Welcome to Biolink Model Toolkit’s documentation!

Contents:

Installation
- For users
- For developers

class bmt.toolkit.Toolkit(schema: Union[str, TextIO, SchemaDefinition] = 'https://raw.githubusercontent.com/biolink/biolink-model/v4.2.2/biolink-model.yaml', predicate_map: str = 'https://raw.githubusercontent.com/biolink/biolink-model/v4.2.2/predicate_mapping.yaml')

Provides a series of methods for performing lookups on the Biolink Model

Parameters

schema: Union[str, TextIO, SchemaDefinition]: The path or url to an instance of the biolink-model.yaml file.

ancestors(name: str, mixin: bool = True) → List[str]: Deprecated since version 0.2.0: This will be removed in 1.0. Use get_ancestors method instead

children(name: str, mixin: bool = True) → List[str]: Deprecated since version 0.2.0: This will be removed in 1.0. Use get_children method instead

descendents(name: str, mixin: bool = True) → List[str]: Deprecated since version 0.2.0: This will be removed in 1.0. Use get_descendants method instead

filter_values_on_slot(slot_values: List[str], definition: SlotDefinition, field: str, formatted: bool = True) → bool

Parameters

slot_values: List[str]: List of (Biolink CURIE) slot values to be matched against target slot field values.
definition: SlotDefinition: Slot definition containing the embedded target field.
field: str: Name of embedded (slot) field rooting the tree of elements against which the slot_values are to be matched.
formatted: bool = True: Use of Biolink CURIE identifiers assumed when True (default: True)

Returns

bool: Returns ‘True’ if any match is found for at least one entry in the slot_values, against the target field values.

get_all_associations(formatted: bool = False) → List[str]

Get all associations from Biolink Model.

This method returns a list of names or (optionally) curies designating classes that are descendants of the class association.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_by_mapping(uriorcurie: str) → List[str]: Deprecated since version 0.1.1: This will be removed in 1.0. Use get_all_elements_by_mapping method instead

get_all_classes(formatted: bool = False) → List[str]

Get all classes from Biolink Model.

This method returns a list containing all the classes defined in the model.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_edge_properties(formatted: bool = False) → List[str]

Get all edge properties from Biolink Model.

This method returns a list containing all the slots that are descendants of the slot association slot.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_elements(formatted: bool = False) → List[str]

Get all elements from Biolink Model.

This method returns a list containing all classes, slots, and types defined in the model.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_elements_by_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find all Biolink elements that correspond to the given identifier as part of its mappings.

Parameters

identifier: str: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_all_entities(formatted: bool = False) → List[str]

Get all entities from Biolink Model.

This method returns a list containing all the classes that are descendants of the class named thing.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_multivalued_slots() → List[str]

Gets a list of names of all multivalued slots.

Returns

List[str]: The names of all multivalued slots

get_all_node_properties(formatted: bool = False) → List[str]

Get all node properties from Biolink Model.

This method returns a list containing all the slots that are descendants of the slot node property.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_predicates_with_class_domain(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Given a class, get all Biolink predicates where the class is the domain.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its domain
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_predicates_with_class_range(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True)

Given a class, get all Biolink predicates where the class is the range.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its range
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_properties_with_class_domain(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Given a class, get all Biolink properties where the class is the domain.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its domain
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_properties_with_class_range(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Given a class, get all Biolink properties where the class is the range.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its range
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_slots(formatted: bool = False) → List[str]

Get all slots from Biolink Model.

This method returns a list containing all the slots defined in the model.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_all_slots_with_class_domain(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Given a class, get all the slots where the class is the domain.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its domain
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_slots_with_class_range(class_name, check_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Given a class, get all the slots where the class is the range.

Parameters

class_name: str: The name or alias of a class in the Biolink Model
check_ancestors: bool: Whether or not to lookup slots that include ancestors of the given class as its range
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: A list of slots

get_all_types(formatted: bool = False) → List[str]

Get all types from Biolink Model.

