function chado_get_organism_scientific_name

3.x tripal_chado.organism.api.inc chado_get_organism_scientific_name($organism)

Returns the full scientific name of an organism.

Parameters

$organism: An organism object.

Return value

The full scientific name of the organism.

Related topics

Chado Organism
Provides API functions specificially for managing organism records in Chado.
5 calls to chado_get_organism_scientific_name()
chado_autocomplete_organism in tripal_chado/api/modules/tripal_chado.organism.api.inc
This function is intended to be used in autocomplete forms for searching for organisms that begin with the provided string.
TaxonomyImporter::findOrganism in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc
Checks the Chado database to see if the organism already exists.
TaxonomyImporter::rebuildTree in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc
Iterates through all existing organisms and rebuilds the taxonomy tree.
TaxonomyImporter::updateExisting in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc
Imports details from NCBI Taxonomy for organisms that alrady exist.
tripal_get_organism_scientific_name in tripal_chado/api/modules/tripal_chado.module.DEPRECATED.api.inc
Returns the full scientific name of an organism.

File

tripal_chado/api/modules/tripal_chado.organism.api.inc, line 145
Provides API functions specificially for managing feature records in Chado.

Code

function chado_get_organism_scientific_name($organism) {
  $name = $organism->genus . ' ' . $organism->species;

  // For Chado v1.3 we have a type_id and infraspecific name.
  if (property_exists($organism, 'type_id')) {
    $rank = '';
    // For organism objects crated using chado_generate_var.
    if (is_object($organism->type_id)) {
      if ($organism->type_id) {
        $rank = $organism->type_id->name;
      }
    }
    else {
      $rank_term = chado_get_cvterm(array('cvterm_id' => $organism->type_id));
      if ($rank_term) {
        $rank = $rank_term->name;
      }
    }

    if ($rank) {
      $rank = chado_abbreviate_infraspecific_rank($rank);
      $name .= ' ' . $rank . ' ' . $organism->infraspecific_name;
    }
    else if ($organism->infraspecific_name) {
      $name .= ' ' . $organism->infraspecific_name;
    }
  }
  return $name;
}