Epidemiology, News, Press, Product

Less Prep, More Insights: GIDEON R for Epidemiology-Related Research

Author Chandana Balasubramanian, 03-08-2021

Table of contents

We are excited to introduce the GIDEON R Package, released this month as a beta test for our researchers worldwide. GIDEON R is an efficient plug-and-play statistical tool for all researchers to clean, analyze, and visualize their epidemiological data from the GIDEON database. There is no need to program your own REST API queries. 

In the past 3 years, ~200 research papers used GIDEON data

EXCLUSIVE SNEAK PEEK FOR EXISTING GIDEON CUSTOMERS

  • All existing GIDEON customers get early access to experience and test the GIDEON R Beta package. Click here to download the package.
  • Let us know what you think! Email us at kristina@gideononline.com and tell us what you liked and what could be improved.
  • Your comments help us refine and launch the best version of GIDEON R for your research needs.
GIDEON R package in use

Image: GIDEON R package in use

 

Over 189 scientific studies that leveraged GIDEON’s (Global Infectious Diseases and Epidemiology Network) database were published in just the past three years. This number is rapidly growing as many researchers turn to the extensive infectious disease database for epidemiological insights and cross-discipline studies. 

The GIDEON database is a valuable web-based reference of infectious diseases and their global occurrences since the 1900s. As of 2020, researchers also get to customize and build their statistical tools to analyze data using the GIDEON API or Application Programming Interface (API). 

While GIDEON’s massive global database of infectious diseases and the GIDEON API are potent tools, GIDEON R allows you to boost your analytics to the next level. 

Why use GIDEON R?

R, the free, open-source programming language, has transformed how researchers prep, clean, and wrangle large databases to get good information. With minimal coding required, researchers can clean and set up their data faster and conduct reproducible steps during data analysis. 

R is quickly gaining in popularity with researchers. R programming is a part of the standard data analytics curriculum in universities like Harvard and the Imperial College in London. It is fast becoming a mainstay in Public Health and epidemiological research studies and reports. In the UK, the O Health foundation, an independent charity, developed an NHS-R community to help leverage the power of R for the NHS (National Health System). Teams of experts trained NHS analysts to use and embed R into the NHS to help improve the delivery of care.  

Using the GIDEON R package brings you more efficiency to:

  • Investigate 25,000+ ongoing and historical infectious disease outbreaks,
  • Produce granular outbreak maps for chosen diseases in a given year range
  • Study the emergence of zoonotic diseases in a particular country,   
  • Evaluate epidemiological situations around the globe, 
  • Retrieve a wealth of information on 360+ infectious diseases, 2,000+ pathogens, and 30,000+ trade names of drugs and vaccines.

The GIDEON R package brings all the convenience and efficiency of the free, open-source programming language R to the world of epidemiological research. 

Benefits of using GIDEON R include…

  • Simplicity: 

There is no need to learn how to work with a REST API client to parse the GIDEON database. With GIDEON R, you can hit the ground running and start crunching your data. 

Working with a GIDEON REST API offers you greater and complete control over how your program manipulates data. However, it requires users to possess programming skills and may also mean an investment in rigorous manual and automatic testing to ensure it functions well under pressure. Your team will need to spend considerable time testing, sequencing API calls correctly, validating parameters, and fixing any other issues before beginning the analysis. GIDEON R gives researchers familiar with R the ability to skip this part of the process and get straight to the analytics.  

  • Reproducibility: 

GIDEON R allows you to create scripts for your entire data analysis process and run a simulation. This way, even if you make a mild edit to the data, the whole process can be run again with the reassurance of reproducibility. As a researcher, you can then focus on developing and analyzing different runs without worrying about the analytical method changing. 

  • Flexibility

Epidemiological research is complex and challenging. No two studies will ever be precisely the same. R offers a considerable toolkit of statistical modeling tools that epidemiologists require, including logistic and Poisson regression and Cox proportional hazard models. 

  • Better Visualization

With R, data comes to life. Using R for data visualization is like the famous scene in the classic movie ‘The Wizard of Oz’ when Dorothy steps out of her dull black and white house and into the dazzling technicolor land of Oz. 

R can create any type of graph or charts – fast ones for analysis and even publication-ready charts with minimum code. R offers in-built functions and libraries to generate basic maps like bar charts, histograms, and scatter plots. It can also create advanced visualization tools like heat and mosaic maps, 3D graphs, or correlograms in vivid technicolor for your exploratory data analysis, presentations, and publications.

