openapi: 3.0.1 info: contact: email: edeutsch@systemsbiology.org description: TRAPI 1.6 endpoint for the NCATS Biomedical Translator Reasoner called ARAX license: name: Apache 2.0 url: http://www.apache.org/licenses/LICENSE-2.0.html termsOfService: https://github.com/RTXteam/RTX/blob/master/LICENSE title: ARAX Translator Reasoner - TRAPI 1.6.0 version: 1.6.2 x-translator: component: ARA team: - Expander Agent infores: infores:arax biolink-version: 4.2.5 externalDocs: description: The values for component and team are restricted according to this external JSON schema. See schema and examples at url url: https://github.com/NCATSTranslator/translator_extensions/blob/production/x-translator/ x-trapi: version: 1.6.0 asyncquery: true pathfinderquery: true multicuriequery: false operations: - lookup - lookup_and_score - overlay_compute_ngd - overlay_compute_jaccard - overlay_fisher_exact_test - overlay_connect_knodes - filter_results_top_n - bind - fill - filter_kgraph_orphans - filter_kgraph_top_n - filter_kgraph_std_dev - filter_kgraph_percentile - filter_kgraph_discrete_kedge_attribute - filter_kgraph_continuous_kedge_attribute - sort_results_score - sort_results_edge_attribute - sort_results_node_attribute - annotate_nodes - score - complete_results externalDocs: description: The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url url: https://github.com/NCATSTranslator/translator_extensions/blob/production/x-trapi/ externalDocs: description: Documentation for the NCATS Biomedical Translator Reasoners web services url: https://github.com/NCATSTranslator/ReasonerAPI servers: - description: ARAX TRAPI 1.6 endpoint - production url: https://arax.transltr.io/api/arax/v1.4 x-maturity: production - description: ARAX TRAPI 1.6 endpoint - testing url: https://arax.test.transltr.io/api/arax/v1.4 x-maturity: testing - description: ARAX TRAPI 1.6 endpoint - staging url: https://arax.ci.transltr.io/api/arax/v1.4 x-maturity: staging - description: ARAX TRAPI 1.6 endpoint - development url: https://arax.ncats.io/beta/api/arax/v1.4 x-maturity: development - description: ARAX TRAPI 1.6 endpoint - development url: https://arax.ncats.io/test/api/arax/v1.4 x-maturity: development - description: ARAX TRAPI 1.6 endpoint - development url: https://arax.ncats.io/devED/api/arax/v1.4 x-maturity: development - description: ARAX TRAPI 1.6 endpoint - development url: https://arax.ncats.io/devLM/api/arax/v1.4 x-maturity: development tags: - description: Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult. externalDocs: description: Documentation for the reasoner predicates function url: https://arax.ncats.io/overview.html#predicates name: meta_knowledge_graph - description: Initiate a query and wait to receive the response externalDocs: description: Documentation for the reasoner query function url: https://arax.ncats.io/overview.html#query name: query - description: Initiate a query with a callback to receive the response externalDocs: description: Documentation for the reasoner asynchquery function url: https://arax.ncats.io/overview.html#asyncquery name: asyncquery - description: Retrieve the current status of a previously submitted asyncquery given its job_id name: asyncquery_status - description: Required for SmartAPI validation of x-translator name: translator - description: Required for SmartAPI validation of x-trapi name: trapi - description: Request a previously stored response from the server externalDocs: description: Documentation for the reasoner response function url: https://arax.ncats.io/overview.html#response name: response - description: Translate natural language question into a standardized query externalDocs: description: Documentation for the reasoner translate function url: https://arax.ncats.io/overview.html#translate name: translate - description: Return identifier and type of some entity in the knowledge graph externalDocs: description: Documentation for the reasoner entity function url: https://arax.ncats.io/overview.html#entity name: entity - description: Return a list of example questions that the reasoner can answer externalDocs: description: Documentation for the reasoner exampleQuestions function url: https://arax.ncats.io/overview.html#exampleQuestions name: exampleQuestions - description: Query to get the Normalized Google Distance between two MeSH terms based on co-occurance in all PubMed article annotations externalDocs: description: Documentation for the reasoner PubmedMeshNgd function url: https://arax.ncats.io/overview.html#PubmedMeshNgd name: PubmedMeshNgd - description: Return status information about the endpoint name: status paths: /PubmedMeshNgd/{term1}/{term2}: get: operationId: pubmed_mesh_ngd parameters: - description: First of two terms. Order not important. example: PTGS2 explode: false in: path name: term1 required: true schema: type: string style: simple - description: Second of two terms. Order not important. example: acetaminophen explode: false in: path name: term2 required: true schema: type: string style: simple responses: "200": content: application/json: schema: $ref: '#/components/schemas/MeshNgdResponse' description: successful operation "400": description: Invalid terms summary: Query to get the Normalized Google Distance between two MeSH terms based on co-occurrence in all PubMed article annotations tags: - PubmedMeshNgd x-openapi-router-controller: openapi_server.controllers.pubmed_mesh_ngd_controller /asyncquery: post: operationId: asyncquery requestBody: content: application/json: schema: $ref: '#/components/schemas/AsyncQuery' description: Query information to be submitted required: true responses: "200": content: application/json: schema: $ref: '#/components/schemas/AsyncQueryResponse' description: The query is accepted for processing and the Response will be sent to the callback url when complete. "400": content: application/json: schema: type: string description: Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized). "413": content: application/json: schema: type: string description: Payload too large. Indicates that batch size was over the limit specified in x-trapi. "429": content: application/json: schema: type: string description: Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. "500": content: application/json: schema: type: string description: Internal server error. "501": content: application/json: schema: type: string description: Not implemented. summary: Initiate a query with a callback to receive the response tags: - asyncquery x-openapi-router-controller: openapi_server.controllers.asyncquery_controller /asyncquery_status/{job_id}: get: operationId: asyncquery_status parameters: - description: Identifier of the job for status request example: 800000 explode: false in: path name: job_id required: true schema: type: string style: simple responses: "200": content: application/json: schema: $ref: '#/components/schemas/AsyncQueryStatusResponse' description: Returns the status and current logs of a previously submitted asyncquery. "404": description: job_id not found "501": content: application/json: schema: type: string description: Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status. summary: Retrieve the current status of a previously submitted asyncquery given its job_id tags: - asyncquery_status x-openapi-router-controller: openapi_server.controllers.asyncquery_status_controller /entity: get: operationId: get_entity parameters: - description: A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings. explode: true in: query name: q required: true schema: example: - MESH:D014867 - NCIT:C34373 items: type: string type: array style: form responses: "200": content: application/json: schema: type: object description: successful operation "404": description: Entity not found summary: Obtain CURIE and synonym information about a search term tags: - entity x-openapi-router-controller: openapi_server.controllers.entity_controller post: operationId: post_entity requestBody: content: application/json: schema: type: object description: List of terms to get information about required: true responses: "200": content: application/json: schema: $ref: '#/components/schemas/EntityQuery' description: successful operation "404": description: Entity not found summary: Obtain CURIE and synonym information about search terms tags: - entity x-openapi-router-controller: openapi_server.controllers.entity_controller /exampleQuestions: get: operationId: example_questions responses: "200": content: application/json: schema: items: type: object type: array description: successful operation summary: Request a list of example questions that ARAX can answer tags: - exampleQuestions x-openapi-router-controller: openapi_server.controllers.example_questions_controller /meta_knowledge_graph: get: operationId: meta_knowledge_graph parameters: - description: Provide meta_knowledge_graph information in a format other than the default. Default value is 'full'. Also permitted is 'simple' explode: true in: query name: format required: false schema: type: string style: form responses: "200": content: application/json: schema: $ref: '#/components/schemas/MetaKnowledgeGraph' description: Returns meta knowledge graph representation of this TRAPI web service. summary: Meta knowledge graph representation of this TRAPI web service. tags: - meta_knowledge_graph x-openapi-router-controller: