Jama workflow

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.