tripal_cv.owl_loader.php File Reference

Functions
	tripal_cv_parse_owl ($filename)
	tripal_owl_check_class_depedencies (OWLStanza $stanza, $vocab_db_name, &$deps)
	tripal_owl_handle_object_property ($stanza, $vocabs)
	tripal_owl_handle_annotation_property ($stanza, $vocabs)
	tripal_owl_handle_description ($stanza, $vocabs)
	tripal_owl_handle_class (OWLStanza $stanza, $vocabs)

Detailed Description

@add file from header

Function Documentation

tripal_cv_parse_owl()

tripal_cv_parse_owl

(

$filename

)

Parses an OWL XML file and imports the CV terms into Chado

Parameters

$filename

The full path to the OWL XML file.

Returns

No return value.

Exceptions

Exception

tripal_owl_check_class_depedencies()

tripal_owl_check_class_depedencies	(	OWLStanza	$stanza,
			$vocab_db_name,
		&	$deps
	)

Checks for required vocabularies that are not loaded into Chado.

Some vocabularies use terms from other ontologies. If this is happens we need to ensure that the dependent vocabularies are present in the database prior to loading this one. This function adds to the $deps array all of the database names and term accessions that are missing in Chado.

Parameters

$stanza	The OWLStanza object for the current stanza from the OWL file.
$vocab_db_name	The name of the database for the vocabulary being loded.
$deps	The dependencies array. The missing databases are provided in array using a 'db' key, and missing terms are in a second array using a 'dbxref' key.

tripal_owl_handle_annotation_property()

tripal_owl_handle_annotation_property	(		$stanza,
			$vocabs
	)

Parameters

$stanza
$vocabs

Exceptions

Exception

tripal_owl_handle_class()

tripal_owl_handle_class	(	OWLStanza	$stanza,
			$vocabs
	)

The function goes through owl:Class stanza to insert new vocabularies.

Parameters

$stanza	The OWLStanza object for the current stanza from the OWL file.
$vocabs

Exceptions

Exception

tripal_owl_handle_description()

tripal_owl_handle_description	(		$stanza,
			$vocabs
	)

Parameters

$stanza
$vocabs

Exceptions

Exception

tripal_owl_handle_object_property()

tripal_owl_handle_object_property	(		$stanza,
			$vocabs
	)

Parameters

$stanza
$vocabs

Exceptions

Exception