Bio::Tools::EUtilities::Info(3) interface class for storing einfo data


#### should not create instance directly; Bio::Tools::EUtilities does this ####
my $info = Bio::Tools::EUtilities->new(-eutil => 'einfo',
-file => 'einfo.xml');
# can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles)
# print available databases (if data is present)
print join(', ',$info->get_available_databases),"\n";
# get database info
my $db = $info->get_database; # in case you forgot...
my $desc = $info->get_description;
my $nm = $info->get_menu_name;
my $ct = $info->get_record_count;
my $dt = $info->get_last_update;
# EUtilDataI interface methods
my $eutil = $info->eutil;
my $type = $info->datatype;
# iterate through Field and Link objects
while (my $field = $info->next_Field) {
print "Field code: ",$field->get_field_code,"\n";
print "Field name: ",$field->get_field_name,"\n";
print "Field desc: ",$field->get_field_description,"\n";
print "DB : ",$field->get_database,"\n";
print "Term ct : ",$field->get_term_count,"\n";
for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) {
print "\tField $att\n" if $field->$att;
my @fields = $info->get_Fields; # grab them all (useful for grep)
while (my $link = $info->next_LinkInfo) {
print "Link name: ",$link->get_link_name,"\n";
print "Link desc: ",$link->get_link_description,"\n";
print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database()
print "DBTo: ",$link->get_dbto,"\n"; # database linked to
my @links = $info->get_LinkInfo; # grab them all (useful for grep)
$info->rewind(); # rewinds all iterators
$info->rewind('links'); # rewinds Link iterator
$info->rewind('fields'); # rewinds Field iterator


This class handles data output (XML) from einfo.

Einfo is capable of returning two types of information:

  • A list of all available databases (when called w/o parameters)
  • Information about a specific database.

The latter information includes the database description, record count, and date/time stamp for the last update, among other things. It also includes a list of fields (indices by which record data is stored which can be used in queries) and links (crossrefs between related records in other databases at NCBI). Data from the latter two are stored in two small subclasses (FieldInfo and LinkInfo) which can be iterated through or retrieved all at once, as demonstrated above. NOTE: Methods described for the LinkInfo and FieldInfo subclasses are unique to those classes (as they retrieve data unique to those data types).

Further documentation for Link and Field subclass methods is included below.

For more information on einfo see:


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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title    : rewind
 Usage    : $info->rewind() # rewinds all (default)
            $info->rewind('links') # rewinds only links
 Function : 'rewinds' (resets) specified interators (all if no arg)
 Returns  : none
 Args     : [OPTIONAL] String: 
            'all'    - all iterators (default)
            'linkinfo'  - LinkInfo objects only
            'fieldinfo' - FieldInfo objects only


 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting
 Note     : Used generally for debugging and for various print methods