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Registry: every screened shotgun-metagenome study

Every screened shotgun-metagenome project in ENA, NCBI SRA and DDBJ (64,369), classified for human host, body site, life stage and assay; ✓ marks the projects in the catalog.

About this page

Is the registry all human? No. The registry holds every shotgun-metagenome study reached by the enumeration — INSDC BioProjects deposited in ENA, NCBI SRA or DDBJ and enumerated through ENA's mirror — and classifies each for human host (registry_studies.host_human): 6,652 host human = yes, 246 mixed (human and non-human material), 13,696 unknown and 43,775 no, out of 64,369 studies in release R2026.25. The 6,898 human studies (yes + mixed) are the headline number on this site; the explorer below shows them by default and lets you include the unknown and non-human rows.

Registry explorer

Filters the 64,369 registry studies in your browser — by default the 6,898 human studies (host human = yes or mixed); tick unknown / no to widen. Runs using DuckDB-WASM over data/registry_studies.parquet (9.0 MB); nothing is sent to a server. Click a row for every column, the evidence rows behind host / body site / life stage. The URL updates with your filters so you can share a view. Registry-only studies have no page on this site (they link to ENA); catalog studies link to their study page. Opening registry/index.html?study=PRJ… filters to that study and opens its record.

✓ = in the curated catalog (has a project page with per-sample metadata). Click any row to see why a study is — or is not — in the catalog.

Loading DuckDB-WASM (from cdn.jsdelivr.net, pinned 1.29.0) and the registry table…

Title word or study accession Body site (any of the study's sites) Life stage (any of the study's stages) Scope membership Assay Access Host human (default: human studies = yes + mixed)

yes mixed include unknown include no (non-human)

Classification stage Catalog Minimum samples

Columns shown are a subset; the CSV export carries all 51 columns of the filtered rows. Full table: registry_studies.parquet. Per-slice enumeration completeness: registry_universe_audit.csv. The run-level table (registry_runs_v1.20.0.parquet, 2,334,512 rows, ≈70 MB, 46 ENA fields + found_by) is attached to the GitHub Release of the data repository, not a site file.

Scopes

Scope memberships derive deterministically from (host, body sites, life stages, assay) — see config/scope.yaml. A study can belong to several scopes. Click a scope for its definition, counts and largest studies.

scope	definition	studies	runs	BioSamples
All human shotgun metagenomes (registry)	Every ENA study with ≥ 1 human-host shotgun-DNA metagenome run; archive-only metadata (route R1), Sandpiper profiles, papers and authors.	4,675	929,502	782,606	explore
Infant gut (0–3 y) curated	Human gut/stool shotgun metagenomes from subjects aged 0–1,100 days (the Infant Gut Shotgun-Metagenome Catalog).	389	182,725	160,955	explore
Child / adolescent gut (3–18 y)	Human gut/stool shotgun metagenomes from children and adolescents.	406	147,159	117,487	explore
Adult gut (≥ 18 y)	Human gut/stool shotgun metagenomes from adults and the elderly — first curated scope after infant_gut (external gold curatedMetagenomicData).	1,389	369,164	315,610	explore
Oral cavity	Saliva, plaque, tongue and other oral-cavity shotgun metagenomes (all ages).	613	140,572	106,761	explore
Skin	Skin shotgun metagenomes (all ages).	273	77,062	54,553	explore
Vaginal / urogenital	Vaginal, cervical, urinary and seminal shotgun metagenomes.	289	67,023	64,720	explore
Respiratory tract	Nasal / nasopharyngeal and lower-respiratory shotgun metagenomes.	827	117,408	100,048	explore
Human milk	Breast-milk and colostrum shotgun metagenomes.	64	22,569	20,282	explore
Blood / tissue	Blood, tissue-biopsy and sterile-site-fluid shotgun metagenomes.	1,251	161,229	119,909	explore
Other body site	Eye/ear and other stated human sites not covered above.	278	45,273	25,908	explore
Body site unknown	Human studies whose body site could not be determined from the archive record; the site-classification queue.	828	57,717	50,519	explore

