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maziyarpanahi
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mining-pubmed-literature

Search PubMed and PMC for biomedical literature and citation metadata.

5.0k|615|Updated Oct 4, 2025
Search Tags:#ncbi#pubmed#pmc#biomedical literature#e-utilities#research corpus#mesh search
One-click install
npx skills add https://github.com/maziyarpanahi/openmed --skill mining-pubmed-literature
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: mining-pubmed-literature
Source: https://github.com/maziyarpanahi/openmed/tree/main/skills/mining-pubmed-literature
Command: npx skills add https://github.com/maziyarpanahi/openmed --skill mining-pubmed-literature

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill removes the friction of finding, retrieving, and organizing biomedical literature from PubMed and PMC, helping researchers gather reliable evidence without manually navigating records or downloading abstracts one at a time.

Core Features & Use Cases

  • Targeted Literature Search: Build reproducible PubMed queries using MeSH terms, title and abstract fields, author filters, publication dates, and article types.
  • Record Retrieval: Use NCBI E-utilities to search for PMIDs, fetch abstracts or PMC full text, and retrieve structured citation metadata such as titles, authors, journals, and dates.
  • Corpus Preparation: Assemble literature collections for summarization, evidence tables, biomedical named entity recognition, or knowledge graph construction.
  • OpenMed Integration: Search for evidence using diseases, drugs, and genes extracted by OpenMed, or analyze retrieved abstracts with OpenMed biomedical models.

Quick Start

Use this Skill to search PubMed for recent studies on metformin and type 2 diabetes, retrieve their abstracts and citation metadata, and prepare the results for biomedical entity extraction.

Frequently Asked Questions about mining-pubmed-literature

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

FAQPage Schema
How do I search PubMed for biomedical literature using MeSH terms and filters?▼

To search PubMed for biomedical literature, you can build reproducible queries using MeSH terms, title and abstract fields, author filters, publication dates, and article types. This targets specific evidence gathering without manual record navigation.

Can I use NCBI E-utilities to retrieve abstracts and citation metadata from PMC?▼

Yes, you can retrieve abstracts and structured citation metadata from PMC by using NCBI E-utilities. The process utilizes ESearch, EFetch, and ESummary to fetch PMIDs, full text records, titles, authors, journals, and dates.

What is the best way to build a research corpus from biomedical literature for entity recognition?▼

The best way to build a research corpus for biomedical named entity recognition is to assemble literature collections by retrieving structured abstracts and citation metadata. This prepares the text data for subsequent entity extraction and knowledge graph construction.

Does searching PubMed through E-utilities require an API key to avoid rate limits?▼

Searching PubMed through E-utilities provides optional API key support to ensure rate-limit compliance. While you can execute ESearch and EFetch requests without one, an API key is recommended for higher volume retrieval workflows.

Can I analyze retrieved PubMed abstracts with biomedical models like OpenMed?▼

Yes, you can analyze retrieved PubMed abstracts with OpenMed biomedical models. This integration allows you to search for evidence using extracted diseases, drugs, and genes, or process the fetched literature directly through the models.

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