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If not specified in the request, this will start at the beginning of the results.","in":"query","name":"offset","schema":{"type":"string"}},{"description":"Amount of records to return in a given page.","in":"query","name":"limit","schema":{"default":1000,"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Tool"},"type":"array"}}},"description":"An array of Tools that match the filter."}},"security":[{"BEARER":[]}],"summary":"List all tools","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}":{"get":{"description":"This endpoint returns one specific tool (which has ToolVersions nested inside it).","operationId":"toolsIdGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Tool"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Tool"}}},"description":"A tool."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be found."}},"security":[{"BEARER":[]}],"summary":"List one specific tool, acts as an anchor for self references","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions":{"get":{"description":"Returns all versions of the specified tool.","operationId":"toolsIdVersionsGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersion"},"type":"array"}}},"description":"An array of tool versions."}},"security":[{"BEARER":[]}],"summary":"List versions of a tool","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/containerfile":{"get":{"description":"Returns the container specifications(s) for the specified image. 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We recommend that versions use semantic versioning https://semver.org/spec/v2.0.0.html  (For example, `1.0.0` instead of `develop`)","in":"path","name":"version_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/FileWrapper"},"type":"array"}}},"description":"The tool payload."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"There are no container specifications for this tool."}},"security":[{"BEARER":[]}],"summary":"Get the container specification(s) for the specified image.","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}":{"get":{"description":"This endpoint returns one specific tool version.","operationId":"toolsIdVersionsVersionIdGet","parameters":[{"description":"A unique identifier of the tool, scoped to this registry, for example `123456`.","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"An identifier of the tool version, scoped to this registry, for example `v1`. 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Unencoded paths such 'sampleDirectory/foo.cwl' should also be allowed.","in":"path","name":"relative_path","required":true,"schema":{"pattern":".+","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/FileWrapper"}},"text/plain":{"schema":{"$ref":"#/components/schemas/FileWrapper"}}},"description":"The tool descriptor."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}},"text/plain":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":"The tool can not be output in the specified type."}},"security":[{"BEARER":[]}],"summary":"Get additional tool descriptor files relative to the main file","tags":["GA4GHV20"]}},"/ga4gh/trs/v2/tools/{id}/versions/{version_id}/{type}/files":{"get":{"description":"Get a list of objects that contain the relative path and file type. 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","operationId":"toolsGet_1","parameters":[{"in":"query","name":"id","schema":{"type":"string"}},{"in":"query","name":"alias","schema":{"type":"string"}},{"in":"query","name":"registry","schema":{"type":"string"}},{"in":"query","name":"organization","schema":{"type":"string"}},{"in":"query","name":"name","schema":{"type":"string"}},{"in":"query","name":"toolname","schema":{"type":"string"}},{"in":"query","name":"description","schema":{"type":"string"}},{"in":"query","name":"author","schema":{"type":"string"}},{"in":"query","name":"checker","schema":{"type":"boolean"}},{"in":"query","name":"offset","schema":{"type":"string"}},{"in":"query","name":"limit","schema":{"default":1000,"format":"int32","type":"integer"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolV20beta"},"type":"array"}}},"description":"An array of Tools that match the filter."}},"summary":"List all tools","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}":{"get":{"description":"This endpoint returns one specific tool (which has ToolVersions nested inside it)","operationId":"toolsIdGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ToolV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ToolV20beta"}}},"description":"A tool."},"404":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}},"text/plain":{"schema":{"$ref":"#/components/schemas/ErrorV20beta"}}},"description":"The tool can not be found."}},"summary":"List one specific tool, acts as an anchor for self references","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions":{"get":{"description":"Returns all versions of the specified tool","operationId":"toolsIdVersionsGet_1","parameters":[{"in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersionV20beta"},"type":"array"}},"text/plain":{"schema":{"items":{"$ref":"#/components/schemas/ToolVersionV20beta"},"type":"array"}}},"description":"An array of tool versions"}},"summary":"List versions of a tool","tags":["GA4GHV20BETA"]}},"/api/ga4gh/v2/tools/{id}/versions/{version_id}/containerfile":{"get":{"description":"Returns the container specifications(s) for the specified image. 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metadata (CWL and Dockerfile))","name":"containers"},{"description":"List and modify tags for containers","name":"containertags"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [1.0.0](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/1.0.0) and is considered final (not subject to change)","name":"GA4GHV1"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [2.0.0-beta.2](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/2.0.0-beta.2) . Integrators are welcome to use these endpoints but they are subject to change based on community input.","name":"GA4GHV20BETA"},{"description":"A curated subset of resources proposed as a common standard for tool repositories. Implements TRS [2.0.1](https://github.com/ga4gh/tool-registry-service-schemas/releases/tag/2.0.1).","name":"GA4GHV20"},{"description":"Optional experimental extensions of the GA4GH API","name":"extendedGA4GH"},{"description":"List, modify, refresh, and delete tokens for external services","name":"tokens"},{"description":"List and register workflows in the dockstore (CWL, Nextflow, WDL)","name":"workflows"},{"description":"Interactions with the Dockstore-support's ToolTester application","name":"toolTester"},{"description":"List and modify notifications for users of Dockstore","name":"curation"},{"description":"Created and modify hosted entries in the dockstore","name":"hosted"},{"description":"List, modify, and manage end users of the dockstore","name":"users"},{"description":"Information about Dockstore like RSS, sitemap, lists of dependencies, etc.","name":"metadata"},{"description":"Query lambda events triggered by GitHub Apps","name":"lambdaEvents"}]},{"components":{"schemas":{"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":{"attributes":{"description":"The attributes of this particular Analysis.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edge_bindings":{"additionalProperties":{"items":{"$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"},"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The id of the resource generating this Analysis"},"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"},"scoring_method":{"description":"An identifier and link to an explanation for the method used to generate the score","nullable":true,"type":"string"},"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"}},"required":["resource_id","edge_bindings"],"type":"object"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"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"},"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","nullable":false,"pattern":"^https?://","type":"string"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"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.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"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.","properties":{"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"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","properties":{"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":{"$ref":"#/components/schemas/LogEntry"},"minItems":1,"nullable":false,"type":"array"},"response_url":{"description":"Optional URL that can be queried to restrieve the full TRAPI Response.","example":"https://arax.ncats.io/api/arax/v1.3/response/116481","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes: Queued, Running, Completed, Failed","example":"Running","nullable":false,"type":"string"}},"required":["status","description","logs"],"type":"object"},"Attribute":{"additionalProperties":false,"description":"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with sub-attributes (for example to provide confidence intervals on a value).","properties":{"attribute_source":{"description":"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.","example":"UniProtKB","nullable":true,"type":"string"},"attribute_type_id":{"$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"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"type":"string"},"original_attribute_name":{"description":"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.","example":"p-value","nullable":true,"type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153},"value_type_id":{"description":"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_1187","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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,"type":"string"}},"required":["attribute_type_id","value"],"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"}]},"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","type":"string"},"not":{"default":false,"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","==="],"type":"string"},"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},"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},"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}},"required":["name","id","operator","value"],"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":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"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"}},"required":["edges","attributes"],"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]*$","type":"string"},"BiolinkPredicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","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/"},"type":"string"},"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":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"object":{"description":"Corresponds to the map key CURIE of the object concept node of this relationship edge.","example":"UniProtKB:P00738","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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":[{"$ref":"#/components/schemas/BiolinkPredicate"}]},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"type":"array"},"sources":{"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":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"type":"array"},"subject":{"description":"Corresponds to the map key CURIE of the subject concept node of this relationship edge.","example":"MONDO:0011382","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["object","predicate","subject","sources"],"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":{"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":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","nullable":false,"type":"string"}},"required":["id","attributes"],"type":"object"},"KnowledgeGraph":{"additionalProperties":true,"description":"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$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"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["nodes","edges"],"type":"object"},"LogEntry":{"additionalProperties":true,"description":"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.","properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"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":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["timestamp","message"],"type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"},"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.","properties":{"auxiliary_graphs":{"additionalProperties":{"$ref":"#/components/schemas/AuxiliaryGraph"},"description":"Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key.","nullable":true,"type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"results":{"description":"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"minItems":0,"nullable":true,"type":"array"}},"type":"object"},"MetaAttribute":{"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)","example":"biolink:p_value"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"}},"required":["attribute_type_id"],"type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","properties":{"association":{"$ref":"#/components/schemas/BiolinkEntity","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"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"knowledge_types":{"description":"A list of knowledge_types that are supported by the service. If the knowledge_types is null, this means that only 'lookup' is supported. Currently allowed values are 'lookup' or 'inferred'.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"},"object":{"$ref":"#/components/schemas/BiolinkEntity","description":"Object node category of this relationship edge.","example":"biolink:Protein"},"predicate":{"$ref":"#/components/schemas/BiolinkPredicate","description":"Biolink relationship between the subject and object categories.","example":"biolink:affects"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"type":"array"},"subject":{"$ref":"#/components/schemas/BiolinkEntity","description":"Subject node category of this relationship edge.","example":"biolink:ChemicalEntity"}},"required":["subject","predicate","object"],"type":"object"},"MetaKnowledgeGraph":{"description":"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.","properties":{"edges":{"description":"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.","items":{"$ref":"#/components/schemas/MetaEdge"},"type":"array"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/MetaNode"},"description":"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.","type":"object"}},"required":["nodes","edges"],"type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"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,"type":"array"}},"required":["id_prefixes"],"type":"object"},"MetaQualifier":{"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":["expression","activity","abundance","degradation"],"type":"string"},"type":"array"},"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of the qualifier type.","example":"biolink:subject_aspect_qualifier","nullable":false}},"required":["qualifier_type_id"],"type":"object"},"Node":{"additionalProperties":false,"description":"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"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":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":false,"type":"array"},"is_set":{"description":"Indicates that the node represents a set of entities. If this property is missing or null, it is assumed to be false.","nullable":true,"type":"boolean"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"required":["categories","attributes"],"type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id","attributes"],"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":{"attribute_constraints":{"default":[],"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":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"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":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"subject":{"description":"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.","example":"https://omim.org/entry/603903","type":"string"}},"required":["subject","object"],"type":"object"},"QNode":{"additionalProperties":true,"description":"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"categories":{"description":"These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"A CURIE identifier (or list of identifiers) for this node.  The 'ids' field will hold a list of CURIEs only in the case of a BATCH set_interpretation, where each CURIE is queried  separately. If a list of queried CURIEs is to be considered as a   set (as under a MANY or ALL set_interpretation), the 'ids' field  will hold a single id representing this set, and the individual members  of this set will be captured in a separate 'member_ids' field.  Note that the set id MUST be created as a UUID by the system that  defines the queried set, using a centralized nodenorm service.  