openapi: 3.0.3 info: description: A TRAPI/Reasoner Standard API for BioThings Explorer (BTE) version: 3.0.0 title: BioThings Explorer (BTE) TRAPI contact: email: asu@scripps.edu name: Andrew Su url: https://github.com/andrewsu termsOfService: https://biothings.io/about x-translator: component: ARA team: - Exploring Agent biolink-version: "4.2.2" infores: "infores:biothings-explorer" x-trapi: version: 1.5.0 multicuriequery: false pathfinderquery: true ## dev instance only asyncquery: true operations: ## look at https://standards.ncats.io/operation.json for details. - lookup_and_score ## /query endpoints have a limit of 15 requests/client/min ## /meta_knowledge_graph endpoints have a limit of 30 requests/client/min ## other endpoints don't have rate limits rate_limit: 15 batch_size_limit: 150 test_data_location: default: url: "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/sri-test-bte-ara.json" servers: ## ITRB Production and Test deployments are made by ITRB when we make a change request. ## These deployments use a snapshot of the staging instance. ## ITRB CI / staging deployments are made by our team. ## non-ITRB dev deployments are made by our team. ## We have full control on when / what branches for modules are used - url: https://bte.transltr.io/v1 description: ITRB Production server x-maturity: production - url: https://bte.test.transltr.io/v1 description: ITRB Test server x-maturity: testing - url: https://bte.ci.transltr.io/v1 description: ITRB CI server x-maturity: staging - url: https://api.bte.ncats.io/v1 description: Non-ITRB dev (internal use) x-maturity: development tags: - name: "1.5.0" - name: meta_knowledge_graph - name: query - name: asyncquery - name: asyncquery_status - name: translator - name: trapi - name: biothings ## Note: BTE has custom behavior so DO NOT blindly copy-paste the TRAPI specs / schemas into the document below ## instead go through it and copy-paste in sections as-needed ## examples are using MyVariant-specific query paths: ## copied directly from TRAPI spec /meta_knowledge_graph: get: tags: - meta_knowledge_graph summary: Meta knowledge graph representation of this TRAPI web service. responses: '200': description: >- Returns meta knowledge graph representation of this TRAPI web service. content: application/json: schema: $ref: '#/components/schemas/MetaKnowledgeGraph' ## copied from /meta_knowledge_graph above and modified: BTE-specific endpoint /smartapi/{smartapi_id}/meta_knowledge_graph: get: tags: - meta_knowledge_graph summary: TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation) parameters: - description: >- SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js in: path name: smartapi_id required: true example: 09c8782d9f4027712e65b95424adba79 ## MyVariant schema: type: string responses: '200': description: >- Returns a TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation) content: application/json: schema: $ref: '#/components/schemas/MetaKnowledgeGraph' ## copied from /meta_knowledge_graph above and modified: BTE-specific endpoint /team/{team_name}/meta_knowledge_graph: get: tags: - meta_knowledge_graph summary: TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation) parameters: - description: >- Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry in: path name: team_name required: true example: "Service Provider" schema: type: string enum: - Multiomics Provider - Text Mining Provider - Service Provider responses: '200': description: >- Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation) content: application/json: schema: $ref: '#/components/schemas/MetaKnowledgeGraph' ## modified TRAPI spec: example and BTE-specific parameters, used by developers running local instances of BTE /query: post: tags: - query summary: Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response parameters: - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean - description: Dryrun a pathfinder query (logs the tempalted-queries BTE would make without running them) in: query name: dryrun_pathfinder required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/Query' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. content: application/json: schema: $ref: '#/components/schemas/Response' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## copied from /query above and modified: BTE-specific endpoint /smartapi/{smartapi_id}/query: post: tags: - query summary: Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API parameters: - description: >- SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js in: path name: smartapi_id required: true example: 09c8782d9f4027712e65b95424adba79 ## MyVariant schema: type: string - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/Query' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. content: application/json: schema: $ref: '#/components/schemas/Response' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## copied from /query above and modified: BTE-specific endpoint /team/{team_name}/query: post: tags: - query summary: >- Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name parameters: - description: >- Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry in: path name: team_name required: true example: "Service Provider" schema: type: string enum: - Multiomics Provider - Text Mining Provider - Service Provider - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/Query' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized. content: application/json: schema: $ref: '#/components/schemas/Response' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## modified TRAPI spec: summary sections tell users that AsyncQuery schema was changed to make callback optional /asyncquery: post: tags: - asyncquery summary: >- Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. parameters: - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean - description: Dryrun a pathfinder query (logs the tempalted-queries BTE would make without running them) in: query name: dryrun_pathfinder required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/AsyncQuery' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. content: application/json: schema: $ref: '#/components/schemas/AsyncQueryResponse' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## copied from /asyncquery above and modified: BTE-specific endpoint /smartapi/{smartapi_id}/asyncquery: post: tags: - asyncquery summary: >- This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API. Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. parameters: - description: >- SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js in: path name: smartapi_id required: true example: 09c8782d9f4027712e65b95424adba79 ## MyVariant schema: type: string - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/AsyncQuery' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. content: application/json: schema: $ref: '#/components/schemas/AsyncQueryResponse' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## copied from /asyncquery above and modified: BTE-specific endpoint /team/{team_name}/asyncquery: post: tags: - asyncquery summary: >- This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name. Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. parameters: - description: >- Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry in: path name: team_name required: true example: "Service Provider" schema: type: string enum: - Multiomics Provider - Text Mining Provider - Service Provider - description: Legacy option to explicitly enable/disable caching. in: query name: caching required: false schema: type: boolean - description: Dryrun a query (logs the queries BTE would make without running them) in: query name: dryrun required: false schema: type: boolean requestBody: description: Query information to be submitted required: true content: application/json: schema: $ref: '#/components/schemas/AsyncQuery' ## should use MyVariant to answer this example: message: query_graph: nodes: n0: ids: - "DBSNP:rs121913521" categories: - "biolink:SequenceVariant" n1: categories: - "biolink:Disease" edges: e1: subject: "n0" object: "n1" responses: '200': description: >- The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response. content: application/json: schema: $ref: '#/components/schemas/AsyncQueryResponse' '400': 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). content: application/json: schema: type: string '413': description: >- Payload too large. Indicates that batch size was over the limit specified in x-trapi. content: application/json: schema: type: string '429': description: >- Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi. content: application/json: schema: type: string '500': description: >- Internal server error. content: application/json: schema: type: string '501': description: >- Not implemented. content: application/json: schema: type: string ## custom: removed example so SmartAPI registry uptime check won't fail /asyncquery_status/{job_id}: get: tags: - asyncquery_status summary: >- Retrieve the current status of a previously submitted asyncquery given its job_id operationId: asyncquery_status parameters: - in: path name: job_id description: Identifier of the job for status request # example: rXEOAosN3L required: true schema: type: string - description: >- When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query. If it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). in: query name: log_level required: false schema: type: string enum: - ERROR - WARNING - INFO - DEBUG responses: '200': description: >- Returns the status and current logs of a previously submitted asyncquery. content: application/json: schema: $ref: '#/components/schemas/AsyncQueryStatusResponse' '404': description: job_id not found '501': 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. content: application/json: schema: type: string ## custom endpoint: copied and modified asyncquery_status endpoint spec /asyncquery_response/{job_id}: get: tags: - asyncquery_response summary: >- If the previously submitted asyncquery is still pending/in-progress, this endpoint will return the same response as the asyncquery_status endpoint (status, logs). But if the asyncquery job is finished, the complete TRAPI response to the query will be returned operationId: asyncquery_response parameters: - in: path name: job_id description: Identifier of the job for status request # example: rXEOAosN3L required: true schema: type: string - description: >- When specified, the TRAPI logs returned will be of this level of importance or higher. This setting will override the log_level setting in the job's TRAPI query. If it's not specified, BTE will use the log_level setting in the job's TRAPI query or return all logs (the default). in: query name: log_level required: false schema: type: string enum: - ERROR - WARNING - INFO - DEBUG responses: '200': description: >- Response format