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data/controlled_vocab/AL_Medium.xml  view on Meta::CPAN

<?xml version="1.0" standalone="yes"?>
<controlled_vocabulary db_table="ArrayLayout" db_column="medium" cv_table="AL_Medium">
  <comment type="definition">Referred to in the Array Layout Spots table and used to describe the medium on which the the probe is deposited	
</comment>
<term name="glass_slide"
        description="user sequence features are spotted on a rigid silicon-based support medium"/>
<term name="nylon_membrane"
        description="user sequence features are spotted on a nylon-coated flexible medium"/>
<term name="nitrocellulose"
        description="user sequence features are spotted on a nitrocellulose medium"/>
<term name="gel_sieve"
        description="target sequence features are separated through a size sieving procedure"/>
<term name="mag_bead"
        description="target sequence features are separated by magnetic bead attachment"/>
<term name="sequence_instance"
        description="target sequence features are  sequenced fragments whose frequency of occurrence is recorded"/>

scripts/db2xml.pl.in  view on Meta::CPAN

    $es_node->setAttribute('citation_ids',do_citation($es_db->cit_obj));
  } else {
    # not all experiments have citations, so this is not a warning
  }

  # get the owner's contact information
  my $owner_id = do_contact($es_db->provider_con_obj);
  $es_node->setAttribute('owner_contact_id', $owner_id);

  # do the group
  my $gid = do_group($es_db->gs_obj);
  $es_node->setAttribute('group_id', $gid);

  # add an experiment_factors_list to the header
  do_factor_list($es_header_node,$es_db);
  my %column2name = %{Bio::Genex::ExperimentSet->column2name()};
  foreach my $column (keys %column2name) {
    # because we are under the restrictions of 'use strict'
    # we need this to get away with the dynamic cuteness of 
    # $obj->$func_name()
    no strict 'subs';
    

scripts/db2xml.pl.in  view on Meta::CPAN

      # don't enter it if it already exists
      my $id = do_scanner($hardware_db);
      $am_node->setAttribute('scanner_hw_id',$id);
    }

    # get the owner's contact information
    my $owner_id = do_contact($am_db->us_obj->con_obj);
    $am_node->setAttribute('owner_contact_id', $owner_id);

    # do the group
    my $gid = do_group($am_db->gs_obj);
    $am_node->setAttribute('group_id', $gid);

    # handle the ArrayMeasurement columns general to all
    # measurements in the hybridization group
    foreach my $column (@ARRAY_COLUMNS) {
      if ($column =~ /^(?:hybridization_stringency|
			instance_code|
		       )
	              $/x) {
	$am_node->setAttribute($ARRAY2GENEXML{$column},$am_db->$column());
      } else {