| --- |
| title: README |
| emoji: 🐨 |
| colorFrom: pink |
| colorTo: purple |
| sdk: static |
| pinned: false |
| --- |
| |
| # EPI-Eval |
|
|
| A curated collection of large epidemiological datasets, normalized to a single |
| schema so they can be searched, joined, and benchmarked against each other. |
|
|
| ## What we track |
|
|
| Time-series surveillance data on infectious disease — primarily respiratory |
| viruses (flu, COVID-19, RSV) and arboviral disease (dengue, Zika, |
| chikungunya), with smaller coverage of notifiable, mortality, wastewater, and |
| behavioural / search signals. Sources come from CDC, WHO, ECDC, PAHO, OWID, |
| and national public-health agencies; we re-publish them as Parquet with a |
| consistent set of row-level columns (`date`, `location_id`, `location_level`, |
| optional `condition` / `case_status` / `as_of`) and a metadata header |
| describing pathogens, geography, cadence, and per-column units. |
|
|
| ## Why |
|
|
| Forecasting and modeling work routinely stalls on data plumbing — finding the |
| canonical version of a series, normalizing geography codes, reconciling |
| reporting cadences, tracking when a source was last revised. The goal of this |
| org is to do that work once, in the open. |
|
|
| ## Schema |
|
|
| Every dataset card on this org uses the same frontmatter format |
| ([schema v0.1](https://github.com/ChrisHarig/apart-forecasting-tool/blob/main/upload_pipeline/schema/schema_v0.1.md)), |
| validated against a controlled vocabulary |
| ([`vocabularies.yaml`](https://github.com/ChrisHarig/apart-forecasting-tool/blob/main/upload_pipeline/schema/vocabularies.yaml)). |
| Curated metadata (pathogens, license, units) lives alongside computed metadata |
| (time coverage, row count, observed cadence) generated at ingest. |
|
|
| ## Contributing a dataset |
|
|
| The ingest pipeline is in |
| [`apart-forecasting-tool/upload_pipeline`](https://github.com/ChrisHarig/apart-forecasting-tool/tree/main/upload_pipeline). |
| A new dataset is one `ingest.py` + `card.yaml` under |
| `upload_pipeline/sources/<source_id>/`; the validator confirms schema fit |
| before upload. Each new truth dataset auto-creates an empty |
| `<id>-predictions` companion at upload time. |
|
|
| ## Datasets (21) |
|
|
| ### Respiratory |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [CDC FluSurv-NET — weekly flu hospitalisation rates](https://huggingface.co/datasets/EPI-Eval/delphi-flusurv) | influenza | US | weekly | |
| | [CDC NHSN Hospital Respiratory Data (HRD)](https://huggingface.co/datasets/EPI-Eval/nhsn-hrd) | influenza, sars-cov-2, rsv | US | weekly | |
| | [CDC NREVSS — weekly RSV test specimens and positives](https://huggingface.co/datasets/EPI-Eval/cdc-nrevss-rsv) | rsv | US | weekly | |
| | [COVID Tracking Project — US states daily (archived)](https://huggingface.co/datasets/EPI-Eval/covid-tracking-project) | sars-cov-2 | US | daily | |
| | [COVID-19 Forecast Hub — hospital admissions target](https://huggingface.co/datasets/EPI-Eval/covid19-forecast-hub) | sars-cov-2 | US | weekly | |
| | [ECDC ERVISS — ILI/ARI primary-care consultation rates](https://huggingface.co/datasets/EPI-Eval/ecdc-erviss) | influenza, sars-cov-2, rsv | multiple (30 countries) | weekly | |
| | [Flu MetroCast Hub — sub-state flu hosp forecast target](https://huggingface.co/datasets/EPI-Eval/flu-metrocast-hub) | influenza | US | weekly | |
| | [FluSight Forecast Hub — flu hospital admission target](https://huggingface.co/datasets/EPI-Eval/flusight-forecast-hub) | influenza | US | weekly | |
| | [JHU CSSE COVID-19 — global daily (archived)](https://huggingface.co/datasets/EPI-Eval/jhu-csse-covid) | sars-cov-2 | multiple | daily | |
| | [NYT COVID-19 — US county daily](https://huggingface.co/datasets/EPI-Eval/nyt-covid) | sars-cov-2 | US | daily | |
| | [OWID COVID-19 — global daily compiled](https://huggingface.co/datasets/EPI-Eval/owid-covid) | sars-cov-2 | multiple | daily | |
| | [PHAC Respiratory Virus Detection Surveillance — Canada weekly](https://huggingface.co/datasets/EPI-Eval/canada-fluwatch) | influenza, influenza-a, influenza-b +7 | CA | weekly | |
| | [RSV Forecast Hub — RSV hospital admissions target](https://huggingface.co/datasets/EPI-Eval/rsv-forecast-hub) | rsv | US | weekly | |
| | [UKHSA Dashboard — England COVID-19 daily metrics](https://huggingface.co/datasets/EPI-Eval/ukhsa-covid-daily) | sars-cov-2 | GB | daily | |
| | [UKHSA Dashboard — England flu / COVID-19 / RSV weekly](https://huggingface.co/datasets/EPI-Eval/ukhsa-respiratory) | influenza, sars-cov-2, rsv | GB | weekly | |
|
|
| ### Syndromic / ED |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [CDC NSSP / ESSENCE — ED visits for ILI / COVID / RSV](https://huggingface.co/datasets/EPI-Eval/cdc-nssp) | influenza, sars-cov-2, rsv | US | weekly | |
|
|
| ### Arboviral |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [OpenDengue — national dengue case counts (V1.3)](https://huggingface.co/datasets/EPI-Eval/opendengue) | dengue | multiple | irregular | |
|
|
| ### Mobility & contact |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [Google Community Mobility Reports — global daily](https://huggingface.co/datasets/EPI-Eval/global-mobility) | — | multiple | daily | |
|
|
| ### Search & behavioural |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [Wikipedia pageviews — disease-article daily views](https://huggingface.co/datasets/EPI-Eval/wikipedia-pageviews) | influenza, sars-cov-2, rsv +6 | multiple | daily | |
|
|
| ### Notifiable / other |
|
|
| | Dataset | Pathogens | Geography | Cadence | |
| | --- | --- | --- | --- | |
| | [OWID Mpox — global daily compiled](https://huggingface.co/datasets/EPI-Eval/owid-mpox) | mpox | multiple | daily | |
| | [WHO Global TB — annual country estimates](https://huggingface.co/datasets/EPI-Eval/who-tb-burden) | tuberculosis | multiple | annual | |
|
|
| ## Predictions |
|
|
| Each truth dataset has a companion `EPI-Eval/<id>-predictions` repo that |
| accumulates community-submitted forecasts. Schema is long-format: one row per |
| `(target_date, [dim values…], quantile, value)`, with `quantile = NULL` |
| reserved for the point estimate. Forecasters submit through the |
| [EPI-Eval dashboard](https://github.com/ChrisHarig/apart-forecasting-tool); |
| a maintainer reviews each PR before merging, and merged predictions show up |
| on the corresponding truth dataset's *Show predictions* toggle in the |
| dashboard, with a per-submitter leaderboard (MAE / WIS / rWIS / coverage). |
|
|
| ## Status |
|
|
| Active. Coverage and dataset list grow through PRs to the upload pipeline. |
|
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|