Primary body site (body_site_primary)

value	studies	runs
unknown_site Body site unknown	13,879	380,561
gut_stool Gut / stool	3,411	767,594
blood_tissue Blood / tissue / internal fluids	1,233	82,380
respiratory_lower Lower respiratory	523	51,984
oral Oral cavity	452	50,691
vaginal_urogenital Vaginal / urogenital	260	40,431
skin Skin	252	36,609
nasal_nasopharyngeal Nasal / nasopharyngeal	201	19,876
other_site Other human site	174	9,218
multi_site Multiple sites	150	71,388
eye_ear Eye / ear	61	5,452
milk Human milk	27	1,813

Primary life stage (life_stage_primary)

value	studies	runs
unknown_age Age unknown	17,755	843,036
adult Adult	1,702	350,259
infant Infant / toddler	454	197,973
child Child	443	51,977
mixed_ages Mixed ages	86	53,023
elderly Elderly	80	11,964
neonate Neonate	53	6,138
adolescent Adolescent	32	1,950

Assay (assay)

value	studies	runs
shotgun_dna Shotgun DNA metagenome	45,355	1,750,099
other Other / non-shotgun	17,327	382,529
isolate_genome Cultured isolate genome	526	30,417
amplicon_misfiled Amplicon deposited as WGS	391	52,085
mixed Mixed assays	357	75,461
rna RNA / metatranscriptome	181	7,043
amplicon Amplicon (16S/18S/ITS)	132	22,529
unknown Unknown	97	11,302
assembly_only Assembly-only deposit	3	3,047

Scope membership (a study counts once per scope) (scope_memberships)

value	studies	runs
human_all All human shotgun metagenomes (registry)	4,675	929,502
gut_adult Adult gut (≥ 18 y)	1,389	369,164
blood_tissue Blood / tissue	1,251	161,229
unknown_site Body site unknown	828	57,717
respiratory Respiratory tract	827	117,408
oral Oral cavity	613	140,572
gut_child Child / adolescent gut (3–18 y)	406	147,159
infant_gut Infant gut (0–3 y)	389	182,725
vaginal_urogenital Vaginal / urogenital	289	67,023
other_site Other body site	278	45,273
skin Skin	273	77,062
milk Human milk	64	22,569

Classification stage (classification_stage)

value	studies	runs
deterministic_rule ENA-field rule (host taxon 9606, library fields, numeric age with unit)	52,142	862,817
sonnet_x2 two replicate model classifications in agreement	5,164	643,443
deterministic_prior prior carried over from an earlier triage (reason code / body-site call) or deterministic term match	4,808	524,690
opus_adjudicated replicate disagreement adjudicated by the stronger model	1,663	243,379
pending not yet classified	417	21,564
owner_decision study-level decision by the catalog owner (config/registry_overrides.yaml)	96	20,336
curator_audit study-level host/assay audit of the archive records (config/registry_overrides.yaml)	79	18,283

Host human (host_human)

value	studies	runs
no	43,775	819,394
unknown	13,696	343,492
yes	6,652	1,118,016
mixed	246	53,610

Access (access)

value	studies	runs
open	64,368	2,321,267
controlled	1	13,245

What a registry row is

Each study carries archive-only metadata (route R1): host, body site(s) anchored to UBERON, life stage(s), assay, access, and the classification stage that produced them, each committed value with an evidence row (labelled source, ≤ 12-word quote). Registry rows are classifications, not inclusions: a study can carry several body sites and life stages; rows at stage pending have not been classified yet. The curated tier goes deeper — per-sample fields recovered from supplementary tables and papers (routes R2–R4) — and is built scope by scope; the catalog (human gut, all ages: 2,798 studies with study pages) is the first curated scope. See Methods › Registry classification for the cascade, the vocabularies and what the confidence means.

6,898

human studies (host human = yes 6,652 + mixed 246), 1,171,626 runs · 64,369 INSDC BioProjects screened in total

2,334,512

sequencing runs

637,397

BioSamples with harvested attributes (registry_biosamples.parquet, 4,381 studies): body site known for 51 %, age 16 %, sex 19 %

838,702

runs with a Sandpiper community profile (36 % of runs; 37,328 studies)

2,027,594

BioSamples

43,775

non-human (host human = no) · 13,696 unknown — screened and kept for provenance, excluded from the default explorer view

63,952

classified (99%) · 417 pending

body-site scopes; 2,798 studies are in the curated catalog (human gut, all ages)

Registry: every screened shotgun-metagenome study

Registry explorer

Scopes

Facets

What a registry row is