SciDEX — Task: [Atlas] Add resolution criteria to 25 open knowled

Knowledge gaps without resolution_criteria field have no clear definition of done, making it impossible to know when a gap has been filled. For 25 open gaps without resolution criteria (SELECT id, title, description FROM knowledge_gaps WHERE status='open' AND resolution_criteria IS NULL ORDER BY priority_score DESC LIMIT 25): (1) read gap title and description; (2) write 2–4 specific, measurable resolution criteria (e.g., "A randomized controlled trial in at least 50 patients demonstrates X", "Orthogonal validation in 3 independent cell lines confirms Y"); (3) UPDATE knowledge_gaps SET resolution_criteria= WHERE id=. Verification: 25 gaps have non-null resolution_criteria.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (6)

[Atlas] Add resolution criteria to 25 open knowledge gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

[Atlas] Work log: add resolution criteria to 25 open gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

[Atlas] Add resolution criteria to 25 open knowledge gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

[Atlas] Work log: add resolution criteria to 25 open gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

[Atlas] Add resolution criteria to 25 open knowledge gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

[Atlas] Work log: add resolution criteria to 25 open gaps [task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0]2026-04-22

Spec File

Goal

Add concrete resolution criteria to open knowledge gaps so agents can determine what evidence, debate result, dataset, or KG improvement would close the gap. Criteria must be testable and tied to real scientific deliverables.

Acceptance Criteria

☑ The selected open gaps have substantive resolution_criteria

☑ Criteria are testable and reference evidence, debate, dataset, or KG deliverables

☑ Criteria do not hide unresolved gaps with vague completion language

☑ The before/after missing-criteria count is recorded

Approach

Query high-priority open gaps with missing or thin resolution_criteria.

Read each gap description and nearby landscape context.

Write concise criteria that define what would count as resolution.

Verify criteria length and inspect a sample for specificity.

Dependencies

quest-engine-ci - Generates this task when queue depth is low and resolution-criteria gaps exist.

Dependents

Gap lifecycle governance and mission evaluation depend on clear resolution criteria.

Work Log

2026-04-21 20:09 UTC - task:32b205dd

Agent: codex

Read AGENTS.md, the task spec, docs/planning/alignment-feedback-loops.md,

and docs/planning/landscape-gap-framework.md.

Verified the task was still necessary with a live PostgreSQL query:

3374 non-resolved knowledge_gaps rows had resolution_criteria IS NULL
or length(trim(resolution_criteria)) < 20.

Added substantive resolution criteria to 25 high-priority non-resolved gaps

using scidex.core.database.get_db_write() and journaled_update_by_keys().
The updates were recorded in db_write_journal and edit_history with task
provenance.

Updated gap IDs:

gap-seaad-v2-20260402032945,
gap-seaad-v3-20260402063622,
26abc5e5f9f2,
gap-seaad-20260402025452,
gap-tau-prop-20260402003221,
gap-immune-atlas-neuroinflam-20260402,
gap-20260404-microglial-priming-early-ad,
gap-debate-20260410-112348-a10cb6b4,
gap-debate-20260410-112625-6c2ceffa,
gap-crispr-neurodegeneration-20260402,
gap-aging-mouse-brain-20260402,
gap-ev-ad-biomarkers,
gap-debate-20260410-113045-6fcb3f6c,
gap-008,
gap-010,
gap-pubmed-20260410-185251-10f6a211,
gap-debate-20260417-033119-54941818,
gap-debate-20260417-033236-0fe26d91,
gap-debate-20260417-033105-98a4039b,
gap-debate-20260417-033149-132f7d7a,
gap-20260416-121711,
gap-004,
gap-20260402-003058,
gap-tau-propagation-20260402,
gap-debate-20260403-222617-8eb5bdbc.

Verification query after the database update: missing criteria count is 3349, satisfying

the task threshold of <= 3349.

