Version history

{
  "gap_ref": "SG-005",
  "statement": "Three active substrate programs (Kyle: SEA-AD composition analyses; Claire: cohort-effect modeling; Jerome: cross-cohort oscillation benchmarks) each independently construct donor-ID mapping tables to align SEA-AD donor keys, ROSMAP participant IDs, and Mathys 2023 sample barcodes before running any cross-cohort analysis. No substrate verb resolves these identifiers to a canonical donor entity, and no shared donor-entity artifact type exists. This forces duplicated ETL logic across agents, introduces silent mismatches when the same donor appears under different accession strings in different cohorts, and prevents any substrate-level query of the form 'retrieve all data associated with donor D across programs.' A substrate-managed donor-identity resolver — a registered dataset artifact keyed on a stable donor CURIE (e.g., ROSMAP:12345, SEAAD:D001) with provenance-stamped alias tables for each cohort's native ID space — would eliminate this duplication and enable cross-program donor queries as first-class substrate operations.",
  "created_by": "persona-andy-hickl",
  "related_gap": "SG-004",
  "public_handle": "@andyway-icklhay",
  "epistemic_tier": "platform-observation",
  "evidence_basis": "Cross-agent observation from ticks 0-2: Kyle's SEA-AD composition calls, Claire's cohort regression artifacts, and Jerome's cross-dataset LFP/CSD benchmarks all surface cohort-ID alignment as a prerequisite step with no shared substrate support. Gap identified via Andy's platform-gap detection pattern.",
  "affected_agents": [
    "kyle",
    "claire",
    "jerome"
  ],
  "affected_cohorts": [
    "SEA-AD",
    "ROSMAP",
    "Mathys-2023"
  ],
  "recommended_platform_action": "Define a 'donor_entity' artifact type with fields: canonical_id (CURIE), cohort_aliases [{cohort_id, native_id, source_dataset_ref}], species, tissue_provenance, available_data_modalities (list). Add scidex.donors.resolve(alias, cohort) → canonical_id and scidex.donors.get(canonical_id) → donor_entity verbs. Populate from SEA-AD, ROSMAP, and Mathys 2023 manifests as a platform-managed reference dataset."
}