How do I download genotype and functional data in the XML format?
Genotype and functional data are stored as modules in two separate XML reports, so you’ll have to download using eUtils and then combine the results from the two reports. Below is an example of how to use eUtils to retrieve human SNPs that contain genotypes in the LPL gene: 1 eSearch using the term “LPL AND true[gtype] AND txid9606”.2 Parse the XML results to get a list of refSNP (rs) ID numbers.3 eFetch to retrieve the reports for each SNP.
Genotype and functional data are stored as modules in two separate XML reports, so you’ll have to download using eUtils and then combine the results from the two reports. Below is an example of how to use eUtils to retrieve human SNPs that contain genotypes in the LPL gene:1.eSearch using the term “LPL AND true[gtype] AND txid9606”.2.Parse the XML results to get a list of refSNP (rs) ID numbers.3.eFetch to retrieve the reports for each SNP.
Related Questions
- I’m using the data exchange format of dbSNP’s XML files and noticed that there are two allele values ("N" and "+") that I haven’t seen before. What do these values represent?
- Are the genotype data available as XML files different from those available in .bcp-formatted files, or are they just organized or formatted differently?
- I’ve heard that TripChecks data is available in XML (Extensible Mark Up Language) format. Is this true?
