Datasets:
File size: 6,790 Bytes
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"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",
"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_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)",
"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_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_raw": "tissue as written in GEO",
"disease_ontology_ids": "MONDO terms judged true for this sample (most specific only; list, may be empty)",
"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_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_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_basis": "release v3, or the GEO series text for corrected / named studies",
"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_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",
"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; null for a field corrected by hand",
"annotation_low_confidence": "fields with model confidence below 0.6 (list); fields corrected by hand are not listed",
"metadata_flags": "consistency flags for review (list): normal_but_disease_text, tumour_marked_normal, low_confidence_annotation, feature_species_differs, ..."
}
} |