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Downloads & releases

Data package 1.20.0 (release R2026.25, built 2026-10-12).

About this page

Start with gut_studies.parquet (one row per catalog study) and gut_sample_metadata_wide.parquet (one row per sample); the evidence behind every value is in gut_sample_determinations.parquet; the registry of all human shotgun metagenomes is registry_studies.parquet. Column definitions: data dictionary.

Whole package: data_package_v1.20.0.zip (171.6 MB) GitHub Release data-v1.20.0

Catalog tables (human gut, all ages)

file	rows	size	description
gut_metadata_contradictions.parquet	8,853	113.1 KB
gut_pass_coverage.csv	2,798	187.0 KB
gut_relatedness.parquet	6,572	345.0 KB
gut_relations.parquet	1,122	34.1 KB
gut_runs.parquet	718,658	30.2 MB
gut_sample_determinations.parquet	4,216,259	43.3 MB	Long form: one row per sample × field with route, scope, confidence, evidence_source, evidence_locator and a verbatim evidence quote (≤ 12 words).
gut_sample_determinations_conflicts.parquet	167,355	3.3 MB
gut_sample_metadata_wide.parquet	602,163	21.7 MB	Start here (samples). One row per sample: identifiers, body-site code/class, age_category (+ basis), every field with __route and __confidence, infant extension fields, infant_scope flag.
gut_sandpiper_pca_loadings.parquet	383	36.8 KB
gut_sandpiper_pca_scores.parquet	335,956	12.4 MB
gut_sandpiper_pca_variance.csv	5	531 B
gut_sandpiper_sample_summary.parquet	339,626	23.3 MB
gut_sandpiper_study_coverage.csv	2,837	555.1 KB
gut_sandpiper_study_panels.parquet	26,060	322.8 KB	Per-project mean top-12 genera over profiled gut samples (project-page composition bar).
gut_studies.parquet	2,946	3.0 MB	Start here (studies). One row per catalog study: registry classification, linked papers, per-field coverage (cov_*), age-category and health-condition distributions, curated depth and source.

Registry tables (all human shotgun metagenomes)

file	rows	size	description
registry_authors.parquet	52,110	3.2 MB	Study × author × paper rows for the registry studies (Europe PMC author lists).
registry_bioproject_records.parquet	4,217	911.4 KB	NCBI BioProject records (title, description, umbrella, organisation) for the registry studies.
registry_biosamples.parquet	637,397	4.2 MB	Registry sample tier: one row per harvested BioSample with normalised body site, life stage / age, sex, country.
registry_studies.parquet	64,369	9.0 MB	Registry tier: one row per ENA study with a human shotgun-metagenome signal — host, body sites (UBERON-anchored codes), life stages, assay, access, classification stage, scope memberships, harvested-sample roll-ups.
registry_study_papers.parquet	6,998	624.4 KB	Study ↔ paper links of the registry studies (PMID/PMCID/DOI, relation own_data/unsure, method, confidence).
registry_universe_audit.csv	35	9.2 KB	Registry enumeration audit: per ENA slice, archive count vs rows pulled and completeness.

Release documents

file	rows	size	description
CHANGELOG.md		62.3 KB	Version history.
DATA_DICTIONARY.md		99.2 KB	Every column, every vocabulary.
README.md		23.0 KB	Package overview and how to read a value.
RELEASE_NOTES_R2026.1.md		4.9 KB
RELEASE_NOTES_R2026.10.md		5.1 KB
RELEASE_NOTES_R2026.11.md		5.2 KB
RELEASE_NOTES_R2026.12.md		6.6 KB
RELEASE_NOTES_R2026.13.md		6.9 KB
RELEASE_NOTES_R2026.14.md		5.6 KB
RELEASE_NOTES_R2026.15.md		6.2 KB
RELEASE_NOTES_R2026.16.md		5.9 KB
RELEASE_NOTES_R2026.17.md		6.0 KB
RELEASE_NOTES_R2026.18.md		6.0 KB
RELEASE_NOTES_R2026.19.md		6.1 KB
RELEASE_NOTES_R2026.2.md		4.2 KB
RELEASE_NOTES_R2026.20.md		6.5 KB
RELEASE_NOTES_R2026.21.md		5.8 KB
RELEASE_NOTES_R2026.22.md		5.9 KB
RELEASE_NOTES_R2026.23.md		6.8 KB
RELEASE_NOTES_R2026.24.md		5.7 KB
RELEASE_NOTES_R2026.25.md		6.1 KB
RELEASE_NOTES_R2026.3.md		4.3 KB
RELEASE_NOTES_R2026.4.md		4.1 KB
RELEASE_NOTES_R2026.5.md		4.4 KB
RELEASE_NOTES_R2026.6.md		4.1 KB
RELEASE_NOTES_R2026.7.md		4.1 KB
RELEASE_NOTES_R2026.8.md		4.0 KB
RELEASE_NOTES_R2026.9.md		5.1 KB
VERSION.json		17.2 KB	Package version, release id, release tag, build date, sha256 + rows per table.
getting_started.ipynb		49.3 KB	Notebook: load, filter, join, plot.
releases.csv	30	3.1 KB	Release registry: one row per release id (release date, package version, tags, DOI, headline counts).

Infant extension tables (deep infant-field curation of the infant studies; also present in the catalog tables)

file	rows	size	description
APPLY_FINDINGS_DIFF.md		942 B
APPLY_GAPFILL_PRJNA1140720.json		4.1 KB
AUTHORS_REPORT.md		8.6 KB	Author index: sources, coverage, caveats.
DATAFIX_REPORT.md		13.1 KB
DATA_MODEL_FIX_REPORT.md		14.3 KB	v1.2 data-model fix (age scope, parents, history).
EXTRACTION_REPORT.md		14.8 KB	Infant-field extraction report.
GUT_SANDPIPER_REPORT.md		15.0 KB
REGISTRY_REPORT.md		43.1 KB	Registry build report.
SANDPIPER_REPORT.md		20.5 KB	Sandpiper join: source, method, validation, caveats.
apply_findings_log.csv	4	631 B
authors.parquet	28,367	737.7 KB	Infant extension: study × author × paper rows.
authors_index.json		6.5 MB	Infant extension: author search index.
bitemporal_log.json		1.9 KB
cohorts.csv	373	167.4 KB	Infant extension: curated cohort clusters with unique-infant estimates (the site's cohort pages carry these names).
confidence_tiers.csv	29	4.2 KB	Infant extension: engine confidence tiers.
confirmations.parquet	0	4.3 KB
contribute_worklist.csv	439	397.7 KB	Infant extension: contribution worklist of the infant fields.
contribute_worklist_fields.csv	2,634	386.8 KB	Infant extension: worklist study × field.
extraction_gold_eval_hires.csv	6	326 B	Infant extension: precision/recall vs curatedMetagenomicData.
field_coverage_summary.csv	19	1.5 KB	Infant extension: coverage per infant field.
human_review_queue.csv	52	48.3 KB	Infant extension: studies the infant triage could not decide.
organisations.parquet	18,888	439.4 KB	Infant extension: organisation strings per study.
organisations_index.json		873.4 KB	Infant extension: organisation index.
parent_biosamples.parquet	16	62.4 KB	Infant extension: parent BioSamples of run-level rows.
review_amplicon_runs.csv	39	4.7 KB
review_genomic_only_samples.csv	3,158	380.4 KB
review_named_microbe_metagenomic_samples.csv	70	11.0 KB
runs.parquet	174,172	8.4 MB	Infant extension: run → sample → study for the infant studies.
sample_determinations.parquet	619,647	6.8 MB	Infant extension: evidence rows of the infant-field curation.
sample_determinations_all.parquet	620,963	6.8 MB	Infant extension, bitemporal: current + retired rows with release_added / release_retired.
sample_determinations_superseded.parquet	223	17.4 KB	Infant extension: subset of value_history (v1.1 layout).
sample_metadata_wide.csv.gz	154,356	11.2 MB	Infant extension table as gzip-compressed CSV.
sample_metadata_wide.parquet	153,238	12.3 MB	Infant extension: the deep infant-gut curation (delivery mode, feeding, gestational age, birth weight …) for the infant studies; these rows are also in gut_sample_metadata_wide (curated_source = infant_catalog).
sample_metadata_wide_excluded_by_review.parquet	1,118	146.6 KB
sample_subjects.parquet	154,356	2.8 MB	Infant extension: subject and timepoint resolution per sample.
sample_unit_classification.csv	11,116	2.0 MB	Infant extension: per-BioSample multi-run classification.
sample_unit_classification_by_study.csv	67	6.9 KB	Infant extension: per-study sample-unit class.
sandpiper_auditor_candidate_runs.csv	375	49.6 KB
sandpiper_flag_definitions.json		5.5 KB	Sandpiper's published QC flag definitions.
sandpiper_flag_table.csv	20	4.0 KB	QC-flag vocabulary.
sandpiper_run_qc.parquet	174,172	8.6 MB	Infant-study runs: profiled or miss reason, QC fields.
sandpiper_sample_summary.parquet	79,473	10.0 MB	Sandpiper/SingleM per-sample summary for the infant studies (sp_* columns, QC flags, URL).
sandpiper_study_coverage.csv	389	79.9 KB	Per infant study: runs/samples profiled.
sandpiper_study_panel_status.csv	389	27.2 KB
sandpiper_study_panels.parquet	4,656	73.1 KB	Per-study mean top phyla / genera (infant studies).
sandpiper_study_qc_flags.csv	389	73.2 KB	Per infant study: flag fractions.
sandpiper_top_genera.parquet	1,049,958	4.6 MB	Top-15 genera per profiled infant-study sample.
study_authors_summary.csv	9,579	963.9 KB	Infant extension: first/last author and organisations per screened study.
study_field_coverage_matrix.csv	371	32.2 KB	Infant extension: coverage per infant study × field.
study_metadata_wide.csv	389	480.0 KB	Same table as CSV.
study_metadata_wide.parquet	389	226.0 KB	Infant extension: one row per infant study with infant-field coverage, triage evidence and recoverability tiers.
study_paper_links.csv	973	172.6 KB	Infant extension: curated study ↔ paper links.
study_verdict_history.parquet	32,233	1.0 MB	Infant extension: every triage-stage verdict per screened study.
tier_field_precision.csv	49	2.5 KB	Infant extension: precision per route × tier vs the cMD gold join.
universe_studies_all.parquet	9,581	1.1 MB	Infant extension: the 9.6 k studies screened for the infant extension with verdict and reason.
value_history.parquet	46,587	569.1 KB	Infant extension: superseded / rejected values with reason.

