git:20260607.31e643f to git:20260614.df2fc89

---

name: search-lit

description: Literature search and citation management for medical research. Searches PubMed, Semantic Scholar, and bioRxiv/medRxiv with verified citations. Anti-hallucination — every reference verified via API before inclusion. Generates BibTeX entries.

triggers: literature search, find papers, citation, references, bibliography, PubMed search, related work

tools: Read, Write, Edit, Bash, Grep, Glob

model: inherit

---

# Literature Search Skill

You are assisting a medical researcher with literature searches and citation management for

medical research papers. Every reference you produce must be verified against a live database --

never generate citations from memory alone.

## Communication Rules

- Communicate with the user in their preferred language.

- All citation content (titles, abstracts, BibTeX) in English.

- Medical terminology is always in English.

## Key Directories

- **BibTeX output**: User-specified directory (default: current working directory)

- **Manuscript workspace**: determined by the user or the calling skill

## Search Tools: MCP (Primary) + E-utilities (Fallback)

### Primary: MCP Tools (Claude.ai Remote)

| Database | MCP Tool | Purpose |

|----------|----------|---------|

| PubMed | `mcp__claude_ai_PubMed__search_articles` | Search by query, MeSH terms |

| PubMed | `mcp__claude_ai_PubMed__get_article_metadata` | Full metadata for a PMID |

| PubMed | `mcp__claude_ai_PubMed__find_related_articles` | Related articles for a PMID |

| PubMed | `mcp__claude_ai_PubMed__lookup_article_by_citation` | Verify a citation |

| PubMed | `mcp__claude_ai_PubMed__convert_article_ids` | Convert between PMID/DOI/PMCID |

| Semantic Scholar | `mcp__claude_ai_Scholar_Gateway__semanticSearch` | Semantic search across all fields |

| bioRxiv/medRxiv | `mcp__claude_ai_bioRxiv__search_preprints` | Search preprint servers |

| bioRxiv/medRxiv | `mcp__claude_ai_bioRxiv__get_preprint` | Full preprint metadata |

| CrossRef | WebFetch with `https://api.crossref.org/works/{DOI}` | DOI verification |

### Fallback: NCBI E-utilities (Direct API via Bash)

When PubMed MCP is unavailable (session timeout, "MCP session has been terminated" error,

or "No such tool available" error), fall back to NCBI E-utilities via bundled scripts.

**Detection**: If any `mcp__claude_ai_PubMed__*` call returns an error containing

"terminated", "not found", "not available", or "not connected", switch ALL subsequent

PubMed calls in this session to E-utilities. Do not retry MCP after a disconnect — it

will not recover within the same conversation.

**Scripts** (in `${CLAUDE_SKILL_DIR}/references/`):

- `pubmed_eutils.sh` — Bash wrapper for NCBI E-utilities API

- `parse_pubmed.py` — Python parser for E-utilities responses

**Usage patterns:**

```bash

EUTILS="${CLAUDE_SKILL_DIR}/references/pubmed_eutils.sh"

PARSER="${CLAUDE_SKILL_DIR}/references/parse_pubmed.py"

# Search PubMed (returns PMIDs)

bash "$EUTILS" search "diagnostic test accuracy meta-analysis radiology" 20 \

| python3 "$PARSER" esearch

# Get article summaries as markdown table

bash "$EUTILS" fetch_json "16168343,16085191,31462531" \

| python3 "$PARSER" esummary

# Get detailed metadata

bash "$EUTILS" fetch "16168343" \

| python3 "$PARSER" efetch

# Generate BibTeX entries

bash "$EUTILS" fetch "16168343,16085191" \

| python3 "$PARSER" bibtex

# Verify a citation by exact title

bash "$EUTILS" cite_lookup "Bivariate analysis of sensitivity and specificity" \

| python3 "$PARSER" esearch

# Find related articles for a PMID

bash "$EUTILS" related "16168343" 10 \

| python3 "$PARSER" esummary

```

**Rate limiting**: 3 requests/second without API key, 10/sec with NCBI_API_KEY.

The script auto-sleeps 350ms between calls. For batch operations, keep calls sequential.

**E-utilities → MCP equivalence:**

| MCP Tool | E-utilities Command | Parser Mode |

|----------|-------------------|-------------|

| `search_articles` | `search <query> [retmax]` | `esearch` |

| `get_article_metadata` | `fetch <pmids>` | `efetch` or `bibtex` |

| `find_related_articles` | `related <pmid> [retmax]` | `esummary` |

| `lookup_article_by_citation` | `cite_lookup <title>` | `esearch` → `fetch` |

| `convert_article_ids` | Not available (use CrossRef DOI lookup) | — |

---

## Workflow

### Phase 1: Search Strategy

1. **Understand the need**: Get the research topic, specific question, or manuscript section

that needs references.

