DATA_MODEL_FIX_REPORT — data package v1.2 (release v12), 2026-09-26

Implements Reviewer B findings B1, B2, B3, B8, B9, B10, B14, B15 deterministically (no LLM calls; 0 tokens). Inputs: data_package_v1(.1) tables, the v11 release bundle, the superseded/rejected/dropped/adult-age/r1_rejected tables, human-review rounds, the 56 triage-stage tables in the artifact store, gold_extract.parquet (B8 precision table only). Every new determination row passed curation_kernel_ext.validate_row.

Before → after

B1 — age_scope (sample level)

• infant_evidenced: 67,598
• age_unknown_no_study_estimate: 49,556
• age_unknown_mixed_study: 14,410
• adult_flagged: 9,559
• study_all_infant: 7,097
• non_infant_role: 5,986

Rule (precedence order): adult_flagged (committed age > 1,100 d) > non_infant_role (mother/other from attr_role, sample_name_token, body_site_raw, body_site_class=linked) > infant_evidenced (age ≤ 1,100 d, preterm_status or gestational_age_weeks on the sample — 53,669 / 13,110 / 112 — or on another sample of the same resolved subject, 707) > study_all_infant (triage n_infant_samples_est ≥ 0.9 × n_infant_scope_samples; 66 studies) > age_unknown_mixed_study (estimate < 0.9; the 0.9–0.99 band is empty so 0.5 and 0.9 give the same partition) > age_unknown_no_study_estimate (253 studies where triage gave no numeric estimate — TEDDY, MOMmy, Codiversification, HMP2-IBD… — labelled unknown, not all-infant, because their triage quotes describe mixed cohorts; this sixth value and non_infant_role extend Reviewer B's four-value list). Headline coverage now uses age_scope ∈ {infant_evidenced, study_all_infant} (n = 74,695): age ≤ 1,100 d on 53,669 (71.9%), preterm 32,426 (43.4%), delivery 23,473 (31.4%), antibiotics 13,027 (17.4%), feeding 11,842 (15.9%). Exposure values on adults: probiotic 3,534 of 8,989, antibiotics 4,970 of 22,718. Mixed-age deposits (mixed_age_deposit, > 50 % of rows mixed/adult): 61 studies, 23,403 rows. Largest: | study_accession | study_title | n_sample_rows | n_infant_evidenced | n_age_unknown_mixed_study | n_adult_flagged | n_infant_samples_est | |:------------------|:---------------------------------------------------------------------------------------------------------------|----------------:|---------------------:|----------------------------:|------------------:|-----------------------:| | PRJNA1468137 | Maternal influences on infant gut microbiome and health | 4749 | 0 | 4577 | 0 | 2200 | | PRJEB11419 | American Gut Project | 7024 | 79 | 2362 | 4583 | 39 | | PRJNA1257550 | Role of gut microbiota in eczema development | 1737 | 0 | 1737 | 0 | 1000 | | PRJNA695570 | Human gut metagenomes of healthy mothers and their children | 1767 | 763 | 536 | 468 | 600 | | PRJNA1356541 | Metagenomic strain tracking among children in urban and rural communities in low- and middle-income countries. | 511 | 0 | 511 | 0 | 150 | | PRJNA1081952 | BRISC microbiome sub study | 1422 | 940 | 482 | 0 | 1000 | | PRJNA1274946 | Siblings are Reservoirs for Microbial Metabolic Processes that Influence Allergy Development | 353 | 0 | 353 | 0 | 150 | | PRJNA1273620 | Maternal-Prenatal Signature Underlying Offspring Atopic Dermatitis Susceptibility | 325 | 0 | 325 | 0 | 150 |

