Renamed chado_linker_fileds

tripal_chado/includes/TripalFields/chado_linker__cvterm_widget.inc

@@ -117,7 +117,7 @@ class chado_linker__cvterm_widget extends TripalFieldWidget {
       '#default_value' => $uname,
       '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
       '#ajax' => array(
-        'callback' => "chado_linker__pub_widget_form_ajax_callback",
+        'callback' => "schema__publication_widget_form_ajax_callback",
         'wrapper' => "$table_name-$delta",
         'effect' => 'fade',
         'method' => 'replace'

tripal_chado/includes/TripalFields/chado_linker__featureloc.inc → tripal_chado/includes/TripalFields/data__sequence_coordinates.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__featureloc extends TripalField {
+class data__sequence_coordinates extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -20,7 +20,7 @@ class chado_linker__featureloc extends TripalField {
   public static $term = 'data:2012';
 
   // The default lable for this field.
-  public static $label = 'Sequence Coordinate';
+  public static $label = 'Sequence Coordinates';
 
   // The default description for this field.
   public static $description = 'Locations on reference sequences where the feature is located.';
@@ -45,10 +45,10 @@ class chado_linker__featureloc extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__featureloc_widget';
+  public static $default_widget = 'data__sequence_coordinates_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__featureloc_formatter';
+  public static $default_formatter = 'data__sequence_coordinates_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__featureloc_formatter.inc → tripal_chado/includes/TripalFields/data__sequence_coordinates_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__featureloc_formatter extends TripalFieldFormatter {
+class data__sequence_coordinates_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Aligned Locations';
+  public static $label = 'Sequence Coordinates';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__featureloc');
+  public static $field_types = array('data__sequence_coordinates');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__featureloc_widget.inc → tripal_chado/includes/TripalFields/data__sequence_coordinates_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__featureloc_widget extends TripalFieldWidget {
+class data__sequence_coordinates_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Aligned Locations';
+  public static $label = 'Sequence Coordinates';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__featureloc');
+  public static $field_types = array('data__sequence_coordinates');
 
   /**
    *

tripal_chado/includes/TripalFields/chado_linker__expression.inc → tripal_chado/includes/TripalFields/go__gene_expression.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__expression extends TripalField {
+class go__gene_expression extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -16,14 +16,18 @@ class chado_linker__expression extends TripalField {
   // and [acession] is the unique accession number for the term.  This term
   // must already exist in the vocabulary storage backend. This
   // value should never be changed once fields exist for this type.
-  public static $term = 'local:expression';
+  public static $term = 'GO:0010467';
 
   // The default lable for this field.
-  public static $label = 'Expression';
+  public static $label = 'Gene expression';
 
   // The default description for this field.
-  public static $description = 'Associates an expression with
-          this record.';
+  public static $description = 'The process in which a gene\'s sequence is converted into a 
+      mature gene product or products (proteins or RNA). This includes the production of an 
+      RNA transcript as well as any processing to produce a mature RNA product or an 
+      mRNA (for protein-coding genes) and the translation of that mRNA into protein. 
+      Protein maturation is included when required to form an active form of a product from 
+      an inactive precursor form.';
 
   // Provide a list of global settings. These can be accessed witihn the
   // globalSettingsForm.  When the globalSettingsForm is submitted then
@@ -45,10 +49,10 @@ class chado_linker__expression extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__expression_widget';
+  public static $default_widget = 'go__gene_expression_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__expression_formatter';
+  public static $default_formatter = 'go__gene_expression_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__expression_formatter.inc → tripal_chado/includes/TripalFields/go__gene_expression_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__expression_formatter extends TripalFieldFormatter {
+class go__gene_expression_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Expression';
+  public static $label = 'Gene expression';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__expression');
+  public static $field_types = array('go__gene_expression');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__phenotype_widget.inc → tripal_chado/includes/TripalFields/go__gene_expression_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__phenotype_widget extends TripalFieldWidget {
+class go__gene_expression_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Phenotypes';
+  public static $label = 'Gene expression';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__phenotype');
+  public static $field_types = array('go__gene_expression');
 
   /**
    *
@@ -37,4 +37,5 @@ class chado_linker__phenotype_widget extends TripalFieldWidget {
   public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
 
