Add cv terms needed by the featuremap module

Related topics

File

legacy/tripal_featuremap/tripal_featuremap.install, line 139

Handles installation of the feature map module

Code

function tripal_featuremap_add_cvterms() {

  // add cvterms for the map unit types
  tripal_insert_cvterm(
  array(
    'name' => 'cM',
    'definition' => 'Centimorgan units',
    'cv_name' => 'featuremap_units',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'bp',
    'definition' => 'Base pairs units',
    'cv_name' => 'featuremap_units',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'bin_unit',
    'definition' => 'The bin unit',
    'cv_name' => 'featuremap_units',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'marker_order',
    'definition' => 'Units simply to define marker order.',
    'cv_name' => 'featuremap_units',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'undefined',
    'definition' => 'A catch-all for an undefined unit type',
    'cv_name' => 'featuremap_units',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );

  // featurepos properties
  tripal_insert_cvterm(
  array(
    'name' => 'start',
    'definition' => 'The start coordinate for a map feature.',
    'cv_name' => 'featurepos_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'stop',
    'definition' => 'The end coordinate for a map feature',
    'cv_name' => 'featurepos_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );

  // add cvterms for map properties
  tripal_insert_cvterm(
  array(
    'name' => 'Map Dbxref',
    'definition' => 'A unique identifer for the map in a remote database.  The '
      . 'format is a database abbreviation and a unique accession separated '
      . 'by a colon.  (e.g. Gramene:tsh1996a)',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Map Type',
    'definition' => 'The type of Map (e.g. QTL, Physical, etc.)',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Genome Group',
    'definition' => '',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'URL',
    'definition' => 'A univeral resource locator (URL) reference where the '
      . 'publication can be found.  For maps found online, this would be '
      . 'the web address for the map.',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Population Type',
    'definition' => 'A brief description of the population type used to generate '
      . 'the map (e.g. RIL, F2, BC1, etc).',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Population Size',
    'definition' => 'The size of the population used to construct the map.',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Methods',
    'definition' => 'A brief description of the methods used to construct the map.',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );
  tripal_insert_cvterm(
  array(
    'name' => 'Software',
    'definition' => 'The software used to construct the map.',
    'cv_name' => 'featuremap_property',
    'is_relationship' => 0,
    'db_name' => 'tripal'
  ), 
  array('update_existing' => TRUE)
  );

}