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

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)

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)

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)

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.

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.

vfb_connect.owl.owlery_query_tools.gen_short_form(iri)[source]

Generate short_form (string) from an iri string, assuming short_form delimiters, in order of precedence: ‘#’ ‘/’. :param iri: An iri string :return: short_form

Module contents