AgentSkillsCN

literature-review

通过Semantic Scholar、OpenAlex、Crossref和PubMed API搜索学术来源，协助撰写文献综述。当用户需要查找某个主题的论文、获取特定DOI的详细信息或用正确引用起草文献综述的部分时使用。

SKILL.md
--- frontmatter
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

VariablePurposeDefault
USER_EMAILEmail for polite API accessanonymous@example.org
CLAWDBOT_EMAILFallback if USER_EMAIL not set—
SEMANTIC_SCHOLAR_API_KEYOptional S2 API key for higher rate limits—
OPENALEX_API_KEYOptional OpenAlex API key—

Workflows

1. Broad Search (All Bases)

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

bash
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.
bash
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.

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

4. Getting Full Details (S2)

Retrieve detailed metadata including TL;DR summaries.

bash
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.