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bp_biblio.pl

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 1 (Commandes utilisateur)

NAME

biblio.PLS - bioperl client for accessing and querying a bibliographic repository.

SYNOPSIS

Usage:
   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>]
 
 

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

   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
   MEDLINE2005/10693778
   MEDLINE2005/10977099
   MEDLINE2005/11726920
   MEDLINE2005/12225585
   MEDLINE2005/12227734
   biblio.PLS -i `cat b.tmp` -g 10693778
   <MedlineCitation Status="Completed">
    ...
   </MedlineCitation>
 
   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
   MEDLINE2005/JournalArticle/properties
   MEDLINENEW/resource_types
   MEDLINE2005/resource_types
   MEDLINE2005/Person/properties
   MEDLINE2005/*/publication_type
   MEDLINENEW/JournalArticle/properties
   repository_subsets
   MEDLINE2005/*/citation_subset
 
   biblio.PLS -Vv::MEDLINE2005/JournalArticle/properties
   AllText
   ID
   PMID
   ISSN
   ...
 
 

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
 
 

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
   biblio.PLS -c
 
 

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
 
 

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Martin Senger

Email martin.senger@gmail.com

HISTORY

Written February 2002 Updated July 2005
Si, grandi par la diérèse,
Le loriot a trois syllabes,
Avec l'alliante synérèse,
Le loriot n'a que deux syllabes.
-- Kaeser, Pascal