Grounding and name standardization (indra.ontology.standardize)

indra.ontology.standardize.get_standard_agent(name, db_refs, ontology=None, ns_order=None, **kwargs)[source]

Get a standard agent based on the name, db_refs, and a any other kwargs.

namestr

The name of the agent that may not be standardized.

db_refsdict

A dict of db refs that may not be standardized, i.e., may be missing an available UP ID corresponding to an existing HGNC ID.

ontologyOptional[indra.ontology.IndraOntology]

An IndraOntology object, if not provided, the default BioOntology is used.

ns_orderOptional[list]

A list of namespaces which are in order of priority with higher priority namespaces appearing earlier in the list.

kwargs :

Keyword arguments to pass to Agent.__init__().

Returns:

A standard agent

Return type:

Agent

indra.ontology.standardize.get_standard_name(db_refs, ontology=None, ns_order=None)[source]

Return a standardized name for a given db refs dict.

Parameters:

  • db_refs (dict) – A dict of db refs that may not be standardized, i.e., may be missing an available UP ID corresponding to an existing HGNC ID.

  • ontology (Optional[indra.ontology.IndraOntology]) – An IndraOntology object, if not provided, the default BioOntology is used.

  • ns_order (Optional[list]) – A list of namespaces which are in order of priority with higher priority namespaces appearing earlier in the list.

Returns:

The standard name based on the db refs, None if not available.

Return type:

str or None

indra.ontology.standardize.standardize_agent_name(agent, standardize_refs=True, ontology=None, ns_order=None)[source]

Standardize the name of an Agent based on grounding information.

The priority of which namespace is used as the bases for the standard name depends on

Parameters:

  • agent (indra.statements.Agent) – An INDRA Agent whose name attribute should be standardized based on grounding information.

  • standardize_refs (Optional[bool]) – If True, this function assumes that the Agent’s db_refs need to be standardized, e.g., HGNC mapped to UP. Default: True

  • ontology (Optional[indra.ontology.IndraOntology]) – An IndraOntology object, if not provided, the default BioOntology is used.

  • ns_order (Optional[list]) – A list of namespaces which are in order of priority with higher priority namespaces appearing earlier in the list.

Returns:

True if a new name was set, False otherwise.

Return type:

bool

indra.ontology.standardize.standardize_db_refs(db_refs, ontology=None, ns_order=None)[source]

Return a standardized db refs dict for a given db refs dict.

Parameters:

  • db_refs (dict) – A dict of db refs that may not be standardized, i.e., may be missing an available UP ID corresponding to an existing HGNC ID.

  • ontology (Optional[indra.ontology.IndraOntology]) – An IndraOntology object, if not provided, the default BioOntology is used.

  • ns_order (Optional[list]) – A list of namespaces which are in order of priority with higher priority namespaces appearing earlier in the list.

Returns:

The db_refs dict with standardized entries.

Return type:

dict

indra.ontology.standardize.standardize_name_db_refs(db_refs, ontology=None, ns_order=None)[source]

Return a standardized name and db refs dict for a given db refs dict.

Parameters:

  • db_refs (dict) – A dict of db refs that may not be standardized, i.e., may be missing an available UP ID corresponding to an existing HGNC ID.

  • ontology (Optional[indra.ontology.IndraOntology]) – An IndraOntology object, if not provided, the default BioOntology is used.

  • ns_order (Optional[list]) – A list of namespaces which are in order of priority with higher priority namespaces appearing earlier in the list.

Returns:

  • str or None – The standard name based on the db refs, None if not available.

  • dict – The db_refs dict with standardized entries.