Bio clinical databases dbsnp queries

Skill FridrichMethod/awesome-skills/skills/bio-clinical-databases-dbsnp-queries

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Install

npx -y skills add FridrichMethod/awesome-skills --skill bio-clinical-databases-dbsnp-queries

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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.

SKILL.md

4.7 KB, as published. Nobody here has run it

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> then help(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 = '[email protected]'

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