{ "openapi": "3.1.0", "info": { "title": "Node Normalization", "version": "1.0.0", "x-translator": { "component": "Utility", "team": [ "Standards Reference Implementation Team" ], "infores": "infores:sri-node-normalizer" }, "x-trapi": { "version": "1.5.0", "operations": [ "annotate_nodes" ] }, "contact": { "email": "bizon@renci.org", "name": "Chris Bizon", "x-id": "https://github.com/cbizon", "x-role": "responsible developer" }, "termsOfService": "https://toss.apps.renci.org/tos?service_long=Node+Normalization&provider_long=the+Translator+Consortium", "description": "Node Normalization takes a CURIE, and returns:
  1. The preferred CURIE for this entity
  2. All other known equivalent identifiers for the entity
  3. Semantic types for the entity as defined by the BioLink Model
The data served by Node Normalization is created by Babel, which attempts to find identifier equivalences, and makes sure that CURIE prefixes are BioLink Model Compliant. To determine whether Node Normalization is likely to be useful, check /get_semantic_types, which lists the BioLink semantic types for which normalization has been attempted, and /get_curie_prefixes, which lists the number of times each prefix is used for a semantic type." }, "paths": { "/status": { "get": { "summary": "Status information on this NodeNorm instance", "tags": ["health"], "description": "Returns information about this NodeNorm instance and the elasticsearch instance backing it.", "operationId": "status", "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "type": "object", "title": "Response Status Get" } } } } } } }, "/get_normalized_nodes": { "get": { "summary": "Get the equivalent identifiers and semantic types for the curie(s) entered.", "tags": ["translator"], "description": "Returns the equivalent identifiers and semantic types for the curie(s)", "operationId": "get_normalized_node_handler_get_normalized_nodes_get", "parameters": [ { "description": "List of curies to normalize", "required": false, "schema": { "items": { "type": "string" }, "type": "array", "minItems": 1, "title": "Curie", "description": "List of curies to normalize", "default": [] }, "example": [ "MESH:D014867", "NCIT:C34373" ], "name": "curie", "in": "query" }, { "description": "Whether to apply gene/protein conflation", "required": false, "schema": { "type": "boolean", "title": "Conflate", "description": "Whether to apply gene/protein conflation", "default": true }, "name": "conflate", "in": "query" }, { "description": "Whether to apply drug/chemical conflation", "required": false, "schema": { "type": "boolean", "title": "Drug Chemical Conflate", "description": "Whether to apply drug/chemical conflation", "default": false }, "name": "drug_chemical_conflate", "in": "query" }, { "description": "Whether to return curie descriptions when possible", "required": false, "schema": { "type": "boolean", "title": "Description", "description": "Whether to return curie descriptions when possible", "default": false }, "name": "description", "in": "query" }, { "description": "Whether to return individual types for equivalent identifiers", "required": false, "schema": { "type": "boolean", "title": "Individual Types", "description": "Whether to return individual types for equivalent identifiers", "default": false }, "name": "individual_types", "in": "query" } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } }, "post": { "summary": "Get the equivalent identifiers and semantic types for the curie(s) entered.", "tags": ["translator"], "description": "Returns the equivalent identifiers and semantic types for the curie(s). Use the `conflate` flag to choose whether to apply conflation.", "operationId": "get_normalized_node_handler_post_get_normalized_nodes_post", "requestBody": { "content": { "application/json": { "schema": { "$ref": "#/components/schemas/CurieList" } } }, "required": true }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": {} } } }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/get_setid": { "get": { "summary": "Normalize and deduplicate a set of identifiers and return a single hash that represents this set.", "tags": ["translator"], "operationId": "get_setid_get_setid_get", "parameters": [ { "description": "Set of curies to normalize", "required": false, "schema": { "items": { "type": "string" }, "type": "array", "minItems": 1, "title": "Curie", "description": "Set of curies to normalize", "default": [] }, "example": [ "MESH:D014867", "NCIT:C34373", "UNII:63M8RYN44N", "RUBBISH:1234" ], "name": "curie", "in": "query" }, { "description": "Set of conflations to apply", "required": false, "schema": { "items": { "type": "string" }, "type": "array", "title": "Conflation", "description": "Set of conflations to apply", "default": [] }, "example": [ "GeneProtein", "DrugChemical" ], "name": "conflation", "in": "query" } ], "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SetIDResponse" } } } }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } }, "post": { "summary": "Normalize and deduplicate a set of identifiers and return a single hash that represents this set.", "tags": ["translator"], "operationId": "get_setid_get_setid_post", "requestBody": { "content": { "application/json": { "schema": { "items": { "$ref": "#/components/schemas/SetIDQuery" }, "type": "array", "title": "Sets", "description": "Set of identifiers to normalize", "default": [] }, "example": [ { "curies": [ "MESH:D014867", "NCIT:C34373" ] }, { "curies": [ "NCIT:C34373", "MESH:D014867", "UNII:63M8RYN44N", "RUBBISH:1234" ], "conflations": [ "GeneProtein", "DrugChemical" ] } ] } } }, "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "items": { "$ref": "#/components/schemas/SetIDResponse" }, "type": "array", "title": "Response Get Setid Get Setid Post" } } } }, "422": { "description": "Validation Error", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/HTTPValidationError" } } } } } } }, "/get_semantic_types": { "get": { "summary": "Return a list of BioLink semantic types for which normalization has been attempted.", "tags": ["metadata"], "description": "Returns a distinct set of the semantic types discovered in the compendium data.", "operationId": "get_semantic_types_handler_get_semantic_types_get", "responses": { "200": { "description": "Successful Response", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/SemanticTypes" } } } } } } }, "/get_allowed_conflations": { "get": { "tags": ["metadata"], "description": "Returns a list of allowed conflation options", "responses": { "200": { "content": { "application/json": { "schema": { "example": { "conflations": [ "GeneProtein", "DrugChemical" ], "type": "object", "description": "Results", "summary": "Return a list of named conflations.", "tags": [ "Interfaces" ] } } } } } } } } }, "components": { "schemas": { "AboveOrBelowEnum": { "type": "string", "enum": [ "above", "below" ], "title": "AboveOrBelowEnum", "description": "'above' or 'below'." }, "Analysis": { "properties": { "resource_id": { "type": "string", "title": "resource infores" }, "edge_bindings": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_str__HashableSet_EdgeBinding__" } ], "title": "list of edge bindings" }, "score": { "type": "number", "format": "float", "title": "Score" }, "support_graphs": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_str_" } ], "title": "Support Graphs", "nullable": true }, "scoring_method": { "type": "string", "title": "Scoring Method", "nullable": true }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "type": "object", "required": [ "resource_id", "edge_bindings" ], "title": "analysis", "description": "Analysis." }, "AnnotateEdgesParameters": { "properties": { "attributes": { "$ref": "#/components/schemas/HashableSequence_str_" } }, "type": "object", "title": "AnnotateEdgesParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "AnnotateNodesParameters": { "properties": { "attributes": { "$ref": "#/components/schemas/HashableSequence_str_" } }, "type": "object", "title": "AnnotateNodesParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "AscOrDescEnum": { "type": "string", "enum": [ "ascending", "descending" ], "title": "AscOrDescEnum", "description": "'ascending' or 'descending'." }, "AsyncQuery": { "properties": { "callback": { "type": "string", "pattern": "^https?://", "format": "uri", "title": "Callback" }, "message": { "allOf": [ { "$ref": "#/components/schemas/Message" } ], "title": "message" }, "log_level": { "allOf": [ { "$ref": "#/components/schemas/LogLevel" } ], "title": "log_level", "nullable": true }, "workflow": { "$ref": "#/components/schemas/Workflow" } }, "type": "object", "required": [ "callback", "message" ], "title": "query", "description": "AsyncQuery.", "x-body-name": "request_body" }, "Attribute": { "properties": { "attribute_type_id": { "type": "string", "title": "type" }, "value": { "title": "value" }, "value_type_id": { "type": "string", "title": "value_type_id", "nullable": true }, "original_attribute_name": { "type": "string", "title": "Original Attribute Name", "nullable": true }, "value_url": { "type": "string", "title": "Value Url", "nullable": true }, "attribute_source": { "type": "string", "title": "Attribute Source", "nullable": true }, "description": { "type": "string", "title": "Description", "nullable": true }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_SubAttribute_" } ], "title": "Attributes", "nullable": true } }, "additionalProperties": false, "type": "object", "required": [ "attribute_type_id", "value" ], "title": "Attribute", "description": "Node/edge attribute." }, "AttributeConstraint": { "properties": { "name": { "type": "string", "title": "name", "nullable": false }, "id": { "type": "string", "title": "id", "nullable": false }, "not": { "type": "boolean", "title": "not", "default": false }, "operator": { "allOf": [ { "$ref": "#/components/schemas/Operator" } ], "title": "operator" }, "value": { "title": "value" }, "unit_id": { "title": "unit_id" }, "unit_name": { "title": "unit_name" } }, "additionalProperties": false, "type": "object", "required": [ "name", "id", "operator", "value" ], "title": "AttributeConstraint", "description": "QNode or QEdge attribute constraint." }, "AuxiliaryGraph": { "properties": { "edges": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_str_" } ], "title": "edges in auxiliary graph" }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "type": "object", "required": [ "edges" ], "title": "auxiliary graph", "description": "Auxiliary Graph" }, "AuxiliaryGraphs": { "$ref": "#/components/schemas/HashableMapping_str__AuxiliaryGraph_", "title": "auxiliary graphs", "description": "Auxiliary Graphs" }, "ConflationList": { "properties": { "conflations": { "items": {}, "type": "array", "title": "Conflations" } }, "type": "object", "required": [ "conflations" ], "title": "ConflationList" }, "CurieList": { "properties": { "curies": { "items": { "type": "string" }, "type": "array", "minItems": 1, "title": "List of CURIEs to normalize" }, "conflate": { "type": "boolean", "title": "Whether to apply gene/protein conflation", "default": true }, "description": { "type": "boolean", "title": "Whether to return CURIE descriptions when possible", "default": false }, "drug_chemical_conflate": { "type": "boolean", "title": "Whether to apply drug/chemical conflation", "default": false }, "individual_types": { "type": "boolean", "title": "Whether to return individual types for equivalent identifiers", "default": false } }, "type": "object", "required": [ "curies" ], "title": "CurieList", "description": "Curie list input model", "example": { "curies": [ "MESH:D014867", "NCIT:C34373" ], "conflate": true, "description": false, "drug_chemical_conflate": false } }, "CuriePivot": { "properties": { "curie_prefix": { "additionalProperties": { "type": "string" }, "type": "object", "title": "Curie Prefix" } }, "type": "object", "required": [ "curie_prefix" ], "title": "CuriePivot" }, "Edge": { "properties": { "subject": { "type": "string", "title": "subject node id" }, "object": { "type": "string", "title": "object node id" }, "predicate": { "type": "string", "pattern": "^biolink:[a-z][a-z_]*$", "title": "edge predicate" }, "sources": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_RetrievalSource_" } ], "title": "list of source retrievals" }, "qualifiers": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Qualifier_" } ], "title": "Qualifiers", "nullable": true }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "additionalProperties": false, "type": "object", "required": [ "subject", "object", "predicate", "sources" ], "title": "knowledge-graph edge", "description": "Knowledge graph edge." }, "EdgeBinding": { "properties": { "id": { "type": "string", "title": "knowledge graph id" }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "type": "object", "required": [ "id" ], "title": "edge binding", "description": "Edge binding.", "example": { "id": "string" } }, "EnrichResultsParameters": { "properties": { "pvalue_threshold": { "type": "number", "maximum": 1.0, "minimum": 0.0, "title": "Pvalue Threshold", "default": 0.000001 }, "qnode_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "predicates_to_exclude": { "$ref": "#/components/schemas/HashableSequence_BiolinkPredicate_" } }, "type": "object", "title": "EnrichResultsParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FillAllowParameters": { "properties": { "allowlist": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" } }, "additionalProperties": false, "type": "object", "title": "FillAllowParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FillDenyParameters": { "properties": { "denylist": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" } }, "additionalProperties": false, "type": "object", "title": "FillDenyParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FillParameters": { "anyOf": [ { "$ref": "#/components/schemas/FillAllowParameters" }, { "$ref": "#/components/schemas/FillDenyParameters" } ], "title": "FillParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphContinuousKedgeAttributeParameters": { "properties": { "edge_attribute": { "type": "string", "title": "Edge Attribute" }, "threshold": { "type": "number", "title": "Threshold" }, "remove_above_or_below": { "$ref": "#/components/schemas/AboveOrBelowEnum" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qnode_keys": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_str_" } ], "title": "Qnode Keys", "default": [] } }, "type": "object", "required": [ "edge_attribute", "threshold", "remove_above_or_below" ], "title": "FilterKgraphContinuousKedgeAttributeParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphDiscreteKedgeAttributeParameters": { "properties": { "edge_attribute": { "type": "string", "title": "Edge Attribute" }, "remove_value": { "title": "Remove Value" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qnode_keys": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_str_" } ], "title": "Qnode Keys", "default": [] } }, "type": "object", "required": [ "edge_attribute" ], "title": "FilterKgraphDiscreteKedgeAttributeParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphDiscreteKnodeAttributeParameters": { "properties": { "node_attribute": { "type": "string", "title": "Node Attribute" }, "remove_value": { "title": "Remove Value" }, "qnode_keys": { "$ref": "#/components/schemas/HashableSequence_str_" } }, "type": "object", "required": [ "node_attribute" ], "title": "FilterKgraphDiscreteKnodeAttributeParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphPercentileParameters": { "properties": { "edge_attribute": { "type": "string", "title": "Edge Attribute" }, "threshold": { "type": "number", "maximum": 100.0, "minimum": 0.0, "title": "Threshold", "default": 95 }, "remove_above_or_below": { "allOf": [ { "$ref": "#/components/schemas/AboveOrBelowEnum" } ], "default": "below" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qnode_keys": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_str_" } ], "title": "Qnode Keys", "default": [] } }, "type": "object", "required": [ "edge_attribute" ], "title": "FilterKgraphPercentileParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphStdDevParameters": { "properties": { "edge_attribute": { "type": "string", "title": "Edge Attribute" }, "plus_or_minus_std_dev": { "allOf": [ { "$ref": "#/components/schemas/PlusOrMinusEnum" } ], "default": "plus" }, "num_sigma": { "type": "number", "minimum": 0.0, "title": "Num Sigma", "default": 1 }, "remove_above_or_below": { "allOf": [ { "$ref": "#/components/schemas/AboveOrBelowEnum" } ], "default": "below" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qnode_keys": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_str_" } ], "title": "Qnode Keys", "default": [] } }, "type": "object", "required": [ "edge_attribute" ], "title": "FilterKgraphStdDevParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterKgraphTopNParameters": { "properties": { "edge_attribute": { "type": "string", "title": "Edge Attribute" }, "max_edges": { "type": "integer", "maximum": 0.0, "title": "Max Edges", "default": 50 }, "remove_top_or_bottom": { "allOf": [ { "$ref": "#/components/schemas/TopOrBottomEnum" } ], "default": "top" }, "qedge_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "qnode_keys": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_str_" } ], "title": "Qnode Keys", "default": [] } }, "type": "object", "required": [ "edge_attribute" ], "title": "FilterKgraphTopNParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "FilterResultsTopNParameters": { "properties": { "max_results": { "type": "integer", "minimum": 0.0, "title": "Max Results" } }, "additionalProperties": false, "type": "object", "required": [ "max_results" ], "title": "FilterResultsTopNParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "HTTPValidationError": { "properties": { "detail": { "items": { "$ref": "#/components/schemas/ValidationError" }, "type": "array", "title": "Detail" } }, "type": "object", "title": "HTTPValidationError" }, "HashableMapping_CURIE__Node_": { "additionalProperties": { "$ref": "#/components/schemas/Node" }, "type": "object", "title": "HashableMapping[CURIE, Node]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_EdgeIdentifier__Edge_": { "additionalProperties": { "$ref": "#/components/schemas/Edge" }, "type": "object", "title": "HashableMapping[EdgeIdentifier, Edge]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_str__AuxiliaryGraph_": { "additionalProperties": { "$ref": "#/components/schemas/AuxiliaryGraph" }, "type": "object", "title": "HashableMapping[str, AuxiliaryGraph]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_str__HashableSet_EdgeBinding__": { "additionalProperties": { "$ref": "#/components/schemas/HashableSet_EdgeBinding_" }, "type": "object", "title": "HashableMapping[str, HashableSet[EdgeBinding]]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_str__HashableSet_NodeBinding__": { "additionalProperties": { "$ref": "#/components/schemas/HashableSet_NodeBinding_" }, "type": "object", "title": "HashableMapping[str, HashableSet[NodeBinding]]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_str__QEdge_": { "additionalProperties": { "$ref": "#/components/schemas/QEdge" }, "type": "object", "title": "HashableMapping[str, QEdge]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableMapping_str__QNode_": { "additionalProperties": { "$ref": "#/components/schemas/QNode" }, "type": "object", "title": "HashableMapping[str, QNode]", "description": "Custom class that implements MutableMapping and is hashable", "default": {} }, "HashableSequence_AttributeConstraint_": { "items": { "$ref": "#/components/schemas/AttributeConstraint" }, "type": "array", "title": "HashableSequence[AttributeConstraint]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_BiolinkEntity_": { "items": { "type": "string", "pattern": "^biolink:[A-Z][a-zA-Z]*$" }, "type": "array", "title": "HashableSequence[BiolinkEntity]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_BiolinkPredicate_": { "items": { "type": "string", "pattern": "^biolink:[a-z][a-z_]*$" }, "type": "array", "title": "HashableSequence[BiolinkPredicate]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_CURIE_": { "items": { "type": "string" }, "type": "array", "title": "HashableSequence[CURIE]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_Operation_": { "items": { "$ref": "#/components/schemas/Operation" }, "type": "array", "title": "HashableSequence[Operation]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_QualifierConstraint_": { "items": { "$ref": "#/components/schemas/QualifierConstraint" }, "type": "array", "title": "HashableSequence[QualifierConstraint]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_Qualifier_": { "items": { "$ref": "#/components/schemas/Qualifier" }, "type": "array", "title": "HashableSequence[Qualifier]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_RecursiveAttribute_": { "items": { "$ref": "#/components/schemas/RecursiveAttribute" }, "type": "array", "title": "HashableSequence[RecursiveAttribute]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_Result_": { "items": { "$ref": "#/components/schemas/Result" }, "type": "array", "title": "HashableSequence[Result]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_SubAttribute_": { "items": { "$ref": "#/components/schemas/SubAttribute" }, "type": "array", "title": "HashableSequence[SubAttribute]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSequence_str_": { "items": { "type": "string" }, "type": "array", "title": "HashableSequence[str]", "description": "Custom class that implements MutableSequence and is