Literature Parsing Skill
OfficialExtract GEO data from literature.
AuthorTianGzlab
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates the process of finding and downloading omics datasets mentioned in scientific literature, streamlining the initial steps of bioinformatics research.
Core Features & Use Cases
- Input Flexibility: Accepts URLs, DOIs, PubMed IDs, local PDFs, or raw text as input.
- Metadata Extraction: Identifies and extracts key information like GEO accessions (GSE, GSM), organism, tissue, and technology.
- Automated Download: Downloads relevant datasets from GEO based on extracted accessions.
- Use Case: You find a promising new paper on bioRxiv. Paste the URL into OmicsClaw, and it will automatically extract the GEO accession number, download the associated data, and prepare it for analysis.
Quick Start
Use the literature skill to parse the URL https://pubmed.ncbi.nlm.nih.gov/12345.
Dependency Matrix
Required Modules
pypdfrequestsbeautifulsoup4
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: Literature Parsing Skill Download link: https://github.com/TianGzlab/OmicsClaw/archive/main.zip#literature-parsing-skill Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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