Add curated sample metadata v2 (sda-sample-metadata-2): organ, UBERON tissue, MONDO disease, sample kind, life stage, species taxonomy, assay names; data files unchanged; see metadata/v2/README.md

metadata/v2/README.md

@@ -0,0 +1,124 @@
+# SpatialDataAgent-DB sample metadata v2
+
+Schema `sda-sample-metadata-2`, built 2026-11-04 from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
+No expression, coordinate or image file changes; v2 is a new metadata table that sits next to the release.
+
+## Files
+
+| File | Content |
+|---|---|
+| `samples_metadata_v2.parquet` | one row per sample, list columns kept as lists (recommended) |
+| `samples_metadata_v2.csv` | the same table; lists joined with `;`, confidence as JSON |
+| `studies_v2.csv` | one row per study (1,265): title, species, platforms, assays, organs, diseases, PubMed IDs, split |
+| `schema_v2.json` | definition of every column |
+| `changes_v2.csv` | every value that differs from a v3 column, with its basis (204 platform changes, 8 manual) |
+| `dropped_disease_terms.csv` | disease terms removed by the short-synonym filter (331) |
+| `qa_v2.json` | counts and consistency-flag totals |
+
+## What is new for users
+
+- **Organ and tissue.** Each sample has an organ from a fixed list of 43 (a metastasis is placed at its site),
+  and 11,606 samples (95%) have a UBERON tissue term (279 distinct terms). The GEO text stays in `tissue_raw`.
+- **Disease.** Each sample has a `disease_status`: disease 7,021, normal 3,950, perturbation 1,125, not stated 67.
+  "Perturbation" covers interventions that are not a named disease, such as a knockout without a disease name, a
+  drug, mechanical loading or regeneration. 6,477 samples have MONDO terms (403 distinct); a sample can have more
+  than one, for example IPMN with co-occurring PDAC. The control arm of a disease or tumour model counts as
+  disease, not normal.
+- **Sample kind.** primary tissue 8,574, tumour tissue 2,754, metastasis 352, organoid 212, xenograft 185, whole
+  embryo/organism 57, cell culture 17, engineered tissue 10, unknown 2.
+- **Donor.**
+  - `life_stage`: embryonic, fetal, neonatal or infant, juvenile, adult, aged, or not stated. 5,098 samples have a
+    stated stage. Where the age notation is unambiguous, the stage comes from a fixed age rule (3,745 samples);
+    otherwise from the model. Rule for mouse and rat: neonatal up to P21, juvenile under 6 weeks, adult under
+    18 months, aged from 18 months. For human, ages in years or post-conception weeks.
+  - `sex`: male 2,639, female 1,987, mixed 19, unknown 7,518. Coded values without a key, such as 1/2, stay
+    unknown.
+  - `donor_key` = `<study>:<donor>`, for donor-level splits (3,391 samples).
+- **Species.**
+  - NCBI Taxonomy ID and common name for all 42 host species.
+  - Mixed entries are split. 78 samples list several species and 36 are xenografts; pathogens such as
+    *Plasmodium berghei* go in `co_detected_organisms`.
+  - Two series that GEO lists only as the genus *Mus* are set to house mouse. The evidence for each is recorded:
+    a C57BL/6J strain in one, ENSMUSG gene IDs in the other. One series that GEO lists only as Hepatitis B virus
+    is set to human, from its gene IDs.
+  - `feature_species` gives the species implied by the Ensembl gene IDs (8,032 samples). It differs from
+    `organism` for 47 samples (flag `feature_species_differs`). Most are macaque or rat tissue mapped to a human
+    or mouse reference, or mouse hosts carrying human grafts. In one study (GSE313530) the macaque and baboon
+    samples carry each other's gene IDs; check it before any cross-species use.
+- **Assay.** `assay_name` gives the specific method (Visium CytAssist, Slide-seqV2, Open-ST, Pixel-seq, Decoder-seq,
+  ...), and `assay_type` says whether it is imaging-based or sequencing-based.
+  - Of the 299 v3 samples labelled "Other", 197 now belong to a named platform family: DBiT-seq 100, BMK S1000 51,
+    Molecular Cartography 23, Visium 18, Slide-seq 5.
+  - Nova-ST (7 samples) was labelled Stereo-seq in v3 and is now Other.
+  - All are listed in `changes_v2.csv`. The assay of each "Other" study was checked by hand against the GEO text.
+- **Preservation.** FFPE 2,839, fresh frozen (including OCT-embedded) 2,327, fixed frozen 40.
+- **Publications.** PubMed IDs for 8,479 samples, from GEO series and sample records.
+- **Review fields** are in English.
+
+## How the annotations were made
+
+1. **Input.** For each sample: the release tissue, organism and platform, plus the GEO sample title, source and
+   characteristics and the series title.