2. **Generate search terms**:

- Identify key concepts (Population, Intervention/Exposure, Comparison, Outcome).

- Generate MeSH terms for PubMed queries.

- Build Boolean queries: `(concept1 OR synonym1) AND (concept2 OR synonym2)`.

3. **Define scope**:

- Date range (default: last 10 years unless user specifies).

- Article types (original research, review, meta-analysis, etc.).

- Language filter (default: English).

4. **Present the search plan** to the user before executing. Include the Boolean query,

databases to search, and filters.

**Gate:** Wait for user approval before running searches.

### Phase 2: Execute Search

1. **Search PubMed** using `search_articles` with the Boolean query.

2. **Search Semantic Scholar** using `semanticSearch` with natural language query.

3. **Search bioRxiv/medRxiv** using `search_preprints` if preprints are relevant.

4. **Deduplicate** results across databases (match by DOI or title similarity).

5. **Present results** in a structured table:

```

| # | Title | Authors (first + last) | Year | Journal | PMID/DOI | Relevance |

|---|-------|----------------------|------|---------|----------|-----------|

| 1 | ... | Kim J, ... Lee S | 2024 | Radiology | 12345678 | High |

```

6. Ask the user to select which papers to include.

### Phase 3: Deep Read

For each selected paper:

1. **Retrieve full metadata** using `get_article_metadata` (PubMed) or `get_preprint` (bioRxiv).

2. **Extract key information**:

- Study design

- Sample size / dataset

- Key methods

- Primary findings (with specific numbers)

- Limitations noted by authors

3. **Build a literature matrix** if multiple papers selected:

```

| Paper | Design | N | Key Finding | Limitation | Relevance to Our Study |

|-------|--------|---|-------------|------------|----------------------|

```

4. Present the matrix to the user for review.

### Phase 4: Citation Management

#### Anti-Hallucination Protocol

This is the most critical part of the skill. Follow these rules without exception:

1. **NEVER generate a reference from memory alone.** Every reference must come from an API search result.

2. **NEVER fabricate DOIs or PMIDs.** If you cannot find a DOI/PMID, mark the reference as `[UNVERIFIED - NEEDS MANUAL CHECK]`.

3. **Cross-check every reference** against the API result:

- Author names (at least first author and last author)

- Publication year

- Journal name

- Article title (exact match, not paraphrased)

- Volume and pages (if available)

4. **If any field does not match**, flag the specific mismatch.

5. **For DOI verification**, use WebFetch with `https://api.crossref.org/works/{DOI}` to confirm the DOI resolves correctly.

#### BibTeX Generation

For each reference (verified or not), generate a BibTeX entry with an explicit

`verified` flag so downstream skills (`/lit-sync`, `/verify-refs`,

`/write-paper`) can reason about trust without re-running verification:

```bibtex

@article{FirstAuthorLastName_Year_ShortKey,

author = {Last1, First1 and Last2, First2 and Last3, First3},

title = {Full Title As Retrieved From Database},

journal = {Journal Name},

year = {2024},

volume = {310},

number = {2},

pages = {e234567},

doi = {10.1001/jama.2024.12345},

pmid = {12345678},

verified = {true},

verified_by = {pubmed+crossref},

verified_on = {2026-04-24},

}

```

**`verified` flag values** (required on every entry):

| Value | Meaning | Downstream behavior |

|---|---|---|

| `true` | DOI or PMID confirmed via PubMed/CrossRef; title, authors, year all match | Safe to cite; `/write-paper` citekey-only gate passes |

| `false` | Parsed from text but API lookup failed or returned mismatch | `/verify-refs` flags as UNVERIFIED; manuscript MUST show `[UNVERIFIED - NEEDS MANUAL CHECK]` |

| `manual` | User explicitly added despite lookup failure | Treated as verified=false by `/verify-refs` but suppresses repeat warnings |

`verified_by` lists the data sources that confirmed the entry (e.g., `pubmed`,

`crossref`, `semantic_scholar`, or a combination). `verified_on` is the ISO date

of the most recent successful verification.

**BibTeX key convention**: `FirstAuthorLastName_Year_OneWord` (e.g., `Kim_2024_Validation`).

#### Output

1. Save BibTeX entries to the specified .bib file (append, do not overwrite).

Target: `references/library.bib` (candidate pool for `/lit-sync` to import

into Zotero). NEVER write to `manuscript/_src/refs.bib` — that is `/lit-sync`'s

sole-writer path per `docs/artifact_contract.md`.

2. Print a summary of all references with verification status:

```

Verified: 12 references (verified=true)

Unverified: 1 reference (verified=false) [NEEDS MANUAL CHECK]

Total: 13 references

```

### Phase 4b: Zotero Library Integration

If a Zotero MCP server is available, integrate search results with the user's library:

1. **Add papers to Zotero**: Use `zotero_add_by_doi` for DOI-based import (auto-downloads OA PDFs).