Note also that downstream systems MUST re-use the original set UUID  in the messages they create/send, which will facilitate merging or  caching operations.","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"member_ids":{"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.","items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$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'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a \"ChemicalX - affects - ?Gene\" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type \"biolink:object_aspect_qualifier\" with a qualifier_value of \"expression\".","properties":{"qualifier_set":{"description":"A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"type":"object"},"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.","properties":{"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"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"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"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$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"},"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"}},"required":["nodes","edges"],"type":"object"},"QueryOptions":{"description":"Additional query options that apply to COHD","properties":{"biolink_only":{"description":"Whether to only include nodes in the knowledge graph and results that are Biolink compliant (as defined by ontology_targets). Default: true","example":true,"type":"boolean"},"confidence_interval":{"description":"Criteria that the results are significant to the specified criteria level. This only applies when the method is 'obsExpRatio'. Default: not required.","example":0.99,"type":"number"},"dataset_id":{"description":"The COHD dataset to query","example":3,"type":"integer"},"local_oxo":{"description":"Whether to use the local implementation of OxO or the real implementation of OxO. Note, the local OxO implementation may contain outdated definitions and xrefs but runs faster. The real OxO has the most updated definitions and xrefs, but is slower (~1-2 seconds/concept). Default: true","example":false,"type":"boolean"},"max_results":{"description":"The maximum number of results to be returned.","example":10,"type":"integer"},"min_cooccurrence":{"description":"Criteria that the results have a minimum co-occurrence count. Default: not required.","example":50,"type":"integer"},"threshold":{"description":"Criteria threshold to apply to the association metric. chiSquare: p-value < threshold. obsExpRatio: abs(ln_ratio) >= threshold. relativeFrequency: relative_frequency >= threshold.","example":0.5,"type":"number"}},"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"],"type":"string"},"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.","properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","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"},"minItems":0,"nullable":false,"type":"array"},"message":{"description":"Contains the knowledge of the response (query graph, knowledge graph, and results).","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"schema_version":{"description":"Version label of the TRAPI schema used in this document","example":"1.4.0","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps that were executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object"},"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 a list of Analysis objects.","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"minItems":0,"nullable":false,"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"minItems":1,"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.","nullable":false,"type":"object"}},"required":["node_bindings","analyses"],"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":{"$ref":"#/components/schemas/CURIE","description":"The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.","example":"infores:drugbank","nullable":false},"resource_role":{"$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."},"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"},"nullable":true,"type":"array"},"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"},"nullable":true,"type":"array"}},"required":["resource_id","resource_role"],"type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"info":{"contact":{"email":"ct2865@cumc.columbia.edu","name":"Casey Ta","url":"http://chunhualab.org/","x-role":"responsible developer"},"description":"The Columbia Open Health Data (COHD) TRAPI API provides access to associations derived from clinical data between\ndiseases, phenotypic features, drugs, procedures, and demographic features.\n\nCOHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/)\nas a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/),\n[Tatonetti Lab](http://tatonettilab.org/), and the\n[NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program.\nThis work was supported in part by grants: NCATS OT2TR003434, NCATS OT3TR002027, NLM R01LM009886-08A1, and\nNIGMS R01GM107145.\n\nThe following external resources may be useful:\n[OHDSI](https://www.ohdsi.org/)\n[OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki)\n[Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy)\n[Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy,\nconcept sets)\n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://cohd.nsides.io/terms/","title":"COHD TRAPI","version":"6.5.0","x-translator":{"biolink-version":"4.1.6","component":"KP","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/"},"infores":"infores:cohd","team":["Clinical Data Provider"]},"x-trapi":{"asyncquery":false,"batch_size_limit":100,"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/"},"multicuriequery":true,"operations":["lookup_and_score"],"pathfinderquery":false,"rate_limit":10,"test_data_location":{"default":{"url":"https://raw.githubusercontent.com/WengLab-InformaticsResearch/cohd_api/master/cohd/translator/sri_testing_triples.json"}},"version":"1.5.0"}},"openapi":"3.0.1","paths":{"/meta_knowledge_graph":{"get":{"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"]}},"/query":{"post":{"description":"Query the COHD API following the [NCATS Translator Reasoner Standard API](https://github.com/NCATSTranslator/ReasonerAPI). Only single hop queries are supported. See the example query_graph.\nThe COHD data are natively represented using OMOP. COHD will attempt to map between Biolink and OMOP both in the input and response.","operationId":"query","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:9053\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Procedure\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"predicates\": [\"biolink:correlated_with\"],\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  },\n  \"query_options\": {\n    \"dataset_id\": 3,\n    \"confidence_interval\": 0.99,\n    \"min_cooccurrence\": 50,\n    \"threshold\": 0.5,\n    \"local_oxo\": true,\n    \"max_results\": 50,\n    \"biolink_only\": true\n  }\n}","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":"Query COHD following NCATS Translator Reasoner Standard API. Initiate a query and wait to receive a Response","tags":["query"]}}},"servers":[{"description":"COHD ITRB Production Server","url":"https://cohd-api.transltr.io/api","x-maturity":"production"},{"description":"COHD ITRB Test Server","url":"https://cohd-api.test.transltr.io/api","x-maturity":"testing"},{"description":"COHD ITRB CI Server","url":"https://cohd-api.ci.transltr.io/api","x-maturity":"staging"},{"description":"COHD Development Server","url":"https://cohd.io/api","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, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"basePath":"/v2","definitions":{"ApiResponse":{"properties":{"code":{"format":"int32","type":"integer"},"message":{"type":"string"},"type":{"type":"string"}},"type":"object"},"Category":{"properties":{"id":{"format":"int64","type":"integer"},"name":{"type":"string"}},"type":"object","xml":{"name":"Category"}},"Order":{"properties":{"complete":{"default":false,"type":"boolean"},"id":{"format":"int64","type":"integer"},"petId":{"format":"int64","type":"integer"},"quantity":{"format":"int32","type":"integer"},"shipDate":{"format":"date-time","type":"string"},"status":{"description":"Order Status","enum":["placed","approved","delivered"],"type":"string"}},"type":"object","xml":{"name":"Order"}},"Pet":{"properties":{"category":{"$ref":"#/definitions/Category"},"id":{"format":"int64","type":"integer"},"name":{"example":"doggie","type":"string"},"photoUrls":{"items":{"type":"string"},"type":"array","xml":{"name":"photoUrl","wrapped":true}},"status":{"description":"pet status in the store","enum":["available","pending","sold"],"type":"string"},"tags":{"items":{"$ref":"#/definitions/Tag"},"type":"array","xml":{"name":"tag","wrapped":true}}},"required":["name","photoUrls"],"type":"object","xml":{"name":"Pet"}},"Tag":{"properties":{"id":{"format":"int64","type":"integer"},"name":{"type":"string"}},"type":"object","xml":{"name":"Tag"}},"User":{"properties":{"email":{"type":"string"},"firstName":{"type":"string"},"id":{"format":"int64","type":"integer"},"lastName":{"type":"string"},"password":{"type":"string"},"phone":{"type":"string"},"userStatus":{"description":"User Status","format":"int32","type":"integer"},"username":{"type":"string"}},"type":"object","xml":{"name":"User"}}},"externalDocs":{"description":"Find out more about Swagger","url":"http://swagger.io"},"host":"petstore.fancy.io","info":{"contact":{"email":"apiteam@fancy.io","x-chat":"https://de.wikipedia.org/wiki/Chat","x-issueTracker":"https://www.atlassian.com/de/software/jira"},"description":"This is a sample server Petstore server.","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://fancy.io/terms/","title":"Fancy Petstore","version":"1.0.0"},"paths":{"/pet":{"post":{"consumes":["application/json","application/xml"],"description":"","operationId":"addPet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"405":{"description":"Invalid input"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Add a new pet to the store","tags":["pet"]},"put":{"consumes":["application/json","application/xml"],"description":"","operationId":"updatePet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"},"405":{"description":"Validation exception"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Update an existing pet","tags":["pet"]}},"/pet/findByStatus":{"get":{"description":"Multiple status values can be provided with comma separated strings","operationId":"findPetsByStatus","parameters":[{"collectionFormat":"multi","description":"Status values that need to be considered for filter","in":"query","items":{"default":"available","enum":["available","pending","sold"],"type":"string"},"name":"status","required":true,"type":"array"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"items":{"$ref":"#/definitions/Pet"},"type":"array"}},"400":{"description":"Invalid status value"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Finds Pets by status","tags":["pet"]}},"/pet/findByTags":{"get":{"deprecated":true,"description":"Muliple tags can be provided with comma separated strings. Use         tag1, tag2, tag3 for testing.","operationId":"findPetsByTags","parameters":[{"collectionFormat":"multi","description":"Tags to filter by","in":"query","items":{"type":"string"},"name":"tags","required":true,"type":"array"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"items":{"$ref":"#/definitions/Pet"},"type":"array"}},"400":{"description":"Invalid tag value"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Finds Pets by tags","tags":["pet"]}},"/pet/{petId}":{"delete":{"description":"","operationId":"deletePet","parameters":[{"in":"header","name":"api_key","required":false,"type":"string"},{"description":"Pet id to delete","format":"int64","in":"path","name":"petId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Deletes a pet","tags":["pet"]},"get":{"description":"Returns a single pet","operationId":"getPetById","parameters":[{"description":"ID of pet to return","format":"int64","in":"path","name":"petId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Pet"}},"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"}},"security":[{"api_key":[]}],"summary":"Find pet by ID","tags":["pet"]},"post":{"consumes":["application/x-www-form-urlencoded"],"description":"","operationId":"updatePetWithForm","parameters":[{"description":"ID of pet that needs to be updated","format":"int64","in":"path","name":"petId","required":true,"type":"integer"},{"description":"Updated name of the pet","in":"formData","name":"name","required":false,"type":"string"},{"description":"Updated status of the pet","in":"formData","name":"status","required":false,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"405":{"description":"Invalid input"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Updates a pet in the store with form data","tags":["pet"]}},"/pet/{petId}/uploadImage":{"post":{"consumes":["multipart/form-data"],"description":"","operationId":"uploadFile","parameters":[{"description":"ID of pet to update","format":"int64","in":"path","name":"petId","required":true,"type":"integer"},{"description":"Additional data to pass to server","in":"formData","name":"additionalMetadata","required":false,"type":"string"},{"description":"file to upload","in":"formData","name":"file","required":false,"type":"file"}],"produces":["application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/ApiResponse"}}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"uploads an image","tags":["pet"]}},"/store/inventory":{"get":{"description":"Returns a map of status codes to quantities","operationId":"getInventory","parameters":[],"produces":["application/json"],"responses":{"200":{"description":"successful operation","schema":{"additionalProperties":{"format":"int32","type":"integer"},"type":"object"}}},"security":[{"api_key":[]}],"summary":"Returns pet inventories by status","tags":["store"]}},"/store/order":{"post":{"description":"","operationId":"placeOrder","parameters":[{"description":"order placed for purchasing the pet","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Order"}}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Order"}},"400":{"description":"Invalid Order"}},"summary":"Place an order for a pet","tags":["store"]}},"/store/order/{orderId}":{"delete":{"description":"For valid response try integer IDs with positive integer value.         Negative or non-integer values will generate API errors","operationId":"deleteOrder","parameters":[{"description":"ID of the order that needs to be deleted","format":"int64","in":"path","minimum":1.0,"name":"orderId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Order not found"}},"summary":"Delete purchase order by ID","tags":["store"]},"get":{"description":"For valid response try integer IDs with value >= 1 and <= 10.         Other values will generated exceptions","operationId":"getOrderById","parameters":[{"description":"ID of pet that needs to be fetched","format":"int64","in":"path","maximum":10.0,"minimum":1.0,"name":"orderId","required":true,"type":"integer"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/Order"}},"400":{"description":"Invalid ID supplied"},"404":{"description":"Order not found"}},"summary":"Find purchase order by ID","tags":["store"]}},"/user":{"post":{"description":"This can only be done by the logged in user.","operationId":"createUser","parameters":[{"description":"Created user object","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/User"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Create user","tags":["user"]}},"/user/createWithArray":{"post":{"description":"","operationId":"createUsersWithArrayInput","parameters":[{"description":"List of user object","in":"body","name":"body","required":true,"schema":{"items":{"$ref":"#/definitions/User"},"type":"array"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Creates list of users with given input array","tags":["user"]}},"/user/createWithList":{"post":{"description":"","operationId":"createUsersWithListInput","parameters":[{"description":"List of user object","in":"body","name":"body","required":true,"schema":{"items":{"$ref":"#/definitions/User"},"type":"array"}}],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Creates list of users with given input array","tags":["user"]}},"/user/login":{"get":{"description":"","operationId":"loginUser","parameters":[{"description":"The user name for login","in":"query","name":"username","required":true,"type":"string"},{"description":"The password for login in clear text","in":"query","name":"password","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","headers":{"X-Expires-After":{"description":"date in UTC when token expires","format":"date-time","type":"string"},"X-Rate-Limit":{"description":"calls per hour allowed by the user","format":"int32","type":"integer"}},"schema":{"type":"string"}},"400":{"description":"Invalid username/password supplied"}},"summary":"Logs user into the system","tags":["user"]}},"/user/logout":{"get":{"description":"","operationId":"logoutUser","parameters":[],"produces":["application/xml","application/json"],"responses":{"default":{"description":"successful operation"}},"summary":"Logs out current logged in user session","tags":["user"]}},"/user/{username}":{"delete":{"description":"This can only be done by the logged in user.","operationId":"deleteUser","parameters":[{"description":"The name that needs to be deleted","in":"path","name":"username","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid username supplied"},"404":{"description":"User not found"}},"summary":"Delete user","tags":["user"]},"get":{"description":"","operationId":"getUserByName","parameters":[{"description":"The name that needs to be fetched. Use user1 for testing. ","in":"path","name":"username","required":true,"type":"string"}],"produces":["application/xml","application/json"],"responses":{"200":{"description":"successful operation","schema":{"$ref":"#/definitions/User"}},"400":{"description":"Invalid username supplied"},"404":{"description":"User not found"}},"summary":"Get user by user name","tags":["user"]},"put":{"description":"This can only be done by the logged in user.","operationId":"updateUser","parameters":[{"description":"name that need to be updated","in":"path","name":"username","required":true,"type":"string"},{"description":"Updated user object","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/User"}}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid user supplied"},"404":{"description":"User not found"}},"summary":"Updated user","tags":["user"]}}},"schemes":["https","http"],"securityDefinitions":{"api_key":{"in":"header","name":"api_key","type":"apiKey"},"petstore_auth":{"authorizationUrl":"http://petstore.swagger.io/oauth/dialog","flow":"implicit","scopes":{"read:pets":"read your pets","write:pets":"modify pets in your account"},"type":"oauth2"}},"swagger":"2.0","tags":[{"description":"Everything about your Pets","externalDocs":{"description":"Find out more","url":"http://fancy.io"},"name":"pet"},{"description":"Access to Petstore orders","name":"store"},{"description":"Operations about user","externalDocs":{"description":"Find out more about our fancy store","url":"http://fancy.io"},"name":"user"}],"x-externalServices":[{"description":"Pact Broker","url":"https://github.com/pact-foundation/pact_broker"},{"description":"Dynatrace","url":"https://www.dynatrace.de/"}]},{"components":{"schemas":{"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":{"attributes":{"description":"The attributes of this particular Analysis.