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) | |
@add file from header
tripal_cv_parse_owl | ( | $filename | ) |
Parses an OWL XML file and imports the CV terms into Chado
$filename | The full path to the OWL XML file. |
Exception |
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.
$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 | ( | $stanza, | |
$vocabs | |||
) |
$stanza | |
$vocabs |
Exception |
tripal_owl_handle_class | ( | OWLStanza | $stanza, |
$vocabs | |||
) |
The function goes through owl:Class stanza to insert new vocabularies.
$stanza | The OWLStanza object for the current stanza from the OWL file. |
$vocabs |
Exception |
tripal_owl_handle_description | ( | $stanza, | |
$vocabs | |||
) |
$stanza | |
$vocabs |
Exception |
tripal_owl_handle_object_property | ( | $stanza, | |
$vocabs | |||
) |
$stanza | |
$vocabs |
Exception |