Ontology Loader
- 2.x tripal_cv/includes/tripal_cv.obo_loader.inc tripal_obo_loader
- 1.x tripal_cv/includes/obo_loader.inc tripal_obo_loader
Functions to aid in loading ontologies into the chado cv module
Parent topics
File
- tripal_cv/
includes/ tripal_cv.obo_loader.inc, line 7 - Functions to aid in loading ontologies into the chado cv module
Functions
Name |
Location | Description |
|---|---|---|
| tripal_cv_load_obo_v1_2 |
tripal_cv/ |
Imports a given OBO file into Chado. This function is usually called by one of three wrapper functions: tripal_cv_load_obo_v1_2_id, tripal_cv_load_obo_v1_2_file or tirpal_cv_load_obo_v1_2_url. But, it can be called directly if the full path to an… |
| tripal_cv_load_obo_v1_2_file |
tripal_cv/ |
A wrapper function for importing the user specified OBO file into Chado by specifying the filename and path of the OBO. It requires that the file be in OBO v1.2 compatible format. This function is typically executed via the Tripal jobs management… |
| tripal_cv_load_obo_v1_2_id |
tripal_cv/ |
A wrapper function for importing the user specified OBO file into Chado by specifying the obo_id of the OBO. It requires that the file be in OBO v1.2 compatible format. This function is typically executed via the Tripal jobs management after a user… |
| tripal_cv_load_obo_v1_2_url |
tripal_cv/ |
A wrapper function for importing the user specified OBO file into Chado by specifying the remote URL of the OBO. It requires that the file be in OBO v1.2 compatible format. This function is typically executed via the Tripal jobs management after a… |
| tripal_cv_load_update_cvtermpath |
tripal_cv/ |
A function for executing the cvtermpath function of Chado. This function populates the cvtermpath table of Chado for quick lookup of term relationships |
| tripal_cv_obo_add_cvterm_dbxref |
tripal_cv/ |
Adds a database reference to a cvterm |
| tripal_cv_obo_add_cvterm_prop |
tripal_cv/ |
Adds a property to a cvterm |
| tripal_cv_obo_add_dbxref |
tripal_cv/ |
Adds a database cross reference to a cvterm |
| tripal_cv_obo_add_relationship |
tripal_cv/ |
Adds a cvterm relationship |
| tripal_cv_obo_add_synonyms |
tripal_cv/ |
Adds the synonyms to a term |
| tripal_cv_obo_form |
tripal_cv/ |
Provides the form to load an already existing controlled Vocabulary into chado |
| tripal_cv_obo_form_submit |
tripal_cv/ |
The submit function for the load ontology form. It registers a tripal job to import the user specified ontology file |
| tripal_cv_obo_get_term |
tripal_cv/ |
Retreives the term array from the temp loading table for a given term id. |
| tripal_cv_obo_load_typedefs |
tripal_cv/ |
OBO files are divided into a typedefs terms section and vocabulary terms section. This function loads the typedef terms from the OBO. |
| tripal_cv_obo_parse |
tripal_cv/ |
Parse the OBO file and populate the templ loading table |
| tripal_cv_obo_process_term |
tripal_cv/ |
Uses the provided term array to add/update information to Chado about the term including the term, dbxref, synonyms, properties, and relationships. |
| tripal_cv_obo_process_terms |
tripal_cv/ |
OBO files are divided into a typedefs section and a terms section. This function loads the typedef terms from the OBO. |
| tripal_cv_obo_quiterror |
tripal_cv/ |
Immediately terminates loading of the OBO file. |