bio-clinical-databases-dbsnp-queries
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
Installation
Details
Usage
After installing, this skill will be available to your AI coding assistant.
Verify installation:
npx agent-skills-cli listSkill Instructions
name: bio-clinical-databases-dbsnp-queries description: Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information. tool_type: python primary_tool: myvariant
Version Compatibility
Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
dbSNP Queries
"Look up variant information by rsID" → Retrieve variant annotations, genomic coordinates, and cross-references to ClinVar/gnomAD from dbSNP using REST API queries.
- Python:
myvariant.MyVariantInfo().getvariant('rs12345')
Query rsID via myvariant.info
Goal: Retrieve variant information including dbSNP, ClinVar, and gnomAD annotations by rsID.
Approach: Query myvariant.info with the rsID and request specific annotation fields.
import myvariant
mv = myvariant.MyVariantInfo()
def get_rsid_info(rsid):
'''Get variant info by rsID'''
result = mv.getvariant(rsid, fields=['dbsnp', 'clinvar', 'gnomad_exome'])
return result
result = get_rsid_info('rs121913527')
Query via NCBI Entrez
Goal: Search and fetch dbSNP records directly from NCBI using Entrez E-utilities.
Approach: Use BioPython Entrez esearch to find SNP IDs, then efetch to retrieve full XML records.
from Bio import Entrez
import xml.etree.ElementTree as ET
Entrez.email = 'your@email.com'
def search_dbsnp(rsid):
'''Search dbSNP by rsID'''
handle = Entrez.esearch(db='snp', term=rsid)
record = Entrez.read(handle)
handle.close()
return record
def fetch_dbsnp(snp_id):
'''Fetch dbSNP record by internal ID'''
handle = Entrez.efetch(db='snp', id=snp_id, rettype='xml')
xml_data = handle.read()
handle.close()
return xml_data
Map Coordinates to rsID
Goal: Find the rsID corresponding to a genomic position and allele change.
Approach: Construct an HGVS notation from coordinates and query myvariant.info for the dbSNP rsID field.
def coords_to_rsid(chrom, pos, ref, alt):
'''Find rsID for genomic coordinates'''
mv = myvariant.MyVariantInfo()
# Query by HGVS notation
hgvs = f'chr{chrom}:g.{pos}{ref}>{alt}'
result = mv.getvariant(hgvs, fields=['dbsnp.rsid'])
if result:
return result.get('dbsnp', {}).get('rsid')
return None
Map rsID to Coordinates
def rsid_to_coords(rsid):
'''Get genomic coordinates for rsID'''
mv = myvariant.MyVariantInfo()
result = mv.getvariant(rsid, fields=['dbsnp', 'vcf'])
if not result:
return None
dbsnp = result.get('dbsnp', {})
return {
'chrom': dbsnp.get('chrom'),
'pos': dbsnp.get('hg38', {}).get('start'),
'ref': dbsnp.get('ref'),
'alt': dbsnp.get('alt')
}
Batch rsID Lookup
def batch_rsid_lookup(rsids, fields=None):
'''Look up multiple rsIDs'''
mv = myvariant.MyVariantInfo()
if fields is None:
fields = ['dbsnp', 'clinvar.clinical_significance', 'gnomad_exome.af.af']
results = mv.getvariants(rsids, fields=fields)
return results
Parse dbSNP Annotations
def parse_dbsnp(result):
'''Extract key dbSNP annotations'''
dbsnp = result.get('dbsnp', {})
return {
'rsid': dbsnp.get('rsid'),
'chrom': dbsnp.get('chrom'),
'pos_hg38': dbsnp.get('hg38', {}).get('start'),
'pos_hg19': dbsnp.get('hg19', {}).get('start'),
'ref': dbsnp.get('ref'),
'alt': dbsnp.get('alt'),
'gene': dbsnp.get('gene', {}).get('symbol'),
'class': dbsnp.get('class'), # snv, ins, del, etc.
'validated': dbsnp.get('validated')
}
Variant Classes in dbSNP
| Class | Description |
|---|---|
| snv | Single nucleotide variant |
| ins | Insertion |
| del | Deletion |
| indel | Insertion/deletion |
| mnv | Multiple nucleotide variant |
Query NCBI Variation Services API
import requests
def query_spdi(rsid):
'''Query NCBI Variation Services for SPDI notation'''
url = f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid[2:]}'
response = requests.get(url)
if response.ok:
return response.json()
return None
Related Skills
- myvariant-queries - Aggregated variant queries
- clinvar-lookup - ClinVar pathogenicity
- database-access/entrez-search - General Entrez queries
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