A reproducible picture of open access health facility data in Africa and R tools to support improvement

Background: Open data on the locations and services provided by health facilities have, in some countries, allowed the development of software tools contributing to COVID-19 response. The UN and WHO encourage countries to make health facility location data open, to encourage use and improvement. We provide a summary of open access health facility location data in Africa using re-useable R code. We aim to support data analysts developing software tools to address COVID-19 response in individual countries. In Africa there are currently three main sources of such open data; 1) direct from national ministries of health, 2) a database for sub-Saharan Africa collated and published by a team from KEMRI-Wellcome Trust Research Programme and now hosted by WHO, and 3) The Global Healthsites Mapping Project in collaboration with OpenStreetMap. Methods: We searched for and documented official national facility location data that were openly available. We developed re-useable open-source R code to summarise and visualise facility location data by country from the three sources. This re-useable code is used to provide a web user interface allowing data exploration through maps and plots of facility type. Results: Out of 52 African countries, seven currently provide an official open facility list that can be downloaded and analysed reproducibly. Considering all three sources, there are over 185,000 health facility locations available for Africa. However, there are differences and overlaps between sources and a lack of data on capacities and service provision. Conclusions: These summaries and software tools can be used to encourage greater use of existing health facility location data, incentivise further improvements in the provision of those data by national suppliers, and encourage collaboration within wider data communities. The tools are a part of the afrimapr project, actively developing R building blocks to facilitate the use of health data in Africa.

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A rapid and reproducible picture of open access health facility data in Africa to support the COVID-19 response

Wellcome Open Research ◽

10.12688/wellcomeopenres.16075.1 ◽

2020 ◽

Vol 5 ◽

pp. 157 ◽

Cited By ~ 1

Author(s):

Andy South ◽

Ahmadou Dicko ◽

Mark Herringer ◽

Peter M. Macharia ◽

Joseph Maina ◽

...

Keyword(s):

Open Access ◽

Facility Location ◽

Health Facility ◽

Open Data ◽

Research Programme ◽

Building Blocks ◽

Software Tools ◽

Sub Saharan Africa ◽

African Countries ◽

Location Data

Background: Open data on the locations and services provided by health facilities in some countries have allowed the development of software tools contributing to COVID-19 response. The UN and WHO encourage countries to make health facility location data open, to encourage use and improvement. We provide a summary of open access health facility location data in Africa using re-useable code. We aim to support data analysts developing software tools to address COVID-19 response in individual countries. In Africa there are currently three main sources of such data; 1) direct from national ministries of health, 2) a database for sub-Saharan Africa collated and published by a team from KEMRI-Wellcome Trust Research Programme and now hosted by WHO, and 3) The Global Healthsites Mapping Project in collaboration with OpenStreetMap. Methods: We searched for and documented official national facility location data that were openly available. We developed re-useable open-source R code to summarise and visualise facility location data by country from the three sources. This re-useable code is used to provide a web user interface allowing data exploration through maps and plots of facility type. Results: Out of 53 African countries, seven provide an official open facility list that can be downloaded and analysed reproducibly. Considering all three sources, there are over 185,000 health facility locations available for Africa. However, there are differences and overlaps between sources and a lack of data on capacities and service provision. Conclusions: We suggest that these summaries and tools will encourage greater use of existing health facility location data, incentivise further improvements in the provision of those data by national suppliers, and encourage collaboration within wider data communities. The tools are a part of the afrimapr project, actively developing R building blocks to facilitate the use of health data in Africa.