   }
+  
 }

tripal_chado/includes/TripalFields/chado_linker__featurepos.inc → tripal_chado/includes/TripalFields/ogi__location_on_map.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__featurepos extends TripalField {
+class ogi__location_on_map extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -45,10 +45,10 @@ class chado_linker__featurepos extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__featurepos_widget';
+  public static $default_widget = 'ogi__location_on_map_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__featurepos_formatter';
+  public static $default_formatter = 'ogi__location_on_map_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__featurepos_formatter.inc → tripal_chado/includes/TripalFields/ogi__location_on_map_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__featurepos_formatter extends TripalFieldFormatter {
+class ogi__location_on_map_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Map positions';
+  public static $label = 'Location on Map';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__featurepos');
+  public static $field_types = array('ogi__location_on_map');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__expression_widget.inc → tripal_chado/includes/TripalFields/ogi__location_on_map_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__expression_widget extends TripalFieldWidget {
+class ogi__location_on_map_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Expression';
+  public static $label = 'Location on Map';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__expression');
+  public static $field_types = array('ogi__location_on_map');
 
   /**
    *
@@ -37,5 +37,4 @@ class chado_linker__expression_widget extends TripalFieldWidget {
   public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
 
   }
-  
 }

tripal_chado/includes/TripalFields/chado_linker__dbxref.inc → tripal_chado/includes/TripalFields/sbo__database_cross_reference.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__dbxref extends TripalField {
+class sbo__database_cross_reference extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -19,7 +19,7 @@ class chado_linker__dbxref extends TripalField {
   public static $term = 'SBO:0000554';
 
   // The default lable for this field.
-  public static $label = 'Cross references';
+  public static $label = 'Database cross reference';
 
   // The default description for this field.
   public static $description = 'This record can be cross referenced with a record in
@@ -46,10 +46,10 @@ class chado_linker__dbxref extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__dbxref_widget';
+  public static $default_widget = 'sbo__database_cross_reference_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__dbxref_formatter';
+  public static $default_formatter = 'sbo__database_cross_reference_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
@@ -170,7 +170,7 @@ class chado_linker__dbxref extends TripalField {
  *
  * @param $variables
  */
-function theme_chado_linker__dbxref_widget($variables) {
+function theme_sbo__database_cross_reference_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -202,7 +202,7 @@ function theme_chado_linker__dbxref_widget($variables) {
 /**
  * An Ajax callback for the dbxref widget.
  */
-function chado_linker__dbxref_widget_form_ajax_callback($form, $form_state) {
+function sbo__database_cross_reference_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];

tripal_chado/includes/TripalFields/chado_linker__dbxref_formatter.inc → tripal_chado/includes/TripalFields/sbo__database_cross_reference_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__dbxref_formatter extends TripalFieldFormatter {
+class sbo__database_cross_reference_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Cross references';
+  public static $label = 'Database cross reference';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__dbxref');
+  public static $field_types = array('sbo__database_cross_reference');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__dbxref_widget.inc → tripal_chado/includes/TripalFields/sbo__database_cross_reference_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__dbxref_widget extends TripalFieldWidget {
+class sbo__database_cross_reference_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Cross references';
+  public static $label = 'Database cross reference';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__dbxref');
+  public static $field_types = array('sbo__database_cross_reference');
 
   /**
    *
@@ -63,8 +63,8 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
     
     $widget['#table_name'] = $chado_table;
     $widget['#fkey_field'] = $fkey;
-    //$widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
-    $widget['#theme'] = 'chado_linker__dbxref_widget';
+    //$widget['#element_validate'] = array('sbo__database_cross_reference_widget_validate');
+    $widget['#theme'] = 'sbo__database_cross_reference_widget';
     $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id-$delta'>";
     $widget['#suffix'] =  "</span>";
     
@@ -97,7 +97,7 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
       '#required' => $element['#required'],
       '#default_value' => $db_id,
       '#ajax' => array(
-        'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
+        'callback' => "sbo__database_cross_reference_widget_form_ajax_callback",
         'wrapper' => "$field_name-dbxref--db-id-$delta",
         'effect' => 'fade',
         'method' => 'replace'
@@ -112,7 +112,7 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
       '#size' => 15,
       '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
       '#ajax' => array(
-        'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
+        'callback' => "sbo__database_cross_reference_widget_form_ajax_callback",
         'wrapper' => "$field_name-dbxref--db-id-$delta",
         'effect' => 'fade',
         'method' => 'replace'
@@ -185,19 +185,19 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
       if (!$db_id and $accession) {
         $errors[$field_name][$delta]['und'][] = array(
           'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
+          'error' => 'sbo__database_cross_reference',
         );
       }
       if ($db_id and !$accession) {
         $errors[$field_name][$delta]['und'][] = array(
           'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
+          'error' => 'sbo__database_cross_reference',
         );
       }
       if (!$db_id and !$accession and ($version or $description)) {
         $errors[$field_name][$delta]['und'][] = array(
           'message' => t("A database and the accession must both be provided."),
-          'error' => 'chado_linker__dbxref',
+          'error' => 'sbo__database_cross_reference',
         );
       }
     }

