OpenELIS

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OpenELIS
OpenELIS logo.jpg
Original author(s) Casey Iiams-Hauser
Developer(s) University of Washington, International Training and Education Center for Health
Initial release February 29, 2012 (2012-02-29)[1]
Stable release

2.7.3.4  (October 19, 2023; 13 months ago (2023-10-19))

[±]
Preview release none [±]
Written in Java
Operating system Cross-platform
Type Laboratory informatics software
License(s) Mozilla Public License 2.0
Website openelis-global.org
OpenELIS.org

OpenELIS (aka OpenELIS Global) is a free open-source laboratory information system (LIS) designed to act as a "software and business process framework for the robust functioning of public health laboratories."[2] OpenELIS originally began as an open-source software project with numerous important collaborations, with contributions coming heavily from the Minnesota State Public Health Laboratory and the University of Iowa. The larger international influence of collaborators such as the Association of Public Health Laboratories (APHL), the U.S. Centers for Disease Control and Prevention (CDC), and the University of Washington's International Training and Education Center on HIV (I-TECH) later spread the OpenELIS technology (in the form of separate branches of the software) to other parts of the world, including Vietnam, Haiti, and Côte d'Ivoire. This software has since evolved, having been rewritten in Java Spring, with new technology and features being added.

Product history

Early project evolution

The OpenELIS project evolved out of a partnership between the Public Health Informatics Institute (PHII) and the Association of Public Health Laboratories (APHL) in late 2002, with funding from the Robert Wood Johnson Foundation.[3][4][dead link] The members of the collaboration were tasked with a "ground-up" effort to develop business processes and system requirements for laboratory informatics systems in the realm of public health.[4][5] This work—together with six U.S. states—eventually led to the 2003 publication of a specifications document called Requirements for Public Health Laboratory Information Management Systems, which detailed "all functions that a public health laboratory information system must be capable of supporting."[4][6]

After the publication of this document, representatives from three of the involved six states—Minnesota, Iowa, and Kansas—expressed interest in putting the ideas in the Requirements document into action in the form of an open-source LIMS system. From this desire another collaborative effort occurred to make such software a reality in the form of the Open Electronic Laboratory Information System or OpenELIS. Kansas eventually had to drop out of the project, but Minnesota and Iowa continued on with development in 2004, all while the APHL and the Centers for Disease Control and Prevention (CDC) increased interest in the project through their humanitarian work in parts of Africa and Vietnam.[5] However, as development on the software had been mostly U.S.-centric, an adaptation had to be developed, including language translations and regional addressing. Inevitably, this turned into its own independent branch of the software, including development by local Vietnamese, making the software truly international. Meanwhile domestic development continued in Minnesota and Iowa, with Minnesota's code base sharing similarities with Vietnam's, while Iowa was branching out with its own slightly-modified version.[5]

By early 2008 the Minnesota State Public Health Laboratory was testing its implementation of OpenLIMS, while Vietnam began testing theirs in February at the District Four Health Center in Ho Chi Minh City and the National Institute of Infectious and Tropical Diseases in Hanoi.[3][7] The Vietnam branch in particular was seen by the APHL as "a rare opportunity to learn from the mistakes we've made with laboratory information systems domestically and to implement them right the first time in these other countries."[7]

OpenELIS branches out again

In April 2008, the OpenELIS team reached out to the members and collaborators (including the University of Washington) of the OpenMRS open-source project[8], a project dedicated to supporting the delivery of health care in developing countries.[9] Weeks of discussions led to an agreement to create an OpenELIS developer community as well as a potential connecting of OpenELIS with OpenMRS.[8]

At roughly the same time as OpenELIS was being developed, a different collaboration was occurring in Haiti between the University of Washington's Clinical Informatics Research Group, headed by Dr. Bill Lober, and the University of California, San Francisco. Known as the International Training and Education Center on HIV (I-TECH), this team worked with yet another group called the Clinical Informatics Research Group (CIRG) to improve the electronic medical record (EMR) systems of Haiti. Through their involvement with OpenMRS collaboration, the University of Washington's Clinical Informatics Research Group learned of OpenELIS and thought it ideal for implementing in clinical labs throughout Haiti, including the Haiti National Lab.[10]

By June 2008, work was beginning on a new branch of the OpenELIS software for Haiti, specifically as a branch of the version implemented in Vietnam,[11] though by November a conversion to the Minnesota/Iowa code base was completed "to take advantage of any updates" those development teams made.[12] The seeds for a similar effort were planted in Côte d'Ivoire the following month.[13] That same month a SourceForge beta project for OpenELIS was started.[14].

