gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/gene-database/references/common_workflows.md

Common Gene Database Workflows

This document provides examples of common workflows and use cases for working with NCBI Gene database.

Table of Contents

1. Disease Gene Discovery
2. Gene Annotation Pipeline
3. Cross-Species Gene Comparison
4. Pathway Analysis
5. Variant Analysis
6. Publication Mining

---

Disease Gene Discovery

Use Case

Identify genes associated with a specific disease or phenotype.

Workflow

1. Search by disease name

# Find genes associated with Alzheimer's disease
python scripts/query_gene.py --search "Alzheimer disease[disease]" --organism human --max-results 50

2. Filter by chromosome location

# Find genes on chromosome 17 associated with breast cancer
python scripts/query_gene.py --search "breast cancer[disease] AND 17[chromosome]" --organism human

3. Retrieve detailed information

# Python example: Get gene details for disease-associated genes
import json
from scripts.query_gene import esearch, esummary

# Search for genes
query = "diabetes[disease] AND human[organism]"
gene_ids = esearch(query, retmax=100, api_key="YOUR_KEY")

# Get summaries
summaries = esummary(gene_ids, api_key="YOUR_KEY")

# Extract relevant information
for gene_id in gene_ids:
    if gene_id in summaries['result']:
        gene = summaries['result'][gene_id]
        print(f"{gene['name']}: {gene['description']}")

Expected Output

• List of genes with disease associations
• Gene symbols, descriptions, and chromosomal locations
• Related publications and clinical annotations

---

Gene Annotation Pipeline

Use Case

Annotate a list of gene identifiers with comprehensive metadata.

Workflow

1. Prepare gene list

Create a file genes.txt with gene symbols (one per line):

BRCA1
TP53
EGFR
KRAS

2. Batch lookup

python scripts/batch_gene_lookup.py --file genes.txt --organism human --output annotations.json --api-key YOUR_KEY

3. Parse results

import json

with open('annotations.json', 'r') as f:
    genes = json.load(f)

for gene in genes:
    if 'gene_id' in gene:
        print(f"Symbol: {gene['symbol']}")
        print(f"ID: {gene['gene_id']}")
        print(f"Description: {gene['description']}")
        print(f"Location: chr{gene['chromosome']}:{gene['map_location']}")
        print()

4. Enrich with sequence data

# Get detailed data including sequences for specific genes
python scripts/fetch_gene_data.py --gene-id 672 --verbose > BRCA1_detailed.json

Use Cases

• Creating gene annotation tables for publications
• Validating gene lists before analysis
• Building gene reference databases
• Quality control for genomic pipelines

---

Cross-Species Gene Comparison

Use Case

Find orthologs or compare the same gene across different species.

Workflow

1. Search for gene in multiple organisms

# Find TP53 in human
python scripts/fetch_gene_data.py --symbol TP53 --taxon human

# Find TP53 in mouse
python scripts/fetch_gene_data.py --symbol TP53 --taxon mouse

# Find TP53 in zebrafish
python scripts/fetch_gene_data.py --symbol TP53 --taxon zebrafish

2. Compare gene IDs across species

# Compare gene information across species
species = {
    'human': '9606',
    'mouse': '10090',
    'rat': '10116'
}

gene_symbol = 'TP53'

for organism, taxon_id in species.items():
    # Fetch gene data
    # ... (use fetch_gene_by_symbol)
    print(f"{organism}: {gene_data}")

3. Find orthologs using ELink

# Get HomoloGene links for a gene
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=homologene&id=7157&retmode=json"

Applications

• Evolutionary studies
• Model organism research
• Comparative genomics
• Cross-species experimental design

---

Pathway Analysis

Use Case

Identify genes involved in specific biological pathways or processes.

Workflow

1. Search by Gene Ontology (GO) term

# Find genes involved in apoptosis
python scripts/query_gene.py --search "GO:0006915[biological process]" --organism human --max-results 100

2. Search by pathway name

# Find genes in insulin signaling pathway
python scripts/query_gene.py --search "insulin signaling pathway[pathway]" --organism human

3. Get pathway-related genes

# Example: Get all genes in a specific pathway
import urllib.request
import json

# Search for pathway genes
query = "MAPK signaling pathway[pathway] AND human[organism]"
url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term={query}&retmode=json&retmax=200"

with urllib.request.urlopen(url) as response:
    data = json.loads(response.read().decode())
    gene_ids = data['esearchresult']['idlist']

print(f"Found {len(gene_ids)} genes in MAPK signaling pathway")

4. Batch retrieve gene details

# Get details for all pathway genes
python scripts/batch_gene_lookup.py --ids 5594,5595,5603,5604 --output mapk_genes.json

Applications

• Pathway enrichment analysis
• Gene set analysis
• Systems biology studies
• Drug target identification

---

Variant Analysis

Use Case

Find genes with clinically relevant variants or disease-associated mutations.