openapi_server.controllers.meta_knowledge_graph_controller /query: post: operationId: query requestBody: content: application/json: schema: $ref: '#/components/schemas/Query' description: Query information to be submitted required: true responses: "200": content: application/json: schema: $ref: '#/components/schemas/Response' description: OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. "400": content: application/json: schema: type: string description: Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized). "413": content: application/json: schema: type: string description: Payload too large. Indicates that batch size was over the limit specified in x-trapi. "429": content: application/json: schema: type: string description: Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. "500": content: application/json: schema: type: string description: Internal server error. "501": content: application/json: schema: type: string description: Not implemented. summary: Initiate a query and wait to receive a Response tags: - query x-openapi-router-controller: openapi_server.controllers.query_controller /response: post: operationId: post_response requestBody: content: application/json: schema: type: object description: Object that provides annotation information required: true responses: "200": content: application/json: schema: type: object description: successful operation "400": description: Invalid request summary: Annotate a response tags: - response x-openapi-router-controller: openapi_server.controllers.response_controller /response/{response_id}: get: operationId: get_response parameters: - description: Identifier of the response to return example: 41651 explode: false in: path name: response_id required: true schema: type: string style: simple responses: "200": content: application/json: schema: $ref: '#/components/schemas/Response' description: successful operation "404": description: response_id not found summary: Request a previously stored response from the server tags: - response x-openapi-router-controller: openapi_server.controllers.response_controller /status: get: operationId: get_status parameters: - description: Limit results to the past N hours explode: true in: query name: last_n_hours required: false schema: example: 6 type: integer style: form - description: Identifier of the log entry explode: true in: query name: id required: false schema: example: 10 type: integer style: form - description: PID of an ongoing query to terminate explode: true in: query name: terminate_pid required: false schema: type: integer style: form - description: Authorization string required for certain calls to status explode: true in: query name: authorization required: false schema: type: string style: form - description: 'Switch to control the type of returned status information Possible values are: activity: Show query activity on server [default] smartapi: Summarize Translator endpoints at SmartAPI' explode: true in: query name: mode required: false schema: type: string style: form responses: "200": content: application/json: schema: type: object description: successful operation "404": description: Entity not found summary: Obtain status information about the endpoint tags: - status x-openapi-router-controller: openapi_server.controllers.status_controller /status/logs: get: operationId: get_logs parameters: - description: Specify the log sending mode explode: true in: query name: mode required: false schema: example: tail type: string style: form responses: "200": content: text/plain: schema: type: string description: successful operation "404": description: Logs not found summary: Get log information from the server tags: - status x-openapi-router-controller: openapi_server.controllers.status_controller /translate: post: operationId: translate requestBody: content: application/json: schema: $ref: '#/components/schemas/Question' description: Question information to be translated required: true responses: "200": content: application/json: schema: items: $ref: '#/components/schemas/Query' type: array description: successful operation "400": description: Invalid status value summary: Translate natural language question into a standardized query tags: - translate x-openapi-router-controller: openapi_server.controllers.translate_controller components: schemas: Query: additionalProperties: true description: The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue. example: submitter: submitter bypass_cache: false page_number: 1 operations: "" workflow: - "" - "" log_level: "" enforce_edge_directionality: false return_minimal_metadata: false max_results: 100 stream_progress: false message: query_graph: edges: e00: subject: n00 object: n01 predicates: - biolink:physically_interacts_with nodes: n00: ids: - CHEMBL.COMPOUND:CHEMBL112 n01: categories: - biolink:Protein page_size: 100 properties: message: oneOf: - $ref: '#/components/schemas/Message' nullable: false log_level: description: The least critical level of logs to return nullable: true oneOf: - $ref: '#/components/schemas/LogLevel' workflow: description: List of workflow steps to be executed. items: oneOf: - $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' nullable: true type: array submitter: description: Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution. nullable: true type: string bypass_cache: default: false description: >- Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs). type: boolean stream_progress: default: false description: Set to true in order to receive a stream of LogEntry objects as the query is progressing type: boolean enforce_edge_directionality: default: false description: Set to true in order to enforce edge directionality during queries. By default, edge directionality can be reversed without penalty. type: boolean return_minimal_metadata: default: false description: Set to true in order to return only the most minimal metadata. By default, rich metadata for nodes and edges are supplied, which may cause a very large and slower Response. type: boolean max_results: default: 100 description: Maximum number of individual results to return example: 100 type: integer page_size: default: 100 description: Split the results into pages with this number of results each example: 100 type: integer page_number: default: 1 description: Page number of results when the number of results exceeds the page_size, with page 1 as the first page example: 1 type: integer operations: description: Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned nullable: true oneOf: - $ref: '#/components/schemas/Operations' required: - message title: Query type: object x-body-name: request_body AsyncQuery: additionalProperties: true description: The AsyncQuery class is effectively the same as the Query class but it requires a callback property. properties: callback: description: 'Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of ''Running''. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.' format: uri pattern: ^https?:// type: string message: oneOf: - $ref: '#/components/schemas/Message' nullable: false log_level: description: The least critical level of logs to return nullable: true oneOf: - $ref: '#/components/schemas/LogLevel' workflow: description: List of workflow steps to be executed. items: oneOf: - $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' nullable: true type: array submitter: description: Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution. nullable: true type: string bypass_cache: type: boolean default: false description: >- Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs). required: - callback - message type: object x-body-name: request_body AsyncQueryResponse: additionalProperties: true description: The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query. example: job_id: rXEOAosN3L description: Async_query has been queued status: Accepted properties: status: description: 'One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable' example: Accepted nullable: true type: string description: description: A brief human-readable description of the result of the async_query submission. example: Async_query has been queued nullable: true type: string job_id: description: An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job. example: rXEOAosN3L nullable: false type: string required: - job_id title: AsyncQueryResponse type: object AsyncQueryStatusResponse: additionalProperties: true description: The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query. example: description: Callback URL returned 500 logs: - code: code level: "" message: message timestamp: 2020-09-03T18:13:49Z - code: code level: "" message: message timestamp: 2020-09-03T18:13:49Z status: Running response_url: https://arax.ncats.io/api/arax/v1.3/response/116481 properties: status: description: 'One of a standardized set of short codes: Queued, Running, Completed, Failed' example: Running nullable: false type: string description: description: A brief human-readable description of the current state or summary of the problem if the status is Failed. example: Callback URL returned 500 nullable: false type: string logs: description: A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity. items: $ref: '#/components/schemas/LogEntry' nullable: false type: array response_url: description: Optional URL that can be queried to restrieve the full TRAPI Response. example: https://arax.ncats.io/api/arax/v1.3/response/116481 nullable: true type: string required: - description - logs - status title: AsyncQueryStatusResponse type: object Response: additionalProperties: true description: The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response. example: original_question: what proteins are affected by sickle cell anemia validation_result: '{}' submitter: submitter workflow: - "" - "" query_options: coalesce: true threshold: 0.9 restated_question: Which proteins are affected by sickle cell anemia? biolink_version: 3.1.2 description: Success. 