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
efetchfor full XML records). - DOI Extraction: DOIs are extracted from all sources for cross-referencing and deduplication.
- Automatic Deduplication: When searching multiple sources (
--source allor--source both), results are automatically deduplicated by DOI. - Polite Access: Automatic email identification for OpenAlex/Crossref "Polite Pool" (via
USER_EMAILenv 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
- Extract: Pull key findings from the abstracts found.
- Organize: Group findings into a logical structure (e.g., chronological or thematic).
- 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
citationCountor recent years for a more modern review. - PubMed for Medicine: Use
--source pmfor the most reliable biomedical literature. - Deduplication: Multi-source searches automatically remove duplicates; use single sources if you need raw counts.