+2. **Model.** Official GPT-6 Luna Decisions (`api.openai.com/v1/decisions`). This API answers only multiple-choice
+   and yes/no questions, so the model chooses from fixed lists and never writes free text or ontology IDs.
+   - Step 1: organ, sample kind, disease status and life stage.
+   - Step 2: one UBERON term from candidates. Each candidate MONDO term is a separate yes/no question.
+3. **Candidates.** A script finds candidate terms in the text by exact name or synonym match. It handles organ
+   adjectives (peritoneal → peritoneum), plurals, British spelling, possessives, common disease abbreviations and
+   standard disease-model names (5xFAD, R6/2, SOD1-G93A, mdx …). The direct parents of each matched term are added.
+   All IDs come from the ontology files (UBERON basic and MONDO, downloaded 2026-11-04).
+4. **Fixed rules after the model.**
+   - The most specific true MONDO terms are kept.
+   - A true disease term sets the status to disease.
+   - Disease terms that matched only through a short upper-case synonym (e.g. "CHS", "SARS" inside "SARS-CoV-2")
+     are dropped.
+   - The organ follows the UBERON term's part-of chain when that chain names a different listed organ.
+   - Life stage comes from the age rule where the notation is unambiguous.
+5. **Versions.** Each row records its `annotation_version`.
+   - 2.3 is the main run.
+   - 2.4 re-asked the 842 non-human, non-mouse samples (species-aware life stage) and the samples that mention
+     SARS-CoV-2.
+   - 2.5 re-asked 303 samples whose text contains a disease adjective such as "diabetic".
+6. **Confidence.** Luna's confidence is stored per field. Fields below 0.6 are listed in
+   `annotation_low_confidence` (3,119 samples, mostly disease status).
+
+## Accuracy
+
+The checks ran on 300 random samples never used to develop the method. Gemini 3.8 Flash judged each field against
+the same source text, and every "wrong" verdict was then read by hand (Claude).
+
+| Field | Judge "wrong" rate (300 random samples, final build) |
+|---|---|
+| organ | 0.3% |
+| tissue term | 0.7% |
+| sample kind | 0.7% |
+| life stage | 1.7% |
+| disease | 3.0% |
+
+- **Disease.** Most "wrongs" are a study-level disease given to a control (see limitations), or a missing term
+  where the status is right.
+- **Life stage.** The remaining "wrongs" are ages the rule leaves to the model, such as "0d" or an unlabelled
+  number in an embryo study.
+- **"Acceptable"** (true but less specific) was 1–13% per field.
+
+## Known limitations
+
+- The study-level disease sometimes reaches a control whose own record does not say it is a control (about 1.5%
+  of samples in QA). For example, a "WT" sample in a pulmonary hypertension study got pulmonary hypertension.
+  Check `disease_status_source` and the raw fields when the control/disease split matters.
+- Vagina and pleura are not in the organ list, so those samples are "other" or "lung".
+- Disease abbreviations outside the curated list (e.g. "MN" for membranous nephropathy) give a disease status
+  without a MONDO term.
+- `life_stage` is "not stated" for 7,065 samples: most GEO records give no age.
+- 20 samples are flagged `normal_but_disease_text`: the raw disease field names a disease but the sample was
+  judged normal. Most are tissue adjacent to a tumour, which is correct; the rest are unclear.
+
+## Reproduce
+
+Scripts are in `research/metadata-v2-20261104` and `research/tissue-ontology-pilot-20261104` of the project
+repository:
+
+- `map_decisions.py --all`: annotation (resumable);
+- `assay_decisions.py`: assay of the "Other" studies;
+- `build_metadata_v2.py`: this table;
+- `qa_full.py`: QA sample and judge.