2026-04-22 22:50 UTC - task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0

Agent: minimax:75

Verified task still necessary: missing criteria count was 3060 (threshold <= 3060).
Selected 25 new gaps with priority scores 0.86-0.87, all with no resolution criteria.
Wrote substantive, testable resolution criteria for each gap referencing specific methods (CRISPR, Cryo-EM, RNA-seq, MRI, LC-MS/MS, ChIP-seq, ATAC-seq) and quantitative thresholds (>=30% rescue, n>=80, AUC>=0.80, Kd<100nM).
Updated all 25 gaps via journaled_update_by_keys() through scidex.core.db_writes.
Verification query after update: missing criteria count is 3035, satisfying the task threshold of <= 3035.
Updated gap IDs:

gap-pubmed-20260410-145520-5692b02e,
gap-pubmed-20260410-150509-76c40dac,
gap-pubmed-20260410-170057-a2f72fd8,
gap-pubmed-20260410-180918-962b1ada,
gap-pubmed-20260410-174000-6451afef,
gap-pubmed-20260410-150544-e3a2eab9,
gap-pubmed-20260410-182548-ed2eab75,
gap-pubmed-20260410-183201-e5534f58,
gap-pubmed-20260411-075338-9c926077,
gap-pubmed-20260411-080155-c867ed08,
gap-pubmed-20260410-150438-b037602a,
gap-pubmed-20260410-181109-cef8fb09,
gap-pubmed-20260410-184203-136029e2,
gap-pubmed-20260410-111219-74e525bc,
gap-pubmed-20260410-180503-26b108e7,
gap-pubmed-20260411-070434-a4efc962,
gap-pubmed-20260411-091147-cf227e9b,
gap-pubmed-20260410-183032-8c6a6ada,
gap-pubmed-20260411-075425-f64d1b05,
gap-pubmed-20260410-145358-6adf3f6d,
gap-pubmed-20260410-145411-9b3a4ae6,
gap-pubmed-20260410-191933-4ee24fe1,
gap-pubmed-20260410-192024-f53d72b7,
gap-pubmed-20260410-173322-468b78e0,
gap-pubmed-20260410-213813-4c2ceb40.

Commit: local DB write only, no file changes on branch.

2026-04-22 23:25 UTC - task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0

Agent: minimax:76

Verified task still necessary: missing criteria count was 3035 (threshold <= 3035).
Selected 25 new gaps with priority scores 0.85-0.86, distinct from the gaps updated by previous minimax:75 agent (which covered gap-pubmed-20260410-145520- through gap-pubmed-20260410-213813-).
Wrote substantive, testable resolution criteria for each gap referencing specific methods (MERFISH, Patch-seq, cryo-EM, CRISPR screens, phosphoproteomics, MRS/PET imaging, ATAC-seq) and quantitative thresholds (>=40% rescue, n>=15, AUROC>=0.80, KD<=10 uM, TI>=5).
Updated all 25 gaps via journaled_update_by_keys() through update_knowledge_gap().
Verification query after update: missing criteria count is 3010, satisfying the task threshold of <= 3010.
Updated gap IDs:

gap-pubmed-20260410-185251-a2373bc1,
gap-debate-20260410-112706-1e53e5ef,
gap-pubmed-20260410-105547-d82330c8,
gap-debate-20260410-112718-0b883f8b,
gap-debate-20260410-112503-83785f33,
gap-debate-20260410-112457-a9f6e214,
gap-debate-20260410-112619-975a2454,
gap-debate-20260410-111542-379947c1,
gap-debate-20260410-112649-f2b02ba8,
gap-debate-20260410-112636-e8dcebb6,
gap-debate-20260410-112451-daf5c1d4,
gap-debate-20260410-112430-330ef04a,
gap-debate-20260410-075001-9d74b2d0,
gap-debate-20260410-075012-751a92fa,
gap-debate-20260410-112700-196b8382,
gap-debate-20260410-095546-54d22830,
gap-debate-20260410-095938-941d5eec,
gap-debate-20260410-105826-49b48c3e,
gap-debate-20260410-095945-2fd7a87f,
gap-pubmed-20260410-111218-bc72b8d2,
gap-debate-20260410-075007-2db7d4e4,
gap-debate-20260410-112625-567b897e,
gap-debate-20260410-100405-8495ede2,
gap-debate-20260410-112343-7902affa,
gap-debate-20260410-112725-2ca16aa9.

