Style Journal Rewrite

Source: https://github.com/aipoch/medical-research-skills

Style and Journal Format Adaptation Skill

Trigger Conditions

Triggers

• Style change: "rewrite in XX style", "write like XX", "match this tone"
• Journal format: "format for XX journal", "rewrite following this format", "convert to NC format"
• Adjust reference style or abstract structure

Does Not Trigger

• Factual additions, content expansion
• Proofreading typos
• Complete structural rewrite (unrelated to style/format)
• Adding references only (use find-paper-references)

Requirements

• python-docx: pip install python-docx (required for B4/C4 visual formatting, B1/B2 scripts)

Process

0. Define Boundaries

Determine three things:

• Input format: DOCX / MD / TXT / conversation text?
• Task type: Style only / format only / both?
• Output format: Same as input or specific format requested?

Then branch into the corresponding path below.

1. Extract Target Profile

Read extraction guides from references/:

• Style adaptation → references/style-profile-extraction.md
• Journal format adaptation → references/journal-format-extraction.md

Do not fabricate rules not found in the user's materials.

Path A: Pure Style Adaptation (any input format)

Read references/rewriting-criteria.md directly, rewrite according to profile. Change only expression style, not formatting.

Output matches input format. DOCX: change text only, not styles; MD/TXT: output same format; conversation text: output directly.

After completion, skip to Section 5 QC.

Path B: DOCX + Format Adaptation

Input is .docx, requires journal format changes (may also include style changes).

B1. Structure Layer

• Heading numbering:
  • Reference article has no numbering → run scripts/remove_heading_numbers.py <input> <output>
  • Reference article has numbering but different format → manually edit heading text
• Abstract structure, section order: AI modifies directly

B2. Citation Layer

• End-of-text list numbering: use convert_ref_format.py --ref-list-style to switch between [N] / N.
• In-text citations: use convert_ref_format.py --style to switch superscript (Unicode / font format)
• --range-joiner and --group-separator must be extracted from the reference article's actual writing style, do not assume
• How the reference article combines consecutive citations: observe multi-citation sequences in text, then set parameters

B3. Field Code Detection

Scan w:instrText in DOCX XML:

• Contains ADDIN ZOTERO_ITEM → load format-references-zotero skill, search CSL style → install → Refresh
• Contains {Author, Year, Title} → load format-references-endnote skill, check .ris in same directory → deliver
• Plain text citations (no field codes) → skip this step, B2 already handled

B4. Visual Formatting

python-docx adjusts font, size, line spacing, paragraph spacing, indentation, alignment per paragraph. Use para.runs to set font.name / font.size, use para.paragraph_format for spacing.

**/!** Do NOT use para._element.clear() to clear paragraphs containing field codes — this destroys Zotero/EndNote field codes. B4 only modifies w:rPr and w:pPr.

Path C: MD + Format Adaptation

Input is .md, requires journal format changes (may also include style changes).

C1. Check PMID Markers

MD must contain [PMID:xxxxxxxx] markers to use this path.

• Has markers → continue
• No markers → prompt user: run find-paper-references first to insert PMID markers, then return to this skill

C2. Style and Structure Adjustment

AI directly modifies MD text:

• Remove heading numbers, adjust abstract structure, adjust section order
• Change writing style (if needed)

/!\ Critical constraint: When moving or rewriting sentences with citations, [PMID:xxxxxxxx] markers must follow the text — do not lose, change numbers, or modify spaces.

C3. Hand Off to Citation Formatting Skill

Load the corresponding skill based on user's tool:

• Zotero → Skill("format-references-zotero")
• EndNote → Skill("format-references-endnote")

Both skills do: parse [PMID:xxxxx] → fetch PubMed metadata → download target journal CSL style → output DOCX (in-text citations and bibliography formatted per journal style).

This step replaces all work done by convert_ref_format.py in Path B, with more professional results — citation formatting is driven by Zotero/EndNote engines, avoiding inconsistencies from manual Unicode superscript assembly.

C4. Visual Formatting

python-docx applies journal-required font, size, line spacing, margins, and figure/table caption positioning on the DOCX produced by C3.

Same as B4: only modify w:rPr and w:pPr, do not affect Zotero/EndNote field codes.

C5. Output

Final DOCX = C2 (structure+style) → C3 (citation formatting) → C4 (visual formatting)

4. Output and Delivery

• DOCX → doc.save() → deliver_attachments
• MD → Write() → deliver_attachments
• TXT → Write() → deliver_attachments
• Conversation text → output directly to conversation
• After delivery, summarize changes in one sentence

5. Quality Check

Verify each item:

• Original key information fully preserved, no example content mixed in
• If style target: consistent tone throughout, not just first few paragraphs
• If journal format target:
  • Heading numbering matches reference article
  • Abstract structure matches reference article
  • (DOCX path) Field codes detected, corresponding citation skill executed
  • (MD path) PMID markers intact, citation skill executed
  • Visual formatting (font/size/line spacing) applied
• No fabricated "journal rules" unsupported by user materials
• File opens normally, no formatting issues (MD path: final DOCX opens with working Refresh/Update Citations)

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If execution fails, report the failure point, summarize what can still be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of style-journal-rewrite and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

style-journal-rewrite only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.