# 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