INDRA Network Search
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Network Search Web UI
INDRA Network Search Modules Reference
INDRA Network Search
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Z
A
alg_options() (indra_network_search.query.BreadthFirstSearchQuery method)
(indra_network_search.query.DijkstraQuery method)
(indra_network_search.query.OntologyQuery method)
(indra_network_search.query.PathQuery method)
(indra_network_search.query.Query method)
(indra_network_search.query.ShortestSimplePathsQuery method)
(indra_network_search.query.SubgraphQuery method)
(indra_network_search.query.UIQuery method)
allow_edge (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
allowed_ns (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
api_options() (indra_network_search.query.Query method)
available_nodes (indra_network_search.data_models.__init__.SubgraphResults attribute)
B
basemodel_in_iterable() (in module indra_network_search.data_models.__init__)
basemodels_equal() (in module indra_network_search.data_models.__init__)
belief (indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.EdgeDataByHash attribute)
(indra_network_search.data_models.__init__.StmtData attribute)
belief_cutoff (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
breadth_first_search() (indra_network_search.search_api.IndraNetworkSearchAPI method)
BreadthFirstSearchQuery (class in indra_network_search.query)
BreadthFirstSearchResultManager (class in indra_network_search.result_handler)
C
case_items() (indra_network_search.autocomplete.autocomplete.NodesTrie method)
case_keys() (indra_network_search.autocomplete.autocomplete.NodesTrie method)
check_existence_and_date_s3() (in module indra_network_search.rest_util)
const_c (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
const_tk (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
context_weight (indra_network_search.data_models.__init__.EdgeData attribute)
context_weighted (indra_network_search.data_models.__init__.FilterOptions attribute)
corr_weight (indra_network_search.data_models.__init__.EdgeData attribute)
cull_best_node (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
curated (indra_network_search.data_models.__init__.StmtData attribute)
curated_db_only (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
CurationCache (class in indra_network_search.util.curation_cache)
D
db_url_edge (indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.EdgeDataByHash attribute)
db_url_hash (indra_network_search.data_models.__init__.StmtData attribute)
depth_limit (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
dijkstra() (indra_network_search.search_api.IndraNetworkSearchAPI method)
DijkstraQuery (class in indra_network_search.query)
DijkstraResultManager (class in indra_network_search.result_handler)
direct_multi_interactors() (in module indra_network_search.pathfinding.pathfinding)
downstream (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SharedInteractorsResults attribute)
dump_query_json_to_s3() (in module indra_network_search.rest_util)
dump_query_result_to_s3() (in module indra_network_search.rest_util)
dump_result_json_to_s3() (in module indra_network_search.rest_util)
E
edge (indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.EdgeDataByHash attribute)
edge_data (indra_network_search.data_models.__init__.MultiInteractorsResults attribute)
(indra_network_search.data_models.__init__.Path attribute)
edge_filter (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
edges (indra_network_search.data_models.__init__.SubgraphResults attribute)
english (indra_network_search.data_models.__init__.StmtData attribute)
evidence_count (indra_network_search.data_models.__init__.StmtData attribute)
F
filter_curated (indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
format (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
fplx_expand (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
from_node_names() (indra_network_search.autocomplete.autocomplete.NodesTrie class method)
from_node_ns_id() (indra_network_search.autocomplete.autocomplete.NodesTrie class method)
G
get_all_hashes() (indra_network_search.util.curation_cache.CurationCache method)
get_default_args() (in module indra_network_search.rest_util)
get_filter_options() (indra_network_search.data_models.__init__.NetworkSearchQuery method)
get_graph() (indra_network_search.search_api.IndraNetworkSearchAPI method)
get_hash() (indra_network_search.data_models.__init__.NetworkSearchQuery method)
get_int_sign() (indra_network_search.data_models.__init__.NetworkSearchQuery method)
get_mandatory_args() (in module indra_network_search.rest_util)
get_node() (indra_network_search.search_api.IndraNetworkSearchAPI method)
