gene-database

Files (9)

• SKILL.md
• api_reference.md · references/
• common_workflows.md · references/
• batch_gene_lookup.cpython-313.pyc · scripts/__pycache__/
• fetch_gene_data.cpython-313.pyc · scripts/__pycache__/
• query_gene.cpython-313.pyc · scripts/__pycache__/
• batch_gene_lookup.py · scripts/
• fetch_gene_data.py · scripts/
• query_gene.py · scripts/

SKILL.md (first lines)

# 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 human")
3. The script returns matching Gene IDs

Example query patterns:
- Gene symbol: `insulin[gene name] AND human[organism]`
- Gene with disease: `dystrophin[gene name] AND muscular dystrophy[disease]`
- Chromosome location: `human[organism] AND 17q21[chromosome]`

### Retrieve Gene Information by ID

To fetch detailed information for known Gene IDs:

1. Use `scripts/fetch_gene_data.py` with the Datasets API for comprehensive data
2. Alternatively, use `scripts/query_gene.py` with E-utilities EFetch for specific formats
3. Specify desired output format (JSON, XML, or text)

The Datasets API returns:
- Gene nomenclature and aliases
- Reference sequences (RefSeqs) for transcripts and proteins
- Chromosomal location and mapping
- Gene Ontology (GO) annotations
- Associated publications

### Batch Gene Lookups

For multiple genes simultaneously:

1. Use `scripts/batch_gene_lookup.py` for efficient batch processing
2. Provide a list of gene symbols or IDs
3. Specify the organism for symbol-based queries
4. The script handles rate limiting automatically (10 requests/second with API key)

This workflow is useful for:
- Validating gene lists
- Retrieving metadata for gene panels
- Cross-referencing gene identifiers
- Building gene annotation tables

### Search by Biological Context

To find genes associated with specific biological functions or phenotypes:

1. Use E-utilities with Gene Ontology (GO) terms or phenotype keywords
2. Query by pathway names or disease associations
3. Filter by organism, chromosome, or other attributes

Example searches:
- By GO term: `GO:0006915[biological process]` (apoptosis)
- By phenotype: `diabetes[phenotype] AND mouse[organism]`
- By pathway: `insulin signaling pathway[pathway]`

### API Access Patterns

**Rate Limits:**
- Without API key: 3 requests/second for E-utilities, 5 requests/second for Datasets API
- With API key: 10 requests/second for both APIs

**Authentication:**
Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ to increase rate limits.

**Error Handling:**
Both APIs return standard HTTP status codes. Common errors include:
- 400: Malformed query or invalid parameters
- 429: Rate limit exceeded
- 404: Gene ID not found

Retry failed requests with exponential backoff.

## Script Usage

### query_gene.py

Query NCBI Gene using E-utilities (ESearch, ESummary, EFetch).

```bash
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]"
```

### fetch_gene_data.py

Fetch comprehensive gene data using NCBI Datasets API.

```bash
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
```

### batch_gene_lookup.py

Process multiple gene queries efficiently.

From lamm-mit/scienceclaw, Apache-2.0.

More from lamm-mit/scienceclaw