Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic

Published online: 2021-04-21

Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic Shinji Kobayashi1, Luis Falcón2, Hamish Fraser3, Jørn Braa4, Pamod Amarakoon5, Alvin Marcelo6, Chris Paton7 1 National Institute of Public Health, Saitama, Japan 2 GNU Solidario, GNU Health, Las Palmas de Gran Canaria, Spain 3 Brown Center for Biomedical Informatics, Brown University, Providence, USA 4 University of Oslo, Oslo, Norway 5 University of Colombo, Colombo, Sri Lanka 6 Asia eHealth Information Network, Manilla, Philippines 7 Nuffield Department of Medicine, University of Oxford, Oxford, UK

spread of COVID-19 [5]. “Infodemics” is a Summary 1 Introduction term, which is defined as the rapid spread of Objectives: The emerging COVID-19 pandemic has caused The new coronavirus infection was first information of all kinds, including rumours, one of the world’s worst health disasters compounded by social reported in Wuhan, China in December gossip and unreliable information related confusion with misinformation, the so-called “Infodemic”. In this 2019 and outbreaks spread rapidly all over to epidemics [6]. From the early stage of paper, we discuss how open technology approaches - including the world. The SARS-CoV-2 virus, and COVID-19 pandemic, WHO’s director data sharing, visualization, and tooling - can address the COVID-19, the resulting disease, has caused general, Tedros Adhanom Ghebreyesus said COVID-19 pandemic and infodemic. one of the most rapidly developing health “We’re not just fighting a pandemic; we’re Methods: In response to the call for participation in the 2020 disasters in generations. The World Health fighting an infodemic” (2020 Munich secu- International Medical Informatics Association (IMIA) Yearbook Organization (WHO) declared it a “pandem- rity conference [7]). WHO and public health theme issue on Medical Informatics and the Pandemic, the IMIA ic” on March 11 [1]. As of January 23, 2021, organizations of each country are struggling Open Source Working Group surveyed recent works related to the WHO dashboard reported there had been to ensure that publishers provide accurate the use of Free/Libre/Open Source Software (FLOSS) for this 92,098,879 confirmed cases of COVID-19, information on their websites and media to pandemic. including 2,098,879 deaths in the globe [2]. avoid repeating and spreading such misinfor- Results: FLOSS health care projects including GNU Health, Open- As the disease became more prevalent, mation [8, 9]. In addition, the infodemic has MRS, DHIS2, and others, have responded from the early phase populations became increasingly concerned caused discrimination and prejudice against of this pandemic. Data related to COVID-19 have been published and social unrest has been reported includ- people of Asian origin and stigmatization of from health organizations all over the world. Civic Technology, ing protests against non-pharmaceutical those infected with COVID-19 and health and the collaborative work of FLOSS and open data groups were interventions such as “lockdowns”. Misin- workers [10, 11]. Open source software considered to support collective intelligence on approaches to formation related to COVID-19 propagated and open data initiatives can provide more managing the pandemic. through mass media reports and social accountability and transparency of data Conclusion: FLOSS and open data have been effectively used networks and risk causing panics or undue sources, helping to combat the secrecy of to contribute to managing the COVID-19 pandemic, and open complacency exacerbating the health con- algorithms and data sharing typical of many approaches to collaboration can improve trust in data. sequences of the disease [3]. In the United social media platforms. States, a comment from President Trump Our working group has been studying Keywords about injecting disinfectant misled people free/libre/open-source software (FLOSS) in COVID-19, Public Health, Open data, Free/Libre/Open source into drinking the disinfectant [4]. In Japan, the medical field and extended the scope to software face masks became scarce from February open data and open science [12, 13]. From 2020, and toilet paper disappeared due to the COVID-19 pandemic and infodemic, we Yearb Med Inform 2021:38-43 panic buying because of the mistaken belief have found that open-source and open data http://dx.doi.org/10.1055/s-0041-1726488 that they were made from the same paper as collaborations, termed “Civic Technology’’, masks. The International Telecommunica- worked efficiently against COVID-19, and tion Union has officially denied the rumors report this concept as a working group that the 5G network was associated with the paper here.