depends on status of the job (pending/in-progress vs finished) content: application/json: schema: oneOf: - $ref: '#/components/schemas/AsyncQueryStatusResponse' - $ref: '#/components/schemas/Response' '404': description: job_id not found '501': 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. content: application/json: schema: type: string components: ## look for comments to see parts that have been modified for BTE ## also, many sections have additionalProperties: true ## - Query: comment out workflow.oneOf section since the $ref breaks execution of BTE's api-schema-builder/openapi-validator-middleware ## - AsyncQuery: callback property not required (commented it out of the 'required' field), ## comment out workflow.oneOf section ## - Response: comment out workflow.oneOf section ## - Attribute: comment out type and items. The self-$ref in items breaks BTE, because ## an error occurs in its api-schema-builder/openapi-validator-middleware. ## The type is commented out because there'd be a semantic error for ## specifying an array without items. schemas: Query: 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. x-body-name: request_body type: object properties: message: oneOf: - $ref: '#/components/schemas/Message' nullable: false description: >- The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields. log_level: description: The least critical level of logs to return oneOf: - $ref: '#/components/schemas/LogLevel' nullable: true workflow: description: List of workflow steps to be executed. # oneOf: # - $ref: https://standards.ncats.io/workflow/1.3.5/schema nullable: true submitter: type: string 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 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). additionalProperties: true required: - message AsyncQuery: description: >- The AsyncQuery class is effectively the same as the Query class but it requires a callback property. x-body-name: request_body type: object properties: callback: type: string nullable: false format: uri pattern: ^https?:// 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. message: oneOf: - $ref: '#/components/schemas/Message' nullable: false description: >- The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields. log_level: description: The least critical level of logs to return oneOf: - $ref: '#/components/schemas/LogLevel' nullable: true workflow: description: List of workflow steps to be executed. # oneOf: # - $ref: https://standards.ncats.io/workflow/1.3.5/schema nullable: true submitter: type: string 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 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). additionalProperties: true required: ## BTE does not require the callback property, see the asyncquery ## endpoint summary and 200 response description # - callback - message AsyncQueryResponse: type: object description: >- The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query. properties: status: description: >- One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable type: string example: Accepted nullable: true description: description: >- A brief human-readable description of the result of the async_query submission. type: string example: Async_query has been queued nullable: true 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. type: string example: rXEOAosN3L nullable: false additionalProperties: true required: - job_id AsyncQueryStatusResponse: type: object description: >- The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query. properties: status: description: >- One of a standardized set of short codes: Queued, Running, Completed, Failed type: string example: Running nullable: false description: description: >- A brief human-readable description of the current state or summary of the problem if the status is Failed. type: string example: Callback URL returned 500 nullable: false 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. type: array items: $ref: '#/components/schemas/LogEntry' minItems: 1 nullable: false response_url: description: >- Optional URL that can be queried to restrieve the full TRAPI Response. type: string example: https://arax.ncats.io/api/arax/v1.3/response/116481 nullable: true additionalProperties: true required: - status - description - logs Response: type: object 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. properties: message: description: >- Contains the knowledge of the response (query graph, knowledge graph, and results). oneOf: - $ref: '#/components/schemas/Message' nullable: false status: description: >- One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable type: string example: Success nullable: true description: description: A brief human-readable description of the outcome type: string example: Success. 