A global dataset of pandemic- and epidemic-prone disease outbreaks

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# A global dataset of pandemic- and epidemic-prone disease outbreaks
### Juan Armando Torres Munguía, Ph.D.<br>

**EM-DAT International Disaster Database <br/> Scientific & Technical Advisory Group (STAG) Meeting**<br>

Potchefstroom, South Africa <br/> March 18th, 2024
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# Acknowledgments

This dataset is the result of collaborative work by a team of researchers from the [University of Göttingen](https://www.uni-goettingen.de/) (**Prof. Inmaculada Martínez-Zarzoso, Ph.D** and **M.Sc. Luis Díaz Pavez **), the [University of Groningen](https://www.rug.nl/) (**Prof. Konstantin Wacker, Ph.D**), and the [University of Bordeaux](https://www.u-bordeaux.fr/en) (**Prof. Florina Cristina Badarau, Ph.D **).

The project was made possible through financial support from the [ENLIGHT network](https://enlight-eu.org/), the [German Academic Exchange Service (DAAD)](https://www.daad.de/en/), and the [Federal Ministry of Education and Research (BMBF)](https://www.bmbf.de/bmbf/en/home/home_node.html) in Germany.

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# About this work
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**Torres Munguía, J.A., Badarau, F.C., Díaz Pavez, L.R. et al. A global dataset of pandemic- and epidemic-prone disease outbreaks. Sci Data 9, 683 (2022). https://doi.org/10.1038/s41597-022-01797-2**
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# <svg preserveAspectRatio="none" aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:2.05em;width:2.05em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#FFFFFF;overflow:visible;position:relative;"><path d="M297.2 248.9C311.6 228.3 320 203.2 320 176c0-70.7-57.3-128-128-128S64 105.3 64 176c0 27.2 8.4 52.3 22.8 72.9c3.7 5.3 8.1 11.3 12.8 17.7l0 0c12.9 17.7 28.3 38.9 39.8 59.8c10.4 19 15.7 38.8 18.3 57.5H109c-2.2-12-5.9-23.7-11.8-34.5c-9.9-18-22.2-34.9-34.5-51.8l0 0 0 0c-5.2-7.1-10.4-14.2-15.4-21.4C27.6 247.9 16 213.3 16 176C16 78.8 94.8 0 192 0s176 78.8 176 176c0 37.3-11.6 71.9-31.4 100.3c-5 7.2-10.2 14.3-15.4 21.4l0 0 0 0c-12.3 16.8-24.6 33.7-34.5 51.8c-5.9 10.8-9.6 22.5-11.8 34.5H226.4c2.6-18.7 7.9-38.6 18.3-57.5c11.5-20.9 26.9-42.1 39.8-59.8l0 0 0 0 0 0c4.7-6.4 9-12.4 12.7-17.7zM192 128c-26.5 0-48 21.5-48 48c0 8.8-7.2 16-16 16s-16-7.2-16-16c0-44.2 35.8-80 80-80c8.8 0 16 7.2 16 16s-7.2 16-16 16zm0 384c-44.2 0-80-35.8-80-80V416H272v16c0 44.2-35.8 80-80 80z"/></svg>
## From unstructured administrative records to an accessible, open, global dataset of pandemic- and epidemic-prone disease outbreaks

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<svg preserveAspectRatio="none" aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:2em;width:2em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#FFFFFF;overflow:visible;position:relative;"><path d="M64 96c0-35.3 28.7-64 64-64H512c35.3 0 64 28.7 64 64V352H512V96H128V352H64V96zM0 403.2C0 392.6 8.6 384 19.2 384H620.8c10.6 0 19.2 8.6 19.2 19.2c0 42.4-34.4 76.8-76.8 76.8H76.8C34.4 480 0 445.6 0 403.2zM281 209l-31 31 31 31c9.4 9.4 9.4 24.6 0 33.9s-24.6 9.4-33.9 0l-48-48c-9.4-9.4-9.4-24.6 0-33.9l48-48c9.4-9.4 24.6-9.4 33.9 0s9.4 24.6 0 33.9zM393 175l48 48c9.4 9.4 9.4 24.6 0 33.9l-48 48c-9.4 9.4-24.6 9.4-33.9 0s-9.4-24.6 0-33.9l31-31-31-31c-9.4-9.4-9.4-24.6 0-33.9s24.6-9.4 33.9 0z"/></svg>
### Process
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<svg preserveAspectRatio="none" aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:2em;width:2em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#FFFFFF;overflow:visible;position:relative;"><path d="M32 32c17.7 0 32 14.3 32 32V400c0 8.8 7.2 16 16 16H480c17.7 0 32 14.3 32 32s-14.3 32-32 32H80c-44.2 0-80-35.8-80-80V64C0 46.3 14.3 32 32 32zM160 224c17.7 0 32 14.3 32 32v64c0 17.7-14.3 32-32 32s-32-14.3-32-32V256c0-17.7 14.3-32 32-32zm128-64V320c0 17.7-14.3 32-32 32s-32-14.3-32-32V160c0-17.7 14.3-32 32-32s32 14.3 32 32zm64 32c17.7 0 32 14.3 32 32v96c0 17.7-14.3 32-32 32s-32-14.3-32-32V224c0-17.7 14.3-32 32-32zM480 96V320c0 17.7-14.3 32-32 32s-32-14.3-32-32V96c0-17.7 14.3-32 32-32s32 14.3 32 32z"/></svg>
### Output
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<svg preserveAspectRatio="none" aria-hidden="true" role="img" viewBox="0 0 640 512" style="height:2em;width:2em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#FFFFFF;overflow:visible;position:relative;"><path d="M160 64c0-35.3 28.7-64 64-64H576c35.3 0 64 28.7 64 64V352c0 35.3-28.7 64-64 64H336.8c-11.8-25.5-29.9-47.5-52.4-64H384V320c0-17.7 14.3-32 32-32h64c17.7 0 32 14.3 32 32v32h64V64L224 64v49.1C205.2 102.2 183.3 96 160 96V64zm0 64a96 96 0 1 1 0 192 96 96 0 1 1 0-192zM133.3 352h53.3C260.3 352 320 411.7 320 485.3c0 14.7-11.9 26.7-26.7 26.7H26.7C11.9 512 0 500.1 0 485.3C0 411.7 59.7 352 133.3 352z"/></svg>
### Dashboard
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# Disease Outbreak News (DONs) 
.panelset[
.panel[
.panel-name[Ebola in Gabon (1996)]
.panel-content[
      <iframe src="pages_outbreaks/1996 - Ebola haemorrhagic fever in Gabon (new outbreak) - .html" style="width:100%; height:500px;"></iframe>
    ]
]

.panel[
.panel-name[Influenza in Viet Nam (2004)]
.panel-content[
      <iframe src="pages_outbreaks/Avian influenza – situation in Viet Nam.html" style="width:100%; height:500px;"></iframe>
    ]
]

.panel[
.panel-name[Zika in Panama (2015)]
.panel-content[
      <iframe src="pages_outbreaks/Zika virus infection – Panama.html" style="width:100%; height:500px;"></iframe>
    ]
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The information of the DONs is obtained from an integrated global system coordinated by the WHO. This information is based on epidemiological, clinical, and laboratory investigations conducted by the official public health authorities, institutions, and research networks of the WHO and its partners all over the world.

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# Transforming DONs into statistical data
#### Code

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- **Web scraping information from www.who.int**
- **2721 DONs collected**
]

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- **Data and text mining using R (remove duplicates, subset only diseases)**
]

???

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## After more than 3000 lines of code...

## and some manual imputation.

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# Output

#### The final dataset contains information on 2227 disease outbreaks and provides six key advantages in comparison to existing data:

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** b) A wide geographic coverage of 233 countries and territories around the world.**
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** c) An extensive coverage of 70 infection diseases.**
]

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** d) Standardized concepts and definitions: official country names according to the ISO-316623 and the ICD-10**
]

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# Output

#### The final dataset contains information on 2227 disease outbreaks and provides six key advantages in comparison to existing data:

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.center[<svg preserveAspectRatio="none" aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:2em;width:2.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#153268;overflow:visible;position:relative;"><path d="M288 32c0-17.7-14.3-32-32-32s-32 14.3-32 32V274.7l-73.4-73.4c-12.5-12.5-32.8-12.5-45.3 0s-12.5 32.8 0 45.3l128 128c12.5 12.5 32.8 12.5 45.3 0l128-128c12.5-12.5 12.5-32.8 0-45.3s-32.8-12.5-45.3 0L288 274.7V32zM64 352c-35.3 0-64 28.7-64 64v32c0 35.3 28.7 64 64 64H448c35.3 0 64-28.7 64-64V416c0-35.3-28.7-64-64-64H346.5l-45.3 45.3c-25 25-65.5 25-90.5 0L165.5 352H64zm368 56a24 24 0 1 1 0 48 24 24 0 1 1 0-48z"/></svg>]]
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** f) For transparency, replicability, and reproducibility purposes, we make the data, metadata, and the code to create these data publicly available from Figshare.**
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# Dashboard

.center[[<img src="img/qrcode.png" width="40%"/>](https://jatorresmunguia.shinyapps.io/A_global_dataset_of_disease_outbreaks/) <br> 
**Scan me!** <br> 
**or go to: [s.gwdg.de/hqj0NV](https://s.gwdg.de/hqj0NV)**
]

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# Thank you very much!