tripal_chado/includes/TripalFields/chado_linker__phenotype.inc → tripal_chado/includes/TripalFields/sbo__phenotype.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__phenotype extends TripalField {
+class sbo__phenotype extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -16,13 +16,16 @@ class chado_linker__phenotype extends TripalField {
   // and [acession] is the unique accession number for the term.  This term
   // must already exist in the vocabulary storage backend. This
   // value should never be changed once fields exist for this type.
+  // http://www.ebi.ac.uk/sbo/main/SBO:0000358
   public static $term = 'SBO:0000358';
 
   // The default lable for this field.
-  public static $label = 'Phenotypes';
+  public static $label = 'Phenotype';
 
   // The default description for this field.
-  public static $description = 'Associates phenotypes with this record.';
+  public static $description = 'A biochemical network can generate phenotypes or affects 
+      biological processes. Such processes can take place at different levels and are 
+      independent of the biochemical network itself.';
 
   // Provide a list of global settings. These can be accessed witihn the
   // globalSettingsForm.  When the globalSettingsForm is submitted then
@@ -44,10 +47,10 @@ class chado_linker__phenotype extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__phenotype_widget';
+  public static $default_widget = 'sbo__phenotype_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__phenotype_formatter';
+  public static $default_formatter = 'sbo__phenotype_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__phenotype_formatter.inc → tripal_chado/includes/TripalFields/sbo__phenotype_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__phenotype_formatter extends TripalFieldFormatter {
+class sbo__phenotype_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Phenotypes';
+  public static $label = 'Phenotype';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__phenotype');
+  public static $field_types = array('sbo__phenotype');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__genotype_widget.inc → tripal_chado/includes/TripalFields/sbo__phenotype_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__genotype_widget extends TripalFieldWidget {
+class sbo__phenotype_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Genotypes';
+  public static $label = 'Phenotype';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__genotype');
+  public static $field_types = array('sbo__phenotype');
 
   /**
    *

tripal_chado/includes/TripalFields/chado_linker__relationship.inc → tripal_chado/includes/TripalFields/sbo__relationship.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__relationship extends TripalField {
+class sbo__relationship extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -19,7 +19,7 @@ class chado_linker__relationship extends TripalField {
   public static $term = 'SBO:0000374';
 
   // The default lable for this field.
-  public static $label = 'Relationships';
+  public static $label = 'Relationship';
 
   // The default description for this field.
   public static $description = 'Relationships between records.';
@@ -44,10 +44,10 @@ class chado_linker__relationship extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__relationship_widget';
+  public static $default_widget = 'sbo__relationship_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__relationship_formatter';
+  public static $default_formatter = 'sbo__relationship_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
@@ -377,7 +377,7 @@ class chado_linker__relationship extends TripalField {
           term for the relationship type.'),
       '#collapsed' => TRUE,
       '#collapsible' => TRUE,
-      '#theme' => 'chado_linker__relationship_instance_settings'
+      '#theme' => 'sbo__relationship_instance_settings'
     );
     //     $element['instructions'] = array(
     //       '#type' => 'item',
@@ -420,7 +420,7 @@ class chado_linker__relationship extends TripalField {
       '#options' => $vocs,
       '#default_value' => $this->instance['settings']['relationships']['option2_vocab'],
       '#ajax' => array(
-        'callback' => "chado_linker__relationship_instance_settings_form_ajax_callback",
+        'callback' => "sbo__relationship_instance_settings_form_ajax_callback",
         'wrapper' => 'relationships-option2-parent',
         'effect' => 'fade',
         'method' => 'replace'

tripal_chado/includes/TripalFields/chado_linker__relationship_formatter.inc → tripal_chado/includes/TripalFields/sbo__relationship_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__relationship_formatter extends TripalFieldFormatter {
+class sbo__relationship_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Relationships';
+  public static $label = 'Relationship';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__relationship');
+  public static $field_types = array('sbo__relationship');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__relationship_widget.inc → tripal_chado/includes/TripalFields/sbo__relationship_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__relationship_widget extends TripalFieldWidget {
+class sbo__relationship_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Relationships';
+  public static $label = 'Relationship';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__relationship');
+  public static $field_types = array('sbo__relationship');
 