42 results found. nullable: true logs: description: >- A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. type: array items: $ref: '#/components/schemas/LogEntry' minItems: 0 nullable: false workflow: description: List of workflow steps that were executed. # oneOf: # - $ref: https://standards.ncats.io/workflow/1.3.5/schema nullable: true schema_version: type: string example: 1.4.0 description: Version label of the TRAPI schema used in this document nullable: true biolink_version: type: string example: 3.1.2 description: Version label of the Biolink model used in this document nullable: true additionalProperties: true required: - message Message: 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. type: object 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. type: array items: $ref: '#/components/schemas/Result' nullable: true minItems: 0 query_graph: description: >- QueryGraph object that contains a serialization of a query in the form of a graph oneOf: - $ref: '#/components/schemas/QueryGraph' nullable: true knowledge_graph: description: >- KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message oneOf: - $ref: '#/components/schemas/KnowledgeGraph' nullable: true auxiliary_graphs: type: object description: >- Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key. additionalProperties: $ref: '#/components/schemas/AuxiliaryGraph' nullable: true additionalProperties: false LogEntry: 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. type: object properties: timestamp: type: string format: date-time 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: '2020-09-03T18:13:49+00:00' nullable: false level: oneOf: - $ref: '#/components/schemas/LogLevel' nullable: true code: type: string description: >- One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed nullable: true message: type: string description: A human-readable log message nullable: true additionalProperties: true required: - timestamp - message LogLevel: type: string description: Logging level enum: - ERROR - WARNING - INFO - DEBUG Result: type: object 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 a list of Analysis objects. properties: node_bindings: type: object 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. additionalProperties: type: array items: $ref: '#/components/schemas/NodeBinding' minItems: 1 nullable: false analyses: type: array description: >- The list of all Analysis components that contribute to the result. See below for Analysis components. items: $ref: '#/components/schemas/Analysis' minItems: 0 nullable: false additionalProperties: true required: - node_bindings - analyses NodeBinding: type: object 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: oneOf: - $ref: '#/components/schemas/CURIE' nullable: false description: >- The CURIE of a Node within the Knowledge Graph. query_id: oneOf: - $ref: '#/components/schemas/CURIE' 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. nullable: true attributes: type: array 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' minItems: 0 nullable: false additionalProperties: true required: - id - attributes Analysis: type: object 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: $ref: '#/components/schemas/CURIE' description: The id of the resource generating this Analysis score: type: number format: float example: 163.233 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. nullable: true edge_bindings: type: object 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. additionalProperties: type: array items: $ref: '#/components/schemas/EdgeBinding' support_graphs: type: array 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. nullable: true items: type: string scoring_method: type: string description: >- An identifier and link to an explanation for the method used to generate the score nullable: true attributes: type: array description: >- The attributes of this particular Analysis. items: $ref: '#/components/schemas/Attribute' nullable: true additionalProperties: true required: - resource_id - edge_bindings EdgeBinding: type: object 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: type: string description: The key identifier of a specific KnowledgeGraph Edge. nullable: false attributes: type: array 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' minItems: 0 nullable: false additionalProperties: true required: - id - attributes AuxiliaryGraph: type: object 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: type: array description: >- List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge items: type: string nullable: false minItems: 1 attributes: type: array description: >- Attributes of the Auxiliary Graph items: $ref: '#/components/schemas/Attribute' minItems: 0 nullable: false additionalProperties: true required: - edges - attributes KnowledgeGraph: type: object 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: type: object description: >- Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. additionalProperties: $ref: '#/components/schemas/Node' edges: type: object description: >- Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key. additionalProperties: $ref: '#/components/schemas/Edge' additionalProperties: true required: - nodes - edges QueryGraph: type: object 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: type: object description: >- The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes. additionalProperties: $ref: '#/components/schemas/QNode' edges: type: object 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. additionalProperties: $ref: '#/components/schemas/QEdge' additionalProperties: true required: - nodes - edges QNode: type: object 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: type: array items: $ref: '#/components/schemas/CURIE' minItems: 1 example: ["OMIM:603903"] description: >- A CURIE identifier (or list of identifiers) for this node. The 'ids' field will hold a list of CURIEs only in the case of a BATCH set_interpretation, where each CURIE is queried separately. If a list of queried CURIEs is to be considered as a set (as under a MANY or ALL set_interpretation), the 