scientific-biomedical-pubtator
CommunityBiomedical text annotation via PubTator3.
Data & Analytics#biomedical#knowledge-graph#text-mining#ner#gene-disease#relation-extraction#pubtator
Authornahisaho
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This skill automates biomedical literature annotation by leveraging PubTator3 to recognize genes, diseases, chemicals, mutations, and species, and to extract relationships, enabling scalable knowledge extraction from large literature corpora.
Core Features & Use Cases
- Entity recognition: gene, disease, chemical, mutation, species tagging in biomedical texts.
- Relation extraction: identify GDA, CGA, CDA relationships and build simple knowledge graphs.
- Pipeline automation: end-to-end annotation, search, and dashboard-style summaries for large corpora.
- Use Case: researchers can annotate PubMed articles to populate knowledge graphs for disease-gene or drug-target studies.
Quick Start
Run a PubTator3 annotation on a set of PubMed articles to automatically annotate entities and extract relations.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 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: scientific-biomedical-pubtator Download link: https://github.com/nahisaho/satori/archive/main.zip#scientific-biomedical-pubtator Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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