Reference·TVB-O Ontology

owl

ontology.owl

— title: “Ontology Module for TVB-O” author: Leon Martin.

This module provides a set of functions to interact with the ontology of TVB-O. It includes functions to:

• Retrieve package version.
• Render ontology objects using labels or IRIs.
• Access and extract various parts of the ontology like models, variables, parameters, etc.
• Compare different models based on their parameters.
• Get properties of parameters.

Usage:

from tvbo.ontology import owl as ontology
jansen_rit_model = ontology.get_model("JansenRit")

Author

Leon K. Martin (2023)

Copyright

Copyright (c) 2023 Charité Universitätsmedizin Berlin

Attributes

Name	Description
DATA_DIR
ONTOLOGY_FILENAME
ONTO_DIR
ROOT_DIR
df_tvbo
functional_models
onto

Functions

Name	Description
add_spaces_around_math_chars	Insert spaces around mathematical operator characters in a string.
compare_models	Compares two TVB models based on their parameters or another specified metric.
contains_math_char	Check whether a string contains a mathematical operator character.
create_acronym	Generate a unique upper-case acronym from a camel-case name.
disintersection	Computes the unique elements of two lists.
extract_most_common	Return the most frequently occurring item across several result lists.
filter_cls_list	Filters out classes from a list that have a specific ancestor.
find_best_fuzzy_match	Find the best fuzzy match for a target string in a list of strings, prioritizing strings that start with the target followed by an underscore.
find_variables	Finds a variable in a TVB model.
find_version	Retrieves the package version from the __init__.py file.
get_all_annotations	Collect all distinct values of an annotation property across every class.
get_class_annotation_properties	Return the annotation properties of an ontology class.
get_class_data_properties	Return the data properties of an ontology class.
get_class_object_properties	Return the object properties of an ontology class.
get_class_properties	Collect the label, identifier, annotation, and object properties of a class.
get_coupling_function	Retrieve a coupling-function class by its label or a synonym.
get_coupling_functions	Return all coupling-function classes keyed by their label.
get_def	Retrieve the description or definition of a class based on the specified mode.
get_default_values	Retrieves the default values for a given TVB model’s parameters.
get_definition	Retrieves the definition for a given ontology class.
get_info	Build a formatted text summary of an ontology class with its definition and references.
get_integrator	Retrieve the ontology class for a named integration method.
get_model	Retrieves a specific TVB-O model using its label.
get_model_acronym	Retrieves the acronym for a given TVB model.
get_model_arguments	Retrieves the arguments for a given TVB model.
get_model_coefficients	Retrieves the coefficients for a given TVB model.
get_model_conditionals	Retrieve the conditional derived variables for a given TVB model.
get_model_constants	Retrieve the constants for a given TVB model.
get_model_coupling_terms	Retrieves the coupling terms for a given TVB model.
get_model_cvars	Retrieves the cvars (coupling variables) for a given TVB model.
get_model_derivatives	Retrieves the derivatives for a given TVB model.
get_model_functions	Retrieves the functions for a given TVB model.
get_model_parameters	Retrieves the parameters for a given TVB model.
get_model_statevariables	Retrieves the state variables for a given TVB model.
get_model_suffix	Retrieves the suffix for a given TVB model, based on its acronym.
get_model_variables	Retrieves the variables for a given TVB model.
get_model_vois	Retrieve the variables of interest (VOIs) for a given TVB model.
get_models	Retrieves all TVB-O models of a given type.
get_object_properties	Collect the object-property relationships of an ontology class.
get_onto	Return the loaded TVB-O ontology object.
get_parameters_by_catalogue	Retrieves parameters for a given TVB model, based on a specified parameter catalogue.
get_property_annotation	Retrieves annotations for a given ontology class and property.
get_range	Retrieves the range for a given ontology variable.
get_sorted_dict	Creates a dictionary from a list of ontology classes. The dictionary’s keys are the class labels and its values are the class objects. The dictionary is sorted alphabetically based on its keys.
get_subclass_list	Retrieves subclasses for a given ontology class, up to a specified depth.
get_subclasses	Retrieves the subclasses for a given TVB-O class.
get_superclasses	Retrieves the superclasses for a given TVB-O class.
get_type	Retrieves the type of a TVB class for a given entity.
hangident	Indent a string by a specified amount.
import_model	Import a model from metadata into the ontology.
intersection	Computes the intersection of two lists.
join_set	Join the unique elements of an iterable into a comma-separated string.
ontology_info	Summarize the contents of the TVB-O ontology as component counts.
render_using_iri	Renders the ontology objects using their IRIs.
render_using_label	Renders the ontology objects using their labels.
replace_suffix	Strip the model-specific suffix from an ontology class’s label.
resolve_class	The ontology class name refers to, by IRI fragment or by label.
search_all	Search the ontology by label, synonym, and symbol and return the best match.
search_class	Searches for an ontology class using a given label.
search_in_model	Search a model’s descendant classes by label or definition for a search string.
select_variables	Selects variables from a list based on a given property.
wrap_text	Pretty print a string with automatic line breaks at specified intervals, while preserving existing new lines.

