`tyto`

Subpackages

tyto.endpoint
- tyto.endpoint.endpoint

Submodules

Package Contents

Classes

`Ontology`	The Ontology class provides an abstraction layer for accessing ontologies, and a
`URI`	The URI class wraps the Python string primitive type, enabling the use of inference methods on the represented uniform resource identifier

Functions

configure_cache_size(maxsize=1000)

Set the size of the in-memory cache in order to optimize performance and frequency of queries over the network

Attributes

`Ontobee`	Endpoint instance representing Ontobee. Ontobee is the default linked data server for most OBO Foundry library ontologies, but is also been used for many non-OBO ontologies.
`EBIOntologyLookupService`	The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Hosted by the European Bioinformatics Institute
`SBO`	Ontology instance for Systems Biology Ontology
`SO`	Ontology instance for Sequence Ontology
`NCIT`	Ontology instance for National Cancer Institute Thesaurus
`OM`	Ontology instance for Ontology of Units of Measure
`NCBITaxon`	Ontology instance for NCBI Taxonomy

class tyto.Ontology(path=None, endpoints=None, uri=None)

The Ontology class provides an abstraction layer for accessing ontologies, and a back-end query dispatcher for interfacing with RESTful services, SPARQL endpoints, or local triple stores.

Parameters

path (str, optional) – A path to a local ontology file, defaults to None
endpoints (list, optional) – A list of zero or more Endpoint objects that provide a query interface to an ontology resource, defaults to None
uri – The URI of the ontology

:type str

__getattr__(self, name): Enables use of ontology terms as dynamic attributes, e.g., SO.promoter

_handler(self, method_name, exception, *args): Dispatches queries through Endpoints

get_term_by_uri(self, uri)

Provides the ontology term (rdfs:label) associated with the given URI.

Parameters: uri (str) – A uniform resource identifier corresponding to an ontology term
Returns: A human-readable term or label that corresponds to the given identifier
Return type: string

get_uri_by_term(self, term)

Provides the URI associated with the given ontology term (rdfs:label). The __getattr__ and __getitem__ methods delegate to this method.

Parameters: term (str) – an ontology term
Returns: A human-readable term or label that corresponds to the given identifier
Return type: URI

_sanitize_uri(self, uri): Some Ontology instances may override this method to translate a URI from purl to identifiers.org namespaces

_reverse_sanitize_uri(self, uri): Some Ontology instances may override this method to reverse-translate a URI from identifiers.org back into purl namespace

_sanitize_term(self, term): Some Ontology instances may override this method in order to convert a Pythonic representation of a label into a more human-readable representation, such as replacing underscores with spaces

_reverse_sanitize_term(self, term): Some Ontology instances may override this method to undo the conversion done by _sanitize_term and return a Pythonic label from free text label

__getitem__(self, key)

Enables use of an ontology term as a subscript. This method is a useful alternative to dynamic attributes in case a term contains special characters

Returns: A uniform resource identifier associated with the provided term
Return type: URI

class tyto.URI

Bases: str

The URI class wraps the Python string primitive type, enabling the use of inference methods on the represented uniform resource identifier

Parameters

value (str) – A string value representing a uniform resource identifier
ontology (Ontology) – links a term to a particular Ontology instance

is_child_of(self, parent_uri: str)

Determine whether this URI is an immediate subclass or subtype of the argument URI

Parameters: parent_uri (str) – URI corresponding to the putative parent term
Return type: bool

is_parent_of(self, child_uri: str)

Determine whether this URI is an immediate superclass or supertype of the argument URI

Parameters: parent_uri (str) – URI corresponding to the putative parent term
Return type: bool

is_descendant_of(self, ancestor_uri: str)

Determine whether this URI is a taxonomic subcategory of the argument URI

Parameters: ancestor_uri (str) – URI corresponding to the putative ancestor
Return type: bool

is_ancestor_of(self, descendant_uri: str)

Determine whether this URI is a taxonomic superclass or supertype of the argument URI

Parameters: descendant_uri (str) – URI corresponding to the putative descendant
Return type: bool

is_subtype_of(self, supertype: str)

Alias of is_descendant_of. Determines whether this URI is a derivative subclass or subtype of the argument URI

Parameters: supertype (str) – URI corresponding to the putative supertype
Return type: bool

is_supertype_of(self, subtype: str)

Alias of is_ancestor_of. Determines whether this URI is a superclass or supertype of the argument URI

Parameters: subtype (str) – URI corresponding to the putative subtype
Return type: bool

is_a(self, term: URI)

get_parents(self)

get_children(self)

get_ancestors(self)

get_descendants(self)

tyto.configure_cache_size(maxsize=1000)