Informatics for Integrating Biology and the Bedside (i2b2)

General Information

Technologies must be operated and maintained in accordance with Federal and Department security and privacy policies and guidelines. More information on the proper use of the TRM can be found on the TRM Proper Use Tab/Section.

Website:	Go to site
Description:	Informatics for Integrating Biology and the Bedside (i2b2) is an open-source platform that is National Institutes of Health (NIH) funded National Center for Biomedical Computing (NCBC) based at Partners HealthCare System. This technology is a framework that bridges clinical research data and the vast data banks arising from basic science research to better understand the genetic bases of complex diseases. An i2b2 implementation consists of a data mart of clinical, research, administrative data, and interface to construct and manage queries and data sets. Also, researchers can use i2b2 to perform self-service queries of de-identified data for Health Insurance Portability and Accountability Act (HIPAA) compliant cohort discovery and hypothesis testing. The architecture consists of two major parts. The first part is the back-end infrastructure (the `Hive`) that takes care of security, access rights, and managing the underlying data repository. The second part is an application set of query and mining programs that allows users to ask questions about the data (the Workbench). Data can be saved in a Microsoft Structured Query Language (SQL) Server database, PostgreSQL database, or an Oracle database.
Technology/Standard Usage Requirements:	Users must ensure their use of this technology/standard is consistent with VA policies and standards, including, but not limited to, VA Handbooks 6102 and 6500; VA Directives 6004, 6513, and 6517; and National Institute of Standards and Technology (NIST) standards, including Federal Information Processing Standards (FIPS). Users must ensure sensitive data is properly protected in compliance with all VA regulations. Prior to use of this technology, users should check with their supervisor, Information Security Officer (ISO), Facility Chief Information Officer (CIO), or local Office of Information and Technology (OI&T) representative to ensure that all actions are consistent with current VA policies and procedures prior to implementation.
Section 508 Information:	This technology has been assessed by the Section 508 Office and found non-conformant. The Implementer of this technology has the responsibility to ensure the version deployed is 508-compliant. Section 508 compliance may be reviewed by the Section 508 Office and appropriate remedial action required if necessary. For additional information or assistance regarding Section 508, please contact the Section 508 Office at Section508@va.gov. Please see reference tab for more information concerning product versions.
Decision:	View Decisions

Decision Source:	TRM Mgmt Group
Decision Process:	One-VA TRM v21.4
Decision Date:	04/07/2021 at 12:01:24 UTC
Introduced By:	TRM Request
Vendor Name:	Informatics for Integrating Biology and the Bedside

Vendor Release Information

The Vendor Release table provides the known releases for the TRM Technology, obtained from the vendor (or from the release source).

Version	Release Date	Vendor End of Life Date	Vendor Desupport Date
1.3	01/01/2009
1.4	02/01/2010
1.5	07/15/2010
1.6	10/09/2012
1.7	05/06/2015
1.7.x	01/15/2016

Current Decision Matrix (04/05/2021)

Users must ensure their use of this technology/standard is consistent with VA policies and standards, including, but not limited to, VA Handbooks 6102 and 6500; VA Directives 6004, 6513, and 6517; and National Institute of Standards and Technology (NIST) standards, including Federal Information Processing Standards (FIPS). Users must ensure sensitive data is properly protected in compliance with all VA regulations. Prior to use of this technology, users should check with their supervisor, Information Security Officer (ISO), Facility Chief Information Officer (CIO), or local Office of Information and Technology (OI&T) representative to ensure that all actions are consistent with current VA policies and procedures prior to implementation.

The VA Decision Matrix displays the current and future VA IT position regarding different releases of a TRM entry. These decisions are based upon the best information available as of the most current date. The consumer of this information has the responsibility to consult the organizations responsible for the desktop, testing, and/or production environments to ensure that the target version of the technology will be supported. Any major.minor version that is not listed in the VA Decision Matrix is considered unapproved for use.