IMIA Yearbook of Medical Informatics 2021 39 Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic

ecosystem consists of different components, GNU Health provides an epidemiologi- 2 FLOSS Projects Responses such as Electronic Medical Record (EMR); cal surveillance report. Real-time epidemic to COVID-19 Hospital Management System (HMIS); curves and demographics to assist in studying Laboratory (LIMS); clinical genetics and an- the incidence and prevalence in many infec- As we have previously reported, FLOSS alytics/epidemiology engine, among others. tious as well as non-communicable diseases. projects are increasingly utilized in the med- The Personal Health Record (PHR) compo- The government can study the causes and the ical domain [14–16]. During the COVID-19 nent, MyGNUHealth, will be released in Q1 impact of these conditions on different groups pandemic, FLOSS groups have responded 2021. GNU Health has been implemented of society, ranging from the molecular to the from the early stages, building on large in countries around the globe from primary social determinants of health [23]. installed bases in many Low and Middle-In- care centers, research institutions, to large, In April 2020, GNU Solidario and the come Countries (LMICs) with experience national-level implementations. GNU Health project partnered with the from dealing with previous epidemics in- GNU Health has developed the “Contact European Commission “EUvsVirus hack- cluding Ebola. Well established examples Tracing” package that is being used in the aton” as civil society and public authority are described below (Table 1). context of COVID-19. It’s also useful in the partners, promoting, teaching and showing control of other infectious diseases, such as the benefits of Libre Software in the Public Ebola or tuberculosis. The government of Health domain, particularly in the context of 2.1 GNU Health Entre Ríos, Argentina is currently using the the COVID-19 pandemic [24]. GNU Health is a Libre digital health eco- contact tracing package to track COVID-19 system from the NGO GNU Solidario [17]. cases in the public health institutions of GNU Health is an international, communi- Diamante [21]. ty-driven project that provides the tools for The GNU Health Federation has been 2.2 OpenMRS individuals, health professionals, institutions chosen as the COVID-19 real-time obser- OpenMRS is an open source, standards-based and governments to proactively assess and vatory by the government of Argentina. and modular electronic health record (EHR) improve the underlying determinants of Argentina National Research and Develop- used clinically in at least 44 LMICs [19, health, from the socioeconomic agents to the ment Agency (Agencia de Promoción de la 25]. The main focus has been on the care molecular basis of disease [17]. It manages Investigación, el Desarrollo Tecnológico y of infectious diseases including human the internal processes of a health institution, la Innovación (Agencia I+D+i)) chose Dr. immunodeficiency virus (HIV) and tuber- such as financial management, stock & Sassetti’s project on GNU Health Federation culosis (TB), with versions also supporting pharmacies and patient management. The as an Epidemiological Observatory [22]. care delivery for primary care, maternal and child health, heart disease, cancer, and surgery. It has been used for management of acute epidemic diseases in the past including cholera in Haiti, and a custom version was Table 1 FLOSS response to COVID-19. created for use in an Ebola treatment center in Sierra Leone in 2015. This had a tablet Description COVID-19 response interface designed for use by staff with full personal protective equipment (PPE) [26]. GNU Health Hospital Management / Health Contact tracing package Several mHealth platforms have been information system [17,18] Epidemiological reporting adapted to support epidemic management Laboratory, test management including Ebola and COVID-19 such as Vaccination management CommCare [27], Medical Mobile [28] and OpenMRS Electronic health record [19] A new version for COVID-19 clinical Open Data Kit (ODK) [29], providing effec- management with HL7 tive support for screening and contact tracing Fast Healthcare Interoperability Resource in the community. To ensure a complete pic- (FHIR) resources ture of the disease impact and management Symptom screening form Vaccine management these systems need to work synergistically with EHRs in health facilities. The EHR can DHIS2 Health management Information Contact tracing capture clinical presentations of COVID-19 (District Health system [18] Daily, weekly reporting of COVID-19 patients in primary or urgent care, their Information Software) patients Vaccine Delivery Toolkit clinical treatment, progress and longer term follow up. OpenMRS has a strong focus on LIFE Open access emergency training New open access training scenarios on the open standards and interoperability using (Life-saving Instruction smartphone app [20] management of COVID-19 patients a concept dictionary mapped to ICD10, for Emergencies) SNOMED CT and LOINC [30]. A new

