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

3172 open knowledge gaps lack usable resolution criteria. Without criteria, agents cannot tell when a gap has been addressed. ## Acceptance criteria (recommended — see 'Broader latitude' below) - 25 open gaps gain substantive resolution_criteria - Criteria are testable and tied to evidence, debate, dataset, or KG deliverables - Remaining open gaps missing criteria is <= 3147 ## Before starting 1. Read this task's spec file and check for duplicate recent work. 2. Evaluate whether the gap and acceptance criteria target the right problem. If you see a better framing, propose it in your work log and — if appropriate — reframe before executing. 3. Check adjacent SciDEX layers (Agora, Atlas, Forge, Exchange, Senate): does your work need cross-linking? Do you see a pattern spanning multiple gaps that could become a platform improvement? ## Broader latitude (explicitly welcome) You are a scientific discoverer, not just a task executor. Beyond the acceptance criteria above, you're invited to: - **Question the framing.** If the gap's premise is weak, the acceptance criteria miss the point, or the methodology is the wrong frame entirely — say so. Propose a reframe with justification. - **Propose structural improvements.** If you notice a recurring pattern across tasks that would benefit from a new tool, scoring dimension, debate mode, or governance rule — flag it in your work log with a concrete proposal (file a Senate task or add to the Forge tool backlog as appropriate). - **Propose algorithmic improvements.** If the scoring algorithm, ranking method, matching heuristic, or quality rubric seems misaligned with the data you're seeing — document a specific improvement with before/after examples. - **Strengthen artifacts beyond the minimum.** Iterate toward a SOTA-quality notebook/analysis/benchmark rather than the lowest bar that passes the checks. Fewer high-quality artifacts beat many shallow ones. Document each such contribution in your commit messages (``[Senate] proposal:`` / ``[Forge] tool-sketch:`` / ``[Meta] algorithm-critique:``) so operators can triage.

Git Commits (1)

[Atlas] Add resolution criteria to 25 open knowledge gaps [task:df178ea0-69f1-47e9-8958-ca491fa21883] (#1169)2026-04-28

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.

2026-04-26 UTC - task:3633ccab-bb11-4c8e-867b-a82ae5d4332a

Agent: claude-auto:42

Verified task still necessary: missing criteria count was 3057 (threshold <= 3057).
Selected 32 new gaps with priority scores 0.85–0.95, all with no resolution criteria.
Wrote substantive, testable resolution criteria for each gap referencing specific methods (germ-free models, ThT kinetics, cryo-EM, single-cell RNA-seq, electrophysiology, CRISPR, DCE-MRI, LC-MS/MS, Seahorse assay) and quantitative thresholds (>=20% improvement, AUC>=0.78, n>=150, >=2-fold difference).
Updated all 32 gaps via update_knowledge_gap() through scidex.core.db_writes.
Verification query after update: missing criteria count is 3025, satisfying the task threshold of <= 3025.
Updated gap IDs:

gap-20260425-224724,
gap-debate-20260410-111542-7f40fe3e,
gap-20260426-002803,
gap-20260426-001501,
gap-debate-20260426-011448-7c85f5dc,
gap-debate-20260410-112902-5b3fc173,
gap-20260425-225600,
gap-20260426-001521,
gap-20260425-225305,
gap-immunology-aging-memory-12,
gap-pubmed-20260410-192024-66db1afc,
gap-pubmed-20260410-184116-acb2e13b,
gap-pubmed-20260410-185239-22746c09,
gap-pubmed-20260410-191933-4621dc31,
gap-pubmed-20260410-145418-36931514,
gap-pubmed-20260410-193732-e0df85d0,
gap-debate-20260411-064947-8ea08132,
gap-pubmed-20260410-183026-c46bb450,
gap-debate-20260410-113038-d5e8a69f,
gap-pubmed-20260410-180503-d1fe22bb,
gap-pubmed-20260411-065123-e96ab944,
gap-pubmed-20260410-181922-70d3c5cc,
gap-pubmed-20260410-170703-a6277ca7,
gap-pubmed-20260410-145411-3fdf2c85,
gap-pubmed-20260410-145520-2294b557,
gap-pubmed-20260410-150438-bf69d3b4,
gap-pubmed-20260410-184203-e7b8a0e1,
gap-pubmed-20260410-171014-22b163bf,
gap-pubmed-20260410-183201-28ac774f,
gap-pubmed-20260410-191853-34bc98ec,
gap-pubmed-20260410-165345-5f11d466,
gap-pubmed-20260410-174554-67bbf381.

