- ENVIRONMENT VARIABLES
bp_biblio - bioperl client for accessing and querying a bibliographic repository
bp_biblio [vh] bp_biblio [bcFgOpq] [-l <URL>] bp_biblio [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID> bp_biblio [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \ [-attrs <attrs>]... bp_biblio [Vq] [-l <URL>] bp_biblio [FOq] [-f <filename>]
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 XML MEDLINE citations into a simple hash table and into full Perl objects.
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.
What service to contact:
-l <URL> ... a location where a Bibliographic Query service is provided as a WebService (default: http://www.ebi.ac.uk/openbqs/services/MedlineSRS)
What query collection to use:
Some options do not need to specify a collection, some do.
-i <collection_id> ... the collection ID can be obtained in a previous invocation by specifying argument '-p' (print ID) -find <keywords> [-attrs <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 <keywords> and <attrs> may be comma-delimited multi-values; note that '-find' must be separated from the rest of options by '-'; 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
What to do (with the query collection):
-g <id> ... get citation <id> -c ... get count (a number of citations) -p ... print collection ID (which may be used in the next invocation as an '-i' argument); it implies also '-k' -b ... print citations in a non-XML format (TBD)
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:
-d ... get all citation IDs -n ... get next citation -m [<how_many>] ... get 'how_many' more -r ... reset iteration to the first citation in the collection (now you can use '-n' or '-m' again) -a ... get all citations - as an array -s ... as '-a' 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 '-i')
Options specifying output format of the results:
-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 <filename> ... an XML file to be read and converted
Options dealing with controlled vocabularies:
-Vn ... get all vocabulary names -Vv::<name> ... get all values from vocabulary <name> -Va::<name> ... get everything from vocabulary <name> -Vd::<name>::<value> ... get description of <value> from vocabulary <name> -Ve::<name>::<value> ... return 1 if <value> exists in vocabulary <name>
And the remaining options:
-h ... get help -v ... get version -q ... be quiet (less verbose)
bp_biblio - -find Java -attrs abstract -find perl
Several separate invocations sharing the same query collection:
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 <MedlineCitation Status="Completed"> ... </MedlineCitation> 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
Access to controlled vocabularies:
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 ...
Converting local XML MEDLINE file:
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
HTTPPROXY = <HTTP proxy server>
Use this if you use this script on a machine which needs to access remote HTTP targets via a proxy server. For example:
export HTTPPROXY=http://220.127.116.11:3128 bp_biblio -c
Written February 2002 Updated July 2005
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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list: firstname.lastname@example.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:
Martin Senger <email@example.com>
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