Welcome to the INDRA Network Service documentation!

This documentation covers a tutorial and the modules of the INDRA Network Search and is part of a broader set of INDRA derived applications. To read more about INDRA, see the homepage, the documentation and the project on github.

Contents:

• Network Search Web UI
  • Source and Target
    • Autocompleting source/target inputs
  • Detailed Search Options - General Options
    • Path Length
    • Node Blacklist
    • Max Paths
    • Signed Search
    • Highest Degree Node Culling Frequency
    • Belief Cutoff
    • Allowed Statement Types
    • Allowed Node Namespaces
    • Checkboxes
  • Detailed Search Options - Context and Weighted Search Options
    • Unweighted
    • Belief Weighted
    • DepMap z-score weighted
    • Mesh Context
  • Detailed Search Options - Open Search Options
    • Terminal Namespaces
    • Max Children Per Node (Unweighted Search)
    • Depth Limit (Unweighted Search)
  • Timeout
  • Result Categories
    • Common Parents
    • Shared Targets
    • Shared Regulators
    • Path Results
  • Detailed Results
  • The Graphs Used
• INDRA Network Search Modules Reference
  • Autocomplete (indra_network_search.autocomplete.autocomplete)
    • NodesTrie
  • Data Models (indra_network_search.data_models)
    • ApiOptions
    • BreadthFirstSearchOptions
    • DijkstraOptions
    • EdgeData
    • EdgeDataByHash
    • FilterOptions
    • MultiInteractorsOptions
    • MultiInteractorsRestQuery
    • MultiInteractorsResults
    • NetworkSearchQuery
    • Node
    • OntologyOptions
    • OntologyResults
    • Path
    • PathResultData
    • Results
    • SharedInteractorsOptions
    • SharedInteractorsResults
    • ShortestSimplePathOptions
    • StmtData
    • StmtTypeSupport
    • SubgraphOptions
    • SubgraphRestQuery
    • SubgraphResults
    • basemodel_in_iterable()
    • basemodels_equal()
  • Rest Models (indra_network_search.data_models.rest_models)
    • Health
    • ServerStatus
  • Pathfinding (indra_network_search.pathfinding.pathfinding)
    • direct_multi_interactors()
    • get_subgraph_edges()
    • shared_interactors()
    • shared_parents()
  • Utility Functions (indra_network_search.util)
    • Util (indra_network_search.util.curation_cache)
  • Query Classes (indra_network_search.query)
    • BreadthFirstSearchQuery
    • DijkstraQuery
    • InvalidParametersError
    • MissingParametersError
    • MultiInteractorsQuery
    • OntologyQuery
    • PathQuery
    • Query
    • SharedRegulatorsQuery
    • SharedTargetsQuery
    • ShortestSimplePathsQuery
    • SubgraphQuery
    • UIQuery
  • Query Handler (indra_network_search.query_handler)
    • QueryHandler
  • Rest API (indra_network_search.rest_api)
    • get_prefix_autocomplete()
    • get_xrefs()
    • health()
    • node_id_in_graph()
    • node_name_in_graph()
    • query()
    • server_status()
    • sub_graph()
  • Rest API Utilities (indra_network_search.rest_util)
    • check_existence_and_date_s3()
    • dump_query_json_to_s3()
    • dump_query_result_to_s3()
    • dump_result_json_to_s3()
    • get_default_args()
    • get_mandatory_args()
    • get_query_hash()
    • is_context_weighted()
    • is_weighted()
    • load_indra_graph()
  • Result Handlers (indra_network_search.result_handler)
    • BreadthFirstSearchResultManager
    • DijkstraResultManager
    • MultiInteractorsResultManager
    • OntologyResultManager
    • SharedInteractorsResultManager
    • ShortestSimplePathsResultManager
    • SubgraphResultManager
  • Search API (indra_network_search.search_api)
    • IndraNetworkSearchAPI

Indices and tables

• Index

• Module Index

• Search Page