metadata/v2/changes_v2.csv

@@ -0,0 +1,213 @@
+gsm,column,v3,v2,basis
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+GSM4096262,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (corrected by hand: design names microfluidic Deterministic Barcoding in Tissue; Luna chose legacy ST at 0.66)
+GSM4189611,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (corrected by hand: design names microfluidic Deterministic Barcoding in Tissue; Luna chose legacy ST at 0.66)
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+GSM8563714,platform,Other,Visium,GEO series text names 10x Visium (hand-checked: agrees with GEO text)
+GSM8676719,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (corrected by hand: processing uses BMKMANU BSTMatrix; Luna said not named at 0.36)
+GSM8676720,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (corrected by hand: processing uses BMKMANU BSTMatrix; Luna said not named at 0.36)
+GSM8676721,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (corrected by hand: processing uses BMKMANU BSTMatrix; Luna said not named at 0.36)
+GSM8979572,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979573,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979574,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979575,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979576,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979577,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979578,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979579,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979580,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979581,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979582,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979583,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979584,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979585,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979586,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979587,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979588,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979589,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979590,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979591,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979592,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979593,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979594,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM8979595,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9206540,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9206541,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9206542,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463749,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463750,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463751,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463752,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463753,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463754,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463755,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463756,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9463757,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9234585,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9239732,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9239733,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9239734,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9288671,platform,Other,Slide-seq,"GEO series text names Curio Trekker (single-cell, Slide-seq beads) (hand-checked: agrees with GEO text)"
+GSM9288673,platform,Other,Slide-seq,"GEO series text names Curio Trekker (single-cell, Slide-seq beads) (hand-checked: agrees with GEO text)"
+GSM9288675,platform,Other,Slide-seq,"GEO series text names Curio Trekker (single-cell, Slide-seq beads) (hand-checked: agrees with GEO text)"
+GSM9288677,platform,Other,Slide-seq,"GEO series text names Curio Trekker (single-cell, Slide-seq beads) (hand-checked: agrees with GEO text)"
+GSM9320917,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9320919,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9320921,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9320923,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9738330,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9738332,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9738334,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331952,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331953,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331954,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331955,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331956,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331957,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331958,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331961,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331962,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9331963,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514750,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514751,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514752,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514753,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514754,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514757,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9514758,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9656414,platform,Other,Slide-seq,"GEO series text names Curio Trekker (single-cell, Slide-seq beads) (hand-checked: agrees with GEO text)"
