# owl { #tvbo.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: ```python from tvbo.ontology import owl as ontology jansen_rit_model = ontology.get_model("JansenRit") ``` ## Author {.doc-section .doc-section-author} Leon K. Martin (2023) ## Copyright {.doc-section .doc-section-copyright} Copyright (c) 2023 Charité Universitätsmedizin Berlin ## Attributes | Name | Description | | --- | --- | | [DATA_DIR](#tvbo.ontology.owl.DATA_DIR) | | | [ONTOLOGY_FILENAME](#tvbo.ontology.owl.ONTOLOGY_FILENAME) | | | [ONTO_DIR](#tvbo.ontology.owl.ONTO_DIR) | | | [ROOT_DIR](#tvbo.ontology.owl.ROOT_DIR) | | | [df_tvbo](#tvbo.ontology.owl.df_tvbo) | | | [functional_models](#tvbo.ontology.owl.functional_models) | | | [onto](#tvbo.ontology.owl.onto) | | ## Functions | Name | Description | | --- | --- | | [add_spaces_around_math_chars](#tvbo.ontology.owl.add_spaces_around_math_chars) | Insert spaces around mathematical operator characters in a string. | | [compare_models](#tvbo.ontology.owl.compare_models) | Compares two TVB models based on their parameters or another specified metric. | | [contains_math_char](#tvbo.ontology.owl.contains_math_char) | Check whether a string contains a mathematical operator character. | | [create_acronym](#tvbo.ontology.owl.create_acronym) | Generate a unique upper-case acronym from a camel-case name. | | [disintersection](#tvbo.ontology.owl.disintersection) | Computes the unique elements of two lists. | | [extract_most_common](#tvbo.ontology.owl.extract_most_common) | Return the most frequently occurring item across several result lists. | | [filter_cls_list](#tvbo.ontology.owl.filter_cls_list) | Filters out classes from a list that have a specific ancestor. | | [find_best_fuzzy_match](#tvbo.ontology.owl.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](#tvbo.ontology.owl.find_variables) | Finds a variable in a TVB model. | | [find_version](#tvbo.ontology.owl.find_version) | Retrieves the package version from the `__init__.py` file. | | [get_all_annotations](#tvbo.ontology.owl.get_all_annotations) | Collect all distinct values of an annotation property across every class. | | [get_class_annotation_properties](#tvbo.ontology.owl.get_class_annotation_properties) | Return the annotation properties of an ontology class. | | [get_class_data_properties](#tvbo.ontology.owl.get_class_data_properties) | Return the data properties of an ontology class. | | [get_class_object_properties](#tvbo.ontology.owl.get_class_object_properties) | Return the object properties of an ontology class. | | [get_class_properties](#tvbo.ontology.owl.get_class_properties) | Collect the label, identifier, annotation, and object properties of a class. | | [get_coupling_function](#tvbo.ontology.owl.get_coupling_function) | Retrieve a coupling-function class by its label or a synonym. | | [get_coupling_functions](#tvbo.ontology.owl.get_coupling_functions) | Return all coupling-function classes keyed by their label. | | [get_def](#tvbo.ontology.owl.get_def) | Retrieve the description or definition of a class based on the specified mode. | | [get_default_values](#tvbo.ontology.owl.get_default_values) | Retrieves the default values for a given TVB model's parameters. | | [get_definition](#tvbo.ontology.owl.get_definition) | Retrieves the definition for a given ontology class. | | [get_info](#tvbo.ontology.owl.get_info) | Build a formatted text summary of an ontology class with its definition and references. | | [get_integrator](#tvbo.ontology.owl.get_integrator) | Retrieve the ontology class for a named integration method. | | [get_model](#tvbo.ontology.owl.get_model) | Retrieves a specific TVB-O model using its label. | | [get_model_acronym](#tvbo.ontology.owl.get_model_acronym) | Retrieves the acronym for a given TVB model. | | [get_model_arguments](#tvbo.ontology.owl.get_model_arguments) | Retrieves the arguments for a given TVB model. | | [get_model_coefficients](#tvbo.ontology.owl.get_model_coefficients) | Retrieves the coefficients for a given TVB model. | | [get_model_conditionals](#tvbo.ontology.owl.get_model_conditionals) | Retrieve the conditional derived variables for a given TVB model. | | [get_model_constants](#tvbo.ontology.owl.get_model_constants) | Retrieve the constants for a given TVB model. | | [get_model_coupling_terms](#tvbo.ontology.owl.get_model_coupling_terms) | Retrieves the coupling terms for a given TVB model. | | [get_model_cvars](#tvbo.ontology.owl.get_model_cvars) | Retrieves the cvars (coupling variables) for a given TVB model. | | [get_model_derivatives](#tvbo.ontology.owl.get_model_derivatives) | Retrieves the derivatives for a given TVB model. | | [get_model_functions](#tvbo.ontology.owl.get_model_functions) | Retrieves the functions for a given TVB model. | | [get_model_parameters](#tvbo.ontology.owl.get_model_parameters) | Retrieves the parameters for a given TVB model. | | [get_model_statevariables](#tvbo.ontology.owl.get_model_statevariables) | Retrieves the state variables for a given TVB model. | | [get_model_suffix](#tvbo.ontology.owl.get_model_suffix) | Retrieves the suffix for a given TVB model, based on its acronym. | | [get_model_variables](#tvbo.ontology.owl.get_model_variables) | Retrieves the variables for a given TVB model. | | [get_model_vois](#tvbo.ontology.owl.get_model_vois) | Retrieve the variables of interest (VOIs) for a given TVB model. | | [get_models](#tvbo.ontology.owl.get_models) | Retrieves all TVB-O models of a given type. | | [get_object_properties](#tvbo.ontology.owl.get_object_properties) | Collect the object-property relationships of an ontology class. | | [get_onto](#tvbo.ontology.owl.get_onto) | Return the loaded TVB-O ontology object. | | [get_parameters_by_catalogue](#tvbo.ontology.owl.get_parameters_by_catalogue) | Retrieves parameters for a given TVB model, based on a specified parameter catalogue. | | [get_property_annotation](#tvbo.ontology.owl.get_property_annotation) | Retrieves annotations for a given ontology class and property. | | [get_range](#tvbo.ontology.owl.get_range) | Retrieves the range for a given ontology variable. | | [get_sorted_dict](#tvbo.ontology.owl.