedures; authored by WHO and NCHS
IHTSDO
International Health Terminology Standards Development Organisation (snomed.org); 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
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limited data set
PHI which excludes direct identifiers of the patient, their family, employer, etc. May include city, state, ZIP code, general geographic infoinformation, date of birth (DOB), date of death (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, Social Security Number (SSN), Medical Record Number (MRN), insurance ID, account #’s, license #’s, vehicle IDsID's, device IDs, URLsID's, URL's, IP addresses, biometric IDsID's, 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
M
MITRE
The MITRE Corporation (mitre.org), author of SyntheaTM
N
NCATS
US National Center for Advancing Translational Sciences , part of the NIH (ncats.nih.gov) (say "en-cats")
...
; part of the NIH
NCBCs
US National Centers for Biomedical Computing (wikipedia) are an initiative of the National Institutes of Health (NIH); there are several centers, including the National Center for Biomedical Ontology (NCBO) and the National Center for Integrative Biomedical Informatics (NCIBI)
NCBO
US National Center for Biomedical Ontology (bioontology.org); hosts the BioPortal
NCIBI
US National Center for Biomedical ComputingIntegrative Biomedical Informatics (ncibi.org)
NCHS
US National Center for Health Statistics (cdc.gov/nchs); author of ICD coding standards
NDC
US National Drug Code; coding standard for medications; authored by FDA
NIH
US National Institutes of Health (nih.gov), under DHHS
NLM
US National Library of Medicine (nlm.nih.gov); author of RxNorm and UMLS coding standards
NPO
non-profit organization
O
OCR
HHS Office for Civil Rights (hhs.gov/ocr), 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”), succeeded by OHDSI
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 patient data through database views that mimic the i2b2 CDM
Oracle
relational database management system supported by i2b2
P
PHI
protected health information
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Postgres / PostgreSQL
relational database management system supported by i2b2 (say "post-gress")
project
an i2b2 project is a specific pairing of a patient database (CRC) with a metadata database (ONT); each i2b2 instance can support multiple projects
R
REDCap
Research Electronic Data Capture (projectredcap.org), provided by Vanderbilt University free to NPO’s for conducting research (say "red-cap")
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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"); authored by IHTSDO (SNOMED International)
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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")
SyntheaTM
a synthetic-patient-population generator; creates realistic (but not real) patient data and associated health records in a variety of formats; may be used for setting up a demo database for i2b2 (say "cynthia"); authored by The MITRE Corporation
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; for instance, 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 applicationsthe SHRINE application
tranSMART
software related to i2b2, used for translational studies; incorporates i2b2 CDM, but includes additional databases for genomics, etc. (i2b2i2b2transmart.org)
TriNetX
multi-institution research network, similar to i2b2+SHRINE (say "try-net-ex") (trinetx.com)
U
UMLS
Unified Medical Language System; coding system for all categories of clinical research informatics; authored by NLM
V
VA
US Veterans Administration (va.gov); 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 (who.int) (say "w-h-o", not "who"); author of ICD coding standards
