tripal/tripal_entities/tripal_entities.module

<?php
// http://www.bluespark.com/blog/drupal-entities-part-3-programming-hello-drupal-entity
/**
 * Implement hook_entity_info().
 */
function tripal_entities_entity_info() {
  $entities = array();

  $entities['cvterm'] = array(
    'label' => t('Vocabulary Term'),
    'uri callback' => 'tripal_entities_vocbulary_term_uri',
    'plural label' => t('Vocabulary Terms'),
    'entity class' => 'TrpVocabularyTerm',
    'controller class' => 'TrpVocabularyTermController',
    'fieldable' => TRUE,
    'entity keys' => array(
      'id' => 'internal_id'
    ),
    // Bundles are defined by the model types below
    'bundles' => array(),
  );

  // We want to dynamically add the bundles (or term types) to the entity.
  $values = array(
    'cv_id' => array(
      'name' => 'sequence'
    ),
    'name' => 'gene'
  );
  $cvterm = chado_generate_var('cvterm', $values);
  $bundle_id = 'trp_' . $cvterm->dbxref_id->db_id->name . '_' . $cvterm->dbxref_id->accession;
  $label = preg_replace('/_/', ' ', ucwords($cvterm->name));
  $entities['trp_vocabulary_term']['bundles'][$bundle_id] = array(
    'label' => $label,
  );
  return $entities;
}

function tripal_entities_load($pid = NULL, $reset = FALSE){
  $pids = (isset ($pid) ? array($pid) : array());
  $cvterm = trp_vocabulary_term_load_multiple($pids, $reset);
  return $cvterm ? reset ($cvterm) : FALSE;
}

function tripal_entities_load_multiple($pids = array(), $conditions = array(), $reset = FALSE){
  return entity_load('cvterm', $pids, $conditions, $reset);
}

function tripal_entities_menu() {
  $items['admin/structure/cvterm/manage'] = array(
    'title' => 'Term Admin',
    'description' => 'Manage cvterm structure',
    'page callback' => 'cvterm_info',
    'access arguments' => array('administer cvterms'),
  );
  $items['cvterm/%cvterm'] = array(
    'title callback' => 'cvterm_page_title',
    'title arguments' => array(1),
    'page callback' => 'cvterm_page_view',
    'page arguments' => array(1),
    'access arguments' => array('view cvterms'),
    'type' => MENU_CALLBACK,
  );


  $items['data/gene/add'] = array(
    'title' => 'Add a gene',
    'page callback' => 'cvterm_add',
    'access arguments' => array('create cvterm'),
  );
  return $items;
}

function tripal_entities_permission(){
  return array(
    'administer cvterms' =>  array(
      'title' => t('Administer cvterms'),
      'restrict access' => TRUE,
    ),
    'view postsits' => array(
      'title' => t('View cvterms'),
    )
  );
}


function cvterm_info() {
  return ('Welcome to the administration page for your CV Terms!');
}

function cvterm_page_title($cvterm){
  return $cvterm->pid;
}

function cvterm_page_view($cvterm, $view_mode = 'full'){
  $cvterm->content = array();

  // Build fields content.
  field_attach_prepare_view('cvterm', array($cvterm->pid => $cvterm), $view_mode);
  entity_prepare_view('cvterm', array($cvterm->pid => $cvterm));
  $cvterm->content += field_attach_view('cvterm', $cvterm, $view_mode);

  return $cvterm->content;
}


function tripal_entities_field_extra_fields() {
  $return = array();
  $return['cvterm']['cvterm'] = array(
    'form' => array(
      'note' => array(
        'label' => t('Note'),
        'description' => t('Term Note'),
      ),
    ),
  );

  return $return;
}
function tripal_entities_vocbulary_term_uri($cvterm) {
  return array(
    'path' => 'cvterm/' . $cvterm->id,
  );
}

function cvterm_add() {
  $cvterm = (object) array (
    'pid' => '',
    'type' => 'cvterm',
    'note' => '',
  );

  return drupal_get_form('cvterm_add_form', $cvterm);
}


function cvterm_add_form($form, &$form_state, $cvterm) {
  $form['note'] = array(
    '#type' => 'textfield',
    '#title' => t('Note'),
    '#required' => TRUE,
  );

  $form['submit'] = array(
    '#type' => 'submit',
    '#value' => t('Save'),
  );

  field_attach_form('cvterm', $cvterm, $form, $form_state);

  return $form;
}
function cvterm_add_form_validate($form, &$form_state) {
  $cvterm_submission = (object) $form_state['values'];
  field_attach_form_validate('cvterm', $cvterm_submission, $form, $form_state);
}

function cvterm_add_form_submit($form, &$form_state) {
  $cvterm_submission = (object) $form_state['values'];
  field_attach_submit('cvterm', $cvterm_submission, $form, $form_state);
  $cvterm = cvterm_save($cvterm_submission);
  $form_state['redirect'] = "cvterm/$cvterm->pid";
}

function cvterm_save(&$cvterm) {
  return entity_get_controller('cvterm')->save($cvterm);
}
/**
 *
 *
 */
class TrpVocabularyTermController extends DrupalDefaultEntityController {

  public function save($cvterm) {
//     drupal_write_record('cvterm', $cvterm);
//     field_attach_insert('cvterm', $cvterm);
//     module_invoke_all('entity_insert', 'cvterm', $cvterm);
    return $cvterm;
  }

}