Grounding and name standardization (indra.ontology.standardize)

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.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_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.