IMIA Yearbook of Medical Informatics 2021 40 Kobayashi et al.

module supports the latest versions of the COVID-19 management, and to improve the ing DHIS2 platform. The ICT Agency of the HL7-FHIR (Fast Healthcare Interoperability quality of data collection, coding and export Government announced the requirements on Resources) interoperability standard [31] from OpenMRS to facilitate rapid surveil- their social media networks and volunteer and has been adapted to link OpenMRS lance, prediction modelling and clinical developers, mainly from the private sector, instances to the OpenELIS laboratory infor- research. OpenMRS has several implemen- contributed their time and efforts for the wor- mation system in Haiti. tations that support vaccine management, thy cause of producing a product to monitor Early work has been carried out to adapt primarily for children, these offer platforms COVID status of the country. For the initial OpenMRS to support screening, testing and for rapid scale up of Sars-Cov-2 vaccines two days, over 20 of them volunteered and management of COVID-19, with initial de- administration including tracking patients the effort continued at full pace at least for ployments in Nepal, Haiti and Kenya. In Ne- for second doses and any adverse events. a period of two months during which several pal, Possible Health uses the Bahmni version apps on DHIS2 platform were developed in of OpenMRS. They have added a screening addition to a mobile application for citizens. note to help clinicians assess patients present- 2.3 Sri Lanka and DHIS2 Digital The web apps produced during the hackathon ing with COVID symptoms or assess expo- included contact mapping, visualization, sure risk. It was designed in consultation with COVID-19 Response and intensive care unit bed management official guidelines and physicians who already The COVID-19 digital response package modules. Integration components to ad- use NepalEHR [32]. In Haiti, at the University using the DHIS2 open source software plat- dress bottlenecks in implementation were Hospital of Mirebalais, Partners in Health form [18] was rapidly developed following also designed, such as integration with the and its sister organization in Haiti, Zanmi the pandemic outbreak, with components for immigration information system. With ex- Lasante, have added COVID-19 testing pro- registration of cases, contact tracing, report- panding requirements, several other modules tocols to the OpenMRS order entry system ing daily and weekly summaries and more. A were customized such as quarantine, case along with basic care forms and are deploying configuration package for DHIS2, which can management and laboratory modules. The clinical forms for managing patients admitted easily be downloaded and adapted to meet collaboration with the global community to the hospital. In Kenya, the ministry of individual country needs, was released early facilitated obtaining rapid support from health along with Kenyan and international March (dhis2.org/covid-19). More than 60 DHIS2 core development team for the efforts collaborating organizations have developed countries are using DHIS2 and the intention in the hackathon. Metadata and modules and deployed a version of the “KenyaEMR” was to leverage this existing infrastructure developed in Sri Lanka were shared with the OpenMRS system at national level to collect, and country capacity for rapid deployment. global DHIS2 community and were quickly manage and report COVID-19 case data. This Sri Lanka was the first country to de- adopted by many countries across the world. includes data from mobile health systems and ploy DHIS2 for COVID-19 response. The Thus, the agility of response to changing links to District Health Information Software Ministry of Health in Sri Lanka foresaw requirements supported by the open source 2 (DHIS2) for reporting. the threat of the pandemic from incoming platform with a global community, existing The OpenMRS community have worked tourists and decided to develop an integrated local capacity and multisector collaboration together to develop core tools to support digital surveillance system, which was de- resulted in a successful digital surveillance sys- management of COVID-19. These include: signed within five days based on the DHIS2 tem in a LMIC amidst an ongoing pandemic. • Release of new versions of the OpenMRS platform utilizing the country’s existing concept dictionary with concepts for capacity. There was collaboration with the screening, testing and clinical manage- HISP group supporting DHIS2 development 2.4 Life-saving Instruction for ment. These have been mapped to HL7 at University of Colombo as well as the FHIR profiles led by Dr Andy Kanter; government’s information, communication Emergencies (LIFE) • Creation of WHO COVID-19 screening and technology (ICT) agency in this process. The LIFE project is a collaboration between forms in OpenMRS, and development of The system, which was approved by the the University of Oxford and the KEM- the new FHIR module led by a team at higher administration from the ministry of RI-Wellcome Trust Research Programme in Brown University (Providence, USA); health, was rapidly implemented following Nairobi, Kenya [20]. The project has devel- • Collaborative work with VecnaCares inc brief training. With the change of the disease oped smartphone apps and immersive VR on improving interoperability of Open- landscape and spread, new requirements training experiences to teach healthcare work- MRS with the District Health Information emerged necessitating development of new ers in Africa how to manage medical emer- System – DHIS2 (see below) to allow modules to the existing system which were gencies. The smartphone apps are released as rapid reporting to district and national not achievable by customizing DHIS2. The open access with free downloads through app levels from OpenMRS. ministry decided to develop additional com- stores to the user’s own smartphone. LIFE VR ponents on the DHIS2 platform and launched is accessible for free through the ENGAGE Goals for the next year are to support in- a two-day hackathon to obtain contributions VR platform [33]. After downloading the app, teroperability with mHealth applications from voluntary software developers to design the user is presented with a series of medical using FHIR, to improve decision support for web apps which could be installed on exist- emergencies that they manage by navigating