   /**
    *
@@ -105,8 +105,8 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
     $widget['#fkeys'] = $schema['foreign keys'];
     $widget['#base_table'] = $base_table;
     $widget['#chado_record_id'] = isset($form['#entity']) ? $form['#entity']->chado_record_id : '';
-    //$widget['#element_validate'] = array('chado_linker__relationship_validate');
-    $widget['#theme'] = 'chado_linker__relationship_widget';
+    //$widget['#element_validate'] = array('sbo__relationship_validate');
+    $widget['#theme'] = 'sbo__relationship_widget';
     $widget['#prefix'] =  "<span id='$chado_table-$delta'>";
     $widget['#suffix'] =  "</span>";
     
@@ -287,7 +287,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         '#required' => $element['#required'],
         '#default_value' => $cv_id,
         '#ajax' => array(
-          'callback' => "chado_linker__relationship_widget_form_ajax_callback",
+          'callback' => "sbo__relationship_widget_form_ajax_callback",
           'wrapper' => "$chado_table-$delta",
           'effect' => 'fade',
           'method' => 'replace'
@@ -371,19 +371,19 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       $form_error = FALSE;
       if (!$type_name && !$type_id) {
         $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
+          'error' => 'sbo__relationship',
           'message' => t("Please provide the type of relationship."),
         );
       }
       if ($entity and !$subject_name) {
         $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
+          'error' => 'sbo__relationship',
           'message' => t("Please provide the subject of the relationship."),
         );
       }
       if ($entity and !$object_name) {
         $errors[$this->field['field_name']][$langcode][$delta][] = array(
-          'error' => 'chado_linker__relationship',
+          'error' => 'sbo__relationship',
           'message' => t("Please provide the object of the relationship."),
         );
       }
@@ -405,7 +405,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
           if (count($subject) == 0) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' => t("The subject record cannot be found using the specified id (e.g. [id: xx])."),
             );
           }
@@ -415,13 +415,13 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
           if (count($subject) == 0) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' => t("The subject record cannot be found. Please check spelling."),
             );
           }
           elseif (count($subject) > 1) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' => t("The subject is not unique and therefore the relationship cannot be made."),
             );
           }
@@ -439,7 +439,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
           if (count($subject) == 0) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' => t("The object record cannot be found using the specified id (e.g. [id: xx])."),
             );
           }
@@ -449,13 +449,13 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
           if (count($object) == 0) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' => t("The object record cannot be found. Please check spelling."),
             );;
           }
           elseif (count($object) > 1) {
             $errors[$this->field['field_name']][$langcode][$delta][] = array(
-              'error' => 'chado_linker__relationship',
+              'error' => 'sbo__relationship',
               'message' =>  t("The object is not unique and therefore the relationship cannot be made."),
             );
           }
@@ -467,7 +467,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         $chado_record_id = $entity->chado_record_id;
         if ($object_id != $chado_record_id  and $subject_id != $chado_record_id) {
           $errors[$this->field['field_name']][$langcode][$delta][] = array(
-            'error' => 'chado_linker__relationship',
+            'error' => 'sbo__relationship',
             'message' =>  t("Either the subject or the object in the relationship must refer to this record."),
           );
         }
@@ -475,7 +475,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         // Make sure that the object and subject are not both the same thing.
         if ($object_id == $subject_id) {
           $errors[$this->field['field_name']][$langcode][$delta][] = array(
-            'error' => 'chado_linker__relationship',
+            'error' => 'sbo__relationship',
             'message' =>  t("The subject and the object in the relationship cannot both refer to the same record."),
           );
         }
@@ -548,9 +548,9 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
 
 
 /**
- * Theme function for the chado_linker__relationship_widget.
+ * Theme function for the sbo__relationship_widget.
  */
-function theme_chado_linker__relationship_widget($variables) {
+function theme_sbo__relationship_widget($variables) {
   $element = $variables['element'];
   $field_name = $element['#field_name'];
   $field = field_info_field($field_name);
@@ -579,7 +579,7 @@ function theme_chado_linker__relationship_widget($variables) {
         return $layout;
 }
 
