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keyword-research-harvest

Automate keyword-driven literature harvesting from PubMed, Europe PMC, Crossref, and OpenAlex.

70|4|Updated Apr 23, 2026
Search Tags:#information retrieval#data science#academic research#bibliography management#literature harvesting
One-click install
npx skills add https://github.com/zhongzhx/literature-harvest --skill keyword-research-harvest
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: keyword-research-harvest
Source: https://github.com/zhongzhx/literature-harvest/tree/main
Command: npx skills add https://github.com/zhongzhx/literature-harvest --skill keyword-research-harvest

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill automates the process of harvesting literature based on keyword search, building candidate tables, downloading PDFs or full texts, and deduplicating results, saving you time and effort in research projects.

Core Features & Use Cases

  • Keyword-based Search: Search scholarly APIs (PubMed, Europe PMC, Crossref, OpenAlex) using any topic keywords.
  • Candidate Table Generation: Create a table of candidate literature based on search results.
  • PDF and Full Text Download: Download accessible PDFs or HTML/XML full texts from the candidate table.
  • HTML-to-PDF Second Pass: Attempt to extract PDFs from saved HTML pages.
  • Deduplication: Deduplicate downloaded files to ensure only unique documents are stored.
  • Use Case: Imagine you are conducting a literature review on "genetic engineering". Use this Skill to automatically search for relevant papers, download the PDFs, and organize them into a deduplicated set.

Quick Start

Run the keyword-research-harvest skill with the following command:

keyword-research-harvest run --output-root "my_literature_runs" --config "config.json" --run-name "genetic_engineering_20231001"

Frequently Asked Questions about keyword-research-harvest

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate literature harvesting from PubMed and OpenAlex using keywords?▼

Automate literature harvesting by configuring keyword queries to search scholarly APIs like PubMed, Europe PMC, Crossref, and OpenAlex, which generates a candidate table and downloads accessible PDFs or full texts.

What is the best way to download full text PDFs for academic search results?▼

Downloading full text PDFs for academic search results is handled through a two-pass process: direct PDF download from candidate tables, followed by an HTML-to-PDF extraction pass for saved web pages.

Can I deduplicate downloaded research papers automatically during literature retrieval?▼

Yes, deduplicate downloaded research papers automatically during literature retrieval to ensure only unique documents are stored, preventing redundancy across multiple scholarly API sources like Crossref and Europe PMC.

Do I need to configure sources and queries before running an automated literature search?▼

Yes, configuring sources and keyword queries is required before running automated literature search workflows, ensuring the tool correctly targets specific scholarly databases and builds an accurate candidate table.

How does HTML to PDF conversion work for academic research papers?▼

HTML to PDF conversion for academic research papers works as a second pass mechanism, attempting to extract and save PDFs from downloaded HTML or XML full text pages when direct PDF links are inaccessible.

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