This method returns a list containing all the built-in and defined types in the model.

Parameters

formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_ancestors(name: str, reflexive: bool = True, formatted: bool = False, mixin: bool = True) → List[str]

Gets a list of names of ancestors.

Parameters

name: str: The name of an element in the Biolink Model
reflexive: bool: Whether to include the query element in the list of ancestors
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: The names of the given elements ancestors

get_associations(subject_categories: Optional[List[str]] = None, predicates: Optional[List[str]] = None, object_categories: Optional[List[str]] = None, match_inverses: bool = True, formatted: bool = False) → List[str]

Get associations from Biolink Model constrained by target list of subject categories, predicates and/or object categories.

Note: to get matches to most specific associations, it is recommended that the subject_categories and object_categories lists be limited to the most specific node categories of interest.

This method returns a list of names or (optionally formatted) curies designating classes that are descendants of the class biolink:Association.

Note that the method does not attempt to continue matching input constraints if any category or predicate is deemed unknown to the current Biolink Model: The caller should know well enough to check these, before calling this method! But log warnings are issued as a courtesys to inform them!

Parameters

subject_categories: Optional[List[str]]: List of node categories (as CURIES) that the associations must match for the subject node; default: None
predicates: Optional[List[str]]: List of edge predicates (as CURIES) that the associations allowed for matching associations; default: None
object_categories: Optional[List[str]]: List of node categories (as CURIES) that the associations must match for the object node; default: None
match_inverses: bool: Whether to also return associations with swapped subject and object with inverted qualifiers (as applicable) plus inverse predicates; default: rue
formatted: bool: Whether to format element names as CURIEs; default: False

Returns

List[str]: A list of elements

get_by_mapping(uriorcurie: str) → Optional[str]: Deprecated since version 0.1.1: This will be removed in 1.0. Use get_element_by_mapping method instead

get_children(name: str, formatted: bool = False, mixin: bool = True) → List[str]

Gets a list of names of children.

Parameters

name: str: The name of an element in the Biolink Model
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: The names of the given elements children

get_denormalized_association_slots(formatted) → List[Element]

Gets all association slots that are denormalized

Returns

List[linkml_model.meta.Element]: A list of association slots

get_descendants(name: str, reflexive: bool = True, formatted: bool = False, mixin: bool = True) → List[str]

Gets a list of names of descendants.

Parameters

name: str: The name of an element in the Biolink Model
reflexive: bool: Whether to include the query element in the list of descendants
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin descendants as well as is_a ancestors

Returns

List[str]: The names of the given element’s descendants

get_element(name: str) → Optional[Element]

Gets an element that is identified by the given name, either as its name or as one of its aliases.

Parameters

name: str: The name or alias of an element in the Biolink Model

Returns

Element: The element identified by the given name

get_element_by_broad_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find a Biolink element that corresponds to the given identifier as part of its broad_mappings.

Parameters

identifier: str: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_element_by_close_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find a Biolink element that corresponds to the given identifier as part of its close_mappings.

Parameters

identifier:: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_element_by_exact_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find a Biolink element that corresponds to the given identifier as part of its exact_mappings.

Parameters

identifier: str: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_element_by_mapping(identifier: str, most_specific: bool = False, formatted: bool = False, mixin: bool = True) → Optional[str]

Get a Biolink Model element by mapping. This method return the common ancestor of the set of elements referenced by uriorcurie.

Parameters

identifier: str: The identifier as an IRI or CURIE
most_specific: bool: Whether or not to get the first available mapping in the order of specificity or to get all mappings of varying specificity
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

Optional[str]: The Biolink element (or the common ancestor) corresponding to the given URI/CURIE

get_element_by_narrow_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find a Biolink element that corresponds to the given identifier as part of its narrow_mappings.

Parameters

identifier: str: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_element_by_prefix(identifier: str) → List[str]

Get a Biolink Model element by prefix.