add_spaces_around_math_chars

ontology.owl.add_spaces_around_math_chars(s)

Insert spaces around mathematical operator characters in a string.

Parameters

Name	Type	Description	Default
s		The string to reformat.	required

Returns

Name	Type	Description
	str	The string with a space added on each side of every +, -, *, /,
	str	or = that is not already surrounded by whitespace.

compare_models

ontology.owl.compare_models(model1, model2, by='ParameterCatalogue')

Compares two TVB models based on their parameters or another specified metric.

Parameters

Name	Type	Description	Default
model1	owlready2.ThingClass or str	The first TVB model for comparison.	required
model2	owlready2.ThingClass or str	The second TVB model for comparison.	required
by	str	The metric to use for comparison. Default is “ParameterCatalogue”.	'ParameterCatalogue'

Returns

Name	Type	Description
	pd.DataFrame	pandas.DataFrame: A dataframe comparing the two TVB models based on the specified metric.

contains_math_char

ontology.owl.contains_math_char(s)

Check whether a string contains a mathematical operator character.

Parameters

Name	Type	Description	Default
s		The string to inspect.	required

Returns

Name	Type	Description
	bool	True if s contains any of +, -, *, /, =, or ^.

create_acronym

ontology.owl.create_acronym(text)

Generate a unique upper-case acronym from a camel-case name.

Letters are taken from each capitalised word, extending the acronym until it no longer collides with an existing acronym in the ontology.

Parameters

Name	Type	Description	Default
text		The camel-case text (e.g. a model name) to build an acronym from.	required

Returns

Name	Type	Description
	str	An upper-case acronym that is unique among existing ontology acronyms.

disintersection

ontology.owl.disintersection(lst1, lst2)

Computes the unique elements of two lists.

Parameters

Name	Type	Description	Default
lst1	list	The first list.	required
lst2	list	The second list.	required

Returns

Name	Type	Description
list	list	The elements that are unique to each list.

extract_most_common

ontology.owl.extract_most_common(searches)

Return the most frequently occurring item across several result lists.

Parameters

Name	Type	Description	Default
searches		An iterable of result lists to flatten and tally.	required

Returns

Name	Type	Description
	owlready2.ThingClass | None	The single most common item, or None if the combined results are empty.

filter_cls_list

ontology.owl.filter_cls_list(cls_list, by)

Filters out classes from a list that have a specific ancestor.

Parameters

Name	Type	Description	Default
cls_list	list	The list of classes to be filtered.	required
by	owlready2.ThingClass	The ancestor class to filter by.	required

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The filtered list of classes.

find_best_fuzzy_match

ontology.owl.find_best_fuzzy_match(target, cls_list)

Find the best fuzzy match for a target string in a list of strings, prioritizing strings that start with the target followed by an underscore.

