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Bio::DB::EUtilities::esummary.3pm

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