lit-synthesizer

Search PubMed and bioRxiv, summarize abstracts, and build citation graphs.

Updated May 10, 2026

Search Tags:#citations #bioinformatics #synthesis #literature review #PubMed #bioRxiv

Ready to run

npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill lit-synthesizer-mubashermohammed

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: lit-synthesizer
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/lit-synthesizer
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill lit-synthesizer-mubashermohammed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the process of searching bioinformatics literature, synthesizing results into a structured report, and building citation graphs, saving researchers hours of manual work.

Core Features & Use Cases

PubMed and bioRxiv Search: Automatically search both databases for relevant papers.
Abstract Synthesis: Summarize key findings from retrieved papers.
Citation Graph: Build a citation graph to visualize relationships between papers.
Reproducibility Bundle: Provide a reproducibility bundle for transparency and verifiability.
Use Case: A researcher can easily generate a comprehensive literature review on a specific topic with a single command.

Quick Start

Run the lit-synthesizer skill with the query 'CRISPR off-target effects' and output the results to the 'report' directory.

Frequently Asked Questions about lit-synthesizer

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

FAQPage Schema

How do I automate a bioinformatics literature review across PubMed and bioRxiv?▼

Synthesize bioinformatics abstracts by retrieving papers from PubMed and bioRxiv, summarizing their key findings into a structured report, and mapping their relationships into a visual citation graph for quick literature overview.

Do I need biopython to search PubMed and bioRxiv for literature synthesis?▼

Yes, you need the biopython dependency installed to handle API interactions and data processing for literature synthesis. It provides the necessary modules to query PubMed, fetch abstracts, and process bioinformatics publication data.

How does a citation graph help visualize bioinformatics literature relationships?▼

A citation graph visualizes literature relationships by mapping how retrieved bioinformatics papers reference each other. This network structure helps researchers identify foundational studies, track research trends, and understand the evolution of specific topics.

Can I generate a reproducibility bundle for a PubMed literature search?▼

Yes, generate a reproducibility bundle alongside your synthesized literature report. This bundle captures the search queries, retrieved abstracts, and processing steps from your PubMed and bioRxiv searches, ensuring full transparency and verifiability of your review.

What's the best way to summarize bioinformatics abstracts from multiple databases?▼

The best way to summarize bioinformatics abstracts is using an automated synthesis tool that queries multiple databases like PubMed and bioRxiv simultaneously, extracts key findings, and compiles them into a single structured report with visual citation graphs.