Bio::D...:eutils(3pm)

✨ NAME ✨

Bio::DB::Biblio::eutils — bestie, this is your all-access pass to PubMed's bibliographic query service 💖 (the manual page for it is Bio::D...:eutils(3pm), that's the one you're reading rn).

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🎀 VERSION 🎀

version 1.70 — no cap, that's the number.

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🦋 SYNOPSIS 🦋

Okay so listen. Do NOT use this object directly, fr fr. The vibe is: you go through the Bio::Biblio module and let it do the work for you 🙈

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. Go read that too, bestie, it's giving main character energy 👑

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🌸 ATTRIBUTES 🌸

💜 db

• Title : db
• Usage : $obj->db($newval)
• Function : tells you which 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

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💅 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

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🧚 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. iykyk 💅

🌈 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)

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😭 BUGS AND LIMITATIONS 😭

okay bestie, this is the "we're working on it" section, no drama just facts 💀

• 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.

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🌈 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

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💌 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/

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👑 LEGAL 👑

💜 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

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and that's the whole page bestie!! ✨ this little number was churned out by perl v5.36.0 on 2023-02-14, and the manual it lives in is Bio::D...:eutils(3pm) — go forth and query, you've got this 💖🦋💅