Adds a cvterm relationship

@object_is_relationship Set to 1 if this term is a relationship term @default_db The name of the default database.

Parameters

$cvterm: A database object for the cvterm

$rel: The relationship name

$objname: The relationship term name

$defaultcv: A database object containing a record from the cv table for the default controlled vocabulary

Related topics

File

tripal_cv/includes/tripal_cv.obo_loader.inc, line 947

Functions to aid in loading ontologies into the chado cv module

Code

function tripal_cv_obo_add_relationship($cvterm, $defaultcv, $rel, 
$objname, $object_is_relationship = 0, $default_db = 'OBO_REL') {

  // make sure the relationship cvterm exists
  $term = array(
    'name' => $rel,
    'id' => "$default_db:$rel",
    'definition' => '',
    'is_obsolete' => 0,
    'cv_name' => $defaultcv,
    'is_relationship' => TRUE,
    'db_name' => $default_db
  );
  $relcvterm = tripal_insert_cvterm($term, array('update_existing' => FALSE));

  if (!$relcvterm) {
    tripal_cv_obo_quiterror("Cannot find the relationship term in the current ontology: $rel\n");
  }

  // get the object term
  $oterm = tripal_cv_obo_get_term($objname);
  if (!$oterm) {
    tripal_cv_obo_quiterror("Could not find object term $objname\n");
  }

  $objterm = array();
  $objterm['id'] = $oterm['id'][0];
  $objterm['name'] = $oterm['name'][0];
  if (array_key_exists('def', $oterm)) {
    $objterm['definition'] = $oterm['def'][0];
  }
  if (array_key_exists('subset', $oterm)) {
    $objterm['subset'] = $oterm['subset'][0];
  }
  if (array_key_exists('namespace', $oterm)) {
    $objterm['namespace'] = $oterm['namespace'][0];
  }
  if (array_key_exists('is_obsolete', $oterm)) {
    $objterm['is_obsolete'] = $oterm['is_obsolete'][0];
  }

  $objterm['cv_name'] = $defaultcv;
  $objterm['is_relationship'] = $object_is_relationship;
  $objterm['db_name'] = $default_db;

  $objcvterm = tripal_insert_cvterm($objterm, array('update_existing' => TRUE));
  if (!$objcvterm) {
    tripal_cv_obo_quiterror("Cannot add cvterm " . $oterm['name'][0]);
  }

  // check to see if the cvterm_relationship already exists, if not add it
  $values = array(
    'type_id' => $relcvterm->cvterm_id,
    'subject_id' => $cvterm->cvterm_id,
    'object_id' => $objcvterm->cvterm_id
  );
  $result = chado_select_record('cvterm_relationship', array('*'), $values);
  if (count($result) == 0) {
    $options = array('return_record' => FALSE);
    $success = chado_insert_record('cvterm_relationship', $values, $options);
    if (!$success) {
      tripal_cv_obo_quiterror("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
    }
  }

  return TRUE;
}