food-paper

# Food-Paper — Whole-Process Manuscript System for Food & Nutrition Science Take a food/nutrition study from data and idea to a submission-ready, journal- formatted manuscript, using a team of subagents for each stage of the research and writing process. Original work; architecture informed by open community paper-writing and Nature-style skills (see the repo README Acknowledgements). ## First move — resolve the target journal (once) Before drafting, load **`journal-selector/SKILL.md`** (a shared procedure, not an installed skill) and follow it — it **asks the author which journal they are targeting** (they may answer 'generic' for **APA 7.0** defaults). Do this **once**: record the resolved journal and its constraints and reuse them for every subagent and stage — do **not** ask again. Re-run `journal-selector` only if the author asks to switch journals, or reuse the choice already resolved by `food-pipeline`/an earlier turn. The constraints govern structure, word/abstract limits, reference style, and the figure spec passed to `food-figure`. ## Modes - **full** (default) — the whole pipeline: field → questions → data/stats → figures → argument → draft → polish → self-review. - **plan** — Socratic planning of the paper chapter by chapter (no full draft). - **outline** — detailed outline + evidence map only. - **section** — draft or rewrite one section (intro/methods/results/discussion/abstract). - **stats** — statistical analysis plan/execution guidance only. - **revise** — revise against an existing review (a `food-review` report and/or margin comments on a Word file). Edit **the original `.docx` with Tracked Changes** (do not start a fresh copy), resolving each comment. **Inside `food-pipeline`:** update the existing **Review & Response Report (`.docx`)** in place with each item's response — **no separate response letter**. **Standalone** (real journal reviewers): produce a **point-by-point response letter as a new Word document**. All deliverables are `.docx`, never Markdown. See `references/revision-response.md`. - **format-convert** — convert a draft to the target journal's structure + reference style; output **Markdown, LaTeX (.tex), or DOCX**, and **build a PDF** via Pandoc or `latexmk` (see `references/latex-guide.md`). Yes — this skill can prepare and edit LaTeX drafts. When the source is a Word file, **preserve EndNote/Zotero/Mendeley citation fields** (`references/word-field-codes.md`) — don't flatten field codes into text. - **polish** — language editing to publication-quality English **and removal of AI writing tells** (`polisher` runs `references/human-writing.md`): inflated significance, "-ing" tack-ons, vague attribution ("studies have shown" → a real citation), stock AI vocabulary, "serves as" → "is", filler, hedge **stacking**, generic upbeat endings — then the two-pass check *"what still reads as machine-written?"*. Keeps calibrated hedging, passive Methods, and journal-mandated form; never changes a number, claim scope, or citation. Good for non-native-English drafts and for anything AI helped write. ## Subagent team (dispatch via the Agent tool; independent stages run in parallel) | # | Subagent | Stage of the research process | |---|---|---| | 1 | `intake` | Capture paper type, target journal, data/materials, and goals; set the plan. | | 2 | `literature_lead` | Understand the field — calls the **`food-research`** skill for the evidence base. | | 3 | `question_framer` | Research questions / hypotheses / objectives + the contribution. | | 4 | `data_curator` | Curate the dataset: integrity, units, missing data, metadata, provenance. | | 5 | `statistician` | Statistical plan + analysis appropriate to the food/nutrition design. | | 6 | `viz_designer` | Figures & tables — calls the **`food-figure`** skill at the journal spec. | | 7 | `structure_architect` | Outline mapped to the target journal's structure + evidence map. | | 8 | `argument_builder` | Claim–evidence–reasoning chains; results→discussion logic. | | 9 | `draft_writer` | Draft each section with food-science reporting conventions. | | 10 | `polisher` | Edit to clear, publication-quality scientific English. | | 11 | `citation_manager` | References + in-text citations in the journal's style (APA 7.0 default). | | 12 | `internal_reviewer` | Pre-submission self-review — calls the **`food-review`** panel. | ## Workflow ```mermaid flowchart TD A[intake<br/>type, journal, data, goals] --> JS[journal-selector<br/>load journal constraints] A --> L[literature_lead<br/>-> food-research evidence base] L --> Q[question_framer<br/>RQs / hypotheses / contribution] A --> D[data_curator<br/>curate + check dataset] D --> S[statistician<br/>analysis plan + results] S --> V[viz_designer<br/>-> food-figure figures & tables] Q --> ST[structure_architect<br/>journal-mapped outline + evidence map] S --> ST V --> ST ST --> AR[argument_builder<br/>CER chains, results->discussion] AR --> W[draft_writer<br/>section drafts] W --> P[polisher<br/>publication English] P --> C[citation_manager<br/>journal reference style] C --> IR[internal_reviewer<br/>-> food-review panel] IR -- revise --> W IR -- ready --> OUT[Submission-ready manuscript] ``` ## Food & nutrition reporting defaults (enforced by `draft_writer` / `data_curator` / `statistician`) Composition as g/100 g (basis + AOAC method); sensory panel type/size/scale + ethics; microbial counts log CFU/g with LOD; TPA/rheology parameters + settings; HPLC/GC/LC-MS conditions, LOD/LOQ, recovery, identification by standards/MS-MS; mean ± SD/SEM with n; the statistical model, test, post-hoc, and threshold, with significance shown consistently. Reproducible Methods (cultivar/breed/batch, prep, storage). Ethics/food-safety statements where relevant. ## References (load as needed) - `references/paper-structure.md` — `structure_architect`: IMRaD/review patterns + abstract types. - `references/writing-style.md` — `draft_writer`/`polisher`: scientific style, title/intro rhetoric. - `references/human-writing.md` — **write like a scientist, not a chatbot**: the AI writing tells to remove (inflated significance, vague attribution, stock vocabulary, hedge stacking), the academic exceptions to keep (calibrated hedging, passive Methods, journal-mandated form), and the two-pass check. Canonical for the suite; used by `food-research`, `food-deep-research`, and `food-review` too. - `references/writing-quality-check.md` — self-check before `internal_reviewer`. - `references/statistics-reporting.md` — `statistician`: what to report and which test. - `references/declarations-guide.md` — CRediT, funding, COI, data availability, ethics. - `references/apa7-quickref.md` — default citation style for `citation_manager` (canonical APA 7.0 for the suite). - `references/faithfulness-and-citation.md` — **grounding rules + four-gate citation check; the suite's no-fabrication contract.** Run `scripts/verify_citations.py` on the reference set. - `references/latex-guide.md` — prepare/edit LaTeX drafts and build the PDF (Pandoc / latexmk). - `references/revision-response.md` — **revise mode**: tracked changes (original Word opt-in under `food-pipeline`) + either updating the one **Review & Response Report** in place (pipeline) or a point-by-point response letter (standalone). All `.docx`. - `references/word-field-codes.md` — **preserve EndNote/Zotero/Mendeley citation fields** when editing a `.docx` (don't flatten field codes into visible text); verify with `scripts/check_docx_fields.py`. - `references/privacy-and-confidentiality.md` — **privacy check before delivery** (no local paths/secrets); run `scripts/privacy_scan.py`. ## Grounding (non-negotiable) Write **only** from the user's data and verified literature. Never invent references, DOIs, numbers, or results; unsupported content is marked `[UNVERIFIED]`/`[EVIDENCE GAP]`, never filled from memory. `citation_manager` and `draft_writer` enforce the four-gate citation check in `references/faithfulness-and-citation.md`. ## Handoffs `food-research` (evidence in) → **food-paper** → `food-review` (external panel) → **food-paper** revise. Orchestrated by `food-pipeline`.