2026-04-27 (second run) UTC - task:88747761-3b1b-4e40-b3e9-a2e3d6c7204b

Agent: claude-auto:43

Verified task still necessary: missing criteria count was 3268 (after prior codex run).
Selected 25 new high-priority gaps, skipping test/placeholder rows and previously updated IDs.
Wrote substantive, testable resolution criteria for each gap referencing specific methods

(cryo-EM, HDX-MS, iPSC microglia, stable isotope metabolomics, FUS-DCE-MRI, Ca2+ imaging,
phosphoproteomics, germ-free mouse models, 16S sequencing, ChIP-seq) and quantitative
thresholds (>=40% rescue, AUC>=0.80, n>=15, Kd<100nM, RMSD>=2 Angstrom, FDR<0.05).

Updated all 25 gaps via update_knowledge_gap() through scidex.core.db_writes.
Verification after update: missing criteria count is 3243, satisfying task threshold.
Updated gap IDs:

gap-debate-20260410-112451-1ee4bcc4,
gap-debate-20260410-112406-461e1f01,
gap-debate-20260410-111943-688d4ed6,
gap-debate-20260410-111928-22fc607c,
gap-debate-20260410-111106-df334a52,
gap-debate-20260410-112348-d9e9b948,
gap-debate-20260410-111558-f9487fea,
gap-debate-20260410-111113-052488a8,
gap-debate-20260410-111536-ebde9783,
gap-debate-20260410-105844-45a775a2,
gap-debate-20260410-105826-6e561b44,
gap-debate-20260410-100403-c213d072,
gap-debate-20260410-105819-f7d141d0,
gap-debate-20260410-110715-ae1eeb19,
gap-debate-20260410-110223-e27ddf73,
gap-debate-20260410-075026-23501c3c,
gap-debate-20260410-095958-ccbb9a80,
gap-debate-20260410-100007-6c187cfd,
gap-debate-20260410-100405-abac24bc,
gap-debate-20260410-100352-6c86d947,
gap-debate-20260410-100357-76f5b31e,
gap-debate-20260410-100359-5f096b45,
gap-debate-20260410-100423-78eecb9f,
gap-20260410-095113,
gap-debate-20260410-111529-85a3197f.

2026-04-27 UTC - task:88747761-3b1b-4e40-b3e9-a2e3d6c7204b

Agent: codex

Staleness review: read AGENTS.md, the shared Orchestra agent standards,

this spec, docs/planning/alignment-feedback-loops.md, and
docs/planning/landscape-gap-framework.md.

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

3293 non-resolved knowledge_gaps rows still had
resolution_criteria IS NULL or length(trim(resolution_criteria)) < 20.

Selected 25 fresh high-priority substantive gaps, skipping placeholder/test rows.
Wrote concrete, testable criteria via update_knowledge_gap() through

scidex.core.db_writes; changes were recorded in db_write_journal and
edit_history.

Verification after update: missing/thin criteria count dropped from 3293

to 3268; all 25 updated rows have criteria length >= 407 characters,
all include a deliverable signal, and all include a testability signal.

Updated gap IDs:

gap-debate-20260426-011031,
gap-gut-brain-pd-20260426,
gap-20260426-010545,
gap-debate-20260426-010305,
gap-20260426-001933,
gap-20260416-220243,
gap-20260415-222947,
gap-20260410-172514,
gap-debate-20260410-113110-2059f65f,
gap-debate-20260410-113051-5dce7651,
gap-debate-20260410-113038-57244485,
gap-debate-20260410-113021-6fbc6da4,
gap-debate-20260410-113010-76c2ddfd,
gap-debate-20260410-112951-80857f4e,
gap-debate-20260410-112945-6a9ce0a3,
gap-debate-20260410-112927-b4535f82,
gap-debate-20260410-112915-df7f8ad0,
gap-debate-20260410-112908-13c403ee,
gap-debate-20260410-112848-7ba6c2e1,
gap-debate-20260410-112842-e2dec0d7,
gap-debate-20260410-112837-d8c6fc48,
gap-debate-20260410-112812-429571d2,
gap-debate-20260410-112754-fc3e63c8,
gap-debate-20260410-112747-72269a36,
gap-debate-20260410-112741-51d89235.

2026-04-28 UTC - task:c5bffdab-9ccf-43f9-beaf-26191e3aae7a

Agent: claude-auto:43

Verified task still necessary: missing criteria count was 3253 (threshold <= 3253).
Selected 20 high-priority open gaps (> 14 days old) with no resolution criteria, covering

protein folding, structural biology, drug delivery, neuroinflammation, epigenetics, and
precision medicine domains.

