outbreak.info is a website to increase the accessibility of SARS-CoV-2 and COVID-19 data and research.
- outbreak.info web application: the open source code powering outbreak.info.
- outbreak.network: a lighter weight version of outbreak.info to run the web application locally with your own data source.
- outbreak.info R package: R package to access all the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
- outbreak.info Python package: Python package to access all the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
- api.outbreak.info: Application programming interface (API) to access Research Library metadata and cases & deaths data, available at api.outbreak.info
- outbreak.network API: a lighter weight version of the API code to create local builds with outbreak.network
- Bjorn: pipeline for SARS-CoV-2 mutation counting, lineage classification, and other processing.
- bioRxiv and medRxiv: Harvester of bioRxiv and medRxiv pre-print publications
- ClinicalTrials.gov: Harvester of clinical trials from clinicaltrials.gov
- COVID-19 LST: Harvester of COVID-19 LST level of evidence ratings
- COVID-19 LST Annotations
- COVID-19 LST Report Data
- Data Discovery Engine: Harvester for manually curated metadata from the Data Discovery Engine
- Figshare: Harvester from Figshare COVID-19
- Harvard Dataverse: Harvester for COVID-19 collection of Harvard Dataverse
- Imperial College: Harvester for analyses by Imperial College London
- LitCOVID: LitCOVID publication harvester
- PDB: Harvester of metadata for SARS-CoV-2 structures from the Protein Data Bank
- protocols.io: Harvester of protocol metadata from protocols.io
- WHO Clinical Trials: Harvester of clinical trials from WHO ICTR
- Research Library Schemas: Reusable schemas for Publications, Datasets, ClinicalTrials, Protocols, and Analyses and associated data mappings
- Research Library Tools: Reusable tools for parsers
- Preprint matcher: Code to match preprints to their peer-reviewed publications
- Topic Classifier: Machine learning classification of categories within the Research Library
- Altmetric: code to look up Altmetric ratings for outbreak.info resources
- Cases & deaths: Processing pipeline for cases & deaths data assembled and curated by Johns Hopkins University.