Parameters

Name	Type	Description	Default
target	str	The target string to match.	required
cls_list	list of str	The list of strings to search.	required

Returns

Name	Type	Description
str	owlready2.ThingClass	The string from the list that best matches the target.

find_variables

ontology.owl.find_variables(
    var,
    model,
    type='all',
    include_synonyms=False,
    find_best_match=True,
)

Finds a variable in a TVB model.

Parameters

Name	Type	Description	Default
var	str	The variable to find.	required
model	owlready2.ThingClass or str	The TVB model to search in.	required
type	str	The type of variable to find. Default is “all”.	'all'
include_synonyms	bool	If True, includes synonyms in the search. Default is False.	False
find_best_match	bool	If True, finds the best fuzzy match if multiple matches are found. Default is True.	True

Returns

Name	Type	Description
	owlready2.ThingClass | None	owlready2.ThingClass or None: The found variable class, or None if not found.

find_version

ontology.owl.find_version()

Retrieves the package version from the __init__.py file.

Returns

Name	Type	Description
str	str	The version of the TVBO package.

Raises

Name	Type	Description
	RuntimeError	If the version cannot be found in the __init__.py file.

get_all_annotations

ontology.owl.get_all_annotations(prop)

Collect all distinct values of an annotation property across every class.

Parameters

Name	Type	Description	Default
prop		The name of the annotation property to gather.	required

Returns

Name	Type	Description
	list[str]	A list of the unique annotation values found across all ontology classes.

get_class_annotation_properties

ontology.owl.get_class_annotation_properties(cls)

Return the annotation properties of an ontology class.

Parameters

Name	Type	Description	Default
cls		The ontology class, or its label string to look up in the ontology.	required

Returns

Name	Type	Description
		The annotation_properties mapping for the class.

get_class_data_properties

ontology.owl.get_class_data_properties(cls)

Return the data properties of an ontology class.

Parameters

Name	Type	Description	Default
cls		The ontology class, or its label string to look up in the ontology.	required

Returns

Name	Type	Description
		The data_properties entry for the class.

get_class_object_properties

ontology.owl.get_class_object_properties(cls)

Return the object properties of an ontology class.

Parameters

Name	Type	Description	Default
cls		The ontology class, or its label string to look up in the ontology.	required

Returns

Name	Type	Description
		The list of object-property relationships for the class.

get_class_properties

ontology.owl.get_class_properties(cls)

Collect the label, identifier, annotation, and object properties of a class.

Parameters

Name	Type	Description	Default
cls		The ontology class, or its label string to look up in the ontology.	required

Returns

Name	Type	Description
		A dictionary with the class’s label, identifier,
		annotation_properties, and object_properties.

get_coupling_function

ontology.owl.get_coupling_function(label='Linear', verbose=True)

Retrieve a coupling-function class by its label or a synonym.

Parameters

Name	Type	Description	Default
label		The label (or synonym) of the coupling function to retrieve.	'Linear'
verbose		If True, print the valid coupling functions when the label is not found.	True

Returns

Name	Type	Description
	owlready2.ThingClass | None	The matching coupling-function class, or None if it is not found.

get_coupling_functions

ontology.owl.get_coupling_functions()

Return all coupling-function classes keyed by their label.

Returns

Name	Type	Description
	dict[str, owlready2.ThingClass]	A dictionary mapping each coupling function’s label to its ontology class.

get_def

ontology.owl.get_def(cls, mode='short')

Retrieve the description or definition of a class based on the specified mode.

This function fetches either a short description or a long definition of the given class. If the requested type (short or long) is not available, it attempts to fetch the other type.

Parameters

cls : class The class for which the description or definition is being retrieved. mode : str, optional The mode specifying the type of text to retrieve: ‘short’ for a brief description or ‘long’ for a detailed definition. The default is ‘short’.

Returns:

str The description or definition of the class. If neither is available, it returns None.

get_default_values

ontology.owl.get_default_values(NMM, tvb_name=False, class_as_key=False)

Retrieves the default values for a given TVB model’s parameters.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the default values for.	required
tvb_name	bool	If True, uses the TVB name for the parameter. Default is False.	False

Returns

Name	Type	Description
dict	dict[str, float | bool | int]	A dictionary of parameter names and their default values.

get_definition

ontology.owl.get_definition(tvbo_class)

Retrieves the definition for a given ontology class.