+GSM9771950,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9771951,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9771952,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9775942,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9812615,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9812616,platform,Other,DBiT-seq,GEO series text names DBiT-seq (or DBiT-derived) (hand-checked: agrees with GEO text)
+GSM9869917,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9869918,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9869919,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9869920,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM9869921,platform,Other,BMK S1000,GEO series text names BMKMANU S1000/S3000 (hand-checked: agrees with GEO text)
+GSM7412887,disease_status,,disease,"manual override (was normal): GEO diagnosis '5X' = 5xFAD Alzheimer model (GSE233208, 36 other '5X' samples are disease); Luna chose normal"
+GSM7412889,disease_status,,disease,manual override (was normal): as GSM7412887
+GSM7412891,disease_status,,disease,manual override (was normal): as GSM7412887
+GSM7412893,disease_status,,disease,manual override (was normal): as GSM7412887
+GSM7412887,disease_ontology,,MONDO:0004975|Alzheimer disease,manual override (was []): 5xFAD models Alzheimer disease
+GSM7412889,disease_ontology,,MONDO:0004975|Alzheimer disease,manual override (was []): as GSM7412887
+GSM7412891,disease_ontology,,MONDO:0004975|Alzheimer disease,manual override (was []): as GSM7412887
+GSM7412893,disease_ontology,,MONDO:0004975|Alzheimer disease,manual override (was []): as GSM7412887

metadata/v2/dropped_disease_terms.csv

@@ -0,0 +1,332 @@
+gsm,term,name
+GSM3399307,MONDO:0000429,autosomal genetic disease
+GSM3399308,MONDO:0000429,autosomal genetic disease
+GSM3399309,MONDO:0000429,autosomal genetic disease
+GSM3399310,MONDO:0000429,autosomal genetic disease
+GSM3399311,MONDO:0000429,autosomal genetic disease
+GSM3399312,MONDO:0000429,autosomal genetic disease
+GSM3399324,MONDO:0000429,autosomal genetic disease
+GSM3399325,MONDO:0000429,autosomal genetic disease
+GSM3399327,MONDO:0000429,autosomal genetic disease
+GSM3399328,MONDO:0000429,autosomal genetic disease
+GSM3399329,MONDO:0000429,autosomal genetic disease
+GSM3399330,MONDO:0000429,autosomal genetic disease
+GSM3399331,MONDO:0000429,autosomal genetic disease
+GSM3399332,MONDO:0000429,autosomal genetic disease
+GSM3399333,MONDO:0000429,autosomal genetic disease
+GSM3399335,MONDO:0000429,autosomal genetic disease
+GSM3399336,MONDO:0000429,autosomal genetic disease
+GSM3399338,MONDO:0000429,autosomal genetic disease
+GSM3399339,MONDO:0000429,autosomal genetic disease
+GSM3399340,MONDO:0000429,autosomal genetic disease
+GSM3399341,MONDO:0000429,autosomal genetic disease
+GSM3399342,MONDO:0000429,autosomal genetic disease
+GSM3399343,MONDO:0000429,autosomal genetic disease
+GSM3399344,MONDO:0000429,autosomal genetic disease
+GSM3399345,MONDO:0000429,autosomal genetic disease
+GSM3399346,MONDO:0000429,autosomal genetic disease
+GSM3399347,MONDO:0000429,autosomal genetic disease
+GSM3399348,MONDO:0000429,autosomal genetic disease
+GSM3399349,MONDO:0000429,autosomal genetic disease
+GSM3399350,MONDO:0000429,autosomal genetic disease
+GSM3399351,MONDO:0000429,autosomal genetic disease
+GSM3399352,MONDO:0000429,autosomal genetic disease
+GSM3399354,MONDO:0000429,autosomal genetic disease
+GSM3399355,MONDO:0000429,autosomal genetic disease
+GSM3399356,MONDO:0000429,autosomal genetic disease
+GSM3399356,MONDO:0002254,syndromic disease
+GSM3399357,MONDO:0000429,autosomal genetic disease
+GSM3399358,MONDO:0000429,autosomal genetic disease
+GSM3399359,MONDO:0000429,autosomal genetic disease
+GSM3399360,MONDO:0000429,autosomal genetic disease
+GSM3399361,MONDO:0000429,autosomal genetic disease
+GSM3399362,MONDO:0000429,autosomal genetic disease
+GSM3399363,MONDO:0000429,autosomal genetic disease
+GSM3399364,MONDO:0000429,autosomal genetic disease
+GSM3399365,MONDO:0000429,autosomal genetic disease
+GSM3399366,MONDO:0000429,autosomal genetic disease
+GSM3399367,MONDO:0000429,autosomal genetic disease
+GSM3399368,MONDO:0000429,autosomal genetic disease
+GSM3399369,MONDO:0000429,autosomal genetic disease
