Pnasnexus workflow

PNAS Nexus Workflow Router (pnasnexus-workflow)

Overview

This is the router. It does not replace any specialized skill. It tells you which pnasnexus- skill to use at the current stage* of a manuscript aimed at PNAS Nexus.

PNAS Nexus is not flagship PNAS. It is the gold open-access sibling journal, published by Oxford University Press (OUP) in partnership with the National Academy of Sciences (NAS). Two things reshape the workflow relative to the pnas-skills pack and must be settled early: (1) it is fully open access with an article processing charge (APC) and a CC BY / CC BY-NC license choice (pnasnexus-openaccess), and (2) it has no Direct/Contributed submission track — every paper goes through standard editor-assigned peer review. PNAS Nexus also has a transfer route from flagship PNAS that carries reviews over (pnasnexus-fit).

When to trigger

• "What should I do next with this draft?"
• A draft arrives and you must diagnose the current bottleneck.
• The user just had a paper declined by PNAS and is considering the PNAS Nexus transfer.
• The user is unsure about open-access cost, waivers, or which license to pick.
• Reviews arrive from PNAS Nexus and you need to switch into rebuttal mode.

The single most important gate

Route to pnasnexus-fit first, always. The first question is "is this high-quality, broadly significant, multidisciplinary research that the PNAS Nexus readership across biological/health/medical, physical sciences & engineering, and social & political sciences would value?" PNAS Nexus is positioned as a complementary, broad-scope sibling to PNAS — including via a transfer route for sound work declined at PNAS — so pnasnexus-fit also handles the "we were declined at PNAS, is the transfer right?" decision.

Settle open access early. Because every PNAS Nexus article is OA and carries an APC, confirm funding, eligibility for a waiver/discount, and license choice before you invest in polishing — run pnasnexus-openaccess right after pnasnexus-fit.

Routing table

Current symptom	Next skill
Not sure the result fits PNAS Nexus, or deciding whether to transfer from PNAS	pnasnexus-fit
Unsure about the APC, waivers/discounts, license (CC BY vs CC BY-NC), or funder compliance	pnasnexus-openaccess
No Significance Statement, or it is outside 50–120 words / just restates the abstract	pnasnexus-significance
Abstract too long/narrow, has headings, or conflated with the significance statement	pnasnexus-abstract
Unsure of article type; structure unclear; Methods misplaced; over the page budget; no classification	pnasnexus-writing
Figures/tables over the graphical-element budget; sizing/fonts/colors non-compliant	pnasnexus-figures
Stats under-reported; n/error bars/tests unclear; not reproducible; considering a Registered Report	pnasnexus-statistics
No data/code deposition plan; raw images not retained; "on request" only	pnasnexus-data
References messy/inconsistent (note: format-neutral at submission)	pnasnexus-citation
About to submit; need a preflight checklist + cover letter	pnasnexus-submission
Received reviews / a revision decision	pnasnexus-rebuttal

Default order

1. pnasnexus-fit — clear the broad-significance bar; confirm PNAS Nexus is the venue (incl. the PNAS transfer call)
2. pnasnexus-openaccess — APC, waiver/discount eligibility, license choice (do this early; it gates submission)
3. pnasnexus-writing — article type, structure, classification, in-text Methods, page budget
4. pnasnexus-figures — finalize display items within the graphical-element budget
5. pnasnexus-statistics — rigor & reproducibility (and whether a Registered Report fits)
6. pnasnexus-data — mandatory data/code deposition + raw-image retention
7. pnasnexus-significance — the 50–120-word Significance Statement (high-value; draft early)
8. pnasnexus-abstract — ≤250-word single-paragraph abstract (late polish)
9. pnasnexus-citation — references (format-neutral at submission; make them clean and consistent)
10. pnasnexus-submission — preflight + cover letter
11. pnasnexus-rebuttal — after review

pnasnexus-significance, pnasnexus-abstract, and pnasnexus-citation are late-stage polish — but the Significance Statement is high-value and editor-facing, so draft it as soon as the claim is locked.

Manuscript state ledger

Keep one ledger per manuscript and update it after every routing decision. The two early gates (fit and open access) are binary and block everything downstream; the rest are progress fields.

PNAS NEXUS ROUTE LEDGER
manuscript: __________________   date: __________
[gate] fit verdict ........ in-scope / transfer-from-PNAS / wrong venue
[gate] APC funding ........ confirmed / waiver-discount pending / unresolved
[gate] license ............ CC BY / CC BY-NC (funder-compatible? Y/N)
article type .............. Research Report / Brief Report / Perspective /
                            Review / Registered Report
page budget ............... current ___ pp vs type budget (Methods in main text)
graphical elements ........ ___ used / budget for type
significance statement .... drafted (50-120 words) Y/N
abstract .................. single paragraph, <=250 words Y/N
data + code deposition .... repository chosen + raw images retained Y/N
references ................ internally consistent (style-neutral at submission)
next skill ................ pnasnexus-______

Decision shortcuts

• "PNAS declined us — should we accept the PNAS Nexus transfer?" → pnasnexus-fit
• "How much will open access cost, and can we get a waiver?" → pnasnexus-openaccess
• "Which license — CC BY or CC BY-NC?" → pnasnexus-openaccess
• "Is a co-author who is an NAS member able to 'contribute' this paper?" → pnasnexus-openaccess / pnasnexus-fit (no — PNAS Nexus has no Contributed track)
• "What article type is this — Research Report, Brief Report, Perspective, Review?" → pnasnexus-writing
• "Where do Materials and Methods go?" → pnasnexus-writing (in the main text)
• "Do I really have to deposit the data and code?" → pnasnexus-data (yes — mandatory, with retraction teeth)

How PNAS Nexus differs from flagship PNAS (do not transcribe PNAS facts here)

• Business model: PNAS Nexus is fully gold open access with an APC; flagship PNAS is hybrid. Cost, waivers, and license choice are real workflow steps here (pnasnexus-openaccess).
• No submission tracks: PNAS Nexus has no Direct vs Contributed (NAS-member) choice — all editor-assigned peer review. The pnas-track skill has no equivalent; its slot is taken by pnasnexus-openaccess.
• Transfer route in: sound work declined by PNAS can be transferred to PNAS Nexus with reviews carried over (pnasnexus-fit).
• Scope & board: broader, explicitly cross-disciplinary; the editorial board spans the NAS, NAE, and NAM.
• Length: page-based budgets and named article types (Research Report ≈6 pp / 12 max, Brief Report, Perspective, Review, Registered Reports) — pnasnexus-writing.
• References: format-neutral at submission — not the strict numbered-by-appearance PNAS demands up front (pnasnexus-citation).
• Significance Statement: 50–120 words (note the minimum) (pnasnexus-significance).

Anti-patterns

• Do not skip pnasnexus-fit and start polishing prose.
• Do not defer the open-access/APC/license decision to the final upload — it gates submission (pnasnexus-openaccess).
• Do not assume a Direct/Contributed track exists — it does not.
• Do not copy length, reference-style, or fee facts from the flagship pnas-skills pack; PNAS Nexus differs.
• Do not generate a rebuttal before the main text is actually revised.