UMDB is a searchable urban microbiome database built for discovery, comparison, and reuse.

UMDB turns public repository metadata into a browsable and downloadable resource for urban metagenomics and related environmental sequencing studies. It combines BioProject-level search, SRR-level provenance, database summaries, geography views, and cohort export workflows in one public release.

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Why UMDB Exists

Discover

Find urban sequencing studies quickly

Search BioProjects, cities, countries, assay classes, and sequencing centers with a dedicated explorer designed for public urban environmental omics records.

Compare

See the database as a landscape

Use summary analytics and geographic views to understand how the current release is distributed across years, locations, assay classes, and institutions.

Reuse

Move from metadata to cohorts

Export matched result sets as JSON bundles, accession lists, and raw-read download scripts so the database supports actual downstream study assembly rather than passive browsing.

Database Overview

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Core Workflow

BioProject Explorer

The dedicated explorer page groups SRR-level records into BioProjects, supports natural-language search, and exposes project expansion, cohort bundling, and download-oriented actions.

Open Explorer

High-Level Summary

Analytics Dashboard

Review release-wide counts, distribution charts, summary tables, and statistical tests that describe the current database snapshot in manuscript-friendly terms.

Open Analytics

Visual Exploration

Analytics and Map

Explore filtered year-by-location analytics and a global country map to understand where public urban sequencing activity is concentrated within the current release.

Current Release Snapshot

For Collaborators

Transparent methodology The public methods page explains provenance, enrichment, caveats, and the logic behind key database fields.
Inspectable release artifacts The database is distributed as a manifest plus part files in docs/db/, which makes the release easy to inspect and archive.
Human and machine access UMDB supports browser exploration, JSON distribution, run bundling, and raw-read download preparation from one public interface.
Geography-aware views The analytics and map pages make it easier to understand how the indexed database is distributed across place and time.