Legend:

White	Approved: The technology/standard has been approved for use.
Yellow	Approved w/Constraints: The technology/standard can be used within the specified constraints located below the decision matrix in the footnote[1] and on the General tab.
Gray	Unapproved: This technology or standard can be used only if a POA&M review is conducted and signed by the Authorizing Official Designated Representative (AODR) as designated by the Authorizing Official (AO) or designee and based upon a recommendation from the POA&M Compliance Enforcement, has been granted to the project team or organization that wishes to use the technology.
Orange	Divest: VA has decided to divest itself on the use of the technology/standard. As a result, all projects currently utilizing the technology/standard must plan to eliminate their use of the technology/standard. Additional information on when the entry is projected to become unapproved may be found on the Decision tab for the specific entry.
Black	Prohibited: The technology/standard is not (currently) permitted to be used under any circumstances.
Blue	Planning/Evaluation Constraint:The period of time this technology is currently being evaluated, reviewed, and tested in controlled environments. Use of this technology is strictly controlled and not available for use within the general population. If a customer would like to use this technology, please work with your local or Regional OI&T office and contact the appropriate evaluation office displayed in the notes below the decision matrix. The Local or Regional OI&T office should submit an inquiry to the TRM if they require further assistance or if the evaluating office is not listed in the notes below.

Release/Version Information:

VA decisions for specific versions may include a ‘.x’ wildcard, which denotes a decision that pertains to a range of multiple versions.

For example, a technology approved with a decision for 7.x would cover any version of 7.(Anything) - 7.(Anything). However, a 7.4.x decision would cover any version of 7.4.(Anything), but would not cover any version of 7.5.x or 7.6.x on the TRM.

VA decisions for specific versions may include ‘+’ symbols; which denotes that the decision for the version specified also includes versions greater than what is specified but is not to exceed or affect previous decimal places.

For example, a technology approved with a decision for 12.6.4+ would cover any version that is greater than 12.6.4, but would not exceed the .6 decimal ie: 12.6.401 is ok, 12.6.5 is ok, 12.6.9 is ok, however 12.7.0 or 13.0 is not.

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Decision Constraints


[1]	Federal Information Processing Standards (FIPS) 140-2 certified encryption must be used to encrypt data in transit if Personal Identifiable Information (PII), Personal Health Information (PHI), or Veteran Affairs (VA) sensitive information is involved or additional mitigating controls must be documented in an approved System Security Plan (SSP).

[2]	Users should check with their supervisor, Information Security Office (ISO) or local OIT representative for permission to download and use this software. Downloaded software must always be scanned for viruses prior to installation to prevent adware or malware. Freeware may only be downloaded directly from the primary site that the creator of the software has advertised for public download and user or development community engagement. Users should note, any attempt by the installation process to install any additional, unrelated software is not approved and the user should take the proper steps to decline those installations.

[3]	Veterans Affairs (VA) users must ensure VA sensitive data is properly protected in compliance with all VA regulations. All instances of deployment using this technology should be reviewed by the local ISO (Information Security Officer) to ensure compliance with VA Handbook 6500.

[4]	Per the May 5th, 2015 memorandum from the VA Chief Information Security Officer (CISO) FIPS 140-2 Validate Full Disk Encryption (FOE) for Data at Rest in Database Management Systems (DBMS) and in accordance with Federal requirements and VA policy, database management must use Federal Information Processing Standards (FIPS) 140-2 compliant encryption to protect the confidentiality and integrity of VA information at rest at the application level. If FIPS 140-2 encryption at the application level is not technically possible, FIPS 140-2 compliant full disk encryption (FOE) must be implemented on the hard drive where the DBMS resides. Appropriate access enforcement and physical security control must also be implemented. All instances of deployment using this technology should be reviewed to ensure compliance with VA Handbook 6500 and National Institute of Standards and Technology (NIST) standards. It is the responsibility of the system owner to work with the local CIO (or designee) and Information Security Officer (ISO) to ensure that a compliant DBMS technology is selected and that if needed, mitigating controls are in place and documented in a System Security Plan (SSP).

[5]	Technology must remain patched and operated in accordance with Federal and Department security policies and guidelines in order to mitigate known and future security vulnerabilities.

