Pubmed(3pm)

NAME
RefDB::Pubmed - Perl extension for converting Pubmed bibliographic data to RIS

SYNOPSIS
  use RefDB::Pubmed;
  my $infile = "-";

  my $pm = new RefDB::Pubmed;

  $pm->in($infile);

  while ((my $set = $pm->next_pubmed_set())) {
      $set->parse_pmset();
      $set->convert_pmset();
      $set->dump_pmset_as_ris();
  }

DESCRIPTION
RefDB::Pubmed allows one to convert Pubmed/Medline bibliographic data to the RIS format understood by RefDB and most other bibliographic software. Data can be provided as a string or they can be read from a file/stream.

FEEDBACK
Send bug reports, questions, and comments to the refdb-users mailing list at:

refdb-users@lists.sourceforge.net

For list information and archives, please visit:

http://lists.sourceforge.net/lists/listinfo/refdb-users

AUTHOR
Markus Hoenicka, markus@mhoenicka.de

SEE ALSO
This module is part of the RefDB package, a reference manager and bibliography tool for markup languages. Please visit http://refdb.sourceforge.net for further information.

PMSet package
This helper package defines methods to deal with a Pubmed dataset

  new
Title : new

Usage : $set = new PMset();

Function: Creates a new PMset object

  parse_pmset
Title : parse_pmset

Usage : $set->parse_pmset();

Function: parses the raw tagged Pubmed data

  convert_pmset
Title : convert_pmset()

Usage : $set->convert_pmset()

Function: Converts the parsed data to RIS data

  dump_pmset_as_ris
Title : dump_pmset_as_ris

Usage : $set->dump_pmset_as_ris()

Function: Dumps the data as a valid RIS set

  dump_pmset_as_pm
Title : dump_pmset_as_pm

Usage : $set->dump_pmset_as_pm()

Function: dumps the parsed data as a Pubmed set. The result differs from the input in that each tag with its associated data is always in a single line whereas the input data may contain continued lines w/o a tag. You can use this function to normalize the Pubmed tagged data.

  _convert_tag
Title : _convert_tag

Usage : $self->_convert_tag($key, $string);

Function: Converts a Pubmed tag line to RIS and adds the result to a list

Argument: string containing the tag, something like 'KW - '
          string containing the data associated with the tag

  _split_mesh
Title : _split_mesh

Usage : $self->_split_mesh($string);

Function: splits a Pubmed MH line into one or more RIS KW lines

Argument: string containing the data associated with the MH tag

  set_print_unmapped
Title : set_print_unmapped

Usage : $pm->set_print_unmapped(1)

Function: switch on or off printing of unmapped Pubmed tags

Argument: 0 (zero) to switch off or non-zero to switch on

  set_converter
Title : set_converter

Usage : $pm->set_converter("from_enc", "to_enc")

Function: creates the iconv character encoding converter to be used

Arguments: from_enc, to_enc: the encoding of the source data and of the output data, respectively

  add_raw_line
Title : add_raw_line

Usage : $set->add_raw_line($_)

Function: adds a raw Pubmed line to the internal list

Argument: string containing a full Pubmed line

Pubmed package
This package defines functions to deal with collections of Pubmed datasets

  new
Title : new

Usage : $pm = new RefDB::Pubmed();

Function: Creates a new Pubmed object

  in
Title : in

Usage : $pm->in($filename)

Function: Opens a file or input stream for reading

Returns : A filehandle or undef if the stream could not be opened

Argument: The path of a file or the name of an input stream

  string
Title : string

Usage : $pm->string($string)

Function: Accepts an input string for parsing

Returns : 1 if Pubmed data, 0 if not Argument: A string containing input data

  next_pubmed_set
Title : next_pubmed_set

Usage : $pm->next_pubmed_set()

Function: Reads the next Pubmed dataset

Returns : A PMset containing the raw Pubmed tagged data, or undef if no data available

  set_print_unmapped
Title : set_print_unmapped

Usage : $pm->set_print_unmapped(1)

Function: switch on or off printing of unmapped Pubmed tags

Argument: 0 (zero) to switch off or non-zero to switch on

  set_encodings
Title : set_encodings

Usage : $pm->set_encodings("from_enc", "to_enc")

Function: set encodings of input and output data

Argument: from_enc, to_enc according to "man iconv_open"