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Social, Behavioral, and Cultural factors of HIV in Malawi: Semi-Automated Systematic Review

Journal of Medical Internet Research ◽

10.2196/18747 ◽

2020 ◽

Vol 22 (8) ◽

pp. e18747

Author(s):

Amaury Thiabaud ◽

Isotta Triulzi ◽

Erol Orel ◽

Kali Tal ◽

Olivia Keiser

Keyword(s):

Systematic Review ◽

Open Access ◽

Hiv Infection ◽

A Priori ◽

Sub Saharan Africa ◽

Topic Modelling ◽

African Countries ◽

Comprehensive Overview ◽

Quantitative Analyses ◽

Sub Saharan

Background Demographic and sociobehavioral factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide in-depth insight into the local behavior and may help to improve HIV prevention. Objective To obtain a comprehensive overview of the sociobehavioral factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature using a newly programmed tool for automatizing part of the systematic review process. Methods Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorize open-access articles published from January 1, 1987 to October 1, 2019 in the PubMed, PubMed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest. Results Our tool extracted 22,709 unique articles; 16,942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics, of which 20 were kept after manual screening. We retrieved 7 more publications after examining the references so that 27 publications were finally included in the review. Reducing the 16,942 articles to 519 potentially relevant articles using the software took 5 days. Several factors contributing to the risk of HIV infection were identified, including religion, gender and relationship dynamics, beliefs, and sociobehavioral attitudes. Conclusions Our software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed dataset” of relevance that could be further developed. It identified known factors and factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

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Social, Behavioral, and Cultural factors of HIV in Malawi: Semi-Automated Systematic Review (Preprint)

10.2196/preprints.18747 ◽

2020 ◽

Author(s):

Amaury Thiabaud ◽

Isotta Triulzi ◽

Erol Orel ◽

Kali Tal ◽

Olivia Keiser

Keyword(s):

Systematic Review ◽

Open Access ◽

Hiv Infection ◽

A Priori ◽

Sub Saharan Africa ◽

Topic Modelling ◽

African Countries ◽

Comprehensive Overview ◽

Quantitative Analyses ◽

Sub Saharan

BACKGROUND Demographic and sociobehavioral factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide in-depth insight into the local behavior and may help to improve HIV prevention. OBJECTIVE To obtain a comprehensive overview of the sociobehavioral factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature using a newly programmed tool for automatizing part of the systematic review process. METHODS Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorize open-access articles published from January 1, 1987 to October 1, 2019 in the PubMed, PubMed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest. RESULTS Our tool extracted 22,709 unique articles; 16,942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics, of which 20 were kept after manual screening. We retrieved 7 more publications after examining the references so that 27 publications were finally included in the review. Reducing the 16,942 articles to 519 potentially relevant articles using the software took 5 days. Several factors contributing to the risk of HIV infection were identified, including religion, gender and relationship dynamics, beliefs, and sociobehavioral attitudes. CONCLUSIONS Our software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed dataset” of relevance that could be further developed. It identified known factors and factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

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Lessons Learnt from Engineering Science Projects Participating in the Horizon 2020 Open Research Data Pilot

Data ◽

10.3390/data6090096 ◽

2021 ◽

Vol 6 (9) ◽

pp. 96

Author(s):

Timothy Austin ◽

Kyriaki Bei ◽

Theodoros Efthymiadis ◽

Elias P. Koumoulos

Keyword(s):

Open Access ◽

Best Practices ◽

Data Management ◽

Open Data ◽

Research Programme ◽

Research Data ◽

Good Effect ◽

Process Data ◽

Horizon 2020 ◽

Open Research

Trends in the sciences are indicative of data management becoming established as a feature of the mainstream research process. In this context, the European Commission introduced an Open Research Data pilot at the start of the Horizon 2020 research programme. This initiative followed the success of the Open Access pilot implemented in the prior (FP7) research programme, which thereafter became an integral component of Horizon 2020. While the Open Access phenomenon can reasonably be argued to be one of many instances of web technologies disrupting established business models (namely publication practices and workflows established over several centuries in the case of Open Access), initiatives designed to promote research data management have no established foundation on which to build. For Open Data to become a reality and, more importantly, to contribute to the scientific process, data management best practices and workflows are required. Furthermore, with the scientific community having operated to good effect in the absence of data management, there is a need to demonstrate the merits of data management. This circumstance is complicated by the lack of the necessary ICT infrastructures, especially interoperability standards, required to facilitate the seamless transfer, aggregation and analysis of research data. Any activity aiming to promote Open Data thus needs to overcome a number of cultural and technological challenges. It is in this context that this paper examines the data management activities and outcomes of a number of projects participating in the Horizon 2020 Open Research Data pilot. The result has been to identify a number of commonly encountered benefits and issues; to assess the utilisation of data management plans; and through the close examination of specific cases, to gain insights into obstacles to data management and potential solutions. Although primarily anecdotal and difficult to quantify, the experiences reported in this paper tend to favour developing data management best practices rather than doggedly pursue the Open Data mantra. While Open Data may prove valuable in certain circumstances, there is good reason to claim that managed access to scientific data of high inherent intellectual and financial value will prove more effective in driving knowledge discovery and innovation.

