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

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 200 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 200 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. 

Dr. Oli prepares medical students for real-life situations

Multi ethnic group of medical students in uniform looking on the x-ray sitting at the desk in the modern classroom
Dr. Oli has created the “GIDEON diagnostic game” where students take on different roles to diagnose a disease

 

Due to the COVID-19 pandemic, universities all over the world had to accelerate their digital teaching programs. This has created a greater need for online tools that support the challenges of preparing students for life after graduation. This is especially true when teaching medical students – it is critically important future health professionals are taught practical and critical thinking techniques that are based on real-life situations.

Dr. Monika Oli has been speaking with Times Higher Education about the challenges of teaching microbiology online and how GIDEON can bring value to the virtual classroom. Dr. Oli explains that traditional teaching techniques may focus on identifying a few pathogens found in most laboratories, which can create “a completely artificial scenario which would never happen in the real world”.

How can a future medical doctor learn to differentiate between diseases with similar symptoms, such as Rocky Mountain Spotted Fever and Lyme disease? In a real-world scenario, you can’t “just open page 510 of the textbook and diagnose the patient…You have to think outside the box” and this is where Dr. Oli brings GIDEON in.

Dr. Oli has created the “GIDEON diagnostic game” where students take on different roles – epidemiologist, doctor, microbiologists, etc. – and use GIDEON’s Bayesian analysis-driven diagnostic tools to help create the list of likely diseases. This is followed by exploring the database to determine the best treatment plan and even speculating whether the patient would have survived or not in a given scenario!

The game proved to be very popular with students. But Dr. Oli didn’t stop there, she further encouraged future medics to analyze issues relevant today by building an exam around secondary infections of COVID-19.

“Many COVID-19 patients get secondary infections that are bacterial, so I built my whole exam around it. Students were given data and had to use GIDEON to analyze the secondary infection, how it should be treated, whether it will contribute to COVID-19 resistance, so the role play continued even during the exams.”

If you are a teacher looking for new ways to engage and challenge your students, GIDEON might be the right tool for the job. Try it free!

Read the original Times Higher Education article here

 

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Bayes in Medicine

Calculator and sthetoscope on blue background

What is Bayesian Analysis and where did it come from?

Sometimes referred to as Bayesian Inference in Mathematics, Bayes’ is a method of statistical inference centered around population information, variables, and evidence to determine the probability of a particular event occurring. In essence, it is the mathematical calculation of how likely something is to happen based on the evidence. 

The creator of the method was Thomas Bayes –  an 18th century English statistician and Presbyterian minister. Although he did not publish his mathematical theories during his life, the publication of his work was post-humously carried out by another famous non-conformist, Richard Price. 

In his life, Thomas Bayes defended Sir Issac Newton’s calculus and explored the concept of probability with a passion, challenging the work of domestic and French contemporaries. 

If he was alive today, Bayes might not believe the impact of his work – and as a minister, he would surely frown over gambling applications using his theorem…

 

How does GIDEON use Bayes’?

Bayesian analysis requires data to be reliable and accurate, which is why GIDEON is uniquely positioned to take advantage of the formula and put millions of data points to use!

GIDEON applies this system to generate a list of likely Infectious Diseases based on the patient’s location, recent travel, and clinical findings. It might sound simple, but with over 200 signs and symptoms for over 360 diseases in 230+ countries and territories, the number of possibilities is vast. 

Regardless of extensive options, the GIDEON application is easy to follow, delivering instantaneous results.

Predicting outcomes in a clinical setting – or future developments of the Infectious Diseases landscape – are currently hot topics, and Bayesian Analysis, combined with a vast epidemiological data set, is ideally suited to help.

GIDEON is not alone in using this method for scientific and medical purposes, as it is also used in the Continuous Individualized Risk Index (CIRI) for identifying the risk of developing cancer over time, assessment of emergency room patients for heart attack, etc, etc.

