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.
Network Search Web UI
This document introduces the web interface of the INDRA Network Search Service
The network search interface with no input or results.
Source and Target
The source and target are the nodes between which to find a path and at least one of source and target is needed to do a search. If only one of source or target is provided, an open ended breadth first search is done instead of a path search. Note that the source and target are not affected by the choice of allowed namespaces (see below at Allowed Node Namespaces).
Autocompleting source/target inputs
Autocompletion of source/target based on prefix and entity identifier are made automatically as an input is typed or pasted into the text boxes. The suggestions are picked from the nodes in the graph and the text box will mark the entered text as correct if it matches an existing node in the graph.
Autocompleting an entity. As an entity name is typed into the source or target text boxes, suggestions from the graph nodes are provided.
Verified entry. Entries are verified as they are being typed or pasted into the text box. When the entered entity is verified to exist in the graph, the text box border will switch to green and a checkmark will appear.
Detailed Search Options - General Options
The general detailed search options contain filters that apply to most searches, regardless of weighting or openness.
The search interface with the general options section expanded.
Path Length
Only paths of this many edges will be returned. Must be a positive integer.
Node Blacklist
Node names entered here are skipped in the path search. This is a good way to avoid nodes of extremely high degree that overwhelms the results and effectively blocks out results that include nodes of lower degree. See also Highest Degree Node Culling Frequency below.
Max Paths
The maximum number of results to return per category in the results. The default and the maximum allowed is 50 results. For unweighted searches this number rarely makes a perceivable difference in response time but for weighted searches keep this number low for a faster response time.
Signed Search
To perform a signed search, click on the drop down menu that says “No sign” and chose a sign. “+” means that the returned paths are upregulations, and “-” means that the returned paths are downregulations. For the purpose of signed search, only statements that imply a clear up- or downregulation are considered. Currently this mean IncreaseAmount and Activation for upregulation, and DecreaseAmount and Inhibition for downregulation.
Highest Degree Node Culling Frequency
Entering a positive integer here allows the path search to include the highest degree node for the first N returned paths, after which that node is added to the Node Blacklist. This is repeated for the second highest degree node for the following N paths, then for the third highest degree node and so forth. Limitations: This option is only applied to unweighted open search and source-target searches.
Belief Cutoff
Any statement with a belief score below this number will be excluded from the edge support. If all statements are excluded from the edge, all paths containing that edge become invalid and are skipped. It is set to zero by default to include all edges. Read more about belief scores in the belief module of INDRA.
Allowed Statement Types
This is a multiselect dropdown which contains multiple statement types to allow in the results. If an edge of a path does not contain any of the selected statement types, the whole path will be skipped from the result. Read more about statement types in the statements module of INDRA.
Allowed Node Namespaces
The namespaces included here are the ones that are allowed on any node visited in the path search. The namespace of the source and target are excluded from this restriction. A namespace in INDRA is the prefix or name of the type of identifier used to uniquely identify an entity from a specific knowledge source. For example, a chemical can be identified using a CHEBI identifier and would then be identified in the CHEBI namespace.
Checkboxes
The following options are available as checkboxes:
Only Database Supported Sources: Check this box to enforce that all edges must be supported by at least one statement sourced from curated databases like PathwayCommons and Signor
Allow Ontological Edges: Check this box to allow directed edges that go from an entity to its ontological parent, e.g. from the NFKB1 sub-unit to the NFkappaB complex.
Include Reverse Search: Check this box to also search for paths with source and target swapped. With this option, the reverse search from target to source is done as well as the original search from source to target. If the timeout is reached (see below) before the reverse search can start, the reverse search will not return any paths. If the timeout is reached during the reverse search, fewer paths than for the original search will be returned.
Include Search for Shared Regulators of Source/Target: Check this box to include a search for common upstream nodes one edge away from both source and target. This option is only available when both source and target specified.
Detailed Search Options - Context and Weighted Search Options
This section of the search options allows control over how to prioritize or weight edges in paths differently. During weighted search, the cost along every path encountered is calculated as the sum of the edge weights along the path. The paths are returned in ascending order of cost.
The different ways of weighting the search are available in the dropdown menu “Weighted Search”. Note: A weighted search is costly and usually takes longer than an unweighted search. It is common that a very heavy weighted search times out, especially for a signed weighted search, even with the highest allowed timeout of 120 seconds.
The weighted search uses a slightly modified version of the Djikstra weighted search employed in Networkx.
The code implemented for the weighted search is available on github in the functions shortest_simple_paths() and open_dijkstra_search() for closed and open paths, respectively.
The search interface with the Context and Weighted search options section expanded.
Unweighted
This is the default option and imposes no weight on the edges and is equivalent to all edges having a unit weight.
Belief Weighted
The belief weight of an edge is calculated as the negative log of the aggregated belief scores of all the statements supporting edge \(e\):
where \(b_i\) is the belief score of supporting statement \(i\) of edge \(e\). Since the belief score is limited to the interval \([0, 1]\), it can interpreted as a probability and the above weight can therefore be seen as the log of the complement to the probability that every supporting statement is incorrect.
DepMap z-score weighted
The z-score edge weight is focused around prioritizing edges between human genes that have been targeted in knockout screens performed at the Broad Institute’s Dependency Map project. The z-score is obtained from first calculating the pearson correlation between all pairs of genes in the gene knockout screen. Then the log of the p-values of the correlations are calculated using the CDF of the beta distribution. Finally the strength of the z-scores are obtained from the p-values and the signs are recuperated from the original correlation matrix.
The edge weight, assuming both nodes are human genes, is calculated by normalizing the difference between the z-score associated with a self-correlation and the strength of the z-score between the two nodes of the edge. In the case that one or both of the nodes of the edge are non-gene entities, the z-score weight is set to 1:
where \(z_0\) is the z-score associated with self correlation and \(z_e\) is the z-score of the edge.
Mesh Context
The context based search allows a search to prioritize or only include connections that are relevant to the provided context. The context is given as MeSH terms.
MeSH IDs: Enter the MeSH IDs, separated by comma, that should be used in the search.
Strict Filtering on MeSH IDs: Check this box to only allow edges with associated with the provided MeSH IDs. If left unchecked, the search is weighted.
Constants \(C\) and \(T_k\): These two constant allow for changing the importance of the context in a weighted context based search. For any edge \(e\), the weight \(w_e\) of the edge in the context based search is calculated in the following way:
Here, refcount is the number of references with the associated MeSH ID(s) that are supporting edge \(e\) and total is the total number of references supporting edge \(e\).
Detailed Search Options - Open Search Options
Options under the Open Search Options are only applied during open searches, i.e. when either of source or target is provided.
The search interface with the Open search options section expanded.
Terminal Namespaces
Namespaces selected here restrict the search to only return paths that end (open search from source) or start (open search from target) on the given namespaces and then not consider these nodes further. For example: if namespace A is selected, then a downstream path might look like this: X->Y->A, but not like this: X->Y->A->Z, where X, Y, Z are all namespaces other than A.
Max Children Per Node (Unweighted Search)
The integer provided here gives a maximum for the number of children to continue to open search from. For example: if N is set here, the first N nodes selected from the starting node are then considered for the next layer in the breadth first search. This option is only available for unweighted searches.
Depth Limit (Unweighted Search)
This option limits how deep, i.e. how many edges, the returned paths are allowed to be/have. This option is only available for unweighted searches.
Timeout
Setting a timeout allows to set a larger (or smaller) timeout than the default 30 seconds timeout. The time since the path search was started is checked before each iteration of data assembly for a returned path during the search. If the time passed is larger than the allowed timeout, the search is stopped. The timeout provided has to be a decimal number smaller than or equal to 120 seconds.
Result Categories
Note: If there are no results for a specific category, that section will be hidden.
Common Parents
This section shows the result of a search for common ontological parents of source and target. For example with GP1BA and GP1BB as source and target, respectively, the Platelet membrane glycoprotein complex shows up as a shared ontological parent.
The result of a search with GP1BA and GP1BB as source and target, respectively, for Common Parents showing the Platelet membrane glycoprotein complex as their shared protein complex.
Path Results
This section show path results per path length, i.e. all paths with the same number of edges share a specific subsection. The division of paths per subsection is done regardless if the path search is weighted or not.
Search results with SIK3 as source and JUN as target with the Shared Regulator section expanded.
Detailed Results
For each result section, excluding Common Parents, there are two levels of detail. Results for Common Parents only have one level of results: name, namespace, identifier and entity lookup. The first level shows path (for Path Results), target (for Shared Targets) or regulator (for Shared Regulators) together with weight (if the search is weighted) the edge, source counts and a link to the INDRA DB for that specific edge.
The second level of results is collapsed by default. To expand it, the circled “+” (\(\oplus\)) need to be clicked. Once expanded, source counts and a link to more specific information in the INDRA DB per statement type are shown.
As the network search results can be filtered in more detail than what is possible using the INDRA DB, the statements shown in the DB can sometimes be a superset of the statements shown in the second level of the results.
Path search results with one of the edges of a path expanded to more detail.
The Graphs Used
The two graphs used for the network search are assembled from a full snapshot of the INDRA DataBase that is updated regularly. Any statement that includes two or three agents are assembled into the support for the edges for the graphs, with one edge containing one or more statements. The two types of graphs used are:
Unsigned directed graph
Signed node directed graph
The edges in the signed graph only contain statements that have clear up- or downreguations associated with them, which currently are IncreaseAmount and Activation for upregulation, and DecreaseAmount and Inhibition for downregulation.
The code assembling the graphs can be found in net_functions.py in the function sif_dump_df_to_digraph() in the depmap_analysis repository.
