Query dbsnp, transform to HTML

Created: 2009-05-21 22:01:55      Last updated: 2009-05-21 23:12:33

This is a XProc worklow. Its input is a list of Entrez queries packed in a html list:

See http://plindenbaum.blogspot.com/2009/05/xml-pipelines-xproc-for-bioinformatics.html

  • "snp_gene_clin"[Filter] AND "snp_pubmed_cited"[Filter] AND 2[CHR]

  • (1000[CHRPOS] : 5000[CHRPOS]) AND 2[CHR] AND "homo sapiens"[Organism]

it queries entrez, download the SNPs as XML and transform the result as an HTML table:


<thead> </thead> <tbody> <t>129</t> </tbody>
rs# dbSnpBuild group build Chrom Position
rs28928870 129 Celera 36_3 chr2 49031258
rs28928870 129 HuRef 36_3 chr2 48924538
rs28928870<!-- a--> 129 reference 36_3 chr2 49044117
rs16858811 129 Celera 36_3 chr2 212796427
rs10171150 129 reference 36_3 chr2 2090
rs10168026CRA_TCAGchr7v2 36_3 chr7 122827
rs10168026 129 Celera 36_3 chr2 71241
rs10168026 129 HuRef 36_3 chr2 4967
rs10168026 129 referenc e 36_3 chr2 4484

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