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Create an INDRA backend

indra_backend.Rd

INDRA is a knowledge graph of mechanisms (activations, phosphorylations, complexes, ...) assembled from the literature and curated databases. The backend queries INDRA CoGEx for networks and grounds gene symbols and chemical names with Gilda, INDRA's grounding service. Curations, which mark evidence as correct or incorrect, come from the INDRA database. backend_capabilities(indra_backend()) lists what it supports.

Usage

indra_backend(
  cogex_url = INDRA_API_URL,
  grounding_url = GILDA_API_URL,
  curation_url = INDRA_DB_URL
)

Arguments

cogex_url

base URL of INDRA CoGEx

grounding_url

base URL of Gilda

curation_url

base URL of the INDRA database, which holds the curations

Value

an IndraBackend object, to pass to convert_ids(), get_entity_properties(), get_network(), get_evidence(), and get_curations()

Details

This function includes third-party software components that are licensed under the BSD 2-Clause License. Include the third-party licensing agreements if redistributing this package or results based on it. See the LICENSE file for details.

See also

NetworkBackend-class

Examples

indra <- indra_backend()
backend_capabilities(indra)$query_types
#> [1] "subnetwork"