Workflow

1. Search for genes with clinical variants

# Find genes with pathogenic variants
python scripts/query_gene.py --search "pathogenic[clinical significance]" --organism human --max-results 50

2. Link to ClinVar database

# Get ClinVar records for a gene
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=clinvar&id=672&retmode=json"

3. Search for pharmacogenomic genes

# Find genes associated with drug response
python scripts/query_gene.py --search "pharmacogenomic[property]" --organism human

4. Get variant summary data

# Example: Get genes with known variants
from scripts.query_gene import esearch, efetch

# Search for genes with variants
gene_ids = esearch("has variants[filter] AND human[organism]", retmax=100)

# Fetch detailed records
for gene_id in gene_ids[:10]:  # First 10
    data = efetch([gene_id], retmode='xml')
    # Parse XML for variant information
    print(f"Gene {gene_id} variant data...")

Applications

• Clinical genetics
• Precision medicine
• Pharmacogenomics
• Genetic counseling

---

Publication Mining

Use Case

Find genes mentioned in recent publications or link genes to literature.

Workflow

1. Search genes mentioned in specific publications

# Find genes mentioned in papers about CRISPR
python scripts/query_gene.py --search "CRISPR[text word]" --organism human --max-results 100

2. Get PubMed articles for a gene

# Get all publications for BRCA1
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=672&retmode=json"

3. Search by author or journal

# Find genes studied by specific research group
python scripts/query_gene.py --search "Smith J[author] AND 2024[pdat]" --organism human

4. Extract gene-publication relationships

# Example: Build gene-publication network
from scripts.query_gene import esearch, esummary
import urllib.request
import json

# Get gene
gene_id = '672'

# Get publications for gene
url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id={gene_id}&retmode=json"

with urllib.request.urlopen(url) as response:
    data = json.loads(response.read().decode())

# Extract PMIDs
pmids = []
for linkset in data.get('linksets', []):
    for linksetdb in linkset.get('linksetdbs', []):
        pmids.extend(linksetdb.get('links', []))

print(f"Gene {gene_id} has {len(pmids)} publications")

Applications

• Literature reviews
• Grant writing
• Knowledge base construction
• Trend analysis in genomics research

---

Advanced Patterns

Combining Multiple Searches

# Example: Find genes at intersection of multiple criteria
def find_genes_multi_criteria(organism='human'):
    # Criteria 1: Disease association
    disease_genes = set(esearch("diabetes[disease] AND human[organism]"))

    # Criteria 2: Chromosome location
    chr_genes = set(esearch("11[chromosome] AND human[organism]"))

    # Criteria 3: Gene type
    coding_genes = set(esearch("protein coding[gene type] AND human[organism]"))

    # Intersection
    candidates = disease_genes & chr_genes & coding_genes

    return list(candidates)

Rate-Limited Batch Processing

import time

def process_genes_with_rate_limit(gene_ids, batch_size=200, delay=0.1):
    results = []

    for i in range(0, len(gene_ids), batch_size):
        batch = gene_ids[i:i + batch_size]

        # Process batch
        batch_results = esummary(batch)
        results.append(batch_results)

        # Rate limit
        time.sleep(delay)

    return results

Error Handling and Retry

import time

def robust_gene_fetch(gene_id, max_retries=3):
    for attempt in range(max_retries):
        try:
            data = fetch_gene_by_id(gene_id)
            return data
        except Exception as e:
            if attempt < max_retries - 1:
                wait = 2 ** attempt  # Exponential backoff
                time.sleep(wait)
            else:
                print(f"Failed to fetch gene {gene_id}: {e}")
                return None

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Tips and Best Practices

1. Start Specific, Then Broaden: Begin with precise queries and expand if needed
2. Use Organism Filters: Always specify organism for gene symbol searches
3. Validate Results: Check gene IDs and symbols for accuracy
4. Cache Frequently Used Data: Store common queries locally
5. Monitor Rate Limits: Use API keys and implement delays
6. Combine APIs: Use E-utilities for search, Datasets API for detailed data
7. Handle Ambiguity: Gene symbols may refer to different genes in different species
8. Check Data Currency: Gene annotations are updated regularly
9. Use Batch Operations: Process multiple genes together when possible
10. Document Your Queries: Keep records of search terms and parameters