IMIA Yearbook of Medical Informatics 2021 41 Using Open Source, Open Data, and Civic Technology to Address the COVID-19 Pandemic and Infodemic

through a realistic 3D environment, gathering are shared in the domestic and international data warehouse, the data are loaded into a together the correct pieces of medical equip- openEHR clinical knowledge repositories dashboard and into a data drop. The sources ment they will need, and then successfully and have been utilized for monitoring pa- range from a case line list, testing aggregates performing the key steps needed to save lives tients and developing digital guidelines for (from laboratories), and a bed tracker (for in emergencies. LIFE was recently evaluated COVID-19 patients [40]. hospitals and clinics). By making the data in a study in Kenya that showed significant open, the government encourages more learning gains between rounds of practice stakeholders to participate in the analysis and using the app [34]. thus promotes transparency and innovation. In response to the COVID-19 pandemic, However, there are limitations for making the LIFE team rapidly developed a series of 3 Open Data for COVID-19 health data open access [12]. Even though COVID-19 open access training scenarios “Open data ‘’ is a movement that promotes contact tracing is important in epidemio- that use an interactive 3D hospital with publication of data with open licenses so that logical investigations, personal identifiable virtual patients to teach clinicians how to they are available “for anyone to use, for any data should not be opened and should only manage patients suspected of being infected purpose, at no cost” [41]. As we described in be shared within public health professionals with the novel coronavirus. Users are taught a previous working group paper, open data on a restrictive basis. It is controversial that to don and doff PPE and ensure that patients is also beneficial for healthcare [12, 42], par- Singapore changed the data policy of contact are isolated and treated in accordance with ticularly in the area of public health [43, 44]. tracing for criminal investigations [54, 55]. WHO guidelines. After completing the train- Using a policy of open data has been shown WHO published an ethical guide for contact ing, users are given feedback on any errors to help curb the Ebola [45] and Zika viruses tracing apps that suggested prohibition of the they have made and are able to repeat the [46]. From the early phase of COVID-19, data use of personal data generated by the public training until they are proficient. was made open by the Chinese government health department [37]. based on the lessons of SARS [47]. The complete sequence of SARS-CoV-2 was shared in GenBank and available for research, clinical

