--- name: jama-workflow description: Use when deciding which jama-* sub-skill to invoke next, or when sequencing a clinical manuscript from scope check through revision for JAMA (Journal of the American Medical Association). Routes — does not replace — the specialized skills. --- # JAMA Manuscript Workflow (jama-workflow) ## Overview This is the router. It does not replace any specialized skill; it tells you **which jama-* skill to use for the stage you are at** when preparing an Original Investigation (or systematic review / meta-analysis) for JAMA. Default assumption: unless the user says the target is a different journal, treat the manuscript as aimed at JAMA — a big-four general medical journal (alongside NEJM, The Lancet, The BMJ) that demands **general medical importance**, a clean **EQUATOR-aligned reporting standard** (CONSORT / STROBE / PRISMA / STARD), prospective **trial registration**, and dedicated **statistical review**. ## When to trigger - "What should I do next?" on a clinical manuscript - A draft is handed over and the current bottleneck is unclear - You are bouncing between design, stats, writing, and reviewer replies - You received JAMA decision letter / reviewer comments and must switch to revision mode ## Routing table | Current symptom | Next skill | |----------------------------------------------------------------------|------------------------------| | Unsure the topic clears JAMA's general-medical-importance bar | `jama-scope-fit` | | Design questions: RCT vs cohort vs diagnostic vs review; ITT, bias | `jama-study-design` | | Need the right EQUATOR checklist + flow diagram (CONSORT/PRISMA…) | `jama-reporting-standards` | | p-values only, no effect sizes/CIs; multiplicity not handled | `jama-statistics` | | Figures/tables cluttered, no CONSORT/PRISMA diagram, units wrong | `jama-figures-tables` | | Abstract not in JAMA structure; no Key Points box | `jama-structured-abstract` | | Trial not registered / registered late; missing IRB, consent, COI | `jama-ethics-registration` | | Prose verbose, jargon-heavy, "spin" in conclusions | `jama-writing-style` | | Need a cover letter pitching importance to the editor | `jama-cover-letter` | | Ready to submit; need the pre-submission preflight | `jama-submission` | | Received reviewer comments / a revise decision | `jama-peer-review-revision` | ## Default order 1. `jama-scope-fit` — decide whether JAMA is the right home before investing more 2. `jama-study-design` — lock the design and its internal-validity safeguards 3. `jama-reporting-standards` — choose and complete the EQUATOR checklist + diagram 4. `jama-statistics` — pre-specified outcomes, effect sizes + 95% CIs, multiplicity 5. `jama-figures-tables` — finalize the flow diagram, baseline table, main exhibits 6. `jama-structured-abstract` — JAMA structured abstract + Key Points box 7. `jama-ethics-registration` — registration, IRB/consent, ICMJE disclosures, data sharing 8. `jama-writing-style` — tighten prose, remove spin, match house style (polish) 9. `jama-cover-letter` — editor-facing pitch of general medical importance 10. `jama-submission` — final preflight against author instructions 11. `jama-peer-review-revision` — response after the decision letter > `jama-structured-abstract` and `jama-writing-style` are **late-stage polish** — do not perfect prose while the design or primary outcome is still unsettled. ## Decision shortcuts - "I have a finding but it's narrow / subspecialty-only" → `jama-scope-fit` - "Reviewers will ask if this is ITT or per-protocol" → `jama-study-design` - "I don't know whether I need CONSORT or STROBE" → `jama-reporting-standards` - "My results are all p < 0.05 with no CIs" → `jama-statistics` - "My RCT has no participant flow diagram" → `jama-figures-tables` - "My abstract is one block paragraph" → `jama-structured-abstract` - "I registered the trial after enrollment started" → `jama-ethics-registration` - "My conclusion overstates a secondary outcome" → `jama-writing-style` - "I need to convince the editor this matters to clinicians" → `jama-cover-letter` - "Submitting tomorrow" → `jama-submission` - "I got three reviews and a major-revision letter" → `jama-peer-review-revision` ## Differences vs. specialty-journal skills If the work is mechanistic, bench, or narrowly subspecialty (e.g., molecular oncology), a specialty journal stack fits better than JAMA. Core contrast: - JAMA: broad clinician readership; demands **general medical importance** and pragmatic clinical relevance. - Specialty / basic-science journals: tolerate narrow scope and mechanistic depth that JAMA would consider off-fit. ## Worked routing example (illustrative) A team hands over a near-complete multicenter randomized clinical trial (illustrative: N = 4,200, 90-day mortality, absolute risk difference -3.3 percentage points [95% CI, -5.9 to -0.7]) bound for the Journal of the American Medical Association, but the abstract is one block paragraph, the registration date is unverified, and the Results report only p-values. Route in dependency order, not symptom order: `jama-ethics-registration` first (registration timing is a hard gate), then `jama-statistics` (effect sizes with CIs, ITT), then `jama-figures-tables` (CONSORT diagram reconciles all 4,200), then `jama-structured-abstract`, with style and submission last. The job is to stop teams from polishing prose while a registration defect sits unaddressed. ## Router output format ``` 【Stage detected】scope / design / stats / exhibits / abstract / ethics / submit / revision 【Hard gate unresolved?】registration timing / primary outcome / none 【Recommended next skill】jama-... 【Why this order】what must precede polish 【Sibling-venue check】NEJM / Lancet / specialty re-route? yes-with-reason / no ``` ## Anti-patterns - **Do not** skip `jama-scope-fit` and polish a manuscript that a JAMA editor will desk-reject for narrow importance. - **Do not** let `jama-figures-tables` beautify exhibits before the reporting standard and primary outcome are settled. - **Do not** let `jama-peer-review-revision` draft a response letter before the manuscript itself is actually revised. - **Do not** defer `jama-ethics-registration` — a retrospectively registered trial cannot be fixed at submission.