| { |
| "index_columns": { |
| "gsm": "GEO sample (canonical GSM of its content group)", |
| "gse": "all GEO series listing the GSM, joined with '+'; the split is computed on this string", |
| "published_gse": "series folder of the sample: samples/<published_gse>/<gsm>", |
| "source_pipeline": "sda-all (agent standardization, independent scorer) or hesrt (H&E Visium/ST, human review)", |
| "source_release": "SDA-All scorer version of the batch, sda-all-gap-20261009, or hesrt-v1.3", |
| "platform": "harmonized platform", |
| "technology": "technology as written by the authors", |
| "organism": "as written in GEO", |
| "tissue": "as written in GEO", |
| "observation_unit": "spot / bin / cell / bead", |
| "n_obs": "observations", |
| "n_vars": "features", |
| "expression_state": "counts (integer X) / non-integer / unknown (SDA-All: as declared and scored)", |
| "verification": "VERIFIED / ATTESTED (SDA-All scorer) or human_visual_review (HESRT)", |
| "expression_sha256": "SHA256 of the sample's spatial.h5ad", |
| "coordinate_units": "units of obsm['spatial']: um / pixel / native_grid / unstated", |
| "um_basis": "verified / declared_unverified / platform_constant / unresolved", |
| "um_per_unit": "micrometres per coordinate unit when known", |
| "has_spatial_um": "obsm['spatial_um'] present (micrometre copy of non-um coordinates)", |
| "has_image": "image.tif present", |
| "image_stain": "stain of image.tif ('(heuristic)' = pixel-only call)", |
| "image_stain_basis": "basis of the stain label", |
| "image_um_per_px": "micrometres per image.tif pixel when known", |
| "image_registration": "VERIFIED / PARTIAL / UNRESOLVED / FAILED / ABSENT (modality acceptance), WITHHELD (HESRT review FAIL: no image delivered), HESRT_HUMAN_REVIEW, empty = no registrable image", |
| "image_sha256": "SHA256 of image.tif", |
| "segmentation": "cell / nucleus boundary acceptance (sources in sample.json)", |
| "molecules": "molecule table acceptance (sources in sample.json)", |
| "molecules_use": "positions_only: molecules without usable cell IDs", |
| "flags": "units_unstated / attested / summary_features_in_matrix / hesrt_review_fail / hesrt_fail_image_released / image_partial_coverage / image_review_fail", |
| "qc_flags": "deposit QC flags (annotation only)", |
| "drop_features": "features to drop before use", |
| "review_decision": "latest author review of this expression file: PASS / FAIL / UNSURE", |
| "review_category": "review category", |
| "review_notes": "review notes", |
| "content_group": "independence unit", |
| "group_kind": "cross_gse_redeposit / library_alias", |
| "aliases": "GSMs with identical content not listed as rows", |
| "split": "train / val / test by series", |
| "sample_dir": "samples/<published_gse>/<gsm>" |
| }, |
| "sample_json": { |
| "$schema": "https://json-schema.org/draft/2020-12/schema", |
| "title": "sda-release-sample-1", |
| "type": "object", |
| "additionalProperties": false, |
| "required": [ |
| "schema", |
| "release_id", |
| "gsm", |
| "gse", |
| "published_gse", |
| "metadata", |
| "expression", |
| "coordinates", |
| "image", |
| "segmentation", |
| "molecules", |
| "quality", |
| "dedup", |
| "split", |
| "provenance" |
| ], |
| "properties": { |
| "schema": { |
| "const": "sda-release-sample-1" |
| }, |
| "release_id": { |
| "type": "string" |
| }, |
| "gsm": { |
| "type": "string", |
| "pattern": "^GSM[0-9]+$" |
| }, |
| "gse": { |
| "type": "array", |
| "items": { |
| "type": "string", |
| "pattern": "^GSE[0-9]+$" |
| }, |
| "minItems": 1 |
| }, |
| "published_gse": { |
| "type": "string", |
| "pattern": "^GSE[0-9]+$" |
| }, |
| "metadata": { |
| "type": "object", |
| "required": [ |
| "organism", |
| "tissue", |
| "platform", |
| "technology" |
| ], |
| "properties": { |
| "organism": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "tissue": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "platform": { |
| "type": "string" |
| }, |
| "technology": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "fields": { |
| "type": "object" |
| }, |
| "field_sources": { |
| "type": "object" |
| } |
| } |
| }, |
| "expression": { |
| "type": "object", |
| "additionalProperties": false, |
| "required": [ |
| "file", |
| "sha256", |
| "n_obs", |
| "n_vars", |
| "state", |
| "observation_unit", |
| "verification" |
| ], |
| "properties": { |
