Lit Review

Multi-Phase Literature Review Workflow

Orchestrate a rigorous, citation-grounded literature review across phases: angles to briefs, parallel paper collection, taxonomic synthesis, direction papers, and self-review loops. Every claim in a final document is traceable back to a paper-card.

When to Use

• Building a corpus-grounded review paper or a set of direction documents
• Multi-strand reviews where breadth + depth must be coordinated across distinct angles (e.g. tools strand, data strand, science strand)
• Reviews where claim-to-evidence traceability matters (grant lit reviews, position papers, white papers)
• Iterative reviews where new papers, refined angles, or updated synthesis must roll forward without losing prior work

When NOT to Use

• Original research IMRAD writing. Use manuscript:manuscript-writing.
• Peer review of a submitted manuscript. Use manuscript:paper-review.
• Journal formatting. Use manuscript:manuscript-formatting.

Two modes

This skill covers two workflows:

• Express mode (single-pass synthesis): thematic synthesis for an Introduction, Background section, or quick standalone review. See [references/single-pass-synthesis.md](references/single-pass-synthesis.md). Pair with [references/review-frameworks.md](references/review-frameworks.md) for PRISMA, PICO, SPIDER, scoping protocol, and risk-of-bias tools.
• Full protocol (multi-phase): citation-traceable corpus reviews and direction papers. Use the Phase 0-4 workflow below.

When in doubt: if the user wants flowing prose for one section, use express mode; if they want a corpus with claim-to-card traceability, use the full protocol.

Workflow Phases

Phase 0: Briefs            -> _briefs/strand-*.md (one brief per strand)
Phase 1: Collection        -> research/collection///{card.md, source.{pdf,md}, meta.json}
                              + INDEX.md + .bib per strand
Phase 2: Synthesis         -> research/synthesis/{-ontology, gap-analysis, scope-diagram, -map}.md
Phase 3: Direction papers  -> direction-papers/-direction.md
Phase 4: Review loop       -> revised direction; may reopen Phase 1 with new gaps

Each angle is realized as a strand; the brief is the strand's dispatch document. Iteration is expected: loop back from any phase. The directory layout is the persistence layer; treat it as the source of truth between sessions.

Phase 0: Define angles and write briefs

Inputs: prior work, gap statement, epic-dev findings (if any), grant call or thesis question.

Output: one brief per strand in _briefs/strand-.md.

Each brief defines:

• Goal (one sentence)
• Scope categories (numbered list, breadth first)
• Per-entry deliverable (cards + source + bib + index)
• Seed material (existing prior-work documents to import)
• Acceptance criteria (count thresholds, breadth thresholds, completeness gates)
• Out-of-scope items
• Sister skills to use (opencite:opencite, manuscript:manuscript-writing)

See [references/brief-template.md](references/brief-template.md) for the full structure.

If the user names a project domain (neuro tools, clinical trials, ML methods, etc.), generate strands by partitioning the topic on dimensions that cannot be merged later without information loss. Common partitions: methods vs. infrastructure vs. application; tools vs. data vs. theory; modality A vs. modality B.

Phase 1: Collection (parallel strand agents)

For each strand, build a corpus of paper-cards under research/collection//. Each entry is a folder with card.md plus source.md plus meta.json, and source.pdf only when redistributable. Per-strand aggregates are INDEX.md and .bib. Use opencite:opencite for all paper operations.

Schema and storage rules: [references/paper-card-schema.md](references/paper-card-schema.md). License-to-redistribution policy and CI rule: [references/license-rules.md](references/license-rules.md).

When parallelizing strands, dispatch one agent per strand. Use the brief as the agent's full context. Do not let strand agents synthesize across strands; that is Phase 2's job.

Phase 2: Synthesis (whole-corpus integration)

Inputs: full collection across all strands.

Outputs (in research/synthesis/):

• -ontology.md per strand: hierarchical category tree of corpus entries
• -map.md (e.g. science-map.md): theme-by-theme inventory of analytic / methodological themes
• -hierarchy.md (e.g. dataset-hierarchy.md): the data layer, when applicable
• gap-analysis.md: three-column comparison of what is covered by prior efforts vs. what the synthesis reveals as uncovered. The third column is the input to Phase 3
• scope-diagram.md: prose plus optional Mermaid/ASCII diagram of corpus boundaries

Bias rules (enforced):

• Gap analysis must list what the corpus does NOT support, not just what it does
• Inter-strand contradictions must be named, not papered over
• Frequency-of-mention is not evidence weight; cite single primary sources where appropriate

See [references/synthesis-templates.md](references/synthesis-templates.md).

Phase 3: Direction papers (citation-grounded essays)

Output: direction-papers/-direction.md per direction (typically one per strand or per gap cluster).

Each direction paper:

• Defends a thesis grounded in the corpus
• Cites every claim back to a specific card path: [](../research/collection///card.md)
• Closes with a flat references section keyed to BibTeX in the strand .bib
• Follows review-paper IMRAD structure and prose discipline (delegate to manuscript:manuscript-writing): no em-dashes, abbreviations defined on first use, descriptive voice not exhortatory

The cite-card cross-link is the load-bearing convention. A claim that does not link to a card is a claim that has not yet been grounded; either ground it (add the card) or remove the claim.

See [references/direction-paper-template.md](references/direction-paper-template.md).