Release assets not on this site

file	description
registry_runs_v1.20.0.parquet	Registry run tier: one row per sequencing run of every registry study (≈ 2 M rows, ≈ 80 MB) — GitHub Release asset data-v1.20.0. — release page
infant_catalog_v1.20.0.sqlite	All package tables as one SQLite database — Release asset. — release page
sandpiper_profiles.parquet	Full sample × rank × taxon Sandpiper profiles of the infant studies (≈100 MB) — Release asset. — release page
gut_sandpiper_sample_genus_v1.20.0_part*.parquet	Genus-level Sandpiper relative abundances for every profiled catalog sample (long table: sample_key, genus, relabund, coverage; ≈ 185 MB in < 90 MB parts, concatenate the parts) — Release asset. — release page
gut_sandpiper_sample_species_v1.20.0_part*.parquet	Species-level Sandpiper relative abundances (relabund ≥ 0.001; ≈ 200 MB in parts) — Release asset. — release page

Site data files

path	files	size	description
data/gut_sample_metadata_wide.parquet	1	21.7 MB	Sample table loaded by the explorer (one row per catalog sample)
data/gut_studies.parquet	1	3.0 MB	Study table loaded by the explorer
data/gut_sample_determinations.parquet	1	43.3 MB	Evidence rows (sample × field with verbatim quote)
data/registry_studies.parquet	1	9.0 MB	Registry tier, loaded by the registry explorer
data/studies/<PRJ>.csv.gz\|.parquet	2798	17.7 MB	Per-study sample slices (gzip CSV + parquet)
data/studies/<PRJ>_determinations.csv.gz	2798	29.7 MB	Per-study evidence rows (gzip CSV, mtime 0)
data/cohorts/<COH>.csv.gz\|.parquet	180	13.8 MB	Per-cohort sample slices (multi-study cohorts)
data/catalog_cohorts.csv	1	17.0 KB	Cohort list (id, name, studies, papers)
data/studies_index.json	1	1.3 MB	Study index used by the Studies table
data/contribute_worklist.json	1	223.1 KB	Contribution worklist (one object per open study)
data/package/	101	160.7 MB	The complete package, file by file, plus the zip
authors/idx/<letter>.json	27	1.3 MB	Author index shards

Integrity: manifest.json (SHA-256 of every data file) · VERSION.json (package tables with row counts and SHA-256). Licence: curated tables CC-BY-4.0; archive metadata under INSDC terms.

Cite this release. Microbiome Repo, release R2026.25 (data package 1.20.0), OlmLab, 2026-10-12.

Concept DOI (all versions, resolves to the latest archived release): 10.5281/zenodo.23087712.

Also cite the upstream sources this catalog is built on:

Releases (30, from releases.csv)

Every release is frozen and archived as a GitHub Release of the data repository (tag data-v<package>) and a site tag (site-v<package>). Numbered releases (R<YYYY>.<n>) start with R2026.1; earlier states are identified by their package version. Every fact row carries release_added / release_retired; the Changes pages list what changed in each release.

Release	Date	Package	Data tag	Site tag	DOI	Studies	Samples	Catalog scope	Determinations (current)	Sandpiper	Changes
R2026.25 current	2026-10-12	1.20.0	data-v1.20.0	site-v1.20.0	pending	389	153238	72254	619647	2.0.0	changes
R2026.24	2026-10-10	1.19.1	data-v1.19.1	site-v1.19.1	pending	389	153238	72254	619647	2.0.0	changes
R2026.23	2026-10-10	1.19.0	data-v1.19.0	site-v1.19.0	pending	389	153238	72254	619647	2.0.0	changes
R2026.22	2026-10-09	1.18.2	data-v1.18.2	site-v1.18.2	pending	389	153238	72254	619647	2.0.0	changes
R2026.21	2026-10-09	1.18.1	data-v1.18.1	site-v1.18.1	pending	389	153238	72254	619647	2.0.0	changes
R2026.20	2026-10-09	1.18.0	data-v1.18.0	site-v1.18.0	pending	389	153238	72254	619647	2.0.0	changes
R2026.19	2026-10-09	1.17.1	data-v1.17.1	site-v1.17.1	pending	389	153238	72254	619647	2.0.0	changes
R2026.18	2026-10-09	1.17.0	data-v1.17.0	site-v1.17.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.17	2026-10-08	1.16.0	data-v1.16.0	site-v1.16.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.16	2026-10-08	1.15.0	data-v1.15.0	site-v1.15.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.15	2026-10-01	1.14.0	data-v1.14.0	site-v1.14.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.14	2026-10-01	1.13.1	data-v1.13.1	site-v1.13.1	pending	389	154356	72358	619647	2.0.0	changes
R2026.13	2026-09-30	1.13.0	data-v1.13.0	site-v1.13.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.12	2026-09-29	1.12.0	data-v1.12.0	site-v1.12.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.11	2026-09-28	1.11.0	data-v1.11.0	site-v1.11.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.10	2026-09-28	1.10.1	data-v1.10.1	site-v1.10.1	pending	389	154356	72358	619647	2.0.0	changes
R2026.9	2026-09-28	1.10.0	data-v1.10.0	site-v1.10.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.8	2026-09-28	1.9.0	data-v1.9.0	site-v1.9.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.7	2026-09-28	1.8.0	data-v1.8.0	site-v1.8.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.6	2026-09-28	1.7.1	data-v1.7.1	site-v1.7.1	pending	389	154356	72358	619647	2.0.0	changes
R2026.5	2026-09-27	1.7.0	data-v1.7.0	site-v1.7.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.4	2026-09-27	1.6.0	data-v1.6.0	site-v1.6.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.3	2026-09-27	1.5.0	data-v1.5.0	site-v1.5.0	pending	389	154356	72358	619647	2.0.0	changes
R2026.2	2026-09-27	1.4.0	data-v1.4.0	site-v1.4.0	pending	389	154206	72358	618898	2.0.0	changes
R2026.1	2026-09-26	1.3.0	data-v1.3.0	site-v1.3.0	pending	389	154206	72358	618898	2.0.0	changes
1.2.2	2026-09-26	1.2.2	data-v1.2.2	site-v1.2.2	pending	389	154206	72358	618898	2.0.0	changes
1.2.1	2026-09-26	1.2.1	—	—	pending	389	154206	71795	618898	2.0.0	changes
1.2.0	2026-09-26	1.2.0	—	—	pending	389	154206	—	618898	2.0.0	changes
1.1.0	2026-09-25	1.1.0	—	—	pending	389	154222	—	609584	—	changes
1.0.0	2026-09-25	1.0.0	—	—	pending	389	—	—	—	—	changes

Empty cells are counts the historical changelog does not state; nothing is back-filled by estimate. Historical rows (1.0.0 … 1.2.2) are documented in the package changelog.

