prisma-systematic-review

PRISMA Systematic Review

A systematic review is a method, not a reading pile: protocol first, auditable screening, reproducible counts. Where an ordinary review says "I read some papers and here is my take", a systematic review can answer "how did you search, what did you exclude, and why" — with logs. This skill wires the PRISMA 2020 discipline into the project's literature tools.

Not for: exploring a new area, building a reading list, or drafting an ordinary Related Work section (writing-related-work when enabled) — those need no protocol and no flow diagram.

Scaled-down mode: when full PRISMA is heavier than the occasion but coverage still needs to be defensible (e.g. a Related Work section someone may challenge), keep the two minimal records — the queries as executed and the exclusion reasons — and skip the protocol registration and flow diagram. Say that you are doing so.

When to use

• The user wants a systematic review / systematic survey, not an ad-hoc one
• A Related Work section needs defensible coverage ("how did you search?")
• Meta-analysis preparation (screening + data extraction stage)

Files in this skill

• references/prisma-2020-checklist.md — the 27-item checklist, condensed; read it when drafting the report, not before.
• templates/protocol-outline.md — the protocol skeleton (write this FIRST).
• templates/screening-log.csv — one row per record: source, query, id, decision, reason.
• templates/prisma-flow.md — the flow-diagram counts file to keep current.

Workflow

1. Protocol before searching — draft from templates/protocol-outline.md into the project (research question, PICO/SPIDER framing, inclusion & exclusion criteria, databases, date limits). Persist via research-brief-update or a protocol file after user confirmation.
2. Search & log — run literature-discover per planned query; record each query and hit count in the screening log. Reproducibility means the queries are written down as executed.
3. Screen in two passes — title/abstract pass then full-text pass; every exclusion gets a reason in the log. literature-read for abstracts; literature-read-pdf (intensive list) for full texts.
4. Keep the flow counts current — identified → deduped → screened → excluded (reasons) → included. templates/prisma-flow.md is the file of record; the diagram is generated from it at report time.
5. Include — papers that pass go to the library only with explicit user confirmation (literature-add); otherwise stage them for the session.
6. Synthesize & report — draft the review following the checklist; citations via [@bibkey] / staged [n]; literature-export-bib for the manuscript.

Done when

• Flow-diagram counts reconcile with the screening log (audited against each other).
• Protocol deviations recorded with dates and reasons.
• Included papers are in the library (user-confirmed) or staged; the bibliography is synced.
• Scaled-down mode: the query log and exclusion reasons exist on disk — the rest is optional.

Rules

• Counts in the flow diagram must reconcile with the screening log — audit them against each other before reporting.
• Deviations from the protocol are allowed but must be recorded with dates and reasons.
• Never silently re-run a query with different terms and keep the old count.