Bio::DB::EUtilities::esummary(3)

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

SYNOPSIS
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

DESCRIPTION
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.

"db"
    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)

"id"
    a list of primary ID's (see below)

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

"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

"cookie"
    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
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.

FEEDBACK

  Mailing Lists
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

  Reporting Bugs
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/

AUTHOR
Email cjfields at uiuc dot edu

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

  parse_response
 Title   : parse_response
 Usage   : $db->parse_response($content)
 Function: parse out response for cookie and/or id's
 Returns : none
 Args    : HTTP::Response object
 Throws  : 'NCBI elink nonrecoverable error'

  Methods inherited from Bio::DB::EUtilities
add_cookie

 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

next_cookie

 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

reset_cookies

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

get_all_cookies

 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

get_response

 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)

reset_parameters

 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

count

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

get_db_ids

 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;

get_score

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

get_ids_by_score

 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