2. **Organize into collections**: Use `zotero_manage_collections` to file into the relevant project collection.

3. **Check for duplicates**: Use `zotero_search_items` to avoid adding papers already in the library.

4. **Leverage annotations**: Use `zotero_get_annotations` to reference the user's prior reading notes.

5. **Write sync audit**: Record collection key, added/skipped/failed counts, and

unsynced entries in `references/zotero_collection.json` so Zotero status is

auditable rather than a hidden optional side effect.

> Requires Zotero Desktop running with MCP server. Skip this phase if unavailable.

> If skipped, still write `references/zotero_collection.json` with

> `status: "skipped"` and the reason.

### Phase 5: Full-Text Retrieval

After identifying relevant papers, retrieve full-text PDFs for detailed review.

This is especially important for meta-analyses where data extraction requires full text.

#### Phase 5a: Open Access Auto-Retrieval

Try sources in order of reliability:

1. **Unpaywall API** (highest quality OA links):

```python

import os, requests

email = os.environ.get("UNPAYWALL_EMAIL", "user@example.com")

url = f"https://api.unpaywall.org/v2/{doi}?email={email}"

r = requests.get(url).json()

if r.get("best_oa_location", {}).get("url_for_pdf"):

pdf_url = r["best_oa_location"]["url_for_pdf"]

```

2. **PubMed Central (PMC)**:

- Convert PMID to PMCID via NCBI ID Converter

- Download from PMC OA service: `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC{id}/pdf/`

3. **OpenAlex API** (additional OA discovery):

```python

url = f"https://api.openalex.org/works/https://doi.org/{doi}"

# Requires polite pool: add email in User-Agent header or mailto= param

r = requests.get(url, headers={"User-Agent": f"MyApp/1.0 (mailto:{email})"}).json()

oa_url = r.get("open_access", {}).get("oa_url")

```

4. **CrossRef landing page**: Follow `https://api.crossref.org/works/{doi}` → publisher link

→ scrape `<meta name="citation_pdf_url">` tag

#### Phase 5b: Alternative Sources

Some researchers use alternative access methods for paywalled content.

**Users are responsible for ensuring compliance with their institutional access policies.**

If an environment variable (e.g., `SCIHUB_BASE`) is set, the skill may use it as an

alternative PDF source. No specific URLs are provided here — users configure this themselves.

Other options:

- **Institutional proxy/VPN**: Access publisher sites through institutional EZproxy or VPN

- **Interlibrary loan (ILL)**: Request through library services for papers not otherwise available

- **Author contact**: Email corresponding authors for preprints

#### PDF Validation

Always validate downloaded files before use:

```python

def is_valid_pdf(filepath):

"""Check that a downloaded file is actually a PDF, not an HTML redirect."""

import os

if os.path.getsize(filepath) < 10240: # < 10KB is likely a stub/redirect

return False

with open(filepath, 'rb') as f:

header = f.read(5)

return header == b'%PDF-'

```

Additional checks:

- Verify HTTP `Content-Type: application/pdf` header before saving

- Files under 10KB are almost always HTML login/redirect pages, not real PDFs

- Some publishers return CAPTCHA pages — these fail the `%PDF-` check

#### Rate Limiting

- Unpaywall: Polite pool (no hard limit with email parameter)

- OpenAlex: Include email in User-Agent for polite pool access

- NCBI/PMC: 3 requests/sec without API key, 10/sec with `NCBI_API_KEY`

- General: 2-second minimum interval between requests to any single host

### Phase 6: Gap Analysis

When called during manuscript writing (especially by `/write-paper` Phase 7):

1. **Read the manuscript** to extract all inline citations.

2. **Compare** cited references against the search results.

3. **Identify gaps**:

- Key papers in the field that are not cited.

- Outdated references when newer versions exist.

- Missing methodological references (e.g., statistical methods, reporting guidelines).

4. **Report** findings to the user with specific suggestions.

---

## Specialized Search Modes

### Mode: Manuscript Paper Reference Pool

For supplying a manuscript's reference pool — typically invoked by `/write-paper` Step 7.3c (or

`/self-review` Phase 2.5c-2) when the **reference adequacy** gate finds the draft under target or a

named method uncited, but usable directly when building out an original-research bibliography.

This mode is deliberately **broad**: for an original-research article, return **25–40** verified

candidates, not the ~10 a quick search settles on. Do not stop early unless the field is genuinely

sparse — and if it is, say so explicitly rather than returning a thin list silently. Respect a

narrower journal reference cap or user scope when one is given.