[6]	Veterans Affairs (VA) users must ensure VA sensitive data is properly protected in compliance with all VA regulations. All instances of deployment using this technology should be reviewed by the local ISO (Information Security Officer) to ensure compliance with VA Handbook 6500.

[7]	Per the May 5th, 2015 memorandum from the VA Chief Information Security Officer (CISO) FIPS 140-2 Validate Full Disk Encryption (FOE) for Data at Rest in Database Management Systems (DBMS) and in accordance with Federal requirements and VA policy, database management must use Federal Information Processing Standards (FIPS) 140-2 compliant encryption to protect the confidentiality and integrity of VA information at rest at the application level. If FIPS 140-2 encryption at the application level is not technically possible, FIPS 140-2 compliant full disk encryption (FOE) must be implemented on the hard drive where the DBMS resides. Appropriate access enforcement and physical security control must also be implemented. All instances of deployment using this technology should be reviewed to ensure compliance with VA Handbook 6500 and National Institute of Standards and Technology (NIST) standards. It is the responsibility of the system owner to work with the local CIO (or designee) and Information Security Officer (ISO) to ensure that a compliant DBMS technology is selected and that if needed, mitigating controls are in place and documented in a System Security Plan (SSP).

[8]	An image of the i2b2 server which is installed on Community Enterprise Operating System (CentOS) is available. At the time of writing, use of CentOS is restricted to laboratory and development test systems only. CentOS may not be used for Veterans Information Systems and Technology Architecture (VistA) site mirror test systems or other pre-production verification systems. Applications and strategies developed on systems running CentOS must be tested properly on enterprise level Red Hat platforms prior to production release. CentOS must remain properly patched in order to mitigate known and future security vulnerabilities. Organization security baseline configuration standards for Linux systems must be employed and properly maintained. For more information, please refer to CentOS entry within One-VA TRM. Informatics for Integrating Biology and the Bedside (i2b2) offers the `i2b2 Source` option in which the server is built from scratch. Users must use this option during initial setup/installation to help mitigate concerns.

[9]	An image of the Informatics for Integrating Biology and the Bedside (i2b2) server which is installed on Community Enterprise Operating System (CentOS) is available. At the time of writing, use of CentOS is restricted to laboratory and development test systems only. CentOS may not be used for Veterans Information Systems and Technology Architecture (VistA) site mirror test systems or other pre-production verification systems. Applications and strategies developed on systems running CentOS must be tested properly on enterprise level Red Hat platforms prior to production release. CentOS must remain properly patched in order to mitigate known and future security vulnerabilities. Organization security baseline configuration standards for Linux systems must be employed and properly maintained. For more information, please refer to CentOS entry within One-VA TRM. Informatics for Integrating Biology and the Bedside (i2b2) offers the `i2b2 Source` option in which the server is built from scratch. Users must use this option during initial setup/installation to help mitigate concerns.

[10]	An image of the Informatics for Integrating Biology and the Bedside (i2b2) server which is installed on Community Enterprise Operating System (CentOS) is available. At the time of writing, use of CentOS is restricted to laboratory and development test systems only. CentOS may not be used for Veterans Information Systems and Technology Architecture (VistA) site mirror test systems or other pre-production verification systems. Applications and strategies developed on systems running CentOS must be tested properly on enterprise level Red Hat platforms prior to production release. CentOS must remain properly patched in order to mitigate known and future security vulnerabilities. Organization security baseline configuration standards for Linux systems must be employed and properly maintained. For more information, please refer to CentOS entry within One-VA TRM. Informatics for Integrating Biology and the Bedside (i2b2) offers the `i2b2 Source` option in which the server is built from scratch. Users must use this option during initial setup/installation to help mitigate concerns. Users must ensure that Firefox, Microsoft Internet Explorer (IE), Microsoft Internet Information Services (IIS), Microsoft Structured Query Language (SQL) Server, Oracle Database and PostgreSQL are implemented with VA-approved baselines. (refer to the ‘Category’ tab under ‘Runtime Dependencies’) This technology must use the latest TRM-approved version of Java Development Kit (JDK) - Oracle.