get_prefix_autocomplete() (in module indra_network_search.rest_api)
get_queries() (indra_network_search.query_handler.QueryHandler method)
get_query_hash() (in module indra_network_search.rest_util)
get_results() (indra_network_search.result_handler.MultiInteractorsResultManager method)
(indra_network_search.result_handler.OntologyResultManager method)
(indra_network_search.result_handler.SharedInteractorsResultManager method)
(indra_network_search.result_handler.SubgraphResultManager method)
get_subgraph_edges() (in module indra_network_search.pathfinding.pathfinding)
get_unsigned_node() (indra_network_search.data_models.__init__.Node method)
get_xrefs() (in module indra_network_search.rest_api)
graph_date (indra_network_search.data_models.rest_models.ServerStatus attribute)
H
handle_multi_interactors_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
handle_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
handle_subgraph_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
hash_blacklist (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
hashes (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.Results attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
health() (in module indra_network_search.rest_api)
I
identifier (indra_network_search.data_models.__init__.Node attribute)
ignore_edges (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
ignore_nodes (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
immediate_only (indra_network_search.data_models.__init__.OntologyOptions attribute)
indra_network_search.autocomplete.autocomplete
module
indra_network_search.data_models.__init__
module
indra_network_search.data_models.rest_models
module
indra_network_search.pathfinding.pathfinding
module
indra_network_search.query
module
indra_network_search.query_handler
module
indra_network_search.rest_api
module
indra_network_search.rest_util
module
indra_network_search.result_handler
module
indra_network_search.search_api
module
indra_network_search.util.curation_cache
module
IndraNetworkSearchAPI (class in indra_network_search.search_api)
initial_sign (indra_network_search.data_models.__init__.StmtData attribute)
input_nodes (indra_network_search.data_models.__init__.SubgraphResults attribute)
InvalidParametersError
is_a_part_of (indra_network_search.data_models.__init__.OntologyOptions attribute)
is_context_weighted() (in module indra_network_search.rest_util)
(indra_network_search.data_models.__init__.NetworkSearchQuery method)
is_empty() (indra_network_search.data_models.__init__.EdgeData method)
(indra_network_search.data_models.__init__.OntologyResults method)
(indra_network_search.data_models.__init__.Path method)
(indra_network_search.data_models.__init__.PathResultData method)
(indra_network_search.data_models.__init__.SharedInteractorsResults method)
is_int_gt2() (indra_network_search.data_models.__init__.NetworkSearchQuery class method)
is_overall_weighted() (indra_network_search.data_models.__init__.NetworkSearchQuery method)
is_pos_int() (indra_network_search.data_models.__init__.NetworkSearchQuery class method)
is_positive_int() (indra_network_search.data_models.__init__.NetworkSearchQuery class method)
is_weighted() (in module indra_network_search.rest_util)
K
k_shortest (indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
L
load_indra_graph() (in module indra_network_search.rest_util)
lookup (indra_network_search.data_models.__init__.Node attribute)
M
max_memory (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
max_paths (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.OntologyOptions attribute)
max_per_node (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
max_results (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
mesh_ids (indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
mesh_options() (indra_network_search.query.BreadthFirstSearchQuery method)
(indra_network_search.query.DijkstraQuery method)
(indra_network_search.query.PathQuery method)
(indra_network_search.query.ShortestSimplePathsQuery method)
MissingParametersError
module
indra_network_search.autocomplete.autocomplete
indra_network_search.data_models.__init__
indra_network_search.data_models.rest_models
indra_network_search.pathfinding.pathfinding
indra_network_search.query
indra_network_search.query_handler
indra_network_search.rest_api
indra_network_search.rest_util
indra_network_search.result_handler
indra_network_search.search_api
indra_network_search.util.curation_cache
multi_interactors_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
MultiInteractorsQuery (class in indra_network_search.query)
MultiInteractorsResultManager (class in indra_network_search.result_handler)