2.5 Contact Tracing test, drug/vaccine development [48]. Compre- Digital contact tracing for COVID-19 pa- hensive lists of COVID-19 related data sets 4 Civic Technology Movement tients and citizens was suggested to be effec- are accessible online [49, 50]. “Civic technology (tech)” describes collab- tive to control the outbreak by the experience Johns Hopkins University developed an orations between governments and citizens in Singapore and through mathematical interactive website to visualize COVID-19 using open data and FLOSS [56]. modelling [35]. Both Apple and Google epidemics in China using ArcGIS and open In Japan, the Tokyo Metropolitan Gov- provide contact tracing API to their prod- data from the Chinese CDC [51]. They also ernment commissioned a non-government ucts, iOS, and Android. They limit access provided open data on the number of con- organization, Code for Japan (CfJ), to build to the representative agency of each country firmed COVID-19 cases and deaths. Using a website to display their open-data (https:// to protect the privacy of users. The ethics this data, a number of websites have been catalog.data.metro.tokyo.lg.jp/en/dataset/ and privacy issues around contact tracing constructed for data visualization, analysis t000010d0000000068) on COVID-19 on are still controversial due to stigmatism of and decision-making. The data was shared February 26. CfJ developed and launched the COVID-19 related patients and health work- in Google spreadsheets at first and is now website (https://stopcovid19.metro.tokyo. ers [36, 37] Japan and Germany have also published on GitHub. WHO also shares lg.jp/en) on March 3 after only five days. The developed contact tracing software using the COVID-19 open data on their website [2] (that source code was opened in a GitHub reposi- Google/Apple API as open-source software was itself developed as open-source software). tory that had gathered 12,798 commitments and made it available to the public to show The merits of open data is not only from 97 contributors as of October 6 2020 their transparency [38, 39]. Limitation for availability, but the transparency of data and (https://github.com/tokyo-metropolitan-gov/ the usage of data is also a problem that will decision making could contribute to mitigate covid19). The site was translated into eight be discussed in a later section of this article. “infodemic” [52, 53]. languages and the derived codes covered 30 The Department of Health of the Govern- of 47 prefectures in June, and 43 by October. ment of the Philippines releases COVID-19 We surveyed the relationship between 2.6 openEHR Clinical Models and data1 on a regular basis. The data are culled open data and open-source software for from three data sources once a day, uploaded, COVID-19 based on the Tokyo COVID-19 Digital Guidelines and transformed in the cloud where field site at the end of June. Zhejiang University has an openEHR based restriction and anonymization algorithms are Table 2 shows the ratio of existing open clinical repository of 1.5 million patients. applied. After the transformation in a cloud data and deployment of visualization site They overlayed a COVID-19 screening (COVID-19 Dashboard) for COVID-19. system on the repository by developing 1 https://drive.google.com/drive/folders/1ZPPc- Visualization sites for COVID-19 were de- openEHR templates [40]. The templates VU4M7T-dtRyUceb0pMAd8ickYf8o ployed more in the prefectures that publish

IMIA Yearbook of Medical Informatics 2021 42 Kobayashi et al.

open data for COVID-19 (odds ratio 2.27, Table 2 Association of COVID 19 dashboard deployment and open data Japanese prefectures. Fisher test: p=0.00058). This might suggest that open data by prefecture governments COVID-19 Dashboard deployment had promoted civic technology movements and better public access to critical health data Yes No Total in the pandemic. Open data 20 2 22 In Taiwan, the government restricted the purchase of face masks by citizens due to COVID-19 Not open data 10 15 25 related data the shortage of PPE. To avoid panic buying, the Taiwan government provided open data Total 10 17 47 on real-time mask availability with the lo- cation of pharmacies from February 2020. This helped to support the creation of 110 software projects to effectively visualize face mask distribution on the map until the ing-stigma.html References 12. Kobayashi S, Kane TB, Paton C. The privacy and mid-March, 2020 [57]. 1. WHO Director-General’s opening remarks at the security implications of open data in healthcare. media briefing on COVID-19 - 11 March 2020 Yearb Med Inform 2018 Apr 22;27(1):41–7. [Internet]. [cited 2020 Jul 9]. Available from: 13. Paton C, Kobayashi S. An open science approach https://www.who.int/dg/speeches/detail/who-di- to artificial intelligence in healthcare. Yearb Med rector-general-s-opening-remarks-at-the-media- Inform 2019 Aug;28(1):47–51. 5 Conclusions briefing-on-covid-19---11-march-2020 14. Karopka T, Schmuhl H, Marcelo A, Dal Molin J, 2. WHO Coronavirus Disease (COVID-19) Dash- Wright G. Towards Open Collaborative Health In this pandemic and infodemic, the commu- board | WHO Coronavirus Disease (COVID-19) Informatics - The Role of Free/Libre Open nities supporting FLOSS for medicine, GNU Dashboard [Internet]. [cited 2020 Oct 4]. Available Source Principles. Yearb Med Inform 2011 Health, OpenMRS, DHIS2, and LIFE, have from: https://covid19.who.int/ Aug;20(01):63–72. 15. Paton C, Karopka T. The role of free/libre and open

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IMIA Yearbook of Medical Informatics 2021