Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service
version 1.70
Do not use this object directly, it is recommended to access it and use it through the Bio::Biblio module:
use Bio::Biblio; use Bio::Biblio::IO; my $biblio = Bio::Biblio->new( -access => 'eutils' ); $biblio->find("10336996"); my $xml = $biblio->get_next; my $io = Bio::Biblio::IO->new( -data => $xml, -format => 'medlinexml' ); my $article = $io->next_bibref();
The main documentation details are to be found in Bio::DB::BiblioI.
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)
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
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
Title : reset_retrieval Usage : $biblio->reset_retrieval(); Function: reset cursor in id list, see cursor() Returns : 1 Args : none
Title : get_next Usage : $xml = $biblio->get_next(); Function: return next record as xml Returns : an xml string Args : none
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
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.
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
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
Title : get_vocabulary_names Usage : do not use Function: no-op. this is here only for interface compatibility Returns : empty arrayref Args : none
Title : get_entry_description Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_all_values Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_all_entries Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
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.
Title : exists Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : destroy Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : contains Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
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)
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)
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)
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)
Title : count Usage : $obj->count($newval) Function: Returns : value of count (a scalar) Args : on set, new value (a scalar or undef, optional)
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)
* More testing and debugging needed to ensure that returned citations are properly transferred even if they contain foreign characters. * Maximum record count (MAX_RECORDS) returned currently hard coded to 100K. * Biblio retrieval methods should be more tightly integrated with Bio::Biblio::Ref and Bio::DB::MeSH.
Pub Med Help
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
Entrez Utilities
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
Example code
eg/biblio-eutils.pl
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
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.
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/
Allen Day <allenday@ucla.edu>
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
To install Bio::Biblio, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Biblio
CPAN shell
perl -MCPAN -e shell install Bio::Biblio
For more information on module installation, please visit the detailed CPAN module installation guide.