'ids' field will hold a single id representing this set, and the individual members of this set will be captured in a separate 'member_ids' field. Note that the set id MUST be created as a UUID by the system that defines the queried set, using a centralized nodenorm service. Note also that downstream systems MUST re-use the original set UUID in the messages they create/send, which will facilitate merging or caching operations. nullable: true categories: type: array 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 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 member_ids: type: array description: >- A list of CURIE identifiers for members of a queried set. This field MUST be populated under a set_interpretation of MANY or ALL, when the 'ids' field holds a UUID representing the set itself. This field MUST NOT be used under a set_interpretation of BATCH. nullable: true items: $ref: '#/components/schemas/CURIE' constraints: type: array description: >- A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND) items: $ref: '#/components/schemas/AttributeConstraint' default: [] additionalProperties: true QEdge: type: object 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: type: array 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 subject: type: string example: https://omim.org/entry/603903 description: >- Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge. object: type: string example: https://www.uniprot.org/uniprot/P00738 description: >- Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge. attribute_constraints: type: array description: >- A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND) items: $ref: '#/components/schemas/AttributeConstraint' default: [] qualifier_constraints: type: array 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' default: [] additionalProperties: true required: - subject - object Node: type: object description: >- A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping. properties: name: type: string example: Haptoglobin description: Formal name of the entity nullable: true categories: type: array 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' minItems: 1 nullable: false attributes: type: array description: A list of attributes describing the node items: $ref: '#/components/schemas/Attribute' minItems: 0 nullable: false is_set: type: boolean description: >- Indicates that the node represents a set of entities. If this property is missing or null, it is assumed to be false. nullable: true required: - categories - attributes additionalProperties: false Attribute: type: object 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: $ref: '#/components/schemas/CURIE' description: >- The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge. example: biolink:synonym original_attribute_name: type: string 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 value: description: >- Value of the attribute. May be any data type, including a list. example: 0.000153 value_type_id: oneOf: - $ref: '#/components/schemas/CURIE' 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 attribute_source: type: string 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 value_url: type: string 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 description: type: string description: >- Human-readable description for the attribute and its value. example: Assertion Authored By Dr. Trans L. Ator nullable: true attributes: # type: array 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 required: - attribute_type_id - value additionalProperties: false Edge: type: object 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 oneOf: - $ref: '#/components/schemas/BiolinkPredicate' nullable: false subject: description: >- Corresponds to the map key CURIE of the subject concept node of this relationship edge. example: MONDO:0011382 oneOf: - $ref: '#/components/schemas/CURIE' nullable: false object: description: >- Corresponds to the map key CURIE of the object concept node of this relationship edge. example: UniProtKB:P00738 oneOf: - $ref: '#/components/schemas/CURIE' nullable: false attributes: description: A list of additional attributes for this edge items: $ref: '#/components/schemas/Attribute' nullable: true 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 type: array sources: type: array 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 additionalProperties: false required: - object - predicate - subject - sources Qualifier: additionalProperties: false description: >- An additional nuance attached to an assertion type: object properties: qualifier_type_id: $ref: '#/components/schemas/CURIE' description: >- CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier, biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'. pattern: ^biolink:[a-z][a-z_]*$ example: biolink:subject_aspect_qualifier nullable: false qualifier_value: type: string 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 required: - qualifier_type_id - qualifier_value 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: type: array description: >- A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges. items: $ref: '#/components/schemas/Qualifier' nullable: false required: - qualifier_set type: object BiolinkEntity: description: >- Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name. type: string pattern: ^biolink:[A-Z][a-zA-Z]*$ externalDocs: description: Biolink model entities url: https://biolink.github.io/biolink-model/docs/NamedThing.html