Added Image term

tripal/api/tripal.notice.api.inc

@@ -32,8 +32,8 @@ define('TRIPAL_DEBUG',7);
  * information to the message.
  *
  * @param $type
- *   The catagory to which this message belongs. Can be any string, but the general
- *   practice is to use the name of the module.
+ *   The catagory to which this message belongs. Can be any string, but the
+ *   general practice is to use the name of the module.
  * @param $severity
  *   The severity of the message; one of the following values:
  *     - TRIPAL_CRITICAL: Critical conditions.
@@ -43,16 +43,18 @@ define('TRIPAL_DEBUG',7);
  *     - TRIPAL_INFO: Informational messages.
  *     - TRIPAL_DEBUG: Debug-level messages.
  * @param $message
- *   The message to store in the log. Keep $message translatable by not concatenating
- *   dynamic values into it! Variables in the message should be added by using placeholder
- *   strings alongside the variables argument to declare the value of the placeholders.
- *   See t() for documentation on how $message and $variables interact.
+ *   The message to store in the log. Keep $message translatable by not
+ *   concatenating dynamic values into it! Variables in the message should be
+ *   added by using placeholder strings alongside the variables argument to
+ *   declare the value of the placeholders. See t() for documentation on how
+ *   $message and $variables interact.
  * @param $variables
- *   Array of variables to replace in the message on display or NULL if message is
- *   already translated or not possible to translate.
+ *   Array of variables to replace in the message on display or NULL if message
+ *   is already translated or not possible to translate.
  * @param $options
  *   An array of options. Some available options include:
- *     - print: prints the error message to the terminal screen. Useful when display is the command-line
+ *     - print: prints the error message to the terminal screen. Useful when
+ *       display is the command-line
  *
  * @ingroup tripal_api
  */

tripal_chado/includes/tripal_chado.semweb.inc

@@ -121,6 +121,7 @@ function tripal_chado_populate_vocab_SCHEMA() {
  * Adds the EDAM database and terms.
  */
 function tripal_chado_populate_vocab_EDAM() {
+
   tripal_insert_db(array(
     'name' => 'data',
     'description' => 'Bioinformatics operations, data types, formats, identifiers and topics.',
@@ -173,6 +174,14 @@ function tripal_chado_populate_vocab_EDAM() {
     'definition' => 'A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things).',
   ));
   tripal_associate_chado_semweb_term(NULL, 'uniquename', $term);
+
+  $term = tripal_insert_cvterm(array(
+    'id' => 'data:2968',
+    'name' => 'Image',
+    'cv_name' => 'EDAM',
+    'definition' => 'Biological or biomedical data has been rendered into an image, typically for display on screen.',
+  ));
+  tripal_associate_chado_semweb_term(NULL, 'eimage_id', $term);
 }
 
 /**
@@ -370,7 +379,7 @@ function tripal_chado_populate_vocab_SWO() {
   $term = tripal_insert_cvterm(array(
     'id' => 'SWO:0000001',
     'name' => 'software',
-    'cv_name' => 'schema',
+    'cv_name' => 'swo',
     'definition' => 'Computer software, or generally just software, is any ' .
       'set of machine-readable instructions (most often in the form of a ' .
       'computer program) that conform to a given syntax (sometimes ' .
@@ -379,6 +388,7 @@ function tripal_chado_populate_vocab_SWO() {
       'specific operations.',
   ));
   tripal_associate_chado_semweb_term('analysis', 'program', $term);
+
 }
 
 /**