[11]	Veterans Affairs (VA) users must ensure VA sensitive data is properly protected in compliance with all VA regulations. All instances of deployment using this technology should be reviewed by the local ISO (Information Security Officer) to ensure compliance with VA Handbook 6500.

[12]	Per the May 5th, 2015 memorandum from the VA Chief Information Security Officer (CISO) FIPS 140-2 Validate Full Disk Encryption (FOE) for Data at Rest in Database Management Systems (DBMS) and in accordance with Federal requirements and VA policy, database management must use Federal Information Processing Standards (FIPS) 140-2 compliant encryption to protect the confidentiality and integrity of VA information at rest at the application level. If FIPS 140-2 encryption at the application level is not technically possible, FIPS 140-2 compliant full disk encryption (FOE) must be implemented on the hard drive where the DBMS resides. Appropriate access enforcement and physical security control must also be implemented. All instances of deployment using this technology should be reviewed to ensure compliance with VA Handbook 6500 and National Institute of Standards and Technology (NIST) standards. It is the responsibility of the system owner to work with the local CIO (or designee) and Information Security Officer (ISO) to ensure that a compliant DBMS technology is selected and that if needed, mitigating controls are in place and documented in a System Security Plan (SSP).

Note:

At the time of writing, version 1.7.12 (released 12/01/2019) is the most current version released.

References

The following reference(s) are associated with this entry:
Type	Name	Source	Description
Other	Data Sharing Network (SHRINE)		Shared Health Research Informatics Network (SHRINE) is a web-based software network (based on the prototype model Shared Pathology Informatics Network, (SPIN)) that allows the participating Harvard hospitals to link their respective Informatics for Integrating Biology and the Bedside (i2b2) instances. The SHRINE is used for the sharing of obfuscated, aggregated counts of patients meeting selected inclusion and exclusion criteria for demographics, diagnoses, medications, and labs.

Technology Components

Note: This list may not be complete. No component, listed or unlisted, may be used outside of the technology in which it is released. The usage decision for a component is found in the Decision and Decision Constraints.
Name	Description
Data Repository (CRC) Cell Install	The Data Repository (CRC) Cell manages the storage and querying of the clinical data stored in the demodata tables.
File Repository (FR) Cell Install	The File Repository (FR) Cell manages integrating Biology and the Bedside (i2b2) files between cells and within i2b2 applications such as the i2b2 Workbench.
Informatics for Integrating Biology and the Bedside (i2b2) Administration Module Install	The i2b2 Administration Module (Admin) is a web-based application that is designed to assist with the workflow and overall ease of setting up the i2b2 environment. Users with administration privileges can manage cells, projects, and user. The Admin has to be setup after the Project Management (PM) Cell is installed and before any other installation of i2b2 cells.
Informatics for Integrating Biology and the Bedside (i2b2) Hive	The Hive is a standard, self-aggregating software architecture for the clinical research chart. The software modules of the Hive are called Cells, and represent atomic units of functionality that exist as software programs. Informatics for Integrating Biology and the Bedside (i2b2) cells are application programming interfaces (APIs) for clinical research chart plug-ins. These are the specifications and software APIs that will allow anyone to produce new functional modules for the i2b2 clinical research chart environment.
Informatics for Integrating Biology and the Bedside (i2b2) Server-Common Install	As part of the i2b2, there are a group of common server files that are used by the i2b2 cells. These files are contained in the edu.harvard.i2b2.server-core project which has to be deployed before installing any of the i2b2 Core Cells.
Informatics for Integrating Biology and the Bedside (i2b2) Source	The i2b2 Source is a collection of the i2b2 source code for the i2b2 clients and server. The source code can be used to build the i2b2 Server from scratch.
Informatics for Integrating Biology and the Bedside (i2b2) VMWare	The i2b2 VMWare is a Virtual Machine (VM) Image of a complete i2b2 Server installed on Community Enterprise Operating System (CentOS). If users do not want to install the i2b2 Server from scratch, this VM image can be used to run an instance of i2b2. However, the Informatics for Integrating Biology and the Bedside (i2b2) Source option can be used instead, in which the server is built from scratch.
Informatics for Integrating Biology and the Bedside (i2b2) Web Client Install	The i2b2 Web Client is a web-based interface to the i2b2 Hive. The web client reproduces much of the functionality of the desktop client (Workbench), and one of the primary advantages is the software does not have to be installed on a user`s computer. All an i2b2 user needs to run the web client is a web browser. This may aid in enterprise-wide roll out of the i2b2 across an institution.
Informatics for Integrating Biology and the Bedside (i2b2) Workbench	The i2b2 Workbench is a collection of client-side components that communicate with i2b2 Cells and help aggregate their functionality in the Hive. Each component is designed as an Eclipse-based plug-in that interacts with a hive cell; collectively these plug-ins provide a cohesive entity to tie all the i2b2 cells together. The workbench can be installed as a desktop application or users can chose to use the Asynchronous JavaScript and Extensible Markup Language (XML) (AJAX) Web Client Install version.
Ontology Management (ONT) Cell Install	The Ontology Management (ONT) Cell manages the Informatics for Integrating Biology and the Bedside (i2b2) vocabulary definitions, concepts, and other terminology. This component is accessed by other cells to give semantic meaning to data.
Project Management (PM) Cell Install	Information in the Project Management (PM) Cell is related to the setup and maintenance of the hive, projects, users, and security. The PM Cell needs to be installed prior to the other Integrating Biology and the Bedside (i2b2) Core cells.
Workplace (WORK) Cell Install	The Workplace Framework (WORK) Cell manages and stores project specific Integrating Biology and the Bedside (i2b2) Extensible Markup Language (XML) data objects for a user of a given project.

