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annotation_for_gene_list

Annotate gene lists into TSV/CSV tables with identifiers, GO terms, and pathways.

64|12|Updated Apr 7, 2026
Search Tags:#pathways#disease#annotation#protein#uniprot#gene#go-terms
One-click install
npx skills add https://github.com/MDhewei/bioinfor-claw --skill annotation-for-gene-list
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: annotation_for_gene_list
Source: https://github.com/MDhewei/bioinfor-claw/tree/main/gene-list-analysis/function-annotation-for-gene-list
Command: npx skills add https://github.com/MDhewei/bioinfor-claw --skill annotation-for-gene-list

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pandas, requests, and includes scripts (resource) components.

What problem does it solve?

This skill builds a structured annotation table for one gene or a gene list, delivering a concise yet information-rich view of identity, protein features, domain composition, GO terms, pathway associations, and disease context.

Core Features & Use Cases

  • Aggregate per-gene annotations into a clean, analysis-ready table.
  • Resolve identifiers and aliases via MyGene.info; map to approved symbols and standard IDs (Entrez, Ensembl, UniProt).
  • Retrieve or summarize protein-level information including protein name, length, basic function, GO terms, domains, and disease associations.
  • Provide pathway context via Reactome and KEGG annotations with concise summaries.
  • Output as TSV or CSV for downstream analyses and pipeline integration.
  • Use cases: quick one-gene reports, batch annotation for gene lists, or generating input tables for downstream enrichment or plotting.

Quick Start

Place one gene per line in a text file and run the script to generate a TSV or CSV annotation table.

Frequently Asked Questions about annotation_for_gene_list

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

FAQPage Schema
How do I annotate a list of genes with protein features, GO terms, and disease associations in one table?▼

To annotate a gene list with protein features, GO terms, and disease associations, you place one gene per line in a text file and run the script to generate a structured TSV or CSV table resolving identifiers via MyGene.info and UniProt.

Can I batch annotate genes and export a TSV file for downstream analysis?▼

Yes, you can batch annotate genes and export a TSV or CSV file for downstream analysis. The skill processes a gene list and outputs an analysis-ready table containing identifiers, pathways, and domain details.

What is the best way to map gene aliases to approved symbols and standard IDs like Entrez and Ensembl?▼

The best way to map gene aliases to approved symbols and standard IDs like Entrez and Ensembl is using this annotation skill, which cross-references MyGene.info to resolve identifiers and fetch organism-specific mappings.

Does this gene annotation tool retrieve pathway context from Reactome and KEGG?▼

Yes, this gene annotation tool retrieves pathway context from Reactome and KEGG. It provides concise pathway summaries alongside protein names, lengths, domains, GO terms, and disease associations within the output table.

Do I need pandas and requests installed to run the gene annotation script?▼

Yes, you need pandas and requests installed to run the gene annotation script. These dependencies are required to fetch data from MyGene.info and UniProt APIs and format the results into a structured tabular output.

What are the limitations of using this skill for organism-specific gene annotation?▼

A limitation of using this skill for organism-specific gene annotation is that it relies on cross-referencing external databases like MyGene.info and UniProt, meaning output completeness depends on the availability and accuracy of those external sources.

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