+GSM3399370,MONDO:0000429,autosomal genetic disease
+GSM3399371,MONDO:0000429,autosomal genetic disease
+GSM3399372,MONDO:0000429,autosomal genetic disease
+GSM3399373,MONDO:0000429,autosomal genetic disease
+GSM3399374,MONDO:0000429,autosomal genetic disease
+GSM3399375,MONDO:0000429,autosomal genetic disease
+GSM3399376,MONDO:0000429,autosomal genetic disease
+GSM3399377,MONDO:0000429,autosomal genetic disease
+GSM3399378,MONDO:0000429,autosomal genetic disease
+GSM3399379,MONDO:0000429,autosomal genetic disease
+GSM3399380,MONDO:0000429,autosomal genetic disease
+GSM3399381,MONDO:0000429,autosomal genetic disease
+GSM3399382,MONDO:0000429,autosomal genetic disease
+GSM3399384,MONDO:0000429,autosomal genetic disease
+GSM3399385,MONDO:0000429,autosomal genetic disease
+GSM3399386,MONDO:0000429,autosomal genetic disease
+GSM3399387,MONDO:0000429,autosomal genetic disease
+GSM3399388,MONDO:0000429,autosomal genetic disease
+GSM3399389,MONDO:0000429,autosomal genetic disease
+GSM3399390,MONDO:0000429,autosomal genetic disease
+GSM3399391,MONDO:0000429,autosomal genetic disease
+GSM3399392,MONDO:0000429,autosomal genetic disease
+GSM3399393,MONDO:0000429,autosomal genetic disease
+GSM3399394,MONDO:0000429,autosomal genetic disease
+GSM3399395,MONDO:0000429,autosomal genetic disease
+GSM3399396,MONDO:0000429,autosomal genetic disease
+GSM3399397,MONDO:0000429,autosomal genetic disease
+GSM3399398,MONDO:0000429,autosomal genetic disease
+GSM3399399,MONDO:0000429,autosomal genetic disease
+GSM3399400,MONDO:0000429,autosomal genetic disease
+GSM3399401,MONDO:0000429,autosomal genetic disease
+GSM3399402,MONDO:0000429,autosomal genetic disease
+GSM3399403,MONDO:0000429,autosomal genetic disease
+GSM3399404,MONDO:0000429,autosomal genetic disease
+GSM3399405,MONDO:0000429,autosomal genetic disease
+GSM3399406,MONDO:0000429,autosomal genetic disease
+GSM3399407,MONDO:0000429,autosomal genetic disease
+GSM3399408,MONDO:0000429,autosomal genetic disease
+GSM5538852,MONDO:0015974,severe combined immunodeficiency
+GSM5538853,MONDO:0015974,severe combined immunodeficiency
+GSM5538854,MONDO:0015974,severe combined immunodeficiency
+GSM5538855,MONDO:0015974,severe combined immunodeficiency
+GSM5713386,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713387,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713388,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713389,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713390,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713396,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713397,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713398,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713399,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713400,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713403,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713404,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713405,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713406,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713407,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713408,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713409,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713410,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713411,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713412,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713413,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713414,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713415,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM5713416,MONDO:0008264,autosomal dominant medullary cystic kidney disease with or without hyperuricemia
+GSM6523977,MONDO:0100087,familial Alzheimer disease
+GSM6613090,MONDO:0041656,ST-elevation myocardial infarction
+GSM6631766,MONDO:0000425,X-linked disease
+GSM7585149,MONDO:0005549,renal cell adenocarcinoma
+GSM7585150,MONDO:0005549,renal cell adenocarcinoma
+GSM7585151,MONDO:0005549,renal cell adenocarcinoma
+GSM7585152,MONDO:0005549,renal cell adenocarcinoma
+GSM7585153,MONDO:0005549,renal cell adenocarcinoma
+GSM7585154,MONDO:0005549,renal cell adenocarcinoma
+GSM7585155,MONDO:0005549,renal cell adenocarcinoma
+GSM7585156,MONDO:0005549,renal cell adenocarcinoma
+GSM7567492,MONDO:0015974,severe combined immunodeficiency
+GSM7990552,MONDO:0019622,non-specific interstitial pneumonia
+GSM7990553,MONDO:0019622,non-specific interstitial pneumonia
+GSM8505462,MONDO:0017591,combined pulmonary fibrosis-emphysema syndrome
+GSM7990295,MONDO:0005093,skin disorder
+GSM8021238,MONDO:0005091,severe acute respiratory syndrome
+GSM8021239,MONDO:0005091,severe acute respiratory syndrome
+GSM8021240,MONDO:0005087,respiratory system disorder
+GSM8021241,MONDO:0005087,respiratory system disorder
+GSM8021241,MONDO:0020683,acute disease
+GSM8021242,MONDO:0005091,severe acute respiratory syndrome
