The Client

The purpose of the client is to be the gateway for external access to the content of the databases. Here we define high level access functions for getting data out of the database in a natural way. This is where the queries used by the REST API are defined, and most users looking to access knowledge on the database should use the client if they can, as it is heavily optimized.

Our system utilizes 2 databases, one which represents the “ground truth”, as we know it, and is structured naturally for performing updates on our knowledge; it will always be the most up to date. We also have a “readonly” database that we used for our outward facing services. This database is optimized for fast queries and the content in it is updated weekly. Each database has its own set of access tools.

• The Principal Database Client
  • Access Readings and Text Content (indra_db.client.principal.content)
    • get_content_by_refs()
    • get_reader_output()
  • Submit and Retrieve Curations (indra_db.client.principal.curation)
    • get_curations()
    • get_grounding_curations()
    • submit_curation()
  • Get Raw Statements (indra_db.client.principal.raw_statements)
    • get_raw_stmt_jsons()
    • get_raw_stmt_jsons_from_agents()
    • get_raw_stmt_jsons_from_papers()
• The Readonly Client
  • Construct composable queries (indra_db.client.readonly.query)
    • Query
    • Intersection
    • Union
    • MergeQuery
    • HasAgent
    • FromMeshIds
    • HasHash
    • HasSources
    • HasOnlySource
    • HasReadings
    • HasDatabases
    • SourceQuery
    • SourceIntersection
    • HasType
    • IntrusiveQuery
    • HasNumAgents
    • HasNumEvidence
    • FromPapers
    • EvidenceFilter
    • FromAgentJson
    • HasEvidenceBound
• Miscellaneous Client APIs (Mostly Deprecated)
  • Get Datasets (indra_db.client.datasets)
    • export_relation_dict_to_tsv()
    • get_relation_dict()
    • get_statement_essentials()
  • Get Statements (indra_db.client.statements)
    • get_evidence()
    • get_statements()
    • get_statements_by_gene_role_type()
    • get_statements_by_paper()
    • get_statements_from_hashes()
    • get_support()