Release notes

R2026.25 — package 1.20.0, 2026-10-12 (markdown)

Release notes — R2026.25 (data package 1.20.0, 2026-10-12)

Generated by catalog.release.release_notes from package 1.19.1 (R2026.24, 2026-10-10) → 1.20.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.19.1	1.20.0	added	removed
catalog studies	2,893	2,798	0	95
catalog samples	588,558	573,001	1,520	17,077
sample × field values (current)	4,137,747	4,216,259	+78,512
catalog runs (`gut_runs`)	738,792	718,658	-20,134

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.19.1	cov	n 1.20.0	cov	Δ n
`age_category`	382,141	64.9%	377,233	65.8%	-4,908
`country`	539,556	91.7%	523,605	91.4%	-15,951
`health_condition`	287,466	48.8%	285,987	49.9%	-1,479
`subject_id`	438,961	74.6%	427,176	74.6%	-11,785
`age_at_collection_days`	168,354	28.6%	165,005	28.8%	-3,349
`sex`	192,382	32.7%	192,169	33.5%	-213
`detailed_location`	307,507	52.2%	309,721	54.1%	+2,214
`lifestyle`	19,989	3.4%	18,872	3.3%	-1,117
`collection_date`	435,563	74.0%	440,066	76.8%	+4,503
`intervention`	48,569	8.3%	49,152	8.6%	+583
`antibiotic_exposure`	115,253	19.6%	115,622	20.2%	+369
`bmi`	52,697	9.0%	53,613	9.4%	+916
`timepoint_label`	181,731	30.9%	179,698	31.4%	-2,033
`diet`	14,427	2.5%	16,929	3.0%	+2,502
`smoking_status`	12,472	2.1%	13,957	2.4%	+1,485
`medication`	10,048	1.7%	10,552	1.8%	+504
`stool_consistency_bristol`	3,038	0.5%	3,038	0.5%	+0

Registry (`registry_studies`)

entity	1.19.1	1.20.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.19.1	1.20.0	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.19.1	cov	n 1.20.0	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.20.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.19.1	1.20.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.19.1	prec 1.19.1	rec 1.19.1	cov 1.20.0	prec 1.20.0	rec 1.20.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: gut_metadata_contradictions.parquet, gut_pass_coverage.csv Removed files: none

table	columns added	columns removed
`gut_studies.parquet`	`n_contradicted_samples`, `contradiction_summary`, `n_relations`, `longitudinal_resolved`, `relatedness_resolved`	—

VERSION.json: package_version=1.20.0, previous_release_id=R2026.24, release_id=R2026.25, release_tag=data-v1.20.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.25). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: ≈ 12 M tokens (16 sub-agents + 4 follow-ups re-running shards that duplicated a sibling) (docs/CYCLE_LOG.md row R2026.25)

R2026.24 — package 1.19.1, 2026-10-10 (markdown)

Release notes — R2026.24 (data package 1.19.1, 2026-10-10)

Generated by catalog.release.release_notes from package 1.19.0 (R2026.23, 2026-10-10) → 1.19.1. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.19.0	1.19.1	added	removed
catalog studies	2,893	2,893	0	0
catalog samples	588,558	588,558	0	0
sample × field values (current)	4,127,431	4,137,747	+10,316
catalog runs (`gut_runs`)	738,792	738,792	+0

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.19.0	cov	n 1.19.1	cov	Δ n
`age_category`	382,141	64.9%	382,141	64.9%	+0
`country`	539,556	91.7%	539,556	91.7%	+0
`health_condition`	287,466	48.8%	287,466	48.8%	+0
`subject_id`	434,745	73.9%	438,961	74.6%	+4,216
`age_at_collection_days`	168,354	28.6%	168,354	28.6%	+0
`sex`	192,382	32.7%	192,382	32.7%	+0
`detailed_location`	307,507	52.2%	307,507	52.2%	+0
`lifestyle`	19,989	3.4%	19,989	3.4%	+0
`collection_date`	435,563	74.0%	435,563	74.0%	+0
`intervention`	48,569	8.3%	48,569	8.3%	+0
`antibiotic_exposure`	115,253	19.6%	115,253	19.6%	+0
`bmi`	52,697	9.0%	52,697	9.0%	+0
`timepoint_label`	181,731	30.9%	181,731	30.9%	+0
`diet`	14,427	2.5%	14,427	2.5%	+0
`smoking_status`	12,472	2.1%	12,472	2.1%	+0
`medication`	10,048	1.7%	10,048	1.7%	+0
`stool_consistency_bristol`	3,038	0.5%	3,038	0.5%	+0

Registry (`registry_studies`)

entity	1.19.0	1.19.1	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.19.0	1.19.1	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.19.0	cov	n 1.19.1	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.19.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.19.0	1.19.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.19.0	prec 1.19.0	rec 1.19.0	cov 1.19.1	prec 1.19.1	rec 1.19.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.19.1, previous_release_id=R2026.23, release_id=R2026.24, release_tag=data-v1.19.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.24). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.23 — package 1.19.0, 2026-10-10 (markdown)

Release notes — R2026.23 (data package 1.19.0, 2026-10-10)

Generated by catalog.release.release_notes from package 1.18.2 (R2026.22, 2026-10-09) → 1.19.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.18.2	1.19.0	added	removed
catalog studies	2,893	2,893	0	0
catalog samples	588,558	588,558	0	0
sample × field values (current)	3,920,362	4,127,431	+207,069
catalog runs (`gut_runs`)	738,792	738,792	+0

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.18.2	cov	n 1.19.0	cov	Δ n
`age_category`	382,141	64.9%	382,141	64.9%	+0
`country`	539,556	91.7%	539,556	91.7%	+0
`health_condition`	287,466	48.8%	287,466	48.8%	+0
`subject_id`	319,084	54.2%	434,745	73.9%	+115,661
`age_at_collection_days`	168,354	28.6%	168,354	28.6%	+0
`sex`	192,382	32.7%	192,382	32.7%	+0
`detailed_location`	307,507	52.2%	307,507	52.2%	+0
`lifestyle`	19,989	3.4%	19,989	3.4%	+0
`collection_date`	435,563	74.0%	435,563	74.0%	+0
`intervention`	48,569	8.3%	48,569	8.3%	+0
`antibiotic_exposure`	115,253	19.6%	115,253	19.6%	+0
`bmi`	52,697	9.0%	52,697	9.0%	+0
`timepoint_label`	177,137	30.1%	181,731	30.9%	+4,594
`diet`	14,427	2.5%	14,427	2.5%	+0
`smoking_status`	12,472	2.1%	12,472	2.1%	+0
`medication`	10,048	1.7%	10,048	1.7%	+0
`stool_consistency_bristol`	3,038	0.5%	3,038	0.5%	+0

Registry (`registry_studies`)

entity	1.18.2	1.19.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.18.2	1.19.0	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.18.2	cov	n 1.19.0	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.19.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.18.2	1.19.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.18.2	prec 1.18.2	rec 1.18.2	cov 1.19.0	prec 1.19.0	rec 1.19.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: gut_relatedness.parquet, gut_relations.parquet Removed files: none

table	columns added	columns removed
`gut_sample_metadata_wide.parquet`	`family_id`, `family_id__confidence`, `family_id__route`, `family_role`, `family_role__confidence`, `family_role__route`, `shared_setting_type`, `shared_setting_type__confidence`, `shared_setting_type__route`, `shared_setting_id`, `shared_setting_id__confidence`, `shared_setting_id__route`, `subject_n_samples`, `days_since_first_sample`, `time_axis`, `person_key`	—
`gut_studies.parquet`	`cov_family_id`, `cov_family_role`, `cov_shared_setting_type`, `cov_shared_setting_id`, `n_subjects`, `n_subjects_repeated`, `n_samples_repeated`, `samples_per_subject_median`, `samples_per_subject_max`, `followup_days_median`, `followup_days_max`, `interval_days_median`, `time_axis`, `longitudinal_status`, `n_families`, `n_related_people`, `n_mother_child_families`, `n_twin_sets`, `n_shared_settings`, `family_motifs`, `shared_setting_types`, `relatedness_designs`, `relatedness_summary`, `longitudinal_design`, `sampling_schedule`, `planned_offsets_days`, `time_origin`, `followup_days_stated`	—

VERSION.json: package_version=1.19.0, previous_release_id=R2026.22, release_id=R2026.23, release_tag=data-v1.19.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.23). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.22 — package 1.18.2, 2026-10-09 (markdown)

Release notes — R2026.22 (data package 1.18.2, 2026-10-09)

Generated by catalog.release.release_notes from package 1.18.1 (R2026.21, 2026-10-09) → 1.18.2. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.18.1	1.18.2	added	removed
catalog studies	2,918	2,893	0	25
catalog samples	588,558	588,558	0	0
sample × field values (current)	3,920,362	3,920,362	+0
catalog runs (`gut_runs`)	738,985	738,792	-193

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.18.1	cov	n 1.18.2	cov	Δ n
`age_category`	382,141	64.9%	382,141	64.9%	+0
`country`	539,556	91.7%	539,556	91.7%	+0
`health_condition`	287,466	48.8%	287,466	48.8%	+0
`subject_id`	319,084	54.2%	319,084	54.2%	+0
`age_at_collection_days`	168,354	28.6%	168,354	28.6%	+0
`sex`	192,382	32.7%	192,382	32.7%	+0
`detailed_location`	307,507	52.2%	307,507	52.2%	+0
`lifestyle`	19,989	3.4%	19,989	3.4%	+0
`collection_date`	435,563	74.0%	435,563	74.0%	+0
`intervention`	48,569	8.3%	48,569	8.3%	+0
`antibiotic_exposure`	115,253	19.6%	115,253	19.6%	+0
`bmi`	52,697	9.0%	52,697	9.0%	+0
`timepoint_label`	177,137	30.1%	177,137	30.1%	+0
`diet`	14,427	2.5%	14,427	2.5%	+0
`smoking_status`	12,472	2.1%	12,472	2.1%	+0
`medication`	10,048	1.7%	10,048	1.7%	+0
`stool_consistency_bristol`	3,038	0.5%	3,038	0.5%	+0

Registry (`registry_studies`)

entity	1.18.1	1.18.2	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.18.1	1.18.2	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.18.1	cov	n 1.18.2	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.18.2: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.18.1	1.18.2
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.18.1	prec 1.18.1	rec 1.18.1	cov 1.18.2	prec 1.18.2	rec 1.18.2
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

table	columns added	columns removed
`gut_studies.parquet`	`study_group_id`, `study_group_basis`, `study_group_members`, `study_group_n_samples`	—

VERSION.json: package_version=1.18.2, previous_release_id=R2026.21, release_id=R2026.22, release_tag=data-v1.18.2