N
name (indra_network_search.data_models.__init__.Node attribute)
namespace (indra_network_search.data_models.__init__.Node attribute)
no_filters() (indra_network_search.data_models.__init__.FilterOptions method)
no_node_filters() (indra_network_search.data_models.__init__.FilterOptions method)
no_stmt_filters() (indra_network_search.data_models.__init__.FilterOptions method)
node_blacklist (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
node_filter (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
node_id_in_graph() (in module indra_network_search.rest_api)
node_name_in_graph() (in module indra_network_search.rest_api)
nodes (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SubgraphOptions attribute)
(indra_network_search.data_models.__init__.SubgraphRestQuery attribute)
NodesTrie (class in indra_network_search.autocomplete.autocomplete)
not_in_graph (indra_network_search.data_models.__init__.SubgraphResults attribute)
O
ontology_results (indra_network_search.data_models.__init__.Results attribute)
OntologyQuery (class in indra_network_search.query)
OntologyResultManager (class in indra_network_search.result_handler)
options (indra_network_search.query.BreadthFirstSearchQuery attribute)
(indra_network_search.query.DijkstraQuery attribute)
(indra_network_search.query.MultiInteractorsQuery attribute)
(indra_network_search.query.OntologyQuery attribute)
(indra_network_search.query.ShortestSimplePathsQuery attribute)
(indra_network_search.query.SubgraphQuery attribute)
overall_weighted (indra_network_search.data_models.__init__.FilterOptions attribute)
P
parents (indra_network_search.data_models.__init__.OntologyResults attribute)
path (indra_network_search.data_models.__init__.Path attribute)
path_length (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
path_limit (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.DijkstraOptions attribute)
path_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
path_results (indra_network_search.data_models.__init__.Results attribute)
PathQuery (class in indra_network_search.query)
paths (indra_network_search.data_models.__init__.PathResultData attribute)
position (indra_network_search.data_models.__init__.StmtData attribute)
Q
Query (class in indra_network_search.query)
query() (in module indra_network_search.rest_api)
query_hash (indra_network_search.data_models.__init__.Results attribute)
QueryHandler (class in indra_network_search.query_handler)
R
ref_counts_function (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
regulators (indra_network_search.data_models.__init__.MultiInteractorsResults attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
residue (indra_network_search.data_models.__init__.StmtData attribute)
result_options() (indra_network_search.query.MultiInteractorsQuery method)
(indra_network_search.query.OntologyQuery method)
(indra_network_search.query.PathQuery method)
(indra_network_search.query.Query method)
(indra_network_search.query.SubgraphQuery method)
(indra_network_search.query.UIQuery method)
reverse (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.DijkstraOptions attribute)
reverse_path_results (indra_network_search.data_models.__init__.Results attribute)
reverse_search() (indra_network_search.data_models.__init__.NetworkSearchQuery method)
run_options() (indra_network_search.query.MultiInteractorsQuery method)
(indra_network_search.query.OntologyQuery method)
(indra_network_search.query.PathQuery method)
(indra_network_search.query.Query method)
(indra_network_search.query.SubgraphQuery method)
(indra_network_search.query.UIQuery method)
S
server_status() (in module indra_network_search.rest_api)
set_source_counts() (indra_network_search.data_models.__init__.EdgeData method)
(indra_network_search.data_models.__init__.StmtTypeSupport method)
shared_interactors() (in module indra_network_search.pathfinding.pathfinding)
shared_parents() (in module indra_network_search.pathfinding.pathfinding)
(indra_network_search.search_api.IndraNetworkSearchAPI method)
shared_regulators (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
shared_regulators() (indra_network_search.search_api.IndraNetworkSearchAPI method)
shared_regulators_results (indra_network_search.data_models.__init__.Results attribute)
shared_target_results (indra_network_search.data_models.__init__.Results attribute)
shared_targets() (indra_network_search.search_api.IndraNetworkSearchAPI method)
SharedInteractorsResultManager (class in indra_network_search.result_handler)
SharedRegulatorsQuery (class in indra_network_search.query)
SharedTargetsQuery (class in indra_network_search.query)