hashable", "default": [] }, "HashableSet_Analysis_": { "items": { "$ref": "#/components/schemas/Analysis" }, "type": "array", "uniqueItems": true, "title": "HashableSet[Analysis]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_Attribute_": { "items": { "$ref": "#/components/schemas/Attribute" }, "type": "array", "uniqueItems": true, "title": "HashableSet[Attribute]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_BiolinkEntity_": { "items": { "type": "string", "pattern": "^biolink:[A-Z][a-zA-Z]*$" }, "type": "array", "uniqueItems": true, "title": "HashableSet[BiolinkEntity]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_CURIE_": { "items": { "type": "string" }, "type": "array", "uniqueItems": true, "title": "HashableSet[CURIE]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_EdgeBinding_": { "items": { "$ref": "#/components/schemas/EdgeBinding" }, "type": "array", "uniqueItems": true, "title": "HashableSet[EdgeBinding]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_NodeBinding_": { "items": { "$ref": "#/components/schemas/NodeBinding" }, "type": "array", "uniqueItems": true, "title": "HashableSet[NodeBinding]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_Qualifier_": { "items": { "$ref": "#/components/schemas/Qualifier" }, "type": "array", "uniqueItems": true, "title": "HashableSet[Qualifier]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_RetrievalSource_": { "items": { "$ref": "#/components/schemas/RetrievalSource" }, "type": "array", "uniqueItems": true, "title": "HashableSet[RetrievalSource]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "HashableSet_str_": { "items": { "type": "string" }, "type": "array", "uniqueItems": true, "title": "HashableSet[str]", "description": "Custom class that implements MutableSet and is hashable", "default": [] }, "KnowledgeGraph": { "properties": { "nodes": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_CURIE__Node_" } ], "title": "nodes" }, "edges": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_EdgeIdentifier__Edge_" } ], "title": "edges" } }, "type": "object", "required": [ "nodes", "edges" ], "title": "knowledge graph", "description": "Knowledge graph." }, "KnowledgeType": { "type": "string", "enum": [ "lookup", "inferred" ], "title": "KnowledgeType", "description": "Knowledge Type." }, "LogLevel": { "$ref": "#/components/schemas/LogLevelEnum", "title": "LogLevel", "description": "Log level." }, "LogLevelEnum": { "type": "string", "enum": [ "ERROR", "WARNING", "INFO", "DEBUG" ], "title": "LogLevelEnum", "description": "Log level." }, "Message": { "properties": { "query_graph": { "allOf": [ { "$ref": "#/components/schemas/QueryGraph" } ], "title": "query graph", "nullable": true }, "knowledge_graph": { "allOf": [ { "$ref": "#/components/schemas/KnowledgeGraph" } ], "title": "knowledge graph", "nullable": true }, "results": { "allOf": [ { "$ref": "#/components/schemas/Results" } ], "title": "list of results", "nullable": true }, "auxiliary_graphs": { "allOf": [ { "$ref": "#/components/schemas/AuxiliaryGraphs" } ], "title": "dict of auxiliary graphs", "nullable": true } }, "additionalProperties": false, "type": "object", "title": "message", "description": "Message." }, "Node": { "properties": { "categories": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_BiolinkEntity_" } ], "title": "categories", "nullable": true }, "name": { "type": "string", "title": "Name", "nullable": true }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "additionalProperties": false, "type": "object", "title": "knowledge-graph node", "description": "Knowledge graph node.", "example": { "category": "string" } }, "NodeBinding": { "properties": { "id": { "type": "string", "title": "knowledge graph id" }, "query_id": { "type": "string", "title": "query graph id" }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Attribute_" } ], "title": "Attributes", "nullable": true } }, "type": "object", "required": [ "id" ], "title": "node binding", "description": "Node binding.", "example": { "id": "x:string" } }, "Operation": { "anyOf": [ { "$ref": "#/components/schemas/OperationAnnotate" }, { "$ref": "#/components/schemas/OperationAnnotateEdges" }, { "$ref": "#/components/schemas/OperationAnnotateNodes" }, { "$ref": "#/components/schemas/OperationBind" }, { "$ref": "#/components/schemas/OperationCompleteResults" }, { "$ref": "#/components/schemas/OperationEnrichResults" }, { "$ref": "#/components/schemas/OperationFill" }, { "$ref": "#/components/schemas/OperationFilterKgraph" }, { "$ref": "#/components/schemas/OperationFilterKgraphContinuousKedgeAttribute" }, { "$ref": "#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute" }, { "$ref": "#/components/schemas/OperationFilterKgraphDiscreteKnodeAttribute" }, { "$ref": "#/components/schemas/OperationFilterKgraphOrphans" }, { "$ref": "#/components/schemas/OperationFilterKgraphPercentile" }, { "$ref": "#/components/schemas/OperationFilterKgraphStdDev" }, { "$ref": "#/components/schemas/OperationFilterKgraphTopN" }, { "$ref": "#/components/schemas/OperationFilterResults" }, { "$ref": "#/components/schemas/OperationFilterResultsTopN" }, { "$ref": "#/components/schemas/OperationLookup" }, { "$ref": "#/components/schemas/OperationOverlay" }, { "$ref": "#/components/schemas/OperationOverlayComputeJaccard" }, { "$ref": "#/components/schemas/OperationOverlayComputeNgd" }, { "$ref": "#/components/schemas/OperationOverlayConnectKnodes" }, { "$ref": "#/components/schemas/OperationOverlayFisherExactTest" }, { "$ref": "#/components/schemas/OperationRestate" }, { "$ref": "#/components/schemas/OperationScore" }, { "$ref": "#/components/schemas/OperationSortResults" }, { "$ref": "#/components/schemas/OperationSortResultsEdgeAttribute" }, { "$ref": "#/components/schemas/OperationSortResultsNodeAttribute" }, { "$ref": "#/components/schemas/OperationSortResultsScore" } ], "title": "Operation", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationAnnotate": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/annotate" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationAnnotate", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationAnnotateEdges": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/annotate_edges" }, "parameters": { "$ref": "#/components/schemas/AnnotateEdgesParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationAnnotateEdges", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationAnnotateNodes": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/annotate_nodes" }, "parameters": { "$ref": "#/components/schemas/AnnotateNodesParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationAnnotateNodes", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationBind": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/bind" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationBind", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationCompleteResults": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/complete_results" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationCompleteResults", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationEnrichResults": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/enrich_results" }, "parameters": { "$ref": "#/components/schemas/EnrichResultsParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationEnrichResults", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFill": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/fill" }, "parameters": { "$ref": "#/components/schemas/FillParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationFill", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraph": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationFilterKgraph", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphContinuousKedgeAttribute": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_continuous_kedge_attribute" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphContinuousKedgeAttributeParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphContinuousKedgeAttribute", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphDiscreteKedgeAttribute": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_discrete_kedge_attribute" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphDiscreteKedgeAttributeParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphDiscreteKedgeAttribute", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphDiscreteKnodeAttribute": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_discrete_knode_attribute" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphDiscreteKnodeAttributeParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphDiscreteKnodeAttribute", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphOrphans": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_orphans" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationFilterKgraphOrphans", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphPercentile": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_percentile" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphPercentileParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphPercentile", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphStdDev": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_std_dev" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphStdDevParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphStdDev", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterKgraphTopN": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_kgraph_top_n" }, "parameters": { "$ref": "#/components/schemas/FilterKgraphTopNParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationFilterKgraphTopN", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterResults": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_results" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationFilterResults", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationFilterResultsTopN": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/filter_results_top_n" }, "parameters": { "$ref": "#/components/schemas/FilterResultsTopNParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationFilterResultsTopN", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationLookup": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/lookup" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationLookup", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationOverlay": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/overlay" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationOverlay", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationOverlayComputeJaccard": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/overlay_compute_jaccard" }, "parameters": { "$ref": "#/components/schemas/OverlayComputeJaccardParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationOverlayComputeJaccard", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationOverlayComputeNgd": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/overlay_compute_ngd" }, "parameters": { "$ref": "#/components/schemas/OverlayComputeNgdParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationOverlayComputeNgd", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationOverlayConnectKnodes": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/overlay_connect_knodes" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationOverlayConnectKnodes", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationOverlayFisherExactTest": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/overlay_fisher_exact_test" }, "parameters": { "$ref": "#/components/schemas/OverlayFisherExactTestParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationOverlayFisherExactTest", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationRestate": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/restate" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationRestate", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationScore": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/score" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationScore", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationSortResults": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/sort_results" }, "parameters": { "title": "Parameters" } }, "additionalProperties": false, "type": "object", "required": [ "id" ], "title": "OperationSortResults", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationSortResultsEdgeAttribute": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/sort_results_edge_attribute" }, "parameters": { "$ref": "#/components/schemas/SortResultsEdgeAttributeParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationSortResultsEdgeAttribute", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationSortResultsNodeAttribute": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/sort_results_node_attribute" }, "parameters": { "$ref": "#/components/schemas/SortResultsNodeAttributeParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationSortResultsNodeAttribute", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OperationSortResultsScore": { "properties": { "runner_parameters": { "$ref": "#/components/schemas/RunnerParameters" }, "id": { "$ref": "#/components/schemas/sort_results_score" }, "parameters": { "$ref": "#/components/schemas/SortResultsScoreParameters" } }, "additionalProperties": false, "type": "object", "required": [ "id", "parameters" ], "title": "OperationSortResultsScore", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "Operator": { "type": "string", "enum": [ "==", "===", ">", "<", "matches" ], "title": "Operator", "description": "Operator." }, "OverlayComputeJaccardParameters": { "properties": { "intermediate_node_key": { "type": "string", "title": "Intermediate Node Key" }, "end_node_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "virtual_relation_label": { "type": "string", "title": "Virtual Relation Label" } }, "type": "object", "required": [ "intermediate_node_key", "end_node_keys", "virtual_relation_label" ], "title": "OverlayComputeJaccardParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OverlayComputeNgdParameters": { "properties": { "qnode_keys": { "$ref": "#/components/schemas/HashableSequence_str_" }, "virtual_relation_label": { "type": "string", "title": "Virtual Relation Label" } }, "type": "object", "required": [ "qnode_keys", "virtual_relation_label" ], "title": "OverlayComputeNgdParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "OverlayFisherExactTestParameters": { "properties": { "subject_qnode_key": { "type": "string", "title": "Subject Qnode Key" }, "object_qnode_key": { "type": "string", "title": "Object Qnode Key" }, "virtual_relation_label": { "type": "string", "title": "Virtual Relation Label" }, "rel_edge_key": { "type": "string", "title": "Rel Edge Key" } }, "type": "object", "required": [ "subject_qnode_key", "object_qnode_key", "virtual_relation_label" ], "title": "OverlayFisherExactTestParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "PlusOrMinusEnum": { "type": "string", "enum": [ "plus", "minus" ], "title": "PlusOrMinusEnum", "description": "'plus' or 'minus'." }, "QEdge": { "properties": { "subject": { "type": "string", "title": "subject node id" }, "object": { "type": "string", "title": "object node id" }, "knowledge_type": { "allOf": [ { "$ref": "#/components/schemas/KnowledgeType" } ], "title": "knowledge type" }, "predicates": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_BiolinkPredicate_" } ], "title": "predicates", "nullable": true }, "attribute_constraints": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_AttributeConstraint_" } ], "title": "attribute constraints", "default": { "__root__": [] } }, "qualifier_constraints": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_QualifierConstraint_" } ], "title": "qualifier constraint", "default": { "__root__": [] } } }, "type": "object", "required": [ "subject", "object" ], "title": "query-graph edge", "description": "Query edge." }, "QNode": { "properties": { "ids": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_CURIE_" } ], "title": "ids", "nullable": true }, "categories": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_BiolinkEntity_" } ], "title": "categories", "nullable": true }, "is_set": { "type": "boolean", "title": "Is Set", "default": false }, "constraints": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_AttributeConstraint_" } ], "title": "attribute constraints", "default": { "__root__": [] } } }, "type": "object", "title": "query-graph node", "description": "Query node." }, "Qualifier": { "properties": { "qualifier_type_id": { "type": "string", "pattern": "^biolink:[a-z][a-z_]*$", "title": "type" }, "qualifier_value": { "type": "string", "title": "value" } }, "type": "object", "required": [ "qualifier_type_id", "qualifier_value" ], "title": "Qualifier", "description": "Edge qualifier." }, "QualifierConstraint": { "properties": { "qualifier_set": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_Qualifier_" } ], "title": "qualifier set", "default": { "__root__": [] } } }, "type": "object", "title": "QualifierConstraint", "description": "QEdge