db¶

 Title   : db
 Usage   : $obj->db($newval)
 Function: specifies the database to search.  valid values are:
           pubmed, pmc, journals
           it is also possible to add the following, and i will do
           so on request:
           genome, nucleotide, protein, popset, snp, sequence, taxonomy
           pubmed is default.
 Returns : value of db (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

has_next¶

  Title   : has_next
  Usage   : $has_next = $biblio->has_next();
  Function: check to see if there are more items to be retrieved
  Returns : 1 on true, undef on false
  Args    : none

get_collection_id¶

  Title   : get_collection_id
  Usage   : $id = $biblio->get_collection_id();
  Function: returns WebEnv value from ESearch
  Returns : ESearch WebEnv value as a string
  Args    : none

reset_retrieval¶

  Title   : reset_retrieval
  Usage   : $biblio->reset_retrieval();
  Function: reset cursor in id list, see cursor()
  Returns : 1
  Args    : none

get_next¶

  Title   : get_next
  Usage   : $xml = $biblio->get_next();
  Function: return next record as xml
  Returns : an xml string
  Args    : none

get_more¶

  Title   : get_more
  Usage   : $xml = $biblio->get_more($more);
  Function: returns next $more records concatenated
  Returns : a string containing multiple xml documents
  Args    : an integer representing how many records to retrieve

find¶

  Title   : find
  Usage   : $biblio = $biblio->find($pubmed_query_phrase);
  Function: perform a PubMed query using Entrez ESearch
  Returns : a reference to the object on which the method was called
  Args    : a PubMed query phrase.  See
            http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
            for help on how to construct a query.

get_all_ids¶

  Title   : get_all_ids
  Usage   : @ids = $biblio->get_all_ids();
  Function: return a list of PubMed ids resulting from call to find()
  Returns : a list of PubMed ids, or an empty list
  Args    : none

get_all¶

  Title   : get_all
  Usage   : $xml = $biblio->get_all();
  Function: retrieve all records from query
  Returns : return a large concatenated string of PubMed xml documents
  Args    : none

get_vocabulary_names¶

  Title   : get_vocabulary_names
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : empty arrayref
  Args    : none

get_entry_description¶

  Title   : get_entry_description
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_all_values¶

  Title   : get_all_values
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

get_all_entries¶

  Title   : get_all_entries
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

_initialize¶

 Usage   : my $obj = Bio::Biblio->new(-access => 'eutils' ...);
           (_initialize is internally called from this constructor)
 Returns : 1 on success
 Args    : none

This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object).

Note that this method is called always as an object method (never as a class method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one.

exists¶

  Title   : exists
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

destroy¶

  Title   : destroy
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

contains¶

  Title   : contains
  Usage   : do not use
  Function: no-op.  this is here only for interface compatibility
  Returns : undef
  Args    : none

cursor¶

  Title   : cursor
  Usage   : $obj->cursor($newval)
  Function: holds position in reference collection
  Returns : value of cursor (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

twig¶

  Title   : twig
  Usage   : $obj->twig($newval)
  Function: holds an XML::Twig instance.
  Returns : value of twig (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

ids¶

  Title   : ids
  Usage   : $obj->ids($newval)
  Function: store pubmed ids resulting from find() query
  Returns : value of ids (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

collection_id¶

  Title   : collection_id
  Usage   : $obj->collection_id($newval)
  Function:
  Returns : value of collection_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

count¶

  Title   : count
  Usage   : $obj->count($newval)
  Function:
  Returns : value of count (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

query_key¶

  Title   : query_key
  Usage   : $obj->query_key($newval)
  Function: holds query_key from ESearch document
  Returns : value of query_key (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

Mailing lists¶

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

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

Support¶

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting bugs¶

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

  https://redmine.open-bio.org/projects/bioperl/

Authors¶

Allen Day <allenday@ucla.edu>

Copyright and License¶

This software is Copyright (c) by 2004 Allen Day, University of California, Los Angeles and released under the license of the same terms as the perl 5 programming language system itself