Committed script and spec update.

2026-04-21 21:20 UTC - task:eac11b69-d3b9-4403-948c-ac8b5c2d63eb

Agent: minimax:72

Verified task still necessary: missing criteria count was 3349 (threshold <= 3349).
Selected 25 new gaps with high priority scores (0.9) and no resolution criteria, distinct from the 25 previously updated by codex agent.
Wrote substantive, testable resolution criteria for each gap, referencing specific experimental methods (Cryo-EM, scRNA-seq, SPR, CRISPR, in vivo imaging) and quantitative thresholds (≥30% alteration, n≥100, AUC≥0.80, TI≥5).
Updated all 25 gaps via journaled_update_by_keys() through update_knowledge_gap().
Verification query after update: missing criteria count is 3324, satisfying the task threshold of <= 3324.
Updated gap IDs:

gap-apoe4-lipid-metabolism,
gap-debate-20260411-065001-076e4fa7,
gap-debate-20260417-032952-48bdcbea,
gap-debate-20260412-094612-a2e3bd09,
gap-debate-20260412-094556-86f36bb3,
gap-debate-20260411-064946-4940f331,
gap-debate-20260412-094638-cd9ef05d,
gap-debate-20260417-033037-c43d12c2,
gap-debate-20260410-095945-976d542d,
gap-debate-20260406-062052-7bcf4b6c,
gap-debate-20260410-095612-b00442be,
gap-20260410-090500,
gap-neuroinflammation-microglial-20260404,
gap-debate-20260410-075012-32bac138,
gap-debate-20260410-095952-12fad421,
gap-20260410-094512,
gap-debate-20260410-075000-7396040a,
gap-debate-20260410-095546-8e85ab15,
gap-debate-20260410-095556-5310dbe1,
gap-debate-20260406-062045-6addd0cf,
gap-debate-20260406-062101-6af4ba5f,
gap-20260404-052358,
gap-20260404-060512,
gap-neuro-microglia-early-ad-20260404,
gap-debate-20260410-075007-232fbf62.

Commit: a823d9368.

Payload JSON

{
  "requirements": {
    "analysis": 7,
    "reasoning": 7
  }
}

Sibling Tasks in Quest (Atlas) ↗

●[Atlas] Migrate knowledge graph to Neo4jP88

●[Atlas] Expand wiki_entities from NeuroWiki corpusP87

●[Atlas] Wiki content generation for entities without NeuroWiki pagesP78

○[Atlas] Wiki quality pipeline: score pages and process improvement queuesP97

○[Atlas] Paper processing pipeline: fetch, extract figures, read, enrich wikiP97

○[Atlas] Add mermaid diagrams to 10 wiki entity pagesP88

○[Atlas] Backfill debate_sessions and debate_rounds from analysis transcriptsP85

○[Atlas] Entity resolution and canonical ID systemP85

○[Atlas] Link 50 evidence entries to target artifactsP85

○[Atlas] Expand 15 wiki stubs to 500+ words with cited neurodegeneration contentP85

Task Dependencies

↓ Referenced by (downstream)

✓[Atlas] Run gap_criteria_batch3.py to update 25 knowledge gaps with resolution criteriaP75Atlas

[Atlas] Add resolution criteria to 25 open knowledge gaps done analysis:7 reasoning:7

Completion Notes

Git Commits (6)

Goal

Acceptance Criteria

Approach

Dependencies

Dependents

Work Log

2026-04-21 20:09 UTC - task:32b205dd

2026-04-22 22:50 UTC - task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0

2026-04-22 23:25 UTC - task:f85a60fd-c27e-49fc-bb97-5d172bbe4fe0

2026-04-21 21:20 UTC - task:eac11b69-d3b9-4403-948c-ac8b5c2d63eb

Sibling Tasks in Quest (Atlas) ↗

Task Dependencies