.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.43) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "BP_BIBLIO 1p" .TH BP_BIBLIO 1p "2023-02-14" "perl v5.36.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" bp_biblio \- bioperl client for accessing and querying a bibliographic repository .SH "VERSION" .IX Header "VERSION" version 1.70 .SH "SYNOPSIS" .IX Header "SYNOPSIS" Usage: .PP .Vb 7 \& bp_biblio [vh] \& bp_biblio [bcFgOpq] [\-l ] \& bp_biblio [abcdDeFknmOpqrs] [\-l ] \-i \& bp_biblio [abcdDeFknmOpqrs] [\-l ] \- \-find \e \& [\-attrs ]... \& bp_biblio [Vq] [\-l ] \& bp_biblio [FOq] [\-f ] .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" A client showing how to use Bio::Biblio module, a module for accessing and querying a bibliographic repository. It also shows how to use modules Bio::Biblio::IO::medlinexml Bio::Biblio::IO::medline2ref which converts \s-1XML MEDLINE\s0 citations into a simple hash table and into full Perl objects. .PP It has many options in order to cover as many methods as possible. Because of that, it can be also used as a fully functional command-line client for querying repository and retrieving citations from it. .SH "OPTIONS" .IX Header "OPTIONS" .SS "What service to contact:" .IX Subsection "What service to contact:" .Vb 3 \& \-l ... a location where a Bibliographic Query service is \& provided as a WebService \& (default: http://www.ebi.ac.uk/openbqs/services/MedlineSRS) .Ve .SS "What query collection to use:" .IX Subsection "What query collection to use:" Some options do not need to specify a collection, some do. .PP .Vb 8 \& \-i ... the collection ID can be obtained in a \& previous invocation by specifying argument \& \*(Aq\-p\*(Aq (print ID) \& \-find [\-attrs ] \& ... create a collection from citations \& containing given keywords \- either in all \& default attributes, or only in the given \& attributes; \& \& it is possible to repeat it, for example: \& \-find brazma \-attrs authors \-find \-study \& (the repetitions refine previous results) \& both and may be \& comma\-delimited multi\-values; \& note that \*(Aq\-find\*(Aq must be separated from \& the rest of options by \*(Aq\-\*(Aq; \& \& note that this script is a bit stupid \& regarding quoted keywords, or keywords \& containing commans... TBD better \& \& what XML format is used for citations: \& \-Fm ... MEDLINE (default) \& \-Fp ... PubMed .Ve .SS "What to do (with the query collection):" .IX Subsection "What to do (with the query collection):" .Vb 5 \& \-g ... get citation \& \-c ... get count (a number of citations) \& \-p ... print collection ID (which may be used in the next \& invocation as an \*(Aq\-i\*(Aq argument); it implies also \*(Aq\-k\*(Aq \& \-b ... print citations in a non\-XML format (TBD) .Ve .PP Other options can be used only on a sub-collection \- which can be obtained directly by specifying '\-i' argument, or indirectly by specifying one or more queries by '\-find' arguments: .PP .Vb 10 \& \-d ... get all citation IDs \& \-n ... get next citation \& \-m [] ... get \*(Aqhow_many\*(Aq more \& \-r ... reset iteration to the first citation in the collection \& (now you can use \*(Aq\-n\*(Aq or \*(Aq\-m\*(Aq again) \& \-a ... get all citations \- as an array \& \-s ... as \*(Aq\-a\*(Aq but get it as one string \& \-e ... check if given collection exists and has more citations \& \-k ... keep resulting collection persistent (makes sense only \& when collection IDs are being printed otherwise you \& would not know how to contact the persistent collection \& next time) \& \-D ... destroy given collection (makes sense together with \*(Aq\-i\*(Aq) .Ve .PP Options specifying output format of the results: .PP .Vb 3 \& \-Ox ... output in XML format (default) \& \-Oo ... output as Biblio objects \& \-Or ... output as a raw hashtable \& \& The options above can be used also for converting an XML MEDLINE \& local file without using any SOAP connection at all; \& \& \-f ... an XML file to be read and converted .Ve .PP Options dealing with controlled vocabularies: .PP .Vb 7 \& \-Vn ... get all vocabulary names \& \-Vv:: ... get all values from vocabulary \& \-Va:: ... get everything from vocabulary \& \-Vd:::: ... get description of \& from vocabulary \& \-Ve:::: ... return 1 if exists \& in vocabulary .Ve .PP And the remaining options: .PP .Vb 3 \& \-h ... get help \& \-v ... get version \& \-q ... be quiet (less verbose) .Ve .SH "EXAMPLES" .IX Header "EXAMPLES" .Vb 1 \& bp_biblio \- \-find Java \-attrs abstract \-find perl .Ve .PP Several separate invocations sharing the same query collection: .PP .Vb 11 \& bp_biblio \-p \-q \- \-find Brazma,Robinson > b.tmp \& bp_biblio \-i \`cat b.tmp\` \-d \& MEDLINE2005/10693778 \& MEDLINE2005/10977099 \& MEDLINE2005/11726920 \& MEDLINE2005/12225585 \& MEDLINE2005/12227734 \& bp_biblio \-i \`cat b.tmp\` \-g 10693778 \& \& ... \& \& \& bp_biblio \-i \`cat b.tmp\` \-e \& Exists: 1 Has next: 1 \& \& bp_biblio \-i \`cat b.tmp\` \-D \& Destroyed OK. \& \& bp_biblio \-i \`cat b.tmp\` \-e \& Exists: 0 Has next: 0 .Ve .PP Access to controlled vocabularies: .PP .Vb 9 \& bp_biblio \-Vn \& MEDLINE2005/JournalArticle/properties \& MEDLINENEW/resource_types \& MEDLINE2005/resource_types \& MEDLINE2005/Person/properties \& MEDLINE2005/*/publication_type \& MEDLINENEW/JournalArticle/properties \& repository_subsets \& MEDLINE2005/*/citation_subset \& \& bp_biblio \-Vv::MEDLINE2005/JournalArticle/properties \& AllText \& ID \& PMID \& ISSN \& ... .Ve .PP Converting local \s-1XML MEDLINE\s0 file: .PP .Vb 3 \& bp_biblio \-g 10693778 > a_file.xml \& bp_biblio \-f a_file.xml \-Oo ... to Perl objects \& bp_biblio \-f a_file.xml \-Or ... as a raw hash .Ve .SH "ENVIRONMENT VARIABLES" .IX Header "ENVIRONMENT VARIABLES" .Vb 1 \& HTTPPROXY = .Ve .PP Use this if you use this script on a machine which needs to access remote \s-1HTTP\s0 targets via a proxy server. For example: .PP .Vb 2 \& export HTTPPROXY=http://128.243.220.41:3128 \& bp_biblio \-c .Ve .SH "HISTORY" .IX Header "HISTORY" Written February 2002 Updated July 2005 .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting bugs" .IX Subsection "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: .PP .Vb 1 \& https://redmine.open\-bio.org/projects/bioperl/ .Ve .SH "LEGAL" .IX Header "LEGAL" .SS "Authors" .IX Subsection "Authors" Martin Senger .SS "Copyright and License" .IX Subsection "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