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Social, behavioural, and cultural factors of HIV in Malawi: a semi-automated systematic review

10.1101/2020.03.12.20034702 ◽

2020 ◽

Author(s):

Amaury Thiabaud ◽

Isotta Triulzi ◽

Erol Orel ◽

Kali Tal ◽

Olivia Keiser

Keyword(s):

Open Access ◽

Hiv Infection ◽

A Priori ◽

Sub Saharan Africa ◽

Topic Modelling ◽

African Countries ◽

Comprehensive Overview ◽

Data Set ◽

Sub Saharan ◽

Behavioural Factors

AbstractBackgroundDemographic and socio-behavioural factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide an in-depth insight into the local behaviour, and may help to improve HIV prevention.MethodsTo obtain a comprehensive overview of the socio-behavioural factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature. Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorise open-access articles published from January 1st, 1987 until October 1st, 2019 in Pubmed, Pubmed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest.ResultsOur tool extracted 22’709 unique articles; 16’942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics; 20 of which were kept after hand-screening. We retrieved 7 more publications after examining references so that 27 publications were finally included in the review. Reducing the 16’942 articles to 519 potentially relevant ones by using the software took 5 days. Several factors were identified to contribute to the risk of HIV infection, including religion, gender and relationship dynamics, beliefs, and socio-behavioural attitudes.ConclusionsOur software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed data-set” of relevance which could be further developed. It identified known factors and rare factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

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Crude childhood vaccination coverage in West Africa: Trends and predictors of completeness

Wellcome Open Research ◽

10.12688/wellcomeopenres.10690.1 ◽

2017 ◽

Vol 2 ◽

pp. 12 ◽

Cited By ~ 14

Author(s):

Jacob S. Kazungu ◽

Ifedayo M.O. Adetifa

Keyword(s):

West Africa ◽

Health Facility ◽

Vaccination Coverage ◽

Maternal Education ◽

Sub Saharan Africa ◽

Childhood Vaccination ◽

Demographic And Health Surveys ◽

African Countries ◽

High Coverage ◽

Country Specific

Background: Africa has the lowest childhood vaccination coverage worldwide. If the full benefits of childhood vaccination programmes are to be enjoyed in sub-Saharan Africa, all countries need to improve on vaccine delivery to achieve and sustain high coverage. In this paper, we review trends in vaccination coverage, dropouts between vaccine doses and explored the country-specific predictors of complete vaccination in West Africa. Methods: We utilized datasets from the Demographic and Health Surveys Program, available for Benin, Burkina Faso, The Gambia, Ghana, Guinea, Cote d’Ivoire, Liberia, Mali, Niger, Nigeria, Senegal, Sierra Leone and Togo, to obtain coverage for Bacillus Calmette-Guerin, polio, measles, and diphtheria, pertussis and tetanus (DPT) vaccines in children aged 12 – 23 months. We also calculated the DPT1-to-DPT3 and DPT1-to-measles dropouts, and proportions of the fully immunised child (FIC). Factors predictive of FIC were explored using Chi-squared tests and multivariable logistic regression. Results: Overall, there was a trend of increasing vaccination coverage. The proportion of FIC varied significantly by country (range 24.1-81.4%, mean 49%). DPT1-to-DPT3 dropout was high (range 5.1% -33.9%, mean 16.3%). Similarly, DPT1-measles dropout exceeded 10% in all but four countries. Although no single risk factor was consistently associated with FIC across these countries, maternal education, delivery in a health facility, possessing a vaccine card and a recent post delivery visit to a health facility were the key predictors of complete vaccination. Conclusions: The low numbers of fully immunised children and high dropout between vaccine doses highlights weaknesses and the need to strengthen the healthcare and routine immunization delivery systems in this region. Country-specific correlates of complete vaccination should be explored further to identify interventions required to increase vaccination coverage. Despite the promise of an increasing trend in vaccination coverage in West African countries, more effort is required to attain and maintain global vaccination coverage targets.