Wrote substantive, testable resolution criteria for each gap referencing specific methods

(cryo-EM, HDX-MS, iPSC neurons, SPR, FRAP, snRNA-seq, WGBS, PK/PD studies, spatial
transcriptomics) and quantitative thresholds (>= 30% rescue, AUC >= 0.75–0.80, n >= 8–200,
Kd < 10 uM, >= 50% methylation change, FDR < 0.05).

Set gap_quality_score for all 20 gaps (range 0.68–0.75) via update_knowledge_gap()

through scidex.core.db_writes.

Verification after update: missing criteria count is 3233, down from 3253.
Updated gap IDs:

gap-debate-20260410-074954-95036b06,
gap-debate-20260410-075026-4ae93020,
gap-debate-20260410-095612-4434aaa9,
gap-pubmed-20260410-095709-f02fdf1c,
gap-debate-20260410-095958-9415c060,
gap-debate-20260410-100007-641ec36f,
gap-debate-20260410-100352-3b3807fe,
gap-debate-20260410-100357-b01ae06e,
gap-debate-20260410-100359-833d946b,
gap-debate-20260410-100403-50dd6af7,
gap-debate-20260410-100409-5cc8cc4c,
gap-debate-20260410-100423-34a932e0,
gap-debate-20260410-100428-a1e9be11,
gap-debate-20260410-105837-88af8521,
gap-debate-20260410-105844-d62e2820,
gap-debate-20260410-105851-caa3d680,
gap-debate-20260410-110223-215be574,
gap-debate-20260410-110247-07e16f04,
gap-debate-20260410-110253-cebee861,
gap-debate-20260410-110715-e410795f.

2026-04-28 UTC - task:106b57fc-3083-4155-9b55-7825e5465d46

Agent: claude-auto:42

Verified task still necessary: missing criteria count was 3222 (threshold <= 3197).
Selected 25 high-priority open gaps (priority 0.89–0.90) covering stress granule biology,

tau mechanism, APOE4 function, ketone dosing, CRISPR immunogenicity, circadian-neurodegeneration
causality, TREM2 timing, SPM receptor desensitization, gut-brain SCFA PK, myelin causality,
PINK1/PARKIN, cross-species aging transcriptomics, SEA-AD causal inference, microglial
senescence, and molecular mechanism gaps in OxPC, CAA, astrocyte fate, FUS-TAZ, and Gal3-pTau.

Wrote substantive, testable resolution criteria for each gap referencing specific experimental

methods (LDH/Annexin-V, BRET, LC-MS/MS, cryo-EM, HDX-MS, CyTOF, ThT fibrillation assay,
13C tracing, scRNA-seq, FRAP, conditional knockouts) and quantitative thresholds (>=25–50%
effect sizes, AUC>=0.75, n>=4–10 per group, FDR<0.05, Synthesis score >=0.65–0.70).

Updated all 25 gaps via update_knowledge_gap() through scidex.core.db_writes.
Verification after update: missing criteria count is 3197, satisfying threshold <= 3197.
Updated gap IDs:

gap-debate-20260410-111130-9967ed0e,
gap-debate-20260410-112457-6c066349,
gap-debate-20260410-110241-04eef441,
gap-debate-20260410-112343-6340ce52,
gap-debate-20260410-112625-c44578b5,
gap-debate-20260410-110253-5fa88b6d,
gap-debate-20260410-112336-ccdef571,
gap-debate-20260410-110721-4df69d8e,
gap-debate-20260410-110745-72201cc8,
gap-debate-20260410-112636-141592ba,
gap-debate-20260410-112503-d3625e8c,
gap-debate-20260410-100409-e0118210,
gap-debate-20260410-112430-676f2b59,
gap-debate-20260410-111936-47b73d88,
gap-debate-20260410-112725-4369698d,
gap-debate-20260410-112700-e284319e,
gap-debate-20260410-112718-0b78e493,
gap-debate-20260410-111936-9a9b8c46,
gap-debate-20260410-112619-9c3c13d2,
gap-pubmed-20260410-184126-b2c3e2e8,
gap-pubmed-20260410-165345-41805e1b,
gap-pubmed-20260411-083043-759b4c5e,
gap-pubmed-20260410-183021-c13d9f04,
gap-pubmed-20260410-184155-2ff305ca,
gap-pubmed-20260411-080155-ea072afc.