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.22). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.21 — package 1.18.1, 2026-10-09 (markdown)

Release notes — R2026.21 (data package 1.18.1, 2026-10-09)

Generated by catalog.release.release_notes from package 1.18.0 (R2026.20, 2026-10-09) → 1.18.1. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.18.0	1.18.1	added	removed
catalog studies	2,918	2,918	0	0
catalog samples	587,603	588,558	1,413	458
sample × field values (current)	3,849,193	3,920,362	+71,169
catalog runs (`gut_runs`)	738,985	738,985	+0

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.18.0	cov	n 1.18.1	cov	Δ n
`age_category`	380,206	64.7%	382,141	64.9%	+1,935
`country`	536,847	91.4%	539,556	91.7%	+2,709
`health_condition`	277,223	47.2%	287,466	48.8%	+10,243
`subject_id`	309,272	52.6%	319,084	54.2%	+9,812
`age_at_collection_days`	164,899	28.1%	168,354	28.6%	+3,455
`sex`	189,231	32.2%	192,382	32.7%	+3,151
`detailed_location`	305,035	51.9%	307,507	52.2%	+2,472
`lifestyle`	19,100	3.3%	19,989	3.4%	+889
`collection_date`	426,579	72.6%	435,563	74.0%	+8,984
`intervention`	47,429	8.1%	48,569	8.3%	+1,140
`antibiotic_exposure`	111,237	18.9%	115,253	19.6%	+4,016
`bmi`	50,868	8.7%	52,697	9.0%	+1,829
`timepoint_label`	170,618	29.0%	177,137	30.1%	+6,519
`diet`	14,085	2.4%	14,427	2.5%	+342
`smoking_status`	12,252	2.1%	12,472	2.1%	+220
`medication`	9,449	1.6%	10,048	1.7%	+599
`stool_consistency_bristol`	3,037	0.5%	3,038	0.5%	+1

Registry (`registry_studies`)

entity	1.18.0	1.18.1	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.18.0	1.18.1	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.18.0	cov	n 1.18.1	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.18.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.18.0	1.18.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.18.0	prec 1.18.0	rec 1.18.0	cov 1.18.1	prec 1.18.1	rec 1.18.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.18.1, previous_release_id=R2026.20, release_id=R2026.21, release_tag=data-v1.18.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.21). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.20 — package 1.18.0, 2026-10-09 (markdown)

Release notes — R2026.20 (data package 1.18.0, 2026-10-09)

Generated by catalog.release.release_notes from package 1.17.1 (R2026.19, 2026-10-09) → 1.18.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.17.1	1.18.0	added	removed
catalog studies	2,865	2,918	53	0
catalog samples	571,712	587,603	15,915	24
sample × field values (current)	3,825,853	3,849,193	+23,340
catalog runs (`gut_runs`)	724,147	738,985	+14,838

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.17.1	cov	n 1.18.0	cov	Δ n
`age_category`	371,975	65.1%	380,206	64.7%	+8,231
`country`	524,020	91.7%	536,847	91.4%	+12,827
`health_condition`	275,748	48.2%	277,223	47.2%	+1,475
`subject_id`	309,271	54.1%	309,272	52.6%	+1
`age_at_collection_days`	162,995	28.5%	164,899	28.1%	+1,904
`sex`	187,001	32.7%	189,231	32.2%	+2,230
`detailed_location`	303,665	53.1%	305,035	51.9%	+1,370
`lifestyle`	19,011	3.3%	19,100	3.3%	+89
`collection_date`	426,018	74.5%	426,579	72.6%	+561
`intervention`	47,430	8.3%	47,429	8.1%	-1
`antibiotic_exposure`	110,928	19.4%	111,237	18.9%	+309
`bmi`	50,867	8.9%	50,868	8.7%	+1
`timepoint_label`	170,618	29.8%	170,618	29.0%	+0
`diet`	14,085	2.5%	14,085	2.4%	+0
`smoking_status`	12,252	2.1%	12,252	2.1%	+0
`medication`	9,449	1.7%	9,449	1.6%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

New catalog studies: PRJDB2800, PRJDB8879, PRJEB38742, PRJEB44907, PRJEB47736, PRJEB50505, PRJEB58879, PRJEB60692, PRJEB62678, PRJEB63587, PRJEB66487, PRJEB74035, PRJEB75353, PRJEB75807, PRJEB76399, PRJEB86785, PRJEB86881, PRJNA1064103, PRJNA1079071, PRJNA1082417, PRJNA1088910, PRJNA1125836, PRJNA1145114, PRJNA1192252, PRJNA1277853, PRJNA1372070, PRJNA1372073, PRJNA1423207, PRJNA256106, PRJNA302832, PRJNA308867, PRJNA317435, PRJNA336061, PRJNA413199, PRJNA413356, PRJNA427187, PRJNA504921, PRJNA588514, PRJNA648796, PRJNA648797, PRJNA665061, PRJNA715245, PRJNA730689, PRJNA734321, PRJNA790678, PRJNA825696, PRJNA877820, PRJNA879122, PRJNA881338, PRJNA898150, PRJNA912122, PRJNA939268, PRJNA944553

Registry (`registry_studies`)

entity	1.17.1	1.18.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.17.1	1.18.0	added	removed
included studies	389	389	0	0
catalog samples	153,238	153,238	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,254 → 72,254); field list from field_coverage_summary.csv.

field	n 1.17.1	cov	n 1.18.0	cov	Δ n
`probiotic_exposure`	2,573	3.6%	2,573	3.6%	+0
`preterm_status`	32,289	44.7%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	17.0%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.7%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,582	72.8%	52,582	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,267	95.9%	69,267	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,284	8.7%	6,284	8.7%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,296	44.7%	32,296	44.7%	+0
`timepoint_label`	27,035	37.4%	27,035	37.4%	+0
`subject_id`	42,930	59.4%	42,930	59.4%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.18.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.17.1	1.18.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.17.1	prec 1.17.1	rec 1.17.1	cov 1.18.0	prec 1.18.0	rec 1.18.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: gut_sandpiper_study_panels.parquet Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.18.0, previous_release_id=R2026.19, release_id=R2026.20, release_tag=data-v1.18.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.20). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.19 — package 1.17.1, 2026-10-09 (markdown)

Release notes — R2026.19 (data package 1.17.1, 2026-10-09)

Generated by catalog.release.release_notes from package 1.17.0 (R2026.18, 2026-10-09) → 1.17.1. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.17.0	1.17.1	added	removed
catalog studies	2,866	2,865	0	1
catalog samples	572,830	571,712	0	1,118
sample × field values (current)	3,825,853	3,825,853	+0
catalog runs (`gut_runs`)	725,265	724,147	-1,118

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.17.0	cov	n 1.17.1	cov	Δ n
`age_category`	373,069	65.1%	371,975	65.1%	-1,094
`country`	525,138	91.7%	524,020	91.7%	-1,118
`health_condition`	276,737	48.3%	275,748	48.2%	-989
`subject_id`	310,389	54.2%	309,271	54.1%	-1,118
`age_at_collection_days`	164,088	28.6%	162,995	28.5%	-1,093
`sex`	188,119	32.8%	187,001	32.7%	-1,118
`detailed_location`	303,665	53.0%	303,665	53.1%	+0
`lifestyle`	20,129	3.5%	19,011	3.3%	-1,118
`collection_date`	426,018	74.4%	426,018	74.5%	+0
`intervention`	47,897	8.4%	47,430	8.3%	-467
`antibiotic_exposure`	110,963	19.4%	110,928	19.4%	-35
`bmi`	51,807	9.0%	50,867	8.9%	-940
`timepoint_label`	171,736	30.0%	170,618	29.8%	-1,118
`diet`	14,085	2.5%	14,085	2.5%	+0
`smoking_status`	12,252	2.1%	12,252	2.1%	+0
`medication`	9,449	1.6%	9,449	1.7%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

Registry (`registry_studies`)

entity	1.17.0	1.17.1	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.17.0	1.17.1	added	removed
included studies	389	389	0	0
catalog samples	154,356	153,238	0	1,118

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,254); field list from field_coverage_summary.csv.

field	n 1.17.0	cov	n 1.17.1	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,573	3.6%	-93
`preterm_status`	32,289	44.6%	32,289	44.7%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	17.0%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.7%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,582	72.8%	-67
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,267	95.9%	-104
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,284	8.7%	-104
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,296	44.7%	-104
`timepoint_label`	27,102	37.5%	27,035	37.4%	-67
`subject_id`	43,034	59.5%	42,930	59.4%	-104

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.17.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

APPLY_FINDINGS_DIFF.md is shipped in the package.