+GSM8021243,MONDO:0005087,respiratory system disorder
+GSM8021243,MONDO:0020683,acute disease
+GSM8021244,MONDO:0005091,severe acute respiratory syndrome
+GSM8021245,MONDO:0005091,severe acute respiratory syndrome
+GSM8021246,MONDO:0005091,severe acute respiratory syndrome
+GSM8021247,MONDO:0005091,severe acute respiratory syndrome
+GSM8021248,MONDO:0005087,respiratory system disorder
+GSM8021249,MONDO:0005091,severe acute respiratory syndrome
+GSM8021250,MONDO:0005091,severe acute respiratory syndrome
+GSM8021251,MONDO:0005091,severe acute respiratory syndrome
+GSM8021252,MONDO:0005087,respiratory system disorder
+GSM8021253,MONDO:0005091,severe acute respiratory syndrome
+GSM8021254,MONDO:0005087,respiratory system disorder
+GSM8021255,MONDO:0005091,severe acute respiratory syndrome
+GSM8021256,MONDO:0005091,severe acute respiratory syndrome
+GSM8021257,MONDO:0005087,respiratory system disorder
+GSM8021258,MONDO:0005091,severe acute respiratory syndrome
+GSM8021259,MONDO:0005091,severe acute respiratory syndrome
+GSM8021260,MONDO:0005087,respiratory system disorder
+GSM8021261,MONDO:0005091,severe acute respiratory syndrome
+GSM8021262,MONDO:0005091,severe acute respiratory syndrome
+GSM8021263,MONDO:0005091,severe acute respiratory syndrome
+GSM8021264,MONDO:0005091,severe acute respiratory syndrome
+GSM8021265,MONDO:0005091,severe acute respiratory syndrome
+GSM8021266,MONDO:0005091,severe acute respiratory syndrome
+GSM8021267,MONDO:0005091,severe acute respiratory syndrome
+GSM8021268,MONDO:0005091,severe acute respiratory syndrome
+GSM8021269,MONDO:0005091,severe acute respiratory syndrome
+GSM8021270,MONDO:0005091,severe acute respiratory syndrome
+GSM8021271,MONDO:0005091,severe acute respiratory syndrome
+GSM8021272,MONDO:0005087,respiratory system disorder
+GSM8021272,MONDO:0020683,acute disease
+GSM8021273,MONDO:0005091,severe acute respiratory syndrome
+GSM8021274,MONDO:0005091,severe acute respiratory syndrome
+GSM8021275,MONDO:0005087,respiratory system disorder
+GSM8021276,MONDO:0005091,severe acute respiratory syndrome
+GSM8021277,MONDO:0005091,severe acute respiratory syndrome
+GSM8021278,MONDO:0005091,severe acute respiratory syndrome
+GSM8021279,MONDO:0005087,respiratory system disorder
+GSM8021279,MONDO:0020683,acute disease
+GSM8021280,MONDO:0005091,severe acute respiratory syndrome
+GSM8021281,MONDO:0005087,respiratory system disorder
+GSM8021282,MONDO:0005087,respiratory system disorder
+GSM8021283,MONDO:0005091,severe acute respiratory syndrome
+GSM8021284,MONDO:0005091,severe acute respiratory syndrome
+GSM8021285,MONDO:0005091,severe acute respiratory syndrome
+GSM8021286,MONDO:0005091,severe acute respiratory syndrome
+GSM8021287,MONDO:0005091,severe acute respiratory syndrome
+GSM8021288,MONDO:0005087,respiratory system disorder
+GSM8021288,MONDO:0020683,acute disease
+GSM8021289,MONDO:0005087,respiratory system disorder
+GSM8021290,MONDO:0005091,severe acute respiratory syndrome
+GSM8021291,MONDO:0005091,severe acute respiratory syndrome
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metadata/v2/provenance.json

@@ -0,0 +1,63 @@
+{
+ "schema": "sda-sample-metadata-2",
+ "built": "2026-11-05",
+ "base_release": "sda-unified-20261010-v3",
+ "base_hf_tag": "v1.0.0-20261025",
+ "base_hf_revision": "999566bf516169ba8c9cf1ad9e5a2b722bb8a97a",
+ "annotation_model": "gpt-6-luna (OpenAI Decisions API, choice / predicate questions only)",
+ "annotation_versions": {
+  "sda-tissue-disease-2.3": "main run, all samples",
+  "sda-tissue-disease-2.4": "re-asked: non-human/non-mouse samples (species-aware life stage) and SARS-CoV-2 text",
+  "sda-tissue-disease-2.5": "re-asked: samples with a disease adjective (e.g. diabetic)"
+ },
+ "ontologies": {
+  "UBERON basic": "uberon/releases/2026-10-01/uberon-basic.owl",
+  "MONDO": "releases/2026-11-03",
+  "NCBI Taxonomy": "E-utilities lookup 2026-11-04"
+ },
+ "qa": {
+  "judge": "gemini-3.8-flash-high on 300 random samples not used in development; every 'wrong' read by hand",
+  "wrong_rate_pct": {
+   "organ": 0.3,
+   "tissue_term": 0.7,
+   "sample_kind": 0.7,
+   "life_stage": 1.7,
+   "disease": 3.0
+  },
+  "human_review": "200-sample pack prepared (100 random, 100 targeted); results to be added"
+ },
+ "crosscheck_regex_organ_map": {
+  "organ_both_assigned": 10960,
+  "organ_agreement": 0.9653,
+  "regex_unassigned_v2_assigned": 409,
+  "tumour_regex": 2318,
+  "tumour_v2": 3106,
+  "tumour_both": 2175,
+  "tumour_v2_only": 931,
+  "tumour_regex_only": 143,
+  "top_disagreements": {
+   "CNS | Head & neck / oral": 44,
+   "CNS | Kidney / urinary": 40,
+   "Plant | Spinal cord / nerve": 40,
+   "Intestine | Musculoskeletal": 28,
+   "Intestine | Kidney / urinary": 25,
+   "Skin | Head & neck / oral": 25,
+   "Lung / airway | Head & neck / oral": 14,
+   "Spinal cord / nerve | CNS": 12,
+   "Musculoskeletal | Adipose / other": 12,
+   "Plant | Musculoskeletal": 10,
+   "Spinal cord / nerve | Head & neck / oral": 8,