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Framework for Monitoring of Road Agency Performance in Rural Road Asset Management

Transportation Research Record Journal of the Transportation Research Board ◽

10.1177/0361198119854088 ◽

2019 ◽

Vol 2673 (12) ◽

pp. 843-854

Author(s):

Charles Bopoto ◽

Robert Geddes ◽

Michael Pinard

Keyword(s):

Rural Communities ◽

Asset Management ◽

Technical Assistance ◽

Building Blocks ◽

Sub Saharan Africa ◽

African Countries ◽

Rural Road ◽

Sub Saharan ◽

Asset Preservation ◽

The Impact

The Research for Community Access Partnership (ReCAP) is providing technical assistance and capacity building initiatives to foster sustainable improvements in asset management performance in selected rural road agencies in Sub-Saharan Africa. Central to the research methodology is the development of a specification to enable road agencies to assess their performance in asset management as a basis for self-improvement. The specification is based on the development of an objectively determinable “road sector sustainability index” which measures the extent to which six building blocks considered essential for achieving effective road asset preservation are satisfied in practice. Periodic measurements of the condition of the project road networks, coupled with the collection of socioeconomic data, are being used to monitor the trend in road asset value, and to assess the effectiveness of, and improvements in, asset management as well as the impact of road condition on the wellbeing of rural communities. This paper outlines methodologies and tools that have been developed and piloted in four Sub-Saharan African countries to assess and monitor performance in rural road asset management and to achieve improvements over time. It summarizes progress achieved in the first 3 years since the project’s inception. The initial findings of the research indicate that severe institutional, funding, and technical shortcomings exist in the participating countries that preclude sustainable road asset preservation. However, following implementation of the methods summarized here, there is now an increased awareness of the importance of adopting a holistic approach to road asset management using simple and sustainable methods.

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GigaByte: Publishing at the Speed of Research

10.31229/osf.io/hj7wx ◽

2020 ◽

Author(s):

Scott C Edmunds ◽

Laurie Goodman

Keyword(s):

Open Access ◽

Data Sharing ◽

Review Process ◽

Open Data ◽

Software Tools ◽

Cutting Edge ◽

Data Sets ◽

Scientific Publishing ◽

Publication Process ◽

Publishing Infrastructure

Current practices in scientific publishing are unsuitable for rapidly changing fields and for presenting updatable data sets and software tools. In this regard, and as part of the need to push scientific publishing to match the needs of modern research, we would like to announce the upcoming launch of GigaByte, an online open-access, open data journal that aims to be a new way to publish research following the software paradigm: CODE, RELEASE, FORK, UPDATE and REPEAT. Following on the success of GigaScience in promoting data sharing and reproducibility of research, its new sister, GigaByte, will aim to take this even further. With a focus on short articles, using a questionnaire-style review process, and combining that with the custom built publishing infrastructure from River Valley Technologies, we now have a cutting edge, XML-first publishing platform designed specifically to make the entire publication process easier, quicker, more interactive, and better suited to the speed needed to communicate modern research.

