UrbanScope BioProject Explorer

A curated, queryable index of environmental sequencing runs grouped by NCBI BioProject. Designed for city-confined metagenomics discovery (built environment, wastewater, transit, air, surfaces).
Loading… — — Source: docs/db/
Database overview
This page loads a manifest and one or more part files containing SRR-level records. Records are aggregated into one row per BioProject and can be expanded to view underlying SRR/SRA runs.
Manifest: docs/db/srr_records_manifest.json → file list, generation timestamp, and total record count.
Parts: docs/db/srr_records_partXXX.json → arrays of SRR records (RunInfo + derived annotations).
What is in each record?
Core fields are sourced from SRA RunInfo and joined with optional enrichments:
  • runinfo_row: SRR, BioProject, BioSample, dates, platform, center
  • bioproject: accession/title (when available)
  • geo: country and city (from BioSample/location parsing)
  • assay: assay class (e.g., WGS, RNA-seq, 16S/ITS)
Use Require Country/City and Exclude (unknown) to keep only geographically resolved projects.
latest_srr.json manifest

Filters

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BioProjects

Matched: — Showing: — Sort: samples ▼
Tip: click a column header to sort · click “Expand” to see SRRs
BioProject Title Runs BioSamples Countries Cities Assays Years Details
Loading manifest…
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Sorting is by BioProject-level aggregates (runs, unique BioSamples, etc.).

Where do the samples come from?

Stats are computed on the currently matched BioProjects (after filters). If your geo fields are empty, you’ll see “(unknown)” buckets — that’s a sign your BioSample enrichment step needs to fill geo.country/geo.city.
Countries (top 15)
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Cities (top 15)
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Files expected under docs/db/: srr_records_manifest.json, srr_records_part000.json, …