Chado CV

Provides API functions specificially for managing controlled vocabulary records in Chado. Please note that Tripal v3 provides a generic set of API functions for working with controlled vocabularies (CVs). This allows for CVs to be stored using any back-end. By default CV's continue to be housed in Chado. Therefore, if you are working directly with controlled vocabulary records inside of a Chado-aware module then these functions can be used.

Parent topics

Chado API
The Tripal Chado (tripal_chado) module provides an application programming interface (API) to support customizations and creation of new extensions using the Chado database schem as a data store.

File

tripal_chado/api/modules/tripal_chado.cv.api.inc, line 10
Provides API functions specificially for managing controlled vocabulary records in Chado.

Functions

Namesort descending Location Description
chado_associate_cvterm tripal_chado/api/modules/tripal_chado.cv.api.inc Add a record to a cvterm linking table (ie: feature_cvterm).
chado_autocomplete_cv tripal_chado/api/modules/tripal_chado.cv.api.inc This function is intended to be used in autocomplete forms.
chado_autocomplete_cvterm tripal_chado/api/modules/tripal_chado.cv.api.inc This function is intended to be used in autocomplete forms for searching for CV terms that begin with the provided string.
chado_get_cv tripal_chado/api/modules/tripal_chado.cv.api.inc Retrieves a chado controlled vocabulary variable
chado_get_cvterm tripal_chado/api/modules/tripal_chado.cv.api.inc Retrieves a chado controlled vocabulary term variable.
chado_get_cvterm_select_options tripal_chado/api/modules/tripal_chado.cv.api.inc Create an options array to be used in a form element which provides a list of all chado cvterms.
chado_get_cv_select_options tripal_chado/api/modules/tripal_chado.cv.api.inc Create an options array to be used in a form element which provides a list of all chado cvs.
chado_get_obo tripal_chado/api/modules/tripal_chado.cv.api.inc Retrieves an OBO record.
chado_insert_cv tripal_chado/api/modules/tripal_chado.cv.api.inc Adds a controlled vocabulary to the CV table of Chado.
chado_insert_cvterm tripal_chado/api/modules/tripal_chado.cv.api.inc Add's a controlled vocabulary term to Chado.
chado_insert_obo tripal_chado/api/modules/tripal_chado.cv.api.inc Add the OBO to the tripal_cv_obo table in the Drupal database.
chado_submit_obo_job tripal_chado/api/modules/tripal_chado.cv.api.inc TODO: deprecate this function
chado_update_cvtermpath tripal_chado/api/modules/tripal_chado.cv.api.inc Duplicate of fill_cvtermpath() stored procedure in Chado.
tripal_update_cvtermpath_old tripal_chado/api/modules/tripal_chado.cv.api.inc Updates the cvtermpath table of Chado for the specified CV.
_chado_update_cvtermpath_loop tripal_chado/api/modules/tripal_chado.cv.api.inc
_chado_update_cvtermpath_loop_increment tripal_chado/api/modules/tripal_chado.cv.api.inc
_chado_update_cvtermpath_root_loop tripal_chado/api/modules/tripal_chado.cv.api.inc Duplicate of _fill_cvtermpath4root() stored procedure in Chado.