Parameters

identifier: str: The identifier as a CURIE

Returns

Optional[str]: The Biolink element corresponding to the given URI/CURIE as available via the id_prefixes mapped to that element.

get_element_by_related_mapping(identifier: str, formatted: bool = False) → List[str]

Given an identifier as IRI/CURIE, find a Biolink element that corresponds to the given identifier as part of its related_mappings.

Parameters

identifier: str: The identifier as an IRI or CURIE
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of Biolink elements that correspond to the given identifier IRI/CURIE

get_inverse_predicate(predicate: Optional[str], formatted: bool = False) → Optional[str]

Utility wrapper of logic to robustly test if a predicate exists and has an inverse.

Parameters

predicate: Optional[str]: CURIE or string name of predicate in the Biolink Model, for which the inverse is sought
formatted: bool: Whether to format element names as CURIEs

Returns

Optional[str]: CURIE string of inverse predicate, if it exists; None otherwise

static get_local_slot_usage(element: Element, slot: str) → Optional[SlotDefinition]

Retrieve the definition of a specified slot from the ‘slot_usage’ defined locally within the class model of the specified Element.

Parameters

element:: Element defining the specified ‘slot’ in its local ‘slot_usage’.
slot: str: Name of the slot whose definition is to be retrieved.

Returns

Optional[SlotDefinition]: None, if not available.

get_model_version() → str

Return the version of the biolink-model in use.

Returns

str: The biolink-model version

get_parent(name: str, formatted: bool = False) → Optional[str]

Gets the name of the parent.

Parameters

name: str: The name of an element in the Biolink Model
formatted: bool: Whether to format element names as CURIEs

Returns

Optional[str]: The name of the given elements parent

get_permissible_value_ancestors(permissible_value: str, enum_name: str, formatted: bool = False) → List[str]

Get ancestors of a permissible value.

This method returns a list containing all the ancestors of a permissible value of a given enum.

Parameters

enum_name: str: The name of the enum
permissible_value: str: The name of the permissible value
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_permissible_value_children(permissible_value: str, enum_name: str) → Optional[Union[str, PermissibleValueText]]

Gets the children of a permissible value in an enumeration.

Parameters:

permissible_value – The permissible value to check.
enum_name – The name of the enumeration.

Returns:

The children of the permissible value.

Raises:

ValueError – If the permissible value or enum is not valid.

get_permissible_value_descendants(permissible_value: str, enum_name: str, formatted: bool = False) → List[str]

Get descendants of a permissible value.

This method returns a list containing all the descendants of a permissible value of a given enum.

Parameters

enum_name: str: The name of the enum
permissible_value: str: The name of the permissible value
formatted: bool: Whether to format element names as CURIEs

Returns

List[str]: A list of elements

get_permissible_value_parent(permissible_value: str, enum_name: str) → str

Get parent of a permissible value.

This method returns a list containing all the parent of a permissible value of a given enum.

Parameters

enum_name: str: The name of the enum
permissible_value: str: The name of the permissible value

Returns

List[str]: A list of elements

get_predicate_mapping(mapped_predicate: str) → Dict[str, str]

Get the predicates that map to a given predicate.

This method returns a list containing all the predicates that map to a given predicate.

Parameters

mapped_predicate: str: The name of the mapped predicate

Returns

Dict[str, str]: A Dictionary of elements, indexed by formatted name

get_slot_domain(slot_name, include_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Get the domain for a given slot.

Parameters

slot_name: str: The name or alias of a slot in the Biolink Model
include_ancestors: bool: Whether or not to include ancestors of the domain class
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: The domain for a given slot

get_slot_range(slot_name, include_ancestors: bool = False, formatted: bool = False, mixin: bool = True) → List[str]

Get the range for a given slot.

