INDRA BioOntology (indra.ontology.bio_ontology)

Module containing the implementation of an IndraOntology for the general biology use case.

class indra.ontology.bio.BioOntology

Represents the ontology used for biology applications.

initialize(rebuild=False)

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.

class indra.ontology.bio.ontology.BioOntology

Represents the ontology used for biology applications.

initialize(rebuild=False)

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.

Generating and caching the BioOntology

The BioOntology is built and cached automatically during runtime. If a cached version already exists, it is loaded from the cache.

To control the build and clean up caches if necessary, one can call

python -m indra.ontology.bio <operation>

to build or clean up the INDRA bio ontology. The script takes a single operation argument which can be as follows:

• build: build the ontology and cache it
• clean: delete the current version of the ontology from the cache
• clean-old: delete all versions of the ontology except the current one
• clean-all: delete all versions of the bio ontology from the cache