---
name: aperivue/search-lit
source: https://app.decimal.ai/s/aperivue-search-lit@2/SKILL.md
source_sha256: b74686fadf73
---

# 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.

#### Record what the source said existed, not only what you downloaded

Search code reports its own haul. Nothing errors when the haul is wrong, and a PRISMA flow built on
a wrong number is fiction that nothing downstream contradicts. Two signatures, both real, both from
a single run:

- **A count that equals a page cap exactly.** arXiv returned 2,000 records — which was the loop's
  own `if start >= 2000: break`, not the total (1,528 once the query was fixed). The round number
  was the only tell. Every source reports a total: `esearchresult.count`,
  `opensearch:totalResults`, `meta.count`. **Record `api_total` beside `downloaded`, and fail loudly
  when `downloaded < api_total`, or when `downloaded` equals a page or loop cap exactly.** Print
  `TRUNCATED` and refuse to write the search record.
- **A boolean that was never applied.** OpenAlex returned 35,345 hits because the query went to
  `search=`, a relevance-ranked free-text parameter that **silently ignores AND/OR**; the parameter
  that honours them is `filter=title_and_abstract.search:` (true count: 5,282). So run the query
  once more with one mandatory clause negated. **If the hit count does not drop, the boolean is
  being ignored** — the engine is ranking, not filtering.

PubMed via E-utilities is the one place where the naive pattern happens to be safe. Everywhere
else, do both.

#### A DOI in a screening row is not necessarily that row's DOI

When a `doi` column was **filled by the pipeline** rather than handed over with the record — matched
against Crossref by title similarity, at some threshold — a wrong match is a valid, resolvable
identifier for a different paper, and nothing downstream can tell. Resolve it and read the title
back before any decision rests on it:

```bash
python3 scripts/check_doi_record_match.py --table 2_Screening/round3.tsv \
        --email <contact> --json qc/doi_record_match.json
```

`DOI_NOT_THIS_RECORD` is a DOI that resolves to another paper; `DOI_IS_CONTAINER` is one that
resolves to an issue, supplement or proceedings rather than an article; `DOI_UNRESOLVED` is
reported rather than dropped. This is not `/verify-refs`, which audits a finished reference list —
it runs at screening, where a wrong DOI is still cheap. In one review two of these appeared within
two days, and one produced a limitation about a "missed eligible paper" that did not exist.

### Phase 2.5: Citation Searching (Snowballing)

Optional but recommended for systematic reviews and thorough background work
(PRISMA item 7, "records identified through citation searching"). Expands a
seed set along the citation graph instead of relying on Boolean recall alone.

Use the deterministic helper `references/snowball.py` (Semantic Scholar Graph
API; nothing generated from memory):

```bash
# Expand seed DOIs/PMIDs in all directions, dedup against the existing pool,
# append verified candidates to references/library.bib
python3 references/snowball.py \
  --seed DOI:10.1148/radiol.2024123,PMID:38000001 \
  --direction all \
  --pool references/library.bib \
  --out references/library.bib
```

- **Directions**: `backward` (references the seeds cite), `forward` (papers
  citing the seeds), `similar` (S2 recommendations), or `all` (default).
- **Dedup**: against the current `references/library.bib` by DOI and
  normalized title, and within the harvested set.
- **Trust flag**: snowball candidates are written `verified=false` +
  `verified_by=semantic_scholar`. They are candidates, not confirmed
  citations — run `/verify-refs` (or Phase 4 verification) to confirm each
  against PubMed/CrossRef before citing.
- **Output contract**: appends to `references/library.bib` only. NEVER writes
  `manuscript/_src/refs.bib` (the script hard-refuses that path).
- **PRISMA line**: the script prints, e.g., `Records identified through
  citation searching (snowballing): N raw (backward=…, forward=…, similar=…);
  after dedup against existing pool: M new candidates.` — record M in the
  PRISMA flow's citation-searching box.

A deterministic, network-free challenge card (recorded fixtures + expected
output + `verify.sh`) lives in `references/snowball_challenge/`.

### 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. **Check for duplicates first**: Use `zotero_search_items` (by DOI) to skip papers already in the library — this search-first step is what dedupes; `zotero_add_by_doi` does not dedupe on its own.
2. **Add papers to Zotero**: Use `zotero_add_by_doi` for DOI-based import (its `attach_mode` argument governs the OA PDF attach attempt at add time).
3. **Organize into collections**: Use `zotero_manage_collections` to file into the relevant project collection.
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

Full-text PDF retrieval is **delegated to `/fulltext-retrieval`** — the single authored
home of the open-access cascade (arXiv → Unpaywall → PMC → OpenAlex → Crossref → landing
page, each validated with a `%PDF-` header + ≥10 KB size). Do **not** re-implement OA
fetching here.

Pass the verified candidate DOIs from `references/library.bib`:

```bash
ENGINE="${MEDSCI_SKILLS_ROOT:-$HOME/workspace/medsci-skills}/skills/fulltext-retrieval/fetch_oa.py"
# extract DOIs from references/library.bib → dois.txt (one per line)
python3 "$ENGINE" dois.txt -o pdfs/ -e <contact-email> --report pdfs/retrieval_report.json
```

For Zotero-resident PDFs and higher-yield, proxy-aware retrieval, use `/lit-sync` Phase 2.7,
which also invokes `/fulltext-retrieval` and triggers Zotero's native "Find Available PDF".

#### Alternative sources (legitimate only)

For DOIs that open access cannot reach (listed in `pdfs/manual_needed.txt`):

- **Institutional access / proxy / VPN** — through your library's own subscriptions.
- **Interlibrary loan (ILL)** — request via library services.
- **Author contact** — email the corresponding author for a copy or preprint.

Never bypass paywalls or publisher access controls, and do not configure unauthorized
PDF mirrors. Rate limits and PDF validation are handled inside `/fulltext-retrieval`.

### 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: Crowding Check

Run **before a study is designed**, not after. The question is not "what has been written about this
topic" — a background search answers that and still leaves the trap open. It is narrower and it is
four questions:

| Ask of | Verdict |
|---|---|
| the **research question** | taken / partly taken / open |
| the **sampling frame** (what population, which records, which years) | taken / partly taken / open |
| the **measurement axis** (what is being coded or measured, and at what granularity) | taken / partly taken / open |
| the **target journal** | already published there / adjacent / open |

Each gets its own verdict. A design can be original on one axis and fully occupied on another, and
collapsing the four into one answer is what hides that.

Why the fourth row is not vanity: a design once matched an existing paper on frame, coding axis
**and** target journal, and that paper was already published in the journal it was first choice
for. A redesign on a different axis then turned out to be partly occupied too — three papers were
already coding the same thing as a single item — which did not kill it but did change the claim
that could honestly be made, from "nobody has looked at this" to "nobody has decomposed it by
provenance". That is a real result of this mode: **most of the time it narrows a claim rather than
ending a project**, and a narrowed claim survives review where the broad one would not.

Search the way a competitor would: the exact frame, the exact measure, and the journal's own site,
not only the topic. Report the four verdicts and the papers behind each, then let the user decide.
`/design-study` and `/orchestrate` should route here first when a new study is being scoped.

### 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.

For a **structured, dedup-aware, PRISMA-countable** expansion (backward +
forward + similar) prefer **Phase 2.5: Citation Searching** with
`references/snowball.py`, which appends verified candidates to
`references/library.bib` and reports a citation-searching count.

### 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.