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](#tvbo.ontology.owl.get_subclass_list) | Retrieves subclasses for a given ontology class, up to a specified depth. | | [get_subclasses](#tvbo.ontology.owl.get_subclasses) | Retrieves the subclasses for a given TVB-O class. | | [get_superclasses](#tvbo.ontology.owl.get_superclasses) | Retrieves the superclasses for a given TVB-O class. | | [get_type](#tvbo.ontology.owl.get_type) | Retrieves the type of a TVB class for a given entity. | | [hangident](#tvbo.ontology.owl.hangident) | Indent a string by a specified amount. | | [import_model](#tvbo.ontology.owl.import_model) | Import a model from metadata into the ontology. | | [intersection](#tvbo.ontology.owl.intersection) | Computes the intersection of two lists. | | [join_set](#tvbo.ontology.owl.join_set) | Join the unique elements of an iterable into a comma-separated string. | | [ontology_info](#tvbo.ontology.owl.ontology_info) | Summarize the contents of the TVB-O ontology as component counts. | | [render_using_iri](#tvbo.ontology.owl.render_using_iri) | Renders the ontology objects using their IRIs. | | [render_using_label](#tvbo.ontology.owl.render_using_label) | Renders the ontology objects using their labels. | | [replace_suffix](#tvbo.ontology.owl.replace_suffix) | Strip the model-specific suffix from an ontology class's label. | | [resolve_class](#tvbo.ontology.owl.resolve_class) | The ontology class *name* refers to, by IRI fragment or by label. | | [search_all](#tvbo.ontology.owl.search_all) | Search the ontology by label, synonym, and symbol and return the best match. | | [search_class](#tvbo.ontology.owl.search_class) | Searches for an ontology class using a given label. | | [search_in_model](#tvbo.ontology.owl.search_in_model) | Search a model's descendant classes by label or definition for a search string. | | [select_variables](#tvbo.ontology.owl.select_variables) | Selects variables from a list based on a given property. | | [wrap_text](#tvbo.ontology.owl.wrap_text) | Pretty print a string with automatic line breaks at specified intervals, while preserving existing new lines. | ### add_spaces_around_math_chars { #tvbo.ontology.owl.add_spaces_around_math_chars } ```python ontology.owl.add_spaces_around_math_chars(s) ``` Insert spaces around mathematical operator characters in a string. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|-------------------------|------------| | s | | The string to reformat. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.compare_models } ```python ontology.owl.compare_models(model1, model2, by='ParameterCatalogue') ``` Compares two TVB models based on their parameters or another specified metric. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------------|-------------------------------------------------------------------------------------------| | | pd.DataFrame | pandas.DataFrame: A dataframe comparing the two TVB models based on the specified metric. | ### contains_math_char { #tvbo.ontology.owl.contains_math_char } ```python ontology.owl.contains_math_char(s) ``` Check whether a string contains a mathematical operator character. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|------------------------|------------| | s | | The string to inspect. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|--------------------------------------------------------------| | | bool | True if `s` contains any of `+`, `-`, `*`, `/`, `=`, or `^`. | ### create_acronym { #tvbo.ontology.owl.create_acronym } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|-------------------------------------------------------------------|------------| | text | | The camel-case text (e.g. a model name) to build an acronym from. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|------------------------------------------------------------------------| | | str | An upper-case acronym that is unique among existing ontology acronyms. | ### disintersection { #tvbo.ontology.owl.disintersection } ```python ontology.owl.disintersection(lst1, lst2) ``` Computes the unique elements of two lists. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|------------------|------------| | lst1 | list | The first list. | _required_ | | lst2 | list | The second list. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|--------------------------------------------| | list | list | The elements that are unique to each list. | ### extract_most_common { #tvbo.ontology.owl.extract_most_common } ```python ontology.owl.extract_most_common(searches) ``` Return the most frequently occurring item across several result lists. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |----------|--------|---------------------------------------------------|------------| | searches | | An iterable of result lists to flatten and tally. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|---------------------------------------------------------------------------| | | owlready2.ThingClass \| None | The single most common item, or `None` if the combined results are empty. | ### filter_cls_list { #tvbo.ontology.owl.filter_cls_list } ```python ontology.owl.filter_cls_list(cls_list, by) ``` Filters out classes from a list that have a specific ancestor. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|-------------------------------| | list | list\[owlready2.ThingClass\] | The filtered list of classes. | ### find_best_fuzzy_match { #tvbo.ontology.owl.find_best_fuzzy_match } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|----------------------|--------------------------------------------------------| | str | owlready2.ThingClass | The string from the list that best matches the target. | ### find_variables { #tvbo.ontology.owl.find_variables } ```python ontology.owl.find_variables( var, model, type='all', include_synonyms=False, find_best_match=True, ) ``` Finds a variable in a TVB model. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|-------------------------------------------------------------------------------| | | owlready2.ThingClass \| None | owlready2.ThingClass or None: The found variable class, or None if not found. | ### find_version { #tvbo.ontology.owl.find_version } ```python ontology.owl.find_version() ``` Retrieves the package version from the `__init__.py` file. #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------| | str | str | The version of the TVBO package. | #### Raises {.doc-section .doc-section-raises} | Name | Type | Description | |--------|--------------|-----------------------------------------------------------| | | RuntimeError | If the version cannot be found in the `__init__.py` file. | ### get_all_annotations { #tvbo.ontology.owl.get_all_annotations } ```python ontology.owl.get_all_annotations(prop) ``` Collect all distinct values of an annotation property across every class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|------------------------------------------------|------------| | prop | | The name of the annotation property to gather. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-------------|---------------------------------------------------------------------------| | | list\[str\] | A list of the unique annotation values found across all ontology classes. | ### get_class_annotation_properties { #tvbo.ontology.owl.get_class_annotation_properties } ```python ontology.owl.get_class_annotation_properties(cls) ``` Return the annotation properties of an ontology class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|---------------------------------------------------------------------|------------| | cls | | The ontology class, or its label string to look up in the ontology. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------------------------| | | | The `annotation_properties` mapping for the class. | ### get_class_data_properties { #tvbo.ontology.owl.get_class_data_properties } ```python ontology.owl.get_class_data_properties(cls) ``` Return the data properties of an ontology class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|---------------------------------------------------------------------|------------| | cls | | The ontology class, or its label string to look up in the ontology. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|--------------------------------------------| | | | The `data_properties` entry for the class. | ### get_class_object_properties { #tvbo.ontology.owl.get_class_object_properties } ```python ontology.owl.get_class_object_properties(cls) ``` Return the object properties of an ontology class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|---------------------------------------------------------------------|------------| | cls | | The ontology class, or its label string to look up in the ontology. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------------------------------| | | | The list of object-property relationships for the class. | ### get_class_properties { #tvbo.ontology.owl.get_class_properties } ```python ontology.owl.get_class_properties(cls) ``` Collect the label, identifier, annotation, and object properties of a class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|---------------------------------------------------------------------|------------| | cls | | The ontology class, or its label string to look up in the ontology. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|------------------------------------------------------| | | | A dictionary with the class's `label`, `identifier`, | | | | `annotation_properties`, and `object_properties`. | ### get_coupling_function { #tvbo.ontology.owl.get_coupling_function } ```python ontology.owl.get_coupling_function(label='Linear', verbose=True) ``` Retrieve a coupling-function class by its label or a synonym. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|---------------------------------------------------------------------| | | owlready2.ThingClass \| None | The matching coupling-function class, or `None` if it is not found. | ### get_coupling_functions { #tvbo.ontology.owl.get_coupling_functions } ```python ontology.owl.get_coupling_functions() ``` Return all coupling-function classes keyed by their label. #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|----------------------------------------------------------------------------| | | dict\[str, owlready2.ThingClass\] | A dictionary mapping each coupling function's label to its ontology class. | ### get_def { #tvbo.ontology.owl.get_def } ```python 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 {.doc-section .doc-section-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: {.doc-section .doc-section-returns} str The description or definition of the class. If neither is available, it returns None. ### get_default_values { #tvbo.ontology.owl.get_default_values } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|-----------------------------------------------------------| | dict | dict\[str, float \| bool \| int\] | A dictionary of parameter names and their default values. | ### get_definition { #tvbo.ontology.owl.get_definition } ```python ontology.owl.get_definition(tvbo_class) ``` Retrieves the definition for a given ontology