shortest_simple_paths() (indra_network_search.search_api.IndraNetworkSearchAPI method)
ShortestSimplePathsQuery (class in indra_network_search.query)
ShortestSimplePathsResultManager (class in indra_network_search.result_handler)
sign (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.Node attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
signed_edges (indra_network_search.data_models.rest_models.ServerStatus attribute)
signed_node_tuple() (indra_network_search.data_models.__init__.Node method)
signed_nodes (indra_network_search.data_models.rest_models.ServerStatus attribute)
source (indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.OntologyResults attribute)
(indra_network_search.data_models.__init__.PathResultData attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
source_counts (indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.StmtData attribute)
(indra_network_search.data_models.__init__.StmtTypeSupport attribute)
source_data (indra_network_search.data_models.__init__.SharedInteractorsResults attribute)
source_filter (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
source_id (indra_network_search.data_models.__init__.OntologyOptions attribute)
source_node (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
source_ns (indra_network_search.data_models.__init__.OntologyOptions attribute)
start (indra_network_search.data_models.__init__.DijkstraOptions attribute)
statements (indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.StmtTypeSupport attribute)
status (indra_network_search.data_models.rest_models.Health attribute)
(indra_network_search.data_models.rest_models.ServerStatus attribute)
stmt_filter (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
stmt_hash (indra_network_search.data_models.__init__.StmtData attribute)
stmt_type (indra_network_search.data_models.__init__.StmtData attribute)
(indra_network_search.data_models.__init__.StmtTypeSupport attribute)
stmt_types (indra_network_search.data_models.__init__.MultiInteractorsOptions attribute)
(indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
stmts (indra_network_search.data_models.__init__.EdgeDataByHash attribute)
strict_mesh_id_filtering (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
sub_graph() (in module indra_network_search.rest_api)
subgraph_query() (indra_network_search.search_api.IndraNetworkSearchAPI method)
SubgraphQuery (class in indra_network_search.query)
SubgraphResultManager (class in indra_network_search.result_handler)
T
target (indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
(indra_network_search.data_models.__init__.OntologyResults attribute)
(indra_network_search.data_models.__init__.PathResultData attribute)
(indra_network_search.data_models.__init__.SharedInteractorsOptions attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
target_data (indra_network_search.data_models.__init__.SharedInteractorsResults attribute)
target_id (indra_network_search.data_models.__init__.OntologyOptions attribute)
target_ns (indra_network_search.data_models.__init__.OntologyOptions attribute)
targets (indra_network_search.data_models.__init__.MultiInteractorsResults attribute)
terminal_ns (indra_network_search.data_models.__init__.BreadthFirstSearchOptions attribute)
(indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
time_limit (indra_network_search.data_models.__init__.Results attribute)
timed_out (indra_network_search.data_models.__init__.Results attribute)
timeout (indra_network_search.data_models.__init__.MultiInteractorsRestQuery attribute)
(indra_network_search.data_models.__init__.SubgraphRestQuery attribute)
two_way (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
U
UIQuery (class in indra_network_search.query)
unsigned_edges (indra_network_search.data_models.rest_models.ServerStatus attribute)
unsigned_nodes (indra_network_search.data_models.rest_models.ServerStatus attribute)
url_by_type (indra_network_search.data_models.__init__.EdgeDataByHash attribute)
user_timeout (indra_network_search.data_models.__init__.ApiOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
W
weight (indra_network_search.data_models.__init__.DijkstraOptions attribute)
(indra_network_search.data_models.__init__.EdgeData attribute)
(indra_network_search.data_models.__init__.EdgeDataByHash attribute)
(indra_network_search.data_models.__init__.ShortestSimplePathOptions attribute)
(indra_network_search.data_models.__init__.StmtData attribute)
weighted (indra_network_search.data_models.__init__.FilterOptions attribute)
(indra_network_search.data_models.__init__.NetworkSearchQuery attribute)
Z
z_score (indra_network_search.data_models.__init__.EdgeData attribute)
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