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edge_bindings":{"additionalProperties":{"items":{"$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"},"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"},"scoring_method":{"description":"An identifier and link to an explanation for the method used to generate the score","nullable":true,"type":"string"},"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"}},"required":["edge_bindings","resource_id"],"title":"Analysis","type":"object"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"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"},"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"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"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"},"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"}},"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":{"description":"Async_query has been queued","job_id":"rXEOAosN3L","status":"Accepted"},"properties":{"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"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"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":"2020-09-03T18:13:49+00:00"},{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"}],"response_url":"https://arax.ncats.io/api/arax/v1.3/response/116481","status":"Running"},"properties":{"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"},"status":{"description":"One of a standardized set of short codes: Queued, Running, Completed, Failed","example":"Running","nullable":false,"type":"string"}},"required":["description","logs","status"],"title":"AsyncQueryStatusResponse","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_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"},"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"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"title":"description","type":"string"},"original_attribute_name":{"description":"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.","example":"p-value","nullable":true,"title":"original_attribute_name","type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153,"title":"value"},"value_type_id":{"description":"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_1187","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"value_type_id"},"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"}},"required":["attribute_type_id","value"],"title":"Attribute","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"},"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"},"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"}},"required":["id","name","operator","value"],"title":"AttributeConstraint","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":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"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"}},"required":["edges"],"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"},"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":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"object":{"description":"Corresponds to the map key CURIE of the object concept node of this relationship edge.","example":"UniProtKB:P00738","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"object"},"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":[{"$ref":"#/components/schemas/BiolinkPredicate"}],"title":"predicate"},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$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":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"title":"sources","type":"array"},"subject":{"description":"Corresponds to the map key CURIE of the subject concept node of this relationship edge.","example":"MONDO:0011382","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"subject"}},"required":["object","predicate","sources","subject"],"title":"Edge","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":{"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":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","type":"string"}},"required":["id"],"title":"EdgeBinding","type":"object"},"EntityQuery":{"example":{"format":"format","terms":["terms","terms"]},"properties":{"format":{"description":"Format of the response (full or compact)","title":"format","type":"string"},"terms":{"description":"List of term strings to search for","items":{"type":"string"},"title":"terms","type":"array"}},"title":"EntityQuery","type":"object"},"KnowledgeGraph":{"additionalProperties":true,"description":"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$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"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["edges","nodes"],"type":"object","x-nullable":true},"LogEntry":{"additionalProperties":true,"description":"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.","example":{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},"properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"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":"2020-09-03T18:13:49+00:00","format":"date-time","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},"MeshNgdResponse":{"example":{"message":"Term 1 'malria' not found in MeSH","result_code":"TermNotFound","value":0.714},"properties":{"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"},"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"},"value":{"description":"Calculated Normalized Google Distance for the two supplied terms","example":0.714,"format":"float","title":"value","type":"number"}},"title":"MeshNgdResponse","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":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"properties":{"auxiliary_graphs":{"additionalProperties":{"$ref":"#/components/schemas/AuxiliaryGraph"},"description":"Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key.","type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"results":{"description":"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\nif present, MAY be used to infer result rankings. If Results are\nnot expected (such as for a query Message), this property SHOULD\nbe null or absent. If Results are expected (such as for a response\nMessage) and no Results are available, this property SHOULD be an\narray with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"nullable":true,"type":"array"}},"title":"Message","type":"object"},"MetaAttribute":{"example":{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"title":"attribute_source","type":"string"},"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"},"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"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","title":"constraint_use","type":"boolean"},"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"}},"required":["attribute_type_id"],"title":"MetaAttribute","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":{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","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"}],"subject":"biolink:PhenotypicFeature"},"properties":{"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]*$","title":"BiolinkEntity","type":"string"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"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"},"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]*$","title":"BiolinkEntity","type":"string"},"predicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","title":"BiolinkPredicate","type":"string"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"title":"qualifiers","type":"array"},"subject":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"}},"required":["object","predicate","subject"],"title":"MetaEdge","type":"object"},"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":{"edges":[{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","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"}],"subject":"biolink:PhenotypicFeature"},{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","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"}],"subject":"biolink:PhenotypicFeature"}],"nodes":{"key":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]}}},"properties":{"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":{"$ref":"#/components/schemas/MetaEdge"},"title":"edges","type":"array"},"nodes":{"additionalProperties":{"$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"}},"required":["edges","nodes"],"title":"MetaKnowledgeGraph","type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","example":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]},"properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"title":"id_prefixes","type":"array"}},"required":["id_prefixes"],"title":"MetaNode","type":"object"},"MetaQualifier":{"example":{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":"[\"expression\",\"activity\",\"abundance\",\"degradation\"]","type":"string"},"title":"applicable_values","type":"array"},"qualifier_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"}},"required":["qualifier_type_id"],"title":"MetaQualifier","type":"object"},"Node":{"additionalProperties":false,"description":"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"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":{"$ref":"#/components/schemas/BiolinkEntity"},"nullable":true,"title":"categories","type":"array"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"title":"name","type":"string"}},"title":"Node","type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id"],"title":"NodeBinding","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":{"$ref":"#/components/schemas/OperationAnnotateEdges_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationAnnotateEdges_parameters":{"properties":{"attributes":{"description":"A list of attributes to annotate the edges with. If not included then all available data will be annotated.","example":["pmids"],"items":{"type":"string"},"title":"attributes","type":"array"}},"title":"OperationAnnotateEdges_parameters","type":"object"},"OperationAnnotateNodes":{"additionalProperties":false,"description":"This operation adds attributes to knowledge graph nodes.","properties":{"id":{"enum":["annotate_nodes"],"type":"string"},"parameters":{"$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"},"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"},"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"},"OperationEnrichResults_parameters":{"properties":{"pvalue_threshold":{"default":1e-6,"description":"The cutoff p-value for enrichment.","example":1e-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"},"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. 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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. 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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":{"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":{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. 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Edges connecting to the removed nodes will also be removed.","properties":{"id":{"enum":["filter_kgraph_discrete_knode_attribute"],"type":"string"},"parameters":{"$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. 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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"},"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. 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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"},"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":{"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"},"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. 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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_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"},"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"},"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"},"OperationLookup":{"additionalProperties":false,"description":"This operation adds knodes/kedges and (complete) results. It is equivalent to the workflow fill + bind + complete_results. 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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"},"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":{"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. 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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"},"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. 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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":{"$ref":"#/components/schemas/OperationSortResultsEdgeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. 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If not provided or empty, all edges will be looked at.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"}},"required":["ascending_or_descending","edge_attribute"],"title":"OperationSortResultsEdgeAttribute_parameters","type":"object"},"OperationSortResultsNodeAttribute":{"additionalProperties":false,"description":"This operation sorts the results by the given node attribute. If in ascending order, the minimum value of the results nodes with the given attribute will be taken while the maximum will be taken for descending order. If a result has no nodes with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value.","properties":{"id":{"enum":["sort_results_node_attribute"],"type":"string"},"parameters":{"$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"},"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":{"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"},"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"},"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":{"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"},"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"},"options":{"additionalProperties":true,"description":"Map of order independent options that apply during processing","example":{"halt_on_warning":false},"type":"object"}},"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":{"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":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"exclude":{"description":"If set to true, then all subgraphs containing this edge are excluded from the final results. (optional)","type":"boolean"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"option_group_id":{"description":"Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ","nullable":true,"type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"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. 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If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"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":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"CURIE identifier for this node","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"is_set":{"default":false,"description":"Set to true if this QNode is a set (deprecated)","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"},"set_id":{"description":"A client-provided identifier for the set described in this QNode","nullable":true,"type":"string"},"set_interpretation":{"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,"type":"string"}},"title":"QNode","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. 