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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
$filenameThe 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
$stanzaThe OWLStanza object for the current stanza from the OWL file.
$vocab_db_nameThe name of the database for the vocabulary being loded.
$depsThe 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
$stanzaThe 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