Take Your Terms from Ontologies (Tyto)

Tyto is a tool that supports standardized annotation practices using terms from controlled vocabularies and ontologies. Tyto allows a user to reference ontology terms in their code using human-readable labels rather than uniform resource identifiers (URIs), thus rendering code more readable and easier to understand.

Examples using dynamic attributes

Tyto allows the user to reference an ontology term as an attribute on an Ontology instance. In the following example, the term promoter is referenced from an Ontology instance representing the Sequence Ontology.

>>> SO.promoter
'https://identifiers.org/SO:0000167'

Some ontology terms have spaces, such as the term functional entity from the Systems Biology Ontology. In these cases, replace the space with an underscore:

>>> SBO.functional_entity
'https://identifiers.org/SBO:0000241'

Example use with subscripts

Some ontology terms may have special characters, especially in the NCBI Taxonomy. In this case, dynamic attributes cannot be used as it would result in invalid Python symbols. Instead, use subscripting:

>>> NCBITaxon['Escherichia coli O157:H-']
'https://identifiers.org/taxonomy:183192'

Query Backend

Tyto’s back-end dynamically queries ontology lookup services for the URI that corresponds to the attribute name or subscript. This dynamic querying approach is in keeping with the principles of the semantic web, in which knowledge is interlinked and distributed across the web rather than concentrated in isolated resources. In this way, Tyto provides up-to-date access to hundreds of ontologies without the need for packaging a large amount of data with the distribution.

Currently Tyto supports queries to Ontobee and the EBI Ontology Lookup Service. In addition, it includes an extensible framework so that users may add their own REST services or SPARQL endpoints. It is also possible to query local OWL files for offline work.

Support for SBOL Ontologies

Tyto was originally developed to support use of the Synthetic Biology Open Language which uses ontologies as a source of standardized terms for annotating synthetic biology data. Tyto provides “out-of-the-box” support for most of the ontologies used in SBOL:

SO: sequence ontology
SBO: systems biology ontology
NCBITaxon: NCBI taxonomy
NCIT: National Cancer Institute Thesaurus
OM: Ontology of Units of Measure

Note

SBOL identifiers standardize on the identifiers.org namespace. By default most ontology lookup services standardize on the purl.org namespace. Tyto’s built-in Ontology interfaces automatically translate from purl.org to identifiers.org namespaces.

Support for Other Ontologies

Ontobee and EBI Ontology Lookup Service host hundreds of ontologies. Even though Tyto has built-in support for only a few of these, it is easy to define your own Ontology interface.

First identify the URI associated with the ontology you wish to use. To do this, use the get_ontologies method on your Endpoint instance to get a dictionary of available ontologies:

>>> for uri, ontology in tyto.EBIOntologyLookupService.get_ontologies().items():
...     print(uri, ontology)
...
http://purl.obolibrary.org/obo/aeo.owl aeo
http://purl.allotrope.org/voc/afo/merged-OLS/REC/2019/05/10 afo
http://purl.obolibrary.org/obo/agro-edit.owl agro
.
.
.

Once you have identified the URI of your desired ontology, instantiate an Ontology, specifying its URI and the lookup service:

>>> from tyto import EBIOntologyLookupService, Ontology
>>> KISAO = Ontology(uri='http://www.biomodels.net/kisao/KISAO_FULL#', endpoints=[EBIOntologyLookupService])
>>> KISAO.Gillespie_direct_algorithm
'http://www.biomodels.net/kisao/KISAO#KISAO_0000029'

Inference

Tyto can be used to reason about the relationships between terms in an ontology.

For example:

>>> SO.inducible_promoter.is_a(SO.promoter)
True
>>> SO.inducible_promoter.is_a(SO.ribosome_entry_site)
False

Other supported inference methods include:

term1.is_a(term2)
term1.is_descendant_of(term2)
term1.is_ancestor_of(term2)
term1.is_child_of(term2)
term1.is_parent_of(term2)

API Reference

This page contains auto-generated API reference documentation 1.

`tyto`

Subpackages

`tyto.endpoint`

Submodules

tyto.endpoint.endpoint

Module 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
`PUG_REST`	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
`PubChemAPI`

class tyto.endpoint.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.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.Endpoint(url)

Bases: QueryBackend, abc.ABC

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

class tyto.endpoint.endpoint.RESTEndpoint(url)

Bases: QueryBackend, abc.ABC

Class for issuing and handling HTTP requests

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

class tyto.endpoint.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.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.endpoint.OntobeeEndpoint

Bases: SPARQLEndpoint

Class which issues SPARQL queries to an endpoint

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

class tyto.endpoint.endpoint.EBIOntologyLookupServiceAPI

Bases: RESTEndpoint

Class for issuing and handling HTTP requests

_load_ontology_ids(self)

