Perl Item XML generation modules

Introduction

In the intermine/perl directory we provide a Perl library for creating files in InterMine "Item XML" format. Files in this format can be loaded into an InterMine database by creating a "source".

The Perl code will need to be installed before use. See InterMinePerl for details.

See also: ItemsAPIJava

Usage

Most code using these modules will follow this pattern:

1. make a model:

    my $model = InterMine::Model->new(file => $model_file);
   

2. make a new InterMine item XML document:

    my $document = InterMine::Item::Document->new(
      model  => $model,
      output => $out_file,
    );
   

3. make an item:

    my $gene = $factory->make_item("Gene");
   

4. set some attributes

    $gene->set(identifier => "CG10811");
   

   or references:

    my $org = $factory->make_item("Organism");
    $org->set(taxonId => 7227);
    $gene->set(organism => $org);
   

   or collections:

    $gene->set(transcripts => [$transcript1, $transcript2]);
   

It is also possible to combine creation and attribute setting in one command:

my $gene = $factory->make_item(
    'Gene',
    identifier  => 'CG10811',
    organism    => $org,
    transcripts => [$transcript1, $transcript2],
);

5. repeat 4 as necessary
6. Call $document->write to write the items to the output.

FlyMine example

Example using the FlyMine model:

  use InterMine::Model;
  use InterMine::Item::Document;

  my $model_file = $ARGV[0] or die;

  my $model   = InterMine::Model->new(file => $model_file);
  my $document = InterMine::Item::Document->new(model => $model);

  my $organism = $document->add_item(
      'Organism',
      taxonId => 7227,
  );

  my $pub1 = $document->add_item(
      'Publication',
      pubMedId => 11700288,
  );
  my $pub2 = $document->add_item(
      'Publication',
      pubMedId => 16496002,
  );

  my $gene = $document->add_item(
      'Gene',
      identifier   => "CG10811",
      organism     => $organism,
      publications => [$pub1, $pub2]
  );

  # write as InterMine Items XML
  $document->write();

Output:

  <items>
     <item id="0_4" class="" implements="Gene">
        <attribute name="identifier" value="CG10811" />
        <collection name="publications">
           <reference ref_id="0_2" />
           <reference ref_id="0_3" />
        </collection>
        <reference name="organism" ref_id="0_1" />
     </item>
     <item id="0_1" class="" implements="Organism">
        <attribute name="taxonId" value="7227" />
     </item>
     <item id="0_2" class="" implements="Publication">
        <attribute name="pubMedId" value="11700288" />
     </item>
     <item id="0_3" class="" implements="Publication">
        <attribute name="pubMedId" value="16496002" />
     </item>
  </items>

Longer example

In bio/scripts there is a longer example: intermine_items_example.pl

The script has three arguments:

• a string describing a DataSet
• a taxon id
• the path to a genomic model file

If you install XML::Writer, the script should run as is from the bio/scripts/ directory

Example command line:

 ./intermine_items_example.pl "FlyMine" 5833 ../../flymine/dbmodel/build/model/genomic_model.xml