class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |------------|-----------------------------|----------------------------------------------------|------------| | tvbo_class | owlready2.ThingClass or str | The ontology class to retrieve the definition for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------------------| | str | str | The definition for the given ontology class. | ### get_info { #tvbo.ontology.owl.get_info } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|------------------------------------------------------------------------|------------| | cls | | The ontology class, or a string naming it by IRI fragment or by label. | _required_ | #### Returns {.doc-section .doc-section-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 {.doc-section .doc-section-raises} | Name | Type | Description | |--------|----------|---------------------------------------------| | | KeyError | If a string names no class in the ontology. | ### get_integrator { #tvbo.ontology.owl.get_integrator } ```python ontology.owl.get_integrator(integration_method='Heun') ``` Retrieve the ontology class for a named integration method. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------------------|--------|-------------------------------------------------|-----------| | integration_method | | The label of the integration method to look up. | `'Heun'` | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model } ```python ontology.owl.get_model(label='JansenRit', model_type='NMM', verbose=False) ``` Retrieves a specific TVB-O model using its label. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|----------------------|-------------------------------------------------------------------| | | owlready2.ThingClass | owlready2.ThingClass: The ontology class for the specified model. | ### get_model_acronym { #tvbo.ontology.owl.get_model_acronym } ```python ontology.owl.get_model_acronym(NMM) ``` Retrieves the acronym for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|--------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the acronym for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-------------|--------------------------------------| | str | str \| None | The acronym for the given TVB model. | ### get_model_arguments { #tvbo.ontology.owl.get_model_arguments } ```python ontology.owl.get_model_arguments(NMM) ``` Retrieves the arguments for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|----------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the arguments for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|---------------------------------------------------------------------------------| | dict | dict\[str, owlready2.ThingClass\] | A dictionary of argument labels and their corresponding ontology class objects. | ### get_model_coefficients { #tvbo.ontology.owl.get_model_coefficients } ```python ontology.owl.get_model_coefficients(NMM) ``` Retrieves the coefficients for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|-------------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the coefficients for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|------------------------------------------------------------------------------------| | dict | dict\[str, owlready2.ThingClass\] | A dictionary of coefficient labels and their corresponding ontology class objects. | ### get_model_conditionals { #tvbo.ontology.owl.get_model_conditionals } ```python ontology.owl.get_model_conditionals(NMM) ``` Retrieve the conditional derived variables for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|----------------------------------------------------------------------|------------| | NMM | | The TVB model to retrieve the conditionals for, or its label string. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_constants } ```python ontology.owl.get_model_constants(NMM, return_as_dict=True) ``` Retrieve the constants for a given TVB model. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_coupling_terms } ```python ontology.owl.get_model_coupling_terms( NMM, only_global=True, return_as_dict=True, ) ``` Retrieves the coupling terms for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|---------------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the coupling terms for. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_cvars } ```python ontology.owl.get_model_cvars(NMM, return_as_dict=True) ``` Retrieves the cvars (coupling variables) for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the cvars for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-------------------------------------------------------------------|------------------------------------| | list | dict\[str, owlready2.ThingClass\] \| list\[owlready2.ThingClass\] | The cvars for the given TVB model. | ### get_model_derivatives { #tvbo.ontology.owl.get_model_derivatives } ```python ontology.owl.get_model_derivatives(NMM, return_as_dict=True) ``` Retrieves the derivatives for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|------------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the derivatives for. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_functions } ```python ontology.owl.get_model_functions(NMM) ``` Retrieves the functions for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|----------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the functions for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|---------------------------------------------------------------------------------| | dict | dict\[str, owlready2.ThingClass\] | A dictionary of function labels and their corresponding ontology class objects. | ### get_model_parameters { #tvbo.ontology.owl.get_model_parameters } ```python ontology.owl.get_model_parameters(NMM, return_as_dict=True) ``` Retrieves the parameters for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|-----------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the parameters for. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_statevariables } ```python ontology.owl.get_model_statevariables(NMM, return_as_dict=True) ``` Retrieves the state variables for a given TVB model. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_model_suffix } ```python ontology.owl.get_model_suffix(NMM) ``` Retrieves the suffix for a given TVB model, based on its acronym. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|-------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the suffix for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|-------------------------------------| | str | str | The suffix for the given TVB model. | ### get_model_variables { #tvbo.ontology.owl.get_model_variables } ```python ontology.owl.get_model_variables(NMM) ``` Retrieves the variables for a given TVB model. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|-----------------------------|----------------------------------------------|------------| | NMM | owlready2.ThingClass or str | The TVB model to retrieve the variables for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|------------------------------------------------| | list | list\[owlready2.ThingClass\] | The list of variables for the given TVB model. | ### get_model_vois { #tvbo.ontology.owl.get_model_vois } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|--------------------------------------------------------------|------------| | model | | The TVB model to retrieve the VOIs for, or its label string. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.get_models } ```python ontology.owl.get_models(model_type='NMM', from_df=False) ``` Retrieves all TVB-O models of a given type. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|-----------------------------------|------------------------------------------------------------------------------| | dict | dict\[str, owlready2.ThingClass\] | A dictionary of model labels and their corresponding ontology class objects. | ### get_object_properties { #tvbo.ontology.owl.get_object_properties } ```python ontology.owl.get_object_properties(ontology_class, include_restriction=True) ``` Collect the object-property relationships of an ontology class. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|------------------------------------------------------------------| | | | A list of single-key dictionaries mapping each property name (or | | | | `"is_a"`) to its target value. | ### get_onto { #tvbo.ontology.owl.get_onto } ```python ontology.owl.get_onto() ``` Return the loaded TVB-O ontology object. #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|------------------------------------------------------| | | owlready2.namespace.Ontology | The loaded `owlready2` ontology backing this module. | ### get_parameters_by_catalogue { #tvbo.ontology.owl.get_parameters_by_catalogue } ```python ontology.owl.get_parameters_by_catalogue(NMM, param_key) ``` Retrieves parameters for a given TVB model, based on a specified parameter catalogue. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------------|---------------------------------------------------------------------------------------| | | pd.DataFrame | pandas.DataFrame: A dataframe of parameters, their definitions, and their categories. | ### get_property_annotation { #tvbo.ontology.owl.get_property_annotation } ```python ontology.owl.get_property_annotation(tvbo_class, property) ``` Retrieves annotations for a given ontology class and property. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|------------------------------------------------------------| | list | list\[owlready2.ThingClass\] | The annotations for the given ontology class and property. | ### get_range { #tvbo.ontology.owl.get_range } ```python ontology.owl.get_range(variable, return_array=False) ``` Retrieves the range for a given ontology variable. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|---------------------|--------------------------------------------------------------------| | | tuple \| np.ndarray | tuple or numpy.ndarray: The range for the given ontology variable. | ### get_sorted_dict { #tvbo.ontology.owl.get_sorted_dict } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |------------|--------|-------------------------------|------------| | class_list | list | The list of ontology classes. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------------------------------------------------| | dict | dict | A sorted dictionary of class labels and their corresponding class objects. | ### get_subclass_list { #tvbo.ontology.owl.get_subclass_list } ```python ontology.owl.get_subclass_list(cls, level=1, exclude_cls=None) ``` Retrieves subclasses for a given ontology class, up to a specified depth. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|------------------------------------------------------| | list | list\[owlready2.ThingClass\] | The list of subclasses for the given ontology class. | ### get_subclasses { #tvbo.ontology.owl.get_subclasses } ```python ontology.owl.get_subclasses(tvbo_class, recursive=False) ``` Retrieves the subclasses for a given TVB-O class. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|---------------------------------------------------| | list | list\[owlready2.ThingClass\] | The list of subclasses for the given TVB-O class. | ### get_superclasses { #tvbo.ontology.owl.get_superclasses } ```python ontology.owl.get_superclasses(tvbo_class) ``` Retrieves the superclasses for a given TVB-O class. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |------------|----------------------|-----------------------------------------------|------------| | tvbo_class | owlready2.ThingClass | The TVB-O class to retrieve superclasses for. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|-----------------------------------------------------| | list | list\[owlready2.ThingClass\] | The list of superclasses for the given TVB-O class. | ### get_type { #tvbo.ontology.owl.get_type } ```python ontology.owl.get_type(c) ``` Retrieves the type of a TVB class for a given entity. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|----------------------|-------------------------|------------| | c | owlready2.ThingClass | The TVB class instance. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|----------------------|-----------------------------| | str | owlready2.ThingClass | The type of the TVB entity. | ### hangident { #tvbo.ontology.owl.hangident } ```python ontology.owl.hangident(text, indent=4) ``` Indent a string by a specified amount. #### Parameters {.doc-section .doc-section-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 { #tvbo.ontology.owl.import_model } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|----------------------|----------------------------------------------------------------| | | owlready2.ThingClass | owlready2.entity.ThingClass: The created ontology model class. | ### intersection { #tvbo.ontology.owl.intersection } ```python ontology.owl.intersection(lst1, lst2) ``` Computes the intersection of two lists. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|------------------|------------| | lst1 | list | The first list. | _required_ | | lst2 | list | The second list. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|------------------------------------------| | list | list | The intersection of the two given lists. | ### join_set { #tvbo.ontology.owl.join_set } ```python ontology.owl.join_set(a) ``` Join the unique elements of an iterable into a comma-separated string. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|-----------------------------------------------------------|------------| | a | | The iterable of strings whose distinct values are joined. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|----------------------------------------------------| | | | A comma-separated string of the distinct elements. | ### ontology_info { #tvbo.ontology.owl.ontology_info } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-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 { #tvbo.ontology.owl.render_using_iri } ```python ontology.owl.render_using_iri(entity) ``` Renders the ontology objects using their IRIs. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|------------------|----------------------------------------------|------------| | entity | owlready2.entity | The ontology class or entity to be rendered. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|---------------------------------------| | str | str | The IRI of the given ontology entity. | ### render_using_label { #tvbo.ontology.owl.render_using_label } ```python ontology.owl.render_using_label(entity) ``` Renders the ontology objects using their labels. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|------------------|----------------------------------------------|------------| | entity | owlready2.entity | The ontology class or entity to be rendered. | _required_ | #### Returns {.doc-section .doc-section-returns} | Name | Type | Description | |--------|--------|-----------------------------------------| | str | str | The label of the given ontology entity. | ### replace_suffix { #tvbo.ontology.owl.replace_suffix } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|---------------------------------------------------------------------|------------| | cls | | The ontology class, or its label string to look up in the ontology. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.resolve_class } ```python 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 {.doc-section .doc-section-raises} | Name | Type | Description | |--------|----------|------------------------------------------------------------| | | KeyError | If no class carries that IRI fragment or that exact label. | ### search_all { #tvbo.ontology.owl.search_all } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-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 { #tvbo.ontology.owl.search_class } ```python ontology.owl.search_class(label) ``` Searches for an ontology class using a given label. #### Parameters {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |--------|--------|----------------------------------------------|------------| | label | str | The label to search for, with regex support. | _required_ | #### Returns {.doc-section .doc-section-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 { #tvbo.ontology.owl.search_in_model } ```python 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 {.doc-section .doc-section-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 {.doc-section .doc-section-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 { #tvbo.ontology.owl.select_variables } ```python ontology.owl.select_variables(variables, property) ``` Selects variables from a list based on a given property. #### Parameters {.doc-section .doc-section-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 {.doc-section .doc-section-returns} | Name | Type | Description | |--------|------------------------------|-------------------------| | list | list\[owlready2.ThingClass\] | The selected variables. | ### wrap_text { #tvbo.ontology.owl.wrap_text } ```python 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 {.doc-section .doc-section-parameters} | Name | Type | Description | Default | |-------------|--------|----------------------------------|------------| | text | str | The text to be printed. | _required_ | | line_length | int | The maximum length of each line. | `100` |