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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":{"bypass_cache":false,"enforce_edge_directionality":false,"log_level":"","max_results":100,"message":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"operations":"","page_number":1,"page_size":100,"return_minimal_metadata":false,"stream_progress":false,"submitter":"submitter","workflow":["",""]},"properties":{"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"},"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"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"max_results":{"default":100,"description":"Maximum number of individual results to return","example":100,"type":"integer"},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"operations":{"description":"Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned","nullable":true,"oneOf":[{"$ref":"#/components/schemas/Operations"}]},"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"},"page_size":{"default":100,"description":"Split the results into pages with this number of results each","example":100,"type":"integer"},"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"},"stream_progress":{"default":false,"description":"Set to true in order to receive a stream of LogEntry objects as the query is progressing","type":"boolean"},"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"},"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"},{"$ref":"#/components/schemas/OperationSortResultsScore"}]},"nullable":true,"type":"array"}},"required":["message"],"title":"Query","type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$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"},"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"}},"required":["edges","nodes"],"type":"object"},"Question":{"additionalProperties":true,"properties":{"language":{"description":"Human language in which the question is posed","enum":["English"],"example":"English","type":"string"},"text":{"description":"Free text question","example":"what genetic conditions offer protection against malaria","type":"string"}},"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"},"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":{"biolink_version":"3.1.2","context":"https://rtx.ncats.io/ns/translator.jsonld","datetime":"2021-01-09T12:34:45","description":"Success. 42 results found.","id":"https://arax.ncats.io/api/rtx/v1.3/response/123","info":"info","job_id":"rXEOAosN3L","logs":[{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"}],"message":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"operations":"","original_question":"what proteins are affected by sickle cell anemia","query_options":{"coalesce":true,"threshold":0.9},"resource_id":"ARAX","restated_question":"Which proteins are affected by sickle cell anemia?","schema_version":"1.4.0","status":"Success","submitter":"submitter","table_column_names":["chemical_substance.name","chemical_substance.id"],"tool_version":"ARAX 0.8.0","total_results_count":0,"type":"TranslatorAPIResponse","validation_result":"{}","workflow":["",""]},"properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","type":"string"},"context":{"description":"JSON-LD context URI","example":"https://rtx.ncats.io/ns/translator.jsonld","type":"string"},"datetime":{"description":"Datetime string for the time that this response was generated","example":"2021-01-09T12:34:45","type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"id":{"description":"URI for this response","example":"https://arax.ncats.io/api/rtx/v1.3/response/123","type":"string"},"info":{"description":"A placholder for including some additional information","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":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"},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"operations":{"description":"Container for one or more Message objects or identifiers for one or more Messages along with the processing plan and options for how those messages were processed and returned","oneOf":[{"$ref":"#/components/schemas/Operations"}]},"original_question":{"description":"The original question text typed in by the user","example":"what proteins are affected by sickle cell anemia","type":"string"},"query_options":{"description":"Dict of options that can be sent with the query. 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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":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"type":"array"},"confidence":{"description":"Confidence metric for this result, a value between (inclusive)\n 0.0 (no confidence) and 1.0 (highest confidence)","example":0.9234,"format":"float","nullable":true,"type":"number"},"description":{"description":"A free text description of this result answer from the reasoner","example":"The genetic condition sickle cell anemia may provide protection from cerebral malaria via genetic alterations of proteins HBB (P68871) and HMOX1 (P09601).","nullable":true,"type":"string"},"essence":{"description":"A single string that is the terse essence of the result (useful for simple answers)","example":"ibuprofen","nullable":true,"type":"string"},"essence_category":{"description":"A Translator BioLink bioentity category of the essence","example":"biolink:ChemicalEntity","nullable":true,"type":"string"},"id":{"description":"URI for this result","example":"result:234","nullable":true,"type":"string"},"node_bindings":{"additionalProperties":{"items":{"$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). 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","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c,  https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"type":"array"},"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"}},"required":["resource_id","resource_role"],"title":"RetrievalSource","type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"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":{"biolink-version":"4.2.5","component":"ARA","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. 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For sources that are from OWL files, source_etl is the URL to the OWL; for other sources, source_etl is a command for one of the python scripts that the generation framework uses to import the source.","example":"http://purl.obolibrary.org/obo/doid.owl","type":"string"},"source_type":{"description":"The type of source file. Possible values are owl, api, ftp, ubkg_edge_node, umls, and simpleknowledge.","example":"owl","type":"string"},"source_version":{"description":"A reference to the version of the source. If the source is an OWL file, the usual version is the date extracted from the VersionIRI of the file; if from a website, the file date. Dates are in format YYYY_MM_DD.","example":"2024_04_22","type":"string"}},"type":"object"},"type":"array"}},"type":"object"},"TermConcept":{"description":"An array of Concepts with preferred terms that exactly match the specified string","properties":{"concepts":{"items":{"description":"a Concept Unique Identifier (CUI)","example":"C0794811","type":"string"},"type":"array"}},"type":"object"},"TermtypeCode":{"description":"A Code with a term that matches a specified string","properties":{"code":{"description":"Identifier for the Code ID, in the format _SAB_:_CODE_.","example":"LNC:LA14283-8","type":"string"},"termtype":{"description":"Term type--i.e., the relationship between the Code and the Term","example":"LA","type":"string"}},"type":"object"}},"securitySchemes":{"umls_key":{"description":"API key for a UMLS licensee account, prefixed with \"UMLS-Key \"--e.g., \"UMLS-Key <my-umls-key>\"","in":"header","name":"Authorization","type":"apiKey"}}},"externalDocs":{"description":"UBKG documentation","url":"https://ubkg.docs.xconsortia.org/api"},"info":{"contact":{"name":"GitHub repository","url":"https://github.com/x-atlas-consortia/ubkg-api"},"description":"The UBKG API provides REST endpoints that return results from queries against a context instance of the [Unified Biomedical Knowledge Graph (UBKG)](https://ubkg.docs.xconsortia.org/). To prevent exceeding service timeouts or payload limits, some endpoints are throttled in both execution time and in the size of its response payload--e.g., to a maximum execution time of 15 seconds and a maximum payload of 9 MB. NOTE - The API requires an Authorization key in the request header in format \"UMLS-Key[space][apikey]\", where apikey is the API key for a UMLS licensee acount.","title":"UBKG API","version":"2.0.0"},"openapi":"3.0.3","paths":{"/codes/{code_id}/codes":{"get":{"operationId":"codes_code_id_codes_get","parameters":[{"description":"the identifier for a Code node, in format _SAB_:_code_ where _SAB_ is an identifier for the source of the code.","in":"path","name":"code_id","required":true,"schema":{"example":"SNOMEDCT_US:254837009","type":"string"}},{"description":"The set of sources (SABs) to which to limit the set of Codes that  link to the same Concept to which the Code with CodeID=_code_id_ links. This set can be specified either a list of values separated by commas (e.g., ?sab=SAB1,SAB,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":false,"schema":{"default":[],"items":{"example":"NCI,MDR","type":"string"},"type":"array","uniqueItems":true}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/CodesCodesObj"},"type":"array"}}},"description":"An array of objects corresponding to Code nodes that share links to the Concept associated with the specified Code, subject to constraints specified in parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded the specified timeout."},"5XX":{"description":"Unknown error"}},"summary":"Returns information on Code nodes that link to the Concept nodes to which the specified code links (i.e., related codes), subject to constraints specified in parameters. [A Concept node in the UBKG can have CODE relationships with (links to) Code nodes from multiple sources (SABs). For example, the Code nodes with code_ids SNOMEDCT_US:254837009, NCI:C9335 and MSH:D001943 link to the Concept with identifier C0006142.]","tags":["codes"]}},"/codes/{code_id}/concepts":{"get":{"operationId":"codes_code_id_concepts_get","parameters":[{"description":"The identifier for the Code node, in format _SAB_:_CODE_ where _SAB_ is an identifier for the source of the code.","in":"path","name":"code_id","required":true,"schema":{"example":"SNOMEDCT_US:79962008","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ConceptDetail"},"type":"array"}}},"description":"An array of Concept nodes that have CODE relationships with the specified Code node"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of Concept nodes that link to the specified Code node. [A Code node can have CODE relationships with (links to) multiple Concept nodes. For example, the Code with identifier SNOMEDCT_US:79962008 links to a set of Concepts that includes C0014863 and C1442913.]","tags":["codes"]}},"/codes/{code_id}/terms":{"get":{"operationId":"codes_code_id_terms_get","parameters":[{"description":"The CodeID for a Code node, in format SAB:CODE.","in":"path","name":"code_id","required":true,"schema":{"example":"SNOMEDCT_US:254837009","type":"string"}},{"description":"optional term type for the term. Can be either a list of values delimited with commas (e.g., ?term_type=PT,SY,FN) or with individual key-value pairs (e.g., ?term_type=PT&term_type=SY&term_type=FN)","in":"query","name":"term_type","required":false,"schema":{"example":"PT","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/CodeTerms"},"type":"array"}}},"description":"An array of Term nodes that have relationships with the specified Code node"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"408":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of Term nodes that link to the specified Code node, subject to constraints specified in parameters.","tags":["codes"]}},"/concepts/{concept_id}/codes":{"get":{"operationId":"concepts_concept_id_codes_get","parameters":[{"description":"The identifier for the Concept (also known as the Concept Unique Identifier, or CUI)","in":"path","name":"concept_id","required":true,"schema":{"example":"C0678222","type":"string"}},{"description":"The set of sources (SABs) to which to limit the set of Codes that link to the specified Concept. Can be either a list of values delimited with commas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":false,"schema":{"default":[],"items":{"example":"MEDLINEPLUS,MSH,MEDCIN","type":"string"},"type":"array","uniqueItems":true}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/ConceptCodes"},"type":"array"}}},"description":"An array of code_ids in format _SAB_:_CODE for the Codes that link to the specified Concept, subject to constraints specified in parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns information on the set of Code nodes that link to the specified Concept, subject to constraints specified in parameters. [A Concept node can have CODE relationships with (links to) multiple Code nodes. For example, the Concept with identifier C0006142 links to a set of Code nodes that include SNOMEDCT_US:254837009, NCI:C9335 and MSH:D001943.]","tags":["concepts"]}},"/concepts/{concept_id}/concepts":{"get":{"operationId":"concepts_concept_id_concepts_get","parameters":[{"description":"The concept identifier (also known as Concept Unique Identifier, or CUI)","in":"path","name":"concept_id","required":true,"schema":{"example":"C4722518","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/SabRelationshipConceptTerm"},"type":"array"}}},"description":"An array of information on Concepts that have relationships with the specified Concept"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of Concepts that have direct relationships with the specified Concept.","tags":["concepts"]}},"/concepts/{concept_id}/definitions":{"get":{"operationId":"concepts_concept_id_definitions_get","parameters":[{"description":"Identifier (also known as a Concept Unique Identifier) for a Concept.","in":"path","name":"concept_id","required":true,"schema":{"example":"C0006142","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/SabDefinition"},"type":"array"}}},"description":"An array of Definitions associated with the Concept."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of Definitions linked to a Concept. [A Definition is usually defined for a Code by a source (SAB), not a Concept; however, in the UBKG, the Definition is associated with the Code's linked Concept. Thus, a Concept may have multiple Definitions.]","tags":["concepts"]}},"/concepts/{concept_id}/nodeobjects":{"get":{"operationId":"concepts_identifier_nodes_get","parameters":[{"description":"The string to match against properties related to Concepts. Related properties include the preferred term for the Concept; the CUI for the Concept; the CodeID for a Code linked to the Concept; and terms for a Code linked to a Concept.","in":"path","name":"concept_id","required":true,"schema":{"example":"Cells","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptNodes"}}},"description":"The set of Concept node objects that match the identifier."