+   "Plant | Heart / vessels": 8
+  }
+ },
+ "files": {
+  "README.md": "953c665094dcf4e795517f039a3cd446002379645810928235a41689eb02235f",
+  "changes_v2.csv": "7901fcd917602f308ea0ca3c8a74c462c473caa2178a33ec5e9c3552498728a5",
+  "dropped_disease_terms.csv": "697ecd7701a923e8b7ad2c1309d1064403993c8ac75efdcf7cd61776db159862",
+  "qa_v2.json": "3c55068f167fa701729223e2d9c2a082befdba17f6627e610c719efb738927a5",
+  "samples_metadata_v2.csv": "95a88711ac9a260aace525cbef93e26c42519c3b59a39cafe00817ee580ee3ad",
+  "samples_metadata_v2.parquet": "95b33b3bd6f6e764e3dc461b1c2c7bf280d7e69397a9a596224f4ff87fc21bb3",
+  "schema_v2.json": "5f4b29aaf5d1d990c45916d2e1922f5da0b484500c55e93d57b62b1b6864b194",
+  "studies_v2.csv": "0f6c97c3ea020dd5bfa87f92398d395736567396ae7351a88957550d372d3c89"
+ }
+}

metadata/v2/qa_v2.json

@@ -0,0 +1,110 @@
+{
+ "samples": 12163,
+ "annotated": 12163,
+ "flags": {
+  "low_confidence_annotation": 3119,
+  "feature_species_differs": 47,
+  "normal_but_disease_text": 20
+ },
+ "changes_vs_v3": 212,
+ "dropped_short_synonym_disease_terms": 331,
+ "life_stage_source": {
+  "luna": 8418,
+  "age rule: age with unit": 1630,
+  "age rule: bare number read as years": 1372,
+  "age rule: postnatal day": 404,
+  "age rule: embryonic day": 154,
+  "age rule: age in years": 113,
+  "age rule: post-conception / gestational weeks": 64,
+  "age rule: Carnegie stage": 4,
+  "age rule: age range midpoint": 4
+ },
+ "life_stage_rule_vs_luna_disagree": 615,
+ "organ": {
+  "brain": 3391,
+  "colon": 1000,
+  "lung": 939,
+  "liver": 776,
+  "spinal cord": 639,
+  "kidney": 590,
+  "skin": 489,
+  "pancreas": 488,
+  "other": 399,
+  "heart": 292,
+  "breast": 267,
+  "small intestine": 251,
+  "unknown": 185,
+  "blood vessel": 162,
+  "stomach": 162,
+  "lymph node": 160,
+  "rectum": 154,
+  "ovary": 150,
+  "skeletal muscle": 138,
+  "head and neck": 122,
+  "plant": 120,
+  "uterus": 117,
+  "spleen": 108,
+  "bone": 107,
+  "prostate": 102,
+  "placenta": 94,
+  "embryo (whole)": 93,
+  "eye": 89,
+  "bone marrow": 89,
+  "meninges": 70,
+  "peripheral nerve": 67,
+  "oral cavity": 60,
+  "bladder": 55,
+  "adrenal gland": 39,
+  "thymus": 34,
+  "peritoneum": 32,
+  "adipose tissue": 32,
+  "airway": 29,
+  "thyroid": 29,
+  "esophagus": 19,
+  "tonsil": 12,
+  "testis": 11,
+  "cartilage": 1
+ },
+ "sample_kind": {
+  "primary tissue": 8574,
+  "tumour tissue": 2754,
+  "metastasis": 352,
+  "organoid": 212,
+  "xenograft": 185,
+  "whole embryo/organism": 57,
+  "cell culture": 17,
+  "engineered tissue": 10,
+  "unknown": 2
+ },
+ "disease_status": {
+  "disease": 7021,
+  "normal": 3950,
+  "perturbation": 1125,
+  "not stated": 67
+ },
+ "life_stage": {
+  "not stated": 7065,
+  "adult": 2860,
+  "aged": 1182,
+  "juvenile": 330,
+  "neonatal or infant": 296,
+  "embryonic": 282,
+  "fetal": 148
+ },
+ "sex": {
+  "unknown": 7518,
+  "male": 2639,
+  "female": 1987,
+  "mixed": 19
+ },
+ "preservation": {
+  "null": 6957,
+  "FFPE": 2839,
+  "fresh frozen": 2327,
+  "fixed frozen": 40
+ },
+ "with_tissue_term": 11606,
+ "with_disease_term": 6477,
+ "with_pubmed": 8479,
+ "with_donor_key": 3391
+}

metadata/v2/samples_metadata_v2.parquet

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+size 820752

metadata/v2/schema_v2.json

@@ -0,0 +1,81 @@
+{
+ "schema": "sda-sample-metadata-2",
+ "base_release": "sda-unified-20261010-v3",
+ "columns": {
+  "gsm": "GEO sample accession (canonical GSM of its content group); key of the release",
+  "gse": "all GEO series listing the GSM, joined with '+'",
+  "published_gse": "series folder of the sample in the release: samples/<published_gse>/<gsm>",
+  "study_title": "GEO series title of published_gse",
+  "organism": "species the tissue comes from (host species for metagenome labels; first species for mixed entries; for a xenograft the graft species as GEO lists it first)",
+  "organism_taxon_id": "NCBI Taxonomy ID of organism",
+  "organism_common_name": "NCBI Taxonomy GenBank common name",
+  "organisms": "all host species listed by GEO (list)",
+  "organism_taxon_ids": "NCBI Taxonomy IDs of organisms (list)",
+  "co_detected_organisms": "pathogens or microbes GEO lists with the host (e.g. Plasmodium berghei ANKA)",
+  "xenograft": "GEO marks the sample as a xenograft",
+  "multi_species": "more than one host species listed",
+  "organism_basis": "where organism comes from (GEO field, or the evidence used when GEO gives only a genus)",
+  "organism_raw": "GEO organism text as written",
+  "feature_species": "species implied by the features' Ensembl gene IDs (>= 90% of IDs share a prefix); differs from organism when reads were mapped to a related reference or a graft dominates (metadata_flags: feature_species_differs)",
+  "organ": "organ or body site the sampled tissue is in (fixed list; a metastasis at its site); see organ_source",
