| 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. |
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
- 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 titleyear: Publication yearauthors: List of author namesabstract: Full abstract text (when available)venue: Journal or conference namecitationCount: 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.
