Get Gene Symbol From A Gene Identifier Eutils Help

Question

[scott.goldweber]

I was wondering if it was possible to get the gene symbol using a gene identifier( or perhaps a taxid?) from the eutils

[Neilfws]

A taxid identifies an organism. It could be linked to all genes for that organism but not "the gene symbol" (assuming you mean "for one gene"). Perhaps you could clarify the question a little?

Answer 1

[ewre]

use esummary would do that if u want to get a symbol related with an entrez id(copied from bioperl eutils howto)

use Bio::DB::EUtilities;

my @ids     = qw(828392 790 470338);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esummary',
                                       -email => '[e-mail]',
                                       -db    => 'gene',
                                       -id    => \@ids);

# iterate through the individual DocSum objects (one per ID)
while (my $ds = $factory->next_DocSum) {
    print "ID: ",$ds->get_id,"\n";
    # flattened mode, iterates through all Item objects
    while (my $item = $ds->next_Item('flattened'))  {
        # not all Items have content, so need to check...
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if $item->get_content;
    }
    print "\n";
}

[Richard Smith]

The URL to to fetch this from the command line is, for example:

curl -g 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=1636,351'

Then you can extract the 'Name' Item in the language of your choice.