Metadata v2.2.2: most-used columns first (organ, disease, tissue, sample kind, organism, life stage, sex, platform); no value changed

Column order only. Every value equals v2.2.1 (checked: parquet and csv equal after reordering). provenance.json hashes updated; card version text updated.

README.md

@@ -251,10 +251,12 @@ catalog has no per-sample license column. See the
 reuse terms and citation, and cite the original studies with the data you use (`sda-db cite` writes BibTeX for
 a selection).
 
-## Curated sample metadata v2 (version 2.2.1, 2026-11-06)
+## Curated sample metadata v2 (version 2.2.2, 2026-11-08)
 
 `metadata/v2/` adds a curated table on top of the same 12,163 samples. No data file changed: the paper release is
-still tag `v1.0.0-20261025`; the current metadata is tag `metadata-v2.2.1-20261106`.
+still tag `v1.0.0-20261025`; the current metadata is tag `metadata-v2.2.2-20261108` (2.2.2 only moves the most-used columns
+to the front: organ, disease status and terms, tissue term, sample kind, organism, life stage, sex, platform; no value
+changed).
 
 In the Dataset Viewer, `metadata_v2` (the default) shows this table and `samples` shows the catalog
 (`catalog/samples.parquet`).

metadata/v2/README.md

@@ -1,6 +1,6 @@
 # SpatialDataAgent-DB sample metadata v2
 
-Schema `sda-sample-metadata-2`, version 2.2.1 (2026-11-06), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
+Schema `sda-sample-metadata-2`, version 2.2.2 (2026-11-08), built 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
@@ -125,6 +125,11 @@ repository:
 
 ## Versions
 
+- **2.2.2** (tag `metadata-v2.2.2-20261108`): column order only. The columns users look for first lead the table
+  (gsm, organ, disease_status, disease_ontology_names, tissue_ontology_name, sample_kind, organism,
+  organism_common_name, life_stage, sex, platform, assay_name, has_image, image_stain, n_obs, study_title,
+  published_gse, gse); the others follow in their former order. No value changed.
+
 - **2.2.1** (tag `metadata-v2.2.1-20261106`): a field corrected by hand no longer carries the model's confidence or
   low-confidence flag, so `annotation_low_confidence` filters keep human-checked samples. The schema text now lists
   every `life_stage_source` value. No label changed.

metadata/v2/provenance.json

@@ -53,16 +53,16 @@
   "tumour_regex_only_after_xenograft": 43
  },
  "files": {
-  "README.md": "edcebb1ce6c92aefb3e7f50ff27c1155d07434fb27f7d4315f945ed7418e6ee5",
+  "README.md": "633883366b4f0829b07579ca8cbdadb8f776a8efe04a32f0ef14e6096971e62e",
   "changes_v2.csv": "9f096e905effabc808c1b5ac142ff8cab3d9a367774ae82757b7406d23e631dc",
   "dropped_disease_terms.csv": "28412ef3f7f7660ea7a85ed46ebcfecec08728dadc549e03510d31a2cce11b80",
   "qa_v2.json": "43002bf2ee515e39c60b81bbd51fc5f313f2ec84a99d1a69a7a1061cf02c8466",
-  "samples_metadata_v2.csv": "16c880338828b9d05c893cde95492255840f6b7d04016e8f11fe8bb0168776b6",
-  "samples_metadata_v2.parquet": "d0be2e6b7284f662872827c767fa71c0f50535fd37b218e9793af04d29b2e5b8",
-  "schema_v2.json": "a0e90e8bf5afa33f23542f60806bf1a235cb4adb42858a4be22f6fbfbdffd05c",
+  "samples_metadata_v2.csv": "9352ad65c498c862b596c2197ac8ac184df760d9fbcfad7283206c7af2fc8549",
+  "samples_metadata_v2.parquet": "c69c25eed912f837122fec75c123ee6f93948f2ce06408d26431ea84b3fb7191",
+  "schema_v2.json": "1c1569b29f9563b84c4c7a22d7acbcc1304476b0d71466e4450a41c212e084cf",
   "studies_v2.csv": "47ae0513a19ebaea9282d8362164b5b898cd143ad7132310cba4d78ee5bb8150"
  },
- "version": "2.2.1",
+ "version": "2.2.2",
  "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": {
@@ -83,5 +83,6 @@
   }
  },
  "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"
+ "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": "2.2.2 (2026-11-08): column order only, no value changed (values = 2.2.1, built 2026-11-06)"
 }

metadata/v2/samples_metadata_v2.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d0be2e6b7284f662872827c767fa71c0f50535fd37b218e9793af04d29b2e5b8
+oid sha256:c69c25eed912f837122fec75c123ee6f93948f2ce06408d26431ea84b3fb7191
 size 822587

metadata/v2/schema_v2.json

@@ -3,12 +3,24 @@
  "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",
+  "organ": "organ or body site the sampled tissue is in (fixed list; a metastasis at its site); see organ_source",
+  "disease_status": "normal / disease / perturbation (experimental intervention that is not a named disease) / not stated; a disease term judged true sets 'disease'",
+  "disease_ontology_names": "MONDO names of disease_ontology_ids",
+  "tissue_ontology_name": "UBERON name of tissue_ontology_id",
+  "sample_kind": "primary tissue / tumour tissue / metastasis / organoid / cell culture / xenograft / whole embryo/organism / engineered tissue / unknown",
   "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",
+  "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",
+  "sex": "male / female / mixed / unknown (coded values without a stated key, e.g. 1/2, stay unknown)",
+  "platform": "harmonised platform family (v3 platform, corrected where the GEO series text names another assay; see changes_v2.csv)",
+  "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",
+  "has_image": "image.tif present",
+  "image_stain": "stain of image.tif",
+  "n_obs": "observations",
+  "study_title": "GEO series title of published_gse",
+  "published_gse": "series folder of the sample in the release: samples/<published_gse>/<gsm>",
+  "gse": "all GEO series listing the GSM, joined with '+'",
+  "organism_taxon_id": "NCBI Taxonomy ID of organism",
   "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)",
@@ -17,45 +29,33 @@
   "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; includes 'age rule: days in an age series'), 'rule: culture or organoid (culture time is not a life stage)', luna (GPT-6 Luna Decisions) or manual",
   "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_source": "extracted field, sample text (the words male / female in title, source or characteristics), manual, or not stated",
   "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",