Individual skill

gene-database

Query the NCBI Gene database via E-utilities and the NCBI Datasets API; use it when you need to search genes by symbol/ID and retrieve annotations (RefSeq, GO, location, phenotype) for single or batch gene lists.

scientific-skills/Evidence Insight/gene-database/SKILL.md

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bioinformatics Repository topic
computational-biology Repository topic
data-analysis Repository topic
ai Repository topic
biology Repository topic
cancer-genomics Repository topic
data-visualization Repository topic
differential-expression Repository topic
genomics Repository topic
medical Repository topic
data Derived category
data-databases Derived category

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SKILL.mdcore · 5,234 bytes
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SKILL.mdcore · 5,234 bytes
SKILL.mdcore · 5,234 bytes
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SKILL.mdcore · 5,234 bytes
SKILL.mdcore · 5,234 bytes
gene-database_audit_result_v1.jsonasset · 11,913 bytes
references/api_reference.mddoc · 9,669 bytes
references/common_workflows.mddoc · 10,973 bytes
scripts/batch_gene_lookup.pyruns · 9,407 bytes
scripts/fetch_gene_data.pyruns · 8,879 bytes
scripts/query_gene.pyruns · 7,660 bytes

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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)

## When to Use

- You have a gene symbol (e.g., **BRCA1**) and need the correct **NCBI Gene ID** for a specific organism.
- You have an NCBI **Gene ID** and need consolidated metadata (aliases, RefSeq accessions, genomic location, GO, literature links).
- You need to **annotate a gene panel** (dozens to thousands of genes) with consistent identifiers and core annotations.
- You want to search genes by **biological context** (GO terms, phenotype/disease keywords, pathway terms) and then retrieve details for the hits.
- You are building a pipeline that must respect **NCBI rate limits** and handle retries for transient API failures.

## Key Features

- Symbol/name search with organism scoping using **E-utilities (ESearch)**.
- Gene record retrieval by ID using **E-utilities (EFetch/ESummary)** in JSON/XML/text-oriented outputs.
- Streamlined, gene-focused retrieval using the **NCBI Datasets API** (metadata + sequences/links in a single workflow).