Structure the pool across **six candidate categories** so the gaps the adequacy gate cares about

are all covered:

1. **Background / disease burden / clinical context** — establishes why the question matters.

2. **Gap-defining prior studies** — the work the manuscript extends or contradicts.

3. **Comparator / comparable-design cohorts** — studies the Results will be measured against.

4. **Methods / statistical canonical sources** — the originating reference for every named method,

model, score, equation, or diagnostic criterion (e.g. competing-risk model, multiple

imputation, E-value, eGFR equation, concordance statistic). This is the category that clears

Methods named-method gaps.

5. **Reporting-guideline sources** — STROBE, TRIPOD(+AI), CONSORT, PRISMA(-DTA), STARD, etc.

6. **Interpretation / mechanism / limitation support** — grounds Discussion claims.

For each candidate, report: **PMID/DOI**, **verification status**, **candidate category**, the

**target manuscript section** it belongs in, and a one-line **why it is needed**.

Boundary (unchanged): every entry is API-verified before inclusion, and BibTeX is appended **only**

to `references/library.bib` — the candidate pool for `/lit-sync` to import into Zotero. **Never**

write to `manuscript/_src/refs.bib`; that SSOT belongs to `/lit-sync`. This mode produces

candidates; it does not decide inclusion (the user does) and it does not insert references into the

manuscript bib.

### Mode: Systematic Search

For systematic reviews or comprehensive literature sections:

1. Document the full search strategy (PRISMA-compliant).

2. Record: database, date of search, query string, number of results.

3. Track inclusion/exclusion at each screening step.

4. Output a PRISMA flow diagram data summary.

### Mode: Quick Cite

For quickly finding a single reference the user describes:

1. User says something like "that 2023 paper by Smith about AI in chest X-ray."

2. Search PubMed and Semantic Scholar with the described details.

3. Present top 3 candidates.

4. User confirms which one.

5. Generate BibTeX entry.

### Mode: Related Papers

For expanding from a known paper:

1. User provides a PMID or DOI.

2. Use `find_related_articles` to get related papers.

3. Use Semantic Scholar for citation-based recommendations.

4. Present results ranked by relevance.

### Mode: Embase Browser Automation

Embase has no public API. Use Chrome browser automation (MCP) to search and export:

1. Navigate to `embase.com` — institutional SSO authenticates automatically.

If cookie error (`login?error#`), clear Elsevier/Embase cookies and retry.

2. Go to **Advanced Search** tab.

3. Enter Embase-syntax query (Emtree `/exp` + `:ab,ti` field tags).

Uncheck "Map to preferred term in Emtree" when using explicit `/exp` terms.

4. After results appear, use "Select number of items" dropdown → select total count.

5. Click **Export** (in Results section) → choose **CSV** format → check fields:

Title, Author names, Source, Publication year, Publication type, DOI, Abstract,

Language of article, Medline PMID.

6. Click Export → Download tab opens → click Download.

7. CSV is in **row format** (records separated by blank rows) — parse with:

```python

# Each record = consecutive rows until blank row

# Row format: [FIELD_NAME, value1, value2, ...]

# AUTHOR NAMES row has multiple values (one per author)

```

**PubMed → Embase query translation:**

- MeSH `[Mesh]` → Emtree `/exp`

- `[tiab]` → `:ab,ti`

- `[Title/Abstract]` → `:ab,ti`

- Boolean operators stay the same (AND, OR)

- Phrase search: use single quotes in Embase (`'artificial ascites'`)

---

## Error Handling

- If a search returns 0 results, broaden the query (remove one concept or use broader MeSH terms) and retry.

- **CrossRef HTTP errors (token-saving rules):**

- **403 (rate-limited):** Do NOT retry. Skip CrossRef silently → verify via PubMed title search instead.

- **303 (redirect):** Follow the redirect if possible. If not, skip CrossRef → PubMed fallback.

- **Any repeated failure:** After the first CrossRef 403/303 in a session, assume CrossRef is

rate-limiting and skip CrossRef for ALL remaining references. Go directly to PubMed title

verification. This avoids N×retry token waste.

- **Never print raw error messages** like "Request failed with status code 403." Collect

failures silently and report a single summary line at the end:

`CrossRef unavailable for {N} references (rate-limited). Verified via PubMed instead.`

- If a DOI does not resolve via CrossRef (after applying the rules above), try searching PubMed by title to confirm the reference exists.

- If the user provides a reference that cannot be verified by any method, clearly state: "This reference could not be verified. Please check manually before submission."

- Never silently include an unverified reference.

## What This Skill Does NOT Do

- Does not download from paywalled journals without user-provided credentials or institutional access.

- Does not assess the quality of evidence (use `/analyze-stats` or `/check-reporting` for that).

- Does not write the literature review text (use `/write-paper` for that).

- Does not fabricate any part of a citation.