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MubasherMohammed
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pubmed-summariser

Retrieve and summarize recent PubMed papers into structured briefings.

Updated May 10, 2026
Search Tags:#bioinformatics#genomics#PubMed#literature search#research briefing
One-click install
npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill pubmed-summariser
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubmed-summariser
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/pubmed-summariser
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill pubmed-summariser

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, xml.etree.ElementTree, clawbio.common.html_report, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the process of searching PubMed and generating a structured research briefing of the top recent English-language papers, saving researchers time and effort.

Core Features & Use Cases

  • PubMed Search: Query PubMed using gene names or disease terms.
  • Structured Briefing: Receive a formatted summary of the top papers, including title, authors, journal, date, and abstract.
  • Dual Output: Provides both a terminal summary and an HTML report for sharing.
  • Use Case: A researcher wants to quickly get an overview of the latest research on a specific gene or disease.

Quick Start

Run the 'pubmed-summariser' skill with the gene name or disease term you are interested in, e.g., 'pubmed-summariser --query "BRCA1"'

Frequently Asked Questions about pubmed-summariser

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

FAQPage Schema
How do I generate a research briefing from PubMed papers for a specific gene?▼

To generate a research briefing from PubMed papers, query the skill with your gene name or disease term to retrieve and summarize top recent English-language papers into a structured overview. It provides titles, authors, journals, dates, and abstracts.

What is the best way to automate PubMed literature search and summarize abstracts?▼

Automating a PubMed literature search is done by querying gene names or disease terms to retrieve top recent papers, automatically parsing XML responses to extract abstracts and metadata into a concise structured research briefing.

Does the PubMed summarizer require Python libraries for XML parsing and HTTP requests?▼

Yes, the PubMed summarizer requires Python libraries including requests for HTTP requests and xml.etree.ElementTree for XML parsing to fetch and process literature data from the PubMed database.

Can I get an HTML report from PubMed search results for sharing with collaborators?▼

Yes, you can get an HTML report from PubMed search results for sharing. The skill provides dual output, delivering both a terminal summary and a formatted HTML report of the structured research briefing.

What information is included in a structured PubMed literature briefing?▼

A structured PubMed literature briefing includes the paper title, authors, journal name, publication date, and abstract summary, providing a concise overview of top recent English-language research papers.

Are there limitations when using a PubMed literature search tool for genomics research?▼

Limitations include being restricted to recent English-language papers retrieved from PubMed using gene or disease terms, and requiring specific Python dependencies for HTTP requests and XML parsing to generate the briefings.

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