`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
`PubChemAPI`
`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
`SBOL2`
`SBOL3`
`EDAM`	EDAM (EMBRACE Data and Methods) is an ontology of common bioinformatics operations, topics, types of data including identifiers, and formats. EDAM comprises common concepts (shared within the bioinformatics community) that apply to semantic annotation of resources.
`PubChem`

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)