esummary documentation.

Bio::DB::EUtilities::esummary - retrieval of NCBI DocSum data from a list
of primary IDs or a Cookie

No package variables defined.

Do not use this module directly.
Use it via the Bio::DB::EUtilities class.

  use Bio::DB::EUtilities;

  my $esearch = Bio::DB::EUtilities->new(-eutil      => 'esearch',
                                         -db         => 'pubmed',
                                         -term       => 'hutP',
                                         -usehistory => 'y');

  $esearch->get_response; # parse the response, fetch a cookie

  my $esummary = Bio::DB::EUtilities->new(-eutil        => 'esummary',
                                       -cookie       => $esearch->next_cookie);

  print $esearch->get_response-content; # prints XML output

WARNING: Please do NOT spam the Entrez web server with multiple requests.
The EUtility ESummary is used to retrieve ducument summaries from a list of
primary IDs or the user's history (stored on the remote server and accessible
using a Cookie. The returned data is processed
for errors, but no further processing is done at this time.

one or more database available through EUtilities if set to 'all', will retrieve
all related ID's from each database (see method get_db_ids to retrieve these)

a list of primary ID's (see below)

reldate

limits results to the number of days preceding today's date

C<mindate>, maxdate

limits results by dates (yyyy/mm/dd format, or by year)

term

limits results by Entrez query (only valid when cmd=neighbor within a single
database)

retmode

set to XML, but can be changed to ref when needed

a Bio::DB::EUtilities::Cookie object (see below)

cmd

command values (see below)

holding

list LinkOut URLs for specified holding provider; used with cmd=llinks
or cmd=llinkslib (rarely used)
Command values are set using the cmd parameter.

prlinks

List the hyperlink to the primary LinkOut provider for multiple IDs and
database. Each ID is processed separately.

prlinks&retmode=ref

Create a hyperlink to the primary LinkOut provider for a single ID and database.

llinks

List LinkOut URLs and Attributes, except PubMed libraries, for multiple IDs
and database. Each ID is processed separately.

llinkslib

List LinkOut URLs and Attributes for multiple IDs and database. Each ID is
processed separately.

lcheck

Check for the existence (Y or N) of an external link in for multiple IDs and
database.

ncheck

Check for the existence of a neighbor link for each ID within a database,
e.g., Related Articles in PubMed.

neighbor

The default setting. Display neighbors and their scores within a database.

neighbor_history

Create history (WebEnv & query_key) for use in other EUtilities.

acheck

Lists Entrez databases links for multiple IDs from a single database.

sub _initialize {

    my ($self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    # set by default
    $self->_eutil($EUTIL);
	my ($retstart, $retmax) =  $self->_rearrange([qw(RETSTART RETMAX)],@args);
    $retstart       && $self->retstart($retstart);
    $retmax         && $self->retmax($retmax);

}

sub parse_response {

    my $self    = shift;
    my $response = shift if @_;
    if (!$response || !$response->isa("HTTP::Response")) {
        $self->throw("Need HTTP::Response object");
    }
    my $xs = XML::Simple->new();
    my $simple = $xs->XMLin($response->content);
    #$self->debug("Response dumper:\n".Dumper($simple));
    # check for errors
    if ($simple->{ERROR}) {
        $self->throw("NCBI esummary nonrecoverable error: ".$simple->{ERROR});
    }

}

General documentation

User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

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.

  http://bugzilla.open-bio.org/

Email cjfields at uiuc dot edu

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

 Title   : cookie
 Usage   : $db->add_cookie($cookie)
 Function: adds an NCBI query cookie to the internal cookie queue
 Returns : none
 Args    : a Bio::DB::EUtilities::Cookie object

 Title   : next_cookie
 Usage   : $cookie = $db->next_cookie
 Function: return a cookie from the internal cookie queue
 Returns : a Bio::DB::EUtilities::Cookie object
 Args    : none

 Title   : reset_cookie
 Usage   : $db->reset_cookie
 Function: resets the internal cookie queue
 Returns : none
 Args    : none

 Title   : get_all_cookies
 Usage   : @cookies = $db->get_all_cookies
 Function: retrieves all cookies from the internal cookie queue; this leaves
           the cookies in the queue intact 
 Returns : none
 Args    : none

 Title   : get_response
 Usage   : $db->get_response($content)
 Function: main method to retrieve data stream; parses out response for cookie
 Returns : HTTP::Response object
 Args    : optional : Bio::DB::EUtilities::Cookie from a previous search
 Throws  : 'not a cookie' exception, response errors (via HTTP::Response)

 Title   : reset_parameters
 Usage   : $db->reset_parameters(@args);
 Function: resets the parameters for a EUtility with args (in @args)
 Returns : none
 Args    : array of arguments (arg1 => value, arg2 => value)

Experimental method at this time

 Title   : count
 Usage   : $count = $db->count;
 Function: return count of number of entries retrieved by query
 Returns : integer
 Args    : none

 Title   : get_db_ids
 Usage   : $count = $elink->get_db_ids($db); # gets array ref of IDs
           @count = $elink->get_db_ids($db); # gets array of IDs
           %hash  = $elink->get_db_ids(); # hash of databases (keys) and array_refs(value)
 Function: returns an array or array ref if a database is the argument,
           otherwise returns a hash of the database (keys) and id_refs (values)
 Returns : array or array ref of ids (arg=database) or hash of
           database-array_refs (no args)
 Args    : database string;

 Title   : get_score
 Usage   : $score = $db->get_score($id);
 Function: gets score for ID (if present)
 Returns : integer (score) 
 Args    : ID values

 Title   : get_ids_by_score
 Usage   : @ids = $db->get_ids_by_score;  # returns IDs
           @ids = $db->get_ids_by_score($score); # get IDs by score
 Function: returns ref of array of ids based on relevancy score from elink;
           To return all ID's above a score, use the normal score value;
           to return all ID's below a score, append the score with '-';
 Returns : ref of array of ID's; if array, an array of IDs
 Args    : integer (score value); returns all if no arg provided

_initialize	No description	Code
parse_response	Description	Code