Different Snp Counts In Dbsnp From Entrez And Eutils

Question

[Andrea_Bio]

Hi

Does anyone know why I might be getting different SNP counts from dbSNP depending on whether i used Entrez or the eutils. I was just looking how many snps there are in cattle and you get about 100,000 in total using Entrez. I looked using the code below using eutils and got about 200,000

my $utils = "http://www.ncbi.nlm.nih.gov/entrez/eutils";

my $esearch = "$utils/esearch.fcgi?" .
              "db=$db&retmax=1&usehistory=y&term=";

my $db = 'snp';

my$query = 'bos+taurus[ORG]';
my $esearch_result = get($esearch . $query);

Many thanks

[Neilfws]

Small correction; search term qualifier should be [ORGN], not [ORG].

Answer 1

[Pierre Lindenbaum]

I got the same number (2210641) with entrez and eutils.

Answer 2

[Mary]

I see 2210641 from bos taurus with the preview/limits option at dbSNP, or 2210642 from an Entrez cross-database search from the NCBI homepage.

Where exactly did you see 100,000?

[Andrea_Bio]

Sorry i wrote down the wrong numbers. I get 275839 when i use eutils and i get 2210641 when i use entrez and select bos taurus as the organism on this page: http://www.ncbi.nlm.nih.gov/snp/limits

[Andrea_Bio]

ESEARCH RESULT:

http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">

My results:

[?][?]275839[?][?]1[?][?]0[?][?]1[?][?]NCID_1_111230488_130.14.22.101_9001_1287777683_1088997682[?][?] [?]20963501[?]

[Andrea_Bio]

also when i change my eutils query to this: my$query = 'bos taurus[ORG] AND snp[SNP_CLASS]'; the result goes down from 275839 to only 494 so I must be doing something very wrong.

[Andrea_Bio]

I think it is modifying the query as i get this in my output: [?]
[?]bos taurus[All Fields][?]
[?]"cattle"[MeSH Terms] OR "cattle"[All Fields] OR ("bos"[All Fields] AND "taurus"[All Fields]) OR "bos taurus"[All Fields][?] [?][?]. How do i stop it doing this?

[Andrea_Bio]

It was my fault - the database was undefined so it was searching medline. Thanks for your help