scientific-writing

# Scientific Writing

## Purpose

Produce clear scientific prose without inventing evidence or concealing uncertainty.
Keep drafting, evidence verification, and submission approval as separate stages.

The accountable human authors control scientific decisions and final approval. AI is
not an author, and generated fluency is never evidence [SW-S01, SW-S03].

## Non-negotiable safety rules

### Confidentiality

Do not send unpublished manuscripts, peer-review or editorial material, sensitive or
restricted data, PHI or other personal data, proprietary content, or source documents
to an external service without:

1. explicit authorization from a person or body empowered to grant it; and
2. a documented review of journal, institutional, funder, consent, ethics, contractual,
   legal, and data-use policy.

When authorization or policy is unclear, keep processing local and use only the minimum
metadata needed. De-identification requires expert review; removing obvious names is
not sufficient. See `references/authorship_ai_confidentiality.md`.

### No fabrication

Never invent or complete:

- citations, references, DOI, PMID, PMCID, ISBN, URLs, or quotations;
- results, data values, denominators, sample sizes, units, effect estimates,
  uncertainty, statistical tests, or significance claims;
- methods, materials, protocol details, software versions, analysis choices, or
  deviations;
- registrations, approvals, consent, ethics statements, participant details, or dates;
- authors, author order, CRediT roles, acknowledgments, or permissions;
- funding, sponsor roles, conflicts, data or code availability, or AI disclosures.

Use an explicit missing, unverified, or not-applicable state. Do not substitute plausible
boilerplate.

### Evidence binding

Every factual or numeric manuscript claim must map to verified evidence IDs. A human
verifier must open the source, confirm the proposition and locator, verify bibliographic
metadata, and record who verified it and when.

Search snippets, generated summaries, memory, and another work's bibliography may aid
discovery but do not verify a claim. See `references/evidence_workflow.md`.

### Scientific fidelity

- Preserve uncertainty and alternative explanations.
- Distinguish confirmatory, exploratory, descriptive, and post hoc work.
- Keep methods and results consistent.
- Reconcile units, denominators, sample sizes, populations, time points, and labels.
- Report negative, null, adverse, unexpected, failed, and inconclusive findings when
  they belong to the study record.
- State concrete limitations and bound generalizability.
- Do not convert association into causation or non-significance into equivalence.

## Intake

Before drafting, obtain or mark unresolved:

- document type, study design, stage, audience, and target venue;
- current author instructions and policy access date;
- protocol, registration, analysis plan, amendments, and reporting guideline;
- manuscript or section scope;
- verified source manifest and claim registry;
- methods, results, tables, figures, and supplements;
- authorship, CRediT, declarations, and approval records;
- confidentiality classification and authorized processing boundary;
- data, code, materials, and repository constraints.

Do not ask for restricted source material if metadata or a local user-run audit is
sufficient.

## Workflow

### 1. Establish the local workspace

For a new draft, optionally generate fail-closed Markdown, JSON, and CSV scaffolds:

```bash
python3 scripts/scaffold_manuscript.py \
  --output-dir ./draft-workspace \
  --document-id local-draft \
  --study-design randomized_trial \
  --guideline consort-2025
```

The generator never overwrites files. Its output is explicitly not submission-ready and
contains placeholders that the linter rejects.

### 2. Select reporting guidance

Choose by actual design and article type, then open the current official statement,
checklist, explanation document, extensions, and target-journal instructions.

```bash
python3 scripts/select_reporting_guidelines.py select \
  --study-design randomized_trial
```

Current major routes researched on 2026-07-24 include CONSORT 2025, SPIRIT 2025,
PRISMA 2020, STROBE, STARD and STARD-AI, TRIPOD+AI, CARE, ARRIVE 2.0, SQUIRE 2.0,
and CHEERS 2022 [SW-S06–SW-S18].

The selector is non-scoring. It does not certify quality, compliance, completeness, or
acceptance. See `references/reporting_guidelines.md`.

### 3. Build the evidence record

Assign:

- `E` IDs to sources in `source_manifest.json`;
- `C` IDs to claims in `claims.csv`;
- `N`, `M`, `O`, and `R` IDs to numeric facts, methods, outcomes, and results in
  `consistency_manifest.json`.

Store a hash of claim text in CSV rather than raw claim text. During drafting, append:

```text
[claim:C001] [evidence:E001,E002]
```

Do not mark a source verified until an accountable human has opened it and confirmed
the exact support.

### 4. Create an evidence outline

Outline only from recorded evidence:

- objective or question;
- section purpose;
- claim IDs and evidence IDs;
- methods and result IDs;
- analysis intent and uncertainty;
- unresolved conflicts or missing information;
- applicable reporting topics.

Keep unsupported content in an unresolved-issues list, not manuscript prose.

### 5. Draft without adding facts

Transform the verified outline into venue-appropriate prose. Preserve all IDs during
drafting.

- Match title and abstract to the completed main text.
- Describe methods as performed.
- Present results in the declared order and analysis population.
- Separate result from interpretation unless the venue combines them.
- Compare with prior evidence only after verifying it.
- Keep conclusions within the observed design, population, and uncertainty.

Use IMRAD only when appropriate. Structured abstracts, lists, combined sections, and
alternative structures depend on study design and venue. See
`references/imrad_structure.md` and `references/writing_principles.md`.

###