Parameters

Name	Type	Description	Default
tvbo_class	owlready2.ThingClass or str	The ontology class to retrieve the definition for.	required

Returns

Name	Type	Description
str	str	The definition for the given ontology class.

get_info

ontology.owl.get_info(cls)

Build a formatted text summary of an ontology class with its definition and references.

A class states as much of itself as it carries. 776 of the ontology’s 1516 classes have no definition and 13 have no label; reading either unconditionally is what made this raise AttributeError on more than half of them. The IRI fragment stands in for a missing label, and a missing definition simply leaves that section out. definition and has_reference are annotation properties TVB-O declares, so a class from an imported ontology — owl:Thing among them — does not carry the properties at all, let alone empty ones.

Parameters

Name	Type	Description	Default
cls		The ontology class, or a string naming it by IRI fragment or by label.	required

Returns

Name	Type	Description
	str	A multi-line string with the class label as a heading, its wrapped
	str	definition when it has one, and a references section when it has references.

Raises

Name	Type	Description
	KeyError	If a string names no class in the ontology.

get_integrator

ontology.owl.get_integrator(integration_method='Heun')

Retrieve the ontology class for a named integration method.

Parameters

Name	Type	Description	Default
integration_method		The label of the integration method to look up.	'Heun'

Returns

Name	Type	Description
	owlready2.ThingClass	The matching integration-method class, or None if none is found. When
	owlready2.ThingClass	several match, the first is returned (with a message printed).

get_model

ontology.owl.get_model(label='JansenRit', model_type='NMM', verbose=False)

Retrieves a specific TVB-O model using its label.

Parameters

Name	Type	Description	Default
label	str	The label of the model to retrieve. Default is “JansenRit”.	'JansenRit'
model_type	str	The type of model to retrieve. Default is “NMM”.	'NMM'

Returns

Name	Type	Description
	owlready2.ThingClass	owlready2.ThingClass: The ontology class for the specified model.

get_model_acronym

ontology.owl.get_model_acronym(NMM)

Retrieves the acronym for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the acronym for.	required

Returns

Name	Type	Description
str	str | None	The acronym for the given TVB model.

get_model_arguments

ontology.owl.get_model_arguments(NMM)

Retrieves the arguments for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the arguments for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass]	A dictionary of argument labels and their corresponding ontology class objects.

get_model_coefficients

ontology.owl.get_model_coefficients(NMM)

Retrieves the coefficients for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the coefficients for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass]	A dictionary of coefficient labels and their corresponding ontology class objects.

get_model_conditionals

ontology.owl.get_model_conditionals(NMM)

Retrieve the conditional derived variables for a given TVB model.

Parameters

Name	Type	Description	Default
NMM		The TVB model to retrieve the conditionals for, or its label string.	required

Returns

Name	Type	Description
	dict[str, owlready2.ThingClass]	A dictionary mapping each suffix-stripped conditional label to its
	dict[str, owlready2.ThingClass]	ontology class object.

get_model_constants

ontology.owl.get_model_constants(NMM, return_as_dict=True)

Retrieve the constants for a given TVB model.

Parameters

Name	Type	Description	Default
NMM		The TVB model to retrieve the constants for, or its label string.	required
return_as_dict		If True, sort and key the constants by their label before suffix stripping.	True

Returns

Name	Type	Description
	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	A dictionary mapping each suffix-stripped constant label to its ontology
	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	class object.

get_model_coupling_terms

ontology.owl.get_model_coupling_terms(
    NMM,
    only_global=True,
    return_as_dict=True,
)

Retrieves the coupling terms for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the coupling terms for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	A dictionary of coupling term labels and their corresponding ontology class objects.

get_model_cvars

ontology.owl.get_model_cvars(NMM, return_as_dict=True)

Retrieves the cvars (coupling variables) for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the cvars for.	required

