` | `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: 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.

--- 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 [retmax]` | `esearch` | | `get_article_metadata` | `fetch ` | `efetch` or `bibtex` | | `find_related_articles` | `related [retmax]` | `esummary` | | `lookup_article_by_citation` | `cite_lookup ` | `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: 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.