B9 — adult_age_flag rule and the 12 contradictions

All 10,305 rows of adult_age_rows.parquet (R1 r1_unit_resolution_v2, 9,567 samples) were re-validated: validate_row ok for all; validate_age(value_normalized,'days') returned age N days outside 0-1100 for all (that message is now in parse_note). One row per sample committed (738 second attributes → not_committed_duplicate). Investigation of the 12 contradictions showed all 12 are maternal samples or maternal ages: PRJEB14941 is a pregnancy cohort ("microbiota at multiple body sites during pregnancy…", Tanzania) whose age attribute is the mother's age and whose dob attribute is the infant's date of birth attached to every sample of the pair — the 5 (+11 outside infant scope) date-arithmetic ages 0–126 d sit on maternal visit samples (titles without the .infant. token); PRJNA716780's six CTRM* mother samples had a supplementary-table age of 30–36 read as months; PRJNA695570 SAMN17618835 has host_age 1388 d (R1) vs a pooled-table 1095 d (R2), R1 wins by precedence. Two further deterministic corrections in PRJEB14941 followed from the same evidence (declared beyond the reviewer's list): 125 title-parser birth → 0 d rows on maternal birth-visit samples superseded; 8 out-of-range ages on .infant. samples rejected because the value equals the mother's age on the same pair code. Open auditor item: PRJEB14941 still has 67 .infant. title-parser ages (birth → 0 d, plausible) and 62 date-arithmetic ages on .infant. samples (plausible); the 751 former role = infant rows of this study are now mostly unknown.

B10 — n_unique_infants_source

B2 / B15 / B14 — counts reconciled from the tables

• Sample table 154,206 rows = 153,701 distinct BioSamples (153,685 BioSample units + 521 run units under 16 parents). Site index must use this table's length (154,206), not 154,222.
• Per-study n_samples/n_runs now come from runs.parquet (sum 154,268 / 174,022); 62 BioSamples carry runs from two BioProjects, so the per-study sum exceeds the sample-table row count by 62; n_sample_rows gives the table count. Only PRJEB49206 changed vs v1.1 (419/457 → 439/477; runs.parquet is the shipped truth).
• Age covered: 54,105 body-site infant-scope samples with age ≤ 1,100 d (v1.1 README 53,802; site 54,150 — the site counted the 16 parent rows and rows since superseded, the README predates the run-unit fix). Age-scope figure: 53,669.
• Gold recall: 22 cMD BioProjects, 18 included, of which 1 by the human-review pass → 17/22 automated, 18/22 final. Both numbers are now stated in the README.
• Multi-run: 57 class-C + 6 class-A studies in sample_unit_classification_by_study.csv; the 61 − 57 = 4 studies with multi-run BioSamples in the sample table (PRJNA1019702, PRJNA1198101, PRJNA613032, PRJNA613054) are cross-study BioSamples (runs from a sibling BioProject on the same BioSample), added as class X_cross_study_biosample; the dictionary's "33 technical" count is withdrawn.
• hires vs full gold: extraction_gold_eval_hires.csv (pipeline evaluator; 3,498 hi-res rows) remains the headline; tier_field_precision.csv re-derives both sets with an explicit, documented value mapping and gives (hires / all): | field | ('n_covered', 'all') | ('n_covered', 'hires') | ('precision', 'all') | ('precision', 'hires') | ('recall', 'all') | ('recall', 'hires') | |:-----------------------|-----------------------:|-------------------------:|-----------------------:|-------------------------:|--------------------:|----------------------:| | age_at_collection_days | 3370 | 3236 | 0.971 | 0.989 | 0.93 | 0.948 | | antibiotic_exposure | 2414 | 2395 | 0.868 | 0.867 | 0.792 | 0.819 | | delivery_mode | 2445 | 2426 | 0.995 | 0.995 | 0.907 | 0.932 | | feeding_mode | 525 | 520 | 0.796 | 0.804 | 0.577 | 0.592 | | gestational_age_weeks | 551 | 551 | 1 | 1 | 0.272 | 0.272 | | preterm_status | 1950 | 1949 | 1 | 1 | 0.961 | 0.961 | The re-derived hires set has 3,530 rows (integer-year age_years rule applied to gold rows without infant_age_days) vs the evaluator's 3,498, and feeding precision differs (0.80 vs 0.89) because the evaluator's feeding mapping is not in the package; treat the tier table as internally consistent but not identical to the shipped evaluator — provisional until the evaluator code is added to the repo.