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a set of \"Concept Node objects\" (or \"concept subgraphs\") that \"match\" the identifier (concept_id). A concept node in the UBKG is the origin of a \"concept subgraph\" that links a Concept node to a set of Code, Term, Definition, and Semantic Type nodes. A \"Concept Node object\" represents this subgraph as a set of Concept properties--i.e., all of the Concept's linked Codes, terms, definitions, and semantic types. A \"match\" is an exact match between an identifier and a text-based property in a Concept Node object. Because an identifier may match properties in more than one Concept Node object, the endpoint can return multiple Concept Node objects.","tags":["concepts"]}},"/concepts/{concept_id}/paths/expand":{"get":{"operationId":"concepts_concept_id_paths_expand_get","parameters":[{"description":"The identifier (also known as Concept Unique Identifier, or CUI) for the Concept from which paths originate.","in":"path","name":"concept_id","required":true,"schema":{"example":"C2720507","type":"string"}},{"description":"The set of sources (SABs) to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited withcommas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":true,"schema":{"example":"SNOMEDCT_US","type":"string"}},{"description":"The set of relationship types to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited with commas (e.g., ?rel=relationship_type1,relationship_type2) or individual key-value pairs (e.g., ?rel=relationship_type1&rel=relationship_type2)","in":"query","name":"rel","required":true,"schema":{"example":"isa","type":"string"}},{"description":"The minimum number of hops in the returned set of expanded paths--e.g., mindepth=2 directs the endpoint to return paths that have at least 2 hops. The minimum must be non-negative and less than the value of _maxdepth_. The default value is 1. Large values of mindepth may result in long queries that exceed the execution time limits.","in":"query","name":"mindepth","required":false,"schema":{"example":1,"type":"string"}},{"description":"The maximum number of hops in the returned set of expanded paths--e.g., maxdepth=4 directs the endpoint to return paths that have no more than 4 hops. The maximum must be non-negative. The default value is _mindepth_ + 2. Large values of maxdepth may result in long queries that exceed the execution time limits.","in":"query","name":"maxdepth","required":false,"schema":{"example":3,"type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of paths to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Return the graph of all Concepts in paths that originate with the specified Concept node, subject to constraints. The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a set of paths that originate from the specified Concept, subject to constraints specified in parameters.","tags":["concepts/paths"]}},"/concepts/{concept_id}/paths/trees":{"get":{"operationId":"concepts_trees_get","parameters":[{"description":"The concept identifier (also known as Concept Unique Identifier, or CUI) of the origin of the spanning tree.","in":"path","name":"concept_id","required":true,"schema":{"example":"C0006142","type":"string"}},{"description":"The set of sources (SABs) to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited with commas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":true,"schema":{"example":"SNOMEDCT_US","type":"string"}},{"description":"The set of relationship types to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited with commas (e.g., ?rel=relationship_type1,relationship_type2) or individual key-value pairs (e.g., ?rel=relationship_type1&rel=relationship_type2).","in":"query","name":"rel","required":true,"schema":{"example":"isa","type":"string"}},{"description":"The minimum number of hops in the spanning tree--e.g., mindepth=1 directs the endpoint to return paths that have at least 1 hop. The minimum must be non-negative and less than the value of _maxdepth_. The only allowed values are 0 or 1. The default value is 0.","in":"query","name":"mindepth","required":false,"schema":{"default":0,"enum":[0,1],"type":"integer"}},{"description":"The maximum number of hops in spanning tree--e.g., maxdepth=4 directs the endpoint to return paths that have no more than 4 hops. The maximum must be non-negative. The default value is _mindepth_ + 2. Large values of maxdepth may result in long queries that exceed the execution time limits.","in":"query","name":"maxdepth","required":false,"schema":{"example":3,"type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of paths to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Return information the paths in the spanning tree that originates from the specified Concept, subject to constraints on relationship type, relationship source, and spanning depth.  The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Return information on the Concepts in the spanning tree that originates from a specified Concept, subject to constraints on relationship type, relationship source, and range of path depths. A spanning tree is the set of paths originating from node that traverse all of the other nodes of a graph.","tags":["concepts/paths"]}},"/concepts/paths/subgraph":{"get":{"operationId":"concepts_subgraph_get","parameters":[{"description":"The set of sources (SABs) to which to limit the relationships in the subgraph. Can be either a list of values delimited with commas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":true,"schema":{"example":"SNOMEDCT_US","type":"string"}},{"description":"The set of relationship types to which to limit the relationships in the subgraph. Can be either a list of values delimited with commas (e.g., ?rel=relationship_type1,relationship_type2) or individual key-value pairs (e.g., ?rel=relationship_type1&rel=relationship_type2)","in":"query","name":"rel","required":true,"schema":{"example":"isa","type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of paths to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Return the set of Concepts linked by the specified relationships from the specified SABs. The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a subgraph of Concept nodes that are connected by a set of specified relationship types defined by a set of specified sources. For example, the endpoint can return the subgraph consisting of nodes that are linked by UBERON's \"part_of\" relationship.","tags":["concepts/paths/subgraph"]}},"/concepts/paths/subgraph/sequential":{"get":{"operationId":"concepts_paths_subgraph_sequential_get","parameters":[{"description":"A sequential set of relationships that specifies the pattern of relationships in the paths in the subgraph. Each element in the set should be in format SAB:relationship type. SAB corresponds to the source in which the relationship was asserted--e.g., \"NCI:is_marked_by_gene_product\" corresponds to the \"is_marked_by_gene_product\" relationship asserted in NCI. The set can be specified with a list of values delimited with commas (e.g., ?relsequence=SAB1:relationshiptype1,SAB2:relationshiptype2) or with individual key-value pairs (e.g., ?relsequence=SAB1:relationship_type1&relsequence=SAB2:relationshiptype2).","in":"query","name":"relsequence","required":true,"schema":{"example":"NCI:is_marked_by_gene_product,NCI:gene_product_encoded_by_gene","type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of paths to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Return the graph of all Concepts in paths with specified sequential relationships, subject to constraints. The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a set of paths with a specified sequence of relationships, subject to constraints specified in parameters.","tags":["concepts/paths/subgraph"]}},"/concepts/{concept_id}/paths/subgraph/sequential":{"get":{"operationId":"concepts_concept_id_paths_subgraph_sequential_get","parameters":[{"description":"The identifier (also known as Concept Unique Identifier, or CUI) for the Concept from which paths originate.","in":"path","name":"concept_id","required":true,"schema":{"example":"C0006142","type":"string"}},{"description":"A sequential set of relationships that specifies the pattern of relationships in the paths in the subgraph. Each element in the set should be in format SAB:relationship type. SAB corresponds to the source in which the relationship was asserted--e.g., \"NCI:is_marked_by_gene_product\" corresponds to the \"is_marked_by_gene_product\" relationship asserted in NCI. The set can be specified with a list of values delimited with commas (e.g., ?relsequence=SAB1:relationshiptype1,SAB2:relationshiptype2) or with individual key-value pairs (e.g., ?relsequence=SAB1:relationship_type1&relsequence=SAB2:relationshiptype2).","in":"query","name":"relsequence","required":true,"schema":{"example":"NCI:is_marked_by_gene_product,NCI:gene_product_encoded_by_gene","type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of paths to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Return the graph of all Concepts in paths that originate with the specified Concept node with specified sequential relationships, subject to constraints. The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a set of paths that originate from the specified Concept with a specified sequence of relationships, subject to constraints specified in parameters.","tags":["concepts/paths/subgraph"]}},"/concepts/{origin_concept_id}/paths/shortestpath/{terminus_concept_id}":{"get":{"operationId":"concepts_shortestpath_get","parameters":[{"description":"The concept identifier (also known as Concept Unique Identifier, or CUI) for the origin of the shortestpath calculation.","in":"path","name":"origin_concept_id","required":true,"schema":{"example":"C2720507","type":"string"}},{"description":"The concept identifier (also known as Concept Unique Identifier, or CUI) for the terminus of the shortestpath calculation.","in":"path","name":"terminus_concept_id","required":true,"schema":{"example":"C1272753","type":"string"}},{"description":"The set of sources (SABs) to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited with commas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":true,"schema":{"example":"SNOMEDCT_US","type":"string"}},{"description":"The set of relationship types to which to limit the relationships in the set of expanded paths. Can be either a list of values delimited with commas (e.g., ?rel=relationship_type1,relationship_type2) or individual key-value pairs (e.g., ?rel=relationship_type1&rel=relationship_type2).","in":"query","name":"rel","required":true,"schema":{"example":"isa","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/ConceptPaths"}}},"description":"Returns the ordered set of Concepts involved in the shortest path, subject to constraints for relationship type and source. The schema of the response corresponds to the Table result frame of the endpoint query in the neo4j browser."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Return the shortest path between two Concepts, using Dykstra's algorithm with default weights, subject to constraints on relationship types (rel) and relationship sources (sab).","tags":["concepts/paths"]}},"/database/server":{"get":{"operationId":"database_info_server_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/DatabaseInfo"}}},"description":"basic information on the UBKG neo4j database"}},"summary":"Returns basic information on the UBKG neo4j database.","tags":["general"]}},"/node-types":{"get":{"operationId":"node_type_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/NodeTypes"}}},"description":"List of node types"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns list of node types (node labels)--e.g., Code, Concept, etc.","tags":["node-types"]}},"/node-types/{node_type}/counts":{"get":{"operationId":"node_type_id_count_get","parameters":[{"description":"a node type","in":"path","name":"node_type","required":true,"schema":{"example":"Code","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/NodeTypeCount"}}},"description":"List of counts by node type"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns counts of nodes in the database for a specified node type (label).","tags":["node-types"]}},"/node-types/{node_type}/counts-by-sab":{"get":{"operationId":"node_type_id_count_by_sab_get","parameters":[{"description":"a node type","in":"path","name":"node_type","required":true,"schema":{"example":"Code","type":"string"}},{"description":"The set of sources (SABs) to which to limit counts by node type. Can be either a list of values delimited with commas (e.g., ?sab=SAB1,SAB2,SAB3) or with individual key-value pairs (e.g., ?sab=SAB1&sab=SAB2&SAB=SAB3).","in":"query","name":"sab","required":true,"schema":{"example":"NCI","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/NodeTypeSabCount"}}},"description":"List of counts by node type, grouped by source, subject to constraints specified in parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns counts of nodes in the database for a specified node type (label), grouped by source (SAB), subject to constraints specified in parameters.","tags":["node-types"]}},"/property-types":{"get":{"operationId":"property_types_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/PropertyTypes"}}},"description":"List of property types"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of property types (keys) for all nodes and relationships","tags":["general"]}},"/relationship-types":{"get":{"operationId":"relationship_types_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/RelationshipTypes"}}},"description":"List of relationship types"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of relationship types","tags":["general"]}},"/sabs":{"get":{"operationId":"sabs_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Sabs"}}},"description":"Returns information on a set of sources."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a list of sources (SABs) in the UBKG. [A source corresponds to a vocabulary, an ontology, or reference. The Source Abbreviation (SAB) is unique acronym that identifies the source.]","tags":["sabs"]}},"/sabs/codes/counts":{"get":{"operationId":"sabs_codes_counts_get","parameters":[{"description":"the number of Codes to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Codes to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SabCodeCounts"}}},"description":"Returns information on a set of sources, subject to constraints from parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a list of sources (SABs), including counts of the codes associated with the sources, subject to constraints from parameters","tags":["sabs"]}},"/sabs/{sab}/codes/counts":{"get":{"operationId":"sabs_codes_counts_sab_get","parameters":[{"description":"A source (SAB) to which to limit the response.","in":"path","name":"sab","required":true,"schema":{"example":"UBERON","type":"string"}},{"description":"the number of Codes to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Codes to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SabCodeDetails"}}},"description":"Returns information on a source, subject to constraints from parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns information for a specified source (SAB), including counts of the codes associated with the source, subject to constraints from parameters","tags":["sabs"]}},"/sabs/{sab}/codes/details":{"get":{"operationId":"sabs_codes_details_sab_get","parameters":[{"description":"A source (SAB) to which to limit the response.","in":"path","name":"sab","required":true,"schema":{"example":"UBERON","type":"string"}},{"description":"the number of Codes to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Codes to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SabCodeDetails"}}},"description":"Returns information on a set of sources and their associated Codes, subject to constraints from parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns including details for codes associated with a specified source (SAB), subject to constraints from parameters","tags":["sabs"]}},"/sabs/{sab}/term-types":{"get":{"operationId":"sabs_term_types_sab_get","parameters":[{"description":"A source (SAB) to which to limit the response.","in":"path","name":"sab","required":true,"schema":{"example":"UBERON","type":"string"}},{"description":"the number of Codes to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Codes to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SabTermTypes"}}},"description":"Returns information on a set of sources and their associated Codes, subject to constraints from parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the list of term types (types of relationship) for relationships between the nodes that are defined by the specified source (SAB)","tags":["sabs"]}},"/semantics/semantic-types":{"get":{"operationId":"semantics_semantic_types_get","parameters":[{"description":"the number of Semantic Types to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Semantic Types to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemanticTypes"}}},"description":"Returns the set of Semantic Type nodes, subject to constaints specified in the parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the complete set of Semantic Type nodes, subject to constraints specified in parameters.","tags":["semantic-types"]}},"/semantics/semantic-types/{identifier}":{"get":{"operationId":"semantics_semantic_types_identifier_get","parameters":[{"description":"The identifier for a Semantic Type node. An identifier may be either a string corresponding to either the name of the Semantic Type (e.g., \"Anatomical Structure\") or the Type Unique Identifier (TUI) of the Semantic Type (e.g., T017).","in":"path","name":"identifier","required":true,"schema":{"example":"T017","type":"string"}},{"description":"the number of paths to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of Semantic Types to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemanticTypes"}}},"description":"Returns the set of Semantic Type nodes, subject to constaints specified in the parameters."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the Semantic Type node that matches the identifier, subject to constraints specified in parameters.","tags":["semantic-types"]}},"/semantics/semantic-types/{identifier}/subtypes":{"get":{"operationId":"semantics_identifier_semantic_subtypes_get","parameters":[{"description":"The identifier for a Semantic Type node. An identifier may be either a string corresponding to either the name of the Semantic Type (e.g., \"Anatomical Structure\") or the Type Unique Identifier (TUI) of the Semantic Type (e.g., T017).","in":"path","name":"identifier","required":true,"schema":{"example":"Anatomical Structure","type":"string"}},{"description":"the number of semantic sub-types to skip in the returned set. The value must be non-negative. The default value is 0.","in":"query","name":"skip","required":false,"schema":{"example":0,"type":"string"}},{"description":"the maximum number of semantic sub-types to return. The value must be non-negative. The default value is the maximum number of rows specified by configuration.","in":"query","name":"limit","required":false,"schema":{"example":10,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/SemanticSubTypes"}}},"description":"Returns the set of Semantic Type nodes that are subtypes of the specified Semantic Type node."