For LaTeX export of a direction paper to a journal review template, delegate to manuscript:manuscript-formatting. The base format is markdown.

Phase 4: Review loop

Self-review the direction paper using manuscript:paper-review. Treat it as a peer review of one's own draft.

Common loop-back triggers:

• Reviewer (self or other) names a claim as ungrounded -> Phase 1 (add cards) or Phase 3 (drop claim)
• Reviewer flags a missing theme -> Phase 0 (new strand or expanded scope) -> Phase 1 (collect)
• Reviewer flags a contradiction in synthesis -> Phase 2 (revise gap analysis or ontology)
• Reviewer flags storyline incoherence -> Phase 3 (restructure with manuscript:manuscript-writing)

Apply [references/rigor-checklist.md](references/rigor-checklist.md) before declaring a direction paper done.

Bootstrapping a new lit review

When the user starts fresh, propose a top-level layout in the working directory or a subdirectory:

/
├── _briefs/
├── research/
│   ├── collection/
│   │   ├── _schema/paper-card.md
│   │   └── /
│   └── synthesis/
└── direction-papers/

Create directories on demand as work progresses; do not pre-create empty trees. The _schema/paper-card.md should be a copy of [references/paper-card-schema.md](references/paper-card-schema.md) so that strand agents have a local reference.

Formalize phases with project:epic-dev

The Phase 0-4 workflow maps cleanly onto the epic/sprint model. When the lit review lives in a git repository with a GitHub remote, delegate phase orchestration (issues, sub-issues, branches, worktrees, state file) to project:epic-dev so the review has the same tracking discipline as feature work. This is opt-in; skip it for non-git note folders or solo scratch reviews.

Recommended mapping:

| Lit-review artifact | epic-dev artifact | |---|---| | The lit review itself | Epic issue + epic branch (feature/issue-{N}-epic-litreview-{slug}) | | Phase 0 (briefs) | Sub-issue, single phase branch; output _briefs/strand-*.md | | Phase 1 (collection) | One sub-issue + worktree per strand for parallel agents; outputs under research/collection// | | Phase 2 (synthesis) | Sub-issue depending on all Phase 1 phases; outputs under research/synthesis/ | | Phase 3 (direction papers) | One sub-issue per direction paper, can run in parallel; outputs under direction-papers/ | | Phase 4 (review loop) | Sub-issue per review pass; loop-back triggers reopen earlier-phase issues rather than mutating closed ones | | .claude/epic.local.md | Phase tracker that survives sessions; complements the directory-as-source-of-truth convention |

When to invoke epic-dev:

• At the start of a fresh multi-strand lit review, after the user agrees on the strand list. Delegate epic + sub-issue creation to project:epic-dev; it will produce the issue tree, worktrees, and state file. Continue Phase 0 brief drafting inside the resulting epic worktree.
• When a Phase 4 review loop spawns new gaps that justify reopening Phase 1 with new strands, create new sub-issues under the existing epic via project:epic-dev --next-phase rather than starting a parallel epic.
• When resuming a stalled review across sessions, project:epic-dev --resume reads .claude/epic.local.md and routes back to the active phase worktree.

When NOT to invoke epic-dev:

• The review is express-mode (single-pass synthesis); the overhead exceeds the value.
• The output lives in a non-git directory (private notes, OneDrive, Notion export staging).
• The user declines GitHub issue tracking for the review.

The cite-card cross-link convention from Phase 3 still applies regardless of whether phases are tracked as epic-dev sub-issues; epic-dev tracks the process, not the traceability.

Sister skills

| Skill | Used for | |---|---| | opencite:opencite | DOI lookup, PDF retrieval, PDF -> markdown, BibTeX export | | manuscript:manuscript-writing | IMRAD / review-paper structure plus prose discipline (abbreviations, voice, transitions) | | manuscript:manuscript-formatting | Journal formatting / LaTeX export | | manuscript:paper-review | Self-review loops on direction-paper drafts | | manuscript:humanizer | Final natural-writing pass on synthesized prose. Lit-review synthesis sections are particularly prone to "evolving landscape", "growing body of work", and significance-inflation patterns; run humanizer before declaring a direction paper or Phase 2 synthesis complete. | | project:epic-dev | Formalize the lit-review phases (epic + sub-issues + worktrees + state file); also an upstream source of research angles when reviewing one's own project |

References

• [references/paper-card-schema.md](references/paper-card-schema.md): card.md frontmatter + sections, meta.json schema, license vocabulary, storage rules
• [references/brief-template.md](references/brief-template.md): per-strand dispatch brief structure
• [references/synthesis-templates.md](references/synthesis-templates.md): ontology, gap-analysis, map, scope-diagram patterns
• [references/direction-paper-template.md](references/direction-paper-template.md): essay structure with cite-card cross-link convention
• [references/license-rules.md](references/license-rules.md): redistribution discipline and CI rules
• [references/rigor-checklist.md](references/rigor-checklist.md): cohesion, storyline, bias-neutrality, traceability acceptance criteria
• [references/single-pass-synthesis.md](references/single-pass-synthesis.md): express-mode thematic synthesis pipeline for Introduction/Background sections
• [references/review-frameworks.md](references/review-frameworks.md): PRISMA, PICO, SPIDER, scoping protocol, risk-of-bias tools

Source & license

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

• Author: neuromechanist
• Source: neuromechanist/research-skills
• License: BSD-3-Clause

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