Ontology Adapter Selectors

In the command line interface and in Python code, descriptors can be used as a shorthand way to refer to either a local or remote ontology, plus a method for parsing/querying it. The OntologyResource that is returned can be used to instantiate an implementation. The descriptors can also be used in the CLI

Note

Ontologies are available in a sometimes bewildering range of formats. One thing that constantly trips people up is the distinction between ontology language and serialization. OWL is an ontology language, not a syntax. OWL has its own syntaxes such as Manchester Syntax, OWL-XML and Functional Syntax’ – additionally it can be *mapped* to RDF, which is its *own* datamodel/language, with its *own* serializations (:term:`Turtle, RDF/XML (NOT the same as OWL-XML), JSON-LD, …). Confusing, huh? We are doing our best in this library to simplify things for you the user, please be patient!

Syntax

A descriptor is EITHER:

prefixed with a scheme OR

is a *path (in which case the scheme is inferred)

Examples

Examples of scheme-less descriptors, implicit implementation:

tests/input/go-nucleus.obo - local OBO Format file loaded with pronto
tests/input/go-nucleus.json - local OBO Graphs json format file loaded with pronto
tests/input/go-nucleus.owl - local OWL rdf/xml format file (loaded with rdflib at the moment, may change)
tests/input/go-nucleus.owl.ttl - local OWL Turtle file (loaded with rdflib at the moment, may change)
tests/input/go-nucleus.db - local sqlite3 db loaded with SqlImplementation
http://purl.obolibrary.org/obo/pato.obo - NOT IMPLEMENTED; download locally for now
http://purl.obolibrary.org/obo/pato.owl - NOT IMPLEMENTED; download locally for now

Examples of explicit schemes:

sparql:tests/input/go-nucleus.owl.ttl - local OWL file in turtle serialization
sparql:tests/input/go-nucleus.owl - local OWL file (RDF/XML assumed unless explicit format option passed)
pronto:tests/input/go-nucleus.obo - local OBO Format file loaded with pronto
pronto:tests/input/go-nucleus.json - local OBO Graphs json format file loaded with pronto
pronto:tests/input/go-nucleus.owl - local OWL rdf/xml format file (loaded with pronto at the moment may change)
pronto:tests/input/go-nucleus.db - local sqlite3 db loaded with SqlImplementation
prontolib:pato.obo - remote OBO Format file loaded from OBO Library with pronto
prontolib:pato.owl - remote owl format file loaded from OBO Library with pronto
sqlite:tests/input/go-nucleus.db - local SQLite file
sqlite:tests/input/go-nucleus.owl - convert OWL to SQLite and query using sql_implementation
sqlite:obo:go - pre-made SQLite from Semantic SQL registry
bioportal: all of bioportal
bioportal:pato pato in bioportal
ontobee: all of ontobee
ontobee:pato pato in ontobee
ols: all of OLS
ols:pato pato in OLS (NOT IMPLEMENTED)
ubergraph: all of OLS
ubergraph:pato pato in ubergraph

See CLI for more examples

Schemes

pronto

Implementation: Pronto / OBO Files Adapter

The slug is a path to a file on disk. Must be in obo or owl or json

prontolib

Implementation: Pronto / OBO Files Adapter

The slug is the name of the resource on obo, e.g. pato.obo, cl.owl

sqlite

Implementation: SQL Database Adapter

The slug is the path to the sqlite .db file on local disk

obosqlite

Implementation: SQL Database Adapter

The slug is the name of the ontology, e.g ‘hp’, ‘uberon’

TODO: download from s3

ontobee

Implementation: Ontobee Adapter

Currently the slug is ignored

ols

Implementation: Ontology Lookup Service (OLS) Adapter

Currently the slug is ignored

bioportal

Implementation: Bioportal Adapter

Currently the slug is ignored

funowl

Implementation: FunOwl Adapter

NOT IMPLEMENTED YET

Functions

oaklib.selector.get_adapter(descriptor: str | Path | InputSpecification, format: str | None = None, implements: Type[T] | None = None, **kwargs) → T[source]

Gets an adapter (implementation) for a given descriptor.

OAK allows for multiple different adapters (aka implementations); for example, SQLImplementation and BioPortalImplementation.

This function allows you to get an adapter for a given descriptor. A descriptor combines a scheme followed by a colon symbol, and then optionally additional information that specifies how to access a particular resource or ontology within that scheme.

Example:

If you omit the scheme then OAK will try to guess the scheme based on the suffix of the descriptor

If you want to pass extra information through to the implementation class, you can do so with keyword arguments:

param descriptor:: The input specification, path to a YAML describing an input specification, or a shorthand string for instantiating an ontology interface
param format:: file format/syntax, e.g obo, turtle
param kwargs:: Keyword arguments to pass through to the implementation class
return:: An instantiated interface

oaklib.selector.add_associations(adapter: AssociationProviderInterface, descriptor: str, format: str | None = None, normalizers: List[Normalizer] | None = None, primary_knowledge_source: str | None = None, aggregator_knowledge_source: str | None = None) → None[source]

Adds associations to an adapter.

Parameters:

adapter
descriptor
format
normalizers

Returns:

oaklib.selector.get_implementation_from_shorthand(descriptor: str, format: str = None) → BasicOntologyInterface[source]

Gets an adapter (implementation) for a given descriptor.

Warning

this is an alias for get_adapter - use this instead, get_implementation_from_shorthand will be deprecated in future.

Parameters:

descriptor
format

Returns:

Deprecated since version Use: get_adapter instead

oaklib.selector.get_implementation_class_from_scheme(scheme: str) → Type[OntologyInterface][source]

Given a selector schema (e.g. sqlite, ubergraph, pronto, etc.) return the adapter class.

Parameters:: scheme
Returns:: adapter (implementation) class that implements the OntologyInterface

oaklib.selector.get_resource_from_shorthand(descriptor: str, format: str | None = None, import_depth: int | None = None) → OntologyResource[source]

Maps from a shorthand descriptor to an OntologyResource.

Parameters:

descriptor
format – file format/syntax, e.g obo, turtle
import_depth – maximum import depth to traverse

Returns: