Question: Download Snp Data From Dbsnp Using Eutils?
0
gravatar for BioInfo1010
7.8 years ago by
BioInfo101010
Pune
BioInfo101010 wrote:

can i download SNPs data(rsID,chromosomal position, function, variation class, contig,contig position,Allele etc..) of a gene from dbSNP using eUtils?

eg. i want to download SNPs data(rsID,chromosomal position, function, variation class, contig,contig position,Allele etc..) of DMD gene using eUtils.

ncbi snp eutils • 3.3k views
ADD COMMENTlink written 7.8 years ago by BioInfo101010
2
gravatar for Pierre Lindenbaum
7.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

Get the ID of your gene: e.g: http://www.ncbi.nlm.nih.gov/gene/4853

retrieves the SNP id with NCBI ELink: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=4853


http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd">
<eLinkResult>

    <LinkSet>
        <DbFrom>gene</DbFrom>
        <IdList>
            <Id>4853</Id>
        </IdList>
        <LinkSetDb>
            <DbTo>snp</DbTo>
            <LinkName>gene_snp</LinkName>
            <Link>
                <Id>207460413</Id>
            </Link>
            <Link>
                <Id>202240453</Id>
            </Link>
             (....)

fetch the SNP data with ncbi efetch:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=snp&id=202240453&retmode=xml

ADD COMMENTlink written 7.8 years ago by Pierre Lindenbaum127k
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