  • Compatibility

R runs on everything. R’s code is platform-independent – which means it does not matter if you use Windows, Mac, or any other system. So, with GIDEON R, you can be sure that your program is compatible with any type of platform you or your team use. This is a significant benefit when working with teams located in different regions and across the globe. 

GIDEON R optimizes how researchers use the GIDEON API to mine the GIDEON infectious disease database for epidemiological research. 

 

Want to be one of the first to try the new GIDEON R package?

  • If you are an existing GIDEON customer, click here to sign up for our beta test. Please give us your feedback at kristina@gideononline.com.
  • If you are not an existing GIDEON customer but would like to be, sign up for a free demo to get started.

 

GIDEON API

The GIDEON API allows medical professionals and researchers pressed for time and resources access to global data on hundreds of diseases, drugs, and bacteria – since 1348 AD. 

With the GIDEON API, you get a direct feed of infectious disease data from around the world at your fingertips. The GIDEON API is based on RESTful principles, and data is refreshed and updated every day, sometimes even multiple times a day. 

The best part? All institutional subscribers to GIDEON get access to the GIDEON API free of charge. 

 

Published articles that used GIDEON

Epidemic infectious disease outbreak with person analyzing virus strain and worldwide situation. SARS-CoV-2 pathogen causing coronavirus covid-19 pandemic disrupting social and economic life

According to Professor Rodolphe Desbordes, Professor of Economics at SKEMA Business School, France, and widely published in International Economics and Economic Development: 

GIDEON was the perfect database for the epidemiological project I had in mind <…> the information provided on each disease was crucial to a better understanding of disease-specific characteristics.

 

GIDEON has a rich history of partnering with researchers and scientists worldwide by offering a wide variety of resources on infectious diseases. You can find data going back to 1348 AD, track outbreaks on an interactive map, identify over 2000+ pathogens, diagnose and compare any number of infectious diseases, drugs, and microbes. 

The GIDEON database contains 23,600 country-specific notes with 3+ million words of text that outline the status of specific infections within each country. Also featured are over 250,000 linked references, 3,000 images, 34,000 graphs, and numerous interactive maps. 

There are more than 189 studies published in just the past three years that use GIDEON’s database to generate meaningful insights. Here are a few of the recent articles published that used GIDEON for their research: 

  • June 2021, Dengue: Alisa Aliaga-Samanez et al. from Spain published the first high-resolution analysis of biogeographic changes in dengue transmission risk. The study informs about the Dengue virus (DENV) making a home in previously low-risk areas and urges the global public health community to implement preventive measures [1]. 

 

  • June 2021, Foodborne Parasitic Diseases: F. Chavez-Ruvalcaba et al. published their review of foodborne parasitic diseases in the neotropics. Since more than one-fifth of the world’s population is infected by one or more intestinal parasites, the authors review the most common ones affecting countries in Central and South America [2]. 

 

  • June 2021, Lyme Borreliosis in Poland: Brzozowska et al. published their study about the tick-borne Lyme Borreliosis in Poland. They found the incidence to be equally significant in urban and rural communities and stressed the importance of widespread awareness and education. The study used GIDEON-generated data to compare Lyme Borreliosis prevalence across the globe [3].  

 

  • May 2021, Control of Intestinal Nematodes in African Green Monkeys (AGMs): A veterinary study by Katalina Cruz et al. tackled the efficacy of antiparasitic treatment and husbandry methods to control nematode infections in AGMs. The authors referred to insights from the GIDEON database to highlight that because AGMs regularly come in contact with humans on the island, they may play a role in the zoonotic parasitic infections commonly found on St. Kitts [4]. 

 

  • May 2021, Emerging Antibiotic-Resistant Pathogens in Iran: As part of their study, Rahder et al. analyzed the reported prevalence of actinomycetes infections worldwide using published global prevalence data sourced from the GIDEON database. They identify infections in Iran affecting immunocompromised and other vulnerable patients and recommend continuous monitoring to better prevent infection and improve therapeutic methods to treat the infections [5]. 

 

  • March 2021, Brucellosis: Battikh et al. from Tunisia used the GIDEON database to analyze the rise in Brucellosis cases in their hospital. They found that osteoarticular involvement was the most common complication of brucellosis in their patient pool. The researchers recommended better animal control practices through vaccinations, occupational and personal hygiene, farm sanitation, and more to lower the number of cases [6]. 

 

  • March 2021, Global Empirical Assessment of Spatial Dynamics of Major Disease Outbreaks: Professor Rodolphe Desbordes presented the spatio-temporal dependence and mortality consequences of the top 15 disease outbreaks in developed or developing countries over ten years. In the article, he states that his team mainly relied on the “under-exploited GIDEON database that provides a worldwide coverage of all infectious diseases [7].”

