scientific-civic-evidence

Extracts LungResect surgical-site infection and postoperative data from EHRs and MINI2 datasets.

3|1|Updated Feb 11, 2026

Search Tags:#bioinformatics #assertions #molecular-profile #variant-interpretation #civic #cancer #evidence-items

Ready to run

npx skills add https://github.com/nahisaho/satori --skill scientific-civic-evidence

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: scientific-civic-evidence
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-civic-evidence
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-civic-evidence

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Enables researchers to efficiently retrieve and interpret clinical evidence for cancer-related variants from the CIViC REST API, aggregating evidence items, gene summaries, molecular profiles, and assertions for downstream analysis.

Core Features & Use Cases

CIViC REST API integration for variant search, gene summaries, evidence extraction, and assertion retrieval.
Pipeline-ready outputs: CSV/structured data for integration into precision oncology workflows.
Use Case: when evaluating a specific cancer variant to gather clinical interpretation, evidence items, and guideline assertions.

Quick Start

Run the CIViC pipeline by calling civic_pipeline with a gene name and optional variant to fetch summaries, variants, evidence, and assertions into an organized output directory.

Frequently Asked Questions about scientific-civic-evidence

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

FAQPage Schema

How do I retrieve clinical evidence for cancer variants from the CIViC API?▼

Retrieve clinical evidence for cancer variants by querying the CIViC REST API to fetch gene summaries, molecular profiles, and assertion items into structured pipeline outputs.

What is the best way to search CIViC for variant interpretation and evidence items?▼

Searching CIViC for variant interpretation involves passing a gene name and optional variant to extract evidence items, assertions, and molecular profiles into an organized output directory.

Can I use Python to fetch CIViC gene summaries and molecular profiles for precision oncology workflows?▼

Use Python with requests and pandas to fetch CIViC gene summaries and molecular profiles, assembling the extracted clinical evidence into CSV files for precision oncology workflows.

Does this approach output structured data for downstream cancer genomics analysis?▼

This approach outputs CSV and structured data formats containing CIViC evidence items, assertions, and variant interpretations ready for integration into downstream cancer genomics analysis pipelines.

What CIViC data types can I extract for cancer variant interpretation?▼

Extract CIViC data types including gene summaries, evidence items, molecular profiles, and clinical assertions to support comprehensive cancer variant interpretation workflows.

Do I need specific Python libraries to run the CIViC evidence retrieval pipeline?▼

Running the CIViC evidence retrieval pipeline requires Python libraries such as requests and pandas to perform API searches, fetch summaries, and assemble structured data outputs.