Parameters

slot_name: str: The name or alias of a slot in the Biolink Model
include_ancestors: bool: Whether or not to include ancestors of the range class
formatted: bool: Whether to format element names as CURIEs
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

List[str]: The range for a given slot

get_slot_usage(element: Element, slot: str) → Optional[SlotDefinition]

Get the definition of a specified slot from the ‘slot_usage’ of a specified Element. A relatively deep search is made within the Element context - local class, parent class and associated mixins - to discover an available ‘slot_usage’ definition for the slot.

Parameters

element:: Element defining the specified ‘slot’ in ‘slot_usage’.
slot: str: Name of the slot whose definition is to be retrieved.

Returns

Optional[SlotDefinition]: None, if not available.

get_value_type_for_slot(slot_name, formatted: bool = False) → str

Get the value type for a given slot.

Parameters

slot_name: str: The name or alias of a slot in the Biolink Model
formatted: bool: Whether to format element names as CURIEs

Returns

str: The slot type

has_inverse(name: str) → bool

Determines whether the given name exists and has an inverse defined in the Biolink Model. An element is a predicate if it descends from RELATED_TO but this is not directly tested here (use the method ‘is_predicate()’ to be sure).

Parameters

name: str: The name or alias of an slot element in the Biolink Model

Returns

bool: That the named element is a slot element with an inverse in the Biolink Model

in_subset(name: str, subset: str) → bool

Determines whether the given name is in a given subset in the Biolink Model.

Parameters

name: str: The name or alias of an element in the Biolink Model.
subset: str: The name of the subset

Returns

bool: That the named element is part of a given subset in Biolink Model

is_association_slot(name: str, mixin: bool = True) → bool

Determines whether the given name is the name of an association slot in the Biolink Model. An element is an association slot if it descends from ASSOCIATION_SLOT

Parameters

name: str: The name or alias of an element in the Biolink Model
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

bool: That the named element is a valid an association slot in Biolink Model

is_category(name: str, mixin: bool = True) → bool

Determines whether the given name is the name of a category in the Biolink Model. An element is a category if it descends from named thing

Parameters

namestr: The name or alias of an element in the Biolink Model
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

bool: That the named element is a valid category in Biolink Model

is_edgelabel(name: str, mixin: bool = True) → bool: Deprecated since version 0.1.1: This will be removed in 1.0. Use is_predicate method instead

is_enum(name: str) → bool

Predicate to test (by name) if a given Biolink Model element is an Enum.

Parameters

namestr: The name or alias of an element in the Biolink Model

Returns

bool: That the named element is a valid enum in the Biolink Model

is_mixin(name: str) → bool

Determines whether the given name is the name of a mixin in the Biolink Model. An element is a mixin if one of its properties is “is_mixin:true”

Parameters

name: str: The name or alias of an element in the Biolink Model

Returns

bool: That the named element is a valid mixin in Biolink Model

is_node_property(name: str, mixin: bool = True) → bool

Determines whether the given name is the name of a node property in the Biolink Model. An element is a node property if it descends from NODE_PROPERTY

Parameters

name: str: The name or alias of an element in the Biolink Model
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

bool: That the named element is a valid node property in Biolink Model

is_permissible_value_of_enum(enum_name: str, value) → bool

method to test (by name) if a candidate ‘permissible value’ is associated with the given Enum

Parameters

enum_namestr: The name or alias of an Enum in the Biolink Model
valueAny: The name or alias of the candidate ‘permissible value’ associated with the given Enum

Returns

bool: That the named element is in the set of ‘permissible values’ of the Enum

is_predicate(name: str, mixin: bool = True) → bool

Determines whether the given name is the name of a relation/predicate in the Biolink Model. An element is a predicate if it descends from RELATED_TO

Parameters

name: str: The name or alias of an element in the Biolink Model
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

bool: That the named element is a valid relation/predicate in Biolink Model

is_qualifier(name: str) → bool

Predicate to test (by name) if a given Biolink Model element is an Edge Qualifier.