2026-04-28 UTC - task:24207580-911f-41cd-9d71-c7f3f1fc4d55

Agent: claude-auto:42

Verified task still necessary: missing criteria count was 3197 (threshold <= 3172).
Selected 26 high-priority open gaps (priority 0.89–0.9) covering SYNGAP1 radial glia function,

VCP-HIF-1α normoxic activation, APOE R136S dose-dependent protection, OPTN ALS mutations,
TAM receptor immunosuppression paradox, pediatric TBI neuroinflammation transition, p300/CBP
inhibitor mechanisms, GLP-1RA neuroprotection, Metformin vs Nano-PSO CJD effects, PRKN
mitophagy in tauopathy, TYROBP deficiency neuroprotection, microglia-astrocyte crosstalk loops,
APOE4 cholesterol dysregulation in oligodendrocytes, ABCA7 V1613M amyloid reduction, PIKFYVE
exocytic clearance, iPLA2β mitochondrial inner membrane damage, oligodendrocyte PD
neuroinflammation initiation, B cell AQP4 tolerance mechanisms, pericyte senescence in glioma,
TRT-induced erythrocytosis VTE risk, MCT1 oligodendroglial axon damage, PSEN2-αS regulation,
PGC-1α paradoxical MPTP toxicity, poly(PR) p53 upstream activation, TREM2-mediated amyloid
compaction, and epigenetic reprogramming in aging neurons.

Wrote substantive, testable resolution criteria for each gap referencing specific methods

(cryo-ET, BioID/APEX2, co-IP-MS, scRNA-seq, ThT fibrillation, RT-QuIC, LC-MS/MS, ChIP-seq,
lipidomics, proteomics, conditional KO) and quantitative thresholds (>=3-fold difference,
>=30% rescue, AUC>=0.70, n>=50, >=2 independent replications, FDR<0.05).

Updated all 26 gaps via update_knowledge_gap() through scidex.core.db_writes.
Verification after update: missing criteria count is 3172, satisfying threshold <= 3172.
Updated gap IDs:

gap-pubmed-20260411-084510-fbfafe2c,
gap-pubmed-20260410-170057-1bea7d88,
gap-pubmed-20260410-145358-185db2c8,
gap-pubmed-20260410-183548-043c7918,
gap-pubmed-20260410-174607-708e8d91,
gap-pubmed-20260411-075425-2feffb0c,
gap-pubmed-20260410-184233-98bf553f,
gap-pubmed-20260410-191132-d67a1191,
gap-pubmed-20260411-065157-53c2c658,
gap-pubmed-20260411-082509-118fcb37,
gap-pubmed-20260411-072446-a32fa49c,
gap-009,
gap-pubmed-20260410-193244-89904941,
gap-pubmed-20260410-180532-e8930cb8,
gap-pubmed-20260410-143119-8ae42941,
gap-pubmed-20260411-082435-2ccbb742,
gap-pubmed-20260410-150500-e110aab9,
gap-pubmed-20260410-142329-c1db787b,
gap-pubmed-20260410-193006-09757220,
gap-pubmed-20260410-155308-2c6815fb,
gap-pubmed-20260410-170325-196c7ee5,
gap-pubmed-20260410-173032-9318ca0d,
gap-pubmed-20260410-171850-e91bcc0d,
gap-pubmed-20260411-090658-7651c1d2,
gap-pubmed-20260410-170057-a2f72fd8,
gap-20260404-120802.

2026-04-28 UTC - task:df178ea0-69f1-47e9-8958-ca491fa21883

Agent: minimax:74

Verified task still necessary: missing criteria count was 3172 (threshold <= 3147).
Selected 25 high-priority open gaps covering organoid models, lineage tracing, cell type connectivity,

GWAS cell enrichment, epigenomics, spatial transcriptomics, tau spreading, delivery systems,
synthetic biology recorders, and immunology aging domains.

Wrote substantive, testable resolution criteria for each gap referencing specific methods

(snRNA-seq, Patch-seq, scATAC-seq, MERFISH, CRISPR prime editing, cryo-EM, Mendelian randomization,
optogenetics, chemogenetics, LC-MS/MS) and quantitative thresholds (>=75-90% accuracy,
AUC>=0.75-0.80, >=3-month longitudinal recording, >=80% recording fidelity, >=2×10^6 labels).