Sandpiper snapshot

	1.17.0	1.17.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.17.0	prec 1.17.0	rec 1.17.0	cov 1.17.1	prec 1.17.1	rec 1.17.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: APPLY_FINDINGS_DIFF.md, apply_findings_log.csv, confirmations.parquet, sample_metadata_wide_excluded_by_review.parquet Removed files: none

table	columns added	columns removed
`gut_studies.parquet`	`src_verified`	`src_expert`
`sample_determinations.parquet`	`decision_stage`	—
`sample_determinations_all.parquet`	`decision_stage`	—

VERSION.json: package_version=1.17.1, previous_release_id=R2026.18, release_id=R2026.19, release_tag=data-v1.17.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.19). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.18 — package 1.17.0, 2026-10-09 (markdown)

Release notes — R2026.18 (data package 1.17.0, 2026-10-09)

Generated by catalog.release.release_notes from package 1.16.0 (R2026.17, 2026-10-08) → 1.17.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.16.0	1.17.0	added	removed
catalog studies	2,883	2,866	0	17
catalog samples	580,407	572,830	0	7,577
sample × field values (current)	3,351,031	3,825,853	+474,822
catalog runs (`gut_runs`)	726,300	725,265	-1,035

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.16.0	cov	n 1.17.0	cov	Δ n
`age_category`	369,851	63.7%	373,069	65.1%	+3,218
`country`	527,221	90.8%	525,138	91.7%	-2,083
`health_condition`	229,765	39.6%	276,737	48.3%	+46,972
`subject_id`	199,219	34.3%	310,389	54.2%	+111,170
`age_at_collection_days`	152,735	26.3%	164,088	28.6%	+11,353
`sex`	179,009	30.8%	188,119	32.8%	+9,110
`detailed_location`	305,460	52.6%	303,665	53.0%	-1,795
`lifestyle`	17,680	3.0%	20,129	3.5%	+2,449
`collection_date`	365,329	62.9%	426,018	74.4%	+60,689
`intervention`	20,242	3.5%	47,897	8.4%	+27,655
`antibiotic_exposure`	98,036	16.9%	110,963	19.4%	+12,927
`bmi`	48,794	8.4%	51,807	9.0%	+3,013
`timepoint_label`	78,320	13.5%	171,736	30.0%	+93,416
`diet`	4,168	0.7%	14,085	2.5%	+9,917
`smoking_status`	4,823	0.8%	12,252	2.1%	+7,429
`medication`	3,829	0.7%	9,449	1.6%	+5,620
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

Registry (`registry_studies`)

entity	1.16.0	1.17.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.16.0	1.17.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.16.0	cov	n 1.17.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.17.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.16.0	1.17.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.16.0	prec 1.16.0	rec 1.16.0	cov 1.17.0	prec 1.17.0	rec 1.17.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: RELEASE_NOTES_R2026.18.md Removed files: none

table	columns added	columns removed
`gut_studies.parquet`	`src_archive`, `src_abstract`, `src_fulltext`, `src_supplement`, `src_external`, `src_contribution`, `src_expert`, `src_detail`, `short_title`, `short_description`, `short_description_model`, `short_description_sources`	—

VERSION.json: package_version=1.17.0, previous_release_id=R2026.17, release_id=R2026.18, release_tag=data-v1.17.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.18). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.17 — package 1.16.0, 2026-10-08 (markdown)

Release notes — R2026.17 (data package 1.16.0, 2026-10-08)

Generated by catalog.release.release_notes from package 1.15.0 (R2026.16, 2026-10-08) → 1.16.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.15.0	1.16.0	added	removed
catalog studies	2,886	2,883	6	9
catalog samples	582,739	580,407	474	2,806
sample × field values (current)	3,212,545	3,351,031	+138,486
catalog runs (`gut_runs`)	726,407	726,300	-107

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.15.0	cov	n 1.16.0	cov	Δ n
`age_category`	368,891	63.3%	369,851	63.7%	+960
`country`	528,167	90.6%	527,221	90.8%	-946
`health_condition`	219,666	37.7%	229,765	39.6%	+10,099
`subject_id`	199,258	34.2%	199,219	34.3%	-39
`age_at_collection_days`	150,537	25.8%	152,735	26.3%	+2,198
`sex`	179,631	30.8%	179,009	30.8%	-622
`detailed_location`	264,581	45.4%	305,460	52.6%	+40,879
`lifestyle`	8,706	1.5%	17,680	3.0%	+8,974
`collection_date`	342,107	58.7%	365,329	62.9%	+23,222
`intervention`	20,242	3.5%	20,242	3.5%	+0
`antibiotic_exposure`	96,609	16.6%	98,036	16.9%	+1,427
`bmi`	40,799	7.0%	48,794	8.4%	+7,995
`timepoint_label`	78,695	13.5%	78,320	13.5%	-375
`diet`	4,168	0.7%	4,168	0.7%	+0
`smoking_status`	4,823	0.8%	4,823	0.8%	+0
`medication`	3,829	0.7%	3,829	0.7%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

New catalog studies: PRJEB6358, PRJNA1441102, PRJNA1501268, PRJNA783956, PRJNA804967, PRJNA895415

Registry (`registry_studies`)

entity	1.15.0	1.16.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.15.0	1.16.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.15.0	cov	n 1.16.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.16.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.15.0	1.16.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.15.0	prec 1.15.0	rec 1.15.0	cov 1.16.0	prec 1.16.0	rec 1.16.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.16.0, previous_release_id=R2026.16, release_id=R2026.17, release_tag=data-v1.16.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.17). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: ≈ 3.1 M billable tokens (3 registry reclass leaves 2.08 M; infant R4 0.74 M; infant R1 0.26 M utility; host audit and new-study harvest small) (docs/CYCLE_LOG.md row R2026.17)

R2026.16 — package 1.15.0, 2026-10-08 (markdown)

Release notes — R2026.16 (data package 1.15.0, 2026-10-08)

Generated by catalog.release.release_notes from package 1.14.0 (R2026.15, 2026-10-01) → 1.15.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.14.0	1.15.0	added	removed
catalog studies	2,886	2,886	0	0
catalog samples	582,739	582,739	0	0
sample × field values (current)	3,212,545	3,212,545	+0
catalog runs (`gut_runs`)	725,401	726,407	+1,006

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.14.0	cov	n 1.15.0	cov	Δ n
`age_category`	368,891	63.3%	368,891	63.3%	+0
`country`	528,167	90.6%	528,167	90.6%	+0
`health_condition`	219,666	37.7%	219,666	37.7%	+0
`subject_id`	199,258	34.2%	199,258	34.2%	+0
`age_at_collection_days`	150,537	25.8%	150,537	25.8%	+0
`sex`	179,631	30.8%	179,631	30.8%	+0
`detailed_location`	264,581	45.4%	264,581	45.4%	+0
`lifestyle`	8,706	1.5%	8,706	1.5%	+0
`collection_date`	342,107	58.7%	342,107	58.7%	+0
`intervention`	20,242	3.5%	20,242	3.5%	+0
`antibiotic_exposure`	96,609	16.6%	96,609	16.6%	+0
`bmi`	40,799	7.0%	40,799	7.0%	+0
`timepoint_label`	78,695	13.5%	78,695	13.5%	+0
`diet`	4,168	0.7%	4,168	0.7%	+0
`smoking_status`	4,823	0.8%	4,823	0.8%	+0
`medication`	3,829	0.7%	3,829	0.7%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

Registry (`registry_studies`)

entity	1.14.0	1.15.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.14.0	1.15.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.14.0	cov	n 1.15.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.15.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.14.0	1.15.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.14.0	prec 1.14.0	rec 1.14.0	cov 1.15.0	prec 1.15.0	rec 1.15.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

table	columns added	columns removed
`gut_runs.parquet`	`run_study_accession`, `base_count_source`	—
`gut_sample_metadata_wide.parquet`	`n_runs`, `seq_gbp`, `seq_reads`, `seq_depth_source`	—
`gut_studies.parquet`	`gbp_per_sample_median`	—

VERSION.json: package_version=1.15.0, previous_release_id=R2026.15, release_id=R2026.16, release_tag=data-v1.15.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.16). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.15 — package 1.14.0, 2026-10-01 (markdown)

Release notes — R2026.15 (data package 1.14.0, 2026-10-01)

Generated by catalog.release.release_notes from package 1.13.1 (R2026.14, 2026-10-01) → 1.14.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.13.1	1.14.0	added	removed
catalog studies	2,886	2,886	0	0
catalog samples	582,739	582,739	0	0
sample × field values (current)	3,172,061	3,212,545	+40,484
catalog runs (`gut_runs`)	725,401	725,401	+0

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.13.1	cov	n 1.14.0	cov	Δ n
`age_category`	368,891	63.3%	368,891	63.3%	+0
`country`	528,167	90.6%	528,167	90.6%	+0
`health_condition`	219,666	37.7%	219,666	37.7%	+0
`subject_id`	199,258	34.2%	199,258	34.2%	+0
`age_at_collection_days`	150,537	25.8%	150,537	25.8%	+0
`sex`	179,631	30.8%	179,631	30.8%	+0
`detailed_location`	264,581	45.4%	264,581	45.4%	+0
`lifestyle`	8,706	1.5%	8,706	1.5%	+0
`collection_date`	342,107	58.7%	342,107	58.7%	+0
`intervention`	0	0.0%	20,242	3.5%	+20,242
`antibiotic_exposure`	96,609	16.6%	96,609	16.6%	+0
`bmi`	40,799	7.0%	40,799	7.0%	+0
`timepoint_label`	78,695	13.5%	78,695	13.5%	+0
`diet`	4,168	0.7%	4,168	0.7%	+0
`smoking_status`	4,823	0.8%	4,823	0.8%	+0
`medication`	3,829	0.7%	3,829	0.7%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

