/sci-search

name: sci-search
description: Academic paper search and metrics analysis. Searches arXiv, PubMed, Web of Science, Springer Nature, Scopus, Semantic Scholar, and OpenAlex simultaneously with journal impact factor data. Triggers on requests to search for papers or find literature.
author: Shuo Zhao         
license: MIT
copyright: © 2026 Shuo Zhao. All rights reserved. 
triggers:
  - 搜索文献
  - 查文献
  - 找论文
  - 最新论文
  - 相关文献
  - 文献检索
  - 影响因子
  - 期刊分区
  - Web of Science
  - WoS
  - SCI检索
  - arXiv
  - PubMed
  - Springer
  - Springer Nature
  - Scopus
  - Elsevier
  - Semantic Scholar
  - OpenAlex
  - find papers
  - search papers
  - literature search
  - impact factor

Sci-Search — Sci Search Skill

Academic paper search and metrics analysis tool for scientific research workflows.

Trigger Phrases

• "搜索关于 [主题] 的高影响因子论文"
• "在 Web of Science 上查找 [主题] 的最新文献"
• "search academic papers on [topic]"
• "find recent papers about [topic] on Web of Science"
• "get impact factor for [topic] papers"

Capabilities

• **Seven-Source Search**: Simultaneously searches arXiv, PubMed, **Web of Science**, **Springer Nature**, **Scopus**, **Semantic Scholar**, and **OpenAlex** (API-key-gated sources activate when keys are configured).
• **Web of Science Integration**: Returns SCI-indexed papers with times-cited counts — the gold standard for academic quality filtering.
• **Springer Nature Integration**: Returns articles from Springer, Nature, Palgrave Macmillan, and other Springer Nature imprints with DOI links.
• **Scopus Integration**: Elsevier's largest abstract and citation database; returns cited-by counts.
• **Semantic Scholar Integration**: AI-powered academic graph with citation counts; no API key required.
• **OpenAlex Integration**: Free and open catalog of 200M+ scholarly works; no API key required.
• **Journal Metrics**: Automatically supplements results with JCR partitions and Impact Factors (IF).
• **Ranking & Highlighting**: Highlights top-tier journals (Nature, Science, Advanced Materials, etc.).
• **Markdown Export**: Generates formatted markdown reports of search results.
• **Source Selection**: Use `--source scopus`, `--source springer`, `--source semantic_scholar`, `--source openalex`, `--source wos`, or `--source all` for all sources.

Configuration

Web of Science API (Recommended for SCI literature)

Add `WOS_API_KEY` to the unified `~/.aut_sci_write/.env` file to enable Web of Science search:

WOS_API_KEY=your_wos_api_key

Apply for a free API key at: https://developer.clarivate.com/apis/wos-starter

The **WoS Starter API** is free to apply for and provides access to the Web of Science Core Collection — the most authoritative index of SCI/SSCI journals.

Springer Nature API (two endpoints)

The Springer Nature API provides two separate endpoints:

**1. Metadata API** (`/meta/v2/json`) — metadata for all Springer Nature content (journals + books). Add `SPRINGER_API_KEY` to `~/.aut_sci_write/.env`:

SPRINGER_API_KEY=your_springer_api_key

**2. Open Access API** (`/openaccess/json`) — full-text OA content from BMC, SpringerOpen, Nature OA articles. Add `SPRINGER_OA_API_KEY` to `~/.aut_sci_write/.env` (falls back to `SPRINGER_API_KEY` if not set):

SPRINGER_OA_API_KEY=your_oa_api_key

Apply for free API keys at: https://dev.springernature.com/

Use `--source springer` for both, `--source springer_meta` for metadata only, or `--source springer_oa` for Open Access only.

Scopus API (Elsevier — largest abstract database)

Add `SCOPUS_API_KEY` to `~/.aut_sci_write/.env` to enable Scopus search:

SCOPUS_API_KEY=your_scopus_api_key

Apply for a free API key at: https://dev.elsevier.com/

The **Scopus Search API** covers 90M+ records across science, technology, medicine, social sciences, and arts & humanities. Requires institutional affiliation for full access.

Semantic Scholar (free, no key required)

Works out of the box. For higher rate limits, optionally add:

SEMANTIC_SCHOLAR_API_KEY=your_key

Request a key at: https://www.semanticscholar.org/product/api#api-key

OpenAlex (free, no key required)

Works out of the box. For polite pool (faster rate limits), optionally add:

OPENALEX_EMAIL=your_email@example.com

Other optional `.env` values (all in `~/.aut_sci_write/.env`)

• `SPRINGER_API_KEY` - Springer Nature Metadata API key (see above)
• `SPRINGER_OA_API_KEY` - Springer Nature Open Access API key (falls back to SPRINGER_API_KEY)
• `SCOPUS_API_KEY` - Elsevier Scopus API key (see above)
• `SEMANTIC_SCHOLAR_API_KEY` - optional, for higher rate limits
• `OPENALEX_EMAIL` - optional, for polite pool access
• `NCBI_API_KEY` - optional PubMed/NCBI E-utilities API key for higher rate limits
• `NCBI_EMAIL` - optional contact email sent to NCBI E-utilities
• `NCBI_TOOL` - optional NCBI tool name; defaults to `sci-search`
• `ZOTERO_USER_ID` — for Zotero integration
• `ZOTERO_API_KEY` — for Zotero integration

Usage

Main script: `./sci_search.py`

# Search all sources (arXiv + PubMed + WoS + Springer + Scopus + Semantic Scholar + OpenAlex)
python skills/sci-search/sci_search.py "perovskite solar cells" --limit 5

# Search Web of Science only
python skills/sci-search/sci_search.py "solid state electrolyte" --source wos --limit 10

# Search PubMed only with NCBI E-utilities
python skills/sci-search/sci_search.py "cancer immunotherapy" --source pubmed --limit 10

# Search Springer Nature only
python skills/sci-search/sci_search.py "machine learning materials science" --source springer --limit 10

# Search Scopus only
python skills/sci-search/sci_search.py "lithium ion battery" --source scopus --limit 10

# Search Semantic Scholar only (no key needed)
python skills/sci-search/sci_search.py "transformer attention mechanism" --source semantic_scholar --limit 10

# Search OpenAlex only (no key needed)
python skills/sci-search/sci_search.py "CRISPR gene editing" --source openalex --limit 10

# Export