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Institutional Repositories in Swaziland: An Exploratory Study

Mousaion ◽

10.25159/2663-659x/4586 ◽

2019 ◽

Vol 36 (2) ◽

Author(s):

Ncamsile Nombulelo Dlamini ◽

Maritha Snyman

Keyword(s):

Open Access ◽

Exploratory Study ◽

Management Strategies ◽

Current Status ◽

Academic Institutions ◽

African Countries ◽

Institutional Repositories ◽

Limited Knowledge ◽

Advocacy Strategies ◽

Awareness Level

The purpose of this paper is to assess the current status of institutional repositories (IRs) in Swaziland’s academic institutions. The factors under discussion are the number of IRs in Swaziland, their usage, the level of awareness of these IRs, and the challenges that prevent the implementation of IRs in Swaziland’s academic institutions. A webometric approach, interviews and semi-structured questionnaires completed by IR managers or librarians working for the Swaziland’s academic institutions were used to collect data for this study. Responses were received from 11 respondents. The findings indicated that there is one IR in Swaziland that is accessible to the institution’s community via the intranet. This IR was, at the time when this study took place, not registered in any of the international registries of repositories, such as the Registry of Open Access Repositories (ROAR) and the Directory of Open Access Repositories (OpenDOAR). Currently, this IR faces problems of insufficient content, a low level of IR awareness, limited knowledge of effective and appropriate IR advocacy strategies and limited knowledge of effective IR implementation and management strategies. Based on the findings and information gained from a literature review of IRs, the paper recommends strategies to academic institutions in Swaziland that may enable them to increase their number of IRs, the awareness level of IRs and consequently the use of IRs. The findings and recommendations may also benefit other African countries in similar situations.

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Crowdsourcing Covid-19 signals in sub-Saharan Africa: Leveraging digital contributor networks for participatory surveillance of Covid-19 symptoms and deaths (Preprint)

10.2196/preprints.26347 ◽

2020 ◽

Author(s):

Ngozi A Erondu ◽

Sagal A Ali ◽

Mohamed Ali ◽

Schadrac C Agbla

Keyword(s):

Public Health ◽

Sub Saharan Africa ◽

Specific Information ◽

Surveillance Systems ◽

Health Seeking ◽

African Countries ◽

Cross Sectional Survey ◽

Local Networks ◽

The World ◽

Sub Saharan

BACKGROUND In sub-Saharan Africa, underreporting of cases and deaths has been attributed to various factors including, weak disease surveillance, low health-seeking behaviour of flu like symptoms, and stigma of Covid-19. There is evidence that SARS-CoV-2 spread mimics transmission patterns of other countries across the world. Since the Covid-19 pandemic has changed the way research can be conducted and in light of restrictions on travel and risks to in-person data collection, innovative approaches to collecting data must be considered. Nearly 50% of Africa’s population is a unique mobile subscriber and it is one of the fastest growing smart-phone marketplaces in the world; hence, mobile phone platforms should be considered to monitor Covid-19 trends in the community. OBJECTIVE We demonstrate the use of digital contributor platforms to survey individuals about cases of flu-like symptoms and instances of unexplained deaths in Ethiopia, Kenya, Nigeria, Somalia, and Zimbabwe. METHODS Rapid cross-sectional survey of individuals with severe flu and pneumonia symptoms and unexplained deaths in Ethiopia, Kenya, Nigeria, Somalia and Zimbabwe RESULTS Using a non-health specific information platform, we found COVID-19 signals in five African countries, specifically: •Across countries, nearly half of the respondents (n=739) knew someone who had severe flu or pneumonia symptoms in recent months. •One in three respondents from Somalia and one in five from Zimbabwe respondents said they knew more than five people recently displaying flu and/or pneumonia symptoms. •In Somalia there were signals that a large number of people might be dying outside of health facilities, specifically in their homes or in IDP or refugee camps. CONCLUSIONS Existing digital contributor platforms with local networks are a non-traditional data source that can provide information from the community to supplement traditional government surveillance systems and academic surveys. We demonstrate that using these distributor networks to for community surveys can provide periodic information on rumours but could also be used to capture local sentiment to inform public health decision-making; for example, these insights could be useful to inform strategies to increase confidence in Covid19 vaccine. As Covid-19 continues to spread somewhat silently across sub-Saharan Africa, regional and national public health entities should consider expanding event-based surveillance sources to include these systems.

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