-function theme_chado_linker__relationship_instance_settings ($variables) {
+function theme_sbo__relationship_instance_settings ($variables) {
   $element = $variables['element'];
   $option1 = $element['option1'];
   $option1_vocabs = $element['option1_vocabs'];
@@ -608,7 +608,7 @@ function theme_chado_linker__relationship_instance_settings ($variables) {
 /**
  * An Ajax callback for the relationshp widget.
  */
-function chado_linker__relationship_widget_form_ajax_callback(&$form, $form_state) {
+function sbo__relationship_widget_form_ajax_callback(&$form, $form_state) {
 
   // Get the triggering element
   $form_element_name = $form_state['triggering_element']['#name'];
@@ -629,7 +629,7 @@ function chado_linker__relationship_widget_form_ajax_callback(&$form, $form_stat
 /**
  * An Ajax callback for the relationshp instance setting form.
  */
-function chado_linker__relationship_instance_settings_form_ajax_callback(&$form, &$form_state) {
+function sbo__relationship_instance_settings_form_ajax_callback(&$form, &$form_state) {
   $acpath  = $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_path'];
   $acpath .=  $form_state['values']['instance']['settings']['relationships']['option2_vocab'] . '/';
   $urlval  = $form['instance']['settings']['relationships']['option2_parent']['#autocomplete_input']['#url_value'];

tripal_chado/includes/TripalFields/chado_linker__synonym.inc → tripal_chado/includes/TripalFields/schema__alternate_name.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__synonym extends TripalField {
+class schema__alternate_name extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -44,10 +44,10 @@ class chado_linker__synonym extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__synonym_widget';
+  public static $default_widget = 'schema__alternate_name_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__synonym_formatter';
+  public static $default_formatter = 'schema__alternate_name_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__synonym_formatter.inc → tripal_chado/includes/TripalFields/schema__alternate_name_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__synonym_formatter extends TripalFieldFormatter {
+class schema__alternate_name_formatter extends TripalFieldFormatter {
   // The default lable for this field.
   public static $label = 'Synonyms';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__synonym');
+  public static $field_types = array('schema__alternate_name');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__synonym_widget.inc → tripal_chado/includes/TripalFields/schema__alternate_name_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__synonym_widget extends TripalFieldWidget {
+class schema__alternate_name_widget extends TripalFieldWidget {
   // The default lable for this field.
   public static $label = 'Synonyms';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__synonym');
+  public static $field_types = array('schema__alternate_name');
 
   /**
    *
@@ -73,7 +73,7 @@ class chado_linker__synonym_widget extends TripalFieldWidget {
     
     $widget['#table_name'] = $table_name;
     $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__synonym_widget';
+    $widget['#theme'] = 'schema__alternate_name_widget';
     $widget['#prefix'] =  "<span id='$table_name-$delta'>";
     $widget['#suffix'] =  "</span>";
     
@@ -209,7 +209,7 @@ class chado_linker__synonym_widget extends TripalFieldWidget {
  *
  * @param $variables
  */
-function theme_chado_linker__synonym_widget($variables) {
+function theme_schema__alternate_name_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields
@@ -240,7 +240,7 @@ function theme_chado_linker__synonym_widget($variables) {
 /**
  * An Ajax callback for the synonym widget.
  */
-function chado_linker__synonym_widget_form_ajax_callback($form, $form_state) {
+function schema__alternate_name_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];

tripal_chado/includes/TripalFields/chado_linker__pub.inc → tripal_chado/includes/TripalFields/schema__publication.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__pub extends TripalField {
+class schema__publication extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -19,7 +19,7 @@ class chado_linker__pub extends TripalField {
   public static $term = 'schema:publication';
 
   // The default lable for this field.
-  public static $label = 'Publications';
+  public static $label = 'Publication';
 
   // The default description for this field.
   public static $description = 'Associates a publication (e.g. journal article,
@@ -45,10 +45,10 @@ class chado_linker__pub extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__pub_widget';
+  public static $default_widget = 'schema__publication_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__pub_formatter';
+  public static $default_formatter = 'schema__publication_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__pub_formatter.inc → tripal_chado/includes/TripalFields/schema__publication_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__pub_formatter extends TripalFieldFormatter {
+class schema__publication_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Publications';
+  public static $label = 'Publication';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__pub');
+  public static $field_types = array('schema__publication');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__pub_widget.inc → tripal_chado/includes/TripalFields/schema__publication_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__pub_widget extends TripalFieldWidget {
+class schema__publication_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Publications';
+  public static $label = 'Publication';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__pub');
+  public static $field_types = array('schema__publication');
 
