`tyto.endpoint`

Submodules

tyto.endpoint.endpoint

Package Contents

Classes

`QueryBackend`	Helper class that provides a standard way to create an ABC using
`SPARQLBuilder`	Mixin class that provides SPARQL queries to SPARQLEndpoint and GraphEndpoint classes
`Endpoint`	Helper class that provides a standard way to create an ABC using
`RESTEndpoint`	Class for issuing and handling HTTP requests
`SPARQLEndpoint`	Class which issues SPARQL queries to an endpoint
`GraphEndpoint`	Class for querying a local graph from a file
`OntobeeEndpoint`	Class which issues SPARQL queries to an endpoint
`EBIOntologyLookupServiceAPI`	Class for issuing and handling HTTP requests

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

class tyto.endpoint.QueryBackend

Bases: abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

abstract get_term_by_uri(self, ontology: Ontology, uri: str)

abstract get_uri_by_term(self, ontology: Ontology, term: str)

class tyto.endpoint.SPARQLBuilder

Mixin class that provides SPARQL queries to SPARQLEndpoint and GraphEndpoint classes

get_term_by_uri(self, ontology, uri)

Query for a term by its URI

Parameters

uri – The URI for the term
ontology – The Ontology to query

Uri

URI

Ontology

Ontology

get_uri_by_term(self, ontology: Ontology, term: str) → str: Query for the URI associated with the given an ontology term (e.g., “promoter”) :param term: The ontology term :term: str :param ontology: The ontology to query :ontology: Ontology

is_child_of(self, ontology: Ontology, child_uri: str, parent_uri: str) → bool

is_parent_of(self, ontology: Ontology, parent_uri: str, child_uri: str) → bool

is_ancestor_of(self, ontology: Ontology, ancestor_uri: str, descendant_uri: str) → bool

is_descendant_of(self, ontology: Ontology, descendant_uri: str, ancestor_uri: str) → bool

get_ontologies(self)

class tyto.endpoint.Endpoint(url)

Bases: QueryBackend, abc.ABC

Helper class that provides a standard way to create an ABC using inheritance.

class tyto.endpoint.RESTEndpoint(url)

Bases: QueryBackend, abc.ABC

Class for issuing and handling HTTP requests

_get_request(self, ontology: Ontology, request: str)

class tyto.endpoint.SPARQLEndpoint(url)

Bases: SPARQLBuilder, Endpoint

Class which issues SPARQL queries to an endpoint

query(self, ontology, sparql, err_msg): Issues SPARQL query

convert(self, response)

Converts standard SPARQL query JSON into a flat list.

See https://www.w3.org/TR/2013/REC-sparql11-results-json-20130321/

class tyto.endpoint.GraphEndpoint(file_path)

Bases: SPARQLBuilder, Endpoint

Class for querying a local graph from a file

is_loaded(self)

load(self)

query(self, ontology, sparql, err_msg)

convert(self, response): Extracts and flattens queried variables from rdflib response into a list

class tyto.endpoint.OntobeeEndpoint

Bases: SPARQLEndpoint