Registry (`registry_studies`)

entity	1.13.1	1.14.0	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.13.1	1.14.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.13.1	cov	n 1.14.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.14.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.13.1	1.14.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.13.1	prec 1.13.1	rec 1.13.1	cov 1.14.0	prec 1.14.0	rec 1.14.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

table	columns added	columns removed
`gut_sample_metadata_wide.parquet`	`intervention`, `intervention__confidence`, `intervention__route`, `intervention_detail`, `intervention_detail__confidence`, `intervention_detail__route`	—
`gut_studies.parquet`	`cov_intervention`, `cov_intervention_detail`, `cov_age_category`, `interventions`, `interventions_unreplicated`, `intervention_design`, `intervention_detail`, `population_condition`, `intervention_evidence_source`, `intervention_evidence_quote`, `intervention_confidence`, `intervention_route`, `intervention_determined_by`	—

VERSION.json: package_version=1.14.0, previous_release_id=R2026.14, release_id=R2026.15, release_tag=data-v1.14.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.15). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.14 — package 1.13.1, 2026-10-01 (markdown)

Release notes — R2026.14 (data package 1.13.1, 2026-10-01)

Generated by catalog.release.release_notes from package 1.13.0 (R2026.13, 2026-09-30) → 1.13.1. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.13.0	1.13.1	added	removed
catalog studies	2,887	2,886	0	1
catalog samples	582,841	582,739	0	102
sample × field values (current)	3,171,459	3,172,061	+602
catalog runs (`gut_runs`)	725,603	725,401	-202

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.13.0	cov	n 1.13.1	cov	Δ n
`age_at_collection_days`	150,537	25.8%	150,537	25.8%	+0
`sex`	179,733	30.8%	179,631	30.8%	-102
`country`	528,167	90.6%	528,167	90.6%	+0
`health_condition`	219,768	37.7%	219,666	37.7%	-102
`subject_id`	199,360	34.2%	199,258	34.2%	-102
`detailed_location`	264,581	45.4%	264,581	45.4%	+0
`lifestyle`	8,706	1.5%	8,706	1.5%	+0
`collection_date`	341,505	58.6%	342,107	58.7%	+602
`antibiotic_exposure`	96,609	16.6%	96,609	16.6%	+0
`bmi`	40,799	7.0%	40,799	7.0%	+0
`timepoint_label`	78,695	13.5%	78,695	13.5%	+0
`diet`	4,168	0.7%	4,168	0.7%	+0
`smoking_status`	4,823	0.8%	4,823	0.8%	+0
`medication`	3,829	0.7%	3,829	0.7%	+0
`stool_consistency_bristol`	3,037	0.5%	3,037	0.5%	+0

Registry (`registry_studies`)

entity	1.13.0	1.13.1	added	removed
registry studies	64,369	64,369	0	0

Infant extension: studies and samples

entity	1.13.0	1.13.1	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.13.0	cov	n 1.13.1	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.13.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.13.0	1.13.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.13.0	prec 1.13.0	rec 1.13.0	cov 1.13.1	prec 1.13.1	rec 1.13.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.13.1, previous_release_id=R2026.13, release_id=R2026.14, release_tag=data-v1.13.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.14). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.13 — package 1.13.0, 2026-09-30 (markdown)

Release notes — R2026.13 (data package 1.13.0, 2026-09-30)

Generated by catalog.release.release_notes from package 1.12.0 (R2026.12, 2026-09-29) → 1.13.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.12.0	1.13.0	added	removed
catalog studies	2,837	2,887	50	0
catalog samples	579,252	582,841	3,589	0
sample × field values (current)	3,136,707	3,171,459	+34,752
catalog runs (`gut_runs`)	721,678	725,603	+3,925

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.12.0	cov	n 1.13.0	cov	Δ n
`age_at_collection_days`	150,537	26.0%	150,537	25.8%	+0
`sex`	179,611	31.0%	179,733	30.8%	+122
`country`	527,707	91.1%	528,167	90.6%	+460
`health_condition`	217,169	37.5%	219,768	37.7%	+2,599
`subject_id`	199,360	34.4%	199,360	34.2%	+0
`detailed_location`	264,324	45.6%	264,581	45.4%	+257
`lifestyle`	10,658	1.8%	8,706	1.5%	-1,952
`collection_date`	340,455	58.8%	341,505	58.6%	+1,050
`antibiotic_exposure`	95,258	16.4%	96,609	16.6%	+1,351
`bmi`	40,799	7.0%	40,799	7.0%	+0
`timepoint_label`	78,695	13.6%	78,695	13.5%	+0
`diet`	0	0.0%	4,168	0.7%	+4,168
`smoking_status`	0	0.0%	4,823	0.8%	+4,823
`medication`	0	0.0%	3,829	0.7%	+3,829
`stool_consistency_bristol`	0	0.0%	3,037	0.5%	+3,037

New catalog studies: PRJDB14272, PRJDB43252, PRJDB43571, PRJEB120967, PRJEB120968, PRJEB120969, PRJEB19677, PRJEB81819, PRJEB87798, PRJEB91792, PRJEB96943, PRJNA1036657, PRJNA1045701, PRJNA1144402, PRJNA1165510, PRJNA1219549, PRJNA1221567, PRJNA1242044, PRJNA1251023, PRJNA1273462, PRJNA1295133, PRJNA1295840, PRJNA1297975, PRJNA1306109, PRJNA1333319, PRJNA1358001, PRJNA1368707, PRJNA1377467, PRJNA1391873, PRJNA1394613, PRJNA1401443, PRJNA1454700, PRJNA1457283, PRJNA1457996, PRJNA293986, PRJNA356544, PRJNA566436, PRJNA594824, PRJNA609594, PRJNA715947, PRJNA755511, PRJNA788147, PRJNA971196, PRJNA982264, SRP000287, SRP005975, SRP006081, SRP006764, SRP012035, SRP057027

Registry (`registry_studies`)

entity	1.12.0	1.13.0	added	removed
registry studies	54,410	64,369	9,959	0

Infant extension: studies and samples

entity	1.12.0	1.13.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.12.0	cov	n 1.13.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.13.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.12.0	1.13.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.12.0	prec 1.12.0	rec 1.12.0	cov 1.13.0	prec 1.13.0	rec 1.13.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

table	columns added	columns removed
`gut_sample_metadata_wide.parquet`	`diet`, `diet__confidence`, `diet__route`, `diet_detail`, `diet_detail__confidence`, `diet_detail__route`, `smoking_status`, `smoking_status__confidence`, `smoking_status__route`, `medication`, `medication__confidence`, `medication__route`, `medication_detail`, `medication_detail__confidence`, `medication_detail__route`, `stool_consistency_bristol`, `stool_consistency_bristol__confidence`, `stool_consistency_bristol__route`	—
`gut_studies.parquet`	`cov_diet`, `cov_diet_detail`, `cov_smoking_status`, `cov_medication`, `cov_medication_detail`, `cov_stool_consistency_bristol`	—

VERSION.json: package_version=1.13.0, previous_release_id=R2026.12, release_id=R2026.13, release_tag=data-v1.13.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.13). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.12 — package 1.12.0, 2026-09-29 (markdown)

Release notes — R2026.12 (data package 1.12.0, 2026-09-29)

Generated by catalog.release.release_notes from package 1.11.0 (R2026.11, 2026-09-28) → 1.12.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.11.0	1.12.0	added	removed
catalog studies	2,837	2,837	0	0
catalog samples	579,252	579,252	0	0
sample × field values (current)	1,861,883	3,136,707	+1,274,824
catalog runs (`gut_runs`)	0	721,678	+721,678

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.11.0	cov	n 1.12.0	cov	Δ n
`age_at_collection_days`	150,537	26.0%	150,537	26.0%	+0
`sex`	179,611	31.0%	179,611	31.0%	+0
`country`	527,707	91.1%	527,707	91.1%	+0
`health_condition`	217,169	37.5%	217,169	37.5%	+0
`subject_id`	199,360	34.4%	199,360	34.4%	+0
`detailed_location`	0	0.0%	264,324	45.6%	+264,324
`lifestyle`	0	0.0%	10,658	1.8%	+10,658
`collection_date`	0	0.0%	340,455	58.8%	+340,455
`antibiotic_exposure`	95,258	16.4%	95,258	16.4%	+0
`bmi`	40,799	7.0%	40,799	7.0%	+0
`timepoint_label`	78,695	13.6%	78,695	13.6%	+0

Registry (`registry_studies`)

entity	1.11.0	1.12.0	added	removed
registry studies	54,410	54,410	0	0

Infant extension: studies and samples

entity	1.11.0	1.12.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.11.0	cov	n 1.12.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.12.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.11.0	1.12.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.11.0	prec 1.11.0	rec 1.11.0	cov 1.12.0	prec 1.12.0	rec 1.12.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: GUT_SANDPIPER_REPORT.md, gut_runs.parquet, gut_sample_determinations_conflicts.parquet, gut_sandpiper_pca_loadings.parquet, gut_sandpiper_pca_scores.parquet, gut_sandpiper_pca_variance.csv, gut_sandpiper_sample_summary.parquet, gut_sandpiper_study_coverage.csv Removed files: none

table	columns added	columns removed
`gut_sample_metadata_wide.parquet`	`collection_date`, `collection_date__confidence`, `collection_date__route`, `location_region`, `location_region__confidence`, `location_region__route`, `location_locality`, `location_locality__confidence`, `location_locality__route`, `location_site`, `location_site__confidence`, `location_site__route`, `latitude`, `latitude__confidence`, `latitude__route`, `longitude`, `longitude__confidence`, `longitude__route`, `lifestyle`, `lifestyle__confidence`, `lifestyle__route`, `lifestyle_detail`, `lifestyle_detail__confidence`, `lifestyle_detail__route`, `detailed_location`, `collection_year`	—
`gut_studies.parquet`	`cov_collection_date`, `cov_location_region`, `cov_location_locality`, `cov_location_site`, `cov_latitude`, `cov_longitude`, `cov_lifestyle`, `cov_lifestyle_detail`, `n_runs_total`, `gbp_per_run_mean`, `gbp_per_run_median`, `instrument_models_top`, `library_layouts`, `sandpiper_profiled_share`	—

VERSION.json: package_version=1.12.0, previous_release_id=R2026.11, release_id=R2026.12, release_tag=data-v1.12.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.12). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.11 — package 1.11.0, 2026-09-28 (markdown)

Release notes — R2026.11 (data package 1.11.0, 2026-09-28)

Generated by catalog.release.release_notes from package 1.10.1 (R2026.10, 2026-09-28) → 1.11.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.10.1	1.11.0	added	removed
catalog studies	2,837	2,837	0	0
catalog samples	579,252	579,252	0	0
sample × field values (current)	1,729,195	1,861,883	+132,688

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.10.1	cov	n 1.11.0	cov	Δ n
`age_at_collection_days`	136,902	23.6%	150,537	26.0%	+13,635
`sex`	165,951	28.6%	179,611	31.0%	+13,660
`bmi`	30,791	5.3%	40,799	7.0%	+10,008
`country`	521,962	90.1%	527,707	91.1%	+5,745
`health_condition`	179,676	31.0%	217,169	37.5%	+37,493
`antibiotic_exposure`	72,338	12.5%	95,258	16.4%	+22,920
`subject_id`	199,360	34.4%	199,360	34.4%	+0
`timepoint_label`	78,695	13.6%	78,695	13.6%	+0

Registry (`registry_studies`)

entity	1.10.1	1.11.0	added	removed
registry studies	54,410	54,410	0	0

Infant extension: studies and samples

entity	1.10.1	1.11.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.10.1	cov	n 1.11.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.11.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.10.1	1.11.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.10.1	prec 1.10.1	rec 1.10.1	cov 1.11.0	prec 1.11.0	rec 1.11.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.11.0, previous_release_id=R2026.10, release_id=R2026.11, release_tag=data-v1.11.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.11). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.10 — package 1.10.1, 2026-09-28 (markdown)

Release notes — R2026.10 (data package 1.10.1, 2026-09-28)

Generated by catalog.release.release_notes from package 1.10.0 (R2026.9, 2026-09-28) → 1.10.1. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.10.0	1.10.1	added	removed
catalog studies	2,837	2,837	0	0
catalog samples	579,252	579,252	0	0
sample × field values (current)	1,729,195	1,729,195	+0

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.10.0	cov	n 1.10.1	cov	Δ n
`age_at_collection_days`	136,902	23.6%	136,902	23.6%	+0
`sex`	165,951	28.6%	165,951	28.6%	+0
`bmi`	30,791	5.3%	30,791	5.3%	+0
`country`	521,962	90.1%	521,962	90.1%	+0
`health_condition`	179,676	31.0%	179,676	31.0%	+0
`antibiotic_exposure`	72,338	12.5%	72,338	12.5%	+0
`subject_id`	199,360	34.4%	199,360	34.4%	+0
`timepoint_label`	78,695	13.6%	78,695	13.6%	+0

Registry (`registry_studies`)

entity	1.10.0	1.10.1	added	removed
registry studies	54,410	54,410	0	0

Infant extension: studies and samples

entity	1.10.0	1.10.1	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.10.0	cov	n 1.10.1	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.10.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.10.0	1.10.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.10.0	prec 1.10.0	rec 1.10.0	cov 1.10.1	prec 1.10.1	rec 1.10.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.10.1, previous_release_id=R2026.9, release_id=R2026.10, release_tag=data-v1.10.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.10). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.9 — package 1.10.0, 2026-09-28 (markdown)

Release notes — R2026.9 (data package 1.10.0, 2026-09-28)

Generated by catalog.release.release_notes from package 1.9.0 (R2026.8, 2026-09-28) → 1.10.0. Every number below is computed from the two packages; dates come from VERSION.json.

Catalog (human gut, all ages: `gut_*` tables)

entity	1.9.0	1.10.0	added	removed
catalog studies	2,837	2,837	0	0
catalog samples	579,252	579,252	0	0
sample × field values (current)	1,787,854	1,729,195	-58,659

Per-field coverage over all catalog samples (gut_sample_metadata_wide):

field	n 1.9.0	cov	n 1.10.0	cov	Δ n
`age_at_collection_days`	136,902	23.6%	136,902	23.6%	+0
`sex`	165,951	28.6%	165,951	28.6%	+0
`bmi`	30,791	5.3%	30,791	5.3%	+0
`country`	521,962	90.1%	521,962	90.1%	+0
`health_condition`	179,676	31.0%	179,676	31.0%	+0
`antibiotic_exposure`	72,338	12.5%	72,338	12.5%	+0
`subject_id`	199,360	34.4%	199,360	34.4%	+0
`timepoint_label`	78,695	13.6%	78,695	13.6%	+0

Registry (`registry_studies`)

entity	1.9.0	1.10.0	added	removed
registry studies	54,410	54,410	0	0

Infant extension: studies and samples

entity	1.9.0	1.10.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Infant extension: per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.9.0	cov	n 1.10.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.10.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.9.0	1.10.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.9.0	prec 1.9.0	rec 1.9.0	cov 1.10.0	prec 1.10.0	rec 1.10.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.10.0, previous_release_id=R2026.8, release_id=R2026.9, release_tag=data-v1.10.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.9). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.8 — package 1.9.0, 2026-09-28 (markdown)

Release notes — R2026.8 (data package 1.9.0, 2026-09-28)

Generated by catalog.release.release_notes from package 1.8.0 (R2026.7, 2026-09-28) → 1.9.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.8.0	1.9.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.8.0	cov	n 1.9.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.9.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.8.0	1.9.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.8.0	prec 1.8.0	rec 1.8.0	cov 1.9.0	prec 1.9.0	rec 1.9.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.9.0, previous_release_id=R2026.7, release_id=R2026.8, release_tag=data-v1.9.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.8). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.7 — package 1.8.0, 2026-09-28 (markdown)

Release notes — R2026.7 (data package 1.8.0, 2026-09-28)

Generated by catalog.release.release_notes from package 1.7.1 (R2026.6, 2026-09-28) → 1.8.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.7.1	1.8.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.7.1	cov	n 1.8.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.8.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.7.1	1.8.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.7.1	prec 1.7.1	rec 1.7.1	cov 1.8.0	prec 1.8.0	rec 1.8.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: gut_sample_determinations.parquet, gut_sample_metadata_wide.parquet, gut_studies.parquet Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.8.0, previous_release_id=R2026.6, release_id=R2026.7, release_tag=data-v1.8.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.7). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.6 — package 1.7.1, 2026-09-28 (markdown)

Release notes — R2026.6 (data package 1.7.1, 2026-09-28)

Generated by catalog.release.release_notes from package 1.7.0 (R2026.5, 2026-09-27) → 1.7.1. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.7.0	1.7.1	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.7.0	cov	n 1.7.1	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.7.1: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.7.0	1.7.1
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.7.0	prec 1.7.0	rec 1.7.0	cov 1.7.1	prec 1.7.1	rec 1.7.1
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: none Removed files: none

table	columns added	columns removed
`registry_authors.parquet`	—	—

VERSION.json: package_version=1.7.1, previous_release_id=R2026.5, release_id=R2026.6, release_tag=data-v1.7.1

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.6). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.5 — package 1.7.0, 2026-09-27 (markdown)

Release notes — R2026.5 (data package 1.7.0, 2026-09-27)

Generated by catalog.release.release_notes from package 1.6.0 (R2026.4, 2026-09-27) → 1.7.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.6.0	1.7.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.6.0	cov	n 1.7.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.7.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.6.0	1.7.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.6.0	prec 1.6.0	rec 1.6.0	cov 1.7.0	prec 1.7.0	rec 1.7.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: registry_authors.parquet, registry_bioproject_records.parquet, registry_biosamples.parquet, registry_study_papers.parquet Removed files: none

table	columns added	columns removed
`registry_studies.parquet`	`n_runs_sandpiper`, `n_biosamples_harvested`, `n_biosamples_with_site`, `n_biosamples_with_age`, `n_biosamples_with_sex`, `sample_body_sites`, `sample_life_stages`, `sample_countries`, `sample_age_days_median`	—

VERSION.json: package_version=1.7.0, previous_release_id=R2026.4, release_id=R2026.5, release_tag=data-v1.7.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.5). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.4 — package 1.6.0, 2026-09-27 (markdown)

Release notes — R2026.4 (data package 1.6.0, 2026-09-27)

Generated by catalog.release.release_notes from package 1.5.0 (R2026.3, 2026-09-27) → 1.6.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.5.0	1.6.0	added	removed
included studies	389	389	0	0
catalog samples	154,356	154,356	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.5.0	cov	n 1.6.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.6.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.5.0	1.6.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.5.0	prec 1.5.0	rec 1.5.0	cov 1.6.0	prec 1.6.0	rec 1.6.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: REGISTRY_REPORT.md, registry_studies.parquet, registry_universe_audit.csv Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.6.0, previous_release_id=R2026.3, release_id=R2026.4, release_tag=data-v1.6.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.4). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.3 — package 1.5.0, 2026-09-27 (markdown)