   /**
    *
@@ -42,7 +42,7 @@ class chado_linker__pub_widget extends TripalFieldWidget {
     
     $widget['#table_name'] = $table_name;
     $widget['#fkey_field'] = $fkey;
-    $widget['#theme'] = 'chado_linker__pub_widget';
+    $widget['#theme'] = 'schema__publication_widget';
     $widget['#prefix'] =  "<span id='$table_name-$delta'>";
     $widget['#suffix'] =  "</span>";
     
@@ -70,7 +70,7 @@ class chado_linker__pub_widget extends TripalFieldWidget {
       '#default_value' => $uname,
       '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/pub',
       '#ajax' => array(
-        'callback' => "chado_linker__pub_widget_form_ajax_callback",
+        'callback' => "schema__publication_widget_form_ajax_callback",
         'wrapper' => "$table_name-$delta",
         'effect' => 'fade',
         'method' => 'replace'
@@ -141,7 +141,7 @@ class chado_linker__pub_widget extends TripalFieldWidget {
 /**
  * An Ajax callback for the pub widget.
  */
-function chado_linker__pub_widget_form_ajax_callback($form, $form_state) {
+function schema__publication_widget_form_ajax_callback($form, $form_state) {
 
   $field_name = $form_state['triggering_element']['#parents'][0];
   $delta = $form_state['triggering_element']['#parents'][2];
@@ -153,7 +153,7 @@ function chado_linker__pub_widget_form_ajax_callback($form, $form_state) {
  *
  * @param $variables
  */
-function theme_chado_linker__pub_widget($variables) {
+function theme_schema__publication_widget($variables) {
   $element = $variables['element'];
 
   // These two fields were added to the widget to help identify the fields

tripal_chado/includes/TripalFields/chado_linker__genotype.inc → tripal_chado/includes/TripalFields/so__genotype.inc

@@ -1,6 +1,6 @@
 <?php
 
-class chado_linker__genotype extends TripalField {
+class so__genotype extends TripalField {
 
 
   // --------------------------------------------------------------------------
@@ -19,7 +19,7 @@ class chado_linker__genotype extends TripalField {
   public static $term = 'SO:0001027';
 
   // The default lable for this field.
-  public static $label = 'Genotypes';
+  public static $label = 'Genotype';
 
   // The default description for this field.
   public static $description = 'Associates an indviddual or organization with
@@ -45,10 +45,10 @@ class chado_linker__genotype extends TripalField {
   public static $storage = 'tripal_no_storage';
 
   // The default widget for this field.
-  public static $default_widget = 'chado_linker__genotype_widget';
+  public static $default_widget = 'so__genotype_widget';
 
   // The default formatter for this field.
-  public static $default_formatter = 'chado_linker__genotype_formatter';
+  public static $default_formatter = 'so__genotype_formatter';
 
   // --------------------------------------------------------------------------
   //              PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE

tripal_chado/includes/TripalFields/chado_linker__genotype_formatter.inc → tripal_chado/includes/TripalFields/so__genotype_formatter.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__genotype_formatter extends TripalFieldFormatter {
+class so__genotype_formatter extends TripalFieldFormatter {
   // The default lable for this field.
-  public static $label = 'Genotypes';
+  public static $label = 'Genotype';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__genotype');
+  public static $field_types = array('so__genotype');
 
   // The list of default settings for this formatter.
   public static $settings = array();

tripal_chado/includes/TripalFields/chado_linker__featurepos_widget.inc → tripal_chado/includes/TripalFields/so__genotype_widget.inc

@@ -1,11 +1,11 @@
 <?php
 
-class chado_linker__featurepos_widget extends TripalFieldWidget {
+class so__genotype_widget extends TripalFieldWidget {
   // The default lable for this field.
-  public static $label = 'Map positions';
+  public static $label = 'Genotype';
 
   // The list of field types for which this formatter is appropriate.
-  public static $field_types = array('chado_linker__featurepos');
+  public static $field_types = array('so__genotype');
 
