Converting Large NCBI Databases into SAS Rosa SJ Lin Division of Statistical Genomics Washington University in Saint Louis June 30, 2008

NCBI (  Contains a large number of databases  Most important are: - GenBank - PubMed - RefSeq - Online Mendelian Inheritance in Man (OMIM) - dbSNP

dbSNP Database

NCBI dbSNP  Contains information about SNPs  Submitted data is given an ss number (e.g. ss )  If data meets criteria a reference SNP is created which had an rs number (e.g. rs530)

dbSNP Data (1) - Each record with various lines and each line with various lengths

dbSNP Data (2)

dbSNP Data (3)

 Various uses of the SCAN, INDEX functions to assist in reading data (1) data ncbisnp ; length rs $12 ; infile din firstobs=1 missover pad; input snpline $132. ; if index(snpline,"updated")>0 then do; rs=compress(scan(snpline,1,"|")); output; end; run;

 Various uses of the SCAN, INDEX functions to assist in reading data (2) if index(snpline,"alleles=")>0 then do; alleles=substr(compress(scan(snpline,2,"|")),9); output; end; if index(snpline,"assembly=reference")>0 then do chrom=input(substr(compress(scan(snpline,3,"|")),5),8.); posc=compress(scan(snpline,4,"|")); output; end;

 Use RETAIN statement - cause a variable to keep its value from one iteration of the DATA step to the next. retain markname rs alleles;

dbSNP Data (4)

Output SAS Dataset

Readings:  Kim L Kolbe etc., SUGI 22: “Advanced Techniques for Reading Difficult and Unusual Flat Files”.  Clinton S Rickards, SUGI 24: “Reading External Files Using SAS ® Software ”.