Finding Rsids Of Snps For A Given Chrname, Start And End Positions For Grch37/Hg19

Question

[burcakotlu]

Hi,

Is there a way to find rsIds of snps for a given chrName, start and end positions for GRCh37/hg19 in java using eutils?

Any idea?

Burçak

Answer 1

[Pierre Lindenbaum]

see the dbsnp FAQ: "How do I extract information from dbSNP by using eutils and specifying the chromosome position interval?" http://www.ncbi.nlm.nih.gov/books/NBK9777/#FTP.how_do_i_extract_information_from_db

[burcakotlu]

Dear Pierre,

Many thanks. Is there an explanation of the output?

Thank you, Burçak

[burcakotlu]

How to parse esearch xml output?

For snps I had to run xjc "ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.3.xsd" for generating java classes.

For parsing an esearch string below which xml schema must I use for generating java classes?

http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=150934518:150934518[Base Position] AND X[CHR] AND txid9606&usehistory=n

Thanks, Burçak