   /**
    *

tripal_chado/includes/tripal_chado.fields.inc

@@ -421,8 +421,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
     $dbxref_table = $table_name . '_dbxref';
     $schema = chado_get_schema($dbxref_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_dbxref';
-    $field_type = 'chado_linker__dbxref';
+    $field_name = 'sbo__database_cross_reference';
+    $field_type = 'sbo__database_cross_reference';
     $info[$field_name] = array(
       'field_name' =>  $field_name,
       'type' => $field_type,
@@ -445,8 +445,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($expression_table)) {
     $schema = chado_get_schema($expression_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_expression';
-    $field_type = 'chado_linker__expression';
+    $field_name = 'go__gene_expression';
+    $field_type = 'go__gene_expression';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -459,7 +459,7 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
         'chado_table' => $expression_table,
         'chado_column' => $pkey,
         'base_table' => $table_name,
-        'semantic_web' => 'local:expression',
+        'semantic_web' => 'GO:0010467',
       ),
     );
   }
@@ -468,8 +468,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if ($table_name == 'feature') {
     $schema = chado_get_schema('featureloc');
     $pkey = $schema['primary key'][0];
-    $field_name = 'featureloc';
-    $field_type = 'chado_linker__featureloc';
+    $field_name = 'data__sequence_coordinates';
+    $field_type = 'data__sequence_coordinates';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -482,7 +482,7 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
         'chado_table' => 'featureloc',
         'chado_column' => $pkey,
         'base_table' => 'feature',
-        'semantic_web' => 'SO:position_of',
+        'semantic_web' => 'data:2012',
       ),
     );
   }
@@ -491,8 +491,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if ($table_name == 'feature') {
     $schema = chado_get_schema('featurepos');
     $pkey = $schema['primary key'][0];
-    $field_name = 'featurepos';
-    $field_type = 'chado_linker__featurepos';
+    $field_name = 'ogi__location_on_map';
+    $field_type = 'ogi__location_on_map';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -505,7 +505,7 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
         'chado_table' => 'featurepos',
         'chado_column' => $pkey,
         'base_table' => 'feature',
-        'semantic_web' => 'SO:position_of',
+        'semantic_web' => 'OGI:0000021',
       ),
     );
   }
@@ -515,8 +515,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($genotype_table)) {
     $schema = chado_get_schema($genotype_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_genotype';
-    $field_type = 'chado_linker__genotype';
+    $field_name = 'so__genotype';
+    $field_type = 'so__genotype';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -539,8 +539,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($phenotype_table)) {
     $schema = chado_get_schema($phenotype_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_phenotype';
-    $field_type = 'chado_linker__phenotype';
+    $field_name = 'sbo__phenotype';
+    $field_type = 'sbo__phenotype';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -582,8 +582,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($pub_table)) {
     $schema = chado_get_schema($pub_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_pub';
-    $field_type = 'chado_linker__pub';
+    $field_name = 'schema__publication';
+    $field_type = 'schema__publication';
     $info[$field_name] =  array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -607,8 +607,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($rel_table)) {
     $schema = chado_get_schema($rel_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_relationship';
-    $field_type = 'chado_linker__relationship';
+    $field_name = 'sbo__relationship';
+    $field_type = 'sbo__relationship';
     $info[$field_name] =  array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -631,8 +631,8 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   if (chado_table_exists($syn_table)) {
     $schema = chado_get_schema($syn_table);
     $pkey = $schema['primary key'][0];
-    $field_name = $table_name . '_synonym';
-    $field_type = 'chado_linker__synonym';
+    $field_name = 'schema__alternate_name';
+    $field_type = 'schema__alternate_name';
     $info[$field_name] =  array(
       'field_name' => $field_name,
       'type' => $field_type,
@@ -1182,19 +1182,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // DBXREF
   $dbxref_table = $table_name . '_dbxref';
   if (chado_table_exists($dbxref_table)) {
-    $field_name = $table_name . '_dbxref';
+    $field_name = 'sbo__database_cross_reference';
     $info[$field_name] =  array(
       'field_name' =>  $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Cross References',
+      'label' => 'Database Cross Reference',
       'description' => 'The IDs where this record may be available in other external online databases.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__dbxref_widget',
+        'type' => 'sbo__database_cross_reference_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1202,7 +1202,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'inline',
-          'type' => 'chado_linker__dbxref_formatter',
+          'type' => 'sbo__database_cross_reference_formatter',
           'settings' => array(),
         ),
       ),
@@ -1212,19 +1212,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // EXPRESSION
   $expression_table = $table_name . '_expression';
   if (chado_table_exists($expression_table)) {
-    $field_name = $table_name . '_expression';
+    $field_name = 'go__gene_expression';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Expression',
+      'label' => 'Gene expression',
       'description' => 'Information about the expression of this record.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__expression_widget',
+        'type' => 'go__gene_expression_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1232,7 +1232,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__expression_formatter',
+          'type' => 'go__gene_expression_formatter',
           'settings' => array(),
         ),
       ),
@@ -1241,12 +1241,12 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
 
