Adds controlled vocabulary terms needed by this module.

Related topics

File

tripal_phylogeny/tripal_phylogeny.install, line 130

Installation of the phylotree module

Code

function tripal_phylogeny_add_cvterms() {

  tripal_insert_cv(
  'tripal_phylogeny', 
  'Terms used by the Tripal phylotree module for phylogenetic and taxonomic trees.'
  );

  // Add the terms used to identify nodes in the tree.
  tripal_insert_cvterm(
  array(
    'name' => 'phylo_leaf',
    'definition' => 'A leaf node in a phylogenetic tree.',
    'cv_name' => 'tripal_phylogeny',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  // Add the terms used to identify nodes in the tree.
  tripal_insert_cvterm(
  array(
    'name' => 'phylo_root',
    'definition' => 'The root node of a phylogenetic tree.',
    'cv_name' => 'tripal_phylogeny',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  // Add the terms used to identify nodes in the tree.
  tripal_insert_cvterm(
  array(
    'name' => 'phylo_interior',
    'definition' => 'An interior node in a phylogenetic tree.',
    'cv_name' => 'tripal_phylogeny',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  // Add the terms used to identify nodes in the tree.
  tripal_insert_cvterm(
  array(
    'name' => 'taxonomy',
    'definition' => 'A term used to indicate if a phylotree is a taxonomic tree',
    'cv_name' => 'tripal_phylogeny',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );

  tripal_insert_cvterm(
  array(
    'name' => 'rank',
    'definition' => 'A taxonmic rank',
    'cv_name' => 'tripal_phylogeny',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );

  //   // ----------------------------------------------
  //   // Add the terms for importing NCBI taxonomy data
  //   $values = array(
  //     'name' => 'taxonomy',
  //     'description' => 'The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.',
  //     'url' => 'http://www.ncbi.nlm.nih.gov/taxonomy',
  //     'urlprefix' => 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=',
  //   );
  //   tripal_insert_db($values);
  //   tripal_insert_cv('taxonomy', 'A taxonomy for NCBI taxonomy ranks');

  //   $terms = array('rank', 'taxid', 'class', 'cohort', 'family', 'forma', 'genus', 'infraclass',
  //     'infraorder', 'kingdom', 'no rank', 'order', 'parvorder', 'phylum',
  //     'species', 'species group', 'species subgroup', 'subclass', 'subcohort',
  //     'subfamily', 'subgenus', 'subkingdom', 'suborder', 'subphylum',
  //     'subspecies', 'subtribe', 'superclass', 'superfamily', 'superkingdom',
  //     'superorder', 'superphylum', 'tribe', 'varietas');
  //   $options = array('update_existing' => TRUE);
  //   foreach ($terms as $term) {
  //     $value = array(
  //       'name' => $term,
  //       'definition' => '',
  //       'cv_name' => 'taxonomy',
  //       'is_relationship' => 0,
  //       'db_name' => 'taxonomy'
  //     );
  //     tripal_insert_cvterm($value, $options);
  //   }

  $terms = array(
    'lineage',
    'genetic_code',
    'genetic_code_name',
    'mitochondrial_genetic_code',
    'mitochondrial_genetic_code_name',
    'division',
    'genbank_common_name',
    'synonym',
    'other_name',
    'equivalent_name',
    'anamorph'
  );
  $options = array('update_existing' => TRUE);
  foreach ($terms as $term) {
    $value = array(
      'name' => $term,
      'definition' => '',
      'cv_name' => 'organism_property',
      'is_relationship' => 0,
      'db_name' => 'tripal'
    );
    tripal_insert_cvterm($value, $options);
  }
}