Medicine aside, Bayes’ has many real-world applications, including computer software for machine learning, security systems, and gambling – and has even been used in a court of law by jurors assessing evidence and determining verdicts. 

 

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Testing the new GIDEON – what did clinicians say?

Testing new GIDEON app on different devices

It is GIDEON’s mission to provide robust support to clinicians, microbiologists, and educators that interface with the infectious diseases field. As such, consulting with our users when developing the product is paramount to ensuring GIDEON continues to meet their expectations. On 12th August GIDEON closed its last alpha testing round, dedicated to gathering feedback on the brand new ‘Diagnose’ module. Medical experts from 26 countries have explored the new interface and shared their thoughts on what works and what can be improved.

WHAT IS ALPHA?

Alpha is an early release of a major product upgrade. Our first alpha testing round was focused on displaying our extensive database in a brand new ‘Explore’ module. The second one was geared towards clinicians who may use GIDEON in Point-of-Care settings to diagnose infectious diseases.

HOW DID IT GO?

The comments were overwhelmingly positive. Here are some of them:

I just had a look and I am blown away both diagnosis modules. They are fantastic!

The product speaks for itself.

Having tried and tested each of the modules, GIDEON does a good job in making it quick and easy for a healthcare professional to access accurate and up to date information and that is the beauty and success of GIDEON.

The look and feel are great.

GIDEON remains an outstanding and easy to use, up to date resource. Commendable. Well done.

We are so grateful for all the positivity as well as constructive criticism – it will make the product better for everyone.

WHAT’S NEXT?

A full beta release is currently planned for mid-September. It’s the same GIDEON data that you know and love, but like you’ve never seen before! The beta will include our brand new Lab module, designed to assist microbiologists. Check out a sneak-peek below:

GIDEON Lab module displayed on a landscape white iPad

Sign up for beta release and receive 1 month of access to the new GIDEON for free!

Join us on Twitter,  Facebook, and LinkedIn

First alpha testing is complete!

Male doctor and female researcher testing GIDEON app

It takes a lot of courage to share a vision with users and critics, but the GIDEON team is in no short supply of that. In our recent alpha testing round, we opened up our brand new interface to medical experts from 25 countries who have very kindly shared their feedback on our successes and shortcomings.

What is alpha?

Quite simply, it is an early release of a major product upgrade. Our first alpha testing round focused on the display of our extensive database in a brand new ‘Explore’ module.

How did we do it?

We opted for feedback gathering mechanisms that support user independence and anonymity. This is different from a focus group, which is prone to leaving some opinions unheard. 

Our Trusted Advisors were a diverse bunch, consisting of 80+ medical professionals – from seasoned experts to students. Some testers have never seen our product before and others have been using GIDEON for years. 

The experience was scary, exciting, and necessary. We cannot thank our Trusted Advisors enough for their insight and valuable time spent exploring our new interface. The feedback has empowered a fruitful fine-tuning exercise, so if you are one of our testers – be sure to check out the implementation of your suggestions in the second alpha release!

Feedback

We are beside ourselves in anticipation of the release of the new interface (date to be confirmed soon) and based on the early feedback we know you are going to love it.

Here is a small sample of the comments we received:

This is a huge improvement. I very much like the general concept. The dark mode is also very nice.

Comprehensive.

Amazing work! So informative and pleasant to use.

Disease comparison is great. What a useful way to compare a differential!

I very much like the ‘fingerprint’ search concept for diseases.

The interface is easy to use.

Maps are amazing!!

Thoughtful, cohesive design.

Links to references are very useful.

What’s next?

We cannot wait to share this new experience with you all. It’s the same GIDEON data that you know and love, but like you’ve never seen before. 

If you are interested in a Bayes-powered Differential Diagnosis that uses one of the most impressive geographical medicine data sets in the world, sign up to test the all-new DIAGNOSE module. The second alpha is just around the corner!

Become our trusted advisor

GIDEON API is in beta!