VA Categories View the VA Categorization Framework

Domain Area	Category	Customer Guidance	Category Locked By ELT Date
Information Management Technologies Business Intelligence and Data Warehouse Platforms	Data Mining Tools
Information Management Technologies Business Intelligence and Data Warehouse Platforms	Clinical Environment and Tools

Open Source

This entry is available as an open source technology.

Operating Systems Supported by the Technology

CentOS Linux - Unapproved
macOS - Approved w/Constraints
Red Hat Enterprise Linux (RHEL) - Approved w/Constraints
Windows Client - Approved w/Constraints
Windows Server - Approved w/Constraints

Technologies/Standards Relationships

Runtime Dependencies:

Comparable Technologies:

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Companion Technologies/Supported Standards:

General Analysis

Adoption Benefits

There are no known common vulnerability exposures (CVEs) or VA Network and Security Operations Center (NSOC) bulletins associated with this technology.
This is a well-documented technology.
This technology may provide efficiencies to those who have researching responsibilities.
This technology`s query interface and flexible data model allows for construction of complex queries of a wide range of data from multiple original source systems.
This technology is available at no cost through open source licensing and supports VA`s open source initiative.
Per vendor, this technology allows for institutions to maintain Health Insurance Portability and Accountability Act of 1996 (HIPAA) and Institutional Review Board (IRB) compliance by providing researchers with a centralized repository of de-identified data and tools for preparatory-to-research type investigation.

Adoption Risks

The technology may collect, store or transmit Personally Identifiable Information (PII)/Protected Health information (PHI) or VA sensitive data.
Due to the frequency of this technology’s updates, the VA may be unable to keep up with the rapid release schedule of this technology and may require a usage model that requires specific versions.
This technology relies on JDK (Java Development Kit) - Oracle which has a rapid release and update schedule.
System scans indicate that this technology is no longer in use within the VA network.

Architectural Benefits

This technology can use a VA-preferred database.
The solution is compatible with virtual machines, therefore consistent with the enterprise Server Virtualize First Policy (VAIQ 7266972 08-27-2012).
This technology is portable across several VA-approved platforms.

Architectural Risks

A server component of this product called `Informatics for Integrating Biology and the Bedside (i2b2) VMWare`, in which a Virtual Machine (VM) Image of a complete i2b2 Server is installed on Community Enterprise Operating System (CentOS), is available and an option for use. However, the server component `Informatics for Integrating Biology and the Bedside (i2b2) Source` can be used instead, in which the server is built from scratch.

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