Reference

bp_biblio(1p)

bioperl client for accessing and querying a bibliographic repository

NAME

bp_biblio - bioperl client for accessing and querying a bibliographic repository

VERSION

version 1.70

SYNOPSIS

Usage:

  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>]

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 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.

OPTIONS

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)

EXAMPLES

  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

ENVIRONMENT VARIABLES

  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://128.243.220.41:3128
  bp_biblio -c

HISTORY

Written February 2002 Updated July 2005

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected]

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 <[email protected]>

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

History