owl package¶
Submodules¶
owl.owlery_query_tools module¶
-
class
vfb_connect.owl.owlery_query_tools.
OWLeryConnect
(endpoint='http://owl.virtualflybrain.org/kbs/vfb/', lookup=None, obo_curies=('FBbt', 'RO', 'BFO'), curies=None)[source]¶ Bases:
object
Wrapper class for querying the VFB OWLery endpoint. Unless you have specialist configuration needs, it is better to access this object with full default configurations from VfbConnect.oc.
- param endpoint
owlery REST endpoint
- param lookup
Dict of name: ID;
- param
obo_curies: list of prefixes for generation of OBO curies. Default: (‘FBbt’, ‘RO’)
- param
curies: Dict of curies
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get_instances
(query, query_by_label=False, direct=False, return_short_forms=False)[source]¶ Generate list of IDs of all instances of class_expression.
- Parameters
class_expression – A valid OWL class expression, e.g. the name of a class.
query_by_label – Optional. If False`, class_expression takes CURIEs instead of labels. Default False
direct – Return direct instances only. Default False
return_short_forms – Optional. If True, returns short_forms instead of IRIs.
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of IRIs or short_forms (depending on return_short_form option)
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get_subclasses
(query, query_by_label=False, direct=False, return_short_forms=False)[source]¶ Generate list of IDs of all subclasses of class_expression.
- Parameters
class_expression – A valid OWL class expression, e.g. the name of a class.
query_by_label – Optional. If False`, class_expression takes CURIEs instead of labels. Default False
direct – Return direct subclasses only. Default False
return_short_forms – Optional. If True, returns short_forms instead of IRIs.
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of IRIs or short_forms (depending on return_short_form option)
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get_superclasses
(query, query_by_label=False, direct=False, return_short_forms=False)[source]¶ Generate list of IDs of all superclasses of class_expression.
- Parameters
class_expression – A valid OWL class expression, e.g. the name (or CURIE) of a class.
query_by_label – Optional. If False`, class_expression takes CURIEs instead of labels. Default False
direct – Return direct instances only. Default False
return_short_forms – Optional. If True, returns short_forms instead of IRIs.
- Returns
Returns a list of terms as nested python data structures following VFB_json or a summary_report_json
- Return type
list of IRIs or short_forms (depending on return_short_form option)
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labels_2_ids
(query_string)[source]¶ Substitutes labels for IDs in a query string
- Parameters
query_string – A OWL class expression in which all labels of OWL entities are single-quoted. Internal
single quotes should be escaped with a backslash. :return: query string in which labels have been converted to unquoted CURIES.
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query
(query_type, return_type, query, query_by_label=False, direct=False, verbose=False)[source]¶ A wrapper for querying Owlery Endpoints. See https://owlery.phenoscape.org/api/ for doc
- Parameters
query_type – Options: subclasses, superclasses,
equivalent, instances, types :param query: ‘Manchester syntax query with owl entities as <iri>,
curie (supporting curies declared on object) or single quoted label (if query_by_label isTrue)
- Parameters
query_by_label – Boolean. Default False.
direct – Boolean. Default False. Determines T/F
:param verbose - print verbose output to stdout for debugging purposes. :return: list of IRIs.