In 2009 and 2010 the University of Washington group continued improving its Haiti branch of the software, demoing it on the University servers as upgrades were being made. In March 2009 the team demonstrated the Minnesota/Iowa and Haiti versions of the OpenELIS software to Joshua Franklin of the University of Washington Biomedical Informatics Core of the Institute of Translational Health Sciences, evaluating it as a potentially useful LIS.[15] As pilot implementations of OpenELIS 1.1 were being installed in Haitian labs, work also continued on the software in Côte d'Ivoire. On October 19, 2010, version 1.0 of the Côte d'Ivoire branch (referred to as "Retro-CI" for the location of its installation, the CDC Retrovirus Cote d′Ivoire [CDC Retro-CI]) of OpenELIS was installed in the country.[16]

2011 brought many changes to OpenELIS. In February 2011 an improved version 1.2 was implemented in Haiti, with a planned expanded version of the software for the Laboratoire National de Santé Publique (LNSP) and other national public health reference laboratories in March.[17] On July 18, 2011, a new 2.0 version of Côte d'Ivoire's branch of OpenELIS was release, featuring a new menu system, better patient demographics handling, and additional bug fixes.[18]

Meanwhile years of work at the University of Iowa were culminating in a beta test of their OpenELIS software in the summer of 2011, eventually leading to a January 1, 2012 deployment of version 2.0 of the software at the University's State Hygienic Laboratory.[3][19][20] Version 1.6.0 of the Vietnam branch was released on February 20, 2012.[21]

Public open-source release and beyond

In 2012, the University of Washington I-TECH began hosting "OpenELIS Global" (now referred to as an Enterprise Laboratory Information System), an international version of the OpenELIS software. The first public open-source release of the software was with version 2.4 on February 29, 2012[1], followed by a 2.5 release on March 30.[22] The incrementation was chosen not as a numerical order of release, but rather as an identifying string as "Version.Pl​annedRelea​se.Unplann​edRelease (build number)," with versions incrementing yearly.[22]

Since then, the software has received regular updates. Following the May 2019 release of version 9.1, work had slowed slightly, apparently in favor of a planned rewrite of the code using Java Spring. In August 2019, I-TECH's Casey Iiams-Hauser (the OpenELIS Global project owner) put out a call for a software development team to tackle the transition to Java Spring and PostgreSQL, with a target date of September 15, 2019.[23] The first release of the new version occurred in January 2020; the release notes stated: "This is a re-write of OpenELIS on modern frameworks and a significant security upgrade. At the end of this process, all tech will be currently supported and up to hardening standards. This software will be certified for use on US Government, and other high-security networks."[24] More recent updates have added support for COVID-19 testing, the FHIR API, ASTM analyzer interfaces, data warehousing, and more.[24]

Features

Known features of OpenELIS Global include[1][22][24]:

  • sample entry
  • results entry
  • user management and administration
  • role-based security
  • reporting
  • data validation
  • workplans
  • patient reports
  • study reports
  • test catalogs
  • workflow management
  • barcoded labels
  • raw data export
  • audit trail logging
  • electronic signatures
  • instrument integration
  • email and SMS support
  • LOINC code compatibility
  • FHIR support
  • English or French language configuration
  • iSante interoperability

Hardware/software requirements

OpenELIS Global can be run in a virtual machine like VirtualBox or it can be built and installed from source code.

Virtual machine

System requirements for an OpenELIS Global virtual machine installation will be based on the requirements to run the virtual machine.

