biblio.PLS(1) bioperl client for accessing and querying a bibliographic



biblio.PLS [vh]
biblio.PLS [bcFgOpq] [-l <URL>]
biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] -i <collection-ID>
biblio.PLS [abcdDeFknmOpqrs] [-l <URL>] - -find <keywords> \
[-attrs <attrs>]...
biblio.PLS [Vq] [-l <URL>]
biblio.PLS [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

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
                          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)


  biblio.PLS - -find Java -attrs abstract -find perl

Several separate invocations sharing the same query collection:

  biblio.PLS -p -q - -find Brazma,Robinson > b.tmp
  biblio.PLS -i `cat b.tmp` -d
  biblio.PLS -i `cat b.tmp` -g 10693778
  <MedlineCitation Status="Completed">
  biblio.PLS -i `cat b.tmp` -e
  Exists: 1       Has next: 1
  biblio.PLS -i `cat b.tmp` -D
  Destroyed OK.
  biblio.PLS -i `cat b.tmp` -e
  Exists: 0       Has next: 0

Access to controlled vocabularies:

  biblio.PLS -Vn
  biblio.PLS -Vv::MEDLINE2005/JournalArticle/properties

Converting local XML MEDLINE file:

  biblio.PLS -g 10693778 > a_file.xml
  biblio.PLS -f a_file.xml -Oo   ... to Perl objects
  biblio.PLS -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=
  biblio.PLS -c


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  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug trackingi system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

AUTHOR - Martin Senger

Email [email protected]


Written February 2002 Updated July 2005