INDRA Network Search Modules Reference
Autocomplete (indra_network_search.autocomplete.autocomplete)
An API wrapping SortedStringTrie from pytrie (see https://github.com/gsakkis/pytrie)
- class indra_network_search.autocomplete.autocomplete.NodesTrie(*args, **kwargs)[source]
A Trie structure that has case insensitive search methods
- case_items(prefix=None, top_n=100)[source]
Case insensitive wrapper around NodeTrie.items()
- Parameters
prefix (
Optional[str]) – The prefix to search- Return type
List[Tuple[str,str,str]]- Returns
Return a list of (name, namespace, id) tuples
- case_keys(prefix=None, top_n=100)[source]
Case insensitive wrapper around NodeTrie.keys()
- Parameters
prefix (
Optional[str]) – The prefix to searchtop_n (
Optional[int]) – The top ranked entities (by node degree)
- Returns
Return a list of this trie’s keys
- Return type
List[str]
- classmethod from_node_names(graph)[source]
Produce a NodesTrie instance from a graph with node names as keys
- Parameters
graph (
Union[DiGraph,MultiDiGraph]) – Graph from which nodes should be searchable. It is assumed the nodes are all keyed by strings- Return type
- Returns
An instance of a NodesTrie containing the node names of the graph as keys and the corresponding (name, ns, id, node degree) tuple as values
- classmethod from_node_ns_id(graph)[source]
Produce a NodesTrie instance from a graph using ns:id as key
- Parameters
graph (
Union[DiGraph,MultiDiGraph]) – Graph from which nodes should be searchable. It is assumed the nodes have the attributes ‘ns’ and ‘id’ accessible via g.nodes[node][‘ns’] and g.nodes[node][‘id’]- Return type
- Returns
An instance of a NodesTrie containing ns:id of each node of the graph as keys and the corresponding (name, ns, id, node degree) tuple as values
Data Models (indra_network_search.data_models)
This module contains all data models used in the repository. They are all built around the the Pydantic BaseModel.
This file contains data models for queries, results and arguments to algorithm functions.
- pydantic model indra_network_search.data_models.__init__.ApiOptions[source]
Options that determine API behaviour
Show JSON schema
{ "title": "ApiOptions", "description": "Options that determine API behaviour", "type": "object", "properties": { "sign": { "title": "Sign", "type": "integer" }, "fplx_expand": { "title": "Fplx Expand", "default": false, "type": "boolean" }, "user_timeout": { "title": "User Timeout", "default": false, "anyOf": [ { "type": "number" }, { "type": "boolean" } ] }, "two_way": { "title": "Two Way", "default": false, "type": "boolean" }, "shared_regulators": { "title": "Shared Regulators", "default": false, "type": "boolean" }, "format": { "title": "Format", "default": "json", "type": "string" } } }
- Fields
- field format: Optional[str] = 'json'
- field fplx_expand: Optional[bool] = False
- field sign: Optional[int] = None
- field two_way: Optional[bool] = False
- field user_timeout: Optional[Union[float, bool]] = False
- pydantic model indra_network_search.data_models.__init__.BreadthFirstSearchOptions[source]
Arguments for indra.explanation.pathfinding.bfs_search
Show JSON schema
{ "title": "BreadthFirstSearchOptions", "description": "Arguments for indra.explanation.pathfinding.bfs_search", "type": "object", "properties": { "source_node": { "title": "Source Node", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "reverse": { "title": "Reverse", "default": false, "type": "boolean" }, "depth_limit": { "title": "Depth Limit", "default": 2, "type": "integer" }, "path_limit": { "title": "Path Limit", "type": "integer" }, "max_per_node": { "title": "Max Per Node", "default": 5, "type": "integer" }, "node_filter": { "title": "Node Filter", "type": "array", "items": { "type": "string" } }, "node_blacklist": { "title": "Node Blacklist", "type": "array", "items": { "type": "string" }, "uniqueItems": true }, "terminal_ns": { "title": "Terminal Ns", "type": "array", "items": { "type": "string" } }, "sign": { "title": "Sign", "type": "integer" }, "max_memory": { "title": "Max Memory", "default": 536870912, "type": "integer" }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "strict_mesh_id_filtering": { "title": "Strict Mesh Id Filtering", "default": false, "type": "boolean" } }, "required": [ "source_node" ] }
- Fields
- field allow_edge: Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]] = None
- field depth_limit: Optional[int] = 2
- field edge_filter: Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]] = None
- field hashes: Optional[List[int]] = None
- field max_memory: Optional[int] = 536870912
- field max_per_node: Optional[int] = 5
- field node_blacklist: Optional[Set[str]] = None
- field node_filter: Optional[List[str]] = None
- field path_limit: Optional[int] = None
- field reverse: Optional[bool] = False
- field sign: Optional[int] = None
- field source_node: Union[str, Tuple[str, int]] [Required]
- field strict_mesh_id_filtering: Optional[bool] = False
- field terminal_ns: Optional[List[str]] = None
- pydantic model indra_network_search.data_models.__init__.DijkstraOptions[source]
Arguments for open_dijkstra_search
Show JSON schema
{ "title": "DijkstraOptions", "description": "Arguments for open_dijkstra_search", "type": "object", "properties": { "start": { "title": "Start", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "reverse": { "title": "Reverse", "default": false, "type": "boolean" }, "path_limit": { "title": "Path Limit", "type": "integer" }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "ignore_nodes": { "title": "Ignore Nodes", "type": "array", "items": { "type": "string" } }, "ignore_edges": { "title": "Ignore Edges", "type": "array", "items": { "type": "array", "items": [ { "type": "string" }, { "type": "string" } ] } }, "terminal_ns": { "title": "Terminal Ns", "type": "array", "items": { "type": "string" } }, "weight": { "title": "Weight", "type": "string" }, "const_c": { "title": "Const C", "default": 1, "type": "integer" }, "const_tk": { "title": "Const Tk", "default": 10, "type": "integer" } }, "required": [ "start" ] }
- Fields
- field const_c: Optional[int] = 1
- field const_tk: Optional[int] = 10
- field hashes: Optional[List[int]] = None
- field ignore_edges: Optional[List[Tuple[str, str]]] = None
- field ignore_nodes: Optional[List[str]] = None
- field path_limit: Optional[int] = None
- field ref_counts_function: Optional[Callable] = None
- field reverse: Optional[bool] = False
- field start: Union[str, Tuple[str, int]] [Required]
- field terminal_ns: Optional[List[str]] = None
- field weight: Optional[str] = None
- pydantic model indra_network_search.data_models.__init__.EdgeData[source]
Data for one single edge
Show JSON schema
{ "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] } } }
- Fields
statements (Dict[str, indra_network_search.data_models.__init__.StmtTypeSupport])belief (indra_network_search.data_models.__init__.ConstrainedFloatValue)weight (indra_network_search.data_models.__init__.ConstrainedFloatValue)corr_weight (Optional[indra_network_search.data_models.__init__.ConstrainedFloatValue])sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])
- field belief: indra_network_search.data_models.__init__.ConstrainedFloatValue [Required]
- Constraints
minimum = 0
maximum = 1
- field context_weight: Union[str, indra_network_search.data_models.__init__.ConstrainedFloatValue, typing_extensions.Literal[N/A]] = 'N/A'
- field corr_weight: Optional[indra_network_search.data_models.__init__.ConstrainedFloatValue] = None
- Constraints
exclusiveMinimum = 0.0
- field db_url_edge: str [Required]
- field edge: List[indra_network_search.data_models.__init__.Node] [Required]
- field sign: Optional[indra_network_search.data_models.__init__.ConstrainedIntValue] [Required]
- Constraints
minimum = 0
maximum = 1
- field source_counts: Dict[str, int] = {}
- field statements: Dict[str, indra_network_search.data_models.__init__.StmtTypeSupport] [Required]
- field weight: indra_network_search.data_models.__init__.ConstrainedFloatValue [Required]
- Constraints
minimum = 0
- field z_score: Optional[float] = None
- pydantic model indra_network_search.data_models.__init__.EdgeDataByHash[source]
Data for one single edge, with data keyed by hash
Show JSON schema
{ "title": "EdgeDataByHash", "description": "Data for one single edge, with data keyed by hash", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "stmts": { "title": "Stmts", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtData" } }, "belief": { "title": "Belief", "type": "number" }, "weight": { "title": "Weight", "type": "number" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "url_by_type": { "title": "Url By Type", "type": "object", "additionalProperties": { "type": "string" } } }, "required": [ "edge", "stmts", "belief", "weight", "db_url_edge", "url_by_type" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] } } }
- Fields
- field belief: float [Required]
- field db_url_edge: str [Required]
- field edge: List[indra_network_search.data_models.__init__.Node] [Required]
- field stmts: Dict[int, indra_network_search.data_models.__init__.StmtData] [Required]
- field url_by_type: Dict[str, str] [Required]
- field weight: float [Required]
- pydantic model indra_network_search.data_models.__init__.FilterOptions[source]
Options for filtering out nodes or edges
Show JSON schema
{ "title": "FilterOptions", "description": "Options for filtering out nodes or edges", "type": "object", "properties": { "stmt_filter": { "title": "Stmt Filter", "default": [], "type": "array", "items": { "type": "string" } }, "allowed_ns": { "title": "Allowed Ns", "default": [], "type": "array", "items": { "type": "string" } }, "node_blacklist": { "title": "Node Blacklist", "default": [], "type": "array", "items": { "type": "string" } }, "path_length": { "title": "Path Length", "type": "integer" }, "belief_cutoff": { "title": "Belief Cutoff", "default": 0.0, "type": "number" }, "curated_db_only": { "title": "Curated Db Only", "default": false, "type": "boolean" }, "max_paths": { "title": "Max Paths", "default": 50, "type": "integer" }, "cull_best_node": { "title": "Cull Best Node", "type": "integer" }, "weighted": { "title": "Weighted", "enum": [ "weight", "context_weight", "corr_weight" ], "type": "string" }, "context_weighted": { "title": "Context Weighted", "default": false, "type": "boolean" }, "overall_weighted": { "title": "Overall Weighted", "default": false, "type": "boolean" } } }