42 results found. message: query_graph: edges: e00: subject: n00 object: n01 predicates: - biolink:physically_interacts_with nodes: n00: ids: - CHEMBL.COMPOUND:CHEMBL112 n01: categories: - biolink:Protein type: TranslatorAPIResponse total_results_count: 0 schema_version: 1.4.0 datetime: 2021-01-09 12:34:45 operations: "" table_column_names: - chemical_substance.name - chemical_substance.id tool_version: ARAX 0.8.0 job_id: rXEOAosN3L context: https://rtx.ncats.io/ns/translator.jsonld resource_id: ARAX id: https://arax.ncats.io/api/rtx/v1.3/response/123 logs: - code: code level: "" message: message timestamp: 2020-09-03T18:13:49Z - code: code level: "" message: message timestamp: 2020-09-03T18:13:49Z status: Success info: info properties: message: oneOf: - $ref: '#/components/schemas/Message' nullable: false status: description: One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable example: Success nullable: true type: string description: description: A brief human-readable description of the outcome example: Success. 42 results found. nullable: true type: string logs: description: A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. items: $ref: '#/components/schemas/LogEntry' nullable: true type: array workflow: description: A list of operations that were executed. items: oneOf: - $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/OperationLookupAndScore' - $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' type: array submitter: description: Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution. nullable: true type: string operations: description: Container for one or more Message objects or identifiers for one or more Messages along with the processing plan and options for how those messages were processed and returned oneOf: - $ref: '#/components/schemas/Operations' job_id: description: An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job. example: rXEOAosN3L nullable: true type: string resource_id: description: Identifier string of the resource that provided this response (one of ARAX, Aragorn, etc.) example: ARAX nullable: true type: string tool_version: description: Version label of the tool that generated this response example: ARAX 0.8.0 type: string schema_version: description: Version label of this TRAPI schema example: 1.4.0 type: string biolink_version: description: Version label of the Biolink model used in this document example: 3.1.2 type: string datetime: description: Datetime string for the time that this response was generated example: 2021-01-09 12:34:45 type: string table_column_names: description: List of column names that corresponds to the row_data for each result example: - chemical_substance.name - chemical_substance.id items: type: string type: array original_question: description: The original question text typed in by the user example: what proteins are affected by sickle cell anemia type: string restated_question: description: A precise restatement of the question, as understood by the Translator, for which the answer applies. The user should verify that the restated question matches the intent of their original question (it might not). example: Which proteins are affected by sickle cell anemia? type: string query_options: description: Dict of options that can be sent with the query. Options are tool specific and not stipulated here example: coalesce: true threshold: 0.9 type: object context: description: JSON-LD context URI example: https://rtx.ncats.io/ns/translator.jsonld type: string type: description: Entity type of this response example: TranslatorAPIResponse type: string id: description: URI for this response example: https://arax.ncats.io/api/rtx/v1.3/response/123 type: string validation_result: description: Validation results and other summary stats computed for this Response. type: object total_results_count: description: The total number of results that were generated prior to any filtering. nullable: true type: integer info: description: A placholder for including some additional information nullable: true type: string required: - message title: Response type: object Message: additionalProperties: false description: 'The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.' example: query_graph: edges: e00: subject: n00 object: n01 predicates: - biolink:physically_interacts_with nodes: n00: ids: - CHEMBL.COMPOUND:CHEMBL112 n01: categories: - biolink:Protein properties: results: description: |- List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it. items: $ref: '#/components/schemas/Result' nullable: true type: array query_graph: description: QueryGraph object that contains a serialization of a query in the form of a graph nullable: true oneOf: - $ref: '#/components/schemas/QueryGraph' knowledge_graph: description: KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message nullable: true oneOf: - $ref: '#/components/schemas/KnowledgeGraph' auxiliary_graphs: additionalProperties: $ref: '#/components/schemas/AuxiliaryGraph' description: Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key. type: object title: Message type: object LogEntry: additionalProperties: true description: The LogEntry object contains information useful for tracing and debugging across Translator components. Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message. example: code: code level: "" message: message timestamp: 2020-09-03T18:13:49Z properties: timestamp: description: Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00). example: 2020-09-03T18:13:49Z format: date-time nullable: false type: string level: nullable: true oneOf: - $ref: '#/components/schemas/LogLevel' code: description: One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed nullable: true type: string message: description: A human-readable log message nullable: false type: string required: - message - timestamp title: LogEntry type: object LogLevel: description: Logging level enum: - ERROR - WARNING - INFO - DEBUG example: DEBUG type: string x-nullable: true Result: additionalProperties: true description: A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings). properties: node_bindings: additionalProperties: items: $ref: '#/components/schemas/NodeBinding' type: array description: The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result. type: object analyses: description: The list of all Analysis components that contribute to the result. See below for Analysis components. items: $ref: '#/components/schemas/Analysis' type: array id: description: URI for this result example: result:234 nullable: true type: string description: description: A free text description of this result answer from the reasoner example: The genetic condition sickle cell anemia may provide protection from cerebral malaria via genetic alterations of proteins HBB (P68871) and HMOX1 (P09601). nullable: true type: string essence: description: A single string that is the terse essence of the result (useful for simple answers) example: ibuprofen nullable: true type: string essence_category: description: A Translator BioLink bioentity category of the essence example: biolink:ChemicalEntity nullable: true type: string row_data: description: An arbitrary list of values that captures the essence of the result that can be turned into a tabular result across all answers (each result is a row) for a user that wants simplified tabular output example: - ibuprofen - CHEMBL:CHEMBL521 items: oneOf: - type: string - type: number nullable: true type: array score: description: A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. example: 163.233 format: float nullable: true type: number score_name: description: Name for the score example: Jaccard distance nullable: true type: string score_direction: description: 'Sorting indicator for the score: one of higher_is_better or lower_is_better' example: lower_is_better nullable: true type: string confidence: description: |- Confidence metric for this result, a value between (inclusive) 0.0 (no confidence) and 1.0 (highest confidence) example: 0.9234 format: float nullable: true type: number result_group: description: An integer group number for results for use in cases where several results should be grouped together. Also useful to control sorting ascending. example: 1 nullable: true type: integer result_group_similarity_score: description: A score that denotes the similarity of this result to other members of the result_group example: 0.95 format: float nullable: true type: number resource_id: description: Identifier string of the resource that provided this result (one of ARAX, Aragorn, etc.) example: ARAX nullable: true type: string required: - analyses - node_bindings title: Result type: object NodeBinding: additionalProperties: true description: An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph. properties: id: description: The CURIE of a Node within the Knowledge Graph. oneOf: - $ref: '#/components/schemas/CURIE' nullable: false query_id: description: An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided. oneOf: - $ref: '#/components/schemas/CURIE' attributes: description: A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result. items: $ref: '#/components/schemas/Attribute' nullable: true type: array required: - id title: NodeBinding type: object Analysis: additionalProperties: true description: An analysis is a dictionary that contains information about the result tied to a particular service. Each Analysis is generated by a single reasoning service, and describes the outputs of analyses performed by the reasoner on a particular Result (e.g. a result score), along with provenance information supporting the analysis (e.g. method or data that supported generation of the score). properties: resource_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string score: description: A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better. example: 163.233 format: float nullable: true type: number edge_bindings: additionalProperties: items: $ref: '#/components/schemas/EdgeBinding' type: array description: The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges. type: object support_graphs: description: This is a list of references to Auxiliary Graph instances that supported the analysis of a Result as performed by the reasoning service. Each item in the list is the key of a single Auxiliary Graph. items: type: string nullable: true type: array scoring_method: description: An identifier and link to an explanation for the method used to generate the score nullable: true type: string attributes: description: The attributes of this particular Analysis. items: $ref: '#/components/schemas/Attribute' nullable: true type: array required: - edge_bindings - resource_id title: Analysis type: object EdgeBinding: additionalProperties: true description: A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners. properties: id: description: The key identifier of a specific KnowledgeGraph Edge. type: string attributes: description: A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result. items: $ref: '#/components/schemas/Attribute' nullable: true type: array required: - id title: EdgeBinding type: object AuxiliaryGraph: additionalProperties: true description: A single AuxiliaryGraph instance that is used by Knowledge Graph Edges and Result Analyses. Edges comprising an Auxiliary Graph are a subset of the Knowledge Graph in the message. Data creators can create an AuxiliaryGraph to assemble a specific collections of edges from the Knowledge Graph into a named graph that can be referenced from an Edge as evidence/explanation supporting that Edge, or from a Result Analysis as information used to generate a score. properties: edges: description: List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge items: type: string minItems: 1 nullable: false type: array attributes: description: Attributes of the Auxiliary Graph items: $ref: '#/components/schemas/Attribute' nullable: true type: array required: - edges type: object KnowledgeGraph: additionalProperties: true description: The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation. properties: nodes: additionalProperties: $ref: '#/components/schemas/Node' description: Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. type: object edges: additionalProperties: $ref: '#/components/schemas/Edge' description: Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. type: object required: - edges - nodes type: object x-nullable: true QueryGraph: additionalProperties: true description: A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element. properties: nodes: additionalProperties: $ref: '#/components/schemas/QNode' description: The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes. type: object edges: additionalProperties: $ref: '#/components/schemas/QEdge' description: The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes. type: object required: - edges - nodes type: object QNode: additionalProperties: true description: A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results. properties: ids: description: CURIE identifier for this node example: - OMIM:603903 items: $ref: '#/components/schemas/CURIE' minItems: 1 nullable: true type: array categories: description: These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided. items: $ref: '#/components/schemas/BiolinkEntity' minItems: 1 nullable: true type: array is_set: type: boolean description: >- Set to true if this QNode is a set (deprecated) default: false set_id: type: string description: >- A client-provided identifier for the set described in this QNode nullable: true set_interpretation: type: string description: >- Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH. enum: - BATCH - ALL - MANY nullable: true constraints: default: [] description: A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND) items: $ref: '#/components/schemas/AttributeConstraint' type: array option_group_id: description: 'Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ' nullable: true type: string title: QNode type: object QEdge: additionalProperties: true description: An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term. properties: knowledge_type: description: Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future. example: lookup nullable: true type: string predicates: description: These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided. items: $ref: '#/components/schemas/BiolinkPredicate' minItems: 1 nullable: true type: array subject: description: Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge. example: https://omim.org/entry/603903 type: string object: description: Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge. example: https://www.uniprot.org/uniprot/P00738 type: string attribute_constraints: default: [] description: A list of attribute contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND) items: $ref: '#/components/schemas/AttributeConstraint' type: array qualifier_constraints: default: [] description: A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time. items: $ref: '#/components/schemas/QualifierConstraint' type: array exclude: description: If set to true, then all subgraphs containing this edge are excluded from the final results. (optional) type: boolean option_group_id: description: 'Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ' nullable: true type: string required: - object - subject title: QEdge type: object Node: additionalProperties: false description: A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping. properties: name: description: Formal name of the entity example: Haptoglobin nullable: true title: name type: string categories: description: These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided. items: $ref: '#/components/schemas/BiolinkEntity' nullable: true title: categories type: array attributes: description: A list of attributes describing the node items: $ref: '#/components/schemas/Attribute' nullable: true title: attributes type: array title: Node type: object Attribute: additionalProperties: false description: Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with sub-attributes (for example to provide confidence intervals on a value). properties: attribute_type_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string original_attribute_name: description: The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term. example: p-value nullable: true title: original_attribute_name type: string value: description: Value of the attribute. May be any data type, including a list. example: 0.000153 title: value value_type_id: description: CURIE describing the semantic type of an attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority. example: EDAM:data_1187 nullable: true oneOf: - $ref: '#/components/schemas/CURIE' title: value_type_id attribute_source: description: The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible. example: UniProtKB nullable: true title: attribute_source type: string value_url: description: Human-consumable URL linking to a web document that provides additional information about an attribute's value (not the node or the edge fom which it hangs). example: https://pubmed.ncbi.nlm.nih.gov/32529952 nullable: true title: value_url type: string description: description: Human-readable description for the attribute and its value. example: Assertion Authored By Dr. Trans L. Ator nullable: true title: description type: string attributes: description: A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute). items: $ref: '#/components/schemas/Attribute' nullable: true title: attributes type: array required: - attribute_type_id - value title: Attribute type: object Edge: additionalProperties: false description: A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge "thought" graph resulting from a query upon the underlying knowledge source. properties: predicate: description: The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided. example: biolink:gene_associated_with_condition nullable: false oneOf: - $ref: '#/components/schemas/BiolinkPredicate' title: predicate