Source code

To build and install from source, you'll need:

  • Ubuntu 20.04 LTS
  • Net Tools
  • Python

More information can be found here.

Videos, screenshots, and other media

Videos

The following YouTube videos exist for OpenELIS Global:

Demos

An online demo of OpenELIS Global can be found on the OpenELIS website.

Documentation

Documentation for OpenELIS Global can be found here.

Entities using OpenELIS

The following entities are known to be utilizing or have used some form of OpenELIS:

CDC Retrovirus Côte d'Ivoire, Clinical Informatics Research Group, Institut Pasteur Côte d'Ivoire, Laboratoire National de Santé Publique - Côte d'Ivoire, Laboratoire National de Santé Publique - Haiti, Minnesota State Public Health Laboratory, State Hygienic Laboratory at the University of Iowa

Further reading

External links

References

  1. ↑ 1.0 1.1 1.2 "OpenELIS Global 2.4 Release Notes". University of Washington I-TECH. 29 February 2012. https://sites.google.com/site/openelisglobal/openelis-global-2-4-release-notes. Retrieved 27 April 2012. 
  2. ↑ "History - OpenELIS Global". University of Washington I-TECH. https://sites.google.com/site/openelisglobal/history. Retrieved 27 April 2012. 
  3. ↑ 3.0 3.1 3.2 "OpenELIS comes home". Lab Link (State Hygienic Laboratory at The University of Iowa) 4 (1). January 2012. http://www.shl.uiowa.edu/publications/lablink/201201/openelis.xml. 
  4. ↑ 4.0 4.1 4.2 Wood, James (February 2009). "Public Health Informatics Institute - Grant Results Reports". Robert Wood Johnson Foundation. http://www.rwjf.org/reports/grr/053531.htm. Retrieved 26 April 2012. 
  5. ↑ 5.0 5.1 5.2 Jones, Jay (2008). "OpenELIS: How a small lab community created a world-wide database" (PDF). PHINews (Centers for Disease Control and Prevention) 2 (4): 6–9. Archived from the original on 11 March 2010. https://web.archive.org/web/20100311000926/http://www.cdc.gov/phin/library/documents/pdf/PHINews%20Volume%202%20Issue%204.pdf. 
  6. ↑ "Requirements for Public Health Laboratory Information Management Systems" (PDF). Association of Public Health Laboratories. September 2003. https://www.aphl.org/aboutAPHL/publications/Documents/INFO-2003-PHL-Requirements-16-Business-Processes.pdf. Retrieved 28 March 2022. 
  7. ↑ 7.0 7.1 Rogers, Karen (Spring 2008). "Realizing the APHL Vision Around the Globe". Association of Public Health Laboratories. Archived from the original on 20 August 2008. https://web.archive.org/web/20080820113137/http://www.aphl.org/AboutAPHL/publications/Pages/Spring2008.aspx. Retrieved 28 March 2022. 
  8. ↑ 8.0 8.1 Blaya, Joaquin (27 April 2008). "Collaboration with OpenELIS, an open source lab information system". Partners In Health Informatics Team. http://pihemr.wordpress.com/2008/04/27/collaboration-with-openelis-an-open-source-lab-information-system/. Retrieved 26 April 2012. 
  9. ↑ Mamlin, Burke W.; Paul G. Biondich; Ben A. Wolfe; Hamish Fraser; Darius Jazayeri; Christian Allen; Justin Miranda; William M. Tierney (2006). "Cooking up an open source EMR for developing countries: OpenMRS - a recipe for successful collaboration". AMIA Annual Symposium Proceedings: 529–33. PMC 1839638. PMID 17238397. https://www.ncbi.nlm.nih.gov/pmc/articles/1839638. 
  10. ↑ "2008 May - OpenELIS Implementation in Haiti". Clinical Informatics Research Group at the University of Washington. May 2008. http://haitilis.wordpress.com/2008/05/. Retrieved 27 April 2012. 