How do you get ‘customer’ data if you are a hospital or a research institute?

You could build a dedicated team for conducting surveys and crawling research papers, even develop your own IT system for storing and accessing this data. How often would you need to revise this data? Monthly? Quarterly? How comprehensive do you think it would be? 

If you are one of the many medical professionals pressed for time and/or money, the above may not be an easy solution to maintain, and when people’s lives are at stake there is no room for failure.

Imagine your organization had access to infectious diseases data collected from all over the globe, from thousands of patients, across hundreds of countries, updated every single day. That would be pretty amazing, right? With GIDEON it is a click away. We offer your organization access to data on hundreds of diseases, drugs, and bacteria, from across the world, dating back from as far as the 1920s – we do the legwork so you can conduct your expert analysis. 

To fully realize the benefits of our comprehensive database, we have developed the GIDEON API so you can leverage a direct feed of continuously updated information between our service and your established processes and tools. The service is now being offered to all our institutional subscribers free of charge.

With a service as broad as GIDEON, we understand that taking on an API integration can be a daunting task, even for a seasoned IT professional. To help make this invaluable feature more accessible to our customers we have written extensive guidance detailing every API call, including examples on the output you should expect. You can access the guidance through this link: API

We are confident building a deeper connection between our service and your systems will empower your analytics and reporting capabilities, bringing new insight to your existing and emerging data trends. Please take a peek at our documentation and let us know when you are ready to give it a go!

2020 is going to be an important and exciting year for GIDEON. We look forward to sharing many more announcements of enhancements and new services throughout the year.

EPUB and Amazon Kindle MOBI format supported by GIDEON eBooks

Now whenever you purchase an eBook from GIDEON, you receive 3 file formats: PDF, EPUB and MOBI to ensure maximum compatibility on all devices.

GIDEON eBooks  support the Amazon Kindle MOBI file format for opening eBooks on Kindle devices directly and EPUB for desktop and mobile devices in addition to PDF.

To transfer a MOBI file: connect your Kindle via USB to your computer and drag and drop the file to your Documents folder. Alternatively you can use Amazon’s Send-To-Kindle

EPUB and PDF eBooks can be opened directly by both desktop and mobile devices.

Example of links in email receipt:

GIDEON in Korean … and any language

Ever since GIDEON launched, one of the top questions from non-native English speakers is when will GIDEON be translated into their local language.
Thanks to the wonders of machine translation built into Google Chrome, the GIDEON web based application can be read in almost any language.
Recently we updated the various tabs to be totally text based rather than graphic based and voila. This is how GIDEON looks in Korean:

Using Chrome right click, Translate and if necessary choose a different language.

 

Read GIDEON ebooks in web app

Since GIDEON first launched ebooks, many app subscribers have wanted to view them. Although the content in the web app is constantly updated and the ebooks are only generated once a year, some users like to view the material in a linear book format.

Now, through the Ebooks tab, app users can read the ebooks:

Ebooks are listed by Country, Disease and Other categories:

Ebooks Country list

The full PDF ebook displays in a new window.


Click Buy to purchase the ebook for offline access.

GIDEON eBooks 2018 Edition

The 2018 edition of GIDEON ebooks has expanded all content, graphs, maps and references based on extensive updates in the GIDEON web application.

New Cross Border events have been added to notes where cases have been imported to and/or exported from that country.

A few of the iconic ebooks in this series:

  • Infectious Diseases of the World – provides a review of every human infectious disease in the world, including disease distribution maps.
  • Global status of [any infectious disease] – the perfect reference source for Clinicians and Epidemiologists.
  • eBooks which provide detailed and up-to-date information on every anti-infective drug and vaccine – key references for every health-care worker.
  • A complete encyclopedia of all human bacteria and yeasts – a must for any laboratory or health-care student.
  • GIDEON Guide to Outbreaks – the most comprehensive list of outbreaks available anywhere.

Available for purchase through:

GIDEON Sign In