[Atlas] Score 8 registered datasets for quality and provenance done analysis:6 reasoning:5

Goal

Populate quality scores for registered datasets so dataset reuse, citation rewards, and governance can prioritize well-documented scientific data. Scores should consider schema completeness, provenance, license clarity, citation coverage, and reuse readiness.

Acceptance Criteria

Approach

Inspect registered datasets and their schema_json, canonical_path, license, and citation metadata.

Evaluate each dataset against a consistent quality rubric.

Persist the score and concise rationale using existing database write patterns.

Verify score ranges and count reduction.

Dependencies

• quest-engine-ci - Generates this task when queue depth is low and unscored datasets exist.

Dependents

• Dataset citation rewards, quality markets, and Atlas governance depend on dataset quality scores.

Work Log

2026-04-27 — Slot codex:52 [task:9df5913c-a054-45b9-a29c-653dd58fe7b1]

• Staleness review: current DB has 53 registered datasets, 20 with quality_score IS NULL; the task's original batch size of 8 is still actionable as a bounded scoring batch, but no longer exhausts all unscored datasets.
• Schema check: live datasets table has quality_score but no quality_notes column; this batch will add a nullable quality_notes text column so the requested rationale can live with the score.
• Planned batch: score the 8 oldest currently unscored datasets (wrap-biomarker, ad-trial-tracker, ukb-ad-gwas, allen-aging-mouse-brain, allen-neural-dynamics, amp-ad-portal, bbb-transcytosis-proteomics, braak-staging-neuropath) using a 4-part rubric: provenance completeness, schema conformance, spot-check accuracy, and domain completeness.
• Verification plan: record before/after unscored counts, insert one dataset_versions audit row per scored dataset, and file specific improvement tasks for any dataset scored below 0.5.
• Implemented with scripts/score_dataset_quality_batch_9df5913c.py; added nullable live DB column datasets.quality_notes because the task required notes but the table only had quality_score.
• Before/after: 20 → 12 datasets with quality_score IS NULL; 8 scored datasets now have non-null quality_score and quality_notes.
• Scores:

- ukb-ad-gwas: 0.36 — generic UKB URL only, no accession/phenotype/schema/row provenance.
- ad-trial-tracker: 0.40 — broad Alzheimer’s Association pages, no structured extract/schema/trial IDs.
- allen-neural-dynamics: 0.42 — broad institutional reference, no pinned release/schema/direct ND scope.
- allen-aging-mouse-brain: 0.46 — no schema/local rows and naming/source normalization needed.
- wrap-biomarker: 0.46 — real WRAP cohort, but no schema/data dictionary/row provenance.
- bbb-transcytosis-proteomics: 0.52 — plausible cited target set, but no row-level curation/schema.
- braak-staging-neuropath: 0.57 — accurate staging references, but no tabular schema/row evidence tiers.
- amp-ad-portal: 0.66 — specific Synapse portal and strong source provenance, but controlled access/no local schema.

• Created 8 dataset_versions audit rows with rubric components, source URLs, notes, and task ID in diff_stat.
• Filed remediation tasks for all datasets with score <0.5: 790cfae9-e501-4fb5-be66-34052fe06760 (WRAP), 0e79463f-4092-406c-b902-002ba3b1ae6b (AD trial tracker), c43a0413-2405-47e6-a25c-6b8c7a95d3b4 (UKB AD GWAS), 1d173c30-6e6f-47d0-bb95-84f29b3a4e8d (Allen aging mouse brain), 64f00534-b410-440b-945f-3dcd9b0fc813 (Allen neural dynamics).
• Verification: python3 -m py_compile scripts/score_dataset_quality_batch_9df5913c.py; SQL check confirmed 53 total datasets, 12 unscored, 8 scored-with-notes for this batch, and 8 task-specific dataset_versions rows.

2026-04-26 — Slot claude-auto:41 [task:af13bd51-396c-4f04-a980-c14b14acc9cc]

• Before: 28 datasets with NULL quality_score (36 total, 8 already scored)
• Scored 25 datasets using 4-dimension rubric (max 10, stored as /10 float):

- data_completeness (0-3): all Biomni parity datasets = 1 (URL+metadata, no schema/local data)
- documentation_quality (0-3): 2 for major open databases (GWAS Catalog, Ensembl, AlphaFold etc.), 1 for minimal
- license_openness (0-2): 2=CC-BY/CC0/public domain, 1=registration free, 0=DUA/restricted application
- reproducibility (0-2): 2=versioned public URL, 1=registration required

• Score distribution: 12 at 0.70 (open + well-documented), 1 at 0.60, 1 at 0.50, 1 at 0.40, 10 at 0.30 (restricted Synapse/ADNI/NIAGADS)
• After: 3 datasets remain unscored (ukb-ad-gwas, wrap-biomarker, ad-trial-tracker — deferred)
• Script: scripts/score_datasets_quality.py
• Score range across all 33 scored datasets: min=0.30, max=0.85, avg=0.57
• Acceptance criteria satisfied: 25 non-null quality_score values, integers 3–7 out of 10 (0.3–0.7 range)