Parameters

namestr: The name or alias of an element in the Biolink Model

Returns

bool: That the named element is a valid edge qualifier in the Biolink Model

is_subproperty_of(predicate: str, name: str, formatted: bool = False) → bool

Checks if a given name is a ‘subproperty_of’ a given predicate. Note: unsure if this method yet captures the full subtlety of ‘subproperty_of’.

Parameters

predicate: str: Target predicate against which a given name is to be searched as a subproperty
name: str: Name to be searched
formatted: bool = False: Input name assumed to be a CURIE

Returns

True if the name is observed to be equivalent to, or a ‘subproperty’ descendant of, the given predicate.

is_symmetric(name: str) → bool

Checks if a given element identified by name, is a symmetric (predicate) slot.

Parameters

name: str: The name or alias of an element in the Biolink Model

Returns

bool: That the named element is tagged as symmetric: true in Biolink Model

is_translator_canonical_predicate(name: str, mixin: bool = True) → bool

Determines whether the given name is the name of a canonical relation/predicate in the Biolink Model. An element is a canonical predicate if it descends from RELATED_TO and is tagged with the annotation ‘biolink:canonical_predicate’

Parameters

name: str: The name or alias of an element in the Biolink Model
mixin: bool: If True, then that means we want to find mixin ancestors as well as is_a ancestors

Returns

bool: That the named element is a valid translator canonical prediacte in Biolink Model

match_association(assoc: Element, subj_cats: List[str], predicates: List[str], obj_cats: List[str], formatted: bool = True) → bool

Match a specified element (assumed to be a child of biolink:Association) to a given set of Subject category – Predicate -> Object category name constraints.

Parameters

assoc: Element: Subclass of biolink:Association to be matched.
subj_cats: List[str]: List of Biolink CURIEs of subject categories.
predicates: List[str]: List of Biolink CURIEs of predicates.
obj_cats: List[str]: List of Biolink CURIEs of object categories.
formatted: bool = True: Use of Biolink CURIE identifiers in ‘subj_cats’, ‘preds’ and ‘obj_cats’ assumed when True (default: True)

Returns

bool:: True if all constraints match the slot_usage of the Association components.

match_slot_usage(element, slot: str, slot_values: List[str], formatted: bool = True) → bool

Match slot_values against expected slot_usage for specified slot in specified (association) element.

Parameters

element: Element: Target element against which slot_usage is being assessed.
slot: str: Name of target slot in given element, against which slot_usage is being assessed.
slot_values: List[str]: List of slot value (strings) e.g. categories, predicates, etc. - being assessed against slot_usage
formatted: bool = True: Use of Biolink CURIE identifiers in slot_values assumed when True (default: True)

Returns

bool: Returns ‘True’ if slot exists and slot_values are compatible with slot usage within the given element (or its immediate parent or mixins); False otherwise

names(formatted: bool = False) → List[str]: Deprecated since version 0.3.0: This will be removed in 1.0. Use get_all_elements method instead

parent(name: str, mixin: bool = True) → Optional[str]: Deprecated since version 0.2.0: This will be removed in 1.0. Use get_parent method instead

validate_edge(subject: str, predicate: str, p_object: str, ancestors: bool = True) → bool

Validates an edge.

Parameters

subject: str: The name or alias of a subject in the Biolink Model
predicate: str: The name or alias of a predicate in the Biolink Model
p_object: str: The name or alias of an object in the Biolink Model
ancestors: bool: Whether to include ancestors of the domain and range classes

Returns

bool: Whether or not the given edge is valid

validate_qualifier(qualifier_type_id: str, qualifier_value: str, associations: Optional[List[str]] = None) → bool

Validates a qualifier.

Parameters

qualifier_type_id: str: The name or alias of a qualifier in the Biolink Model
qualifier_value: str: The value of the qualifier
associations: Optional[List[str]] = None: Optional list of possible biolink:Association subclass (CURIEs) which could resolve the context for qualifier_value validation.

Returns

bool: Whether or not the given qualifier is valid