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### Contact information
[<svg aria-label="Twitter" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>Twitter</title><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> @jtorresmunguia ](https://twitter.com/jtorresmunguia) <br/>
[<svg aria-label="At" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>At</title><path d="M256 64C150 64 64 150 64 256s86 192 192 192c17.7 0 32 14.3 32 32s-14.3 32-32 32C114.6 512 0 397.4 0 256S114.6 0 256 0S512 114.6 512 256v32c0 53-43 96-96 96c-29.3 0-55.6-13.2-73.2-33.9C320 371.1 289.5 384 256 384c-70.7 0-128-57.3-128-128s57.3-128 128-128c27.9 0 53.7 8.9 74.7 24.1c5.7-5 13.1-8.1 21.3-8.1c17.7 0 32 14.3 32 32v80 32c0 17.7 14.3 32 32 32s32-14.3 32-32V256c0-106-86-192-192-192zm64 192a64 64 0 1 0 -128 0 64 64 0 1 0 128 0z"/></svg> jtorres@gwdg.de ](jtorres@gwdg.de) <br/>
[<svg aria-label="File Contract" role="img" viewBox="0 0 384 512" style="height:1em;width:0.75em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>File Contract</title><path d="M64 0C28.7 0 0 28.7 0 64V448c0 35.3 28.7 64 64 64H320c35.3 0 64-28.7 64-64V160H256c-17.7 0-32-14.3-32-32V0H64zM256 0V128H384L256 0zM80 64h64c8.8 0 16 7.2 16 16s-7.2 16-16 16H80c-8.8 0-16-7.2-16-16s7.2-16 16-16zm0 64h64c8.8 0 16 7.2 16 16s-7.2 16-16 16H80c-8.8 0-16-7.2-16-16s7.2-16 16-16zm54.2 253.8c-6.1 20.3-24.8 34.2-46 34.2H80c-8.8 0-16-7.2-16-16s7.2-16 16-16h8.2c7.1 0 13.3-4.6 15.3-11.4l14.9-49.5c3.4-11.3 13.8-19.1 25.6-19.1s22.2 7.7 25.6 19.1l11.6 38.6c7.4-6.2 16.8-9.7 26.8-9.7c15.9 0 30.4 9 37.5 23.2l4.4 8.8H304c8.8 0 16 7.2 16 16s-7.2 16-16 16H240c-6.1 0-11.6-3.4-14.3-8.8l-8.8-17.7c-1.7-3.4-5.1-5.5-8.8-5.5s-7.2 2.1-8.8 5.5l-8.8 17.7c-2.9 5.9-9.2 9.4-15.7 8.8s-12.1-5.1-13.9-11.3L144 349l-9.8 32.8z"/></svg> Read the paper ](https://www.nature.com/articles/s41597-022-01797-2) <br/>
[<svg aria-label="Cloud Arrow Down" role="img" viewBox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>Cloud Arrow Down</title><path d="M144 480C64.5 480 0 415.5 0 336c0-62.8 40.2-116.2 96.2-135.9c-.1-2.7-.2-5.4-.2-8.1c0-88.4 71.6-160 160-160c59.3 0 111 32.2 138.7 80.2C409.9 102 428.3 96 448 96c53 0 96 43 96 96c0 12.2-2.3 23.8-6.4 34.6C596 238.4 640 290.1 640 352c0 70.7-57.3 128-128 128H144zm79-167l80 80c9.4 9.4 24.6 9.4 33.9 0l80-80c9.4-9.4 9.4-24.6 0-33.9s-24.6-9.4-33.9 0l-39 39V184c0-13.3-10.7-24-24-24s-24 10.7-24 24V318.1l-39-39c-9.4-9.4-24.6-9.4-33.9 0s-9.4 24.6 0 33.9z"/></svg> Access to data from Figshare ](https://doi.org/10.6084/m9.figshare.17207183.v2) <br/>
[<svg aria-label="Chart Line" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>Chart Line</title><path d="M64 64c0-17.7-14.3-32-32-32S0 46.3 0 64V400c0 44.2 35.8 80 80 80H480c17.7 0 32-14.3 32-32s-14.3-32-32-32H80c-8.8 0-16-7.2-16-16V64zm406.6 86.6c12.5-12.5 12.5-32.8 0-45.3s-32.8-12.5-45.3 0L320 210.7l-57.4-57.4c-12.5-12.5-32.8-12.5-45.3 0l-112 112c-12.5 12.5-12.5 32.8 0 45.3s32.8 12.5 45.3 0L240 221.3l57.4 57.4c12.5 12.5 32.8 12.5 45.3 0l128-128z"/></svg> Link to dashboard ](https://jatorresmunguia.shinyapps.io/A_global_dataset_of_disease_outbreaks/) <br/>
[<svg aria-label="Person Chalkboard" role="img" viewBox="0 0 640 512" style="height:1em;width:1.25em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><title>Person Chalkboard</title><path d="M192 96a48 48 0 1 0 0-96 48 48 0 1 0 0 96zm-8 384V352h16V480c0 17.7 14.3 32 32 32s32-14.3 32-32V192h56 64 16c17.7 0 32-14.3 32-32s-14.3-32-32-32H384V64H576V256H384V224H320v48c0 26.5 21.5 48 48 48H592c26.5 0 48-21.5 48-48V48c0-26.5-21.5-48-48-48H368c-26.5 0-48 21.5-48 48v80H243.1 177.1c-33.7 0-64.9 17.7-82.3 46.6l-58.3 97c-9.1 15.1-4.2 34.8 10.9 43.9s34.8 4.2 43.9-10.9L120 256.9V480c0 17.7 14.3 32 32 32s32-14.3 32-32z"/></svg> Slides ](https://jatorresmunguia.github.io/A_global_dataset_of_disease_outbreaks_SA_presentation_0324/#30)

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