},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns the set of Semantic Type nodes that are subtypes (have ISA_STY relationship with) the specified Semantic Type, subject to constraints specified in parameters.","tags":["semantic-types"]}},"/terms/{term_id}/codes":{"get":{"operationId":"terms_term_id_codes_get","parameters":[{"description":"The string to match. Subject to timeout. Should be URL-encoded for spaces (%20).","in":"path","name":"term_id","required":true,"schema":{"example":"Breast cancer","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/TermtypeCode"},"type":"array"}}},"description":"An array of Codes with terms that exactly match the specified string"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a list of Code nodes with terms that exactly match the specified string. Terms can be of different types--e.g., preferred terms (PT), synonyms (SY), etc.","tags":["terms"]}},"/terms/{term_id}/concepts":{"get":{"operationId":"terms_term_id_concepts_get","parameters":[{"description":"The string to match. Should be URL-encoded for spaces (%20).","in":"path","name":"term_id","required":true,"schema":{"example":"Breast cancer","type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/TermConcept"},"type":"array"}}},"description":"An array of Concepts with preferred terms that exactly match the specified string"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns a list of Concept nodes with preferred terms that exactly match the specified string.","tags":["terms"]}},"/sources":{"get":{"operationId":"sources_get","parameters":[{"description":"A source (SAB) to which to limit the response.","in":"query","name":"sab","required":false,"schema":{"example":"UBERON","type":"string"}},{"description":"A UBKG context to which to limit the response. Possible values are base_context, data_distillery_context, hubmap_sennet_context. The sources from base_context are included with any other context.","in":"query","name":"context","required":false,"schema":{"enum":["base_context","hubmap_sennet_context","data_distillery_context"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Source"}}},"description":"An array of objects for the specified set of sources"},"303":{"description":"The response size exceeds a limit set by the server. The response content is stored in a file in a AWS S3 bucket. The returned response includes a URL that can be used to download the stored file."},"400":{"description":"Invalid parameter name or value"},"403":{"description":"The response size exceeds a limit set by the server."},"404":{"description":"No response for the specified parameters."},"504":{"description":"The query run time exceeded a timeout set by the server."},"5XX":{"description":"Unknown error"}},"summary":"Returns information on a set of sources (SABs) used to build an instance of the UBKG.","tags":["general"]}}},"security":[{"umls_key":[]}],"servers":[{"description":"Base context instance","url":"https://ubkg.api.xconsortia.org"}],"tags":[{"description":"endpoints about codes from a SAB","name":"codes"},{"description":"endpoints about concepts","name":"concepts"},{"description":"endpoints that return graph representations of paths","name":"concepts/paths"},{"description":"endpoints that return graph representations of subgraphs","name":"concepts/paths/subgraph"},{"description":"structural and source information","name":"general"},{"description":"types (labels) of nodes","name":"node-types"},{"description":"Source ABbreviations (SABs) that identify data sources in the UBKG","name":"sabs"},{"description":"information about semantic types","name":"semantic-types"},{"description":"information linking terms to concepts and codes","name":"terms"}]},{"components":{"schemas":{"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":{"attributes":{"description":"The attributes of this particular Analysis.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edge_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/EdgeBinding"},"type":"array"},"description":"The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges.","type":"object"},"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The id of the resource generating this Analysis"},"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"},"scoring_method":{"description":"An identifier and link to an explanation for the method used to generate the score","nullable":true,"type":"string"},"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"}},"required":["resource_id","edge_bindings"],"type":"object"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"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"},"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","nullable":false,"pattern":"^https?://","type":"string"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"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"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["callback","message"],"type":"object","x-body-name":"request_body"},"AsyncQueryResponse":{"additionalProperties":true,"description":"The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the result of the async_query submission.","example":"Async_query has been queued","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","example":"rXEOAosN3L","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the current state or summary of the problem if the status is Failed.","example":"Callback URL returned 500","nullable":false,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":1,"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"},"status":{"description":"One of a standardized set of short codes: Queued, Running, Completed, Failed","example":"Running","nullable":false,"type":"string"}},"required":["status","description","logs"],"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_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,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.","example":"biolink:synonym"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"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,"type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153},"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":[{"$ref":"#/components/schemas/CURIE"}]},"value_url":{"description":"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).","example":"https://pubmed.ncbi.nlm.nih.gov/32529952","nullable":true,"type":"string"}},"required":["attribute_type_id","value"],"type":"object"},"AttributeConstraint":{"additionalProperties":false,"description":"Generic query constraint for a query node or query edge","properties":{"id":{"description":"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_0844","oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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","type":"string"},"not":{"default":false,"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","==="],"type":"string"},"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},"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},"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}},"required":["name","id","operator","value"],"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":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges","attributes"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","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_]*$","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"type":"string"},"Edge":{"additionalProperties":false,"description":"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \"thought\" graph resulting from a query upon the underlying knowledge source.","properties":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"object":{"description":"Corresponds to the map key CURIE of the object concept node of this relationship edge.","example":"UniProtKB:P00738","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"predicate":{"description":"The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided.","example":"biolink:gene_associated_with_condition","nullable":false,"oneOf":[{"$ref":"#/components/schemas/BiolinkPredicate"}]},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"type":"array"},"sources":{"description":"A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","items":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"type":"array"},"subject":{"description":"Corresponds to the map key CURIE of the subject concept node of this relationship edge.","example":"MONDO:0011382","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["object","predicate","subject","sources"],"type":"object"},"EdgeBinding":{"additionalProperties":true,"description":"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners.","properties":{"attributes":{"description":"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","nullable":false,"type":"string"}},"required":["id","attributes"],"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":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/Edge"},"description":"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"},"nodes":{"additionalProperties":{"$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"}},"required":["nodes","edges"],"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.","properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"timestamp":{"description":"Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00).","example":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["timestamp","message"],"type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","properties":{"auxiliary_graphs":{"additionalProperties":{"$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.","nullable":true,"type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"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":{"$ref":"#/components/schemas/Result"},"minItems":0,"nullable":true,"type":"array"}},"type":"object"},"MetaAttribute":{"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"type":"string"},"attribute_type_id":{"$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"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"}},"required":["attribute_type_id"],"type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","properties":{"association":{"$ref":"#/components/schemas/BiolinkEntity","description":"The Biolink association type (entity) that this edge represents. Associations are classes in Biolink that represent a relationship between two entities. For example, the association 'gene interacts with gene' is represented by the Biolink class, 'biolink:GeneToGeneAssociation'.  If association is filled out, then the testing harness can help validate that the qualifiers are being used correctly.","example":"biolink:ChemicalToGeneAssociation"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"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"},"object":{"$ref":"#/components/schemas/BiolinkEntity","description":"Object node category of this relationship edge.","example":"biolink:Protein"},"predicate":{"$ref":"#/components/schemas/BiolinkPredicate","description":"Biolink relationship between the subject and object categories.","example":"biolink:affects"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"type":"array"},"subject":{"$ref":"#/components/schemas/BiolinkEntity","description":"Subject node category of this relationship edge.","example":"biolink:ChemicalEntity"}},"required":["subject","predicate","object"],"type":"object"},"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.","properties":{"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":{"$ref":"#/components/schemas/MetaEdge"},"type":"array"},"nodes":{"additionalProperties":{"$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.","type":"object"}},"required":["nodes","edges"],"type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"type":"array"}},"required":["id_prefixes"],"type":"object"},"MetaQualifier":{"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":["expression","activity","abundance","degradation"],"type":"string"},"type":"array"},"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of the qualifier type.","example":"biolink:subject_aspect_qualifier","nullable":false}},"required":["qualifier_type_id"],"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":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":false,"type":"array"},"is_set":{"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,"type":"boolean"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"required":["categories","attributes"],"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":{"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":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id","attributes"],"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"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"},"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"},"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":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"qualifier_constraints":{"default":[],"description":"A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time.","items":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"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"}},"required":["subject","object"],"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":{"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":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"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.","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"member_ids":{"description":"A list of CURIE identifiers for members of a queried set. This field MUST be populated under a set_interpretation of MANY or ALL, when the 'ids' field holds a UUID representing the set itself. This field MUST NOT be used under a set_interpretation of BATCH.","items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"},"set_interpretation":{"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,"type":"string"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier, biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"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,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"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":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"type":"object"},"Query":{"additionalProperties":true,"description":"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"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.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"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":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/QEdge"},"description":"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.","type":"object"},"nodes":{"additionalProperties":{"$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"}},"required":["nodes","edges"],"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"],"type":"string"},"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). 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The detailed query syntax for parameter is explained  [here for a core BioThings  API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"subject.umls:C0055723","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases,  there are times you might find it more efficient to make batch queries (e.g., retrieving data  for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query” field in the returned object indicates the matching query term. If a query term has no match,  it will return with a “notfound” field with the value “true”.","parameters":[{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000  maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Optional, specify one or more fields (separated by commas) to search. 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Default: _id","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response 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If the direct ancestor is a Source, the sample must be of type organ.","type":"string","writeOnly":true},"doi_url":{"description":"The url from the doi registry for this entity. e.g. https://doi.org/10.35079/snt289.pcbm.487","readOnly":true,"type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).","type":"string"},"image_files":{"description":"List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"image_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array","writeOnly":true},"image_files_to_remove":{"description":"List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"format":"file_uuid","type":"string"},"type":"array","writeOnly":true},"lab_tissue_sample_id":{"description":"Lab specific id for the sample.","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970","readOnly":true,"type":"integer"},"last_modified_user_displayname":{"description":"The name of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_email":{"description":"The email address of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_sub":{"description":"The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.","readOnly":true,"type":"string"},"metadata_files":{"description":"List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"metadata_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array"},"metadata_files_to_remove":{"description":"List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"format":"file_uuid","type":"string"},"type":"array"},"organ":{"description":"Organ code specifier, only set if sample_type == organ. Valid values found in: [organ types](https://ontology.api.hubmapconsortium.org/organs?application_context=sennet)","enum":["UBERON:0001013","UBERON:0000178","UBERON:0001474","UBERON:0002371","UBERON:0000955","UBERON:0000948","UBERON:0004538","UBERON:0004539","UBERON:0000059","UBERON:0002107","UBERON:0002168","UBERON:0002167","UBERON:0000029","UBERON:0001911","FMA:57991","FMA:57987","UBERON:0005090","UBERON:0010000","UBERON:0002119","UBERON:0002118","UBERON:0001264","UBERON:0001987","UBERON:0002097","UBERON:0002240","UBERON:0002106","UBERON:0002370","FMA:54974","FMA:54973","UBERON:0003126"],"type":"string"},"organ_other":{"description":"The organ type provided by the user if \"other\" organ type is selected","type":"string"},"registered_doi":{"description":"The doi of a the registered entity. e.g. 10.35079/snt289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets.","type":"string"},"rui_location":{"description":"The sample location and orientation in the ancestor organ as specified in the RUI tool. Returned as a json object.","type":"object"},"sample_category":{"description":"The category of the sample. Valid values found in: [sample categories](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C020076&child_sabs=SENNET)","enum":["Block","Organ","Section","Suspension"],"type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"},"visit":{"description":"The visit id for the source/patient when the sample was obtained.","type":"string"}},"type":"object"},"Source":{"properties":{"contacts":{"description":"A list of the people who are the main contacts to get information about the entity.