- Fields
- field allowed_ns: List[indra_network_search.data_models.__init__.ConstrainedStrValue] = []
- field belief_cutoff: float = 0.0
- field context_weighted: bool = False
- field cull_best_node: Optional[int] = None
- field curated_db_only: bool = False
- field max_paths: int = 50
- field node_blacklist: List[str] = []
- field overall_weighted: bool = False
- field path_length: Optional[int] = None
- field stmt_filter: List[indra_network_search.data_models.__init__.ConstrainedStrValue] = []
- field weighted: Optional[typing_extensions.Literal[weight, context_weight, corr_weight]] = None
- pydantic model indra_network_search.data_models.__init__.MultiInteractorsOptions[source]
Multi interactors options
Show JSON schema
{ "title": "MultiInteractorsOptions", "description": "Multi interactors options", "type": "object", "properties": { "nodes": { "title": "Nodes", "type": "array", "items": { "type": "string" } }, "downstream": { "title": "Downstream", "type": "boolean" }, "allowed_ns": { "title": "Allowed Ns", "type": "array", "items": { "type": "string" } }, "stmt_types": { "title": "Stmt Types", "type": "array", "items": { "type": "string" } }, "source_filter": { "title": "Source Filter", "type": "array", "items": { "type": "string" } }, "max_results": { "title": "Max Results", "default": 50, "type": "integer" }, "hash_blacklist": { "title": "Hash Blacklist", "type": "array", "items": { "type": "integer" }, "uniqueItems": true }, "node_blacklist": { "title": "Node Blacklist", "type": "array", "items": { "type": "string" } }, "belief_cutoff": { "title": "Belief Cutoff", "default": 0.0, "type": "number" }, "curated_db_only": { "title": "Curated Db Only", "default": false, "type": "boolean" } }, "required": [ "nodes", "downstream" ] }
- Fields
- field allowed_ns: Optional[List[str]] = None
- field belief_cutoff: float = 0.0
- field curated_db_only: bool = False
- field downstream: bool [Required]
- field hash_blacklist: Optional[Set[int]] = None
- field max_results: int = 50
- field node_blacklist: Optional[List[str]] = None
- field nodes: List[str] [Required]
- field source_filter: Optional[List[str]] = None
- field stmt_types: Optional[List[str]] = None
- pydantic model indra_network_search.data_models.__init__.MultiInteractorsRestQuery[source]
Multi interactors rest query
Show JSON schema
{ "title": "MultiInteractorsRestQuery", "description": "Multi interactors rest query", "type": "object", "properties": { "nodes": { "title": "Nodes", "type": "array", "items": { "type": "string" } }, "downstream": { "title": "Downstream", "type": "boolean" }, "allowed_ns": { "title": "Allowed Ns", "type": "array", "items": { "type": "string", "minLength": 1 } }, "stmt_types": { "title": "Stmt Types", "type": "array", "items": { "type": "string", "minLength": 1 } }, "source_filter": { "title": "Source Filter", "type": "array", "items": { "type": "string", "minLength": 1 } }, "max_results": { "title": "Max Results", "default": 50, "type": "integer" }, "node_blacklist": { "title": "Node Blacklist", "type": "array", "items": { "type": "string" } }, "belief_cutoff": { "title": "Belief Cutoff", "default": 0.0, "type": "number" }, "curated_db_only": { "title": "Curated Db Only", "default": false, "type": "boolean" }, "timeout": { "title": "Timeout", "default": 30, "minimum": 5.0, "maximum": 120.0, "type": "number" } }, "required": [ "nodes", "downstream" ] }
- Fields
allowed_ns (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])stmt_types (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])source_filter (Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]])timeout (indra_network_search.data_models.__init__.ConstrainedFloatValue)
- field allowed_ns: Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]] = None
- field belief_cutoff: float = 0.0
- field curated_db_only: bool = False
- field downstream: bool [Required]
- field max_results: int = 50
- field node_blacklist: Optional[List[str]] = None
- field nodes: List[str] [Required]
- field source_filter: Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]] = None
- field stmt_types: Optional[List[indra_network_search.data_models.__init__.ConstrainedStrValue]] = None
- field timeout: indra_network_search.data_models.__init__.ConstrainedFloatValue = 30
- Constraints
minimum = 5.0
maximum = 120.0
- pydantic model indra_network_search.data_models.__init__.MultiInteractorsResults[source]
Results post direct_multi_interactors
Show JSON schema
{ "title": "MultiInteractorsResults", "description": "Results post direct_multi_interactors", "type": "object", "properties": { "targets": { "title": "Targets", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "regulators": { "title": "Regulators", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "edge_data": { "title": "Edge Data", "default": [], "type": "array", "items": { "$ref": "#/definitions/EdgeData" } } }, "required": [ "targets", "regulators" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] }, "EdgeData": { "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ] } } }
- Fields
- field edge_data: List[indra_network_search.data_models.__init__.EdgeData] = []
- field regulators: List[indra_network_search.data_models.__init__.Node] [Required]
- field targets: List[indra_network_search.data_models.__init__.Node] [Required]
- pydantic model indra_network_search.data_models.__init__.NetworkSearchQuery[source]
The query model for network searches
Show JSON schema
{ "title": "NetworkSearchQuery", "description": "The query model for network searches", "type": "object", "properties": { "source": { "title": "Source", "default": "", "type": "string" }, "target": { "title": "Target", "default": "", "type": "string" }, "stmt_filter": { "title": "Stmt Filter", "default": [], "type": "array", "items": { "type": "string" } }, "filter_curated": { "title": "Filter Curated", "default": true, "type": "boolean" }, "allowed_ns": { "title": "Allowed Ns", "default": [], "type": "array", "items": { "type": "string" } }, "node_blacklist": { "title": "Node Blacklist", "default": [], "type": "array", "items": { "type": "string" } }, "path_length": { "title": "Path Length", "type": "integer" }, "depth_limit": { "title": "Depth Limit", "default": 2, "type": "integer" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "weighted": { "title": "Weighted", "default": "unweighted", "enum": [ "belief", "context", "z_score", "unweighted" ], "type": "string" }, "belief_cutoff": { "title": "Belief Cutoff", "default": 0.0, "anyOf": [ { "type": "number" }, { "type": "boolean" } ] }, "curated_db_only": { "title": "Curated Db Only", "default": false, "type": "boolean" }, "fplx_expand": { "title": "Fplx Expand", "default": false, "type": "boolean" }, "k_shortest": { "title": "K Shortest", "default": 50, "type": "integer" }, "max_per_node": { "title": "Max Per Node", "default": 5, "type": "integer" }, "cull_best_node": { "title": "Cull Best Node", "type": "integer" }, "mesh_ids": { "title": "Mesh Ids", "default": [], "type": "array", "items": { "type": "string" } }, "strict_mesh_id_filtering": { "title": "Strict Mesh Id Filtering", "default": false, "type": "boolean" }, "const_c": { "title": "Const C", "default": 1, "type": "integer" }, "const_tk": { "title": "Const Tk", "default": 10, "type": "integer" }, "user_timeout": { "title": "User Timeout", "default": 30, "anyOf": [ { "type": "number" }, { "type": "boolean" } ] }, "two_way": { "title": "Two Way", "default": false, "type": "boolean" }, "shared_regulators": { "title": "Shared Regulators", "default": false, "type": "boolean" }, "terminal_ns": { "title": "Terminal Ns", "default": [], "type": "array", "items": { "type": "string" } }, "format": { "title": "Format", "default": "json", "type": "string" } }, "additionalProperties": false }
- Config
allow_mutation: bool = False
extra: Extra = forbid
- Fields
source (indra_network_search.data_models.__init__.ConstrainedStrValue)target (indra_network_search.data_models.__init__.ConstrainedStrValue)stmt_filter (List[indra_network_search.data_models.__init__.ConstrainedStrValue])allowed_ns (List[indra_network_search.data_models.__init__.ConstrainedStrValue])sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])weighted (typing_extensions.Literal[belief, context, z_score, unweighted])
- Validators
- field allowed_ns: List[indra_network_search.data_models.__init__.ConstrainedStrValue] = []
- field belief_cutoff: Union[float, bool] = 0.0
- field const_c: int = 1
- field const_tk: int = 10
- field cull_best_node: Optional[int] = None
- Validated by
- field curated_db_only: bool = False
- field depth_limit: int = 2
- field filter_curated: bool = True
- field format: str = 'json'
- field fplx_expand: bool = False
- field k_shortest: int = 50
- field max_per_node: int = 5
- Validated by
- field mesh_ids: List[str] = []
- field node_blacklist: List[str] = []
- field path_length: Optional[int] = None
- Validated by
- field sign: Optional[indra_network_search.data_models.__init__.ConstrainedIntValue] = None
- Constraints
minimum = 0
maximum = 1
- field source: indra_network_search.data_models.__init__.ConstrainedStrValue = ''
- field stmt_filter: List[indra_network_search.data_models.__init__.ConstrainedStrValue] = []
- field strict_mesh_id_filtering: bool = False
- field target: indra_network_search.data_models.__init__.ConstrainedStrValue = ''
- field terminal_ns: List[str] = []
- field two_way: bool = False
- field user_timeout: Union[float, bool] = 30
- field weighted: typing_extensions.Literal[belief, context, z_score, unweighted] = 'unweighted'
- validator is_int_gt2 » cull_best_node[source]
Validate cull_best_node >= 2
- is_overall_weighted()[source]
Return True if this query is weighted
This method is used to determine if a weighted search needs to be done using either of shortest_simple_paths and open_dijkstra_search.
