| { |
| "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/<published_gse>/<gsm>", |
| "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: <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", |
| "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, ..." |
| } |
| } |
