Deep Research

Deep-Research — Source-Validated Literature Review Engine

Answer a hard question properly and hand back a written, formatted, integrity- checked literature review — not just notes. Scope → design → discover → screen by journal ranking → validate sources → extract & verify evidence → synthesize → stress-test → write → review-loop → final report. Original work; architecture informed by open community deep-research skills (see the repo README Acknowledgements). Usable standalone, or as the deep-dive engine called by food-research.

Modes

• quick brief — scope → discover → screen (Tier 1) → light synthesis → short sourced answer. Skips the full validation/compile/review loop.
• full — the default: the complete 12-subagent pipeline below with the iterate-to-saturation and compile↔review loops, ending in a finished review.

Subagent team (dispatch via the Agent tool)

| # | Subagent | Job | |---|---|---| | 1 | research_scope | Comprehensive scope brief: background, problem, significance, central + sub-questions, concepts, boundaries, success criteria. | | 2 | research_architect | Methodology blueprint: review type, search strategy, inclusion criteria, analytical framework, reporting standard, stopping criteria. | | 3 | investigator | Pass 1 discover candidate sources; Pass 2 extract evidence from validated sources only (parallel per sub-question). | | 4 | source_screener | Prioritize candidates by journal ranking (Tier 1 Q1/Q2 + Nature/Science/Cell + other-discipline Q1/Q2; Tier 2 Q3; avoid Tier 4). | | 5 | source_verifier | Validate each prioritized source (existence/DOI, venue legitimacy, retraction, predatory, methodology, COI) → Source Quality Matrix. | | 6 | bibliography | Deduplicate + format references (APA 7.0 default, or target-journal style via journal-selector); build the citation map + .bib/.ris. | | 7 | claim_verifier | Verify each load-bearing claim against its validated source; classify fact/hypothesis/contested/speculation. | | 8 | synthesizer | Evidence matrix, thematic synthesis, conflict reconciliation, evidence grading, coverage advisory, gap agenda, narrative arc. | | 9 | critic | Devil's advocate on the synthesis; loop back to investigate if gaps. | | 10 | compiler | Write & format the literature-review draft (APA 7.0 / target journal); cite by key only; no fabrication. | | 11 | editor | Editorial review of the draft (5 weighted dimensions, verdict + prioritized feedback). | | 12 | ethics_reviewer | Integrity/ethics review of the draft (citation integrity, faithful representation, bias, COI, disclosure). |

Workflow

flowchart TD
    A[research_scopescope brief] --> B[research_architectmethodology blueprint]
    B --> C[investigator Pass 1discover candidate sources]
    C --> D[source_screenerjournal-ranking tiers]
    D --> E[source_verifiervalidate → Source Quality Matrix]
    E --> F[bibliographydedupe + format + citation map]
    E --> G[investigator Pass 2extract evidence from validated sources]
    G --> H[claim_verifierverify claims vs validated sources]
    H --> I[synthesizermatrix, themes, conflicts, grading, gaps]
    I --> J[criticstress-test synthesis]
    J -- gaps --> C
    J -- sound --> K[compilerwrite + format reviewAPA 7.0 / target journal]
    F --> K
    K --> L[editor + ethics_reviewereditorial + integrity review]
    L -- minor/major revision --> K
    L -- accept --> M[Final literature review]

Two loops: (1) evidence loop — critic sends gaps back to investigator (cap ~2–3); (2) writing loop — editor/ethics_reviewer send revisions back to compiler until Accept (cap ~2–3), then deliver.

Source discipline (non-negotiable)

• Investigation and claim-checking operate only on validated sources — those that passed source_screener (ranking) and source_verifier (validity). Retracted/unresolvable sources are excluded and logged.
• Journal ranking favors Tier 1 (Q1/Q2 food-science & nutrition, Nature/Science/Cell families, Q1/Q2 in any other discipline); Tier 2 (Q3) only to fill gaps; Tier 4 avoided.
• Every claim carries a source and locator; inference is labelled as inference.

Formatting

Default APA 7.0. If the user names a target journal, bibliography and compiler call the journal-selector skill to format the review to that journal's structure, limits, and reference style.

Principles

Every claim sourced; fact separated from interpretation; disagreement shown, not averaged; uncertainty surfaced. Upstream evidence beats parametric knowledge — mark missing evidence [EVIDENCE GAP], never fabricate.

References (load as needed)

• references/reasoning-and-fallacies.md — synthesizer/critic: sound argument + fallacies.
• food-research/references/literature-sources.md — databases/APIs for investigator.
• food-research/references/source-quality-hierarchy.md — evidence grading for source_verifier/synthesizer.
• food-research/references/reporting-guidelines.md — EQUATOR/PRISMA/CONSORT/STROBE.
• food-paper/references/apa7-quickref.md — APA 7.0 for bibliography/compiler (default style).
• food-review/references/ethics-integrity-checklist.md — for ethics_reviewer.

Handoff

Standalone → deliver the final review. Called by food-research → return the validated synthesis (or the finished review) to fold into the evidence brief.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: PangenomeAI
• Source: PangenomeAI/academic-skills-food-nutrition
• License: MIT

Install and usage instructions live in the source repository linked above.