  11. ↑ Schwartz, Paul (4 June 2008). "Version Genealogy". Clinical Informatics Research Group at the University of Washington. http://haitilis.wordpress.com/2008/06/04/version-genealogy/. Retrieved 27 April 2012. 
  12. ↑ Lober, Bill (8 December 2008). "Status Reports for last 4 weeks (from Paul)". Clinical Informatics Research Group at the University of Washington. http://haitilis.wordpress.com/2008/12/08/status-reports-for-last-xx-weeks-from-paul/. Retrieved 27 April 2012. 
  13. ↑ Lober, Bill (8 December 2008). "Off to Cote d’Ivoire". Clinical Informatics Research Group at the University of Washington. http://haitilis.wordpress.com/2008/12/08/off-to-cote-divoire/. Retrieved 27 April 2012. 
  14. ↑ "OpenELIS - Laboratory Information System". SourceForge. 2 December 2008. Archived from the original on 24 March 2012. https://web.archive.org/web/20120324153202/http://sourceforge.net/projects/openelis/. Retrieved 28 March 2022. 
  15. ↑ Schwartz, Paul (9 March 2009). "HaitiOpenElis status report for week ending 06/03/2009". Clinical Informatics Research Group at the University of Washington. http://haitilis.wordpress.com/2009/03/09/haitiopenelis-status-report-for-week-ending-06032009/. Retrieved 27 April 2012. 
  16. ↑ Nixon, Laura (19 October 2010). "Training and Installation at RetroCI". Clinical Informatics Research Group at the University of Washington. http://cdilis.wordpress.com/2010/10/19/training-and-installation-at-retroci/. Retrieved 27 April 2012. 
  17. ↑ "Health Informatics in Haiti: Improving Access to Data Improves Care". University of Washington I-TECH. March 2011. Archived from the original on 30 May 2015. https://web.archive.org/web/20150530140917/http://news.go2itech.org/2011/03/health-informatics-in-haiti-improving-access-to-data-improves-care/. Retrieved 28 March 2022. 
  18. ↑ Schwartz, Paul (9 March 2009). "HaitiOpenElis status report for week ending 06/03/2009". Clinical Informatics Research Group at the University of Washington. http://cdilis.wordpress.com/2011/07/19/retroci-release-2-0-july-18th/. Retrieved 27 April 2012. 
  19. ↑ "OpenELIS Version 2". State Hygienic Laboratory at the University of Iowa. 3 January 2012. Archived from the original on 27 June 2011. https://web.archive.org/web/20110627045508/http://openelis.shl.uiowa.edu/?q=node/1. Retrieved 28 March 2022. 
  20. ↑ "Your Test Results". State Hygienic Laboratory at the University of Iowa. 1 January 2012. Archived from the original on 20 March 2012. https://web.archive.org/web/20120320023138/http://www.shl.uiowa.edu/results/index.xml. Retrieved 28 March 2022. 
  21. ↑ "Update Release 1.6.0". Clinical Informatics Research Group at the University of Washington. 20 February 2012. http://vietnamlis.wordpress.com/2012/02/20/update-release-1-6-0/. Retrieved 27 March 2012. 
  22. ↑ 22.0 22.1 22.2 "OpenELIS Global 2.5 Release Notes". University of Washington I-TECH. 30 March 2012. https://sites.google.com/site/openelisglobal/openelis-global-2-5-release-notes. Retrieved 27 April 2012. 
  23. ↑ Liams-Hauser, C. (5 August 2019). "Come work on OpenELIS Global with I-TECH!". OpenMRS Talk. https://talk.openmrs.org/t/come-work-on-openelis-global-with-i-tech-we-are-looking-for-tech-writers-ui-ux-designers-and-devs-an/24221. Retrieved 28 March 2022. 
  24. ↑ 24.0 24.1 24.2 Liams-Hauser, C. (March 2022). "OpenELIS Software Release Roadmap". https://docs.google.com/document/d/1p0zMfoUXRBbr9JyjjMeWRt1dgi7EbOd3IZdP6NCulow/edit?pli=1#heading=h.71anhixmrzil. Retrieved 28 March 2022. 
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