gene-database
NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# NCBI Gene Database ## Overview NCBI Gene is the authoritative curated database for gene-centric information, covering 1M+ genes across hundreds of thousands of taxa. Each gene record includes the official symbol, aliases, full name, functional summary, genomic coordinates (GRCh38/GRCh37), RefSeq accessions, GO annotations, interaction partners, and links to related databases. Access is free via E-utilities REST API (no API key required, though recommended). ## When to Use - Resolving gene aliases and synonyms to the current official HGNC/NCBI symbol - Fetching the NCBI Gene ID (integer) for a gene symbol for downstream API calls (e.g., dbSNP, ClinVar, GEO) - Retrieving curated gene summaries and function descriptions programmatically - Pulling RefSeq mRNA (NM_) and protein (NP_) accessions associated with a gene - Querying GO functional annotations (Biological Process, Molecular Function, Cellular Component) - Finding orthologs across species via the NCBI Datasets v2 orthologs endpoint (legacy E-utilities `gene_gene_homolog` retired with HomoloGene in 2019) - For expression profiles across conditions use `geo-database`; for variant annotations use `clinvar-database` or `ensembl-d
- Overview
- When to Use
- Prerequisites
- Quick Start
- Core API
- Query 1: Search by Symbol, Name, or Function
- Query 2: Fetch Gene Summary (JSON/ESummary)
- Query 3: Fetch Full Gene Record (XML)
- Query 4: Batch Symbol-to-ID Mapping
- Query 5: GO Annotation Retrieval
- Query 6: Cross-Species Orthologs (NCBI Datasets v2)
- Key Concepts
- NCBI Gene ID vs. HGNC ID vs. Ensembl ID
- alive[prop] Filter
pip install requests pandas
What does the gene-database skill do?
NCBI Gene via E-utilities: curated records across 1M+ taxa. Official symbols, aliases, RefSeq IDs, summaries, coordinates, GO, interactions. Use for gene ID resolution and cross-species function queries. For sequences use Ensembl; for expression use geo-database.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.