Documentation
API reference, data formats, and usage guides.
Full Documentation on ReadTheDocs
Complete API reference (all endpoints incl. EcoRisk & SENTINEL-Φ early warning), pathogen catalogue, data sources, import guides, and the early-warning methodology.
infectonet.readthedocs.io
Public API — quick reference
Full API referenceGET
/api/virusesReturns the catalogue of all 50+ pathogens with sequence counts.GET
/api/viruses/:idReturns sequence records for a specific virus. Supports ?page and ?limit.Data Format
Each sequence record contains the following fields where available:
| Field | Description |
|---|---|
| ACCESSION | GenBank / GISAID accession number |
| COUNTRY | Country of sample collection |
| COLLECTION_DATE | ISO 8601 collection date |
| YEAR | Collection year (integer) |
| GENOTYPE | Resolved genotype / clade / lineage |
| LINEAGE | Lineage assignment (e.g. Pango for SARS-CoV-2) |
| clade | Nextstrain clade assignment |
| serotype | Serotype (e.g. DENV-1 to DENV-4 for Dengue) |
| LATITUDE | Approximate latitude of collection location |
| LONGITUDE | Approximate longitude of collection location |
Data Sources & Citation
NCBI GenBank — Benson DA et al. (2018). Nucleic Acids Research.
GISAID — Khare S et al. (2021). Lancet Infectious Diseases.
Nextstrain — Hadfield J et al. (2018). Bioinformatics.
When using InfectoNET data, please cite the original data sources above as well as InfectoNET (preprint forthcoming).