Virtual Ontology (indra.ontology.virtual_ontology)

This module implements a virtual ontology which communicates with a REST service to perform all ontology functions.

class indra.ontology.virtual.ontology.VirtualOntology(*args, backend=None, **kwargs)[source]

A virtual ontology class which uses a remote REST service to perform all operations. It is particularly useful if the host machine has limited resources and keeping the ontology graph in memory is not desirable.

Parameters:

  • url (str) – The base URL of the ontology graph web service.

  • ontology (Optional[str]) – The identifier of the ontology recognized by the web service. Default: bio

get_id_from_name(ns, name)[source]

Return an entity’s ID given its name space and standard name.

Parameters:

  • ns (str) – The name space in which the standard name is defined.

  • name (str) – The standard name defined in the name space.

Returns:

The pair of namespace and ID corresponding to the given standard name in the given name space or None if it’s not available.

get_node_property(ns, id, property)[source]

Return a given property of a given entity.

Parameters:

  • ns (str) – An entity’s name space.

  • id (str) – An entity’s ID.

  • property (str) – The property to look for on the given node.

Returns:

The name associated with the given entity or None if the node is not in the ontology or doesn’t have the given property.

Return type:

str or None

initialize()[source]

Initialize the ontology by adding nodes and edges.

By convention, ontologies are implemented such that the constructor does not add all the nodes and edges, which can take a long time. This function is called automatically when any of the user-facing methods ot IndraOntology is called. This way, the ontology is only fully constructed if it is used.