The exception to self.weighted not being None but still be unweighted is strict mesh id search.
- Return type
bool
- validator is_pos_int » max_per_node[source]
Validate max_per_node >= 1 if given
- validator is_positive_int » path_length[source]
Validate path_length >= 1 if given
- pydantic model indra_network_search.data_models.__init__.Node[source]
Data for a node
Show JSON schema
{ "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }
- Fields
name (Optional[indra_network_search.data_models.__init__.ConstrainedStrValue])namespace (indra_network_search.data_models.__init__.ConstrainedStrValue)identifier (indra_network_search.data_models.__init__.ConstrainedStrValue)lookup (Optional[indra_network_search.data_models.__init__.ConstrainedStrValue])sign (Optional[indra_network_search.data_models.__init__.ConstrainedIntValue])
- field identifier: indra_network_search.data_models.__init__.ConstrainedStrValue [Required]
- Constraints
minLength = 1
- field lookup: Optional[indra_network_search.data_models.__init__.ConstrainedStrValue] [Required]
- Constraints
minLength = 1
- field name: Optional[indra_network_search.data_models.__init__.ConstrainedStrValue] [Required]
- Constraints
minLength = 1
- field namespace: indra_network_search.data_models.__init__.ConstrainedStrValue [Required]
- Constraints
minLength = 1
- field sign: Optional[indra_network_search.data_models.__init__.ConstrainedIntValue] [Required]
- Constraints
minimum = 0
maximum = 1
- pydantic model indra_network_search.data_models.__init__.OntologyOptions[source]
Arguments for indra_network_search.pathfinding.shared_parents
Show JSON schema
{ "title": "OntologyOptions", "description": "Arguments for indra_network_search.pathfinding.shared_parents", "type": "object", "properties": { "source_ns": { "title": "Source Ns", "type": "string" }, "source_id": { "title": "Source Id", "type": "string" }, "target_ns": { "title": "Target Ns", "type": "string" }, "target_id": { "title": "Target Id", "type": "string" }, "max_paths": { "title": "Max Paths", "default": 50, "type": "integer" }, "immediate_only": { "title": "Immediate Only", "default": false, "type": "boolean" }, "is_a_part_of": { "title": "Is A Part Of", "type": "array", "items": { "type": "string" }, "uniqueItems": true } }, "required": [ "source_ns", "source_id", "target_ns", "target_id" ] }
- Fields
- field immediate_only: Optional[bool] = False
- field is_a_part_of: Optional[Set[str]] = None
- field max_paths: int = 50
- field source_id: str [Required]
- field source_ns: str [Required]
- field target_id: str [Required]
- field target_ns: str [Required]
- pydantic model indra_network_search.data_models.__init__.OntologyResults[source]
Results for shared_parents
Show JSON schema
{ "title": "OntologyResults", "description": "Results for shared_parents", "type": "object", "properties": { "source": { "$ref": "#/definitions/Node" }, "target": { "$ref": "#/definitions/Node" }, "parents": { "title": "Parents", "type": "array", "items": { "$ref": "#/definitions/Node" } } }, "required": [ "source", "target", "parents" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] } } }
- Fields
- field parents: List[indra_network_search.data_models.__init__.Node] [Required]
- field source: indra_network_search.data_models.__init__.Node [Required]
- field target: indra_network_search.data_models.__init__.Node [Required]
- pydantic model indra_network_search.data_models.__init__.Path[source]
Results for a single path
Show JSON schema
{ "title": "Path", "description": "Results for a single path", "type": "object", "properties": { "path": { "title": "Path", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "edge_data": { "title": "Edge Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } } }, "required": [ "path", "edge_data" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] }, "EdgeData": { "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ] } } }
- Fields
- field edge_data: List[indra_network_search.data_models.__init__.EdgeData] [Required]
- field path: List[indra_network_search.data_models.__init__.Node] [Required]
- pydantic model indra_network_search.data_models.__init__.PathResultData[source]
Results for any of the path algorithms
Show JSON schema
{ "title": "PathResultData", "description": "Results for any of the path algorithms", "type": "object", "properties": { "source": { "$ref": "#/definitions/Node" }, "target": { "$ref": "#/definitions/Node" }, "paths": { "title": "Paths", "type": "object", "additionalProperties": { "type": "array", "items": { "$ref": "#/definitions/Path" } } } }, "required": [ "paths" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] }, "EdgeData": { "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ] }, "Path": { "title": "Path", "description": "Results for a single path", "type": "object", "properties": { "path": { "title": "Path", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "edge_data": { "title": "Edge Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } } }, "required": [ "path", "edge_data" ] } } }
- Fields
- field paths: Dict[int, List[indra_network_search.data_models.__init__.Path]] [Required]
- field source: Optional[indra_network_search.data_models.__init__.Node] = None
- field target: Optional[indra_network_search.data_models.__init__.Node] = None
- pydantic model indra_network_search.data_models.__init__.Results[source]
The model wrapping all results from the NetworkSearchQuery
Show JSON schema
{ "title": "Results", "description": "The model wrapping all results from the NetworkSearchQuery", "type": "object", "properties": { "query_hash": { "title": "Query Hash", "type": "string" }, "time_limit": { "title": "Time Limit", "type": "number" }, "timed_out": { "title": "Timed Out", "type": "boolean" }, "hashes": { "title": "Hashes", "default": [], "type": "array", "items": { "type": "string" } }, "path_results": { "$ref": "#/definitions/PathResultData" }, "reverse_path_results": { "$ref": "#/definitions/PathResultData" }, "ontology_results": { "$ref": "#/definitions/OntologyResults" }, "shared_target_results": { "$ref": "#/definitions/SharedInteractorsResults" }, "shared_regulators_results": { "$ref": "#/definitions/SharedInteractorsResults" } }, "required": [ "query_hash", "time_limit", "timed_out" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] }, "EdgeData": { "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ] }, "Path": { "title": "Path", "description": "Results for a single path", "type": "object", "properties": { "path": { "title": "Path", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "edge_data": { "title": "Edge Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } } }, "required": [ "path", "edge_data" ] }, "PathResultData": { "title": "PathResultData", "description": "Results for any of the path algorithms", "type": "object", "properties": { "source": { "$ref": "#/definitions/Node" }, "target": { "$ref": "#/definitions/Node" }, "paths": { "title": "Paths", "type": "object", "additionalProperties": { "type": "array", "items": { "$ref": "#/definitions/Path" } } } }, "required": [ "paths" ] }, "OntologyResults": { "title": "OntologyResults", "description": "Results for shared_parents", "type": "object", "properties": { "source": { "$ref": "#/definitions/Node" }, "target": { "$ref": "#/definitions/Node" }, "parents": { "title": "Parents", "type": "array", "items": { "$ref": "#/definitions/Node" } } }, "required": [ "source", "target", "parents" ] }, "SharedInteractorsResults": { "title": "SharedInteractorsResults", "description": "Results for shared targets and shared regulators", "type": "object", "properties": { "source_data": { "title": "Source Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } }, "target_data": { "title": "Target Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } }, "downstream": { "title": "Downstream", "type": "boolean" } }, "required": [ "source_data", "target_data", "downstream" ] } } }
- Fields
path_results (Optional[indra_network_search.data_models.__init__.PathResultData])reverse_path_results (Optional[indra_network_search.data_models.__init__.PathResultData])ontology_results (Optional[indra_network_search.data_models.__init__.OntologyResults])shared_target_results (Optional[indra_network_search.data_models.__init__.SharedInteractorsResults])
- field hashes: List[str] = []
- field ontology_results: Optional[indra_network_search.data_models.__init__.OntologyResults] = None
- field path_results: Optional[indra_network_search.data_models.__init__.PathResultData] = None
- field query_hash: str [Required]
- field reverse_path_results: Optional[indra_network_search.data_models.__init__.PathResultData] = None
- field time_limit: float [Required]
- field timed_out: bool [Required]
Arguments for indra_network_search.pathfinding.shared_interactors
Show JSON schema
{ "title": "SharedInteractorsOptions", "description": "Arguments for indra_network_search.pathfinding.shared_interactors", "type": "object", "properties": { "source": { "title": "Source", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "target": { "title": "Target", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "allowed_ns": { "title": "Allowed Ns", "type": "array", "items": { "type": "string" } }, "stmt_types": { "title": "Stmt Types", "type": "array", "items": { "type": "string" } }, "source_filter": { "title": "Source Filter", "type": "array", "items": { "type": "string" } }, "max_results": { "title": "Max Results", "default": 50, "type": "integer" }, "regulators": { "title": "Regulators", "default": false, "type": "boolean" }, "sign": { "title": "Sign", "type": "integer" } }, "required": [ "source", "target" ] }
- Fields
Results for shared targets and shared regulators
Show JSON schema
{ "title": "SharedInteractorsResults", "description": "Results for shared targets and shared regulators", "type": "object", "properties": { "source_data": { "title": "Source Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } }, "target_data": { "title": "Target Data", "type": "array", "items": { "$ref": "#/definitions/EdgeData" } }, "downstream": { "title": "Downstream", "type": "boolean" } }, "required": [ "source_data", "target_data", "downstream" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "StmtTypeSupport": { "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ] }, "EdgeData": { "title": "EdgeData", "description": "Data for one single edge", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "statements": { "title": "Statements", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtTypeSupport" } }, "belief": { "title": "Belief", "minimum": 0, "maximum": 1, "type": "number" }, "weight": { "title": "Weight", "minimum": 0, "type": "number" }, "context_weight": { "title": "Context Weight", "default": "N/A", "anyOf": [ { "type": "string" }, { "type": "number", "exclusiveMinimum": 0 }, { "enum": [ "N/A" ], "type": "string" } ] }, "z_score": { "title": "Z Score", "type": "number" }, "corr_weight": { "title": "Corr Weight", "exclusiveMinimum": 0.0, "type": "number" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } } }, "required": [ "edge", "statements", "belief", "weight", "db_url_edge" ] } } }
