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"