Qualifier constraint." }, "Query": { "properties": { "message": { "allOf": [ { "$ref": "#/components/schemas/Message" } ], "title": "message" }, "log_level": { "allOf": [ { "$ref": "#/components/schemas/LogLevel" } ], "title": "log_level", "nullable": true }, "workflow": { "$ref": "#/components/schemas/Workflow" } }, "type": "object", "required": [ "message" ], "title": "query", "description": "Request.", "x-body-name": "request_body" }, "QueryGraph": { "properties": { "nodes": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_str__QNode_" } ], "title": "dict of nodes" }, "edges": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_str__QEdge_" } ], "title": "dict of edges" } }, "type": "object", "required": [ "nodes", "edges" ], "title": "simple query graph", "description": "Query graph." }, "RecursiveAttribute": { "properties": { "attribute_type_id": { "type": "string", "title": "type" }, "value": { "title": "value" }, "value_type_id": { "type": "string", "title": "value_type_id", "nullable": true }, "original_attribute_name": { "type": "string", "title": "Original Attribute Name", "nullable": true }, "value_url": { "type": "string", "title": "Value Url", "nullable": true }, "attribute_source": { "type": "string", "title": "Attribute Source", "nullable": true }, "description": { "type": "string", "title": "Description", "nullable": true }, "attributes": { "allOf": [ { "$ref": "#/components/schemas/HashableSequence_RecursiveAttribute_" } ], "title": "Attributes", "nullable": true } }, "additionalProperties": false, "type": "object", "required": [ "attribute_type_id", "value" ], "title": "RecursiveAttribute", "description": "Attribute subattribute." }, "ResourceRoleEnum": { "type": "string", "enum": [ "aggregator_knowledge_source", "primary_knowledge_source", "supporting_data_source" ], "title": "ResourceRoleEnum", "description": "Types of resources" }, "Result": { "properties": { "node_bindings": { "allOf": [ { "$ref": "#/components/schemas/HashableMapping_str__HashableSet_NodeBinding__" } ], "title": "list of node bindings" }, "analyses": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_Analysis_" } ], "title": "list of anlysis blocks" } }, "type": "object", "required": [ "node_bindings", "analyses" ], "title": "result", "description": "Result." }, "Results": { "$ref": "#/components/schemas/HashableSequence_Result_", "title": "results", "description": "Results." }, "RetrievalSource": { "properties": { "resource_id": { "type": "string", "title": "infores for source" }, "resource_role": { "allOf": [ { "$ref": "#/components/schemas/ResourceRoleEnum" } ], "title": "source type" }, "upstream_resource_ids": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_CURIE_" } ], "title": "Upstream Resource Ids", "nullable": true }, "source_record_urls": { "allOf": [ { "$ref": "#/components/schemas/HashableSet_str_" } ], "title": "Source Record Urls", "nullable": true } }, "type": "object", "required": [ "resource_id", "resource_role" ], "title": "RetrievalSource", "description": "A component of source retrieval provenance" }, "RunnerAllowList": { "properties": { "allowlist": { "$ref": "#/components/schemas/HashableSequence_str_" }, "timeout": { "type": "number", "title": "Timeout" } }, "additionalProperties": false, "type": "object", "title": "RunnerAllowList", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "RunnerDenyList": { "properties": { "denylist": { "$ref": "#/components/schemas/HashableSequence_str_" }, "timeout": { "type": "number", "title": "Timeout" } }, "additionalProperties": false, "type": "object", "title": "RunnerDenyList", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "RunnerParameters": { "anyOf": [ { "$ref": "#/components/schemas/RunnerAllowList" }, { "$ref": "#/components/schemas/RunnerDenyList" }, { "$ref": "#/components/schemas/RunnerTimeout" } ], "title": "RunnerParameters", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "RunnerTimeout": { "properties": { "timeout": { "type": "number", "title": "Timeout" } }, "additionalProperties": false, "type": "object", "title": "RunnerTimeout", "description": "Custom base model for all classes\n\nThis provides hash and equality methods." }, "SemanticTypes": { "properties": { "semantic_types": { "additionalProperties": { "items": {}, "type": "array" }, "type": "object", "title": "Semantic Types" } }, "type": "object", "required": [ "semantic_types" ], "title": "SemanticTypes", "example": { "semantic_types": { "types": [ "biolink:CellularComponent", "biolink:NamedThing", "etc." ] } } }, "SemanticTypesInput": { "properties": { "semantic_types": { "items": { "type": "string" }, "type": "array", "title": "list of semantic types" } }, "type": "object", "required": [ "semantic_types" ], "title": "SemanticTypesInput", "description": "Semantic type input model", "example": { "semantic_types": [ "biolink:ChemicalEntity", "biolink:AnatomicalEntity" ] } }, "SetIDQuery": { "properties": { "curies": { "items": { "type": "string" }, "type": "array", "title": "Curies", "description": "Set of curies to normalize", "example": [ "MESH:D014867", "NCIT:C34373" ] }, "conflations": { "items": { "type": "string" }, "type": "array", "title": "Conflations", "description": "Set of conflations to apply", "default": [], "example": [ "GeneProtein", "DrugChemical" ] } }, "type": "object", "required": [ "curies" ], "title": "SetIDQuery", "description": "Query for a single SetID. Includes a set of CURIEs as well as a set of conflations to apply. 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