--- name: "Bio::DB::BiblioI" 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::BiblioI" --- # Bio::DB::BiblioI(3pm) an interface to a Bibliographic Query Service ## NAME Bio::DB::BiblioI - an interface to a Bibliographic Query Service ## VERSION version 1.70 ## SYNOPSIS This is an interface module - you do not instantiate it. Use *Bio::Biblio* module: ``` use Bio::Biblio; my $biblio = Bio::Biblio->new(@args); ``` ## DESCRIPTION This interface describes the methods for accessing a bibliographic repository, for querying it and for retrieving citations from it. The retrieved citations are in XML format and can be converted to perl objects using *Bio::Biblio::IO*. The interface complies (with some simplifications) with the specification described in the **OpenBQS** project. Its home page is at http://www.ebi.ac.uk/~senger/openbqs/. ## ATTRIBUTES ### has\_next ``` Usage : my $is = $biblio->has_next; Returns : 1 or undef Args : none ``` It returns 1 if there is a next citation available in the underlying query collection. Otherwise it returns undef. It throws an exception if this object does not represent any query result - see explanation in method *reset\_retrieval* elsewhere in this document. ### exists ``` Usage : my $exists = $biblio->exists; Returns : 1 or undef Args : none ``` It returns 1 if the underlying query collection represented by the `$biblio` object still exists (on the server side). If you have a collection ID (e.g. stored or printed in a previous session) but you do not have anymore a `"Bio::Biblio"` object representing it this is how you can check the collection existence: ``` use Bio::Biblio; print Bio::Biblio->new(-collection_id => '1014324148861')->exists; ``` It throws an exception if this object does not represent any query result - see explanation in method *reset\_retrieval* elsewhere in this document. ### contains ``` Usage : my $yes = $biblio->contains ($vocabulary_name, $value); Returns : 1 or undef Args : $vocabulary_name defines a vocabulary where to look, and a $value defines what to look for ``` It returns 1 if the given controlled vocabulary contains the given value. For example, when you know, that a vocabulary `"MEDLINE/JournalArticle/properties"` contains value `"COUNTRY"` you can use it in the *find* method: ``` $biblio->find ('United States', 'COUNTRY'); ``` ## METHODS ### get\_collection\_id ``` Usage : my $collection_id = $biblio->get_collection_id; Returns : string identifying a query collection represented by the $biblio object Args : none ``` Every query collection is uniquely identify-able by its collection ID. The returned value can be used to populate another `$biblio` object and then to access that collection. ### get\_count ``` Usage : my $count = $biblio->get_count; Returns : integer Args : none, or a string identifying a query collection ``` It returns a number of citations in the query collection represented by the calling `$biblio` object, or in the collection whose ID is given as an argument. ### find ``` Usage : my $new_biblio = $biblio->find ($keywords, $attrs); my $new_biblio = $biblio->find ('perl', 'abstract'); my $new_biblio = $biblio->find ( [ 'perl', 'Java' ] ); Returns : new Bio::Biblio object representing a new query collection Args : $keywords - what to look for (mandatory) - a comma-delimited list of keywords, or - an array reference with keywords as elements $attrs - where to look in (optional) - a comma-delimited list of attribute names, or - an array reference with attribute names as elements ``` This is the main query method. It looks for the `$keywords` in a default set of attributes, or - if `$attrs` given - only in the given attributes. Because it returns a new Bio::Biblio object which can be again queried it is possible to chain together several invocations: ``` $biblio->find ('Brazma')->find ('Robinson')->get_collection_id; ``` ### reset\_retrieval ``` Usage : $biblio->reset_retrieval; Returns : nothing Args : none ``` It sets an iterator stored in the `$biblio` object back to its beginning. After this, the retrieval methods *has\_next*, *get\_next* and *get\_more* start to iterate the underlying query collection again from its start. It throws an exception if this object does not represent any query result (e.i. it does not contain a collection ID). Note that a collection ID is created automatically when this object was returned by a *find* method, or it can be assigned in a constructor using argument *-collection\_id*. ### get\_next ``` Usage : my $citation = $biblio->get_next; Returns : a citation in an XML format Args : none ``` It returns the next available citation from the underlying query collection. It throws an exception if there are no more citations. In order to avoid this, use it together with the *has\_next* method: ``` my $result = $biblio->find ('brazma', 'authors'); while ( $result->has_next ) { print $result->get_next; } ``` It also throws an exception if this object does not represent any query result - see explanation in the *reset\_retrieval* elsewhere in this document. ### get\_more ``` Usage : my $r_citations = $biblio->get_more (5); Returns : an array reference - each