/ 
bioperl-1.5.2_004-RCf
/ Bio::DB::EUtilities::esummary

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

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.

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.

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

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

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