- Fields
Return True if both source and target data is empty
- pydantic model indra_network_search.data_models.__init__.ShortestSimplePathOptions[source]
Arguments for indra.explanation.pathfinding.shortest_simple_paths
Show JSON schema
{ "title": "ShortestSimplePathOptions", "description": "Arguments for indra.explanation.pathfinding.shortest_simple_paths", "type": "object", "properties": { "source": { "title": "Source", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "target": { "title": "Target", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "weight": { "title": "Weight", "type": "string" }, "ignore_nodes": { "title": "Ignore Nodes", "type": "array", "items": { "type": "string" }, "uniqueItems": true }, "ignore_edges": { "title": "Ignore Edges", "type": "array", "items": { "type": "array", "items": [ { "type": "string" }, { "type": "string" } ] }, "uniqueItems": true }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "strict_mesh_id_filtering": { "title": "Strict Mesh Id Filtering", "default": false, "type": "boolean" }, "const_c": { "title": "Const C", "default": 1, "type": "integer" }, "const_tk": { "title": "Const Tk", "default": 10, "type": "integer" } }, "required": [ "source", "target" ] }
- Fields
- field const_c: Optional[int] = 1
- field const_tk: Optional[int] = 10
- field hashes: Optional[List[int]] = None
- field ignore_edges: Optional[Set[Tuple[str, str]]] = None
- field ignore_nodes: Optional[Set[str]] = None
- field ref_counts_function: Optional[Callable] = None
- field source: Union[str, Tuple[str, int]] [Required]
- field strict_mesh_id_filtering: Optional[bool] = False
- field target: Union[str, Tuple[str, int]] [Required]
- field weight: Optional[str] = None
- pydantic model indra_network_search.data_models.__init__.StmtData[source]
Data for one statement supporting an edge
Show JSON schema
{ "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }
- Fields
- field belief: indra_network_search.data_models.__init__.ConstrainedFloatValue [Required]
- Constraints
minimum = 0.0
maximum = 1.0
- field curated: bool [Required]
- field db_url_hash: str [Required]
- field english: str [Required]
- field evidence_count: indra_network_search.data_models.__init__.ConstrainedIntValue [Required]
- Constraints
minimum = 1
- field initial_sign: Optional[indra_network_search.data_models.__init__.ConstrainedIntValue] = None
- Constraints
minimum = 0
maximum = 1
- field position: Optional[str] = ''
- field residue: Optional[str] = ''
- field source_counts: Dict[str, int] [Required]
- field stmt_hash: Union[int, pydantic.networks.HttpUrl] [Required]
- field stmt_type: str [Required]
- field weight: Optional[float] = None
- pydantic model indra_network_search.data_models.__init__.StmtTypeSupport[source]
Data per statement type
Show JSON schema
{ "title": "StmtTypeSupport", "description": "Data per statement type", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "source_counts": { "title": "Source Counts", "default": {}, "type": "object", "additionalProperties": { "type": "integer" } }, "statements": { "title": "Statements", "type": "array", "items": { "$ref": "#/definitions/StmtData" } } }, "required": [ "stmt_type", "statements" ], "definitions": { "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] } } }
- Fields
- field source_counts: Dict[str, int] = {}
- field statements: List[indra_network_search.data_models.__init__.StmtData] [Required]
- field stmt_type: str [Required]
- pydantic model indra_network_search.data_models.__init__.SubgraphOptions[source]
Argument for indra_network_search.pathfinding.get_subgraph_edges
Show JSON schema
{ "title": "SubgraphOptions", "description": "Argument for indra_network_search.pathfinding.get_subgraph_edges", "type": "object", "properties": { "nodes": { "title": "Nodes", "type": "array", "items": { "$ref": "#/definitions/Node" } } }, "required": [ "nodes" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] } } }
- field nodes: List[indra_network_search.data_models.__init__.Node] [Required]
- pydantic model indra_network_search.data_models.__init__.SubgraphRestQuery[source]
Subgraph query
Show JSON schema
{ "title": "SubgraphRestQuery", "description": "Subgraph query", "type": "object", "properties": { "nodes": { "title": "Nodes", "minItems": 1, "maxItems": 4000, "type": "array", "items": { "$ref": "#/definitions/Node" } } }, "required": [ "nodes" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] } } }
- field nodes: types.ConstrainedListValue[indra_network_search.data_models.__init__.Node] [Required]
- Constraints
minItems = 1
maxItems = 4000
- pydantic model indra_network_search.data_models.__init__.SubgraphResults[source]
Results for get_subgraph_edges
Show JSON schema
{ "title": "SubgraphResults", "description": "Results for get_subgraph_edges", "type": "object", "properties": { "input_nodes": { "title": "Input Nodes", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "not_in_graph": { "title": "Not In Graph", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "available_nodes": { "title": "Available Nodes", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "edges": { "title": "Edges", "type": "array", "items": { "$ref": "#/definitions/EdgeDataByHash" } } }, "required": [ "input_nodes", "not_in_graph", "available_nodes", "edges" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] }, "StmtData": { "title": "StmtData", "description": "Data for one statement supporting an edge", "type": "object", "properties": { "stmt_type": { "title": "Stmt Type", "type": "string" }, "evidence_count": { "title": "Evidence Count", "minimum": 1, "type": "integer" }, "stmt_hash": { "title": "Stmt Hash", "anyOf": [ { "type": "integer" }, { "type": "string", "minLength": 1, "maxLength": 2083, "format": "uri" } ] }, "source_counts": { "title": "Source Counts", "type": "object", "additionalProperties": { "type": "integer" } }, "belief": { "title": "Belief", "minimum": 0.0, "maximum": 1.0, "type": "number" }, "curated": { "title": "Curated", "type": "boolean" }, "english": { "title": "English", "type": "string" }, "weight": { "title": "Weight", "type": "number" }, "residue": { "title": "Residue", "default": "", "type": "string" }, "position": { "title": "Position", "default": "", "type": "string" }, "initial_sign": { "title": "Initial Sign", "minimum": 0, "maximum": 1, "type": "integer" }, "db_url_hash": { "title": "Db Url Hash", "type": "string" } }, "required": [ "stmt_type", "evidence_count", "stmt_hash", "source_counts", "belief", "curated", "english", "db_url_hash" ] }, "EdgeDataByHash": { "title": "EdgeDataByHash", "description": "Data for one single edge, with data keyed by hash", "type": "object", "properties": { "edge": { "title": "Edge", "type": "array", "items": { "$ref": "#/definitions/Node" } }, "stmts": { "title": "Stmts", "type": "object", "additionalProperties": { "$ref": "#/definitions/StmtData" } }, "belief": { "title": "Belief", "type": "number" }, "weight": { "title": "Weight", "type": "number" }, "db_url_edge": { "title": "Db Url Edge", "type": "string" }, "url_by_type": { "title": "Url By Type", "type": "object", "additionalProperties": { "type": "string" } } }, "required": [ "edge", "stmts", "belief", "weight", "db_url_edge", "url_by_type" ] } } }
- Fields
- field available_nodes: List[indra_network_search.data_models.__init__.Node] [Required]
- field edges: List[indra_network_search.data_models.__init__.EdgeDataByHash] [Required]
- field input_nodes: List[indra_network_search.data_models.__init__.Node] [Required]
- field not_in_graph: List[indra_network_search.data_models.__init__.Node] [Required]
- indra_network_search.data_models.__init__.basemodel_in_iterable(basemodel, iterable, any_item, exclude=None)[source]
Test if a basemodel object is part of a collection
- Parameters
basemodel (
BaseModel) – A BaseModel to test membership in iterable foriterable (
Iterable) – An iterable that contains objects to test for equality with basemodelany_item (
bool) – If True, use any() when testing collections for equality, otherwise use all(), i.e. the collections must match exactlyexclude (
Optional[Set[str]]) – A set of field names to exclude from the basemodels
- Return type
bool- Returns
True if basemodel is found in the collection
- indra_network_search.data_models.__init__.basemodels_equal(basemodel, other_basemodel, any_item, exclude=None)[source]
Wrapper to test two basemodels for equality, can exclude irrelevant keys
- Parameters
basemodel (
BaseModel) – BaseModel to test against other_basemodelother_basemodel (
BaseModel) – BaseModel to test against basemodelany_item (
bool) – If True, use any() when testing collections for equality, otherwise use all(), i.e. the collections must match exactlyexclude (
Optional[Set[str]]) – A set of field names to exclude from the basemodels
- Return type
bool- Returns
True if the two models are equal
Rest Models (indra_network_search.data_models.rest_models)
Contains return models from the rest api
- pydantic model indra_network_search.data_models.rest_models.Health[source]
Health status
Show JSON schema
{ "title": "Health", "description": "Health status", "type": "object", "properties": { "status": { "title": "Status", "enum": [ "booting", "available" ], "type": "string" } }, "required": [ "status" ] }
- field status: typing_extensions.Literal[booting, available] [Required]
- pydantic model indra_network_search.data_models.rest_models.ServerStatus[source]
Status with more detail than health
Show JSON schema
{ "title": "ServerStatus", "description": "Status with more detail than health", "type": "object", "properties": { "unsigned_nodes": { "title": "Unsigned Nodes", "type": "integer" }, "signed_nodes": { "title": "Signed Nodes", "type": "integer" }, "unsigned_edges": { "title": "Unsigned Edges", "type": "integer" }, "signed_edges": { "title": "Signed Edges", "type": "integer" }, "graph_date": { "title": "Graph Date", "type": "string", "format": "date" }, "status": { "title": "Status", "enum": [ "booting", "available" ], "type": "string" } }, "required": [ "status" ] }
- Fields
- field graph_date: Optional[datetime.date] = None
- field signed_edges: Optional[int] = None
- field signed_nodes: Optional[int] = None
- field status: typing_extensions.Literal[booting, available] [Required]
- field unsigned_edges: Optional[int] = None
- field unsigned_nodes: Optional[int] = None
Pathfinding (indra_network_search.pathfinding.pathfinding)
Pathfinding algorithms local to this repository
- indra_network_search.pathfinding.pathfinding.direct_multi_interactors(graph, nodes, downstream, allowed_ns=None, stmt_types=None, source_filter=None, max_results=50, hash_blacklist=None, node_blacklist=None, belief_cutoff=0.0, curated_db_only=False)[source]
Find up- or downstream common nodes from a list of nodes
- Parameters
graph (
DiGraph) – The graph to look innodes (
List[Union[str,Tuple[str,int]]]) – The starting nodesdownstream (
bool) – If True, look for shared targets, otherwise look for shared regulatorsallowed_ns (
Optional[List[str]]) – A list of allowed node namespacesstmt_types (
Optional[List[str]]) – A list of allowed statemtent typessource_filter (
Optional[List[str]]) – A list of valid sourcesmax_results (
int) – The maximum number of results to returnhash_blacklist (
Optional[Set[int]]) – A list of hashes to blacklistnode_blacklist (
Optional[List[str]]) – A list of node names to blacklistbelief_cutoff (
float) – If set, an edge will not be allowed if all its supporting statements have belief scores below this valuecurated_db_only (
bool) – If True, only allow edge that have support from curated databases
- Return type
Iterator[Union[str,Tuple[str,int]]]- Returns
An Iterator of the resulting nodes
- indra_network_search.pathfinding.pathfinding.get_subgraph_edges(graph, nodes)[source]
Get the subgraph connecting the provided nodes
- Parameters
graph (
DiGraph) – Graph to look for in and out edges innodes (
List[Dict[str,str]]) – List of dicts of Node instances to look for neighbors in
- Return type
Iterator[Tuple[str,str]]- Returns
A dict keyed by each of the input node names that were present in the graph. For each node, two lists are provided for in-edges and out-edges respectively
Get shared regulators or targets and filter them based on sign
Closely resembles get_st and get_sr from depmap_analysis.scripts.depmap_script_expl_funcs
- Parameters
graph (
DiGraph) – The graph to perform the search insource (
Union[str,Tuple[str,int]]) – Node to look for common up- or downstream neighbors from with targettarget (
Union[str,Tuple[str,int]]) – Node to look for common up- or downstream neighbors from with sourceallowed_ns (
Optional[List[str]]) – If provided, filter common nodes to these namespacesstmt_types (
Optional[List[str]]) – If provided, filter the statements in the supporting edges to these statement typessource_filter (
Optional[List[str]]) – If provided, filter the statements in the supporting edges to those with these sourcesmax_results (
int) – The maximum number of results to returnregulators (
bool) – If True, do shared regulator search (upstream), otherwise do shared target search (downstream). Default False.sign (
Optional[int]) –- If provided, match edges to sign:
positive: edges must have same sign
negative: edges must have opposite sign
hash_blacklist (
Optional[Set[str]]) – A list of hashes to exclude from the edgesnode_blacklist (
Optional[List[str]]) – A list of node names to excludebelief_cutoff (
float) – Exclude statements that are below the cutoff. Default: 0.0 (no cutoff)curated_db_only (
bool) – If True, exclude statements in edge support that only have readers in their sources. Default: False.
- Return type
Iterator[Tuple[List[Union[str,Tuple[str,int]]],List[Union[str,Tuple[str,int]]]]]- Returns
An iterator of regulators or targets to source and target as edges
Get shared ontological parents of source and target
- Parameters
source_ns (
str) – Namespace of sourcesource_id (
str) – Identifier of sourcetarget_ns (
str) – Namespace of targettarget_id (
str) – Identifier of targetimmediate_only (
bool) – Determines if all or just the immediate parents should be returned. Default: False, i.e. all parents.is_a_part_of (
Optional[Set[str]]) – If provided, the parents must be in this set of ids. The set is assumed to be valid ontology labels (see ontology.label()).max_paths (
int) – Maximum number of results to return. Default: 50.
- Return type
Iterator[Tuple[str,Any,Any,str]]- Returns
An iterator of parents to source and target, each parent being a tuple of (name, namespace, id, lookup URL)
Utility Functions (indra_network_search.util)
Query Classes (indra_network_search.query)
This file contains the Query classes mapping incoming rest queries to different algorithms used in the search api.
- class indra_network_search.query.BreadthFirstSearchQuery(query, hash_blacklist=None)[source]
Check queries that will use the bfs_search algorithm
- alg_options()[source]
Match arguments of bfs_search from query
- Return type
Dict[str,Any]- Returns
The argument to provide bfs_search
- mesh_options(graph=None)[source]
Get mesh options for bfs_search
- Parameters
graph (
Optional[DiGraph]) – The graph- Return type
Dict[str,Union[Set,bool,Callable]]- Returns
The mesh option for bfs_search
- options
alias of
indra_network_search.data_models.BreadthFirstSearchOptionsShow JSON schema
{ "title": "BreadthFirstSearchOptions", "description": "Arguments for indra.explanation.pathfinding.bfs_search", "type": "object", "properties": { "source_node": { "title": "Source Node", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "reverse": { "title": "Reverse", "default": false, "type": "boolean" }, "depth_limit": { "title": "Depth Limit", "default": 2, "type": "integer" }, "path_limit": { "title": "Path Limit", "type": "integer" }, "max_per_node": { "title": "Max Per Node", "default": 5, "type": "integer" }, "node_filter": { "title": "Node Filter", "type": "array", "items": { "type": "string" } }, "node_blacklist": { "title": "Node Blacklist", "type": "array", "items": { "type": "string" }, "uniqueItems": true }, "terminal_ns": { "title": "Terminal Ns", "type": "array", "items": { "type": "string" } }, "sign": { "title": "Sign", "type": "integer" }, "max_memory": { "title": "Max Memory", "default": 536870912, "type": "integer" }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "strict_mesh_id_filtering": { "title": "Strict Mesh Id Filtering", "default": false, "type": "boolean" } }, "required": [ "source_node" ] }
- Fields
source_node (Union[str, Tuple[str, int]])reverse (Optional[bool])depth_limit (Optional[int])path_limit (Optional[int])max_per_node (Optional[int])node_filter (Optional[List[str]])node_blacklist (Optional[Set[str]])terminal_ns (Optional[List[str]])sign (Optional[int])max_memory (Optional[int])hashes (Optional[List[int]])allow_edge (Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]])edge_filter (Optional[Callable[[networkx.classes.digraph.DiGraph, Union[str, Tuple[str, int]], Union[str, Tuple[str, int]]], bool]])strict_mesh_id_filtering (Optional[bool])
- class indra_network_search.query.DijkstraQuery(query, hash_blacklist=None)[source]
Check queries that will use the open_dijkstra_search algorithm
- alg_options()[source]
Match arguments of open_dijkstra_search from query
- Return type
Dict[str,Any]- Returns
A dict with arguments for open_dijkstra_search
- mesh_options(graph=None)[source]
Produces mesh arguments matching open_dijkstra_search from query
- Return type
Dict[str,Union[Set,bool,Callable]]- Returns
The mesh options for open_dijkstra_query
- options
alias of
indra_network_search.data_models.DijkstraOptionsShow JSON schema
{ "title": "DijkstraOptions", "description": "Arguments for open_dijkstra_search", "type": "object", "properties": { "start": { "title": "Start", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "reverse": { "title": "Reverse", "default": false, "type": "boolean" }, "path_limit": { "title": "Path Limit", "type": "integer" }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "ignore_nodes": { "title": "Ignore Nodes", "type": "array", "items": { "type": "string" } }, "ignore_edges": { "title": "Ignore Edges", "type": "array", "items": { "type": "array", "items": [ { "type": "string" }, { "type": "string" } ] } }, "terminal_ns": { "title": "Terminal Ns", "type": "array", "items": { "type": "string" } }, "weight": { "title": "Weight", "type": "string" }, "const_c": { "title": "Const C", "default": 1, "type": "integer" }, "const_tk": { "title": "Const Tk", "default": 10, "type": "integer" } }, "required": [ "start" ] }
- Fields
start (Union[str, Tuple[str, int]])reverse (Optional[bool])path_limit (Optional[int])hashes (Optional[List[int]])ignore_nodes (Optional[List[str]])ignore_edges (Optional[List[Tuple[str, str]]])terminal_ns (Optional[List[str]])weight (Optional[str])ref_counts_function (Optional[Callable])const_c (Optional[int])const_tk (Optional[int])
- class indra_network_search.query.MultiInteractorsQuery(rest_query)[source]
Check queries that will use pathfinding.direct_multi_interactors
- options
alias of
indra_network_search.data_models.MultiInteractorsOptionsShow JSON schema
{ "title": "MultiInteractorsOptions", "description": "Multi interactors options", "type": "object", "properties": { "nodes": { "title": "Nodes", "type": "array", "items": { "type": "string" } }, "downstream": { "title": "Downstream", "type": "boolean" }, "allowed_ns": { "title": "Allowed Ns", "type": "array", "items": { "type": "string" } }, "stmt_types": { "title": "Stmt Types", "type": "array", "items": { "type": "string" } }, "source_filter": { "title": "Source Filter", "type": "array", "items": { "type": "string" } }, "max_results": { "title": "Max Results", "default": 50, "type": "integer" }, "hash_blacklist": { "title": "Hash Blacklist", "type": "array", "items": { "type": "integer" }, "uniqueItems": true }, "node_blacklist": { "title": "Node Blacklist", "type": "array", "items": { "type": "string" } }, "belief_cutoff": { "title": "Belief Cutoff", "default": 0.0, "type": "number" }, "curated_db_only": { "title": "Curated Db Only", "default": false, "type": "boolean" } }, "required": [ "nodes", "downstream" ] }
- Fields
nodes (List[str])downstream (bool)allowed_ns (Optional[List[str]])stmt_types (Optional[List[str]])source_filter (Optional[List[str]])max_results (int)hash_blacklist (Optional[Set[int]])node_blacklist (Optional[List[str]])belief_cutoff (float)curated_db_only (bool)
- class indra_network_search.query.OntologyQuery(query)[source]
Check queries that will use shared_parents
- alg_options()[source]
Match arguments of shared_parents from query
- Return type
Dict[str,Any]- Returns
A dict with arguments for shared_parents
- options
alias of
indra_network_search.data_models.OntologyOptionsShow JSON schema
{ "title": "OntologyOptions", "description": "Arguments for indra_network_search.pathfinding.shared_parents", "type": "object", "properties": { "source_ns": { "title": "Source Ns", "type": "string" }, "source_id": { "title": "Source Id", "type": "string" }, "target_ns": { "title": "Target Ns", "type": "string" }, "target_id": { "title": "Target Id", "type": "string" }, "max_paths": { "title": "Max Paths", "default": 50, "type": "integer" }, "immediate_only": { "title": "Immediate Only", "default": false, "type": "boolean" }, "is_a_part_of": { "title": "Is A Part Of", "type": "array", "items": { "type": "string" }, "uniqueItems": true } }, "required": [ "source_ns", "source_id", "target_ns", "target_id" ] }
- Fields
source_ns (str)source_id (str)target_ns (str)target_id (str)max_paths (int)immediate_only (Optional[bool])is_a_part_of (Optional[Set[str]])
- class indra_network_search.query.PathQuery(query, hash_blacklist)[source]
Parent Class for ShortestSimplePaths, Dijkstra and BreadthFirstSearch
- alg_options()[source]
Returns the options for the algorithm used, excl mesh options
- Return type
Dict[str,Any]
- class indra_network_search.query.Query(query)[source]
Parent class to all Query classes
The Query classes are helpers that make sure the methods of the IndraNetworkSearchAPI receive the data needed from a NetworkSearchQuery or other Rest query.
