About
Microbiome Repo was created in the Olm Lab at the University of Colorado Boulder and is funded by Anthropic's AI for Science program.
About this page
It has two tiers: a registry of every shotgun-metagenome study reached in ENA — INSDC BioProjects deposited in ENA, NCBI SRA or DDBJ — classified for human host, body site, life stage, assay and access (6,898 human studies of 64,369), and a curated catalog of the human-gut studies among them, all ages (2,798 studies, 573,001 samples), with per-sample metadata in which every value carries a verbatim evidence quote, a route and a confidence.
How the 2,798 catalog studies are cut from the registry: the study rule, the funnel, and the gut studies left out and why. Methods
Registry enumeration and classification, the four curation routes (R1–R4) and their precedence, evidence and confidence rules, cohorts, releases, limitations. Sources & acknowledgements
Archives, literature, software and models behind the catalog; the external curated resources incorporated as R2 evidence; funding. Fields documentation
All 41 fields grouped core / key / infant extension with vocabulary, coverage, route mix and confidence; the package data dictionary. Downloads & releases
The data package, per-table downloads, the release history and what changed in each release. Contribute
Studies whose core fields are still missing, and how a per-sample table or a paper pointer unlocks them.
Registry → catalog in numbers
| registry studies (every ENA shotgun-metagenome study reached by the enumeration) | 64,369 |
| host human = yes or mixed | 6,898 |
| … with gut / stool among the body sites | 3,588 |
| … host human AND assay shotgun (catalog rule) | 2,819 |
| catalog studies | 2,798 |
Funding
Development of Microbiome Repo is supported by a grant from Anthropic to the Olm Lab (University of Colorado Boulder) for organising human microbiome metadata.
How to cite
Concept DOI (all versions, resolves to the latest archived release): 10.5281/zenodo.23087712.
Documents
- README (README.md)
- Data dictionary (DATA_DICTIONARY.md)
- Changelog (CHANGELOG.md)
- Registry report (REGISTRY_REPORT.md)
- Sandpiper report (SANDPIPER_REPORT.md)
- Authors report (infant extension) (AUTHORS_REPORT.md)
- Data-model fix report (infant extension) (DATA_MODEL_FIX_REPORT.md)
- Infant-extension catalog report (CATALOG_REPORT.md)
- Infant-field extraction report (EXTRACTION_REPORT.md)
- Collections: how membership rules work and how to propose one (COLLECTIONS.md)
- Sandpiper profiles for the whole catalog (report) (GUT_SANDPIPER_REPORT.md)
Code, configuration and vocabularies: microbiome_repo-pipeline; data packages: OlmLab/microbiome_repo-data. Found an error? Use the Flag an issue link on a study or cohort page — it opens a short prefilled GitHub issue.