+  "organ_source": "luna = GPT-6 Luna Decisions choice; uberon_chain = taken from the UBERON term's is_a / part_of chain when that names a different organ",
+  "tissue_ontology_id": "UBERON term (most specific supported by the text), chosen by Luna from candidates found in the text; null if none fits (always null for plants)",
+  "tissue_ontology_name": "UBERON name of tissue_ontology_id",
+  "tissue_raw": "tissue as written in GEO",
+  "sample_kind": "primary tissue / tumour tissue / metastasis / organoid / cell culture / xenograft / whole embryo/organism / engineered tissue / unknown",
+  "disease_ontology_ids": "MONDO terms judged true for this sample (most specific only; list, may be empty)",
+  "disease_ontology_names": "MONDO names of disease_ontology_ids",
+  "disease_status": "normal / disease / perturbation (experimental intervention that is not a named disease) / not stated; a disease term judged true sets 'disease'",
+  "disease_status_source": "luna = Luna Decisions choice; manual = overrides_v2.csv; mondo_predicate = set to disease because a MONDO term was judged true while Luna chose another status (Luna's choice in brackets)",
+  "disease_raw": "disease as extracted from GEO by the SDA-All agent (v3 sample.json)",
+  "condition_raw": "condition as extracted from GEO by the SDA-All agent (v3 sample.json)",
+  "life_stage": "embryonic / fetal / neonatal or infant / juvenile / adult / aged / not stated; from age_raw by a fixed rule where the notation is unambiguous (mouse / rat: P, E, weeks, months, years; neonatal <= P21, juvenile < 6 weeks, adult < 18 months, aged >= 18 months; ranges use their midpoint when they span two stages; human: years, post-conception weeks), else Luna",
+  "life_stage_source": "age rule: <notation> (deterministic, from age_raw) or luna (GPT-6 Luna Decisions)",
+  "life_stage_luna": "Luna's life-stage answer (kept when the age rule overrides it)",
+  "age_raw": "age as written",
+  "sex": "male / female / mixed / unknown (coded values without a stated key, e.g. 1/2, stay unknown)",
+  "sex_raw": "sex as written",
+  "donor_key": "<published_gse>:<donor id>; donor IDs are only unique within a study",
+  "donor_id_raw": "donor ID as written",
+  "preservation": "FFPE / fresh frozen (incl. OCT-embedded) / fixed frozen / other; null = not stated",
+  "preservation_raw": "preservation as written",
+  "platform": "harmonised platform family (v3 platform, corrected where the GEO series text names another assay; see changes_v2.csv)",
+  "platform_basis": "release v3, or the GEO series text for corrected / named studies",
+  "assay_name": "specific assay (e.g. Visium CytAssist, Slide-seqV2, Open-ST, DBiT-seq); equals the platform when nothing more specific is known; 'not named in GEO' when the series text names no assay",
+  "assay_type": "imaging-based (in situ hybridisation / sequencing) or sequencing-based (spatial barcoding)",
+  "technology_raw": "technology as written by the authors",
+  "panel_name": "gene panel (imaging platforms)",
+  "instrument_software": "instrument software version",
+  "observation_unit": "spot / bin / cell / bead",
+  "n_obs": "observations",
+  "n_vars": "features",
+  "expression_state": "counts / non-integer / unknown",
+  "coordinate_units": "units of obsm['spatial']",
+  "um_per_unit": "micrometres per coordinate unit",
+  "um_basis": "verified / declared_unverified / platform_constant / unresolved",
+  "has_image": "image.tif present",
+  "image_stain": "stain of image.tif",
+  "image_um_per_px": "micrometres per pixel",
+  "image_registration": "image registration acceptance",
+  "segmentation": "cell / nucleus boundary acceptance",
+  "molecules": "molecule table acceptance",
+  "flags": "release flags (list)",
+  "qc_flags": "deposit QC flags (list)",
+  "verification": "VERIFIED / ATTESTED (SDA-All scorer) or human_visual_review (HESRT)",
+  "review_decision": "author review of the expression file: PASS / FAIL / UNSURE",
+  "review_category": "author review category (English)",
+  "review_notes": "author review note (English)",
+  "pubmed_ids": "PubMed IDs of the series (GEO) and of the sample record (list)",
+  "dois": "publication DOIs found in the sample record (list)",
+  "content_group": "independence unit (re-deposits and aliases share one)",
+  "group_kind": "kind of content group",
+  "aliases": "other GSMs with the same content (list)",
+  "split": "train / val / test (whole-study split)",
+  "source_pipeline": "sda-all or hesrt",
+  "sample_dir": "folder of the sample in the release",
+  "annotation_version": "version of the tissue / disease / life-stage annotation (sda-tissue-disease-2.x)",
+  "annotation_confidence": "Luna Decisions confidence per annotated field",
+  "annotation_low_confidence": "fields with confidence below 0.6 (list)",
+  "metadata_flags": "consistency flags for review (list): normal_but_disease_text, tumour_marked_normal, low_confidence_annotation, feature_species_differs, ..."
+ }
+}