subject: description: Corresponds to the map key CURIE of the subject concept node of this relationship edge. example: MONDO:0011382 nullable: false oneOf: - $ref: '#/components/schemas/CURIE' title: subject object: description: Corresponds to the map key CURIE of the object concept node of this relationship edge. example: UniProtKB:P00738 nullable: false oneOf: - $ref: '#/components/schemas/CURIE' title: object attributes: description: A list of additional attributes for this edge items: $ref: '#/components/schemas/Attribute' nullable: true title: attributes type: array qualifiers: description: A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge. items: $ref: '#/components/schemas/Qualifier' nullable: true title: qualifiers type: array sources: description: A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. items: $ref: '#/components/schemas/RetrievalSource' minItems: 1 nullable: false title: sources type: array required: - object - predicate - sources - subject title: Edge type: object Qualifier: additionalProperties: false description: An additional nuance attached to an assertion properties: qualifier_type_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string qualifier_value: description: The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge. example: expression nullable: false title: qualifier_value type: string required: - qualifier_type_id - qualifier_value title: Qualifier type: object QualifierConstraint: additionalProperties: false description: Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a "ChemicalX - affects - ?Gene" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type "biolink:object_aspect_qualifier" with a qualifier_value of "expression". properties: qualifier_set: description: A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges. items: $ref: '#/components/schemas/Qualifier' nullable: false title: qualifier_set type: array required: - qualifier_set title: QualifierConstraint type: object BiolinkEntity: description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name. example: biolink:PhenotypicFeature externalDocs: description: Biolink model entities url: https://biolink.github.io/biolink-model/docs/NamedThing.html pattern: ^biolink:[A-Z][a-zA-Z]*$ title: BiolinkEntity type: string BiolinkPredicate: description: CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge. example: biolink:interacts_with externalDocs: description: Biolink model predicates url: https://biolink.github.io/biolink-model/docs/related_to.html pattern: ^biolink:[a-z][a-z_]*$ title: BiolinkPredicate type: string CURIE: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string MetaKnowledgeGraph: description: Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge. example: nodes: key: id_prefixes: - CHEMBL.COMPOUND - INCHIKEY attributes: - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false edges: - predicate: biolink:interacts_with knowledge_types: - knowledge_types - knowledge_types subject: biolink:PhenotypicFeature qualifiers: - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id association: biolink:PhenotypicFeature attributes: - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false object: biolink:PhenotypicFeature - predicate: biolink:interacts_with knowledge_types: - knowledge_types - knowledge_types subject: biolink:PhenotypicFeature qualifiers: - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id association: biolink:PhenotypicFeature attributes: - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false object: biolink:PhenotypicFeature properties: nodes: additionalProperties: $ref: '#/components/schemas/MetaNode' description: Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available. title: nodes type: object edges: description: List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available. items: $ref: '#/components/schemas/MetaEdge' title: edges type: array required: - edges - nodes title: MetaKnowledgeGraph type: object MetaNode: additionalProperties: false description: Description of a node category provided by this TRAPI web service. example: id_prefixes: - CHEMBL.COMPOUND - INCHIKEY attributes: - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false properties: id_prefixes: description: List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input. example: - CHEMBL.COMPOUND - INCHIKEY items: type: string minItems: 1 title: id_prefixes type: array attributes: description: Node attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' nullable: true title: attributes type: array required: - id_prefixes title: MetaNode type: object MetaEdge: additionalProperties: false description: Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class. example: predicate: biolink:interacts_with knowledge_types: - knowledge_types - knowledge_types subject: biolink:PhenotypicFeature qualifiers: - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id - applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id association: biolink:PhenotypicFeature attributes: - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false - attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false object: biolink:PhenotypicFeature properties: subject: description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name. example: biolink:PhenotypicFeature externalDocs: description: Biolink model entities url: https://biolink.github.io/biolink-model/docs/NamedThing.html pattern: ^biolink:[A-Z][a-zA-Z]*$ title: BiolinkEntity type: string predicate: description: CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge. example: biolink:interacts_with externalDocs: description: Biolink model predicates url: https://biolink.github.io/biolink-model/docs/related_to.html pattern: ^biolink:[a-z][a-z_]*$ title: BiolinkPredicate type: string object: description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name. example: biolink:PhenotypicFeature externalDocs: description: Biolink model entities url: https://biolink.github.io/biolink-model/docs/NamedThing.html pattern: ^biolink:[A-Z][a-zA-Z]*$ title: BiolinkEntity type: string knowledge_types: description: A list of knowledge_types that are supported by the service. If the knowledge_types is null, this means that only 'lookup' is supported. Currently allowed values are 'lookup' or 'inferred'. items: type: string minItems: 1 nullable: true title: knowledge_types type: array attributes: description: Edge attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' nullable: true title: attributes type: array qualifiers: description: Qualifiers that are possible to be found on this edge type. items: $ref: '#/components/schemas/MetaQualifier' nullable: true title: qualifiers type: array association: description: Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name. example: biolink:PhenotypicFeature externalDocs: description: Biolink model entities url: https://biolink.github.io/biolink-model/docs/NamedThing.html pattern: ^biolink:[A-Z][a-zA-Z]*$ title: BiolinkEntity type: string required: - object - predicate - subject title: MetaEdge type: object MetaQualifier: example: applicable_values: - '["expression","activity","abundance","degradation"]' - '["expression","activity","abundance","degradation"]' qualifier_type_id: qualifier_type_id properties: qualifier_type_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string applicable_values: description: The list of values that are possible for this qualifier. items: example: '["expression","activity","abundance","degradation"]' type: string title: applicable_values type: array required: - qualifier_type_id title: MetaQualifier type: object MetaAttribute: example: attribute_source: infores:chembl original_attribute_names: - original_attribute_names - original_attribute_names constraint_name: p-value attribute_type_id: attribute_type_id constraint_use: false properties: attribute_type_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string attribute_source: description: Source of an attribute provided by this TRAPI web service. example: infores:chembl nullable: true title: attribute_source type: string original_attribute_names: description: Names of an the attribute as provided by the source. items: type: string minItems: 1 nullable: true title: original_attribute_names type: array constraint_use: default: false description: Indicates whether this attribute can be used as a query constraint. title: constraint_use type: boolean constraint_name: description: Human-readable name or label for the constraint concept. Required whenever constraint_use is true. example: p-value nullable: true title: constraint_name type: string required: - attribute_type_id title: MetaAttribute type: object AttributeConstraint: additionalProperties: false description: Generic query constraint for a query node or query edge properties: id: description: CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority. example: EDAM:data_0844 oneOf: - $ref: '#/components/schemas/CURIE' title: id name: description: Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability. example: molecular mass title: name type: string not: default: false title: not type: boolean operator: description: Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. If the value of the compared attribute is a list, then comparisons are performed between each of the constraint values and each of the attribute