   // FEATURELOC
   if ($table_name == 'feature') {
-    $field_name = 'featureloc';
+    $field_name = 'data__sequence_coordinates';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Aligned Locations',
+      'label' => 'Sequence Coordinates',
       'description' => 'The locations on other genomic sequences where this
         record has been aligned.',
       'required' => FALSE,
@@ -1254,7 +1254,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__featureloc_widget',
+        'type' => 'data__sequence_coordinates_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1262,7 +1262,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__featureloc_formatter',
+          'type' => 'data__sequence_coordinates_formatter',
           'settings' => array(),
         ),
       ),
@@ -1271,19 +1271,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
 
   // FEATUREPOS
   if ($table_name == 'feature') {
-    $field_name = 'featurepos';
+    $field_name = 'ogi__location_on_map';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Map Positions',
+      'label' => 'Location on Map',
       'description' => 'The positions on a genetic map.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__featurepos_widget',
+        'type' => 'ogi__location_on_map_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1291,7 +1291,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__featurepos_formatter',
+          'type' => 'ogi__location_on_map_formatter',
           'settings' => array(),
         ),
       ),
@@ -1301,19 +1301,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // GENOTYPE
   $genotype_table = $table_name . '_genotype';
   if (chado_table_exists($genotype_table)) {
-    $field_name = $table_name . '_genotype';
+    $field_name = 'so__genotype';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Genotypes',
+      'label' => 'Genotype',
       'description' => 'The genotypes associated with this record.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__genotype_widget',
+        'type' => 'so__genotype_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1321,7 +1321,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__genotype_formatter',
+          'type' => 'so__genotype_formatter',
           'settings' => array(),
         ),
       ),
@@ -1331,19 +1331,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // PHENOTYPE
   $phenotype_table = $table_name . '_phenotype';
   if (chado_table_exists($phenotype_table)) {
-    $field_name = $table_name . '_phenotype';
+    $field_name = 'sbo__phenotype';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Phenotypes',
+      'label' => 'Phenotype',
       'description' => 'The phenotypes associated with this record.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__phenotype_widget',
+        'type' => 'sbo__phenotype_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1351,7 +1351,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__phenotype_formatter',
+          'type' => 'sbo__phenotype_formatter',
           'settings' => array(),
         ),
       ),
@@ -1391,12 +1391,12 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // PUBLICATIONS
   $pub_table = $table_name . '_pub';
   if (chado_table_exists($pub_table)) {
-    $field_name = $table_name . '_pub';
+    $field_name = 'schema__publication';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Publications',
+      'label' => 'Publication',
       'description' => 'This record has been referenced or is sourced from
         these publications.',
       'required' => FALSE,
@@ -1404,7 +1404,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__pub_widget',
+        'type' => 'schema__publication_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1412,7 +1412,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__pub_formatter',
+          'type' => 'schema__publication_formatter',
           'settings' => array(),
         ),
       ),
@@ -1423,19 +1423,19 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // If the linker table does not exists then we don't want to add attach.
   $rel_table = $table_name . '_relationship';
   if (chado_table_exists($rel_table)) {
-    $field_name = $table_name . '_relationship';
+    $field_name = 'sbo__relationship';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
       'bundle' => $bundle->name,
-      'label' => 'Relationships',
+      'label' => 'Relationship',
       'description' => 'Other records with relationships to this record.',
       'required' => FALSE,
       'settings' => array(
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__relationship_widget',
+        'type' => 'sbo__relationship_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1443,7 +1443,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'above',
-          'type' => 'chado_linker__relationship_formatter',
+          'type' => 'sbo__relationship_formatter',
           'settings' => array(),
         ),
       ),
@@ -1453,7 +1453,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   // SYNONYMS
   $syn_table = $table_name . '_synonym';
   if (chado_table_exists($syn_table)) {
-    $field_name = $table_name . '_synonym';
+    $field_name = 'schema__alternate_name';
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
@@ -1465,7 +1465,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
         'auto_attach' => FALSE,
       ),
       'widget' => array(
-        'type' => 'chado_linker__synonym_widget',
+        'type' => 'schema__alternate_name_widget',
         'settings' => array(
           'display_label' => 1,
         ),
@@ -1473,7 +1473,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       'display' => array(
         'default' => array(
           'label' => 'inline',
-          'type' => 'chado_linker__synonym_formatter',
+          'type' => 'schema__alternate_name_formatter',
           'settings' => array(),
         ),
       ),