add-journal

Add Journal Skill

You are helping a medical researcher add a new journal to the MedSci Skills profile database. You generate two reference profiles per journal -- a detailed write-paper profile (~100-150 lines) and a compact find-journal profile (~30 lines) -- using the journal's author guidelines as the primary data source.

Communication Rules

• Communicate with the user in their preferred language.
• Journal names, profile content, and URLs are always in English.
• Medical terminology and field names are always in English.
• Section headings within profiles must exactly match the canonical format defined below.

Key Directories

Profiles live in one of two tiers — public (shipped with the skill) or user-local private (per-user, never pushed to git). Pick the correct target in Phase 0 before any extraction.

Public (shipped, must meet verification bar)

• Write-paper: ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/
• Find-journal: ${CLAUDE_SKILL_DIR}/../find-journal/references/journal_profiles/

User-local private (per-user override, optional)

• Write-paper: $HOME/.claude/private-journal-profiles/write-paper/
• Find-journal: $HOME/.claude/private-journal-profiles/find-journal/

Promotion workflow (private → public) is documented in ${CLAUDE_SKILL_DIR}/../find-journal/POLICY.md.

---

Phase 0: Input Collection

Required

1. Journal name -- full official name (e.g., "Journal of Clinical Oncology")
2. Target tier -- public (shipped) or private (user-local only)

Strongly Encouraged

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

Optional

4. Field focus -- e.g., cardiology, oncology, surgery, general medicine, medical education, methodology
5. Tier estimate -- Q1 / Q2 / Q3 (user's best guess)
6. 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.

Public vs. Private target selection

If the user does not state the target tier, ASK explicitly before proceeding. Use these defaults and criteria to guide the question:

• Default to private for any journal outside the user's stated area of deep expertise. Private profiles only live on the user's machine and do not need to clear the public verification bar line-by-line — but the journal's Author Guidelines page must still be the primary source (no inference from adjacent journals, no AI policy copy-paste from the publisher family).
• public is appropriate only when all of the following hold:
  1. The user intends to contribute the profile upstream for other researchers.
  2. The user has opened the journal's homepage and author guidelines page and can attest to each field against the live source, OR can paste the relevant sections.
  3. AI policy wording is transcribed from the journal/publisher's own policy page, not inferred from a sibling journal.
  4. The user has completed or will complete the promotion checklist in ../find-journal/POLICY.md before commit.

If the target is public but the user cannot attest to (2) and (3), switch the target to private and tell the user: promotion to public can happen later after the checklist is cleared.

---

Phase 1: Duplicate Check

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

1. Glob all four directories (public + private across both skills):

   ${CLAUDE_SKILL_DIR}/../write-paper/references/journal_profiles/*.md
   ${CLAUDE_SKILL_DIR}/../find-journal/references/journal_profiles/*.md
   $HOME/.claude/private-journal-profiles/write-paper/*.md
   $HOME/.claude/private-journal-profiles/find-journal/*.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:

Field	Example
Full name	Journal of Clinical Oncology
Abbreviation	J Clin Oncol
Publisher	Wolters Kluwer (ASCO)
ISSN (print/online)	0732-183X / 1527-7755
Frequency	36 issues/year
Impact Factor (with year)	~45.3 (JCR 2023)
OA model	Hybrid
Acceptance rate	~10-15%
Peer review type	Single-blind, 2-3 reviewers
Manuscript types with limits	Table: type, word limit, abstract, references, figures
Abstract format	Structured/unstructured, headings, word limit
Required sections	For Original Article
Statistical requirements	p-value format, CI, effect sizes
Figure specs	DPI, format, color, max count
Cover letter requirements	What to include

For find-journal profile:

Field	Example
Scope paragraph	1-2 sentence scope description
Scope keywords	Comma-separated, 15-20 keywords
Article types	List of accepted types
Classification	Tier (Q1/Q2), OA, Field

--- 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:

Field	Template to Load
Radiology	Radiology.md or European_Radiology.md
General medicine	The_BMJ.md or JAMA.md
Medical education	Medical_Education.md or BMC_Medical_Education.md
AI / digital health	npj_Digital_Medicine.md or JMIR.md
IR / interventional	CVIR.md or JVIR.md
Surgery	Annals_of_Internal_Medicine.md
Other	The_BMJ.md (safest general template)

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

Route to the directory pair chosen in Phase 0 (target = public or private).

If target = public:

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

If target = private:

1. Ensure the private directories exist (create if missing):

   • $HOME/.claude/private-journal-profiles/write-paper/
   • $HOME/.claude/private-journal-profiles/find-journal/

2. Write the write-paper profile to: $HOME/.claude/private-journal-profiles/write-paper/{filename}.md

3. Write the find-journal profile to: $HOME/.claude/private-journal-profiles/find-journal/{filename}.md

Do NOT write private profiles anywhere inside the medsci-skills git tree.

4.3 Update Profile Counts

Skip this phase entirely when target = private — private profiles are not counted in public-facing descriptions.

When target = public: the profile library uses runtime counting via Glob (no hard-coded totals). Do not edit SKILL.md or README.md to update numeric counts.

4.4 Confirmation

Report to user:

• Target tier (public or private) and paths written
• Reminder for public: "Run git add -A && git commit in the medsci-skills repo"
• Reminder for private: "Files are local-only in your private profiles directory (outside this repo) — do not commit to the public repo"

---

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, covering: society affiliation, scope emphasis, impact factor range, and distinguishing features.

---

Error Handling

• If WebFetch fails or is unavailable: ask user to paste content. Never fail silently.
• If author guidelines page is login-gated: ask user to paste accessible portions.
• If insufficient information for a required field: mark as [TODO: verify at journal site].
• If journal exists in one directory but not the other: create only the missing profile.
• If user provides conflicting information: present the conflict and ask for resolution.
• Never fabricate metrics -- mark unknown values explicitly.

---

Skill Interactions

Context	Skill	Interaction
After adding	find-journal	New profile immediately available for journal matching
After adding	write-paper	New profile available as target journal for manuscript formatting
Verification	search-lit	Can verify journal exists in PubMed/NLM catalog if needed

---

What This Skill Does NOT Do

• Does not scrape paywalled content or bypass access restrictions.
• Does not auto-commit changes to git.
• Does not modify existing profiles without user confirmation.
• Does not validate whether a journal is predatory (recommend user check Beall's list or DOAJ).

Anti-Hallucination

• Never fabricate file paths, URLs, DOIs, or package names. Verify existence before recommending.
• Never invent journal metadata, impact factors, or submission policies without verification at the journal's website.
• If a tool, package, or resource does not exist or you are unsure, say so explicitly rather than guessing.