Release notes — R2026.3 (data package 1.5.0, 2026-09-27)

Generated by catalog.release.release_notes from package 1.4.0 (R2026.2, 2026-09-27) → 1.5.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.4.0	1.5.0	added	removed
included studies	389	389	0	0
catalog samples	154,206	154,356	150	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.4.0	cov	n 1.5.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,581 → 9,581 studies; verdict distribution 1.5.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 0 studies new to the universe, 0 removed.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.4.0	1.5.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.4.0	prec 1.4.0	rec 1.4.0	cov 1.5.0	prec 1.5.0	rec 1.5.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: APPLY_GAPFILL_PRJNA1140720.json Removed files: none

table	columns added	columns removed
`sample_metadata_wide.csv.gz`	`body_site`	—

VERSION.json: package_version=1.5.0, previous_release_id=R2026.2, release_id=R2026.3, release_tag=data-v1.5.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 619,647 current + 1,316 retired rows (0 retired in R2026.3). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559
R2026.3	749

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: 0 curation tokens; agent work: 2 leaf frames (worklist data ≈ 31 min, contribute site ≈ 28 min) + gap-fill leaf ≈ 50 min; root ≈ 2 h (docs/CYCLE_LOG.md row R2026.2)

R2026.2 — package 1.4.0, 2026-09-27 (markdown)

Release notes — R2026.2 (data package 1.4.0, 2026-09-27)

Generated by catalog.release.release_notes from package 1.3.0 (R2026.1, 2026-09-26) → 1.4.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.3.0	1.4.0	added	removed
included studies	389	389	0	0
catalog samples	154,206	154,206	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.3.0	cov	n 1.4.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,579 → 9,581 studies; verdict distribution 1.4.0: exclude 9,140, include 389, uncertain 52. 0 flips among studies present in both packages; 2 studies new to the universe, 0 removed.

study	1.3.0	1.4.0
PRJEB108618	(absent)	exclude
PRJEB124241	(absent)	exclude

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.3.0	1.4.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.3.0	prec 1.3.0	rec 1.3.0	cov 1.4.0	prec 1.4.0	rec 1.4.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: contribute_worklist.csv, contribute_worklist_fields.csv Removed files: none

No column changes in tables present in both packages.

VERSION.json: package_version=1.4.0, previous_release_id=R2026.1, release_id=R2026.2, release_tag=data-v1.4.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 618,898 current + 1,316 retired rows (0 retired in R2026.2). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

R2026.1 — package 1.3.0, 2026-09-26 (markdown)

Release notes — R2026.1 (data package 1.3.0, 2026-09-26)

Generated by catalog.release.release_notes from package 1.2.2 (1.2.2, 2026-09-26) → 1.3.0. Every number below is computed from the two packages; dates come from VERSION.json.

Studies and samples

entity	1.2.2	1.3.0	added	removed
included studies	389	389	0	0
catalog samples	154,206	154,206	0	0

Per-field coverage on `catalog_scope`

Recomputed from sample_metadata_wide (non-null values among catalog_scope rows: 72,358 → 72,358); field list from field_coverage_summary.csv.

field	n 1.2.2	cov	n 1.3.0	cov	Δ n
`probiotic_exposure`	2,666	3.7%	2,666	3.7%	+0
`preterm_status`	32,289	44.6%	32,289	44.6%	+0
`gestational_age_weeks`	12,256	16.9%	12,256	16.9%	+0
`delivery_mode`	23,066	31.9%	23,066	31.9%	+0
`feeding_mode`	11,312	15.6%	11,312	15.6%	+0
`antibiotic_exposure`	12,576	17.4%	12,576	17.4%	+0
`age_at_collection_days`	52,649	72.8%	52,649	72.8%	+0
`birth_weight_grams`	10,436	14.4%	10,436	14.4%	+0
`country`	69,371	95.9%	69,371	95.9%	+0
`maternal_antibiotics`	8,317	11.5%	8,317	11.5%	+0
`hmo_supplementation`	1,256	1.7%	1,256	1.7%	+0
`nec_status`	5,302	7.3%	5,302	7.3%	+0
`health_condition`	6,388	8.8%	6,388	8.8%	+0
`multiple_birth`	4,792	6.6%	4,792	6.6%	+0
`sibling_in_study`	3,272	4.5%	3,272	4.5%	+0
`geo_subregion`	26,468	36.6%	26,468	36.6%	+0
`sex`	32,400	44.8%	32,400	44.8%	+0
`timepoint_label`	27,102	37.5%	27,102	37.5%	+0
`subject_id`	43,034	59.5%	43,034	59.5%	+0

Triage verdict flips (`universe_studies_all.triage_verdict`)

Universe 9,579 → 9,579 studies; verdict distribution 1.3.0: exclude 9,138, include 389, uncertain 52. 0 flips.

Findings applied in this release (`value_history` rows new since the previous package)

value_history 46,587 → 46,587 rows; 0 new rows.

Sandpiper snapshot

	1.2.2	1.3.0
sandpiper_version	2.0.0	2.0.0
zenodo_record	20419175	20419175
profiled samples	79,473	79,473

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

field	gold n	cov 1.2.2	prec 1.2.2	rec 1.2.2	cov 1.3.0	prec 1.3.0	rec 1.3.0
`age_days`	3,346	0.959	0.991	0.951	0.959	0.991	0.951
`born_method`	2,546	0.937	0.995	0.932	0.937	0.995	0.932
`feeding_practice`	693	0.648	0.891	0.577	0.648	0.891	0.577
`premature`	1,998	0.961	1.000	0.961	0.961	1.000	0.961
`antibiotics_current_use`	2,534	0.946	0.867	0.820	0.946	0.867	0.820
`gestational_age`	1,998	0.264	1.000	0.264	0.264	1.000	0.264

Schema changes

New files: bitemporal_log.json, releases.csv, sample_determinations_all.parquet Removed files: none

table	columns added	columns removed
`cohorts.csv`	`release_added`, `release_retired`, `package_added`	—
`sample_determinations.parquet`	`release_added`, `release_retired`, `package_added`	—
`sandpiper_run_qc.parquet`	`release_added`, `release_retired`, `package_added`	—
`sandpiper_sample_summary.parquet`	`release_added`, `release_retired`, `package_added`	—
`sandpiper_study_panels.parquet`	`release_added`, `release_retired`, `package_added`	—
`sandpiper_top_genera.parquet`	`release_added`, `release_retired`, `package_added`	—
`study_metadata_wide.csv`	`release_added`, `release_retired`, `package_added`	—
`study_metadata_wide.parquet`	`release_added`, `release_retired`, `package_added`	—
`study_paper_links.csv`	`release_added`, `release_retired`, `package_added`	—
`universe_studies_all.parquet`	`release_added`, `release_retired`, `package_added`	—

VERSION.json: package_version=1.3.0, previous_release_id=1.2.2, release_id=R2026.1, release_tag=data-v1.3.0

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

sample_determinations_all.parquet: 618,898 current + 1,316 retired rows (0 retired in R2026.1). Rule for retired rows: value_history.status in ['superseded', 'moved_to_parent_biosamples', 'recommitted_out_of_scope_host', 'recommitted_out_of_scope_isolate'].

release_added (current determinations)	rows
1.0.0	605,707
1.1.0	3,632
1.2.0	9,559

release_retired (retired determinations)	rows
1.1.0	75
1.2.0	245
1.2.1	295
1.2.2	701

Pre-1.3.0 values of release_added are reconstructed from value_history.change_stage / src_track — see docs/RELEASES.md §3 for exactness per row class.

Token cost

LLM tokens this cycle: not recorded

Downloads & releases

Catalog tables (human gut, all ages)

Registry tables (all human shotgun metagenomes)

Release documents

Infant extension tables (deep infant-field curation of the infant studies; also present in the catalog tables)

Release assets not on this site

Site data files

Releases (30, from releases.csv)

Release notes

Release notes — R2026.25 (data package 1.20.0, 2026-10-12)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Token cost

Release notes — R2026.24 (data package 1.19.1, 2026-10-10)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Token cost

Release notes — R2026.23 (data package 1.19.0, 2026-10-10)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Token cost

Release notes — R2026.22 (data package 1.18.2, 2026-10-09)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Token cost

Release notes — R2026.21 (data package 1.18.1, 2026-10-09)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Token cost

Release notes — R2026.20 (data package 1.18.0, 2026-10-09)

Catalog (human gut, all ages: gut_* tables)

Registry (registry_studies)

Infant extension: studies and samples

Infant extension: per-field coverage on catalog_scope

Triage verdict flips (universe_studies_all.triage_verdict)

Findings applied in this release (value_history rows new since the previous package)

Sandpiper snapshot

Gold metrics (extraction_gold_eval_hires.csv, curatedMetagenomicData hi-res set)

Schema changes

Bitemporal columns (release_added / release_retired / package_added)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`

Triage verdict flips (`universe_studies_all.triage_verdict`)

Findings applied in this release (`value_history` rows new since the previous package)

Gold metrics (`extraction_gold_eval_hires.csv`, curatedMetagenomicData hi-res set)

Bitemporal columns (`release_added` / `release_retired` / `package_added`)

Catalog (human gut, all ages: `gut_*` tables)

Registry (`registry_studies`)

Infant extension: per-field coverage on `catalog_scope`