B8 — confidence tiers

confidence_tiers.csv: 29 route × determiner × scope tiers; discrete values per tier. Precision by tier (hires, age): R1 0.90 → 1.000 (n=194), R1 0.85 (date arithmetic / subject propagation) → 0.700 (n=70), R1 0.75 → 1.000 (n=763), R2 0.85 → 1.000 (n=1,519), R2 0.75 → 0.980 (n=683); feeding R2 0.75 → 0.480 (n=152) vs R2 0.85 → 0.938 (n=368); R3 preterm 0.80 → 1.000 (n=193). No gold for R4 or exposure fields. Dictionary paragraph added.

B3 — histories

study_verdict_history.parquet: 32,231 rows from 56 tables (haiku screen 3,978; Sonnet rubric tier-1 960; Sonnet confirm parts/replicates; Opus adjudication 00/01/linked/rescue/gap/grow/w2/w3/ff/nm/loose/r3/gsa; growth_triage merged outcomes; BioSample re-judge 13; human review 157 + 60; triage_v2 consolidated 9,579; final 9,579). 138 of 389 included studies carry ≥ 2 distinct stage verdicts (include/exclude/uncertain) — the site's "Decision history" panel has content for them. value_history.parquet: 45,591 rows (statuses above); r1_rejected rows that v1.2 committed are marked recommitted_out_of_scope_adult with replaced_by pointing at the current row.

Checks (all pass)

{ "wide_rows": 154206, "subj_rows": 154206, "no_pooled_in_wide": true, "wide_vs_det_mismatches": { "probiotic_exposure": 0, "preterm_status": 0, "gestational_age_weeks": 0, "delivery_mode": 0, "feeding_mode": 0, "antibiotic_exposure": 0, "age_at_collection_days": 0, "birth_weight_grams": 0, "country": 0, "maternal_antibiotics": 0, "hmo_supplementation": 0, "nec_status": 0, "health_condition": 0, "multiple_birth": 0, "sibling_in_study": 0, "geo_subregion": 0, "sex": 0, "timepoint_label": 0, "subject_id": 0 }, "adult_flag_equals_age_gt_1100": true, "adult_flag_rows_have_out_of_scope_note": true, "infant_role_all_evidenced": true, "role_infant_unevidenced": 0, "age_scope_infant_has_no_adult": 0, "biosample_accession_all_SAM": true, "run_accession_only_on_run_units": true, "det_unique_sample_field": true, "det_keys_in_wide": true, "study_n_sample_rows_sum": 154206, "study_n_samples_sum": 154268, "study_n_runs_sum": 174022, "n_unique_infants_est_zero_or_sentinel": 0, "value_history_rows": 45591, "study_verdict_history_rows": 32231, "history_covers_all_catalog_studies": true, "non_age_det_rows_identical": true, "new_adult_rows_validate_row_ok": 9559 }

Not done / declared deviations

• age_scope vocabulary extended by two values (age_unknown_no_study_estimate, non_infant_role).
• Two PRJEB14941 corrections beyond the listed findings (125 superseded title-parser rows, 8 rejected adult rows), both from sample_id_pattern evidence.
• Site templates/generator not touched (out of this track); the package now supplies n_unique_infants_display, mixed_age_deposit, age_scope, parent_biosamples, and the two history tables for the site track.
• Reviewer B's cohort-clustering re-adjudication (B10 second part, ~50k tokens) not done — LLM work excluded from this deterministic track.
• Gold precision tiers are a re-derivation with a documented mapping; the shipped evaluator CSV is unchanged.