literature-review

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.