Add Journal

Required

1. Journal name -- full official name (e.g., "Journal of Clinical Oncology")

Strongly Encouraged

2. Author Guidelines URL -- primary data source for metadata extraction

Optional

3. Field focus -- e.g., cardiology, oncology, surgery, general medicine, medical education, methodology
4. Tier estimate -- Q1 / Q2 / Q3 (user's best guess)
5. ISSN -- if known

If the user provides only a journal name without a URL, ask for the Author Guidelines URL before proceeding. The guidelines page is the single most important data source for accurate profile generation.

Phase 1: Duplicate Check

Before any data extraction, check whether the journal already exists:

1. Glob both directories:

   ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/*.md
   ${CLAUDE_SKILL_DIR}/../find-journal/references/journal_profiles/*.md
   

2. Filename match: Normalize the journal name (spaces to underscores, remove special characters) and check for an exact filename match.

3. Abbreviation match: Grep existing profiles for the journal's common abbreviation (e.g., "JCO" for Journal of Clinical Oncology).

If found:

• Report which directory/directories already have the profile, with file paths.
• If present in only one directory, offer to create the missing counterpart.
• If present in both, offer to update the existing profiles or abort.
• Do NOT proceed to Phase 2 without user direction.

If not found:

• Confirm to user: "No existing profile found. Proceeding with data extraction."

Phase 2: Data Extraction

Path A: WebFetch Available

1. Attempt to fetch the Author Guidelines URL.
2. Parse the page for metadata fields listed in the extraction checklist below.
3. If the page is insufficient (login-gated, JavaScript-heavy, or sparse), fall back to Path B.

Path B: User-Provided Content

1. Ask the user to paste the Author Guidelines content (or key sections).
2. Accept pasted content and extract metadata from it.

Extraction Checklist

Extract the following. Mark any field that cannot be determined as [TODO: verify at journal site].

For write-paper profile:

For find-journal profile:

--- Gate 1: Metadata Confirmation ---

Present extracted metadata as a structured summary. Ask the user:

1. "Is this information accurate? Any corrections?"
2. "What are the common rejection reasons for this journal?" (if not extractable)
3. "How would you position this journal relative to similar journals in the field?"

Do NOT proceed to Phase 3 until user confirms or provides corrections.

Phase 3: Profile Generation

3.1 Load Reference Template

Read ONE existing write-paper profile from a similar field as a format reference:

Also read ONE existing find-journal profile from any field for the compact format reference.

3.2 Generate Write-Paper Profile

Follow the canonical 11-section order exactly:

# Journal Profile: {Full Name}

## Journal Identity

- **Full name**: {name}
- **Abbreviation**: {abbrev}
- **Publisher**: {publisher}
- **ISSN**: {print} (print), {online} (online)
- **Frequency**: {frequency}
- **Impact Factor**: ~{IF} (JCR {year})
- **Open Access**: {OA model}
- **Acceptance rate**: ~{rate}
- **Peer review**: {type}

## Manuscript Types and Word Limits

| Type | Body Word Limit | Abstract | References | Figures/Tables |
|------|----------------|----------|------------|----------------|
| Original Article | {limit} | {limit} | {limit} | {limit} |
| ... | ... | ... | ... | ... |

---

## Abstract Requirements

{Structured or unstructured. Show format as code block if structured.}

---

## Required Sections (Original Article)

1. **Introduction**
2. **Methods**
   - {subsections}
3. **Results**
4. **Discussion**
5. **{Other required sections if any}**

---

## Statistical Reporting

- {p-value format}
- {CI requirements}
- {Effect size requirements}
- {Software identification requirement}
- {Journal-specific statistical requirements}

---

## Figures

- **Maximum**: {N figures/tables}
- **Resolution**: {DPI} minimum
- **Format**: {accepted formats}
- **Color**: {policy}

---

## Common Rejection Reasons

1. {reason}
2. {reason}
3. {reason}
4. {reason}
5. {reason}

---

## Cover Letter

Should include:
- {requirements}

---

## AI Writing Disclosure Policy

- **Requirement level:** {Required / Recommended / Not specified — follows ICMJE recommendations}
- **Permitted scope:** {Language editing only / All tasks / describe specific policy}
- **Disclosure location:** {Methods / Acknowledgments / Cover letter / Submission form}
- **AI-generated images:** {Banned / Must be declared / Not specified}
- **Policy URL:** {URL to journal's AI policy page, or author guidelines URL if no dedicated page}

