tripal/legacy/tripal_pub/theme/templates/tripal_pub_references.tpl.php

<?php
$pub = $variables['node']->pub;

// expand the pub object to include the records from the pub_dbxref table
$options = ['return_array' => 1];
$pub = chado_expand_var($pub, 'table', 'pub_dbxref', $options);
$pub_dbxrefs = $pub->pub_dbxref;

$references = [];
if (count($pub_dbxrefs) > 0) {
  foreach ($pub_dbxrefs as $pub_dbxref) {
    $references[] = $pub_dbxref->dbxref_id;
  }
}

if (count($references) > 0) { ?>
    <div class="tripal_pub-data-block-desc tripal-data-block-desc">This
        publication is also available in the following databases:
    </div><?php

  // the $headers array is an array of fields to use as the colum headers.
  // additional documentation can be found here
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $headers = ['Database', 'Accession'];

  // the $rows array contains an array of rows where each row is an array
  // of values for each column of the table in that row.  Additional documentation
  // can be found here:
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $rows = [];

  foreach ($references as $dbxref) {
    $database = $dbxref->db_id->name . ': ' . $dbxref->db_id->description;
    if ($dbxref->db_id->url) {
      $database = l($dbxref->db_id->name, $dbxref->db_id->url, ['attributes' => ['target' => '_blank']]) . ': ' . $dbxref->db_id->description;
    }
    $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
    if ($dbxref->db_id->urlprefix) {
      $accession = l($accession, tripal_get_dbxref_url($dbxref), ['attributes' => ['target' => '_blank']]);
    }
    if (property_exists($dbxref, 'is_primary')) {
      $accession .= " <i>(primary cross-reference)</i>";
    }

    $rows[] = [
      $database,
      $accession,
    ];
  }
  // the $table array contains the headers and rows array as well as other
  // options for controlling the display of the table.  Additional
  // documentation can be found here:
  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
  $table = [
    'header' => $headers,
    'rows' => $rows,
    'attributes' => [
      'id' => 'tripal_pub-table-references',
      'class' => 'tripal-data-table',
    ],
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => [],
    'empty' => '',
  ];

  // once we have our table array structure defined, we call Drupal's theme_table()
  // function to generate the table.
  print theme_table($table);
}