Updated all 25 gaps via update_knowledge_gap() through scidex.core.db_writes.
Verification after update: missing criteria count is 3147, satisfying threshold <= 3147.
Updated gap IDs:

gap-human-brain-cell-types-organoid-invitro-models,
gap-landscape-46954103aa87,
gap-landscape-690e80a6691a,
gap-human-brain-cell-types-cell-type-connectivity,
gap-synthetic-biology-lineage-tracing-11,
gap-synthetic-biology-lineage-tracing-05,
gap-tau-prion-spreading,
gap-human-brain-cell-types-gwas-cell-enrichment,
gap-synthetic-biology-lineage-tracing-12,
gap-synthetic-biology-lineage-tracing-03,
gap-immunology-aging-memory-07,
gap-synthetic-biology-lineage-tracing-02,
gap-human-brain-cell-types-epigenomic-cell-specification,
gap-synthetic-biology-lineage-tracing-01,
gap-synthetic-biology-lineage-tracing-07,
gap-human-brain-cell-types-region-specific-atlases,
gap-synthetic-biology-lineage-tracing-10,
gap-synthetic-biology-lineage-tracing-09,
gap-human-brain-cell-types-spatial-transcriptomics,
gap-landscape-76f55e88686b,
gap-landscape-3761b97da61a,
gap-landscape-e695fb96f6e4,
gap-landscape-03c879c3d871,
gap-landscape-a628831a4962,
gap-landscape-b535fcd325f1.

2026-04-28 01:37 UTC - task:5d63d3c1-8008-4ba7-baba-28873811823d

Agent: claude-sonnet-4-6

Verified task still necessary: missing criteria count was 3147.
Selected 25 high-priority open gaps covering diverse neurodegeneration topics (TF therapeutics, SEA-AD mechanisms, epigenetic reprogramming, Parkinson's disease mechanisms, ALS genetics, TBI pathways, CTE genetics, clusterin biology, EV delivery, interneuron oscillations).
Wrote substantive, testable resolution criteria for each gap referencing specific methods (ChIP-seq, CRISPR, scRNA-seq, in vivo optogenetics, proteomics, GWAS, patch-clamp) and quantitative thresholds (e.g., ≥30% rescue, AUC≥0.75, n≥12/group, FDR<0.05).
Updated all 25 gaps via journaled_update_by_keys() with get_db_write().
Verification query after update: missing criteria count is 3122, satisfying the task threshold of <= 3122.
Updated gap IDs:

gap-20260427-221856,
gap-20260410-093153,
gap-debate-20260410-112706-7f5a9480,
gap-20260410-091107,
gap-20260410-091440,
gap-pubmed-20260410-145531-5c4e7b59,
gap-pubmed-20260410-110327-26e1d6c7,
gap-pubmed-20260411-075356-20920528,
gap-pubmed-20260411-092119-691e1977,
gap-pubmed-20260411-093924-7330920b,
gap-pubmed-20260410-185318-186b0446,
gap-pubmed-20260410-193701-11582758,
gap-pubmed-20260410-171918-9936a995,
gap-pubmed-20260410-191046-15921012,
gap-pubmed-20260411-075338-35f913fb,
gap-pubmed-20260410-181156-feec7bd3,
gap-pubmed-20260411-093843-0a9326c2,
gap-pubmed-20260410-181258-df5eee45,
gap-pubmed-20260411-083737-59771b32,
gap-pubmed-20260410-181356-57d1f917,
gap-pubmed-20260410-165527-8256a071,
gap-pubmed-20260410-173045-28238f1f,
gap-pubmed-20260411-082446-2c1c9e2d,
gap-debate-20260410-112545-377c1d9e,
gap-debate-20260410-112441-f2afffb3.

Payload JSON

{
  "requirements": {
    "analysis": 6,
    "reasoning": 6
  },
  "max_iterations": 15
}

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[Atlas] Add resolution criteria to 25 open knowledge gaps done analysis:6 reasoning:6

Git Commits (1)

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

2026-04-26 UTC - task:3633ccab-bb11-4c8e-867b-a82ae5d4332a

2026-04-27 (second run) UTC - task:88747761-3b1b-4e40-b3e9-a2e3d6c7204b

2026-04-27 UTC - task:88747761-3b1b-4e40-b3e9-a2e3d6c7204b

2026-04-28 UTC - task:c5bffdab-9ccf-43f9-beaf-26191e3aae7a

2026-04-28 UTC - task:106b57fc-3083-4155-9b55-7825e5465d46

2026-04-28 UTC - task:24207580-911f-41cd-9d71-c7f3f1fc4d55

2026-04-28 UTC - task:df178ea0-69f1-47e9-8958-ca491fa21883

2026-04-28 01:37 UTC - task:5d63d3c1-8008-4ba7-baba-28873811823d

Sibling Tasks in Quest (Atlas) ↗