Returns

Name	Type	Description
list	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	The cvars for the given TVB model.

get_model_derivatives

ontology.owl.get_model_derivatives(NMM, return_as_dict=True)

Retrieves the derivatives for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the derivatives for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	A dictionary of derivative labels and their corresponding ontology class objects.

get_model_functions

ontology.owl.get_model_functions(NMM)

Retrieves the functions for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the functions for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass]	A dictionary of function labels and their corresponding ontology class objects.

get_model_parameters

ontology.owl.get_model_parameters(NMM, return_as_dict=True)

Retrieves the parameters for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the parameters for.	required

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	A dictionary of parameter labels and their corresponding ontology class objects.

get_model_statevariables

ontology.owl.get_model_statevariables(NMM, return_as_dict=True)

Retrieves the state variables for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the state variables for.	required
return_as_dict	bool	If True, returns the state variables as a dictionary. Default is True.	True

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass] | list[owlready2.ThingClass]	A dictionary of state variable labels and their corresponding ontology class objects.

get_model_suffix

ontology.owl.get_model_suffix(NMM)

Retrieves the suffix for a given TVB model, based on its acronym.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the suffix for.	required

Returns

Name	Type	Description
str	str	The suffix for the given TVB model.

get_model_variables

ontology.owl.get_model_variables(NMM)

Retrieves the variables for a given TVB model.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve the variables for.	required

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The list of variables for the given TVB model.

get_model_vois

ontology.owl.get_model_vois(model)

Retrieve the variables of interest (VOIs) for a given TVB model.

Combines the model’s default VOIs with any extra VOIs listed on the model, spacing out operator-based expressions.

Parameters

Name	Type	Description	Default
model		The TVB model to retrieve the VOIs for, or its label string.	required

Returns

Name	Type	Description
	tuple[str]	A sorted tuple of unique VOI names, falling back to the model’s state
	tuple[str]	variables when no VOIs are defined.

get_models

ontology.owl.get_models(model_type='NMM', from_df=False)

Retrieves all TVB-O models of a given type.

Parameters

Name	Type	Description	Default
model_type	str	The type of model to retrieve. Default is “NMM”.	'NMM'
from_df	bool	If True, retrieves models from a dataframe. Default is False.	False

Returns

Name	Type	Description
dict	dict[str, owlready2.ThingClass]	A dictionary of model labels and their corresponding ontology class objects.

get_object_properties

ontology.owl.get_object_properties(ontology_class, include_restriction=True)

Collect the object-property relationships of an ontology class.

Parameters

Name	Type	Description	Default
ontology_class		The ontology class to inspect.	required
include_restriction		If True, include owl:someValuesFrom-style restriction relationships.	True

Returns

Name	Type	Description
		A list of single-key dictionaries mapping each property name (or
		"is_a") to its target value.

get_onto

ontology.owl.get_onto()

Return the loaded TVB-O ontology object.

Returns

Name	Type	Description
	owlready2.namespace.Ontology	The loaded owlready2 ontology backing this module.

get_parameters_by_catalogue

ontology.owl.get_parameters_by_catalogue(NMM, param_key)

Retrieves parameters for a given TVB model, based on a specified parameter catalogue.

Parameters

Name	Type	Description	Default
NMM	owlready2.ThingClass or str	The TVB model to retrieve parameters for.	required
param_key	str	The parameter catalogue to use for retrieving parameters.	required

Returns

Name	Type	Description
	pd.DataFrame	pandas.DataFrame: A dataframe of parameters, their definitions, and their categories.

get_property_annotation

ontology.owl.get_property_annotation(tvbo_class, property)

Retrieves annotations for a given ontology class and property.

Parameters

Name	Type	Description	Default
tvbo_class	owlready2.ThingClass or str	The ontology class to retrieve annotations for.	required
property	str	The property to retrieve annotations for.	required

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The annotations for the given ontology class and property.

get_range

ontology.owl.get_range(variable, return_array=False)

Retrieves the range for a given ontology variable.