example: biolink:PhenotypicFeature 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. type: string pattern: ^biolink:[a-z][a-z_]*$ externalDocs: description: Biolink model predicates url: https://biolink.github.io/biolink-model/docs/related_to.html example: biolink:interacts_with CURIE: type: string 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/ MetaKnowledgeGraph: type: object 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. properties: nodes: type: object 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. additionalProperties: $ref: '#/components/schemas/MetaNode' edges: type: array 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' required: - nodes - edges MetaNode: type: object description: >- Description of a node category provided by this TRAPI web service. properties: id_prefixes: type: array description: >- List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input. items: type: string minItems: 1 example: [CHEMBL.COMPOUND, INCHIKEY] attributes: type: array description: >- Node attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' nullable: true required: - id_prefixes additionalProperties: false MetaEdge: type: object description: >- Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class. properties: subject: $ref: '#/components/schemas/BiolinkEntity' description: >- Subject node category of this relationship edge. example: biolink:ChemicalEntity predicate: $ref: '#/components/schemas/BiolinkPredicate' description: >- Biolink relationship between the subject and object categories. example: biolink:affects object: $ref: '#/components/schemas/BiolinkEntity' description: >- Object node category of this relationship edge. example: biolink:Protein 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 type: array attributes: type: array description: >- Edge attributes provided by this TRAPI web service. items: $ref: '#/components/schemas/MetaAttribute' nullable: true qualifiers: description: >- Qualifiers that are possible to be found on this edge type. items: $ref: '#/components/schemas/MetaQualifier' nullable: true type: array association: description: >- The Biolink association type (entity) that this edge represents. Associations are classes in Biolink that represent a relationship between two entities. For example, the association 'gene interacts with gene' is represented by the Biolink class, 'biolink:GeneToGeneAssociation'. If association is filled out, then the testing harness can help validate that the qualifiers are being used correctly. example: 'biolink:ChemicalToGeneAssociation' $ref: '#/components/schemas/BiolinkEntity' required: - subject - predicate - object additionalProperties: false MetaQualifier: type: object properties: qualifier_type_id: $ref: '#/components/schemas/CURIE' description: >- The CURIE of the qualifier type. example: biolink:subject_aspect_qualifier nullable: false applicable_values: type: array description: >- The list of values that are possible for this qualifier. items: type: string example: [expression, activity, abundance, degradation] required: - qualifier_type_id MetaAttribute: type: object properties: attribute_type_id: $ref: '#/components/schemas/CURIE' description: >- Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot) example: biolink:p_value attribute_source: type: string description: >- Source of an attribute provided by this TRAPI web service. example: infores:chembl nullable: true original_attribute_names: type: array items: type: string description: >- Names of an the attribute as provided by the source. nullable: true minItems: 1 constraint_use: type: boolean description: >- Indicates whether this attribute can be used as a query constraint. default: false constraint_name: type: string description: >- Human-readable name or label for the constraint concept. Required whenever constraint_use is true. example: p-value nullable: true required: - attribute_type_id AttributeConstraint: type: object description: >- Generic query constraint for a query node or query edge properties: id: oneOf: - $ref: '#/components/schemas/CURIE' 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 name: type: string 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 not: type: boolean default: false operator: type: string 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 - === value: example: 57.0 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. unit_id: example: UO:0000222 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. nullable: true unit_name: example: kilodalton 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. nullable: true required: - name - id - operator - value additionalProperties: false RetrievalSource: type: object 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: $ref: '#/components/schemas/CURIE' description: >- The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. example: infores:drugbank nullable: false resource_role: $ref: '#/components/schemas/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. upstream_resource_ids: type: array nullable: true items: $ref: '#/components/schemas/CURIE' 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"] source_record_urls: type: array nullable: true items: type: string 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] required: - resource_id - resource_role additionalProperties: true ResourceRoleEnum: type: string 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