During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research.
outbreak.info is a standardized, searchable platform to discover and explore COVID-19 and SARS-CoV-2 data from the Center for Viral Systems Biology at Scripps Research. It contains three parts: a standardized searchable database of COVID-19 research; customizable real-time surveillance reports on SARS-CoV-2 variants and mutations; and an explorable interface to examine changes in epidemiological data.
Disclaimer: This project is a work-in progress. Please submit an issue if you notice any bugs or want to suggest features.
- Outbreak.api -- repo for the back-end API
- outbreak.info-resources -- data schemas and harvesters for COVID-19 resources
- Clone the repository
- Make sure you have [node & npm] (https://nodejs.org/en/) and Vue & Vue CLI installed.
- In terminal, navigate to the
src
directory of this repository. - Install node_modules by running
npm install
. - Launch a local server with hot-reloads by running
npm run serve
.
Updating curated Variants of Concern (VOCs) / Variants of Interest (VOIs) / Variants under Monitoring (VUMs).
outbreak.info maintains a curated list of VOCs/VOIs/VUMs based on classifications by public health agencies. Additionally, the sublineages associated with a variant are maintained by accessing the data file from the Pango team.
- Edit the curated yaml file. Do not manually edit the curated .json file used by outbreak.info; this file will be dynamically generated by the python script below. Essential components:
pangolin_lineage
: the primary, parent pangolin lineage for the variant. Can also be an array (e.g.["B.1.427", "B.1.429"]
-- specify as a yaml array)who_name
: (if available) the WHO alias for the variantdateModified
: date which outbreak.info classifies it as a VOC/VOI/VUMclassifications
: array containing classifications as per CDC, WHO, PHE, ECDC- Make sure to nest the yaml object under the appropriate section (VOC, VOI, VUM) to ensure it gets classified as the appropriate level of concern.
- Run
python curated_reports_prep/generate_curated_lineages_json.py
. This updates the curated .json file used by outbreak.info. - Edit
updates
admin.js to add a note that a variant has been classified, reclassified, or downgraded. - Commit to the GitHub repo and rebuild the site.
- Run
python curated_reports_prep/generate_curated_lineages_json.py
. This updates the curated .json file used by outbreak.info. - Commit to the GitHub repo and rebuild the site.