    In an interview, Professor Desbordes talked about why having access to data added to his study. He mentioned, “As an applied economist, I value excellent data on a novel and interesting issue more than anything else. The GIDEON database allowed me to publish in an excellent journal and, most importantly, carefully model the spatial diffusion of infectious diseases in a globalized world.”

 

  • March 2021, Ecological Conditions That Increase Vector-Borne and Zoonotic Diseases Outbreaks: Morand and Lajaunie published their findings on how global forest cover changes and oil palm expansions are associated with increased outbreaks of vector-borne and zoonotic disease outbreaks from 1990 – 2016. The authors state, “Here, we examine the global trends between changes in forest cover in recent decades and epidemics of human infectious diseases, using the GIDEON global database, which is the best available dataset on infectious diseases that has already been used in several studies [8].”

 

Want to be an early user and test GIDEON R?

  • All existing GIDEON customers get free access to experience and test the GIDEON R Beta package. Click here to start.
  • Let us know what you think! Email us at kristina@gideononline.com with what you liked and what could be improved.
  • Not an existing GIDEON customer? Don’t worry. We’ve got you covered. Sign up here for a free demo to get started.

Conclusion

GIDEON is one of the most well-known and comprehensive global databases for infectious diseases. Data is refreshed daily, and the GIDEON API allows medical professionals and researchers access to a continuous stream of data. 

The GIDEON R package allows researchers to retrieve, clean, analyze, and visualize infectious disease data in real-time from the GIDEON database without the need to get familiar with API clients and learn to program your own API queries. This improves the efficiency and reproducibility of research methods and results and lowers the time and costs required to learn how to work with REST APIs.

 

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References

[1]  A. A.-S. e. al., “Worldwide dynamic biogeography of zoonotic and anthroponotic dengue,” PLoS Negl. Trop. Dis., vol. 15, no. 6, p. e0009496, 2021. 
[2]  F. Chávez-Ruvalcaba, M. I. Chávez-Ruvalcaba, M. K. Santibañez, J. L. Muñoz-Carrillo, C. A. León and R. R. Martínez, “Foodborne Parasitic Diseases in the Neotropics – a review,” Helminthologia, vol. 58, no. 2, pp. 119-133, 2021. 
[3]  M. Brzozowska, A. Wierzba, A. Śliwczyński, M. Myśliwiec, K. Kozłowski and W. Wierzba, “The problem of Lyme borreliosis infections in urban and rural residents in Poland, based on National Health Fund data,” Annals of Agricultural and Environmental Medicine, vol. 28, no. 2, p. 277–282, 2021. 
[4]  K. Cruz, T. M. Corey, M. Vandenplas, M. Trelis, A. Osuna and P. J. Kelly, “Case report: Control of intestinal nematodes in captiveChlorocebus sabaeus,” Onderstepoort Journal of Veterinary Research, vol. 88, no. 1, pp. 2219-0635, 2021. 
[5]  H. A. Rahdar, S. Mahmoudi, A. Bahador, F. Ghiasvand, H. Sadeghpour and M. M. Feizabadi, “Molecular identification and antibiotic resistance pattern of actinomycetes isolates among immunocompromised patients in Iran, emerging of new infections,” Scientific Reports, vol. 11, 2021. 
[6]  H. Battikh, A. Berriche, R. Zayoud, L. Ammari, R. Abdelmalek, B. Kilani, H. Tiouiri Ben Aissa and M. Zribi, “Clinical and laboratory features of brucellosis in a university hospital in Tunisia,” Infectious Diseases Now, 2021. 
[7]  R. Desbordes, “Spatial dynamics of major infectious diseases outbreaks: A global empirical assessment,” Journal of Mathematical Economics, vol. 93, 2021. 
[8]  S. Morand and C. Lajaunie, “Outbreaks of Vector-Borne and Zoonotic Diseases Are Associated With Changes in Forest Cover and Oil Palm Expansion at Global Scale,” Front. Vet. Sci., vol. 8, p. 230, 2021. 
[9]  R. e. al., “Data proliferation, reconciliation, and synthesis in viral ecology,” bioRxiv, 2021. 
Author
Chandana Balasubramanian

Chandana Balasubramanian is an experienced healthcare executive who writes on the intersection of healthcare and technology. She is the President of Global Insight Advisory Network, and has a Masters degree in Biomedical Engineering from the University of Wisconsin-Madison, USA.

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