Parameters

Name	Type	Description	Default
variable	owlready2.ThingClass or str	The ontology variable to retrieve the range for.	required
return_array	bool	If True, returns the range as an array. Default is False.	False

Returns

Name	Type	Description
	tuple | np.ndarray	tuple or numpy.ndarray: The range for the given ontology variable.

get_sorted_dict

ontology.owl.get_sorted_dict(class_list)

Creates a dictionary from a list of ontology classes. The dictionary’s keys are the class labels and its values are the class objects. The dictionary is sorted alphabetically based on its keys.

Parameters

Name	Type	Description	Default
class_list	list	The list of ontology classes.	required

Returns

Name	Type	Description
dict	dict	A sorted dictionary of class labels and their corresponding class objects.

get_subclass_list

ontology.owl.get_subclass_list(cls, level=1, exclude_cls=None)

Retrieves subclasses for a given ontology class, up to a specified depth.

Parameters

Name	Type	Description	Default
cls	owlready2.ThingClass	The ontology class to retrieve subclasses for.	required
level	int	The depth to retrieve subclasses up to. Default is 1.	1
exclude_cls	owlready2.ThingClass	A class to exclude from the results. Default is None.	None

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The list of subclasses for the given ontology class.

get_subclasses

ontology.owl.get_subclasses(tvbo_class, recursive=False)

Retrieves the subclasses for a given TVB-O class.

Parameters

Name	Type	Description	Default
tvbo_class	owlready2.ThingClass	The TVB-O class to retrieve subclasses for.	required
recursive	bool	If True, retrieves subclasses recursively. Default is False.	False

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The list of subclasses for the given TVB-O class.

get_superclasses

ontology.owl.get_superclasses(tvbo_class)

Retrieves the superclasses for a given TVB-O class.

Parameters

Name	Type	Description	Default
tvbo_class	owlready2.ThingClass	The TVB-O class to retrieve superclasses for.	required

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The list of superclasses for the given TVB-O class.

get_type

ontology.owl.get_type(c)

Retrieves the type of a TVB class for a given entity.

Parameters

Name	Type	Description	Default
c	owlready2.ThingClass	The TVB class instance.	required

Returns

Name	Type	Description
str	owlready2.ThingClass	The type of the TVB entity.

hangident

ontology.owl.hangident(text, indent=4)

Indent a string by a specified amount.

Parameters

Name	Type	Description	Default
text	str	The text to be indented.	required
indent	int	The amount to indent the text by.	4

import_model

ontology.owl.import_model(model_metadata, model_name=None)

Import a model from metadata into the ontology.

Creates ontology subclasses for state variables, parameters, derived variables, and output transforms.

Parameters

Name	Type	Description	Default
model_metadata	Union[str, dict, tvbo_datamodel.Dynamics, tvbo_datamodel.SimulationExperiment]	A Dynamics, SimulationExperiment, dict, or path to a YAML file.	required
model_name	str | None	Name to use for the created ontology class.	None

Returns

Name	Type	Description
	owlready2.ThingClass	owlready2.entity.ThingClass: The created ontology model class.

intersection

ontology.owl.intersection(lst1, lst2)

Computes the intersection of two lists.

Parameters

Name	Type	Description	Default
lst1	list	The first list.	required
lst2	list	The second list.	required

Returns

Name	Type	Description
list	list	The intersection of the two given lists.

join_set

ontology.owl.join_set(a)

Join the unique elements of an iterable into a comma-separated string.

Parameters

Name	Type	Description	Default
a		The iterable of strings whose distinct values are joined.	required

Returns

Name	Type	Description
		A comma-separated string of the distinct elements.

ontology_info

ontology.owl.ontology_info(print_info=True, return_info=False, return_df=False)

Summarize the contents of the TVB-O ontology as component counts.

Parameters

Name	Type	Description	Default
print_info		If True, print the base IRI and a count of each component group.	True
return_info		If True, return the collected components as a Bunch.	False
return_df		If True, return the component counts as a pandas.DataFrame.	False

Returns

Name	Type	Description
		A Bunch of component lists when return_info is set, or a count
		DataFrame indexed by component name when return_df is set; otherwise
		nothing is returned.

render_using_iri

ontology.owl.render_using_iri(entity)

Renders the ontology objects using their IRIs.

