clinvar-database

Name: clinvar-database
Availability: InStock
Author: OwnLab

Query ClinVar variant classifications via E-utilities and FTP downloads.

21|1|Updated Mar 19, 2026

Search Tags:#genomics #annotation #vcf #eutilities #ftp #clinvar #variant-classification

Ready to run

npx skills add https://github.com/OwnLabAI/ownlab --skill clinvar-database-ownlabai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/clinvar-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill clinvar-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar provides a centralized resource of clinically relevant variant interpretations. This Skill enables programmatic access to ClinVar data for automated interpretation, cross-referencing, and downstream annotation of genomic datasets.

Core Features & Use Cases

Query ClinVar by gene, variant, or condition via E-utilities or FTP data.
Retrieve summaries, full records, and cross-references to support variant annotation and literature review.
Use cases include bulk annotation of VCFs, research curation, and data integration for genomic medicine.

Quick Start

Query ClinVar for a BRCA1 pathogenic variant and fetch its summary via E-utilities or download the corresponding XML record for parsing.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema

How do I query ClinVar for variant classifications and clinical significance?▼

You can query ClinVar for variant classifications and clinical significance using programmatic access via E-utilities (esearch, esummary, efetch, elink) or by downloading XML, VCF, and tab-delimited data from FTP. This supports automated interpretation and cross-referencing for genomic datasets.

Can I use this skill for bulk annotation of VCF files with ClinVar data?▼

Yes, bulk annotation of VCF files is a core use case. You can apply this skill to bulk data processing and integration into annotation pipelines to retrieve ClinVar variant classifications for multiple genomic variants simultaneously.

What's the best way to retrieve full ClinVar records for gene- and disease-centered queries?▼

The best way to retrieve full ClinVar records for gene- and disease-centered queries is by applying E-utilities like efetch and esummary. You can fetch complete XML records or tab-delimited files to support variant annotation and literature review.

Does this skill support cross-referencing ClinVar data with other genomic databases?▼

Yes, the skill supports cross-referencing through the E-utilities elink function and FTP data downloads. This enables you to retrieve summaries, full records, and cross-references to support variant annotation and data integration for genomic medicine.

When do I need to download ClinVar FTP data instead of using E-utilities?▼

You need to download ClinVar FTP data instead of using E-utilities when processing bulk datasets in XML, VCF, or tab-delimited formats. FTP downloads are suited for bulk data processing and integration into annotation pipelines, while E-utilities handle targeted queries.

What genomic data formats are supported for ClinVar variant annotation?▼

Supported genomic data formats for ClinVar variant annotation include VCF, XML, and tab-delimited files. These formats allow you to retrieve ClinVar variant classifications and clinical significance for bulk annotation and data integration tasks.