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"created_by_user_displayname":{"description":"The name of the person or process authenticated when creating the object","readOnly":true,"type":"string"},"created_by_user_email":{"description":"The email address of the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_by_user_sub":{"description":"The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_timestamp":{"description":"The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970","readOnly":true,"type":"integer"},"creators":{"description":"A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"data_access_level":{"description":"One of the values: public, consortium","enum":["consortium","public"],"readOnly":true,"type":"string"},"description":{"description":"Free text description of the source","type":"string"},"doi_url":{"description":"The url from the doi registry for this entity. e.g. https://doi.org/10.35079/snt289.pcbm.487","readOnly":true,"type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source, Upload","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of.  This is required on Create/POST if the user creating the Source is a member of more than one write group.  This property cannot be set via PUT (only on Create/POST).","type":"string"},"image_files":{"description":"List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"image_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array","writeOnly":true},"image_files_to_remove":{"description":"List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"format":"file_uuid","type":"string"},"type":"array","writeOnly":true},"lab_source_id":{"description":"A lab specific identifier for the source.","type":"string"},"label":{"description":"Lab provided, de-identified name for the source","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970","readOnly":true,"type":"integer"},"last_modified_user_displayname":{"description":"The name of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_email":{"description":"The email address of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_sub":{"description":"The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.","readOnly":true,"type":"string"},"registered_doi":{"description":"The doi of a the registered entity. e.g. 10.35079/snt289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets.","type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"source_type":{"description":"A high level description of where this source originates from. Valid values found in: [source types](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C050020&child_sabs=SENNET)","enum":["Human","Human Organoid","Mouse","Mouse Organoid"],"type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"}},"type":"object"},"SourceMetadata":{"properties":{"code":{"description":"This is a Code from a source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS source vocabulary terms.","type":"string"},"concept_id":{"description":"This is the Concept ID from the SenNet Knowledge Graph.  Currently limited to UMLS concepts.","type":"string"},"data_type":{"description":"This is the data type of thw record. Numeric types will generally have non-null data_value. Nominal types will generally have null data_value.","enum":["Nominal","Numeric"],"type":"string"},"data_value":{"description":"The data value of the record.","type":"string"},"end_datetime":{"description":"This is the approximate time difference in seconds between the procurement and the end of this event (this is to construct time series records of clinical data for event-level data not source-level data). An empty of zero value designates missing data or that this field is not applicable for the concept","type":"integer"},"graph_version":{"description":"This is the version of the SenNet Knowledge Graph that the Concept appears in, currently the version of UMLS that is used.","type":"string"},"grouping_code":{"description":"This is a Code from a source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS vocabulary codes. This code corresponds to the grouping_concept.","type":"string"},"grouping_concept":{"description":"This is the Concept ID from the SenNet Knowledge Graph, currently limited to UMLS concetps, that is to be used for grouping the record.","type":"string"},"grouping_concept_preferred_term":{"description":"This is the preferred display term for the facet in which this record should be counted for faceted search in the portal. It may or may not correspond to a term in UMLS for the grouping concept.","type":"string"},"grouping_sab":{"description":"This is a grouping for the source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code.","type":"string"},"numeric_operator":{"description":"This is the numeric operator for the data value .This enables inputing thresholds and ranges for data values by using greater than or less than.","enum":["EQ","GT","LT"],"type":"string"},"preferred_term":{"description":"This is the preferred display term for the item. It may or may not correspond to a term in UMLS for this concept.","type":"string"},"sab":{"description":"This is the source vocabulary in the SenNet Knowledge Graph.  Currently limited to UMLS source vocabularies.","type":"string"},"start_datetime":{"description":"This is the approximate time difference in seconds between the procurement and the start of this event (this is to construct time series records of clinical data for event-level data not source-level data). An empty or zero value designates missing data or that this field is not applicable for the concept.","type":"integer"},"units":{"description":"This are the units for the data value.","type":"string"}},"type":"object"},"Upload":{"properties":{"created_by_user_displayname":{"description":"The name of the person or process authenticated when creating the object","readOnly":true,"type":"string"},"created_by_user_email":{"description":"The email address of the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_by_user_sub":{"description":"The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_timestamp":{"description":"The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970","readOnly":true,"type":"integer"},"dataset_uuids_to_link":{"description":"List of datasets to add to the Upload. Provide as a json array of the dataset UUIDs like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"type":"string"},"type":"array","writeOnly":true},"dataset_uuids_to_unlink":{"description":"List of datasets to remove from a Upload. Provide as a json array of the dataset UUIDs like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"type":"string"},"type":"array","writeOnly":true},"datasets":{"description":"The datasets that are contained in this Upload.","items":{"$ref":"#/components/schemas/Dataset"},"readOnly":true,"type":"array"},"description":{"description":"Free text description of the data being submitted.","type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source, Upload","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970","readOnly":true,"type":"integer"},"last_modified_user_displayname":{"description":"The name of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_email":{"description":"The email address of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_sub":{"description":"The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.","readOnly":true,"type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"status":{"description":"One of: New|Valid|Invalid|Error|Submitted","type":"string"},"title":{"description":"Title of the datasets, a sentance or less","type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"},"validation_message":{"description":"A message from the validataion tools describing what is invalid with the upload.","type":"string"}},"type":"object"}},"securitySchemes":{"BearerAuth":{"description":"Globus Bearer token to authorize requests","scheme":"bearer","type":"http"}}},"info":{"contact":{"email":"help@sennetconsortium.org","name":"SenNet Help Desk"},"description":"The SenNet Entity API is a standard RESTful web service with create, update and read operations for the standard SenNet provenance graph entities.","license":{"name":"MIT License","url":"https://github.com/sennetconsortium/entity-api/blob/main/license.txt"},"title":"SenNet Entity API","version":"1.10.5"},"openapi":"3.0.0","paths":{"/entities/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID (32 digit hexadecimal number)","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The properties to not be included in the JSON response of the entity.","in":"query","name":"exclude","required":false,"schema":{"type":"string"}},{"description":"Specifies a single property to be returned from the entity JSON.","in":"query","name":"property","required":false,"schema":{"enum":["data_access_level","status"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}},"description":"The json of the **[Source](http://somewhere.org)**, **[Sample](http://somewhere.org)**, **[Dataset](http://somewhere.org)**, or **[Upload](http://somewhere.org)**"},"400":{"description":"Invalid or misformatted entity identifier was provided."},"401":{"description":"The user's bearer token has expired or the user did not supply a valid token."},"403":{"description":"The user is not authorized to retrieve the referenced entity."},"404":{"description":"The target entity could not be found."},"500":{"description":"An unexpected error occurred."}},"summary":"Retrieve a provenance entity by id. Entity types of Source, Sample, Dataset, and Upload.","tags":["entities"]},"put":{"parameters":[{"description":"The SenNet ID (e.g. SNT123.ABCD.456) or UUID of target entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}},"description":"The entity was successfully updated and is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Update the properties of a given Source, Sample, Dataset or Upload","tags":["entities"]}},"/entity-types":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"An array of entity types is returned"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to use this method"},"500":{"description":"Internal error"}},"summary":"Get a list of all the available entity types defined in the schema yaml","tags":["entities types"]}},"/ancestors/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the ancestor list for an Entity. The ancestors are the nodes connected \"upstream\" from the current node. This list traverses all the levels in the graph.","tags":["ancestors"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the ancestor list for an Entity. The ancestors are the nodes connected \"upstream\" from the current node. This list traverses all the levels in the graph.","tags":["ancestors"]}},"/descendants/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of descendants is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the descendant list for an Entity. The descendants are the nodes \"downstream\" from the current node.  This list traverses all the levels in the graph. Returns all descendants as an array of Entities.","tags":["descendants"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the descendant list for an Entity. The descendants are the nodes \"downstream\" from the current node.  This list traverses all the levels in the graph. Returns all descendants as an array of Entities.","tags":["descendants"]}},"/parents/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of parent entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the immediate parent list for an Entity. The parents are the nodes connected one level \"upstream\" from the current node.  This list only goes to the next higher level in the graph.","tags":["parents"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the immediate parent list for an Entity. The parents are the nodes connected one level \"upstream\" from the current node.  This list only goes to the next higher level in the graph.","tags":["parents"]}},"/children/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of children entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the list of children directly connected to an Entity. The children are the nodes one level below the current node. This list only returns the items one level below in the graph.","tags":["children"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the list of children directly connected to an Entity. The children are the nodes one level below the current node. This list only returns the items one level below in the graph.","tags":["children"]}},"/entities/{id}/siblings":{"get":{"parameters":[{"description":"The unique identifier of entity.  This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true will have no effect. If the string is 'true', datasets that are have newer revisions will be included, otherwise by default they are not included.","in":"query","name":"include-old-revisions","required":false,"schema":{"enum":["true","false"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'new', 'qa', and 'published' will raise an error. If a valid status is provided, only results matching that status (if they are datasets) will be returned","in":"query","name":"status","required":false,"schema":{"enum":["new","qa","published"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. If property_key=uuid is provided, rather than entire dictionary representations of each node, only the list of matching uuid's will be returned","in":"query","name":"property_key","required":false,"schema":{"enum":["uuid"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of sibling entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the siblings list for an Entity.  The siblings have the same direct ancestor.  This list does not include all nodes whom have common ancestors, only the direct ancestor.","tags":["entities"]}},"/entities/{id}/tuplets":{"get":{"parameters":[{"description":"The unique identifier of entity.  This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'new', 'qa', and 'published' will raise an error. If a valid status is provided, only results matching that status (if they are datasets) will be returned","in":"query","name":"status","required":false,"schema":{"enum":["new","qa","published"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. If property_key=uuid is provided, rather than entire dictionary representations of each node, only the list of matching uuid's will be returned","in":"query","name":"property_key","required":false,"schema":{"enum":["uuid"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of tuplet entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the tuplets list for an Entity.  