- api_options()[source]
These options are used when IndraNetworkSearchAPI handles the query
The options here impact decisions on which extra search algorithms to include and which graph to pick
- Return type
Dict[str,Any]- Returns
A dict of ApiOptions
Check queries that will use shared_interactors(regulators=True)
Check queries that will use shared_interactors(regulators=False)
- class indra_network_search.query.ShortestSimplePathsQuery(query, hash_blacklist=None)[source]
Check queries that will use the shortest_simple_paths algorithm
- alg_options()[source]
Match arguments of shortest_simple_paths from query
- Return type
Dict[str,Any]- Returns
A dict with arguments for shortest_simple_paths
- mesh_options(graph=None)[source]
Match input to shortest_simple_paths
- Return type
Dict[str,Union[Set,int,bool,Callable]]- Returns
The mesh options for shortest_simple_paths
- options
alias of
indra_network_search.data_models.ShortestSimplePathOptionsShow JSON schema
{ "title": "ShortestSimplePathOptions", "description": "Arguments for indra.explanation.pathfinding.shortest_simple_paths", "type": "object", "properties": { "source": { "title": "Source", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "target": { "title": "Target", "anyOf": [ { "type": "string" }, { "type": "array", "items": [ { "type": "string" }, { "type": "integer" } ] } ] }, "weight": { "title": "Weight", "type": "string" }, "ignore_nodes": { "title": "Ignore Nodes", "type": "array", "items": { "type": "string" }, "uniqueItems": true }, "ignore_edges": { "title": "Ignore Edges", "type": "array", "items": { "type": "array", "items": [ { "type": "string" }, { "type": "string" } ] }, "uniqueItems": true }, "hashes": { "title": "Hashes", "type": "array", "items": { "type": "integer" } }, "strict_mesh_id_filtering": { "title": "Strict Mesh Id Filtering", "default": false, "type": "boolean" }, "const_c": { "title": "Const C", "default": 1, "type": "integer" }, "const_tk": { "title": "Const Tk", "default": 10, "type": "integer" } }, "required": [ "source", "target" ] }
- Fields
source (Union[str, Tuple[str, int]])target (Union[str, Tuple[str, int]])weight (Optional[str])ignore_nodes (Optional[Set[str]])ignore_edges (Optional[Set[Tuple[str, str]]])hashes (Optional[List[int]])ref_counts_function (Optional[Callable])strict_mesh_id_filtering (Optional[bool])const_c (Optional[int])const_tk (Optional[int])
- class indra_network_search.query.SubgraphQuery(query)[source]
Check queries that gets the subgraph
- alg_options(graph)[source]
Match arguments of get_subgraph_edges
- Parameters
graph (
DiGraph) – The graph the search will be performed with- Return type
Dict[str,List[Node]]- Returns
A dict with the arguments for get_subgraph_edges
- options
alias of
indra_network_search.data_models.SubgraphOptionsShow JSON schema
{ "title": "SubgraphOptions", "description": "Argument for indra_network_search.pathfinding.get_subgraph_edges", "type": "object", "properties": { "nodes": { "title": "Nodes", "type": "array", "items": { "$ref": "#/definitions/Node" } } }, "required": [ "nodes" ], "definitions": { "Node": { "title": "Node", "description": "Data for a node", "type": "object", "properties": { "name": { "title": "Name", "minLength": 1, "type": "string" }, "namespace": { "title": "Namespace", "minLength": 1, "type": "string" }, "identifier": { "title": "Identifier", "minLength": 1, "type": "string" }, "lookup": { "title": "Lookup", "minLength": 1, "type": "string" }, "sign": { "title": "Sign", "minimum": 0, "maximum": 1, "type": "integer" } }, "required": [ "namespace", "identifier" ] } } }
- Fields
nodes (List[indra_network_search.data_models.Node])
Query Handler (indra_network_search.query_handler)
The QueryHandler’s job is to act as a middle layer between the network search functionalities and the REST API that receives queries.
- class indra_network_search.query_handler.QueryHandler(rest_query, curation_cache=<indra_network_search.util.curation_cache.CurationCache object>)[source]
Maps queries from the REST API to a method of the IndraNetworkSearchAPI
The QueryHandler’s job is to act as a middle layer between the methods of the IndraNetworkSearchAPI and the REST API. It figures out which queries are eligible from the input query.
Rest API (indra_network_search.rest_api)
This documentation is here for completeness and for code documentation purposes. For a better description of the Rest API, read the API docs.
The IndraNetworkSearch REST API
- indra_network_search.rest_api.get_prefix_autocomplete(prefix=Query(Ellipsis), max_res=Query(100))[source]
Get the case-insensitive node names with (ns, id) starting in prefix
- Parameters
prefix (
str) – The prefix of a node name to search for. Note: for prefixes of 1 and 2 characters, only exact matches are returned. For 3+ characters, prefix matching is done. If the prefix contains ‘:’, an namespace:id search is done.max_res (
int) – The top ranked (by node degree) results will be returned, cut off at this many results.
- Return type
List[Tuple[str,str,str]]- Returns
A list of tuples of (node name, namespace, identifier)
- indra_network_search.rest_api.get_xrefs(ns, id)[source]
Get all cross-refs given a namespace and ID
- Parameters
ns (
str) – The namespace of the entity to find cross-refs forid (
str) – The identifier of the entity to find cross-regs for
- Return type
List[List[str]]- Returns
A list of tuples containing namespace, identifier, lookup url to identifiers.org
- indra_network_search.rest_api.node_id_in_graph(db_name=Query(Ellipsis), db_id=Query(Ellipsis))[source]
Check if a node by provided db name and db id exists
- Parameters
db_name (
str) – The database name, e.g. hgnc, chebi or updb_id (
str) – The identifier for the entity in the given database, e.g. 11018
- Return type
Optional[Node]- Returns
When a match is found, the full information of the node is returned
- indra_network_search.rest_api.node_name_in_graph(node_name=Query(Ellipsis))[source]
Check if node by provided name (case sensitive) exists in graph
- Parameters
node_name (
str) – The name of the node to check- Return type
Optional[Node]- Returns
When a match is found, the full information of the node is returned
- indra_network_search.rest_api.query(search_query, background_tasks)[source]
Interface with IndraNetworkSearchAPI.handle_query
- Parameters
search_query (NetworkSearchQuery) – Query to the NetworkSearchQuery
- Returns
- Return type
- async indra_network_search.rest_api.server_status()[source]
Returns the status of the server and some info about the loaded graphs
- Returns
- indra_network_search.rest_api.sub_graph(search_query)[source]
Interface with IndraNetworkSearchAPI.handle_subgraph_query
- Parameters
search_query (SubgraphRestQuery) – Query to for IndraNetworkSearchAPI.handle_subgraph_query
- Returns
- Return type
Rest API Utilities (indra_network_search.rest_util)
Utility functions for the Network Search API and Rest API
- indra_network_search.rest_util.check_existence_and_date_s3(query_hash)[source]
Check if a query hash has corresponding result and query json on S3
- Parameters
query_hash (
Union[int,str]) – The query hash to check- Return type
Dict[str,str]- Returns
Dict with S3 key for query and corresponding result, if they exist
- indra_network_search.rest_util.dump_query_json_to_s3(query_hash, json_obj, get_url=False)[source]
Dump a query json to S3
- Parameters
query_hash (
Union[str,int]) – The query hash associated with the queryjson_obj (
Dict) – The json object to uploadget_url (
bool) – If True return the S3 url of the object. Default: False.
