gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
npx skills add LeonChaoX/qinyan-academic-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.
# Gene Database ## Overview NCBI Gene is a comprehensive database integrating gene information from diverse species. It provides nomenclature, reference sequences (RefSeqs), chromosomal maps, biological pathways, genetic variations, phenotypes, and cross-references to global genomic resources. ## When to Use This Skill This skill should be used when working with gene data including searching by gene symbol or ID, retrieving gene sequences and metadata, analyzing gene functions and pathways, or performing batch gene lookups. ## Quick Start NCBI provides two main APIs for gene data access: 1. **E-utilities** (Traditional): Full-featured API for all Entrez databases with flexible querying 2. **NCBI Datasets API** (Newer): Optimized for gene data retrieval with simplified workflows Choose E-utilities for complex queries and cross-database searches. Choose Datasets API for straightforward gene data retrieval with metadata and sequences in a single request. ## Common Workflows ### Search Genes by Symbol or Name To search for genes by symbol or name across organisms: 1. Use the `scripts/query_gene.py` script with E-utilities ESearch 2. Specify the gene symbol and organism (e.g., "BRCA1 in
- Overview
- When to Use This Skill
- Quick Start
- Common Workflows
- Search Genes by Symbol or Name
- Retrieve Gene Information by ID
- Batch Gene Lookups
- Search by Biological Context
- API Access Patterns
- Script Usage
- querygene.py
- fetchgenedata.py
- batchgenelookup.py
- API References
python scripts/query_gene.py --search "BRCA1" --organism "human" python scripts/query_gene.py --id 672 --format json python scripts/query_gene.py --search "insulin[gene] AND diabetes[disease]" python scripts/fetch_gene_data.py --gene-id 672 python scripts/fetch_gene_data.py --symbol BRCA1 --taxon human python scripts/fetch_gene_data.py --symbol TP53 --taxon "Homo sapiens" --output json python scripts/batch_gene_lookup.py --file gene_list.txt --organism human python scripts/batch_gene_lookup.py --ids 672,7157,5594 --output results.json
What does the gene-database skill do?
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-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 LeonChaoX/qinyan-academic-skills, a repository with 759 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.