| { |
| "schema": "sda-sample-metadata-2", |
| "built": "2026-11-06", |
| "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 (100 random, 100 targeted) read by a human reviewer offline; the errors found were corrected in 2.2; per-field accuracy from that review not yet computed" |
| }, |
| "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 |
| }, |
| "tumour_v2_incl_xenograft_disease": 3265, |
| "tumour_regex_only_after_xenograft": 43 |
| }, |
| "files": { |
| "README.md": "633883366b4f0829b07579ca8cbdadb8f776a8efe04a32f0ef14e6096971e62e", |
| "changes_v2.csv": "9f096e905effabc808c1b5ac142ff8cab3d9a367774ae82757b7406d23e631dc", |
| "dropped_disease_terms.csv": "28412ef3f7f7660ea7a85ed46ebcfecec08728dadc549e03510d31a2cce11b80", |
| "qa_v2.json": "a8120c035389e56aeb8667358d8df555501e864acb2656d9d9cdba6c63f14775", |
| "samples_metadata_v2.csv": "14abf0323606e0246ce6d2cdb63ff4d3b25c7e2daa55b664e79fe9a8ace575f6", |
| "samples_metadata_v2.parquet": "c41e8e9fc5ed172729d08fb881142bdd8f06f70646f6da45132ff870f6aeb598", |
| "schema_v2.json": "1c1569b29f9563b84c4c7a22d7acbcc1304476b0d71466e4450a41c212e084cf", |
| "studies_v2.csv": "1369bee55ef19aad2bf5d9819fec955331d6c31144174fa19a991e0ee52947aa" |
| }, |
| "version": "2.2.4", |
| "changes_from_2.0": "one name per assay (ASSAY_CANON, 261 rows); assay_type of 6 ISS (Cartana) samples (GSE227046) now imaging-based; um_per_unit and image_um_per_px copied exactly from the release parquet; organ, tissue, disease, life stage and other annotations unchanged", |
| "sensitivity_balanced_r2_series_units": { |
| "human": { |
| "organ": 0.355, |
| "platform": 0.109, |
| "paper_regex": [ |
| 0.321, |
| 0.125 |
| ] |
| }, |
| "mouse": { |
| "organ": 0.48, |
| "platform": 0.194, |
| "paper_regex": [ |
| 0.47, |
| 0.179 |
| ] |
| } |
| }, |
| "changes_from_2.1": "rules: non-human-animal MONDO terms removed from human samples (16); culture/organoid/engineered life stage = not stated; sex from male/female words in sample text (77); rodent day ages in age series; manual corrections in 10 samples (overrides_v2.csv); new column sex_source", |
| "changes_from_2.2": "manually corrected fields: model confidence set to null and removed from annotation_low_confidence; schema text for life_stage_source; no label changed", |
| "version_note": "2.2.4 (2026-11-11): the image of 9 misaligned HESRT samples was removed; no annotation changed (other values = 2.2.3)", |
| "changes_from_2.2.2": "12 samples re-converted (catalog-derived columns updated; curated annotations unchanged) and 6 samples withdrawn (rows removed): 12,163 -> 12,157 samples, 1,265 -> 1,264 studies. No other row changed.", |
| "changes_from_2.2.3": "9 samples (GSE229175 x4, GSE302160 x2, GSM8925216, GSM8770960, GSM9317397): has_image False, image_stain and image_um_per_px empty, image_registration WITHHELD, flag image_review_fail, review_decision FAIL. 12,157 samples and 1,264 studies as before. No other row changed." |
| } |