<!-- Use WebFetch to check the journal's Author Guidelines for AI policy.
     If no specific AI policy found, use ICMJE default:
     - Requirement level: Not specified — follows ICMJE recommendations
     - Permitted scope: Language editing only — per ICMJE 2025
     - Disclosure location: Methods
     - AI-generated images: Not specified
     - Policy URL: [author guidelines URL] (no dedicated AI policy page)
     Add [VERIFY] tag if uncertain about any field. -->

---

## Author Guidelines URL

{URL}

---

## Positioning

{When to submit here. When NOT to submit here.}

| Dimension | {This Journal} | {Competitor 1} | {Competitor 2} |
|-----------|---------------|----------------|----------------|
| Society | ... | ... | ... |
| Scope | ... | ... | ... |
| Impact factor | ... | ... | ... |
| Emphasis | ... | ... | ... |

3.3 Generate Find-Journal Profile

Follow the canonical 5-section format exactly:

# {Full Name}

## Identity
- **Abbreviation:** {abbrev}
- **Publisher:** {publisher}
- **ISSN:** {print} / {online}
- **Homepage:** {URL}
- **Author guidelines:** {URL}

## Scope
{1-2 sentence scope description.}

## Scope Keywords
{comma-separated keywords, 15-20 terms}

## Article Types Accepted
- Original Article
- Review Article
- ...

## Classification
- **Tier:** {Q1/Q2}
- **Open Access:** {Full OA / Hybrid / Subscription}
- **Field:** {field}

## Special Notes
{2-3 sentences on positioning, unique aspects, society affiliation.} AI policy: {1-line summary from write-paper profile's AI Writing Disclosure Policy section — e.g., "language editing only, dual disclosure required, AI images banned." or "follows ICMJE — disclose AI use in Methods."}

--- Gate 2: Profile Review ---

Present BOTH complete draft profiles to the user. Ask:

1. "Review these profiles. Any corrections needed?"
2. "Is the Scope paragraph accurate?"
3. "Are the Common Rejection Reasons realistic?"

Do NOT write files until user approves both profiles.

Phase 4: Write Files and Update Counts

4.1 Determine Filename

Convert journal name to filename: spaces to underscores, remove special characters.

Examples:

• "Journal of Clinical Oncology" -> Journal_of_Clinical_Oncology.md
• "JACC" -> JACC.md
• "The Lancet Oncology" -> The_Lancet_Oncology.md
• "JAMA Network Open" -> JAMA_Network_Open.md

4.2 Write Profile Files

1. Write the write-paper profile to: ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/{filename}.md

2. Write the find-journal profile to: ${CLAUDE_SKILL_DIR}/../find-journal/references/journal_profiles/{filename}.md

4.3 Update Profile Counts

After writing, count the actual files in both directories using Glob:

Glob: ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/*.md
Glob: ${CLAUDE_SKILL_DIR}/../find-journal/references/journal_profiles/*.md

Compute total = find-journal count + write-paper count.

Update all count references in these files:

find-journal/SKILL.md -- update every occurrence of the old counts:

• Frontmatter description: line (total count)
• Body paragraph referencing total count
• Key Directories section (local count, write-paper count)
• Phase 3.1 "yields N profiles total (X + Y)"
• Case Report Mode section (total count)
• Error Handling section (total count)

Use Grep to find all numeric count references before updating. Use replace_all when the same number appears multiple times.

README.md -- update:

• "Depth per skill" row: "(N journal profiles, ...)"
• find-journal row in Available Now table: "against N journal scope profiles"

4.4 Confirmation

Report to user:

• Files written (paths)
• New counts: find-journal local, write-paper, total
• Files updated with new counts
• Reminder: "Run git add -A && git commit to commit changes"

Batch Mode

When the user wants to add multiple journals in one session:

1. Collect all journal names and URLs upfront.
2. Run Phase 1 (duplicate check) for all journals first.
3. For each journal, run Phases 2-3 individually with gates.
4. Write all files in a single Phase 4 pass (one count update at the end).

This avoids updating counts N times for N journals.

Quality Standards

Never Fabricate

• Impact Factor, acceptance rate, APC, ISSN, or peer review timelines.
• Mark unknown values as [TODO: verify at journal site].
• Use approximate ranges (e.g., "~15-20%") only when the source supports it.

Statistical Reporting Section Is Mandatory

Every write-paper profile MUST include a Statistical Reporting section. If the journal's author guidelines do not specify statistical requirements, use these defaults and note they should be verified:

• Report exact p-values to 2-3 significant figures; use p < 0.001 below that threshold.
• 95% CI for primary outcomes.
• Effect sizes with clinically meaningful units.
• Statistical software and version must be identified.

Positioning Section Should Compare

The Positioning section should include a comparison table against 2-3 similar journals,