| "file": { |
| "const": "spatial.h5ad" |
| }, |
| "sha256": { |
| "type": "string", |
| "pattern": "^[0-9a-f]{64}$" |
| }, |
| "n_obs": { |
| "type": "integer", |
| "minimum": 1 |
| }, |
| "n_vars": { |
| "type": "integer", |
| "minimum": 1 |
| }, |
| "state": { |
| "type": "string" |
| }, |
| "observation_unit": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "verification": { |
| "type": "string" |
| } |
| } |
| }, |
| "coordinates": { |
| "type": "object", |
| "additionalProperties": false, |
| "required": [ |
| "obsm_key", |
| "units", |
| "um_basis", |
| "spatial_um" |
| ], |
| "properties": { |
| "obsm_key": { |
| "const": "spatial" |
| }, |
| "units": { |
| "enum": [ |
| "mm", |
| "native_grid", |
| "nm", |
| "pixel", |
| "um", |
| "unstated" |
| ] |
| }, |
| "um_basis": { |
| "enum": [ |
| "declared_unverified", |
| "platform_constant", |
| "unresolved", |
| "verified" |
| ] |
| }, |
| "um_per_unit": { |
| "type": [ |
| "number", |
| "null" |
| ] |
| }, |
| "um_basis_detail": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "spatial_um": { |
| "type": "boolean" |
| } |
| } |
| }, |
| "image": { |
| "oneOf": [ |
| { |
| "type": "null" |
| }, |
| { |
| "type": "object", |
| "additionalProperties": false, |
| "required": [ |
| "file", |
| "sha256", |
| "shape", |
| "dtype", |
| "channels", |
| "stain", |
| "um_per_px", |
| "spatial_to_pixel", |
| "registration", |
| "inside_fraction", |
| "source" |
| ], |
| "properties": { |
| "file": { |
| "const": "image.tif" |
| }, |
| "sha256": { |
| "type": "string", |
| "pattern": "^[0-9a-f]{64}$" |
| }, |
| "shape": { |
| "type": "array", |
| "items": { |
| "type": "integer" |
| }, |
| "minItems": 2, |
| "maxItems": 2 |
| }, |
| "dtype": { |
| "enum": [ |
| "uint8", |
| "uint16" |
| ] |
| }, |
| "channels": { |
| "type": "array", |
| "items": { |
| "type": "string" |
| }, |
| "minItems": 1 |
| }, |
| "stain": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "stain_basis": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "um_per_px": { |
| "type": [ |
| "number", |
| "null" |
| ] |
| }, |
| "spatial_to_pixel": { |
| "type": "array", |
| "minItems": 3, |
| "maxItems": 3, |
| "items": { |
| "type": "array", |
| "items": { |
| "type": "number" |
| }, |
| "minItems": 3, |
| "maxItems": 3 |
| } |
| }, |
| "registration": { |
| "type": "string" |
| }, |
| "review": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "inside_fraction": { |
| "type": "number", |
| "minimum": 0, |
| "maximum": 1 |
| }, |
| "source": { |
| "type": "array" |
| } |
| } |
| } |
| ] |
| }, |
| "segmentation": { |
| "type": [ |
| "object", |
| "null" |
| ] |
| }, |
| "molecules": { |
| "type": [ |
| "object", |
| "null" |
| ] |
| }, |
| "quality": { |
| "type": "object", |
| "required": [ |
| "flags", |
| "qc_flags", |
| "drop_features", |
| "review" |
| ], |
| "properties": { |
| "flags": { |
| "type": "array", |
| "items": { |
| "type": "string" |
| } |
| }, |
| "qc_flags": { |
| "type": "array", |
| "items": { |
| "type": "string" |
| } |
| }, |
| "drop_features": { |
| "type": "array", |
| "items": { |
| "type": "string" |
| } |
| }, |
| "review": { |
| "type": [ |
| "object", |
| "null" |
| ] |
| } |
| } |
| }, |
| "dedup": { |
| "type": "object", |
| "required": [ |
| "content_group", |
| "group_kind", |
| "aliases" |
| ], |
| "properties": { |
| "content_group": { |
| "type": "string" |
| }, |
| "group_kind": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| }, |
| "aliases": { |
| "type": "array", |
| "items": { |
| "type": "string" |
| } |
| } |
| } |
| }, |
| "split": { |
| "enum": [ |
| "train", |
| "val", |
| "test" |
| ] |
| }, |
| "provenance": { |
| "type": "object", |
| "required": [ |
| "pipeline", |
| "source_release", |
| "files" |
| ], |
| "properties": { |
| "pipeline": { |
| "enum": [ |
| "sda-all", |
| "hesrt" |
| ] |
| }, |
| "source_release": { |
| "type": "string" |
| }, |
| "files": { |
| "type": "array", |
| "items": { |
| "type": "object", |
| "required": [ |
| "role", |
| "path" |
| ], |
| "properties": { |
| "role": { |
| "type": "string" |
| }, |
| "path": { |
| "type": "string" |
| }, |
| "sha256": { |
| "type": [ |
| "string", |
| "null" |
| ] |
| } |
| } |
| } |
| } |
| } |
| } |
| } |
| }, |
| "sample_folder": [ |
| "image.tif", |
| "sample.json", |
| "spatial.h5ad" |
| ] |
| } |
|
|
