{ "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//", "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: (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": ":; 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; 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, ..." } }