Parameters

Name	Type	Description	Default
entity	owlready2.entity	The ontology class or entity to be rendered.	required

Returns

Name	Type	Description
str	str	The IRI of the given ontology entity.

render_using_label

ontology.owl.render_using_label(entity)

Renders the ontology objects using their labels.

Parameters

Name	Type	Description	Default
entity	owlready2.entity	The ontology class or entity to be rendered.	required

Returns

Name	Type	Description
str	str	The label of the given ontology entity.

replace_suffix

ontology.owl.replace_suffix(cls)

Strip the model-specific suffix from an ontology class’s label.

The suffix is derived from the acronyms of the class’s neural-mass-model, coupling, or data-type ancestors.

Parameters

Name	Type	Description	Default
cls		The ontology class, or its label string to look up in the ontology.	required

Returns

Name	Type	Description
	str	The class label with any matching ancestor suffix removed. The original
	str	label (or string) is returned when no suffix matches.

resolve_class

ontology.owl.resolve_class(name)

The ontology class name refers to, by IRI fragment or by label.

onto[...] resolves a fragment only within the ontology’s own IRI, so every class reached through an import — Annotation, Space, the UBERON and NCBITaxon terms — is invisible to it. The imported classes are searched here too.

Both lookups are exact. The ontology’s own label_search matches loosely, which is right for a search box and wrong for resolving a name: it answers 'Annotation' with 'annotation criteria application', a different class, with no sign that it guessed. A name that matches nothing raises rather than yielding None for the caller to fail on later.

Raises

Name	Type	Description
	KeyError	If no class carries that IRI fragment or that exact label.

search_all

ontology.owl.search_all(search_term, from_class=None, case_sensitive=False)

Search the ontology by label, synonym, and symbol and return the best match.

Parameters

Name	Type	Description	Default
search_term		The prefix to search for.	required
from_class		Restrict the search to this class’s descendants; if None, search all ontology classes.	None
case_sensitive		If True, perform a case-sensitive search.	False

Returns

Name	Type	Description
	owlready2.ThingClass | None	The class matching across the most search dimensions, or None if
	owlready2.ThingClass | None	nothing matches.

search_class

ontology.owl.search_class(label)

Searches for an ontology class using a given label.

Parameters

Name	Type	Description	Default
label	str	The label to search for, with regex support.	required

Returns

Name	Type	Description
	owlready2.ThingClass | owlready2.triplelite._SearchList	owlready2.ThingClass or owlready2.triplelite._SearchList:
	owlready2.ThingClass | owlready2.triplelite._SearchList	The ontology class(es) that match the given label.

search_in_model

ontology.owl.search_in_model(search_str, model, wildcards=True)

Search a model’s descendant classes by label or definition for a search string.

Parameters

Name	Type	Description	Default
search_str		The text to search for.	required
model	owlready2.ThingClass	The TVB model to search within, or its label string.	required
wildcards		If True, wrap search_str in * wildcards; otherwise append the model’s suffix to the search string.	True

Returns

Name	Type	Description
	owlready2.ThingClass | list[owlready2.ThingClass] | None	The single matching class when exactly one is found, None when none
	owlready2.ThingClass | list[owlready2.ThingClass] | None	match, or the list of matching classes otherwise.

select_variables

ontology.owl.select_variables(variables, property)

Selects variables from a list based on a given property.

Parameters

Name	Type	Description	Default
variables	list	The list of variables to select from.	required
property	str	The property to use for selecting variables.	required

Returns

Name	Type	Description
list	list[owlready2.ThingClass]	The selected variables.

wrap_text

ontology.owl.wrap_text(text, line_length=100, line_breaks='\n')

Pretty print a string with automatic line breaks at specified intervals, while preserving existing new lines.

Parameters

Name	Type	Description	Default
text	str	The text to be printed.	required
line_length	int	The maximum length of each line.	100