element has a citation in an XML format Args : an integer 'how_many' citations to return; default is 1 - but it is assigned with warning ``` It returns the next *how\_many* available citations from the underlying query collection. It does not throw any exception if 'how\_many' is more than currently available - it simply returns less. However, it throws an exception if used again without calling first *reset\_retrieval*. It also throws an exception if this object does not represent any query result - see explanation in method *reset\_retrieval* elsewhere in this document. ### get\_all\_ids ``` Usage : my $r_ids = $biblio->get_all_ids; Returns : an array reference - each element has a citation identifier Args : none ``` The identifiers of all citations in the underlying query collection are returned. A usual pattern is to use them then in the *get\_by\_id* method: ``` my $biblio = $repository->find ('brazma')->find ('robinson'); foreach my $id ( @{ $biblio->get_all_ids } ) { print $biblio->get_by_id ($id); } ``` It throws an exception if this object does not represent any query result - see explanation in method *reset\_retrieval* elsewhere in this document. ### get\_by\_id ``` Usage : my $citation = $biblio->get_by_id ('12368254'); Returns : a citation in an XML format Args : a citation identifier (PMID for Medline) ``` It returns a citation - disregarding if the citation is or is not in the underlying query collection (of course, it must be in the repository). ### get\_all ``` Usage : my $all = $biblio->get_all; Returns : a (big) string with all citations in an XML format Args : none ``` It returns an XML valid string (which means that individual citations are also surrounded by a "set" XML tag) representing all citations from the underlying query collection. Note that some servers may limit the number of citations which can be returned by this method. In such case you need either to refine further your query collection (using *find* method) or to retrieve results by iteration (methods *has\_next*, *get\_next*, *get\_more*). It throws an exception if this object does not represent any query result - see explanation in method *reset\_retrieval* elsewhere in this document. ### destroy ``` Usage : $biblio->destroy; Returns : nothing Args : none ``` It sends a message to the remote server to forget (or free, or destroy - whatever server choose to do) the query collection represented by this object. It throws an exception if this object does not represent any query collection. ### get\_vocabulary\_names ``` Usage : print join ("\n", @{ $biblio->get_vocabulary_names }); Returns : an array reference - each element has a name of a controlled vocabulary Args : none ``` The controlled vocabularies allow to introspect bibliographic repositories and to find what citation resource types (such as journal and book articles, patents or technical reports) are provided by the repository, what attributes they have, eventually what attribute values are allowed. This method returns names of all available controlled vocabularies. The names can than be used in other methods dealing with vocabularies: *contains*, *get\_entry\_description*, *get\_all\_values*, and *get\_all\_entries*. ### get\_entry\_description ``` Usage : $biblio->get_entry_description ($voc_name, $value); Returns : a string with a desciption Args : $voc_name defines a vocabulary where to look, and a $value defines whose description to return ``` Each vocabulary entry has its value (mandatory attribute), and can have a description (optional attribute). The description may be just a human readable explanation of an attribute, or it can have more exact meaning. For example, the server implementation of the bibliographic query service provided by the EBI puts into attribute descriptions words *queryable* and/or *retrievable* to distinguish the role of the attributes. It throws an exception if either vocabulary or value do not exist. ### get\_all\_values ``` Usage : $biblio->get_all_values ($vocabulary_name); Returns : an array reference - each element has a value (scalar) from the given controlled vocabulary Args : $vocabulary_name defines a vocabulary whose values are being returned ``` It returns all values of the given vocabulary. It throws an exception if the vocabulary does not exist. ### get\_all\_entries ``` Usage : $biblio->get_all_entries ($vocabulary_name); Returns : a hash reference - keys are vocabulary values and values are their descriptions Args : $vocabulary_name defines a vocabulary whose entries are being returned ``` It returns pairs of values and their descriptions of the whole vocabulary. It throws an exception if the vocabulary does not exist. This is one way how to get it and print it: ``` my $name = 'MEDLINE2005/JournalArticle/properties'; use Data::Dumper; print Data::Dumper->Dump ( [$biblio->get_all_entries ($name)], ['All entries']); ``` ## 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 Martin Senger \ ### Copyright and License This software is Copyright (c) by 2002 European Bioinformatics Institute and released under the license of the same terms as the perl 5 programming language system itself