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

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

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

get_parents(self, ontology: Ontology, uri: str)

get_children(self, ontology: Ontology, uri: str)

get_descendants(self, ontology: Ontology, uri: str)

get_ancestors(self, ontology: Ontology, uri: str)

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

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

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

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

get_ontologies(self)

convert(self, response)

query(self, query)

class tyto.endpoint.endpoint.PUG_REST

Bases: RESTEndpoint

Class for issuing and handling HTTP requests

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

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

tyto.endpoint.endpoint.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.

tyto.endpoint.endpoint.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

tyto.endpoint.endpoint.PubChemAPI

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
`PUG_REST`	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
`PubChemAPI`

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

Class which issues SPARQL queries to an endpoint

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

class tyto.endpoint.EBIOntologyLookupServiceAPI

Bases: RESTEndpoint

Class for issuing and handling HTTP requests

_load_ontology_ids(self)

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

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

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

get_parents(self, ontology: Ontology, uri: str)

get_children(self, ontology: Ontology, uri: str)

get_descendants(self, ontology: Ontology, uri: str)

get_ancestors(self, ontology: Ontology, uri: str)

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

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

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

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

get_ontologies(self)

convert(self, response)

query(self, query)

class tyto.endpoint.PUG_REST

Bases: RESTEndpoint

Class for issuing and handling HTTP requests

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

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

tyto.endpoint.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.

tyto.endpoint.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

tyto.endpoint.PubChemAPI

Submodules

`tyto.edam`

Module Contents

tyto.edam.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.

`tyto.ncbi_taxon`

Module Contents

tyto.ncbi_taxon.NCBITaxon: Ontology instance for NCBI Taxonomy

tyto.ncbi_taxon._sanitize_uri

tyto.ncbi_taxon._reverse_sanitize_uri

`tyto.ncit`

Module Contents

tyto.ncit.NCIT: Ontology instance for National Cancer Institute Thesaurus

tyto.ncit._sanitize_uri

tyto.ncit._reverse_sanitize_uri

`tyto.om`

Module Contents

tyto.om.OM: Ontology instance for Ontology of Units of Measure

tyto.om._sanitize_term

tyto.om._reverse_sanitize_term

`tyto.pubchem`

Module Contents

tyto.pubchem.PubChem

`tyto.sbo`

Module Contents

tyto.sbo.SBO: Ontology instance for Systems Biology Ontology

tyto.sbo._sanitize_uri

tyto.sbo._reverse_sanitize_uri

`tyto.sbol2`

Module Contents

tyto.sbol2.SBOL2

`tyto.sbol3`

Module Contents

tyto.sbol3.SBOL3

`tyto.so`

Module Contents

tyto.so.SO: Ontology instance for Sequence Ontology

tyto.so._sanitize_uri

tyto.so._reverse_sanitize_uri

tyto.so._sanitize_term

`tyto.tyto`

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

Functions

`installation_path`(relative_path)
`multi_replace`(target_uri, old_namespaces, new_namespace)
`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

LOGGER

tyto.tyto.LOGGER

class tyto.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.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)

class tyto.tyto.Term

Bases: URI

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

__repr__(self): Return repr(self).

tyto.tyto.installation_path(relative_path)

tyto.tyto.multi_replace(target_uri, old_namespaces, new_namespace)

tyto.tyto.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

Parameters: maxsize (int) – The maximum number of cached query results

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)

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

Parameters: maxsize (int) – The maximum number of cached query results

tyto.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.

tyto.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

tyto.PubChemAPI

tyto.SBO: Ontology instance for Systems Biology Ontology

tyto.SO: Ontology instance for Sequence Ontology

tyto.NCIT: Ontology instance for National Cancer Institute Thesaurus

tyto.OM: Ontology instance for Ontology of Units of Measure

tyto.NCBITaxon: Ontology instance for NCBI Taxonomy

tyto.SBOL2

tyto.SBOL3

tyto.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.

tyto.PubChem

`App`

Created on 26 May 2021

@author: gokselmisirli

Module Contents

Classes

`Measure`
`Identified`

Attributes

`sbol3`
`prov`
`om`

App.sbol3

App.prov

App.om

class App.Measure

Bases: Thing

label = Measure

class App.Identified

Bases: Thing

label = Identified

1: Created with sphinx-autoapi

Take Your Terms from Ontologies (Tyto)

Examples using dynamic attributes

Example use with subscripts

Query Backend

Support for SBOL Ontologies

Support for Other Ontologies

Inference

API Reference

Subpackages

Submodules

Package Contents

Submodules

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Module Contents

Package Contents

Classes

Functions

Attributes

Module Contents

Classes

Attributes

Indices and tables