The tuplets have the same parent activity node.","tags":["entities"]}},"/entities/{id}/provenance":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"Determines which node labels are allowed or not allowed to be returned in the provenance result. Formatting of filter follows the syntax of 'labelFilter' config param of the neo4j subgraph method. (e.g. -Publication|-Collection)","in":"query","name":"filter","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{}},"description":"Successful operation"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the provenance of the given entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get Provenance Data for Entity. This returns a PROV JSON compliant representation of the entity's provenance. Refer to this document for more information regarding [PROV JSON format](https://www.w3.org/Submission/2013/SUBM-prov-json-20130424/)","tags":["entities"]}},"/entities/type/{type_a}/instanceof/{type_b}":{"get":{"parameters":[{"description":"The unique identifier of entity (e.g. Published)","in":"path","name":"type_a","required":true,"schema":{"type":"string"}},{"description":"The Entity Type Class as defined in entity-api-spec.yaml (e.g. Dataset)","in":"path","name":"type_b","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Instanceof"}}},"description":"An object with the attribute 'instanceof' that has a value of either 'true' of 'false'"},"400":{"description":"Invalid or misformatted entity identifie"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to retrieve the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Determines if the Entity type type_a is an instance of type_b","tags":["entities"]}},"/entities/{id}/ancestor-organs":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Sample"},"type":"array"}}},"description":"An array of Samples (sub-type organ) are returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to retrieve the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve a list of ancestor organ(s) of a given UUID","tags":["entities"]}},"/entities/{entity_type}":{"post":{"parameters":[{"description":"One of the target entity types (case-insensitive since will be normalized): Source, Sample, Dataset, Upload","in":"path","name":"entity_type","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]},"type":"array"}}},"description":"The entity was successfully created and is returned"},"400":{"description":"Invalid entity type provided"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to create the entity"},"500":{"description":"Internal error"}},"summary":"Create a new entity of the target type","tags":["entities"]}},"/entities/multiple-samples/{count}":{"post":{"parameters":[{"description":"The number of samples to be created","in":"path","name":"count","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"properties":{"sennet_id":{"type":"string"},"uuid":{"type":"string"}},"type":"object"},"type":"array"}}},"description":"The samples were successfully created. An array of objects each containing a UUID and SenNet ID associated with each newly created sample."},"400":{"description":"Invalid json input"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"500":{"description":"Internal error"}},"summary":"Create multiple samples from the same source entity. 'count' samples will be generated each with individual UUIDs and SenNet IDs.","tags":["entities"]}},"/doi/redirect/{id}":{"get":{"parameters":[{"description":"The SenNet ID (e.g. SNT123.ABCD.456) or UUID of the target collection","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"307":{"description":"Redirect to the entities landing page"},"400":{"description":"Invalid or misformatted collection identifier"},"500":{"description":"Internal error"}},"summary":"Redirect a request from a doi service","tags":["doi"]}},"/entities/{id}/globus-url":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"url","type":"string"}}},"description":"Returns the Globus service URL pointing to the Dataset or Upload data is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the Globus URL to the given Dataset or Upload entity","tags":["entities"]}},"/entities/{id}/pipeline-message":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"text","type":"string"}}},"description":"Returns the pipeline message for the given Dataset"},"400":{"description":"Invalid or misformatted entity identifier or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the pipeline message for the given Dataset","tags":["entities"]}},"/entities/{id}/validation-message":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"text","type":"string"}}},"description":"Returns the validation message for the given Upload"},"400":{"description":"Invalid or misformatted entity identifier or the given entity is not an Upload"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the validation message for the given Upload","tags":["entities"]}},"/datasets/{id}/latest-revision":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Dataset"}}},"description":"Successful operation"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the latest revision of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve the latest (newest) revision of a given Dataset. Public/Consortium access rules apply - if no token/consortium access then must be for a public dataset and the returned Dataset must be the latest public version. If the given dataset itself is the latest revision, meaning it has no next revisions, this dataset gets returned.","tags":["datasets"]}},"/datasets/{id}/revision":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"The revision number (integer) on successful operation"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve the calculated revision number of a Dataset. The calculated revision is number is based on the [:REVISION_OF] relationships to the oldest dataset in a revision chain. Where the oldest dataset = 1 and each newer version is incremented by one (1, 2, 3 ...). Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in SenNet-Read group is sent with the request then a 403 response should be returned.","tags":["datasets"]}},"/datasets/{id}/revisions":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true will have no effect. If the string is 'true', the full dataset for each revision will be included in the response","in":"query","name":"include_dataset","required":false,"schema":{"enum":["true","false"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"dataset":{"$ref":"#/components/schemas/Dataset"},"revision_number":{"description":"The number in the revision chain of this dataset where 1 is the oldest revision","type":"integer"},"uuid":{"description":"The uuid of a dataset","type":"string"}},"type":"object"}}},"description":"The list of revised datasets that the referenced dataset is a member of including the index number of the revision, where 1 is the oldest version of any revision chain"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"From a given ID of a versioned dataset, retrieve a list of every dataset in the chain ordered from most recent to oldest. The revision number, as well as the dataset UUID will be included. An optional parameter ?include_dataset=true will include the full dataset for each revision as well. Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in SenNet-Read group is sent with the request then a 403 response should be returned. If the given id is published, but later revisions are not and the user is not in SenNet-Read group, only published revisions will be returned. The field next_revision_uuid will not be returned if the next revision is unpublished","tags":["datasets"]}},"/datasets/{id}/retract":{"put":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either a SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"retraction_reason":{"description":"Free text describing why the dataset was retracted","type":"string"}},"type":"object"}}},"description":"A json body with a single, required retraction_reason parameter contianing the reason why the dataset is being retracted."},"responses":{"200":{"description":"The complete dataset with modified sub_status and retraction_reason"},"400":{"description":"Invalid or misformatted entity identifier, the given entity is not a Dataset, is not published or the required retraction_reason was not included in a json body"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the retract the given dataset. The user must be a member of the SenNet-Data-Admin group"},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retracts a dataset after it has been published. Requires a json body with a single field {retraction_reason: string}. The dataset for the given id is modified to include this new retraction_reason field and sets the dataset property sub_status to Retracted. The complete modified dataset is returned. Requires that the dataset being retracted has already been published (dataset.status == Published. Requires a user token with membership in the SenNet-Data-Admin group otherwise then a 403 will be returned.","tags":["datasets"]}},"/datasets/prov-info":{"get":{"parameters":[{"description":"A case insensitive string. Any value besides 'json' will have no effect. If the string is 'json', provenance info will be returned as a json. Otherwise, it will be returned as a tsv file","in":"query","name":"format","required":false,"schema":{"enum":["json","tsv"],"type":"string"}},{"description":"The UUID of the group","in":"query","name":"group_uuid","required":false,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true or false will cause a 400 exception.","in":"query","name":"has_rui_info","required":false,"schema":{"enum":["true","false"],"type":"string"}},{"description":"Case insensitive string for 2 character organ code. Values must be present on organ yaml or a 400 exception is raised","in":"query","name":"organ","required":false,"schema":{"type":"string"}},{"description":"Case insensitive string indicating the current status of a dataset","in":"query","name":"dataset_status","required":false,"schema":{"enum":["qa","new","published"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"dataset_created_by_email":{"description":"The email address of the person who created the dataset","type":"string"},"dataset_data_types":{"description":"The data/assay types (can be multiple types for pipeline derived data, so a comma separated list for tsv output or a json array for json output)","type":"string"},"dataset_date_time_created":{"description":"The date/time that the dataset was created","type":"string"},"dataset_date_time_modified":{"description":"The date/time that the dataset was last modified","type":"string"},"dataset_group_name":{"description":"The name of the data provider group who created the dataset","type":"string"},"dataset_group_uuid":{"description":"The internal id for the data provider group","type":"string"},"dataset_lab_id":{"description":"The identifier used by the data provider","type":"string"},"dataset_modified_by_email":{"description":"The email address of the person who last modified the dataset","type":"string"},"dataset_portl_url":{"description":"The url to open the dataset in the data portal","type":"string"},"dataset_sennet_id":{"description":"The SenNet ID of the dataset like SNT123.ABCD.456","type":"string"},"dataset_status":{"description":"The status of the dataset New, QA, Published, etc ...","type":"string"},"dataset_uuid":{"description":"The UUID of the dataset","type":"string"},"first_sample_portal_url":{"items":{"description":"The URL to the data portal for this sample nearest to this dataset in the provenance chain","type":"string"},"type":"array"},"first_sample_sennet_id":{"items":{"description":"The SenNet ID of the tissue sample nearest to this dataset in the provenance chain","type":"string"},"type":"array"},"first_sample_submission_id":{"items":{"description":"The Submission ID of the tissue sample nearest to this dataset in the provenance chain","type":"string"},"type":"array"},"first_sample_type":{"items":{"description":"The tissue type of the sample nearest to this dataset in the provenance chain","type":"string"},"type":"array"},"first_sample_uuid":{"items":{"description":"The UUID of the tissue sample nearest to this dataset in the provenance chain","type":"string"},"type":"array"},"organ_sennet_id":{"items":{"description":"The SenNet ID of the organ associated to this dataset in the provenance chain","type":"string"},"type":"array"},"organ_submission_id":{"items":{"description":"The submission ID of the organ associated to this dataset in the provenance chain","type":"string"},"type":"array"},"organ_type":{"items":{"description":"The organ type of the organ associated to this dataset in the provenance chain (return the organ code resolved to the organ name via the organ.yaml file)","type":"string"},"type":"array"},"organ_uuid":{"items":{"description":"The UUID of the organ associated to this dataset in the provenance chain","type":"string"},"type":"array"},"rui_location_sennet_id":{"items":{"description":"The SenNet ID of the tissue sample that contains RUI location json for this dataset","type":"string"},"type":"array"},"rui_location_submission_id":{"items":{"description":"The Submission ID of the tissue sample that contains RUI location json for this dataset","type":"string"},"type":"array"},"rui_location_uuid":{"items":{"description":"The UUID of the tissue sample that contains RUI location json for this dataset","type":"string"},"type":"array"},"sample_metadata_sennet_id":{"items":{"description":"The SenNet ID of tissue sample(s) containing sample metadata","type":"string"},"type":"array"},"sample_metadata_submission_id":{"items":{"description":"The Submission ID of the tissue sample(s) containing sample metadata","type":"string"},"type":"array"},"sample_metadata_uuid":{"items":{"description":"The UUID of the tissue sample(s) containing sample metadata","type":"string"},"type":"array"},"source:submission_id":{"items":{"description":"The Submission ID of the source associated to this dataset in the provenance chain","type":"string"},"type":"array"},"source_group_name":{"items":{"description":"The name of the SenNet group where this source originated (resolved to the group name from the group_uuid property resolved to displayname via the groups mapping file","type":"string"},"type":"array"},"source_sennet_id":{"items":{"description":"The SenNet ID of the source associated to this dataset in the provenance chain","type":"string"},"type":"array"},"source_uuid":{"items":{"description":"The UUID of the source associated to this dataset in the provenance 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This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID (32 digit hexadecimal number)","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'json' will have no effect. If the string is 'json', provenance info will be returned as a json. Otherwise, it will be returned as a tsv file","in":"query","name":"format","required":false,"schema":{"enum":["json","tsv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"dataset_created_by_email":{"description":"The email address of the person who created the dataset","type":"string"},"dataset_data_types":{"description":"The data/assay types (can be multiple types for pipeline derived data, so a comma separated list for tsv output or a json array for json output)","type":"string"},"dataset_date_time_created":{"description":"The date/time that the dataset was created","type":"string"},"dataset_date_time_modified":{"description":"The date/time that the dataset was last modified","type":"string"},"dataset_group_name":{"description":"The name of the data provider group who created the dataset","type":"string"},"dataset_group_uuid":{"description":"The internal id for the data provider 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Allowed values are \"Multi-Assay Split\"","type":"string"},"datasets":{"items":{"$ref":"#/components/schemas/Dataset"},"type":"array"},"direct_ancestor_uuids":{"description":"The UUID for the parent multi assay dataset","type":"string"},"group_uuid":{"description":"The group UUID for the new component datasets","type":"string"}},"type":"object"}}},"required":true},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Dataset"},"type":"array"}}},"description":"The entities were successfully created and are returned."},"400":{"description":"Invalid input."},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The given dataset is unpublished and the user does not have the authorization to view it."},"404":{"description":"Not found. No matching datasets were found, or the none were found that the user is authorized to see."},"500":{"description":"Internal error"}},"summary":"Create multiple component datasets from a single Multi-Assay ancestor","tags":["datasets"]}},"/datasets/{id}/organs":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Sample"},"type":"array"}}},"description":"A list of entity_type == Sample with sample_category == organ associated with the dataset id"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve a list of all of the samples that are organs that are associated with the dataset id","tags":["datasets"]}},"/datasets/{id}/samples":{"get":{"parameters":[{"description":"The unique identifier of entity.  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This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Source"},"type":"array"}}},"description":"A list of entity_type == Source that are associated with the dataset id"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve a list of all of the sources that are associated with the dataset id","tags":["datasets"]}},"/entities/{id}/uploads":{"get":{"parameters":[{"description":"The unique identifier of entity.  This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. 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This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Dataset"},"type":"array"}}},"description":"A list of entity_type == Dataset that are associated with the upload id"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve a list of all of the datasets that are associated with the upload id","tags":["uploads"]},"post":{"parameters":[{"description":"The unique identifier of entity. 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This identifier can be either an SenNet ID (e.g. HBM123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. 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This identifier can be either an SenNet ID (e.g. HBM123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. 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