values, and any one true evaluation counts as an overall true (e.g., [1,2,3] == [6,7,2] is true). The == operator is therefore a broad interpretation of inclusion. The '===' operator requires that the constraint value and the attribute value be the same data type, length, content, and order (e.g. only [1,2,3] === [1,2,3]). The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, not matches means does not match, and not === means the match between the constraint and attribute values are not exact. The '==' operator SHOULD NOT be used in a manner that describes an "is a" subclass relationship for the parent QNode. enum: - == - '>' - < - matches - === title: operator type: string value: description: Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR) unless the '===' operator is used. If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages. example: 57.0 title: value unit_id: description: CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units. example: UO:0000222 nullable: true title: unit_id unit_name: description: Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability. example: kilodalton nullable: true title: unit_name required: - id - name - operator - value title: AttributeConstraint type: object RetrievalSource: additionalProperties: true description: Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved. properties: resource_id: description: A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI. externalDocs: url: https://www.w3.org/TR/2010/NOTE-curie-20101216/ title: CURIE type: string resource_role: $ref: '#/components/schemas/ResourceRoleEnum' upstream_resource_ids: description: An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact. example: - infores:automat-mychem-info - infores:molepro items: $ref: '#/components/schemas/CURIE' type: array source_record_urls: description: 'A URL linking to a specific web page or document provided by the source, that contains a record of the knowledge expressed in the Edge. If the knowledge is contained in more than one web page on an Information Resource''s site, urls MAY be provided for each. For example, Therapeutic Targets Database (TTD) has separate web pages for ''Imatinib'' and its protein target KIT, both of which hold the claim that ''the KIT protein is a therapeutic target for Imatinib''. ' example: '[https://db.idrblab.net/ttd/data/drug/details/d0az3c, https://db.idrblab.net/ttd/data/target/details/t57700]' items: type: string type: array required: - resource_id - resource_role title: RetrievalSource type: object ResourceRoleEnum: description: The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources. This enumeration is found in Biolink Model, but is repeated here for convenience. enum: - primary_knowledge_source - aggregator_knowledge_source - supporting_data_source title: ResourceRoleEnum type: string Operations: additionalProperties: true description: Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned nullable: true properties: message_uris: description: List of URIs for Message or Response objects to fetch and process example: - https://arax.ncats.io/api/arax/v1.3/response/38 items: type: string type: array messages: description: List of Message objects to process items: $ref: '#/components/schemas/Message' type: array actions: description: List of order-dependent operations to execute example: - add_qnode(name=acetaminophen, key=n00) - add_qnode(category=biolink:Protein, key=n01) - add_qedge(subject=n01, object=n00, key=e00) - expand(edge_key=e00) - resultify() - filter_results(action=limit_number_of_results, max_results=10) items: type: string type: array options: additionalProperties: true description: Map of order independent options that apply during processing example: halt_on_warning: false type: object type: object Question: additionalProperties: true properties: text: description: Free text question example: what genetic conditions offer protection against malaria type: string language: description: Human language in which the question is posed enum: - English example: English type: string type: object MeshNgdResponse: example: result_code: TermNotFound message: Term 1 'malria' not found in MeSH value: 0.714 properties: result_code: description: Set to OK for success, or some other short string to indicate and error (e.g., TermNotFound, etc.) example: TermNotFound title: result_code type: string message: description: Extended message denoting the success or mode of failure for request example: Term 1 'malria' not found in MeSH title: message type: string value: description: Calculated Normalized Google Distance for the two supplied terms example: 0.714 format: float title: value type: number title: MeshNgdResponse type: object EntityQuery: example: terms: - terms - terms format: format properties: terms: description: List of term strings to search for items: type: string title: terms type: array format: description: Format of the response (full or compact) title: format type: string title: EntityQuery type: object OperationAnnotate: additionalProperties: false description: This operation adds attributes to knowledge graph elements. properties: id: enum: - annotate type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationAnnotateEdges: additionalProperties: false description: This operation adds attributes to knowledge graph edges. properties: id: enum: - annotate_edges type: string parameters: $ref: '#/components/schemas/OperationAnnotateEdges_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationAnnotateNodes: additionalProperties: false description: This operation adds attributes to knowledge graph nodes. properties: id: enum: - annotate_nodes type: string parameters: $ref: '#/components/schemas/OperationAnnotateNodes_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationBind: additionalProperties: false description: This operation adds results binding kgraph elements to qgraph elements. properties: id: enum: - bind type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationCompleteResults: additionalProperties: false description: This operation combines partial results into complete results. properties: id: enum: - complete_results type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationEnrichResults: additionalProperties: false description: Create new results by applying enrichment analysis to existing results. In particular, combines results by transforming a qnode into a set, formed of knodes that share a property or relation more often than expected by chance. properties: id: enum: - enrich_results type: string parameters: $ref: '#/components/schemas/OperationEnrichResults_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationFill: additionalProperties: false description: This operation adds knodes and kedges. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. properties: id: enum: - fill type: string parameters: oneOf: - additionalProperties: false properties: allowlist: description: List of knowledge providers/sources that may be used to provide knowledge. example: - icees items: type: string minLength: 1 type: array qedge_keys: description: A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled. example: - e00 items: type: string type: array type: object - additionalProperties: false properties: denylist: description: List of knowledge providers/sources that may NOT be used to provide knowledge. example: - ctd items: type: string minLength: 1 type: array qedge_keys: description: A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled. example: - e00 items: type: string type: array type: object type: object runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationFilterKgraph: additionalProperties: false description: This operation removes kgraph elements (nodes and/or edges). properties: id: enum: - filter_kgraph type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationFilterKgraphContinuousKedgeAttribute: additionalProperties: false description: This operation removes kgraph edges based on the value of a continuous edge attribute. Edges without the given attribute are left alone. properties: id: enum: - filter_kgraph_continuous_kedge_attribute type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphContinuousKedgeAttribute_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterKgraphDiscreteKedgeAttribute: additionalProperties: false description: This operation removes kgraph edges which have a discrete attribute containing the specified value. Edges without the given attribute are left alone. properties: id: enum: - filter_kgraph_discrete_kedge_attribute type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterKgraphDiscreteKnodeAttribute: additionalProperties: false description: This operation removes kgraph nodes which have a discrete attribute containing the specified value. In TRAPI 1.1+ this will look in the `attribute_type_id` and `original_attribute_name` attribute fields for the attribute name. Node without the given attribute are left alone. Edges connecting to the removed nodes will also be removed. properties: id: enum: - filter_kgraph_discrete_knode_attribute type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphDiscreteKnodeAttribute_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterKgraphOrphans: additionalProperties: false description: This operation removes kgraph elements that are not referenced by any results. properties: id: enum: - filter_kgraph_orphans type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationFilterKgraphPercentile: additionalProperties: false description: This operation removes kgraph edges that have attribute values are below/above the given percentile. properties: id: enum: - filter_kgraph_percentile type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphPercentile_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterKgraphStdDev: additionalProperties: false description: This operation removes kgraph edges that have attribute values are below/above the mean +/- n standard deviations. properties: id: enum: - filter_kgraph_std_dev type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphStdDev_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterKgraphTopN: additionalProperties: false description: This operation removes kgraph edges that have attribute values are below/above the top/bottom n values. properties: id: enum: - filter_kgraph_top_n type: string parameters: $ref: '#/components/schemas/OperationFilterKgraphTopN_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationFilterResults: additionalProperties: false description: This operation allows the TRAPI server to remove elements from the list of results. properties: id: enum: - filter_results type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationFilterResultsTopN: additionalProperties: false description: This operation truncates the results to at most `max_results` that appear in the TRAPI JSON message. properties: id: enum: - filter_results_top_n type: string parameters: $ref: '#/components/schemas/OperationFilterResultsTopN_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationLookup: additionalProperties: false description: This operation adds knodes/kedges and (complete) results. It is equivalent to the workflow fill + bind + complete_results. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. properties: id: enum: - lookup type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationLookupAndScore: additionalProperties: false description: This operation adds knodes/kedges, (complete) results, and scores (to the results). It is equivalent to the workflow fill + bind + complete_results + score. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected. properties: id: enum: - lookup_and_score type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationOverlay: additionalProperties: false description: This operation adds additional qedges and/or kedges and/or result edge bindings. properties: id: enum: - overlay type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationOverlayComputeJaccard: additionalProperties: false description: This operation computes the Jaccard Similarity which measures how many intermediate_node_key nodes are directly connected to both the end_node_keys nodes for all pairs of nodes with corresponding keys. It will then add edges to the knowledge graph along with edge attributes (with the property name jaccard_index) between each start_node_key and object_node_key. A query graph edge will also be added using the key specified by virtual_relation_label. This is used for purposes such as "find me all drugs (start_node_key) that have many proteins (intermediate_node_key) in common with this disease (end_node_key)." This can be used for downstream filtering to concentrate on relevant bioentities. properties: id: enum: - overlay_compute_jaccard type: string parameters: $ref: '#/components/schemas/OperationOverlayComputeJaccard_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationOverlayComputeNgd: additionalProperties: false description: This operation computes the normalized Google distance (co-occurrence frequency) in PubMed abstracts and adds virual edges between qnodes AND/OR knodes AND/OR results edge bindings. If no publications are found infinity is returned. properties: id: enum: - overlay_compute_ngd type: string parameters: $ref: '#/components/schemas/OperationOverlayComputeNgd_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationOverlayConnectKnodes: additionalProperties: false description: Given a TRAPI message, create new kedges between existing knodes. These may be created using arbitrary methods or data sources, though provenance should be attached to the new kedges. Each new kedge is also added to all results containing node bindings to both the subject and object knodes. This may be independent of any qedge connections, i.e. kedges can be created between any nodes in the kgraph. properties: id: enum: - overlay_connect_knodes type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationOverlayFisherExactTest: additionalProperties: false description: Fisher exact test computes the Fisher's Exact Test p-values of the connection between a list of given nodes with specified query id (subject_qnode_key e.g. n01) to their adjacent nodes with specified query id (object_qnode_key e.g. n02) in the message knowledge graph. This information is then added as an edge attribute to a virtual edge which is then added to the query graph and knowledge graph. It can also allow you to filter out the user-defined insignificance of connections based on a specified p-value cutoff or return the top n smallest p-value of connections and only add their corresponding virtual edges to the knowledge graph. properties: id: enum: - overlay_fisher_exact_test type: string parameters: $ref: '#/components/schemas/OperationOverlayFisherExactTest_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationRestate: additionalProperties: false description: This operation modifies the query graph. properties: id: enum: - restate type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationScore: additionalProperties: false description: This operation adds scores to results. properties: id: enum: - score type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationSortResults: additionalProperties: false description: This operation allows the TRAPI server to sort the elements of the list of results. properties: id: enum: - sort_results type: string parameters: {} runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id type: object OperationSortResultsEdgeAttribute: additionalProperties: false description: This operation sorts the results by the given edge attribute. If in ascending order, the minimum value of the results edges with the given attribute will be taken while the maximum will be taken for descending order. If a result has no edges with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value. properties: id: enum: - sort_results_edge_attribute type: string parameters: $ref: '#/components/schemas/OperationSortResultsEdgeAttribute_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationSortResultsNodeAttribute: additionalProperties: false description: This operation sorts the results by the given node attribute. If in ascending order, the minimum value of the results nodes with the given attribute will be taken while the maximum will be taken for descending order. If a result has no nodes with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value. properties: id: enum: - sort_results_node_attribute type: string parameters: $ref: '#/components/schemas/OperationSortResultsNodeAttribute_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationSortResultsScore: additionalProperties: false description: This operation sorts the results by the result score. If `max_results` is given, it truncates the results to at most the given value. properties: id: enum: - sort_results_score type: string parameters: $ref: '#/components/schemas/OperationSortResultsScore_parameters' runner_parameters: oneOf: - properties: allowlist: description: List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array - properties: denylist: description: List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner. example: - infores:aragorn items: type: string minLength: 1 type: array type: object unique: default: true type: boolean required: - id - parameters type: object OperationAnnotateEdges_parameters: properties: attributes: description: A list of attributes to annotate the edges with. If not included then all available data will be annotated. example: - pmids items: type: string title: attributes type: array title: OperationAnnotateEdges_parameters type: object OperationAnnotateNodes_parameters: properties: attributes: description: A list of attributes to annotate the nodes with. If not included then all available data will be annotated. example: - pmids items: type: string title: attributes type: array title: OperationAnnotateNodes_parameters type: object OperationEnrichResults_parameters: properties: pvalue_threshold: default: 0.0000010 description: The cutoff p-value for enrichment. example: 1.0E-7 maximum: 1 minimum: 0 title: pvalue_threshold type: number qnode_keys: description: If specified, then only knodes bound to these qnodes will be examined for enrichment and combination. example: - n01 items: type: string title: qnode_keys type: array title: OperationEnrichResults_parameters type: object OperationFilterKgraphContinuousKedgeAttribute_parameters: properties: edge_attribute: description: The name of the edge attribute to filter on. example: normalized_google_distance title: edge_attribute type: string qedge_keys: description: This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on. example: - e01 items: type: string title: qedge_keys type: array qnode_keys: default: [] description: This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. example: - n01 items: type: string title: qnode_keys type: array remove_above_or_below: description: Indicates whether to remove above or below the given threshold. enum: - above - below title: remove_above_or_below type: string threshold: description: The value to compare attribute values to. example: 1.2 title: threshold type: number required: - edge_attribute - remove_above_or_below - threshold title: OperationFilterKgraphContinuousKedgeAttribute_parameters type: object OperationFilterKgraphDiscreteKedgeAttribute_parameters: properties: edge_attribute: description: The name of the edge attribute to filter on. example: provided_by title: edge_attribute type: string qedge_keys: description: This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on. example: - e01 items: type: string title: qedge_keys type: array qnode_keys: default: [] description: This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed example: - n01 items: type: string title: qnode_keys type: array remove_value: description: The value for which all edges containing this value in the specified edge_attribute should be removed. example: infores:semmeddb title: remove_value required: - edge_attribute - remove_value title: OperationFilterKgraphDiscreteKedgeAttribute_parameters type: object OperationFilterKgraphDiscreteKnodeAttribute_parameters: properties: node_attribute: description: The name of the node attribute to filter on. example: molecule_type title: node_attribute type: string qnode_keys: description: This indicates if you only want to remove nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, all nodes will be considered when filtering. example: - n01 items: type: string title: qnode_keys type: array remove_value: description: The value for which all edges containing this value in the specified edge_attribute should be removed. example: small_molecule title: remove_value required: - node_attribute - remove_value title: OperationFilterKgraphDiscreteKnodeAttribute_parameters type: object OperationFilterKgraphPercentile_parameters: properties: edge_attribute: description: The name of the edge attribute to filter on. example: normalized_google_distance title: edge_attribute type: string qedge_keys: description: This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. example: - e01 items: type: string title: qedge_keys type: array qnode_keys: default: [] description: This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. example: - n01 items: type: string title: qnode_keys type: array remove_above_or_below: default: below description: Indicates whether to remove above or below the given threshold. enum: - above - below title: remove_above_or_below type: string threshold: default: 95 description: The percentile to threshold on. example: 96.8 maximum: 100 minimum: 0 title: threshold type: number required: - edge_attribute title: OperationFilterKgraphPercentile_parameters type: object OperationFilterKgraphStdDev_parameters: properties: edge_attribute: description: The name of the edge attribute to filter on. example: normalized_google_distance title: edge_attribute type: string num_sigma: default: 1 description: The number of standard deviations to threshold on. example: 1.2 minimum: 0 title: num_sigma type: number plus_or_minus_std_dev: default: plus description: Indicate whether or not the threshold should be found using plus or minus the standard deviation. E.g. when plus_or_minus_std_dev is set to plus will set the cutoff for filtering as the mean + num_sigma * std_dev while setting plus_or_minus_std_dev to minus will set the cutoff as the mean - num_sigma * std_dev. enum: - plus - minus title: plus_or_minus_std_dev type: string qedge_keys: description: This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. example: - e01 items: type: string title: qedge_keys type: array qnode_keys: default: [] description: This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. example: - n01 items: type: string title: qnode_keys type: array remove_above_or_below: default: below description: Indictes whether to remove above or below the given threshold. enum: - above - below title: remove_above_or_below type: string required: - edge_attribute title: OperationFilterKgraphStdDev_parameters type: object OperationFilterKgraphTopN_parameters: properties: edge_attribute: description: The name of the edge attribute to filter on. example: normalized_google_distance title: edge_attribute type: string keep_top_or_bottom: default: top description: Indicate whether or not the the top or bottom n values should be kept. enum: - top - bottom title: keep_top_or_bottom type: string max_edges: default: 50 description: The number of edges to keep. example: 10 minimum: 0 title: max_edges type: integer qedge_keys: description: This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on. example: - e01 items: type: string title: qedge_keys type: array qnode_keys: default: [] description: This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed. example: - n01 items: type: string title: qnode_keys type: array required: - edge_attribute title: OperationFilterKgraphTopN_parameters type: object OperationFilterResultsTopN_parameters: properties: max_results: description: The maximum number of results to return. example: 50 minimum: 0 title: max_results type: integer required: - max_results title: OperationFilterResultsTopN_parameters type: object OperationOverlayComputeJaccard_parameters: properties: end_node_keys: description: A list of qnode keys specifying the ending nodes. example: - n0 - n2 items: type: string title: end_node_keys type: array intermediate_node_key: description: A qnode key specifying the intermediate node. example: n1 title: intermediate_node_key type: string virtual_relation_label: description: The key of the query graph edge that corresponds to the knowledge graph edges that were added by this operation. example: J1 title: virtual_relation_label type: string required: - end_node_keys - intermediate_node_key - virtual_relation_label title: OperationOverlayComputeJaccard_parameters type: object OperationOverlayComputeNgd_parameters: properties: qnode_keys: description: A list of qnode keys to overlay pairwise edges onto. Must be be a list of at least 2 valid qnodes. example: - n00 - n01 items: type: string title: qnode_keys type: array virtual_relation_label: description: An label to help identify the virtual edge in the relation field example: NGD1 title: virtual_relation_label type: string required: - qnode_keys - virtual_relation_label title: OperationOverlayComputeNgd_parameters type: object OperationOverlayFisherExactTest_parameters: properties: object_qnode_key: description: A specific object query node id. example: n2 title: object_qnode_key type: string rel_edge_key: description: A specific Qedge id connected to both subject nodes and object nodes in message KG (optional, otherwise all edges connected to both subject nodes and object nodes in message KG are considered). example: e01 title: rel_edge_key type: string subject_qnode_key: description: A specific subject query node id. example: n1 title: subject_qnode_key type: string virtual_relation_label: description: An label to help identify the virtual edge. example: f1 title: virtual_relation_label type: string required: - object_qnode_key - subject_qnode_key - virtual_relation_label title: OperationOverlayFisherExactTest_parameters type: object OperationSortResultsEdgeAttribute_parameters: properties: ascending_or_descending: description: Indicates whether results should be sorted in ascending or descending order. enum: - ascending - descending title: ascending_or_descending type: string edge_attribute: description: The name of the edge attribute to order by. example: normalized_google_distance title: edge_attribute type: string qedge_keys: description: This indicates if you only want to consider edges with specific edge_keys. If not provided or empty, all edges will be looked at. example: - e01 items: type: string title: qedge_keys type: array required: - ascending_or_descending - edge_attribute title: OperationSortResultsEdgeAttribute_parameters type: object OperationSortResultsNodeAttribute_parameters: properties: ascending_or_descending: description: Indicates whether results should be sorted in ascending or descending order. enum: - ascending - descending title: ascending_or_descending type: string node_attribute: description: The name of the node attribute to order by. example: normalized_google_distance title: node_attribute type: string qnode_keys: description: This indicates if you only want to consider nodes with specific node_keys. If not provided or empty, all nodes will be looked at. example: - e01 items: type: string title: qnode_keys type: array required: - ascending_or_descending - node_attribute title: OperationSortResultsNodeAttribute_parameters type: object OperationSortResultsScore_parameters: properties: ascending_or_descending: description: Indicates whether results should be sorted in ascending or descending order. enum: - ascending - descending title: ascending_or_descending type: string required: - ascending_or_descending title: OperationSortResultsScore_parameters type: object