--- name: "Bio::DB::Biblio::eutils" section: "3pm" platform: "linux" package: "libbio-biblio-perl" version: "1.70-2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::DB::Biblio::eutils" --- # Bio::DB::Biblio::eutils(3pm) access to PubMed's bibliographic query service ## NAME Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service ## VERSION version 1.70 ## SYNOPSIS 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. ## ATTRIBUTES ### 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 ``` ## METHODS ### 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 ``` ## INTERNAL METHODS ### \_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) ``` ## BUGS AND LIMITATIONS \* 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. ## SEE ALSO - • 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* ## 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 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/ ``` ## LEGAL ### Authors Allen Day \ ### 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