Literature Review

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name: literature-review version: 1.2.0 description: Assistance with writing literature reviews by searching for academic sources via Semantic Scholar, OpenAlex, Crossref and PubMed APIs. Use when the user needs to find papers on a topic, get details for specific DOIs, or draft sections of a literature review with proper citations.

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Literature Review

Help write academic literature reviews using a multi-engine search integration (S2, OA, CR, PM).

Capabilities

Multi-Source Search: Find relevant academic papers using Semantic Scholar (S2), OpenAlex (OA), Crossref (CR), and PubMed (PM).

Full Abstracts: All sources now return complete abstracts (PubMed uses efetch for full XML records).

DOI Extraction: DOIs are extracted from all sources for cross-referencing and deduplication.

Automatic Deduplication: When searching multiple sources (--source all or --source both), results are automatically deduplicated by DOI.

Polite Access: Automatic email identification for OpenAlex/Crossref "Polite Pool" (via USER_EMAIL env var).

Abstract Reconstruction: Reconstructs abstracts from OpenAlex inverted index format.

Synthesis: Group papers by theme and draft review sections based on metadata.

Environment Variables

| Variable | Purpose | Default | |----------|---------|---------| | USER_EMAIL | Email for polite API access | anonymous@example.org | | CLAWDBOT_EMAIL | Fallback if USER_EMAIL not set | — | | SEMANTIC_SCHOLAR_API_KEY | Optional S2 API key for higher rate limits | — | | OPENALEX_API_KEY | Optional OpenAlex API key | — |

Workflows

1. Broad Search (All Bases)

Get a comprehensive overview from all major academic databases. Results are automatically deduplicated by DOI.

python3 scripts/lit_search.py search "impact of glycyrrhiza on bifidobacterium" --limit 5 --source all

2. Targeted Search

OpenAlex (oa): Fast and comprehensive, good abstracts.

Semantic Scholar (s2): High-quality citation data and TL;DRs.

Crossref (cr): Precise DOI-based metadata (no abstracts).

PubMed (pm): Gold standard for biomedical research, full abstracts and PMIDs.

python3 scripts/lit_search.py search "prebiotic effects of liquorice" --source pm

3. Comparing Sources

Search both S2 and OA simultaneously to ensure nothing is missed. Deduplicated by default.

python3 scripts/lit_search.py search "Bifidobacterium infantis growth" --source both

4. Getting Full Details (S2)

Retrieve detailed metadata including TL;DR summaries.

python3 scripts/lit_search.py details "DOI:10.1016/j.foodchem.2023.136000"

5. Writing the Review

1. Extract: Pull key findings from the abstracts found. 2. Organize: Group findings into a logical structure (e.g., chronological or thematic). 3. Draft: Use the "Think step-by-step" approach to synthesize multiple sources into a coherent narrative.

Output Format

Each result includes:

id: Source-specific identifier (PMID for PubMed, OpenAlex ID, S2 paper ID, DOI for Crossref)

doi: DOI when available (used for deduplication)

title: Paper title

year: Publication year

authors: List of author names

abstract: Full abstract text (when available)

venue: Journal or conference name

citationCount: Citation count (S2, OA)

source: Which database the result came from

Tips for Success

Citations: Always cross-reference the DOI or PMID for accuracy in bibliography.

Filtering: Focus on papers with higher citationCount or recent years for a more modern review.

PubMed for Medicine: Use --source pm for the most reliable biomedical literature.

Deduplication: Multi-source searches automatically remove duplicates; use single sources if you need raw counts.