- Return type
Optional[str]- Returns
Optionally return the S3 url of the json file
- indra_network_search.rest_util.dump_query_result_to_s3(filename, json_obj, get_url=False)[source]
Dump a result or query json from the network search to S3
- Parameters
filename (
str) – The filename to usejson_obj (
Dict) – The json object to uploadget_url (
bool) – If True return the S3 url of the object. Default: False.
- Return type
Optional[str]- Returns
Optionally return the S3 url of the json file
- indra_network_search.rest_util.dump_result_json_to_s3(query_hash, json_obj, get_url=False)[source]
Dump a result json to S3
- Parameters
query_hash (
Union[str,int]) – The query hash associated with the resultjson_obj (
Dict) – The json object to uploadget_url (
bool) – If True return the S3 url of the object. Default: False.
- Return type
Optional[str]- Returns
Optionally return the S3 url of the json file
- indra_network_search.rest_util.get_default_args(func)[source]
Returns the default args of a function as a dictionary
Returns a dictionary of {arg: default} of the arguments that have default values. Arguments without default values and **kwargs type arguments are excluded.
Code copied from: https://stackoverflow.com/a/12627202/10478812
- Parameters
func (
Callable) – Function to find default arguments for- Return type
Dict[str,Any]- Returns
A dictionary with the default values keyed by argument name
- indra_network_search.rest_util.get_mandatory_args(func)[source]
Returns the mandatory args for a function as a set
Returns the set of arguments names of a functions that are mandatory, i.e. does not have a default value. **kwargs type arguments are ignored.
- Parameters
func (
Callable) – Function to find mandatory arguments for- Return type
Set[str]- Returns
The of mandatory arguments
- indra_network_search.rest_util.get_query_hash(query_json, ignore_keys=None)[source]
Create an FNV-1a 32-bit hash from the query json
- Parameters
query_json (
Dict) – A json compatible query dictignore_keys (
Union[Set,List,None]) – A list or set of keys to ignore in the query_json. By default, no keys are ignored. Default: None.
- Return type
int- Returns
An FNV-1a 32-bit hash of the query json ignoring the keys in ignore_keys
- indra_network_search.rest_util.get_queryable_stmt_types()[source]
Return Statement class names that can be used for querying.
- indra_network_search.rest_util.get_s3_client(unsigned=True)[source]
Return a boto3 S3 client with optional unsigned config.
- Parameters
unsigned (Optional[bool]) – If True, the client will be using unsigned mode in which public resources can be accessed without credentials. Default: True
- Returns
A client object to AWS S3.
- Return type
botocore.client.S3
- indra_network_search.rest_util.is_context_weighted(mesh_id_list, strict_filtering)[source]
Return True if context weighted
- Parameters
mesh_id_list (
List[str]) – A list of mesh idsstrict_filtering (
bool) – whether to run strict context filtering or not
- Return type
bool- Returns
True for the combination of mesh ids being present and unstrict filtering, otherwise False
- indra_network_search.rest_util.is_weighted(weighted, mesh_ids, strict_mesh_filtering)[source]
Return True if the combination is either weighted or context weighted
- Parameters
weighted (
bool) – If a query is weighted or notmesh_ids (
List[str]) – A list of mesh idsstrict_mesh_filtering (bool) – whether to run strict context filtering or not
- Return type
bool- Returns
True if the combination is either weighted or context weighted
- indra_network_search.rest_util.list_chunk_gen(lst, size=1000)[source]
Given list, generate chunks <= size
- indra_network_search.rest_util.load_indra_graph(unsigned_graph=True, unsigned_multi_graph=False, sign_edge_graph=False, sign_node_graph=True, use_cache=False)[source]
Return a tuple of graphs to be used in the network search API
- Parameters
unsigned_graph (
bool) – Load the latest unsigned graph. Default: True.unsigned_multi_graph (
bool) – Load the latest unsigned multi graph. Default: False.sign_node_graph (
bool) – Load the latest signed node graph. Default: True.sign_edge_graph (
bool) – Load the latest signed edge graph. Default: False.use_cache (
bool) – If True, try to load files from the designated local cache
- Returns
- Returns, as a tuple:
unsigned graph
unsigned multi graph
signed edge graph
signed node graph
If a graph was not chosen to be loaded or wasn’t found, None will be returned in its place in the tuple.
- Return type
Tuple[nx.DiGraph, nx.MultiDiGraph, nx.MultiDiGraph, nx.DiGraph]
Result Handlers (indra_network_search.result_handler)
Handles the aggregation of results from the IndraNetworkSearchAPI
The result manager deals with things like:
Stopping path iteration when timeout is reached
Keeping count of number of paths returned
Filtering results when it’s not done in the algorithm
- class indra_network_search.result_handler.BreadthFirstSearchResultManager(path_generator, graph, filter_options, source, target, reverse, timeout=30)[source]
Handles results from bfs_search
- class indra_network_search.result_handler.DijkstraResultManager(path_generator, graph, filter_options, source, target, reverse, timeout=30, hash_blacklist=None)[source]
Handles results from open_dijkstra_search
- class indra_network_search.result_handler.MultiInteractorsResultManager(path_generator, graph, input_nodes, filter_options, downstream, timeout=30)[source]
Handles results from pathfinding.direct_multi_interactors
- class indra_network_search.result_handler.OntologyResultManager(path_generator, graph, filter_options, source, target)[source]
Handles results from shared_parents
Handles results from shared_interactors, both up and downstream
downstream is True for shared targets and False for shared regulators
Execute the result assembly with the loaded generator
- Return type
SharedInteractorsResults- Returns
Results for shared_interactors as a BaseModel
- class indra_network_search.result_handler.ShortestSimplePathsResultManager(path_generator, graph, filter_options, source, target, timeout=30, hash_blacklist=None)[source]
Handles results from shortest_simple_paths
Search API (indra_network_search.search_api)
The INDRA Network Search API
This class represents an API that executes search queries
Queries for specific searches are found in indra_network_search.query
- class indra_network_search.search_api.IndraNetworkSearchAPI(unsigned_graph, signed_node_graph)[source]
The search API class
- breadth_first_search(breadth_first_search_query, is_signed)[source]
Get results from running bfs_search
- Parameters
breadth_first_search_query (
BreadthFirstSearchQuery) – The input query holding the options to the algorithmis_signed (
bool) – Whether the query is signed or not
- Return type
- Returns
An instance of the BreadthFirstSearchResultManager, holding results from running bfs_search
- dijkstra(dijkstra_query, is_signed)[source]
Get results from running open_dijkstra_search
- Parameters
dijkstra_query (
DijkstraQuery) – The input query holding options for open_dijkstra_search and DijkstraResultManageris_signed (
bool) – Whether the query is signed or not
- Return type
- Returns
An instance of the DijkstraResultManager, holding results from running open_dijkstra_search
- get_node(node_name)[source]
Returns an instance of a Node matching the input name, if it exists
- Parameters
node_name (
str) – Name of node to look up- Return type
Optional[Node]- Returns
An instance of a node corresponding to the input name
- handle_multi_interactors_query(multi_interactors_rest_query)[source]
Interface with pathfinding.direct_multi_interactors
- Parameters
multi_interactors_rest_query (
MultiInteractorsRestQuery) – The input query holding options for direct multi interactors- Return type
MultiInteractorsResults- Returns
Results holding node and edge data
- handle_query(rest_query)[source]
Handle a NetworkSearchQuery and return the corresponding results
- Parameters
rest_query (
NetworkSearchQuery) – A query from the rest api with all relevant information to execute path queries and other related queries. See available queries in indra_network_search.query- Return type
Results- Returns
A model containing all results from the query. For more information about the data structure, see indra_network_search.data_models
- handle_subgraph_query(subgraph_rest_query)[source]
Interface for handling queries to get_subgraph_edges
- Parameters
subgraph_rest_query (
SubgraphRestQuery) – A rest query containing the list of nodes needed for get_subgraph_edges- Return type
SubgraphResults- Returns
The data put together from the results of get_subgraph_edges
- multi_interactors_query(query)[source]
Run direct_multi_interactors and return the result manager
- Parameters
query (
MultiInteractorsQuery) – An instance of MultiInteractorsQuery, that interfaces with the algorithm and the result manager- Return type
- Returns
A MultiInteractorsResultManager holding the results of running direct_multi_interactors
Get results from running shared_parents
- Parameters
ontology_query (
OntologyQuery) – The input query holding options for shared_parents- Return type
- Returns
An instance of the OntologyResultManager, holding results from running shared_parents
Get results from running shared_interactors looking for regulators
- Parameters
shared_regulators_query (
SharedRegulatorsQuery) – The input query holding options for shared_interactorsis_signed (
bool) – Whether the query is signed or not
- Return type
- Returns
An instance of the SharedInteractorsResultManager, holding results from running shared_interactors looking for regulators
Get results from running shared_interactors looking for targets
- Parameters
shared_targets_query (
SharedTargetsQuery) – The input query holding options for shared_interactorsis_signed (
bool) – Whether the query is signed or not
- Return type
- Returns
An instance of the SharedInteractorsResultManager, holding results from running shared_interactors looking for targets
- shortest_simple_paths(shortest_simple_paths_query, is_signed)[source]
Get results from running shortest_simple_paths
- Parameters
shortest_simple_paths_query (
ShortestSimplePathsQuery) – The input query holding the options to the algorithmis_signed (
bool) – Whether the query is signed or not
- Return type
- Returns
An instance of the ShortestSimplePathsResultManager, holding results from running shortest_simple_paths_query
- subgraph_query(query)[source]
Get results from running get_subgraph_edges
- Parameters
query (
SubgraphQuery) – The input query holding the options for get_subgraph_edges- Return type
- Returns
An instance of the SubgraphResultManager, holding results from running get_subgraph_edges